R39K5B last accessed: 2022-11-04

ensembl
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:06.364802

Other names: e!, ensembl

Ensembl aims to provide a centralized resource for geneticists, molecular biologists and other researchers studying the genomes of our own species and other vertebrates and model organisms. Ensembl is one of several well known genome browsers for the retrieval of genomic information.

Webpage:

www.ensembl.org

Licence:

Name: Ensembl - specific / no license
URL: https://www.ensembl.org/info/about/legal/disclaimer.html

Publications: (63)

Publications
More detailed information about this field from each metasource.

GENCODE: the reference human genome annotation for The ENCODE Project
PMID: 22955987
metasource: Fairsharing.org
version: FAIRsharing.org: Ensembl; Ensembl; DOI: https://doi.org/10.25504/FAIRsharing.fx0mw7; Last edited: July 8, 2021, 1:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

The Ensembl Variant Effect Predictor
PMID: 27268795
metasource: Fairsharing.org
version: FAIRsharing.org: Ensembl; Ensembl; DOI: https://doi.org/10.25504/FAIRsharing.fx0mw7; Last edited: July 8, 2021, 1:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

Ensembl 2018
PMID: 29155950
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929

Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor
PMID: 20562413
metasource: Fairsharing.org
version: FAIRsharing.org: Ensembl; Ensembl; DOI: https://doi.org/10.25504/FAIRsharing.fx0mw7; Last edited: July 8, 2021, 1:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

Ensembl 2014
PMID: 24316576
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929

metasource: Fairsharing.org
version: FAIRsharing.org: Ensembl; Ensembl; DOI: https://doi.org/10.25504/FAIRsharing.fx0mw7; Last edited: July 8, 2021, 1:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

Ensembl 2016
PMID: 26687719
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929

metasource: Fairsharing.org
version: FAIRsharing.org: Ensembl; Ensembl; DOI: https://doi.org/10.25504/FAIRsharing.fx0mw7; Last edited: July 8, 2021, 1:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

Ensembl 2015
PMID: 25352552
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929

metasource: Fairsharing.org
version: FAIRsharing.org: Ensembl; Ensembl; DOI: https://doi.org/10.25504/FAIRsharing.fx0mw7; Last edited: July 8, 2021, 1:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

The Ensembl genome database project
PMID: 11752248
metasource: Fairsharing.org
version: FAIRsharing.org: Ensembl; Ensembl; DOI: https://doi.org/10.25504/FAIRsharing.fx0mw7; Last edited: July 8, 2021, 1:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:06.364802

Ensembl 2020
PMID: 31691826
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929

metasource: Fairsharing.org
version: FAIRsharing.org: Ensembl; Ensembl; DOI: https://doi.org/10.25504/FAIRsharing.fx0mw7; Last edited: July 8, 2021, 1:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates
PMID: 19029536
metasource: Fairsharing.org
version: FAIRsharing.org: Ensembl; Ensembl; DOI: https://doi.org/10.25504/FAIRsharing.fx0mw7; Last edited: July 8, 2021, 1:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

Ensembl 2013
PMID: 23203987
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929

metasource: Fairsharing.org
version: FAIRsharing.org: Ensembl; Ensembl; DOI: https://doi.org/10.25504/FAIRsharing.fx0mw7; Last edited: July 8, 2021, 1:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

Ensembl BioMarts: a hub for data retrieval across taxonomic space
PMID: 21785142
metasource: Fairsharing.org
version: FAIRsharing.org: Ensembl; Ensembl; DOI: https://doi.org/10.25504/FAIRsharing.fx0mw7; Last edited: July 8, 2021, 1:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

Ensembl 2012
PMID: 22086963
metasource: Fairsharing.org
version: FAIRsharing.org: Ensembl; Ensembl; DOI: https://doi.org/10.25504/FAIRsharing.fx0mw7; Last edited: July 8, 2021, 1:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

Ensembl 2009
PMID: 19033362
metasource: Fairsharing.org
version: FAIRsharing.org: Ensembl; Ensembl; DOI: https://doi.org/10.25504/FAIRsharing.fx0mw7; Last edited: July 8, 2021, 1:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:06.364802

Ensembl 2007
PMID: 17148474
metasource: Fairsharing.org
version: FAIRsharing.org: Ensembl; Ensembl; DOI: https://doi.org/10.25504/FAIRsharing.fx0mw7; Last edited: July 8, 2021, 1:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:06.364802

Ensembl 2011
PMID: 21045057
metasource: Fairsharing.org
version: FAIRsharing.org: Ensembl; Ensembl; DOI: https://doi.org/10.25504/FAIRsharing.fx0mw7; Last edited: July 8, 2021, 1:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

Ensembl 2019
PMID: 30407521
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929

metasource: Fairsharing.org
version: FAIRsharing.org: Ensembl; Ensembl; DOI: https://doi.org/10.25504/FAIRsharing.fx0mw7; Last edited: July 8, 2021, 1:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

The Ensembl gene annotation system
PMID: 27337980
metasource: Fairsharing.org
version: FAIRsharing.org: Ensembl; Ensembl; DOI: https://doi.org/10.25504/FAIRsharing.fx0mw7; Last edited: July 8, 2021, 1:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

Ensembl 2017
PMID: 27899575
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929

metasource: Fairsharing.org
version: FAIRsharing.org: Ensembl; Ensembl; DOI: https://doi.org/10.25504/FAIRsharing.fx0mw7; Last edited: July 8, 2021, 1:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

Ensembl 2008
PMID: 18000006
metasource: Fairsharing.org
version: FAIRsharing.org: Ensembl; Ensembl; DOI: https://doi.org/10.25504/FAIRsharing.fx0mw7; Last edited: July 8, 2021, 1:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:06.364802

The ensembl regulatory build
PMID: 25887522
metasource: Fairsharing.org
version: FAIRsharing.org: Ensembl; Ensembl; DOI: https://doi.org/10.25504/FAIRsharing.fx0mw7; Last edited: July 8, 2021, 1:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

metasource: Fairsharing.org
version: FAIRsharing.org: Ensembl; Ensembl; DOI: https://doi.org/10.25504/FAIRsharing.fx0mw7; Last edited: July 8, 2021, 1:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

The Ensembl automatic gene annotation system
PMID: 15123590
metasource: Fairsharing.org
version: FAIRsharing.org: Ensembl; Ensembl; DOI: https://doi.org/10.25504/FAIRsharing.fx0mw7; Last edited: July 8, 2021, 1:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

Ensembl 2005
PMID: 15608235
metasource: Fairsharing.org
version: FAIRsharing.org: Ensembl; Ensembl; DOI: https://doi.org/10.25504/FAIRsharing.fx0mw7; Last edited: July 8, 2021, 1:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:06.364802

Ensembl 2006
PMID: 16381931
metasource: Fairsharing.org
version: FAIRsharing.org: Ensembl; Ensembl; DOI: https://doi.org/10.25504/FAIRsharing.fx0mw7; Last edited: July 8, 2021, 1:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

metasource: Fairsharing.org
version: FAIRsharing.org: Ensembl; Ensembl; DOI: https://doi.org/10.25504/FAIRsharing.fx0mw7; Last edited: July 8, 2021, 1:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:06.364802

Ensembl's 10th year
PMID: 19906699
metasource: Fairsharing.org
version: FAIRsharing.org: Ensembl; Ensembl; DOI: https://doi.org/10.25504/FAIRsharing.fx0mw7; Last edited: July 8, 2021, 1:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:06.364802

Ensembl comparative genomics resources
PMID: 26896847
metasource: Fairsharing.org
version: FAIRsharing.org: Ensembl; Ensembl; DOI: https://doi.org/10.25504/FAIRsharing.fx0mw7; Last edited: July 8, 2021, 1:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

Genome-wide nucleotide-level mammalian ancestor reconstruction
PMID: 18849525
metasource: Fairsharing.org
version: FAIRsharing.org: Ensembl; Ensembl; DOI: https://doi.org/10.25504/FAIRsharing.fx0mw7; Last edited: July 8, 2021, 1:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

Ensembl 2002: accommodating comparative genomics
PMID: 12519943
metasource: Fairsharing.org
version: FAIRsharing.org: Ensembl; Ensembl; DOI: https://doi.org/10.25504/FAIRsharing.fx0mw7; Last edited: July 8, 2021, 1:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

metasource: Fairsharing.org
version: FAIRsharing.org: Ensembl; Ensembl; DOI: https://doi.org/10.25504/FAIRsharing.fx0mw7; Last edited: July 8, 2021, 1:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:06.364802

Ensembl 2004
PMID: 14681459
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:06.364802

The Ensembl REST API: Ensembl Data for Any Language
PMID: 25236461
metasource: Fairsharing.org
version: FAIRsharing.org: Ensembl; Ensembl; DOI: https://doi.org/10.25504/FAIRsharing.fx0mw7; Last edited: July 8, 2021, 1:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

metasource: Fairsharing.org
version: FAIRsharing.org: Ensembl; Ensembl; DOI: https://doi.org/10.25504/FAIRsharing.fx0mw7; Last edited: July 8, 2021, 1:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

Ensembl comparative genomics resources
PMID: 27141089
metasource: Fairsharing.org
version: FAIRsharing.org: Ensembl; Ensembl; DOI: https://doi.org/10.25504/FAIRsharing.fx0mw7; Last edited: July 8, 2021, 1:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

Ensembl variation resources
PMID: 20459805
metasource: Fairsharing.org
version: FAIRsharing.org: Ensembl; Ensembl; DOI: https://doi.org/10.25504/FAIRsharing.fx0mw7; Last edited: July 8, 2021, 1:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

The Ensembl core software libraries
PMID: 15123588
metasource: Fairsharing.org
version: FAIRsharing.org: Ensembl; Ensembl; DOI: https://doi.org/10.25504/FAIRsharing.fx0mw7; Last edited: July 8, 2021, 1:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

The Ensembl Web site: mechanics of a genome browser
PMID: 15123591
metasource: Fairsharing.org
version: FAIRsharing.org: Ensembl; Ensembl; DOI: https://doi.org/10.25504/FAIRsharing.fx0mw7; Last edited: July 8, 2021, 1:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

Incorporating RNA-seq data into the zebrafish Ensembl genebuild
PMID: 22798491
metasource: Fairsharing.org
version: FAIRsharing.org: Ensembl; Ensembl; DOI: https://doi.org/10.25504/FAIRsharing.fx0mw7; Last edited: July 8, 2021, 1:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

The Ensembl analysis pipeline
PMID: 15123589
metasource: Fairsharing.org
version: FAIRsharing.org: Ensembl; Ensembl; DOI: https://doi.org/10.25504/FAIRsharing.fx0mw7; Last edited: July 8, 2021, 1:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

ESTGenes: alternative splicing from ESTs in Ensembl
PMID: 15123595
metasource: Fairsharing.org
version: FAIRsharing.org: Ensembl; Ensembl; DOI: https://doi.org/10.25504/FAIRsharing.fx0mw7; Last edited: July 8, 2021, 1:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

WiggleTools: parallel processing of large collections of genome-wide datasets for visualization and statistical analysis
PMID: 24363377
metasource: Fairsharing.org
version: FAIRsharing.org: Ensembl; Ensembl; DOI: https://doi.org/10.25504/FAIRsharing.fx0mw7; Last edited: July 8, 2021, 1:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

Ensembl regulation resources
PMID: 26888907
metasource: Fairsharing.org
version: FAIRsharing.org: Ensembl; Ensembl; DOI: https://doi.org/10.25504/FAIRsharing.fx0mw7; Last edited: July 8, 2021, 1:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

A database and API for variation, dense genotyping and resequencing data
PMID: 20459810
metasource: Fairsharing.org
version: FAIRsharing.org: Ensembl; Ensembl; DOI: https://doi.org/10.25504/FAIRsharing.fx0mw7; Last edited: July 8, 2021, 1:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

eHive: an artificial intelligence workflow system for genomic analysis
PMID: 20459813
metasource: Fairsharing.org
version: FAIRsharing.org: Ensembl; Ensembl; DOI: https://doi.org/10.25504/FAIRsharing.fx0mw7; Last edited: July 8, 2021, 1:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

Touring Ensembl: a practical guide to genome browsing
PMID: 20459808
metasource: Fairsharing.org
version: FAIRsharing.org: Ensembl; Ensembl; DOI: https://doi.org/10.25504/FAIRsharing.fx0mw7; Last edited: July 8, 2021, 1:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

Genome browsing with Ensembl: a practical overview
PMID: 17967807
metasource: Fairsharing.org
version: FAIRsharing.org: Ensembl; Ensembl; DOI: https://doi.org/10.25504/FAIRsharing.fx0mw7; Last edited: July 8, 2021, 1:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

ncRNA orthologies in the vertebrate lineage
PMID: 26980512
metasource: Fairsharing.org
version: FAIRsharing.org: Ensembl; Ensembl; DOI: https://doi.org/10.25504/FAIRsharing.fx0mw7; Last edited: July 8, 2021, 1:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

TranscriptSNPView: a genome-wide catalog of mouse coding variation
PMID: 16874317
metasource: Fairsharing.org
version: FAIRsharing.org: Ensembl; Ensembl; DOI: https://doi.org/10.25504/FAIRsharing.fx0mw7; Last edited: July 8, 2021, 1:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

Genome information resources - developments at Ensembl
PMID: 15145580
metasource: Fairsharing.org
version: FAIRsharing.org: Ensembl; Ensembl; DOI: https://doi.org/10.25504/FAIRsharing.fx0mw7; Last edited: July 8, 2021, 1:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

The Ensembl computing architecture
PMID: 15123594
metasource: Fairsharing.org
version: FAIRsharing.org: Ensembl; Ensembl; DOI: https://doi.org/10.25504/FAIRsharing.fx0mw7; Last edited: July 8, 2021, 1:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

http://dx.doi.org/10.1093/nar/gku1010
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929

metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:06.364802

http://dx.doi.org/10.1093/nar/gkt1196
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929

http://dx.doi.org/10.1093/nar/gks1236
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929

http://dx.doi.org/10.1093/nar/gkr991
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929

http://dx.doi.org/10.1093/nar/gkq1064
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929

http://dx.doi.org/10.1093/nar/gkp972
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929

http://dx.doi.org/10.1093/nar/gkn828
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929

http://dx.doi.org/10.1093/nar/gkm988
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929

http://dx.doi.org/10.1093/nar/gkl996
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929

http://dx.doi.org/10.1093/nar/gkj133
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929

http://dx.doi.org/10.1093/nar/gki138
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929

http://nar.oxfordjournals.org/cgi/content/full/32/suppl_1/D468
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929

http://nar.oxfordjournals.org/cgi/content/full/31/1/38
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929

http://nar.oxfordjournals.org/cgi/content/full/30/1/38
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929

Disease and phenotype data at Ensembl
PMID: 21400687
metasource: Fairsharing.org
version: FAIRsharing.org: Ensembl; Ensembl; DOI: https://doi.org/10.25504/FAIRsharing.fx0mw7; Last edited: July 8, 2021, 1:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

https://doi.org/10.1093/nar/gkaa942
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

GENCODE: the reference human genome annotation for The ENCODE Project PubMed citations: 2315.

2315 articles citing: GENCODE: the reference human genome annotation for The ENCODE Project

RNA sequencing reveals dynamic expression of spleen lncRNAs and mRNAs in Beagle dogs infected by Toxocara canis. PMID:35927758
Exploring the lncRNA localization landscape within the retinal pigment epithelium under normal and stress conditions. PMID:35883037
Chronology of natural selection in Oceanian genomes. PMID:35880026
Oncogene addiction to GNAS in GNASR201 mutant tumors. PMID:35879396
Functional interplay between long non-coding RNAs and Breast CSCs. PMID:35864503
ISR8/IRF1-AS1 Is Relevant for IFNα and NF-κB Responses. PMID:35860270
Adipose methylome integrative-omic analyses reveal genetic and dietary metabolic health drivers and insulin resistance classifiers. PMID:35843982
Non-coding de novo mutations in chromatin interactions are implicated in autism spectrum disorder. PMID:35840799
Cancer type classification using plasma cell-free RNAs derived from human and microbes. PMID:35816095
Monocytic-Myeloid Derived Suppressor Cells Suppress T-Cell Responses in Recovered SARS CoV2-Infected Individuals. PMID:35812392
Bioinformatics Approaches for Determining the Functional Impact of Repetitive Elements on Non-coding RNAs. PMID:35796972
Construction of a Prognostic Immune-Related LncRNA Risk Model for Gastric Cancer. PMID:35794986
Comprehensive Analysis of LINC01615 in Head and Neck Squamous Cell Carcinoma: A Hub Biomarker Identified by Machine Learning and Experimental Validation. PMID:35794984
Exploring the Potential of Pyroptosis-Related Genes in Predicting Prognosis and Immunological Characteristics of Pancreatic Cancer From the Perspective of Genome and Transcriptome. PMID:35785176
Temporal Whole-Transcriptomic Analysis of Characterized In Vitro and Ex Vivo Primary Nasal Epithelia. PMID:35784475
DESSO-DB: A web database for sequence and shape motif analyses and identification. PMID:35782725
Integrative mRNA and Long Noncoding RNA Analysis Reveals the Regulatory Network of Floral Bud Induction in Longan (Dimocarpus longan Lour.). PMID:35774802
Microbiota, not host origin drives ex vivo intestinal epithelial responses. PMID:35758256
The origin of bladder cancer from mucosal field effects. PMID:35747385
Unexpected Effect of IL-1β on the Function of GABAA Receptors in Pediatric Focal Cortical Dysplasia. PMID:35741692
Non-Coding RNA Networks as Potential Novel Biomarker and Therapeutic Target for Sepsis and Sepsis-Related Multi-Organ Failure. PMID:35741168
The Long Non-Coding RNA GOMAFU in Schizophrenia: Function, Disease Risk, and Beyond. PMID:35741078
Construction and validation of N6-methyladenosine long non-coding RNAs signature of prognostic value for early biochemical recurrence of prostate cancer. PMID:35731271
The intestinal microbiota influences the microenvironment of metastatic colon cancer by targeting miRNAs. PMID:35712898
X chromosome inactivation in the human placenta is patchy and distinct from adult tissues. PMID:35712697
A multifunctional locus controls motor neuron differentiation through short and long noncoding RNAs. PMID:35698802
Somatic point mutations are enriched in non-coding RNAs with possible regulatory function in breast cancer. PMID:35672401
The clinical efficiency of transcriptome-based endometrial receptivity assessment (Tb-ERA) in Chinese patients with recurrent implantation failure (RIF): A study protocol for a prospective randomized controlled trial. PMID:35669489
Tangled quest of post-COVID-19 infection-caused neuropathology and what 3P nano-bio-medicine can solve? PMID:35668839
Evaluating the Immune Response in Treatment-Naive Hospitalised Patients With Influenza and COVID-19. PMID:35663963
The LINC01929/miR-6875-5p/ADAMTS12 Axis in the ceRNA Network Regulates the Development of Advanced Bladder Cancer. PMID:35646642
Deep Splicer: A CNN Model for Splice Site Prediction in Genetic Sequences. PMID:35627292
Paired guide RNA CRISPR-Cas9 screening for protein-coding genes and lncRNAs involved in transdifferentiation of human B-cells to macrophages. PMID:35619054
Senescence-induced endothelial phenotypes underpin immune-mediated senescence surveillance. PMID:35618311
Identification of Long Noncoding RNAs Involved in Eyelid Pigmentation of Hereford Cattle. PMID:35601493
Berberine and Oligomeric Proanthocyanidins Exhibit Synergistic Efficacy Through Regulation of PI3K-Akt Signaling Pathway in Colorectal Cancer. PMID:35600365
Immune Subtype Profiling and Establishment of Prognostic Immune-Related lncRNA Pairs in Human Ovarian Cancer. PMID:35578596
Progresses in epigenetic studies of asthma from the perspective of high-throughput analysis technologies: a narrative review. PMID:35571411
The Role of Non-Coding RNAs in the Human Placenta. PMID:35563893
The Role of Epigenetics in Primary Biliary Cholangitis. PMID:35563266
Skin-Expressing lncRNAs in Inflammatory Responses. PMID:35559048
Multi-ancestry genetic study of type 2 diabetes highlights the power of diverse populations for discovery and translation. PMID:35551307
Identification of Prognostic Biomarkers for Glioblastoma Based on Transcriptome and Proteome Association Analysis. PMID:35538679
A genome-wide CRISPR-Cas9 knockout screen identifies essential and growth-restricting genes in human trophoblast stem cells. PMID:35538076
Spatial epitranscriptomics reveals A-to-I editome specific to cancer stem cell microniches. PMID:35534484
Dynamic and widespread control of poly(A) tail length during macrophage activation. PMID:35512831
Native RNA or cDNA Sequencing for Transcriptomic Analysis: A Case Study on Saccharomyces cerevisiae. PMID:35497361
Classification of non-coding variants with high pathogenic impact. PMID:35486646
Allele-specific H3K9me3 and DNA methylation co-marked CpG-rich regions serve as potential imprinting control regions in pre-implantation embryo. PMID:35484247
MafB, WDR77, and ß-catenin interact with each other and have similar genome association profiles. PMID:35482762
Asymptomatic SARS-CoV-2 Infection Is Associated With Higher Levels of Serum IL-17C, Matrix Metalloproteinase 10 and Fibroblast Growth Factors Than Mild Symptomatic COVID-19. PMID:35479098
SETDB1 fuels the lung cancer phenotype by modulating epigenome, 3D genome organization and chromatin mechanical properties. PMID:35474385
Intraspecific de novo gene birth revealed by presence-absence variant genes in Caenorhabditis elegans. PMID:35464238
Specification of CNS macrophage subsets occurs postnatally in defined niches. PMID:35444273
Tandem Exon Duplications Expanding the Alternative Splicing Repertoire. PMID:35441045
circFAM120B functions as a tumor suppressor in esophageal squamous cell carcinoma via the miR-661/PPM1L axis and the PKR/p38 MAPK/EMT pathway. PMID:35436983
Construction of the Six-lncRNA Prognosis Signature as a Novel Biomarker in Esophageal Squamous Cell Carcinoma. PMID:35432441
REIA: A database for cancer A-to-I RNA editing with interactive analysis. PMID:35414795
Non-coding RNA LEVER sequestration of PRC2 can mediate long range gene regulation. PMID:35411071
Profiling Blood Serum Extracellular Vesicles in Plaque Psoriasis and Psoriatic Arthritis Patients Reveals Potential Disease Biomarkers. PMID:35409365
DUX4 is a multifunctional factor priming human embryonic genome activation. PMID:35402882
CRISPRs in the human genome are differentially expressed between malignant and normal adjacent to tumor tissue. PMID:35396392
Expansion of Schizophrenia Gene Network Knowledge Using Machine Learning Selected Signals From Dorsolateral Prefrontal Cortex and Amygdala RNA-seq Data. PMID:35386517
Ancestry adjustment improves genome-wide estimates of regional intolerance. PMID:35385101
Identification and evaluation of circulating small extracellular vesicle microRNAs as diagnostic biomarkers for patients with indeterminate pulmonary nodules. PMID:35366907
A single-cell analysis of breast cancer cell lines to study tumour heterogeneity and drug response. PMID:35361816
Paleozoic Protein Fossils Illuminate the Evolution of Vertebrate Genomes and Transposable Elements. PMID:35348724
Genome-wide Analysis Reflects Novel 5-Hydroxymethylcytosines Implicated in Diabetic Nephropathy and the Biomarker Potential. PMID:35342902
Analysis of Ferroptosis-Related LncRNAs Signatures Associated with Tumor Immune Infiltration and Experimental Validation in Clear Cell Renal Cell Carcinoma. PMID:35342303
METRO: Multi-ancestry transcriptome-wide association studies for powerful gene-trait association detection. PMID:35334221
Screening and Identification of Putative Long Non-Coding RNA in Childhood Obesity: Evaluation of Their Transcriptional Levels. PMID:35327332
SWI/SNF Antagonism of PRC2 Mediates Estrogen-Induced Progesterone Receptor Expression. PMID:35326450
Modelling the genetic aetiology of complex disease: human-mouse conservation of noncoding features and disease-associated loci. PMID:35317627
StemSC: a cross-dataset human stemness index for single-cell samples. PMID:35313979
Viral long non-coding RNA regulates virus life-cycle and pathogenicity. PMID:35301646
Integrating the Epigenome and Transcriptome of Hepatocellular Carcinoma to Identify Systematic Enhancer Aberrations and Establish an Aberrant Enhancer-Related Prognostic Signature. PMID:35300417
ArhGEF12 activates Rap1A and not RhoA in human dermal microvascular endothelial cells to reduce tumor necrosis factor-induced leak. PMID:35294066
Electrical modulation of transplanted stem cells improves functional recovery in a rodent model of stroke. PMID:35292643
SCAPE: a mixture model revealing single-cell polyadenylation diversity and cellular dynamics during cell differentiation and reprogramming. PMID:35288753
Predicting exon criticality from protein sequence. PMID:35286381
Derivation, Comprehensive Analysis, and Assay Validation of a Pyroptosis-Related lncRNA Prognostic Signature in Patients With Ovarian Cancer. PMID:35280739
C10orf99/GPR15L Regulates Proinflammatory Response of Keratinocytes and Barrier Formation of the Skin. PMID:35273606
Linc-RAM promotes muscle cell differentiation via regulating glycogen phosphorylase activity. PMID:35254536
Methylation- and homologous recombination deficiency-related mutant genes predict the prognosis of lung adenocarcinoma. PMID:35238419
TADA-a machine learning tool for functional annotation-based prioritisation of pathogenic CNVs. PMID:35232478
Remodeling the tumor microenvironment via blockade of LAIR-1 and TGF-β signaling enables PD-L1-mediated tumor eradication. PMID:35230974
Computational Resources for the Interpretation of Variations in Cancer. PMID:35230689
LncRNA Biomarkers of Inflammation and Cancer. PMID:35220568
The Complexity of the Mammalian Transcriptome. PMID:35220563
A multi-dimensional integrative scoring framework for predicting functional variants in the human genome. PMID:35216679
Single-cell eQTL analysis of activated T cell subsets reveals activation and cell type-dependent effects of disease-risk variants. PMID:35213211
Novel Genetic Prognostic Signature for Lung Adenocarcinoma Identified by Differences in Gene Expression Profiles of Low- and High-Grade Histological Subtypes. PMID:35204661
Functional Interactions Between lncRNAs/circRNAs and miRNAs: Insights Into Rheumatoid Arthritis. PMID:35197980
Tumor ENPP1 (CD203a)/Haptoglobin Axis Exploits Myeloid-Derived Suppressor Cells to Promote Post-Radiotherapy Local Recurrence in Breast Cancer. PMID:35191482
A comparison of experimental assays and analytical methods for genome-wide identification of active enhancers. PMID:35177836
Robust Transcriptional Profiling and Identification of Differentially Expressed Genes With Low Input RNA Sequencing of Adult Hippocampal Neural Stem and Progenitor Populations. PMID:35173579
Identification of Circulating lncRNAs Associated with Gallbladder Cancer Risk by Tissue-Based Preselection, Cis-eQTL Validation, and Analysis of Association with Genotype-Based Expression. PMID:35158906
Serum RNAs can predict lung cancer up to 10 years prior to diagnosis. PMID:35147498
Secreted Toxins From Staphylococcus aureus Strains Isolated From Keratinocyte Skin Cancers Mediate Pro-tumorigenic Inflammatory Responses in the Skin. PMID:35145494
The Carbon Footprint of Bioinformatics. PMID:35143670
Bioinformatic Analyses of the Ferroptosis-Related lncRNAs Signature for Ovarian Cancer. PMID:35127813
Multi-omic profiling of peritoneal metastases in gastric cancer identifies molecular subtypes and therapeutic vulnerabilities. PMID:35121863
A seven-lncRNA signature for predicting prognosis in breast carcinoma. PMID:35116701
CECR2 drives breast cancer metastasis by promoting NF-κB signaling and macrophage-mediated immune suppression. PMID:35108062
Four groups of type 2 diabetes contribute to the etiological and clinical heterogeneity in newly diagnosed individuals: An IMI DIRECT study. PMID:35106505
Haplotype-based inference of the distribution of fitness effects. PMID:35100400
GenomeTornadoPlot: A novel R package for CNV visualization and focality analysis. PMID:35099519
Long Non-coding RNA ZFPM2-AS1: A Novel Biomarker in the Pathogenesis of Human Cancers. PMID:35098483
CBX2 and EZH2 cooperatively promote the growth and metastasis of lung adenocarcinoma. PMID:35070495
Integrated clinical characteristics and omics analysis identifies a ferroptosis and iron-metabolism-related lncRNA signature for predicting prognosis and therapeutic responses in ovarian cancer. PMID:35057848
Transcriptional Analysis-Based Alterations Affecting Neuritogenesis of the Peripheral Nervous System in Psoriasis. PMID:35054504
Murine roseolovirus does not accelerate amyloid-β pathology and human roseoloviruses are not over-represented in Alzheimer disease brains. PMID:35033173
Down-regulation of the brain-specific cell-adhesion molecule contactin-3 in tuberous sclerosis complex during the early postnatal period. PMID:35030990
Role of cardiolipins, mitochondria, and autophagy in the differentiation process activated by all-trans retinoic acid in acute promyelocytic leukemia. PMID:35013142
Titanium with nanotopography attenuates the osteoclast-induced disruption of osteoblast differentiation by regulating histone methylation. PMID:35012895
Genomic studies controvert the existence of the CUX1 p75 isoform. PMID:34997000
Limb development genes underlie variation in human fingerprint patterns. PMID:34995520
Universal annotation of the human genome through integration of over a thousand epigenomic datasets. PMID:34991667
JAFFAL: detecting fusion genes with long-read transcriptome sequencing. PMID:34991664
The importance of enhancer methylation for epigenetic regulation of tumorigenesis in squamous lung cancer. PMID:34987166
Deconvolving Clinically Relevant Cellular Immune Cross-talk from Bulk Gene Expression Using CODEFACS and LIRICS Stratifies Patients with Melanoma to Anti-PD-1 Therapy. PMID:34983745
Screening and analysis of RNAs associated with activated memory CD4 and CD8 T cells in liver cancer. PMID:34980144
LncRNA PCAT19 induced by SP1 and acted as oncogene in gastric cancer competitively binding to miR429 and upregulating DHX9. PMID:34976174
m6A Modification-Mediated DUXAP8 Regulation of Malignant Phenotype and Chemotherapy Resistance of Hepatocellular Carcinoma Through miR-584-5p/MAPK1/ERK Pathway Axis. PMID:34957112
Network Integration Analysis and Immune Infiltration Analysis Reveal Potential Biomarkers for Primary Open-Angle Glaucoma. PMID:34926471
Evolving features of human cortical development and the emerging roles of non-coding RNAs in neural progenitor cell diversity and function. PMID:34921638
Alternative polyadenylation is a determinant of oncogenic Ras function. PMID:34919436
Control of Foxp3 induction and maintenance by sequential histone acetylation and DNA demethylation. PMID:34910919
β2-spectrin (SPTBN1) as a therapeutic target for diet-induced liver disease and preventing cancer development. PMID:34910547
Emerging Roles of Long Noncoding RNAs in Immuno-Oncology. PMID:34900986
Long non-coding RNAs as possible therapeutic targets in protozoa, and in Schistosoma and other helminths. PMID:34859292
Integrative Analysis of Epigenome and Transcriptome Data Reveals Aberrantly Methylated Promoters and Enhancers in Hepatocellular Carcinoma. PMID:34858848
Key Markers Involved in the Anticolon Cancer Response of CD8+ T Cells through the Regulation of Cholesterol Metabolism. PMID:34858500
An autoimmune stem-like CD8 T cell population drives type 1 diabetes. PMID:34847567
Analysis of the long noncoding RNA profiles of RD and SH-SY5Y cells infected with coxsackievirus B5, using RNA sequencing. PMID:34839420
Predictive modeling of gene expression regulation. PMID:34837938
Whole-genome analysis of Nigerian patients with breast cancer reveals ethnic-driven somatic evolution and distinct genomic subtypes. PMID:34836952
ATR inhibition enables complete tumour regression in ALK-driven NB mouse models. PMID:34819497
A novel role for vaping in mitochondrial gene dysregulation and inflammation fundamental to disease development. PMID:34815430
Genome-wide identification and characterization of circular RNA m6A modification in pancreatic cancer. PMID:34798904
Potential biomarkers of abnormal osseointegration of implants in type II diabetes mellitus. PMID:34794414
PP2A is a therapeutically targetable driver of cell fate decisions via a c-Myc/p21 axis in human and murine acute myeloid leukemia. PMID:34788382
Muscle fibrosis and maladaptation occur progressively in CKD and are rescued by dialysis. PMID:34784301
Differential Expression Profiles of lncRNA Following LPS-Induced Inflammation in Bovine Mammary Epithelial Cells. PMID:34778437
Novel and Annotated Long Noncoding RNAs Associated with Ischemia in the Human Heart. PMID:34768754
ASB2 is a direct target of FLI1 that sustains NF-κB pathway activation in germinal center-derived diffuse large B-cell lymphoma. PMID:34763718
The Role of Long Non-coding RNAs in Human Imprinting Disorders: Prospective Therapeutic Targets. PMID:34760887
Klf5 establishes bi-potential cell fate by dual regulation of ICM and TE specification genes. PMID:34758315
FusionGDB 2.0: fusion gene annotation updates aided by deep learning. PMID:34755868
An integrated multi-omic analysis of iPSC-derived motor neurons from C9ORF72 ALS patients. PMID:34746695
Comprehensive analysis of N6 -methyladenosine-related long non-coding RNAs for prognosis prediction in liver hepatocellular carcinoma. PMID:34741346
Haplotype-aware variant calling with PEPPER-Margin-DeepVariant enables high accuracy in nanopore long-reads. PMID:34725481
Derivation and Comprehensive Analysis of Aging Patterns in Patients with Bladder Cancer. PMID:34721733
Robust Virus-Specific Adaptive Immunity in COVID-19 Patients with SARS-CoV-2 Δ382 Variant Infection. PMID:34716845
Somatic driver mutation prevalence in 1844 prostate cancers identifies ZNRF3 loss as a predictor of metastatic relapse. PMID:34716314
NanoMethViz: An R/Bioconductor package for visualizing long-read methylation data. PMID:34695109
Machine learning applications for therapeutic tasks with genomics data. PMID:34693370
Muscle Regeneration and RNA: New Perspectives for Ancient Molecules. PMID:34685492
Anthocyanins from Aristotelia chilensis Prevent Olanzapine-Induced Hepatic-Lipid Accumulation but Not Insulin Resistance in Skeletal Muscle Cells. PMID:34684731
IL-1-driven stromal-neutrophil interactions define a subset of patients with inflammatory bowel disease that does not respond to therapies. PMID:34675383
Quantifying full-length circular RNAs in cancer. PMID:34663689
Comprehensive Genomic Characterization Analysis Identifies an Oncogenic Pseudogene RP11-3543B.1 in Human Gastric Cancer. PMID:34660601
The key role of NLRP3 and STING in APOL1-associated podocytopathy. PMID:34651582
Building the mega single-cell transcriptome ocular meta-atlas. PMID:34651173
Benchmarking sequencing methods and tools that facilitate the study of alternative polyadenylation. PMID:34649612
Thousands of Qatari genomes inform human migration history and improve imputation of Arab haplotypes. PMID:34642339
Chromatin Velocity reveals epigenetic dynamics by single-cell profiling of heterochromatin and euchromatin. PMID:34635836
Diverse functional elements in RNA predicted transcriptome-wide by orthogonal RNA structure probing. PMID:34634799
Cohesin Core Complex Gene Dosage Contributes to Germinal Center Derived Lymphoma Phenotypes and Outcomes. PMID:34621263
Multi-tiered analyses of honey bees that resist or succumb to parasitic mites and viruses. PMID:34610790
Targeting mutant p53 for cancer therapy: direct and indirect strategies. PMID:34583722
High frequency of intron retention and clustered H3K4me3-marked nucleosomes in short first introns of human long non-coding RNAs. PMID:34579770
Full-length transcriptome analysis and identification of transcript structures in Eimeria necatrix from different developmental stages by single-molecule real-time sequencing. PMID:34579769
Gene Expression Analysis in Patients with Cocaine-Induced Midline Destructive Lesions. PMID:34577784
Performance Evaluation of SpliceAI for the Prediction of Splicing of NF1 Variants. PMID:34573290
TP53 loss initiates chromosomal instability in fallopian tube epithelial cells. PMID:34569598
Comprehensive analyses of glycolysis-related lncRNAs for ovarian cancer patients. PMID:34560889
HIV reprograms host m6Am RNA methylome by viral Vpr protein-mediated degradation of PCIF1. PMID:34545078
Characterization of the Potential Role of NTPCR in Epithelial Ovarian Cancer by Integrating Transcriptomic and Metabolomic Analysis. PMID:34539736
ISOTOPE: ISOform-guided prediction of epiTOPEs in cancer. PMID:34529669
Integrative Epigenome Map of the Normal Human Prostate Provides Insights Into Prostate Cancer Predisposition. PMID:34513844
Predicting Target Genes of San-Huang-Chai-Zhu Formula in Treating ANIT-Induced Acute Intrahepatic Cholestasis Rat Model via Bioinformatics Analysis Combined with Experimental Validation. PMID:34512777
Epigenetic Regulation of the Vascular Endothelium by Angiogenic LncRNAs. PMID:34512715
Integrative analysis of epigenetics data identifies gene-specific regulatory elements. PMID:34508352
A Novel Regulatory Player in the Innate Immune System: Long Non-Coding RNAs. PMID:34502451
Identifying the Main Functional Pathways Associated with Cognitive Resilience to Alzheimer's Disease. PMID:34502030
A compendium of uniformly processed human gene expression and splicing quantitative trait loci. PMID:34493866
A pair of long intergenic non-coding RNA LINC00887 variants act antagonistically to control Carbonic Anhydrase IX transcription upon hypoxia in tongue squamous carcinoma progression. PMID:34493285
The regulatory pattern of target gene expression by aberrant enhancer methylation in glioblastoma. PMID:34482818
Molecular genetic evaluation of pediatric renovascular hypertension due to renal artery stenosis and abdominal aortic coarctation in neurofibromatosis type 1. PMID:34476477
UV-induced reduction in Polycomb repression promotes epidermal pigmentation. PMID:34473941
Precision medicine in diabetes: A non-invasive prenatal diagnostic test for the determination of fetal glucokinase mutations. PMID:34469064
Cap analysis of gene expression (CAGE) and noncoding regulatory elements. PMID:34468849
YAP and TAZ are transcriptional co-activators of AP-1 proteins and STAT3 during breast cellular transformation. PMID:34463254
An approach to gene-based testing accounting for dependence of tests among nearby genes. PMID:34459489
RP11-616M22.7 recapitulates imatinib resistance in gastrointestinal stromal tumor. PMID:34458010
Genome-wide profiling of alternative splicing in glioblastoma and their clinical value. PMID:34445990
High Concentration of an ISS-N1-Targeting Antisense Oligonucleotide Causes Massive Perturbation of the Transcriptome. PMID:34445083
Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review. PMID:34439912
Absent from DNA and protein: genomic characterization of nullomers and nullpeptides across functional categories and evolution. PMID:34433494
Developmental dynamics of voltage-gated sodium channel isoform expression in the human and mouse brain. PMID:34425903
The impact of LncRNA dysregulation on clinicopathology and survival of pancreatic cancer: a systematic review and meta-analysis (PRISMA compliant). PMID:34425840
The endogenous mex-3 3´UTR is required for germline repression and contributes to optimal fecundity in C. elegans. PMID:34424904
Non-redundant functions of H2A.Z.1 and H2A.Z.2 in chromosome segregation and cell cycle progression. PMID:34423893
Long Non-coding RNA RP11-395G23.3 Acts as a Competing Endogenous RNA of miR-124-3p to Regulate ROR1 in Anaplastic Thyroid Carcinoma. PMID:34421987
A novel immune signature to predict the prognosis of patients with hepatocellular carcinoma. PMID:34414957
X-linked recessive TLR7 deficiency in ~1% of men under 60 years old with life-threatening COVID-19. PMID:34413140
Mechanism-Centric Approaches for Biomarker Detection and Precision Therapeutics in Cancer. PMID:34408770
Long Noncoding RNAs as Emerging Regulators of COVID-19. PMID:34408749
Single-cell evaluation reveals shifts in the tumor-immune niches that shape and maintain aggressive lesions in the breast. PMID:34408137
Intussusceptive Angiogenesis in Human Metastatic Malignant Melanoma. PMID:34400131
LncRNA OGFRP1 acts as an oncogene in NSCLC via miR-4640-5p/eIF5A axis. PMID:34389018
Precision treatment exploration of breast cancer based on heterogeneity analysis of lncRNAs at the single-cell level. PMID:34388989
Transcriptomic and Epigenetic Profiling of Fibroblasts in Idiopathic Pulmonary Fibrosis. PMID:34370624
Four Prognosis-Associated lncRNAs Serve as Biomarkers in Ovarian Cancer. PMID:34367239
A Tissue-Specific Landscape of Alternative Polyadenylation, lncRNAs, TFs, and Gene Co-expression Networks in Liriodendron chinense. PMID:34367224
SDE2 is an essential gene required for ribosome biogenesis and the regulation of alternative splicing. PMID:34365507
Cloud Computing Based Immunopeptidomics Utilizing Community Curated Variant Libraries Simplifies and Improves Neo-Antigen Discovery in Metastatic Melanoma. PMID:34359654
Integrated Analysis of Long Non-Coding RNA and mRNA Expression Profiles in Testes of Calves and Sexually Mature Wandong Bulls (Bos taurus). PMID:34359134
Hippocampal Transcriptome Changes After Subarachnoid Hemorrhage in Mice. PMID:34354664
Comprehensive analysis of lncRNAs involved in skeletal muscle development in ZBED6-knockout Bama pigs. PMID:34348644
Pre-pregnancy BMI-associated miRNA and mRNA expression signatures in the placenta highlight a sexually-dimorphic response to maternal underweight status. PMID:34344912
Progesterone receptor antagonists reverse stem cell expansion and the paracrine effectors of progesterone action in the mouse mammary gland. PMID:34344445
Transgenic mice for in vivo epigenome editing with CRISPR-based systems. PMID:34341582
Plasmodium falciparum transcription in different clinical presentations of malaria associates with circulation time of infected erythrocytes. PMID:34330920
Systematic Profiling of mRNA Splicing Reveals the Prognostic Predictor and Potential Therapeutic Target for Glioblastoma Multiforme. PMID:34326872
The genomic landscape of 85 advanced neuroendocrine neoplasms reveals subtype-heterogeneity and potential therapeutic targets. PMID:34326338
lncRNA-PACER upregulates COX-2 and PGE2 through the NF-κB pathway to promote the proliferation and invasion of colorectal-cancer cells. PMID:34316376
Tissue-specific expression of p73 and p63 isoforms in human tissues. PMID:34315849
Web tools to perform long non-coding RNAs analysis in oncology research. PMID:34296748
Gucy2d selectively marks inhibitory dynorphin neurons in the spinal dorsal horn but is dispensable for pain and itch sensitivity. PMID:34296052
Seizure-mediated iron accumulation and dysregulated iron metabolism after status epilepticus and in temporal lobe epilepsy. PMID:34292399
Single-cell Long Non-coding RNA Landscape of T Cells in Human Cancer Immunity. PMID:34284134
Functional annotation of noncoding mutations in cancer. PMID:34282050
Splicing in the Diagnosis of Rare Disease: Advances and Challenges. PMID:34276790
Long Non-coding RNAs: Mechanisms, Experimental, and Computational Approaches in Identification, Characterization, and Their Biomarker Potential in Cancer. PMID:34276764
The circulatory small non-coding RNA landscape in community-acquired pneumonia on intensive care unit admission. PMID:34272809
Epithelial Splicing Regulatory Protein 1 Is Overexpressed in Breast Cancer and Predicts Poor Prognosis for Breast Cancer Patients. PMID:34262011
Comparing the Predictivity of Human Placental Gene, microRNA, and CpG Methylation Signatures in Relation to Perinatal Outcomes. PMID:34255065
DNA damage repair: historical perspectives, mechanistic pathways and clinical translation for targeted cancer therapy. PMID:34238917
Identification and validation of lncRNAs involved in m6A regulation for patients with ovarian cancer. PMID:34238292
A DNA methylation profile of long non-coding RNAs can predict OS in prostate cancer. PMID:34238128
Software Options for the Analysis of MS-Proteomic Data. PMID:34236654
EZH2-induced lysine K362 methylation enhances TMPRSS2-ERG oncogenic activity in prostate cancer. PMID:34230470
ACE2-lentiviral transduction enables mouse SARS-CoV-2 infection and mapping of receptor interactions. PMID:34214142
EGFR in Cancer: Signaling Mechanisms, Drugs, and Acquired Resistance. PMID:34206026
Predicting the Risk Genes of Autism Spectrum Disorders. PMID:34194469
Contribution of genetic and epigenetic changes to escape from X-chromosome inactivation. PMID:34187555
Single-cell analysis of mouse and human prostate reveals novel fibroblasts with specialized distribution and microenvironment interactions. PMID:34173975
Construction of lncRNA-Mediated ceRNA Network for Investigating Immune Pathogenesis of Ischemic Stroke. PMID:34173933
Dealing with Pseudogenes in Molecular Diagnostics in the Next Generation Sequencing Era. PMID:34165726
Pseudogene Profiling for Cancer Subtype Classification. PMID:34165723
GENCODE Pseudogenes. PMID:34165709
rigrag: high-resolution mapping of genic targeting preferences during HIV-1 integration in vitro and in vivo. PMID:34165568
KCNQ1OT1 lncRNA affects the proliferation, apoptosis, and chemoresistance of small cell lung cancer cells via the JAK2/STAT3 axis. PMID:34164525
Experimental Validation of the Noncoding Potential for lncRNAs. PMID:34160810
Probing the signaling requirements for naive human pluripotency by high-throughput chemical screening. PMID:34133938
Potential prognostic markers and significant lncRNA-mRNA co-expression pairs in laryngeal squamous cell carcinoma. PMID:34131588
Fine-mapping, trans-ancestral and genomic analyses identify causal variants, cells, genes and drug targets for type 1 diabetes. PMID:34127860
Comprehensive analysis of suppressor of cytokine signaling proteins in human breast Cancer. PMID:34120621
H2A.Z acetylation by lincZNF337-AS1 via KAT5 implicated in the transcriptional misregulation in cancer signaling pathway in hepatocellular carcinoma. PMID:34120148
CD27hiCD38hi plasmablasts are activated B cells of mixed origin with distinct function. PMID:34113823
Time trajectories in the transcriptomic response to exercise - a meta-analysis. PMID:34108459
Identification of DNA methylation biomarkers for risk of liver metastasis in early-stage colorectal cancer. PMID:34108011
A microRNA expression and regulatory element activity atlas of the mouse immune system. PMID:34099919
RNA structure probing reveals the structural basis of Dicer binding and cleavage. PMID:34099665
Multiple Omics Integration Reveals Key Circular RNAs in Hepatocellular Carcinoma. PMID:34094907
Bone marrow mesenchymal stem cells and their derived exosomes resolve doxorubicin-induced chemobrain: critical role of their miRNA cargo. PMID:34090498
Identification of 3'-UTR single nucleotide variants and prediction of select protein imbalance in mesial temporal lobe epilepsy patients. PMID:34086756
A panel of 8-lncRNA predicts prognosis of breast cancer patients and migration of breast cancer cells. PMID:34086679
An Informatics Pipeline for Profiling and Annotating RNA Modifications. PMID:34085236
Oncogenic Landscape of Somatic Mutations Perturbing Pan-Cancer lncRNA-ceRNA Regulation. PMID:34079798
The landscape and biological relevance of aberrant alternative splicing events in esophageal squamous cell carcinoma. PMID:34079089
Decoding LncRNAs. PMID:34072257
The Detection and Bioinformatic Analysis of Alternative 3' UTR Isoforms as Potential Cancer Biomarkers. PMID:34070203
HERV-K(HML7) Integrations in the Human Genome: Comprehensive Characterization and Comparative Analysis in Non-Human Primates. PMID:34069102
Human Endogenous Retroviruses (HERVs) and Mammalian Apparent LTRs Retrotransposons (MaLRs) Are Dynamically Modulated in Different Stages of Immunity. PMID:34062989
Long Non-coding RNA RUNDC3A-AS1 Promotes Lung Metastasis of Thyroid Cancer via Targeting the miR-182-5p/ADAM9. PMID:34046406
Pan-cancer characterization of long non-coding RNA and DNA methylation mediated transcriptional dysregulation. PMID:34044218
Lantern: an integrative repository of functional annotations for lncRNAs in the human genome. PMID:34039271
BRIO: a web server for RNA sequence and structure motif scan. PMID:34038531
Association of FAAH p.Pro129Thr and COMT p.Ala72Ser with schizophrenia and comorbid substance use through next-generation sequencing: an exploratory analysis. PMID:34037083
Phenotypic plasticity underlies local invasion and distant metastasis in colon cancer. PMID:34036938
Selection of Optimal Bioinformatic Tools and Proper Reference for Reducing the Alignment Error in Targeted Sequencing Data. PMID:34026589
Interpretation of deep learning in genomics and epigenomics. PMID:34020542
Identity and compatibility of reference genome resources. PMID:34017945
Interpreting type 1 diabetes risk with genetics and single-cell epigenomics. PMID:34012112
Targeted RNA-seq improves efficiency, resolution, and accuracy of allele specific expression for human term placentas. PMID:34009305
Generation of an isoform-level transcriptome atlas of macrophage activation. PMID:34000296
Glucocorticoid signaling in pancreatic islets modulates gene regulatory programs and genetic risk of type 2 diabetes. PMID:33983929
Dynamic imaging of nascent RNA reveals general principles of transcription dynamics and stochastic splice site selection. PMID:33979654
Asymptomatic COVID-19: disease tolerance with efficient anti-viral immunity against SARS-CoV-2. PMID:33961735
Kidney Diseases: The Age of Molecular Markers. PMID:33959903
A Human Endogenous Bornavirus-Like Nucleoprotein Encodes a Mitochondrial Protein Associated with Cell Viability. PMID:33952640
Intergenic RNA mainly derives from nascent transcripts of known genes. PMID:33952325
Activation of HERV-K(HML-2) disrupts cortical patterning and neuronal differentiation by increasing NTRK3. PMID:33951478
Tumor necrosis factor-induced ArhGEF10 selectively activates RhoB contributing to human microvascular endothelial cell tight junction disruption. PMID:33948992
lncRNA PVT1 in the Pathogenesis and Clinical Management of Renal Cell Carcinoma. PMID:33947142
Detection of new drivers of frequent B-cell lymphoid neoplasms using an integrated analysis of whole genomes. PMID:33945543
Transcriptome prediction performance across machine learning models and diverse ancestries. PMID:33937878
Topography of transcriptionally active chromatin in glioblastoma. PMID:33931443
Loss of RET Promotes Mesenchymal Identity in Neuroblastoma Cells. PMID:33921066
Meningeal lymphatics affect microglia responses and anti-Aβ immunotherapy. PMID:33911285
Identification of candidate PAX2-regulated genes implicated in human kidney development. PMID:33907292
Human brain region-specific variably methylated regions are enriched for heritability of distinct neuropsychiatric traits. PMID:33888138
The cis-regulatory effects of modern human-specific variants. PMID:33885362
Genomic Landscapes of Noncoding RNAs Regulating VEGFA and VEGFC Expression in Endothelial Cells. PMID:33875575
Conserved long-range base pairings are associated with pre-mRNA processing of human genes. PMID:33863890
A genome-wide atlas of co-essential modules assigns function to uncharacterized genes. PMID:33859415
Human KIT+ myeloid cells facilitate visceral metastasis by melanoma. PMID:33857287
A Transcription Start Site Map in Human Pancreatic Islets Reveals Functional Regulatory Signatures. PMID:33849996
Uncovering transcriptional dark matter via gene annotation independent single-cell RNA sequencing analysis. PMID:33846360
A large-scale genome-wide gene expression analysis in peripheral blood identifies very few differentially expressed genes related to antidepressant treatment and response in patients with major depressive disorder. PMID:33833401
The structure, function and evolution of a complete human chromosome 8. PMID:33828295
An extended catalogue of tandem alternative splice sites in human tissue transcriptomes. PMID:33826604
Human-lineage-specific genomic elements are associated with neurodegenerative disease and APOE transcript usage. PMID:33824317
Vitamin D receptor upregulates lncRNA TOPORS-AS1 which inhibits the Wnt/β-catenin pathway and associates with favorable prognosis of ovarian cancer. PMID:33820921
Machine Learning Reduced Gene/Non-Coding RNA Features That Classify Schizophrenia Patients Accurately and Highlight Insightful Gene Clusters. PMID:33805976
CALINCA-A Novel Pipeline for the Identification of lncRNAs in Podocyte Disease. PMID:33804736
Differential Methylation in the GSTT1 Regulatory Region in Sudden Unexplained Death and Sudden Unexpected Death in Epilepsy. PMID:33801838
HIV-1 integration sites in CD4+ T cells during primary, chronic, and late presentation of HIV-1 infection. PMID:33784259
Evidence for additive and synergistic action of mammalian enhancers during cell fate determination. PMID:33770473
A transcription-centric model of SNP-age interaction. PMID:33770080
Neuronal enhancers are hotspots for DNA single-strand break repair. PMID:33767446
Aripiprazole as a Candidate Treatment of COVID-19 Identified Through Genomic Analysis. PMID:33762960
Fine-mapping of two differentiated thyroid carcinoma susceptibility loci at 2q35 and 8p12 in Europeans, Melanesians and Polynesians. PMID:33747362
COX2 regulates senescence secretome composition and senescence surveillance through PGE2. PMID:33730589
Mutant non-coding RNA resource in mouse embryonic stem cells. PMID:33729986
Coronary artery disease: differential expression of ceRNAs and interaction analyses. PMID:33708856
Most non-canonical proteins uniquely populate the proteome or immunopeptidome. PMID:33691108
Day-night and seasonal variation of human gene expression across tissues. PMID:33688644
An intriguing characteristic of enhancer-promoter interactions. PMID:33685407
Genomic and Transcriptomic Analyses Reveals ZNF124 as a Critical Regulator in Highly Aggressive Medulloblastomas. PMID:33681213
Non-Coding RNAs in Retinoic Acid as Differentiation and Disease Drivers. PMID:33671241
RNA-Seq Implies Divergent Regulation Patterns of LincRNA on Spermatogenesis and Testis Growth in Goats. PMID:33653002
Human DNA methylation signatures differentiate persistent from resolving MRSA bacteremia. PMID:33649198
A potential association of RNF219-AS1 with ADHD: Evidence from categorical analysis of clinical phenotypes and from quantitative exploration of executive function and white matter microstructure endophenotypes. PMID:33644999
Genome-Wide Identification and Characterization of Potato Long Non-coding RNAs Associated With Phytophthora infestans Resistance. PMID:33643350
Potential Molecular Mechanism of TNF Superfamily-Related Genes in Glioblastoma Multiforme Based on Transcriptome and Epigenome. PMID:33643183
Exome-wide age-of-onset analysis reveals exonic variants in ERN1 and SPPL2C associated with Alzheimer's disease. PMID:33637690
Identification and Characterisation of Putative Enhancer Elements in Mouse Embryonic Stem Cells. PMID:33623376
Annotation of chromatin states in 66 complete mouse epigenomes during development. PMID:33619351
Uniform genomic data analysis in the NCI Genomic Data Commons. PMID:33619257
Chromatin Looping Links Target Genes with Genetic Risk Loci for Dermatological Traits. PMID:33607115
Polycomb complexes redundantly maintain epidermal stem cell identity during development. PMID:33602871
Genetic Effects on Transcriptome Profiles in Colon Epithelium Provide Functional Insights for Genetic Risk Loci. PMID:33601062
CD4+ T cells from children with active juvenile idiopathic arthritis show altered chromatin features associated with transcriptional abnormalities. PMID:33597588
Novel DNA methylation signatures of tobacco smoking with trans-ethnic effects. PMID:33593402
CIITA-Transduced Glioblastoma Cells Uncover a Rich Repertoire of Clinically Relevant Tumor-Associated HLA-II Antigens. PMID:33592498
Identification of Functional lncRNAs Associated With Ovarian Endometriosis Based on a ceRNA Network. PMID:33584822
Novel insights into the interaction between long non-coding RNAs and microRNAs in glioma. PMID:33582947
PRMT5 inhibition disrupts splicing and stemness in glioblastoma. PMID:33579912
Benchmark study comparing liftover tools for genome conversion of epigenome sequencing data. PMID:33575605
Alterations of 5-hydroxymethylation in circulating cell-free DNA reflect molecular distinctions of subtypes of non-Hodgkin lymphoma. PMID:33574286
Reintroduction of the archaic variant of NOVA1 in cortical organoids alters neurodevelopment. PMID:33574182
Eight-lncRNA signature of cervical cancer were identified by integrating DNA methylation, copy number variation and transcriptome data. PMID:33557879
Role of Transposable Elements in Gene Regulation in the Human Genome. PMID:33557056
Inhibitory effect of sodium butyrate on colorectal cancer cells and construction of the related molecular network. PMID:33549042
Biphasic Activation of WNT Signaling Facilitates the Derivation of Midbrain Dopamine Neurons from hESCs for Translational Use. PMID:33545081
Dual functions of SPOP and ERG dictate androgen therapy responses in prostate cancer. PMID:33531470
Consequences of aneuploidy in human fibroblasts with trisomy 21. PMID:33526671
Competing endogenous RNA network analysis explores the key lncRNAs, miRNAs, and mRNAs in type 1 diabetes. PMID:33526014
MicroRNA Profiles in Monocyte-Derived Macrophages Generated by Interleukin-27 and Human Serum: Identification of a Novel HIV-Inhibiting and Autophagy-Inducing MicroRNA. PMID:33525571
Integrating quantitative proteomics with accurate genome profiling of transcription factors by greenCUT&RUN. PMID:33524153
Gene expression signatures of target tissues in type 1 diabetes, lupus erythematosus, multiple sclerosis, and rheumatoid arthritis. PMID:33523973
Identification of Potential Prognostic Competing Triplets in High-Grade Serous Ovarian Cancer. PMID:33519912
Long Non-Coding RNA FENDRR: Gene Structure, Expression, and Biological Relevance. PMID:33513839
Cell-to-Cell Adhesion and Neurogenesis in Human Cortical Development: A Study Comparing 2D Monolayers with 3D Organoid Cultures. PMID:33513360
Inferring time series chromatin states for promoter-enhancer pairs based on Hi-C data. PMID:33509077
Systematic analysis of binding of transcription factors to noncoding variants. PMID:33505025
Detection of aberrant splicing events in RNA-seq data using FRASER. PMID:33483494
Transcriptome network analyses in human coronavirus infections suggest a rational use of immunomodulatory drugs for COVID-19 therapy. PMID:33482326
A novel five-lncRNA signature panel improves high-risk survival prediction in patients with cholangiocarcinoma. PMID:33472169
Compression of quantification uncertainty for scRNA-seq counts. PMID:33471073
A spatially resolved brain region- and cell type-specific isoform atlas of the postnatal mouse brain. PMID:33469025
Long Non-Coding RNAs and Their Potential Roles in the Vector-Host-Pathogen Triad. PMID:33466803
Genome-wide landscape of RNA-binding protein target site dysregulation reveals a major impact on psychiatric disorder risk. PMID:33462483
DeepLPI: a multimodal deep learning method for predicting the interactions between lncRNAs and protein isoforms. PMID:33461501
PacBio full-length transcriptome of wild apple (Malus sieversii) provides insights into canker disease dynamic response. PMID:33446096
Blood-derived mitochondrial DNA copy number is associated with gene expression across multiple tissues and is predictive for incident neurodegenerative disease. PMID:33441415
Injection site vaccinology of a recombinant vaccinia-based vector reveals diverse innate immune signatures. PMID:33439897
Longitudinal saliva omics responses to immune perturbation: a case study. PMID:33436912
Differential contribution of transcriptomic regulatory layers in the definition of neuronal identity. PMID:33436550
The Functions and Unique Features of LncRNAs in Cancer Development and Tumorigenesis. PMID:33435206
Multi-trait transcriptome-wide association studies with probabilistic Mendelian randomization. PMID:33434493
Smc3 dosage regulates B cell transit through germinal centers and restricts their malignant transformation. PMID:33432228
Induced organoids derived from patients with ulcerative colitis recapitulate colitic reactivity. PMID:33431859
Diabetes induced renal complications by leukocyte activation of nuclear factor κ-B and its regulated genes expression. PMID:33424337
Comprehensive characterisation of intronic mis-splicing mutations in human cancers. PMID:33420369
A cross-platform approach identifies genetic regulators of human metabolism and health. PMID:33414548
ALK ligand ALKAL2 potentiates MYCN-driven neuroblastoma in the absence of ALK mutation. PMID:33411331
Genome-wide identification and characterization of long non-coding RNAs conferring resistance to Colletotrichum gloeosporioides in walnut (Juglans regia). PMID:33407106
Unbiased RNA-Seq-driven identification and validation of reference genes for quantitative RT-PCR analyses of pooled cancer exosomes. PMID:33407103
Sex-dimorphic genetic effects and novel loci for fasting glucose and insulin variability. PMID:33402679
Mitochondrial DNA alterations underlie an irreversible shift to aerobic glycolysis in fumarate hydratase-deficient renal cancer. PMID:33402335
TLR3 controls constitutive IFN-β antiviral immunity in human fibroblasts and cortical neurons. PMID:33393505
Transcriptomic analysis identifies a tumor subtype mRNA classifier for invasive non-functioning pituitary neuroendocrine tumor diagnostics. PMID:33391466
Identification of Critical Genes and Proteins for Stent Restenosis Induced by Esophageal Benign Hyperplasia in Esophageal Cancer. PMID:33391336
Pressure-Driven Mitochondrial Transfer Pipeline Generates Mammalian Cells of Desired Genetic Combinations and Fates. PMID:33378680
Common cell type nomenclature for the mammalian brain. PMID:33372656
Sex and age influence gonadal steroid hormone receptor distributions relative to estrogen receptor β-containing neurons in the mouse hypothalamic paraventricular nucleus. PMID:33341960
Single cell analysis reveals distinct immune landscapes in transplant and primary sarcomas that determine response or resistance to immunotherapy. PMID:33335088
FAN-C: a feature-rich framework for the analysis and visualisation of chromosome conformation capture data. PMID:33334380
AnnoLnc: A One-Stop Portal to Systematically Annotate Novel Human Long Noncoding RNAs. PMID:33326073
Integrating comprehensive functional annotations to boost power and accuracy in gene-based association analysis. PMID:33320851
Liftoff: accurate mapping of gene annotations. PMID:33320174
Functional interaction between long non-coding RNA and microRNA in rheumatoid arthritis. PMID:33319382
The computational approaches of lncRNA identification based on coding potential: Status quo and challenges. PMID:33304463
Our emerging understanding of the roles of long non-coding RNAs in normal liver function, disease, and malignancy. PMID:33294829
MicroRNA expression data of pluripotent and somatic cells and identification of cell type-specific MicroRNAs in pigs. PMID:33294536
CoolMPS: evaluation of antibody labeling based massively parallel non-coding RNA sequencing. PMID:33290507
Screening of T Cell-Related Long Noncoding RNA-MicroRNA-mRNA Regulatory Networks in Non-Small-Cell Lung Cancer. PMID:33274216
Immune-Related Four-lncRNA Signature for Patients with Cervical Cancer. PMID:33274204
GENCODE 2021. PMID:33270111
Deep whole-genome sequencing of multiple proband tissues and parental blood reveals the complex genetic etiology of congenital diaphragmatic hernias. PMID:33263113
dbNSFP v4: a comprehensive database of transcript-specific functional predictions and annotations for human nonsynonymous and splice-site SNVs. PMID:33261662
Improvement of Disease Resistance in Livestock: Application of Immunogenomics and CRISPR/Cas9 Technology. PMID:33260762
Genomic and transcriptomic alterations associated with drug vulnerabilities and prognosis in adenocarcinoma at the gastroesophageal junction. PMID:33257699
Serum RNA Profiling in the 10-Years Period Prior to Diagnosis of Testicular Germ Cell Tumor. PMID:33251139
ProTECT-Prediction of T-Cell Epitopes for Cancer Therapy. PMID:33244314
NAIL: an evolutionarily conserved lncRNA essential for licensing coordinated activation of p38 and NFκB in colitis. PMID:33239342
Global transcriptomic profiling of microcystin-LR or -RR treated hepatocytes (HepaRG). PMID:33235993
An integrative atlas of chicken long non-coding genes and their annotations across 25 tissues. PMID:33235280
A Detailed Flow Cytometric Analysis of Immune Activity Profiles in Molecular Subtypes of Colorectal Cancer. PMID:33228141
Molecular Features of Cancers Exhibiting Exceptional Responses to Treatment. PMID:33217343
Atypical UV Photoproducts Induce Non-canonical Mutation Classes Associated with Driver Mutations in Melanoma. PMID:33207206
Genome-Wide Identification of Long Non-coding RNAs in the Gravid Ectoparasite Varroa destructor. PMID:33193688
Plant miRNAs Reduce Cancer Cell Proliferation by Targeting MALAT1 and NEAT1: A Beneficial Cross-Kingdom Interaction. PMID:33193626
Proteoform Identification by Combining RNA-Seq and Top-Down Mass Spectrometry. PMID:33183009
Integrated analysis of transcriptomic and metabolomic data demonstrates the significant role of pyruvate carboxylase in the progression of ovarian cancer. PMID:33177242
deepBase v3.0: expression atlas and interactive analysis of ncRNAs from thousands of deep-sequencing data. PMID:33175131
Transcriptional analysis of metastatic uveal melanoma survival nominates NRP1 as a therapeutic target. PMID:33170593
SVFX: a machine learning framework to quantify the pathogenicity of structural variants. PMID:33168059
Prediction of enhancer-promoter interactions using the cross-cell type information and domain adversarial neural network. PMID:33160328
Towards a better understanding of the low recall of insertion variants with short-read based variant callers. PMID:33148192
Cross-resistance of cisplatin selected cells to anti-microtubule agents: Role of general survival mechanisms. PMID:33129114
Long non-coding RNAs (lncRNAs) in spermatogenesis and male infertility. PMID:33126901
Illuminating the dark side of the human transcriptome with long read transcript sequencing. PMID:33126848
A small protein encoded by a putative lncRNA regulates apoptosis and tumorigenicity in human colorectal cancer cells. PMID:33112233
mTOR-dependent translation amplifies microglia priming in aging mice. PMID:33108356
Combined genetic analysis of juvenile idiopathic arthritis clinical subtypes identifies novel risk loci, target genes and key regulatory mechanisms. PMID:33106285
LncRNAs in adaptive immunity: role in physiological and pathological conditions. PMID:33094664
PLA2G6 guards placental trophoblasts against ferroptotic injury. PMID:33087576
Network-Based Coexpression Analysis Identifies Functional and Prognostic Long Noncoding RNAs in Hepatocellular Carcinoma. PMID:33083449
Retinoic Acid Sensitivity of Triple-Negative Breast Cancer Cells Characterized by Constitutive Activation of the notch1 Pathway: The Role of Rarβ. PMID:33081033
Metformin alters skeletal muscle transcriptome adaptations to resistance training in older adults. PMID:33071237
Host gene expression modulated by Zika virus infection of human-293 cells. PMID:33059318
An enhanced genetic model of relapsed IGH-translocated multiple myeloma evolutionary dynamics. PMID:33057009
Pan-cancer analysis reveals TAp63-regulated oncogenic lncRNAs that promote cancer progression through AKT activation. PMID:33056990
A systematic evaluation of bioinformatics tools for identification of long noncoding RNAs. PMID:33055239
Identification of male infertility-related long non-coding RNAs and their functions based on a competing endogenous RNA network. PMID:33054493
LncExpDB: an expression database of human long non-coding RNAs. PMID:33045751
Genetic variant effects on gene expression in human pancreatic islets and their implications for T2D. PMID:32999275
Effects of germline and somatic events in candidate BRCA-like genes on breast-tumor signatures. PMID:32997669
Long noncoding RNA AANCR modulates innate antiviral responses by blocking miR-210-dependent MITA downregulation in teleost fish, Miichthys miiuy. PMID:32997329
Targeted Inhibition of the NUP98-NSD1 Fusion Oncogene in Acute Myeloid Leukemia. PMID:32993115
Swan: a library for the analysis and visualization of long-read transcriptomes. PMID:32991665
Integrative genomics identifies a convergent molecular subtype that links epigenomic with transcriptomic differences in autism. PMID:32978376
Long non-coding RNA AGAP2-AS1 increases the invasiveness of papillary thyroid cancer. PMID:32960785
PRAM: a novel pooling approach for discovering intergenic transcripts from large-scale RNA sequencing experiments. PMID:32958497
IDH1/2 mutations in acute myeloid leukemia patients and risk of coronary artery disease and cardiac dysfunction-a retrospective propensity score analysis. PMID:32948843
Network analysis of KLF5 targets showing the potential oncogenic role of SNHG12 in colorectal cancer. PMID:32943987
The Landscape of Micro-Inversions Provide Clues for Population Genetic Analysis of Humans. PMID:32929667
Incomplete annotation has a disproportionate impact on our understanding of Mendelian and complex neurogenetic disorders. PMID:32917675
A Quantitative Proteome Map of the Human Body. PMID:32916130
Scavenger: A pipeline for recovery of unaligned reads utilising similarity with aligned reads. PMID:32913631
A polyclonal allelic expression assay for detecting regulatory effects of transcript variants. PMID:32912286
Identification and Characterization of Copy Number-Associated Driver Genes in Esophageal Squamous Cell Carcinoma. PMID:32908901
A role for microRNAs in the epigenetic control of sexually dimorphic gene expression in the human placenta. PMID:32901510
p53 drives a transcriptional program that elicits a non-cell-autonomous response and alters cell state in vivo. PMID:32900967
Radiation induces dynamic changes to the T cell repertoire in renal cell carcinoma patients. PMID:32900949
Three-dimensional facial-image analysis to predict heterogeneity of the human ageing rate and the impact of lifestyle. PMID:32895578
Roles of miRNA and lncRNA in triple-negative breast cancer. PMID:32893525
Genome-wide identification of differentially methylated promoters and enhancers associated with response to anti-PD-1 therapy in non-small cell lung cancer. PMID:32879421
Long non-coding RNA CASC8 polymorphisms are associated with the risk of esophageal cancer in a Chinese population. PMID:32875717
The genomic landscape of Mongolian hepatocellular carcinoma. PMID:32873799
Genome-wide analysis of long non-coding RNAs in adult tissues of the melon fly, Zeugodacus cucurbitae (Coquillett). PMID:32867696
Learning the properties of adaptive regions with functional data analysis. PMID:32853200
Genome-Wide Transcriptional Analysis Reveals Alternative Splicing Event Profiles in Hepatocellular Carcinoma and Their Prognostic Significance. PMID:32849842
Systematic Evaluation of the Diagnostic and Prognostic Significance of Competitive Endogenous RNA Networks in Prostate Cancer. PMID:32849794
Identifying Circular RNA and Predicting Its Regulatory Interactions by Machine Learning. PMID:32849764
Dynamic incorporation of multiple in silico functional annotations empowers rare variant association analysis of large whole-genome sequencing studies at scale. PMID:32839606
Daxx maintains endogenous retroviral silencing and restricts cellular plasticity in vivo. PMID:32821827
Intrinsic Endocardial Defects Contribute to Hypoplastic Left Heart Syndrome. PMID:32810435
Concentration-dependent splicing is enabled by Rbfox motifs of intermediate affinity. PMID:32807990
Promoter CpG Density Predicts Downstream Gene Loss-of-Function Intolerance. PMID:32800095
Ybx1 fine-tunes PRC2 activities to control embryonic brain development. PMID:32792512
circRNAome Profiling in Oral Carcinoma Unveils a Novel circFLNB that Mediates Tumour Growth-Regulating Transcriptional Response. PMID:32785098
Splicing Anomalies in Myeloproliferative Neoplasms: Paving the Way for New Therapeutic Venues. PMID:32784800
The role of exome sequencing in newborn screening for inborn errors of metabolism. PMID:32778825
The Long Non-coding Road to Atherosclerosis. PMID:32772181
CD163+ cytokine-producing cDC2 stimulate intratumoral type 1 T cell responses in HPV16-induced oropharyngeal cancer. PMID:32771994
Dynamic changes in the epigenomic landscape regulate human organogenesis and link to developmental disorders. PMID:32764605
Demystifying "drop-outs" in single-cell UMI data. PMID:32762710
Comprehensive Network Analysis Reveals Alternative Splicing-Related lncRNAs in Hepatocellular Carcinoma. PMID:32760422
A limited set of transcriptional programs define major cell types. PMID:32759341
Tousled-Like Kinases Suppress Innate Immune Signaling Triggered by Alternative Lengthening of Telomeres. PMID:32755577
LncRNA AY343892 inhibits breast cancer development by positively regulating BRCA1-mediated transcription of PTEN. PMID:32754899
MYBPC3 Haplotype Linked to Hypertrophic Cardiomyopathy in Rhesus Macaques (Macaca mulatta). PMID:32753092
Identification of the key genes and characterizations of Tumor Immune Microenvironment in Lung Adenocarcinoma (LUAD) and Lung Squamous Cell Carcinoma (LUSC). PMID:32742444
Supervised enhancer prediction with epigenetic pattern recognition and targeted validation. PMID:32737473
Testing and controlling for horizontal pleiotropy with probabilistic Mendelian randomization in transcriptome-wide association studies. PMID:32737316
Methodologies for Transcript Profiling Using Long-Read Technologies. PMID:32733532
Improving the diversity of captured full-length isoforms using a normalized single-molecule RNA-sequencing method. PMID:32732980
Perspectives on ENCODE. PMID:32728248
Spatiotemporal DNA methylome dynamics of the developing mouse fetus. PMID:32728242
An atlas of dynamic chromatin landscapes in mouse fetal development. PMID:32728240
Transcriptional activity and strain-specific history of mouse pseudogenes. PMID:32728065
RADAR: annotation and prioritization of variants in the post-transcriptional regulome of RNA-binding proteins. PMID:32727537
HOTTIP polymorphism may affect gastric cancer susceptibility by altering HOTTIP expression. PMID:32725141
Placental genomic and epigenomic signatures associated with infant birth weight highlight mechanisms involved in collagen and growth factor signaling. PMID:32721520
MiT/TFE factors control ER-phagy via transcriptional regulation of FAM134B. PMID:32716134
Altered Long Noncoding RNA Expression Profile in Multiple Myeloma Patients with Bisphosphonate-Induced Osteonecrosis of the Jaw. PMID:32714991
The Heterogeneous Landscape and Early Evolution of Pathogen-Associated CpG Dinucleotides in SARS-CoV-2. PMID:32714120
The RNA exosome shapes the expression of key protein-coding genes. PMID:32710631
Cell type-specific novel long non-coding RNA and circular RNA in the BLUEPRINT hematopoietic transcriptomes atlas. PMID:32703790
Comprehensive Analysis of Differentially Expressed lncRNAs in Gastric Cancer. PMID:32695786
Genetic architecture of complex traits and disease risk predictors. PMID:32694572
Reference genome and transcriptome informed by the sex chromosome complement of the sample increase ability to detect sex differences in gene expression from RNA-Seq data. PMID:32693839
The long non-coding RNA HLNC1 potentiates hepatocellular carcinoma progression via interaction with USP49. PMID:32691951
Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes. PMID:32686750
Long noncoding RNA MARL regulates antiviral responses through suppression miR-122-dependent MAVS downregulation in lower vertebrates. PMID:32678830
RNA-Seq Transcriptome Analysis Reveals Long Terminal Repeat Retrotransposon Modulation in Human Peripheral Blood Mononuclear Cells after In Vivo Lipopolysaccharide Injection. PMID:32669333
Modeling Secondary Iron Overload Cardiomyopathy with Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes. PMID:32668256
Systematic Characterization of Recurrent Genomic Alterations in Cyclin-Dependent Kinases Reveals Potential Therapeutic Strategies for Cancer Treatment. PMID:32668240
Unified inference of missense variant effects and gene constraints in the human genome. PMID:32667917
Total Functional Score of Enhancer Elements Identifies Lineage-Specific Enhancers That Drive Differentiation of Pancreatic Cells. PMID:32655276
Chromosome-level de novo assembly of the pig-tailed macaque genome using linked-read sequencing and HiC proximity scaffolding. PMID:32649757
Macrocyclization of a Ligand Targeting a Toxic RNA Dramatically Improves Potency. PMID:32649032
DrugSniper, a Tool to Exploit Loss-Of-Function Screens, Identifies CREBBP as a Predictive Biomarker of VOLASERTIB in Small Cell Lung Carcinoma (SCLC). PMID:32645997
miR-7 Reduces Breast Cancer Stem Cell Metastasis via Inhibiting RELA to Decrease ESAM Expression. PMID:32637582
Characterization of cell-free breast cancer patient-derived scaffolds using liquid chromatography-mass spectrometry/mass spectrometry data and RNA sequencing data. PMID:32637480
Network of clinically-relevant lncRNAs-mRNAs associated with prognosis of hepatocellular carcinoma patients. PMID:32636408
Impact of Losing hRpn13 Pru or UCHL5 on Proteasome Clearance of Ubiquitinated Proteins and RA190 Cytotoxicity. PMID:32631902
Bioinformatic analysis of the potential molecular mechanism of PAK7 expression in glioblastoma. PMID:32626960
Germline de novo mutation rates on exons versus introns in humans. PMID:32620809
Insights into lncRNAs in Alzheimer's disease mechanisms. PMID:32605500
Quantification of translation uncovers the functions of the alternative transcriptome. PMID:32601440
Co-administration of 5α-reductase Inhibitors Worsens the Adverse Metabolic Effects of Prescribed Glucocorticoids. PMID:32594135
Long non-coding RNA profiling of pediatric Medulloblastoma. PMID:32591022
Deletion of Glutathione S-Transferase Omega 1 Activates Type I Interferon Genes and Downregulates Tissue Factor. PMID:32571799
The Long Noncoding RNA NEAT1 Promotes Sarcoma Metastasis by Regulating RNA Splicing Pathways. PMID:32561656
Intellectual disability-associated gene ftsj1 is responsible for 2'-O-methylation of specific tRNAs. PMID:32558197
Inferring changes in histone modification during cell differentiation by ancestral state estimation based on phylogenetic trees of cell types: Human hematopoiesis as a model case. PMID:32550550
Long Noncoding RNAs in Diffuse Large B-Cell Lymphoma: Current Advances and Perspectives. PMID:32547063
Weighted Gene Coexpression Network Analysis Reveals the Dynamic Transcriptome Regulation and Prognostic Biomarkers of Hepatocellular Carcinoma. PMID:32523331
Properties of structural variants and short tandem repeats associated with gene expression and complex traits. PMID:32522982
WHSC1 monomethylates histone H1 and induces stem-cell like features in squamous cell carcinoma of the head and neck. PMID:32497898
Genomic analyses of early responses to radiation inglioblastoma reveal new alterations at transcription,splicing, and translation levels. PMID:32488114
The lncRNA RUNX1-IT1 regulates C-FOS transcription by interacting with RUNX1 in the process of pancreatic cancer proliferation, migration and invasion. PMID:32487998
The Impact of Recessive Deleterious Variation on Signals of Adaptive Introgression in Human Populations. PMID:32487519
Hypermethylation of the miR-155 gene in the whole blood and decreased plasma level of miR-155 in rheumatoid arthritis. PMID:32484820
Skeletal muscle enhancer interactions identify genes controlling whole-body metabolism. PMID:32483258
Dynamic TF-lncRNA Regulatory Networks Revealed Prognostic Signatures in the Development of Ovarian Cancer. PMID:32478062
Frequent upregulation of G9a promotes RelB-dependent proliferation and survival in multiple myeloma. PMID:32477831
Discovery of a transcriptomic core of genes shared in 8 primary retinoblastoma with a novel detection score analysis. PMID:32474753
Age-dependent effect of APOE and polygenic component on Alzheimer's disease. PMID:32464432
HOTTIP Predicts Poor Survival in Gastric Cancer Patients and Contributes to Cisplatin Resistance by Sponging miR-216a-5p. PMID:32457911
Geminin is required for Hox gene regulation to pattern the developing limb. PMID:32450229
SNHG7 is a lncRNA oncogene controlled by Insulin-like Growth Factor signaling through a negative feedback loop to tightly regulate proliferation. PMID:32444795
miRactDB characterizes miRNA-gene relation switch between normal and cancer tissues across pan-cancer. PMID:32436932
Progress, Challenges, and Surprises in Annotating the Human Genome. PMID:32421357
Codon usage similarity between viral and some host genes suggests a codon-specific translational regulation. PMID:32395662
ORF Capture-Seq as a versatile method for targeted identification of full-length isoforms. PMID:32393825
Transcriptome analysis of neural progenitor cells derived from Lowe syndrome induced pluripotent stem cells: identification of candidate genes for the neurodevelopmental and eye manifestations. PMID:32393163
Identification of Key Players Involved in CoCl2 Hypoxia Induced Pulmonary Artery Hypertension in vitro. PMID:32391042
All-Trans Retinoic Acid Stimulates Viral Mimicry, Interferon Responses and Antigen Presentation in Breast-Cancer Cells. PMID:32384653
A human lung tumor microenvironment interactome identifies clinically relevant cell-type cross-talk. PMID:32381040
Comprehensive Molecular Characterization Identifies Distinct Genomic and Immune Hallmarks of Renal Medullary Carcinoma. PMID:32359397
Long non-coding RNA RAMS11 promotes metastatic colorectal cancer progression. PMID:32358485
Blood-based biomarkers for early detection of esophageal squamous cell carcinoma. PMID:32351288
CircAtlas: an integrated resource of one million highly accurate circular RNAs from 1070 vertebrate transcriptomes. PMID:32345360
Comprehensive Analysis of HERV Transcriptome in HIV+ Cells: Absence of HML2 Activation and General Downregulation of Individual HERV Loci. PMID:32340287
The Construction and Analysis of the Aberrant lncRNA-miRNA-mRNA Network in Adipose Tissue from Type 2 Diabetes Individuals with Obesity. PMID:32337289
Myogenic Progenitor Cell Lineage Specification by CRISPR/Cas9-Based Transcriptional Activators. PMID:32330446
Predicting target genes of non-coding regulatory variants with IRT. PMID:32330225
O-GlcNAc regulates gene expression by controlling detained intron splicing. PMID:32329777
Transcriptome Analyses of lncRNAs in A2E-Stressed Retinal Epithelial Cells Unveil Advanced Links between Metabolic Impairments Related to Oxidative Stress and Retinitis Pigmentosa. PMID:32326576
STAT3-dependent analysis reveals PDK4 as independent predictor of recurrence in prostate cancer. PMID:32323921
Detection of Allosteric Effects of lncRNA Secondary Structures Altered by SNPs in Human Diseases. PMID:32322582
Genome‑wide DNA methylation regulation analysis of long non‑coding RNAs in glioblastoma. PMID:32319552
Effect for Human Genomic Variation During the BMP4-Induced Conversion From Pluripotent Stem Cells to Trophoblast. PMID:32318089
Complete characterization of the human immune cell transcriptome using accurate full-length cDNA sequencing. PMID:32312742
Leveraging gene co-expression patterns to infer trait-relevant tissues in genome-wide association studies. PMID:32310941
DolphinNext: a distributed data processing platform for high throughput genomics. PMID:32306927
Dermal Adipocyte Lipolysis and Myofibroblast Conversion Are Required for Efficient Skin Repair. PMID:32302523
Ex Vivo Organoid Cultures Reveal the Importance of the Tumor Microenvironment for Maintenance of Colorectal Cancer Stem Cells. PMID:32290033
Misuse of RPKM or TPM normalization when comparing across samples and sequencing protocols. PMID:32284352
Comparability of the small RNA secretome across human biofluids concomitantly collected from healthy adults. PMID:32275679
Modulator-Dependent RBPs Changes Alternative Splicing Outcomes in Kidney Cancer. PMID:32273884
Whole-Genome and RNA Sequencing Reveal Variation and Transcriptomic Coordination in the Developing Human Prefrontal Cortex. PMID:32268104
Differences in gene-expression profiles in breast cancer between African and European-ancestry women. PMID:32267939
The UCSC repeat browser allows discovery and visualization of evolutionary conflict across repeat families. PMID:32266012
Identification of Autophagy-Associated Biomarkers and Corresponding Regulatory Factors in the Progression of Colorectal Cancer. PMID:32265986
Lats1/2 Sustain Intestinal Stem Cells and Wnt Activation through TEAD-Dependent and Independent Transcription. PMID:32259481
Integrative Analysis of NSCLC Identifies LINC01234 as an Oncogenic lncRNA that Interacts with HNRNPA2B1 and Regulates miR-106b Biogenesis. PMID:32246902
The Emerging Role of ncRNAs and RNA-Binding Proteins in Mitotic Apparatus Formation. PMID:32245090
A genomic and epigenomic atlas of prostate cancer in Asian populations. PMID:32238934
U1 snRNP regulates chromatin retention of noncoding RNAs. PMID:32238924
Tumor suppressor and oncogenic role of long non-coding RNAs in cancer. PMID:32232211
Genomic and Transcriptomic Analysis Identified Novel Putative Cassava lncRNAs Involved in Cold and Drought Stress. PMID:32231066
dbMTS: A comprehensive database of putative human microRNA target site SNVs and their functional predictions. PMID:32227657
Long noncoding RNA LINC00844-mediated molecular network regulates expression of drug metabolizing enzymes and nuclear receptors in human liver cells. PMID:32222775
Evidence of constraint in the 3D genome for trans-splicing in human cells. PMID:32221814
Genetic Architecture of Gene Expression in European and African Americans: An eQTL Mapping Study in GENOA. PMID:32220292
CLING: Candidate Cancer-Related lncRNA Prioritization via Integrating Multiple Biological Networks. PMID:32211391
DNA methylation disruption reshapes the hematopoietic differentiation landscape. PMID:32203468
An autoinhibitory intramolecular interaction proof-reads RNA recognition by the essential splicing factor U2AF2. PMID:32188783
RUNX1 and RUNX2 transcription factors function in opposing roles to regulate breast cancer stem cells. PMID:32180230
MoAIMS: efficient software for detection of enriched regions of MeRIP-Seq. PMID:32171255
COMPSRA: a COMprehensive Platform for Small RNA-Seq data Analysis. PMID:32165660
Identification of lncRNA-associated differential subnetworks in oesophageal squamous cell carcinoma by differential co-expression analysis. PMID:32164040
Cystic renal-epithelial derived induced pluripotent stem cells from polycystic kidney disease patients. PMID:32163234
Beyond classic editing: innovative CRISPR approaches for functional studies of long non-coding RNA. PMID:32161809
Targeting MYCN-expressing triple-negative breast cancer with BET and MEK inhibitors. PMID:32161105
Integrated proteogenomic deep sequencing and analytics accurately identify non-canonical peptides in tumor immunopeptidomes. PMID:32157095
Men1 maintains exocrine pancreas homeostasis in response to inflammation and oncogenic stress. PMID:32156729
Differential expression analysis comparing EBV uninfected to infected human cell lines identifies induced non-micro small non-coding RNAs. PMID:32154466
The X-linked trichothiodystrophy-causing gene RNF113A links the spliceosome to cell survival upon DNA damage. PMID:32152280
MiR-7 reduces the BCSC subset by inhibiting XIST to modulate the miR-92b/Slug/ESA axis and inhibit tumor growth. PMID:32143670
Graph embedding and unsupervised learning predict genomic sub-compartments from HiC chromatin interaction data. PMID:32127534
Expert curation of the human and mouse olfactory receptor gene repertoires identifies conserved coding regions split across two exons. PMID:32126975
Long Non-Coding RNA H19 Promotes Porcine Satellite Cell Differentiation by Interacting with TDP43. PMID:32121115
Inferring lncRNA Functional Similarity Based on Integrating Heterogeneous Network Data. PMID:32117916
PAX1 is essential for development and function of the human thymus. PMID:32111619
Single-cell transcriptome analysis reveals TOX as a promoting factor for T cell exhaustion and a predictor for anti-PD-1 responses in human cancer. PMID:32111241
Genome-wide Association Analysis in Humans Links Nucleotide Metabolism to Leukocyte Telomere Length. PMID:32109421
Candidate silencer elements for the human and mouse genomes. PMID:32103011
Pathway-guided analysis identifies Myc-dependent alternative pre-mRNA splicing in aggressive prostate cancers. PMID:32086391
Passenger Mutations in More Than 2,500 Cancer Genomes: Overall Molecular Functional Impact and Consequences. PMID:32084333
PVT1 Long Non-coding RNA in Gastrointestinal Cancer. PMID:32083000
A lncRNA survey finds increases in neuroprotective LINC-PINT in Parkinson's disease substantia nigra. PMID:32080970
Skeletal Muscle Regeneration in Advanced Diabetic Peripheral Neuropathy. PMID:32059624
Exploration of databases and methods supporting drug repurposing: a comprehensive survey. PMID:32055842
A living biobank of ovarian cancer ex vivo models reveals profound mitotic heterogeneity. PMID:32054838
Novel Mutation Hotspots within Non-Coding Regulatory Regions of the Chronic Lymphocytic Leukemia Genome. PMID:32051441
Derivation of trophoblast stem cells from naïve human pluripotent stem cells. PMID:32048992
Variations and expression features of CYP2D6 contribute to schizophrenia risk. PMID:32047265
Chromatin-enriched RNAs mark active and repressive cis-regulation: An analysis of nuclear RNA-seq. PMID:32040509
CLEAR: coverage-based limiting-cell experiment analysis for RNA-seq. PMID:32039730
Systematic dissection of biases in whole-exome and whole-genome sequencing reveals major determinants of coding sequence coverage. PMID:32029882
Single-cell ATAC-Seq in human pancreatic islets and deep learning upscaling of rare cells reveals cell-specific type 2 diabetes regulatory signatures. PMID:32029221
Integrative prediction of gene expression with chromatin accessibility and conformation data. PMID:32029002
Genomic basis for RNA alterations in cancer. PMID:32025019
Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. PMID:32025015
Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis. PMID:32024996
Combined burden and functional impact tests for cancer driver discovery using DriverPower. PMID:32024818
Genomic footprints of activated telomere maintenance mechanisms in cancer. PMID:32024817
Multiplatform Molecular Profiling Reveals Epigenomic Intratumor Heterogeneity in Ependymoma. PMID:32023450
Progress in understanding the relationship between long noncoding RNA and endometriosis. PMID:32021971
Characterization of the human GnRH neuron developmental transcriptome using a GNRH1-TdTomato reporter line in human pluripotent stem cells. PMID:31996360
Refgenie: a reference genome resource manager. PMID:31995185
Longitudinal assessment of tumor development using cancer avatars derived from genetically engineered pluripotent stem cells. PMID:31992716
Functional and transcriptomic characterization of cisplatin-resistant AGS and MKN-28 gastric cancer cell lines. PMID:31990955
Whole-genome fingerprint of the DNA methylome during chemically induced differentiation of the human AML cell line HL-60/S4. PMID:31988093
Effect of eleutheroside B1 on non‑coding RNAs and protein profiles of influenza A virus‑infected A549 cells. PMID:31985023
Single-cell transcriptomics from human pancreatic islets: sample preparation matters. PMID:31984226
Reducing the structure bias of RNA-Seq reveals a large number of non-annotated non-coding RNA. PMID:31980822
Transcriptional analysis of THP-1 cells infected with Leishmania infantum indicates no activation of the inflammasome platform. PMID:31961876
Up-regulated LINC01234 promotes non-small-cell lung cancer cell metastasis by activating VAV3 and repressing BTG2 expression. PMID:31959200
Epigenetic plasticity of enhancers in cancer. PMID:31944157
YB-3 substitutes YB-1 in global mRNA binding. PMID:31944153
Targeting the Oncogenic Long Non-coding RNA SLNCR1 by Blocking Its Sequence-Specific Binding to the Androgen Receptor. PMID:31940495
Structural variation and its potential impact on genome instability: Novel discoveries in the EGFR landscape by long-read sequencing. PMID:31940362
Hepatic Tumor Formation in Adult Mice Developmentally Exposed to Organotin. PMID:31939706
Differential functional roles of fibroblasts and pericytes in the formation of tissue-engineered microvascular networks in vitro. PMID:31934351
miR-373 inhibits nasopharyngeal carcinoma cell migration and invasion by targeting MARCH5. PMID:31934093
Comprehensive transcriptome analysis of cochlear spiral ganglion neurons at multiple ages. PMID:31913118
Fine-mapping of 150 breast cancer risk regions identifies 191 likely target genes. PMID:31911677
Non-coding RNAs underlie genetic predisposition to breast cancer. PMID:31910864
Profiling of lincRNAs in human pluripotent stem cell derived forebrain neural progenitor cells. PMID:31909251
When Long Noncoding Becomes Protein Coding. PMID:31907280
LINC01714 Enhances Gemcitabine Sensitivity by Modulating FOXO3 Phosphorylation in Cholangiocarcinoma. PMID:31902744
Uncovering Biological Factors That Regulate Hepatocellular Carcinoma Growth Using Patient-Derived Xenograft Assays. PMID:31899548
In silico identification of EP400 and TIA1 as critical transcription factors involved in human hepatocellular carcinoma relapse. PMID:31897208
Cellular and molecular characterization of multiplex autism in human induced pluripotent stem cell-derived neurons. PMID:31893020
Learning distributed representations of RNA and protein sequences and its application for predicting lncRNA-protein interactions. PMID:31890140
A network view of microRNA and gene interactions in different pathological stages of colon cancer. PMID:31888617
Discovering Rare Genes Contributing to Cancer Stemness and Invasive Potential by GBM Single-Cell Transcriptional Analysis. PMID:31888172
Circ_MDM2_000139, Circ_ATF2_001418, Circ_CDC25C_002079, and Circ_BIRC6_001271 Are Involved in the Functions of XAV939 in Non-Small Cell Lung Cancer. PMID:31885751
Small noncoding RNA discovery and profiling with sRNAtools based on high-throughput sequencing. PMID:31885040
Deep sequencing and automated histochemistry of human tissue slice cultures improve their usability as preclinical model for cancer research. PMID:31882946
Deep mixed model for marginal epistasis detection and population stratification correction in genome-wide association studies. PMID:31881907
Predicted Archaic 3D Genome Organization Reveals Genes Related to Head and Spinal Cord Separating Modern from Archaic Humans. PMID:31878147
Targeted sequencing of the LRRTM gene family in suicide attempters with bipolar disorder. PMID:31854516
Integrative analyses of noncoding RNAs reveal the potential mechanisms augmenting tumor malignancy in lung adenocarcinoma. PMID:31853539
A 10-year prediagnostic follow-up study shows that serum RNA signals are highly dynamic in lung carcinogenesis. PMID:31851411
RHPCG: a database of the Regulation of the Hippo Pathway in Cancer Genome. PMID:31848596
Insights into malaria susceptibility using genome-wide data on 17,000 individuals from Africa, Asia and Oceania. PMID:31844061
The coding and non-coding transcriptional landscape of subependymal giant cell astrocytomas. PMID:31834371
A developmental landscape of 3D-cultured human pre-gastrulation embryos. PMID:31830756
Nonequilibrium Biophysical Processes Influence the Large-Scale Architecture of the Cell Nucleus. PMID:31818465
Re-annotation of 191 developmental and epileptic encephalopathy-associated genes unmasks de novo variants in SCN1A. PMID:31814998
GraphClust2: Annotation and discovery of structured RNAs with scalable and accessible integrative clustering. PMID:31808801
The distributions of protein coding genes within chromatin domains in relation to human disease. PMID:31805995
miR-181c Activates Mitochondrial Calcium Uptake by Regulating MICU1 in the Heart. PMID:31801413
Subendothelial stiffness alters endothelial cell traction force generation while exerting a minimal effect on the transcriptome. PMID:31796790
Meglumine acridone acetate, the ionic salt of CMA and N-methylglucamine, induces apoptosis in human PBMCs via the mitochondrial pathway. PMID:31796757
Multimodal Long Noncoding RNA Interaction Networks: Control Panels for Cell Fate Specification. PMID:31796550
Causal association of type 2 diabetes with amyotrophic lateral sclerosis: new evidence from Mendelian randomization using GWAS summary statistics. PMID:31796040
A novel RNA sequencing-based risk score model to predict papillary thyroid carcinoma recurrence. PMID:31792675
LncDisAP: a computation model for LncRNA-disease association prediction based on multiple biological datasets. PMID:31787106
Translated Long Non-Coding Ribonucleic Acid ZFAS1 Promotes Cancer Cell Migration by Elevating Reactive Oxygen Species Production in Hepatocellular Carcinoma. PMID:31781169
Characterization of Hepatocellular Carcinoma Cell Lines Using a Fractionation-Then-Sequencing Approach Reveals Nuclear-Enriched HCC-Associated lncRNAs. PMID:31781161
Common DNA sequence variation influences 3-dimensional conformation of the human genome. PMID:31779666
Machine Learning Approaches for the Prioritization of Genomic Variants Impacting Pre-mRNA Splicing. PMID:31779139
Heritability of skewed X-inactivation in female twins is tissue-specific and associated with age. PMID:31767861
DNA methylation aging clocks: challenges and recommendations. PMID:31767039
Recurrent somatic mutations reveal new insights into consequences of mutagenic processes in cancer. PMID:31765368
Midbrain microglia mediate a specific immunosuppressive response under inflammatory conditions. PMID:31757220
Long noncoding RNAs in lipid metabolism: literature review and conservation analysis across species. PMID:31752679
A single ChIP-seq dataset is sufficient for comprehensive analysis of motifs co-occurrence with MCOT package. PMID:31750523
The genomic landscape of metastatic castration-resistant prostate cancers reveals multiple distinct genotypes with potential clinical impact. PMID:31748536
Systematic genetic analysis of the MHC region reveals mechanistic underpinnings of HLA type associations with disease. PMID:31746734
Transposable element expression in tumors is associated with immune infiltration and increased antigenicity. PMID:31745090
Comparative genomic analysis of eutherian connexin genes. PMID:31729432
A Simple RNA Target Capture NGS Strategy for Fusion Genes Assessment in the Diagnostics of Pediatric B-cell Acute Lymphoblastic Leukemia. PMID:31723839
Recurrent functional misinterpretation of RNA-seq data caused by sample-specific gene length bias. PMID:31714939
LncTarD: a manually-curated database of experimentally-supported functional lncRNA-target regulations in human diseases. PMID:31713618
Immunological observations and transcriptomic analysis of trimester-specific full-term placentas from three Zika virus-infected women. PMID:31709049
ILF3 contributes to the establishment of the antiviral type I interferon program. PMID:31701124
Emerging Roles of Long Non-Coding RNAs as Drivers of Brain Evolution. PMID:31698782
Long-read sequencing reveals the complex splicing profile of the psychiatric risk gene CACNA1C in human brain. PMID:31695164
AIDE: annotation-assisted isoform discovery with high precision. PMID:31694868
The long noncoding RNA lncNB1 promotes tumorigenesis by interacting with ribosomal protein RPL35. PMID:31690716
Improving single-cell transcriptome sequencing efficiency with a microfluidic phase-switch device. PMID:31688860
Differentiation of Long Non-Coding RNA and mRNA Expression Profiles in Male and Female Aedes albopictus. PMID:31681418
Enhancer LncRNAs Influence Chromatin Interactions in Different Ways. PMID:31681405
The impact of proinflammatory cytokines on the β-cell regulatory landscape provides insights into the genetics of type 1 diabetes. PMID:31676868
A multi-sample approach increases the accuracy of transcript assembly. PMID:31676772
GWAS for systemic sclerosis identifies multiple risk loci and highlights fibrotic and vasculopathy pathways. PMID:31672989
Systematic Discovery of Endogenous Human Ribonucleoprotein Complexes. PMID:31665645
Metabolic reprogramming associated with aggressiveness occurs in the G-CIMP-high molecular subtypes of IDH1mut lower grade gliomas. PMID:31665443
Double triage to identify poorly annotated genes in maize: The missing link in community curation. PMID:31658277
Comparative Genomics Analysis Reveals High Levels of Differential Retrotransposition among Primates from the Hominidae and the Cercopithecidae Families. PMID:31651947
Genome-wide microhomologies enable precise template-free editing of biologically relevant deletion mutations. PMID:31649251
The RNA-binding ubiquitin ligase MKRN1 functions in ribosome-associated quality control of poly(A) translation. PMID:31640799
Loss of Imprinting in Human Placentas Is Widespread, Coordinated, and Predicts Birth Phenotypes. PMID:31639821
Comprehensive RNA-Seq Data Analysis Identifies Key mRNAs and lncRNAs in Atrial Fibrillation. PMID:31632440
LncRNA LINC01116 Promotes Cancer Cell Proliferation, Migration And Invasion In Gastric Cancer By Positively Interacting With lncRNA CASC11. PMID:31632064
Identifying regulatory pathways of spleen tyrosine kinase expression in human basophils. PMID:31629804
A Balanced Translocation in Kallmann Syndrome Implicates a Long Noncoding RNA, RMST, as a GnRH Neuronal Regulator. PMID:31628846
Genetic Control of Expression and Splicing in Developing Human Brain Informs Disease Mechanisms. PMID:31626773
The caudate nucleus undergoes dramatic and unique transcriptional changes in human prodromal Huntington's disease brain. PMID:31619230
Profiling of tRNA Halves and YRNA Fragments in Serum and Tissue From Oral Squamous Cell Carcinoma Patients Identify Key Role of 5' tRNA-Val-CAC-2-1 Half. PMID:31616639
DNA sequence-dependent chromatin architecture and nuclear hubs formation. PMID:31601866
DC3 is a method for deconvolution and coupled clustering from bulk and single-cell genomics data. PMID:31601804
The U1 spliceosomal RNA is recurrently mutated in multiple cancers. PMID:31597163
An atlas of cortical circular RNA expression in Alzheimer disease brains demonstrates clinical and pathological associations. PMID:31591557
LncRNA LUCAT1 as a novel prognostic biomarker for patients with papillary thyroid cancer. PMID:31591432
Long non-coding RNAs in cutaneous biology and proliferative skin diseases: Advances and perspectives. PMID:31588640
Realizing the potential of full-length transcriptome sequencing. PMID:31587638
Systematic profiling of alternative splicing events and splicing factors in left- and right-sided colon cancer. PMID:31586988
Plasma extracellular vesicle microRNAs for pulmonary ground-glass nodules. PMID:31579436
SFTA1P, LINC00968, GATA6-AS1, TBX5-AS1, and FEZF1-AS1 are crucial long non-coding RNAs associated with the prognosis of lung squamous cell carcinoma. PMID:31579094
The genomic landscape of metastatic breast cancer highlights changes in mutation and signature frequencies. PMID:31570896
Landscape of stimulation-responsive chromatin across diverse human immune cells. PMID:31570894
Allele-specific NKX2-5 binding underlies multiple genetic associations with human electrocardiographic traits. PMID:31570892
c-Maf regulates the plasticity of group 3 innate lymphoid cells by restraining the type 1 program. PMID:31570496
Prognostic implications of 5-hydroxymethylcytosines from circulating cell-free DNA in diffuse large B-cell lymphoma. PMID:31570490
Expression of microRNA in human retinal pigment epithelial cells following infection with Zaire ebolavirus. PMID:31570108
LNRLMI: Linear neighbour representation for predicting lncRNA-miRNA interactions. PMID:31568653
Crosstalk of mRNA, miRNA, lncRNA, and circRNA and Their Regulatory Pattern in Pulmonary Fibrosis. PMID:31561125
LINC01133 inhibits breast cancer invasion and metastasis by negatively regulating SOX4 expression through EZH2. PMID:31557401
Network-based method for drug target discovery at the isoform level. PMID:31554914
The Long Noncoding RNA HEAL Regulates HIV-1 Replication through Epigenetic Regulation of the HIV-1 Promoter. PMID:31551335
LINC00461 affects the survival of patients with renal cell carcinoma by acting as a competing endogenous RNA for microRNA‑942. PMID:31545458
Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci. PMID:31537640
Multi-omics profiling reveals key signaling pathways in ovarian cancer controlled by STAT3. PMID:31534498
Evolutionary and functional impact of common polymorphic inversions in the human genome. PMID:31530810
Sequence determinants of polyadenylation-mediated regulation. PMID:31530582
Expression of ZNF695 Transcript Variants in Childhood B-Cell Acute Lymphoblastic Leukemia. PMID:31527520
A comprehensive, multidisciplinary, precision medicine approach to discover effective therapy for an undiagnosed, progressive, fibroinflammatory disease. PMID:31520587
Gene expression profiling of single cells from archival tissue with laser-capture microdissection and Smart-3SEQ. PMID:31519740
Effect of hyperoside on cervical cancer cells and transcriptome analysis of differentially expressed genes. PMID:31516392
Possible Molecular Mechanisms for the Roles of MicroRNA-21 Played in Lung Cancer. PMID:31506038
Identifying targets for preventing epilepsy using systems biology of the human brain. PMID:31493467
A polygenic resilience score moderates the genetic risk for schizophrenia. PMID:31492941
Mitigation of off-target toxicity in CRISPR-Cas9 screens for essential non-coding elements. PMID:31492858
Interrogating Mutant Allele Expression via Customized Reference Genomes to Define Influential Cancer Mutations. PMID:31484939
Comprehensive analysis of long noncoding RNA (lncRNA)-chromatin interactions reveals lncRNA functions dependent on binding diverse regulatory elements. PMID:31484726
PredLnc-GFStack: A Global Sequence Feature Based on a Stacked Ensemble Learning Method for Predicting lncRNAs from Transcripts. PMID:31484412
Graph Convolutional Network and Convolutional Neural Network Based Method for Predicting lncRNA-Disease Associations. PMID:31480350
NET-CAGE characterizes the dynamics and topology of human transcribed cis-regulatory elements. PMID:31477927
Identification of lung-adenocarcinoma-related long non-coding RNAs by random walking on a competing endogenous RNA network. PMID:31475209
Getting the Entire Message: Progress in Isoform Sequencing. PMID:31475029
Long intergenic noncoding RNA profiles of pheochromocytoma and paraganglioma: A novel prognostic biomarker. PMID:31469413
Maximizing binary interactome mapping with a minimal number of assays. PMID:31467278
Long non-coding RNA LINC01225 promotes proliferation, invasion and migration of gastric cancer via Wnt/β-catenin signalling pathway. PMID:31460694
Modeling and analysis of RNA-seq data: a review from a statistical perspective. PMID:31456901
Exome sequencing of 457 autism families recruited online provides evidence for autism risk genes. PMID:31452935
Mapping eGFR loci to the renal transcriptome and phenome in the VA Million Veteran Program. PMID:31451708
Harnessing the tissue and plasma lncRNA-peptidome to discover peptide-based cancer biomarkers. PMID:31444383
A Phase Ib Study of the Combination of Personalized Autologous Dendritic Cell Vaccine, Aspirin, and Standard of Care Adjuvant Chemotherapy Followed by Nivolumab for Resected Pancreatic Adenocarcinoma-A Proof of Antigen Discovery Feasibility in Three Patients. PMID:31440238
The role of long non-coding RNAs in cardiac development and disease. PMID:31435517
Replication timing networks reveal a link between transcription regulatory circuits and replication timing control. PMID:31434679
Six-mRNA risk score system and nomogram constructed for patients with ovarian cancer. PMID:31423184
The nuclear hypoxia-regulated NLUCAT1 long non-coding RNA contributes to an aggressive phenotype in lung adenocarcinoma through regulation of oxidative stress. PMID:31417181
Application of the High-throughput TAB-Array for the Discovery of Novel 5-Hydroxymethylcytosine Biomarkers in Pancreatic Ductal Adenocarcinoma. PMID:31413874
EPIP: a novel approach for condition-specific enhancer-promoter interaction prediction. PMID:31410461
Whole genome and transcriptome sequencing of post-mortem cardiac tissues from sudden cardiac death victims identifies a gene regulatory variant in NEXN. PMID:31392414
Molecular architecture of lineage allocation and tissue organization in early mouse embryo. PMID:31391582
ARID1A and PI3-kinase pathway mutations in the endometrium drive epithelial transdifferentiation and collective invasion. PMID:31391455
Applications of the Soil, Plant and Rumen Microbiomes in Pastoral Agriculture. PMID:31380386
Functional genetic variants can mediate their regulatory effects through alteration of transcription factor binding. PMID:31375681
Prediction of regulatory motifs from human Chip-sequencing data using a deep learning framework. PMID:31372637
A Comprehensive Study of Vesicular and Non-Vesicular miRNAs from a Volume of Cerebrospinal Fluid Compatible with Clinical Practice. PMID:31367240
Beyond sequencing: re-visiting annotations for PJL as a test case. PMID:31366397
HUPAN: a pan-genome analysis pipeline for human genomes. PMID:31366358
The long noncoding RNA MALAT1 predicts human pancreatic islet isolation quality. PMID:31361602
Scarcity of Recurrent Regulatory Driver Mutations in Colorectal Cancer Revealed by Targeted Deep Sequencing. PMID:31360895
Mitochondrial oxidative stress-induced transcript variants of ATF3 mediate lipotoxic brain microvascular injury. PMID:31356870
An expanded landscape of human long noncoding RNA. PMID:31350901
Integrative analysis of loss-of-function variants in clinical and genomic data reveals novel genes associated with cardiovascular traits. PMID:31345219
Predicting functional long non-coding RNAs validated by low throughput experiments. PMID:31345106
Before and After: Comparison of Legacy and Harmonized TCGA Genomic Data Commons' Data. PMID:31344359
Eye in a Disk: eyeIntegration Human Pan-Eye and Body Transcriptome Database Version 1.0. PMID:31343654
Benchmark and integration of resources for the estimation of human transcription factor activities. PMID:31340985
Impact of sequencing depth and technology on de novo RNA-Seq assembly. PMID:31337347
Long Non-Coding RNA Function in CD4+ T Cells: What We Know and What Next? PMID:31336952
Identification of DNA motifs that regulate DNA methylation. PMID:31334813
AKR1D1 is a novel regulator of metabolic phenotype in human hepatocytes and is dysregulated in non-alcoholic fatty liver disease. PMID:31330134
Simultaneous RNA purification and size selection using on-chip isotachophoresis with an ionic spacer. PMID:31328753
Activation of neuronal genes via LINE-1 elements upon global DNA demethylation in human neural progenitors. PMID:31320637
NEAT1 is overexpressed in Parkinson's disease substantia nigra and confers drug-inducible neuroprotection from oxidative stress. PMID:31311324
Genome-Wide Identification and Characterization of Long Non-Coding RNAs in Peanut. PMID:31311183
Vitamin D differentially regulates colon stem cells in patient-derived normal and tumor organoids. PMID:31306552
FOXA2 Is Required for Enhancer Priming during Pancreatic Differentiation. PMID:31291575
Correlations between Genetic Polymorphisms in Long Non-Coding RNA PRNCR1 and Gastric Cancer Risk in a Korean Population. PMID:31288430
Systematic discovery of conservation states for single-nucleotide annotation of the human genome. PMID:31286065
The construction and analysis of the aberrant lncRNA-miRNA-mRNA network in non-small cell lung cancer. PMID:31285869
Gene-based analysis in HRC imputed genome wide association data identifies three novel genes for Alzheimer's disease. PMID:31283791
Predicting drug-free remission in rheumatoid arthritis: A prospective interventional cohort study. PMID:31280933
Leukocyte transcriptional signatures dependent on LPS dosage in human endotoxemia. PMID:31280495
Uncovering biomarker genes with enriched classification potential from Hallmark gene sets. PMID:31278367
TNF-α Differentially Regulates Cell Cycle Genes in Promyelocytic and Granulocytic HL-60/S4 Cells. PMID:31263060
Detecting the long non‑coding RNA signature related to spinal cord ependymal tumor subtype using a genome‑wide methylome analysis approach. PMID:31257484
Conditional Activation of NF-κB Inducing Kinase (NIK) in the Osteolineage Enhances Both Basal and Loading-Induced Bone Formation. PMID:31246323
3.5KJPNv2: an allele frequency panel of 3552 Japanese individuals including the X chromosome. PMID:31240104
Integration of CLIP experiments of RNA-binding proteins: a novel approach to predict context-dependent splicing factors from transcriptomic data. PMID:31238884
Haplotypes spanning centromeric regions reveal persistence of large blocks of archaic DNA. PMID:31237235
Molecular Traits of Long Non-protein Coding RNAs from Diverse Plant Species Show Little Evidence of Phylogenetic Relationships. PMID:31235560
Genome-Wide Analysis of Long Non-Coding RNA Profiles in Canine Oral Melanomas. PMID:31234577
PhenoScanner V2: an expanded tool for searching human genotype-phenotype associations. PMID:31233103
Accumulating computational resource usage of genomic data analysis workflow to optimize cloud computing instance selection. PMID:31222199
Two Separation-of-Function Isoforms of Human TPP1 Dictate Telomerase Regulation in Somatic and Germ Cells. PMID:31216472
p73 regulates epidermal wound healing and induced keratinocyte programming. PMID:31216312
Phytochemicals as Modulators of Long Non-Coding RNAs and Inhibitors of Cancer-Related Carbonic Anhydrases. PMID:31208095
TOX is a critical regulator of tumour-specific T cell differentiation. PMID:31207604
Evolutionary perspectives on polygenic selection, missing heritability, and GWAS. PMID:31201529
Computational Methods for Mapping, Assembly and Quantification for Coding and Non-coding Transcripts. PMID:31193391
Identification of Breast Cancer Stem Cell Related Genes Using Functional Cellular Assays Combined With Single-Cell RNA Sequencing in MDA-MB-231 Cells. PMID:31191614
LncRNA-Disease Association Prediction Using Two-Side Sparse Self-Representation. PMID:31191605
LncRRIsearch: A Web Server for lncRNA-RNA Interaction Prediction Integrated With Tissue-Specific Expression and Subcellular Localization Data. PMID:31191601
RNA sequencing uncovers the key long non-coding RNAs and potential molecular mechanism contributing to XAV939-mediated inhibition of non-small cell lung cancer. PMID:31186710
Codon usage optimization in pluripotent embryonic stem cells. PMID:31174582
Comprehensive Characterization of the Human Endogenous Retrovirus HERV-K(HML-6) Group: Overview of Structure, Phylogeny, and Contribution to the Human Genome. PMID:31167914
Phosphorylation of TET2 by AMPK is indispensable in myogenic differentiation. PMID:31164154
Integrative Analysis of Somatic Mutations in Non-coding Regions Altering RNA Secondary Structures in Cancer Genomes. PMID:31160636
Haplotype-aware diplotyping from noisy long reads. PMID:31159868
Bridging the gap between reference and real transcriptomes. PMID:31159855
Comprehensive functional profiling of long non-coding RNAs through a novel pan-cancer integration approach and modular analysis of their protein-coding gene association networks. PMID:31159744
CircRNA-100338 Is Associated With mTOR Signaling Pathway and Poor Prognosis in Hepatocellular Carcinoma. PMID:31157168
Novel Approaches in Ovarian Cancer Research against Heterogeneity, Late Diagnosis, Drug Resistance, and Transcoelomic Metastases. PMID:31146417
Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism risk. PMID:31133750
Genetic analyses of human fetal retinal pigment epithelium gene expression suggest ocular disease mechanisms. PMID:31123710
MetaDome: Pathogenicity analysis of genetic variants through aggregation of homologous human protein domains. PMID:31116477
Genetics of heart rate in heart failure patients (GenHRate). PMID:31113495
Epigenetic evolution and lineage histories of chronic lymphocytic leukaemia. PMID:31092926
Identification of Cancer Drivers at CTCF Insulators in 1,962 Whole Genomes. PMID:31078526
A Quantitative and Predictive Model for RNA Binding by Human Pumilio Proteins. PMID:31078383
Tissue-specific genes as an underutilized resource in drug discovery. PMID:31076736
Large-scale in-silico identification of a tumor-specific antigen pool for targeted immunotherapy in triple-negative breast cancer. PMID:31069014
Pancreatic islet chromatin accessibility and conformation reveals distal enhancer networks of type 2 diabetes risk. PMID:31064983
Human transposons are an abundant supply of transcription factor binding sites and promoter activities in breast cancer cell lines. PMID:31061680
A five lncRNA signature for prognosis prediction in hepatocellular carcinoma. PMID:31059056
Differential methylation of enhancer at IGF2 is associated with abnormal dopamine synthesis in major psychosis. PMID:31053723
Identification and Quantification of Proteoforms by Mass Spectrometry. PMID:31050378
EpiAlign: an alignment-based bioinformatic tool for comparing chromatin state sequences. PMID:31045217
Loss of Nuclear TDP-43 Is Associated with Decondensation of LINE Retrotransposons. PMID:31042469
ClinOmicsTrailbc: a visual analytics tool for breast cancer treatment stratification. PMID:31038669
Complement C7 is a novel risk gene for Alzheimer's disease in Han Chinese. PMID:31032141
A Panel of 12-lncRNA Signature Predicts Survival of Pancreatic Adenocarcinoma. PMID:31031865
Targeted, High-Resolution RNA Sequencing of Non-coding Genomic Regions Associated With Neuropsychiatric Functions. PMID:31031799
PseudoFuN: Deriving functional potentials of pseudogenes from integrative relationships with genes and microRNAs across 32 cancers. PMID:31029062
African evolutionary history inferred from whole genome sequence data of 44 indigenous African populations. PMID:31023338
RNA Sequencing Analyses of Gene Expression during Epstein-Barr Virus Infection of Primary B Lymphocytes. PMID:31019051
Transcriptome Alterations in Liver Metastases of Colorectal Cancer After Acquired Resistance to Cetuximab. PMID:31018951
An integrated analysis reveals the oncogenic function of lncRNA LINC00511 in human ovarian cancer. PMID:31016892
Corrupted coordination of epigenetic modifications leads to diverging chromatin states and transcriptional heterogeneity in CLL. PMID:31015400
SNHG15 is a bifunctional MYC-regulated noncoding locus encoding a lncRNA that promotes cell proliferation, invasion and drug resistance in colorectal cancer by interacting with AIF. PMID:31014355
Applications of ENCODE data to Systematic Analyses via Data Integration. PMID:31011690
BayesPI-BAR2: A New Python Package for Predicting Functional Non-coding Mutations in Cancer Patient Cohorts. PMID:31001324
NF-κB Signaling and IL-4 Signaling Regulate SATB1 Expression via Alternative Promoter Usage During Th2 Differentiation. PMID:31001272
Evidence for an oncogenic role of HOXC6 in human non-small cell lung cancer. PMID:30993034
Prediction of Long Non-Coding RNAs Based on Deep Learning. PMID:30987229
Integrated Transcriptomic and Proteomic Analysis of Primary Human Umbilical Vein Endothelial Cells. PMID:30983154
Promoter-Intrinsic and Local Chromatin Features Determine Gene Repression in LADs. PMID:30982597
Mapping the transcriptional diversity of genetically and anatomically defined cell populations in the mouse brain. PMID:30977723
Pan-cancer analysis on microRNA-associated gene activation. PMID:30956173
exceRpt: A Comprehensive Analytic Platform for Extracellular RNA Profiling. PMID:30956140
High resolution discovery of chromatin interactions. PMID:30953075
PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing data. PMID:30951143
ADAR1 promotes robust hypoxia signaling via distinct regulation of multiple HIF-1α-inhibiting factors. PMID:30948460
TranscriptAchilles: a genome-wide platform to predict isoform biomarkers of gene essentiality in cancer. PMID:30942869
The lncRNA Neat1 promotes activation of inflammasomes in macrophages. PMID:30940803
Transposable elements drive widespread expression of oncogenes in human cancers. PMID:30926969
Electrotaxis of Glioblastoma and Medulloblastoma Spheroidal Aggregates. PMID:30926929
Combinatorial interactions of genetic variants in human cardiomyopathy. PMID:30923642
FactorNet: A deep learning framework for predicting cell type specific transcription factor binding from nucleotide-resolution sequential data. PMID:30922998
Diagnosis of fusion genes using targeted RNA sequencing. PMID:30918253
Dual RNA-Seq of Human Leprosy Lesions Identifies Bacterial Determinants Linked to Host Immune Response. PMID:30917313
Integrative transcriptomic analysis suggests new autoregulatory splicing events coupled with nonsense-mediated mRNA decay. PMID:30916337
Developing a network view of type 2 diabetes risk pathways through integration of genetic, genomic and functional data. PMID:30914061
Contribution of ultrarare variants in mTOR pathway genes to sporadic focal epilepsies. PMID:30911571
Functional and transcriptomic characterization of carboplatin-resistant A2780 ovarian cancer cell line. PMID:30894224
Transcriptome Analysis of the Human Tibial Nerve Identifies Sexually Dimorphic Expression of Genes Involved in Pain, Inflammation, and Neuro-Immunity. PMID:30890918
The Proteogenomic Landscape of Curable Prostate Cancer. PMID:30889379
HOXC6 promotes migration, invasion and proliferation of esophageal squamous cell carcinoma cells via modulating expression of genes involved in malignant phenotypes. PMID:30886783
Genetic Association of Olanzapine Treatment Response in Han Chinese Schizophrenia Patients. PMID:30886581
Long Noncoding RNA MPRL Promotes Mitochondrial Fission and Cisplatin Chemosensitivity via Disruption of Pre-miRNA Processing. PMID:30885939
Evaluating and sharing global genetic ancestry in biomedical datasets. PMID:30869786
Liquid Biopsies in Lung Cancer: Four Emerging Technologies and Potential Clinical Applications. PMID:30866571
Genome-wide analysis of long non-coding RNA expression profile in porcine circovirus 2-infected intestinal porcine epithelial cell line by RNA sequencing. PMID:30863688
Correlations of lncRNAs with cervical lymph node metastasis and prognosis of papillary thyroid carcinoma. PMID:30863094
Drug repositioning in epilepsy reveals novel antiseizure candidates. PMID:30847362
The cellular landscape of mid-size noncoding RNA. PMID:30843375
svist4get: a simple visualization tool for genomic tracks from sequencing experiments. PMID:30841857
Multi-Omics Approaches to Study Long Non-coding RNA Function in Atherosclerosis. PMID:30838214
Integrative Analysis Reveals Key Circular RNA in Atrial Fibrillation. PMID:30838031
Shortage of Cellular ATP as a Cause of Diseases and Strategies to Enhance ATP. PMID:30837873
Drug Repurposing: The Anthelmintics Niclosamide and Nitazoxanide Are Potent TMEM16A Antagonists That Fully Bronchodilate Airways. PMID:30837866
Shared and unique genomic structural variants of different histological components within testicular germ cell tumours identified with mate pair sequencing. PMID:30837548
Subtle changes in chromatin loop contact propensity are associated with differential gene regulation and expression. PMID:30837461
Revealing Gene Function and Transcription Relationship by Reconstructing Gene-Level Chromatin Interaction. PMID:30828411
Genetic meta-analysis of diagnosed Alzheimer's disease identifies new risk loci and implicates Aβ, tau, immunity and lipid processing. PMID:30820047
Circular RNA expression profiles in neonatal rats following hypoxic-ischemic brain damage. PMID:30816430
RREB1-induced upregulation of the lncRNA AGAP2-AS1 regulates the proliferation and migration of pancreatic cancer partly through suppressing ANKRD1 and ANGPTL4. PMID:30814490
BGFE: A Deep Learning Model for ncRNA-Protein Interaction Predictions Based on Improved Sequence Information. PMID:30813451
Identification of lncRNA TRPM2-AS/miR-140-3p/PYCR1 axis's proliferates and anti-apoptotic effect on breast cancer using co-expression network analysis. PMID:30810442
Extensive epigenomic integration of the glucocorticoid response in primary human monocytes and in vitro derived macrophages. PMID:30809020
SELER: a database of super-enhancer-associated lncRNA- directed transcriptional regulation in human cancers. PMID:30806704
New guidelines for DNA methylome studies regarding 5-hydroxymethylcytosine for understanding transcriptional regulation. PMID:30782641
CVm6A: A Visualization and Exploration Database for m⁶As in Cell Lines. PMID:30781586
Long non-coding RNAs discriminate the stages and gene regulatory states of human humoral immune response. PMID:30778059
Hypomorphic Mutations in TONSL Cause SPONASTRIME Dysplasia. PMID:30773278
Role of Noncoding RNAs in the Pathogenesis of Abdominal Aortic Aneurysm. PMID:30763215
Epigenetic findings in periodontitis in UK twins: a cross-sectional study. PMID:30760334
Whole-genome sequencing identifies ADGRG6 enhancer mutations and FRS2 duplications as angiogenesis-related drivers in bladder cancer. PMID:30755618
Histone deacetylase inhibitors induce complex host responses that contribute to differential potencies of these compounds in HIV reactivation. PMID:30745362
PUMILIO hyperactivity drives premature aging of Norad-deficient mice. PMID:30735131
Proposal for Modification of Cahan's Criteria Utilizing Molecular Genetic Analyses for Cases without Baseline Histopathology: A Unique Method Applicable to Primary Radiosurgery. PMID:30733895
RNA-Seq Signatures Normalized by mRNA Abundance Allow Absolute Deconvolution of Human Immune Cell Types. PMID:30726743
RNA-Seq profiling in peripheral blood mononuclear cells of amyotrophic lateral sclerosis patients and controls. PMID:30720798
The circRNA-microRNA code: emerging implications for cancer diagnosis and treatment. PMID:30719845
Differentiation of human pluripotent stem cells into neurons or cortical organoids requires transcriptional co-regulation by UTX and 53BP1. PMID:30718900
The methylome of the celiac intestinal epithelium harbours genotype-independent alterations in the HLA region. PMID:30718669
Identification of the targets of hematoporphyrin derivative in lung adenocarcinoma using integrated network analysis. PMID:30717818
Prohibitin: A hypothetical target for sex-based new therapeutics for metabolic and immune diseases. PMID:30717609
Bioinformatics analysis to identify the key genes affecting the progression and prognosis of hepatocellular carcinoma. PMID:30705088
Generative modeling of multi-mapping reads with mHi-C advances analysis of Hi-C studies. PMID:30702424
Detection of RNA-DNA binding sites in long noncoding RNAs. PMID:30698727
GARFIELD classifies disease-relevant genomic features through integration of functional annotations with association signals. PMID:30692680
EnhancerDB: a resource of transcriptional regulation in the context of enhancers. PMID:30689845
High-throughput functional analysis of lncRNA core promoters elucidates rules governing tissue specificity. PMID:30683753
Multiple-gene targeting and mismatch tolerance can confound analysis of genome-wide pooled CRISPR screens. PMID:30683138
Immune regulation by glucocorticoids can be linked to cell type-dependent transcriptional responses. PMID:30674564
Enhancer hijacking activates oncogenic transcription factor NR4A3 in acinic cell carcinomas of the salivary glands. PMID:30664630
Incorporation of long non-coding RNA expression profile in the 2017 ELN risk classification can improve prognostic prediction of acute myeloid leukemia patients. PMID:30662003
Propofol Suppresses Proinflammatory Cytokine Production by Increasing ABCA1 Expression via Mediation by the Long Noncoding RNA LOC286367. PMID:30647536
pblat: a multithread blat algorithm speeding up aligning sequences to genomes. PMID:30646844
Neuronal brain-region-specific DNA methylation and chromatin accessibility are associated with neuropsychiatric trait heritability. PMID:30643296
Invited Review: Long non-coding RNAs: important regulators in the development, function and disorders of the central nervous system. PMID:30636336
The Circulating Transcriptome as a Source of Biomarkers for Melanoma. PMID:30634628
Treatment of two mitochondrial disease patients with a combination of febuxostat and inosine that enhances cellular ATP. PMID:30631120
Accurate prediction of cell type-specific transcription factor binding. PMID:30630522
West Nile Virus-Inclusive Single-Cell RNA Sequencing Reveals Heterogeneity in the Type I Interferon Response within Single Cells. PMID:30626670
Interpreting Non-coding Genetic Variation in Multiple Sclerosis Genome-Wide Associated Regions. PMID:30619471
The Role of Histone Methyltransferases and Long Non-coding RNAs in the Regulation of T Cell Fate Decisions. PMID:30619315
Antisense Transcription in Loci Associated to Hereditary Neurodegenerative Diseases. PMID:30610612
Isolation and genome-wide characterization of cellular DNA:RNA triplex structures. PMID:30605520
Trans-ethnic kidney function association study reveals putative causal genes and effects on kidney-specific disease aetiologies. PMID:30604766
Balancing yield, purity and practicality: a modified differential ultracentrifugation protocol for efficient isolation of small extracellular vesicles from human serum. PMID:30604646
Oligomeric proanthocyanidins (OPCs) from grape seed extract suppress the activity of ABC transporters in overcoming chemoresistance in colorectal cancer cells. PMID:30596962
A longitudinal systems immunologic investigation of acute Zika virus infection in an individual infected while traveling to Caracas, Venezuela. PMID:30596671
Discerning novel splice junctions derived from RNA-seq alignment: a deep learning approach. PMID:30591034
Ancient exapted transposable elements promote nuclear enrichment of human long noncoding RNAs. PMID:30587508
Pathogenicity and selective constraint on variation near splice sites. PMID:30587507
Current perspectives in assessing humoral immunity after measles vaccination. PMID:30585753
RNA element discovery from germ cell to blastocyst. PMID:30576549
Generation of an immortalized human choroid endothelial cell line (iChEC-1) using an endothelial cell specific promoter. PMID:30571950
Anchor: trans-cell type prediction of transcription factor binding sites. PMID:30567711
Measures of co-expression for improved function prediction of long non-coding RNAs. PMID:30567492
A Cellular Anatomy of the Normal Adult Human Prostate and Prostatic Urethra. PMID:30566875
Relative impact of indels versus SNPs on complex disease. PMID:30565766
An evolutionary framework for measuring epigenomic information and estimating cell-type-specific fitness consequences. PMID:30559490
Co-expression of long non-coding RNAs and autism risk genes in the developing human brain. PMID:30547845
Long noncoding RNAs of single hematopoietic stem and progenitor cells in healthy and dysplastic human bone marrow. PMID:30545929
Transcriptome and epigenome landscape of human cortical development modeled in organoids. PMID:30545853
Genome-wide de novo risk score implicates promoter variation in autism spectrum disorder. PMID:30545852
Significantly altered peripheral blood cell DNA methylation profile as a result of immediate effect of metformin use in healthy individuals. PMID:30545422
Mapping of γ/δ T cells reveals Vδ2+ T cells resistance to senescence. PMID:30528453
Bi-allelic TMEM94 Truncating Variants Are Associated with Neurodevelopmental Delay, Congenital Heart Defects, and Distinct Facial Dysmorphism. PMID:30526868
Rapid reversible changes in compartments and local chromatin organization revealed by hyperosmotic shock. PMID:30523037
The transcription factors TFE3 and TFEB amplify p53 dependent transcriptional programs in response to DNA damage. PMID:30520728
Circulating small non-coding RNAs associated with age, sex, smoking, body mass and physical activity. PMID:30518766
Interactome determination of a Long Noncoding RNA implicated in Embryonic Stem Cell Self-Renewal. PMID:30514857
Transcript- and protein-level analyses of the response of human eosinophils to glucocorticoids. PMID:30512017
Multifocal Versus Conventional Unifocal Diverticulitis: A Comparison of Clinical and Transcriptomic Characteristics. PMID:30511196
OUTRIDER: A Statistical Method for Detecting Aberrantly Expressed Genes in RNA Sequencing Data. PMID:30503520
CHESS: a new human gene catalog curated from thousands of large-scale RNA sequencing experiments reveals extensive transcriptional noise. PMID:30486838
Discovery of the first genome-wide significant risk loci for attention deficit/hyperactivity disorder. PMID:30478444
Pooled extracellular receptor-ligand interaction screening using CRISPR activation. PMID:30477585
SMuRF: a novel tool to identify regulatory elements enriched for somatic point mutations. PMID:30477433
MIR sequences recruit zinc finger protein ZNF768 to expressed genes. PMID:30476274
Long non-coding RNAs in hematological malignancies: translating basic techniques into diagnostic and therapeutic strategies. PMID:30466456
Hepatic gene body hypermethylation is a shared epigenetic signature of murine longevity. PMID:30462643
BPLLDA: Predicting lncRNA-Disease Associations Based on Simple Paths With Limited Lengths in a Heterogeneous Network. PMID:30459803
ASGAL: aligning RNA-Seq data to a splicing graph to detect novel alternative splicing events. PMID:30458725
CARM1 methylates MED12 to regulate its RNA-binding ability. PMID:30456381
Widespread roles of enhancer-like transposable elements in cell identity and long-range genomic interactions. PMID:30455182
Insights into mammalian transcription control by systematic analysis of ChIP sequencing data. PMID:30453943
Impact of Genetic Polymorphisms on Human Immune Cell Gene Expression. PMID:30449622
RNAct: Protein-RNA interaction predictions for model organisms with supporting experimental data. PMID:30445601
Splicing of long non-coding RNAs primarily depends on polypyrimidine tract and 5' splice-site sequences due to weak interactions with SR proteins. PMID:30445574
PAVOOC: designing CRISPR sgRNAs using 3D protein structures and functional domain annotations. PMID:30445568
Micro-Inversions In Human Cancer Genomes. PMID:30440635
Expression of mitochondrial dysfunction-related genes and pathways in paclitaxel-induced peripheral neuropathy in breast cancer survivors. PMID:30426838
Non-coding RNAome of RPE cells under oxidative stress suggests unknown regulative aspects of Retinitis pigmentosa etiopathogenesis. PMID:30413775
Ongoing human chromosome end extension revealed by analysis of BioNano and nanopore data. PMID:30413723
The DEK Oncoprotein Functions in Ovarian Cancer Growth and Survival. PMID:30412857
A Potential Competitive Endogenous RNA Pathway Involved in Chronic Spinal Cord Injury. PMID:30411720
FusionGDB: fusion gene annotation DataBase. PMID:30407583
Update of the FANTOM web resource: expansion to provide additional transcriptome atlases. PMID:30407557
Lnc2Cancer v2.0: updated database of experimentally supported long non-coding RNAs in human cancers. PMID:30407549
The UCSC Genome Browser database: 2019 update. PMID:30407534
WebCircRNA: Classifying the Circular RNA Potential of Coding and Noncoding RNA. PMID:30404245
Localizing and Classifying Adaptive Targets with Trend Filtered Regression. PMID:30398642
Longitudinal personal DNA methylome dynamics in a human with a chronic condition. PMID:30397358
A Prognostic Signature for Lower Grade Gliomas Based on Expression of Long Non-Coding RNAs. PMID:30392137
A phylogenomic study quantifies competing mechanisms for pseudogenization in prokaryotes-The Mycobacterium leprae case. PMID:30383852
Improved Macaca fascicularis gene annotation reveals evolution of gene expression profiles in multiple tissues. PMID:30382841
LncRNA2Target v2.0: a comprehensive database for target genes of lncRNAs in human and mouse. PMID:30380072
Whole-Genome Alignment and Comparative Annotation. PMID:30379572
Tumor suppressor PNRC1 blocks rRNA maturation by recruiting the decapping complex to the nucleolus. PMID:30373810
LNCipedia 5: towards a reference set of human long non-coding RNAs. PMID:30371849
DUXAP8, a pseudogene derived lncRNA, promotes growth of pancreatic carcinoma cells by epigenetically silencing CDKN1A and KLF2. PMID:30367681
Cancer type prediction based on copy number aberration and chromatin 3D structure with convolutional neural networks. PMID:30367576
CircRNA-associated ceRNA network reveals ErbB and Hippo signaling pathways in hypopharyngeal cancer. PMID:30365065
EWAS Atlas: a curated knowledgebase of epigenome-wide association studies. PMID:30364969
Discordant roles for FGF ligands in lung branching morphogenesis between human and mouse. PMID:30357827
GENCODE reference annotation for the human and mouse genomes. PMID:30357393
CORUM: the comprehensive resource of mammalian protein complexes-2019. PMID:30357367
Genome-wide map of human and mouse transcription factor binding sites aggregated from ChIP-Seq data. PMID:30352610
Deleterious variation shapes the genomic landscape of introgression. PMID:30346959
From De Novo to "De Nono": The Majority of Novel Protein-Coding Genes Identified with Phylostratigraphy Are Old Genes or Recent Duplicates. PMID:30346517
Bridging Synaptic and Epigenetic Maintenance Mechanisms of the Engram. PMID:30344478
Smoking induces coordinated DNA methylation and gene expression changes in adipose tissue with consequences for metabolic health. PMID:30342560
SeqOthello: querying RNA-seq experiments at scale. PMID:30340508
Discovering in vivo cytokine-eQTL interactions from a lupus clinical trial. PMID:30340504
Up-regulation of the kinase gene SGK1 by progesterone activates the AP-1-NDRG1 axis in both PR-positive and -negative breast cancer cells. PMID:30337371
Comprehensive analysis of long noncoding RNA expression in dorsal root ganglion reveals cell-type specificity and dysregulation after nerve injury. PMID:30335683
PopHumanScan: the online catalog of human genome adaptation. PMID:30335169
Long noncoding RNA NBAT1 inhibits autophagy via suppression of ATG7 in non-small cell lung cancer. PMID:30323972
Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells. PMID:30320766
Dlk1-Dio3 locus-derived lncRNAs perpetuate postmitotic motor neuron cell fate and subtype identity. PMID:30311912
New players in chronic lung disease identified at the European Respiratory Society International Congress in Paris 2018: from microRNAs to extracellular vesicles. PMID:30310685
Thyroid hormone signaling specifies cone subtypes in human retinal organoids. PMID:30309916
Examining the contribution of smoking and HPV towards the etiology of oral cavity squamous cell carcinoma using high-throughput sequencing: A prospective observational study. PMID:30308005
Complement receptor CD46 co-stimulates optimal human CD8+ T cell effector function via fatty acid metabolism. PMID:30305631
Expression analysis of lncRNA AK370814 involved in the barley vitamin B6 salvage pathway under salinity. PMID:30298351
Epigenomic map of human liver reveals principles of zonated morphogenic and metabolic control. PMID:30297808
Shark genomes provide insights into elasmobranch evolution and the origin of vertebrates. PMID:30297745
Long non-coding RNA AFAP1-AS1 plays an oncogenic role in promoting cell migration in non-small cell lung cancer. PMID:30293090
Repurposing of promoters and enhancers during mammalian evolution. PMID:30287902
Single-cell transcriptomes reveal the mechanism for a breast cancer prognostic gene panel. PMID:30279960
Long Noncoding RNA Signature and Disease Outcome in Estrogen Receptor-Positive Breast Cancer Patients Treated with Tamoxifen. PMID:30275856
Renal compartment-specific genetic variation analyses identify new pathways in chronic kidney disease. PMID:30275566
Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci. PMID:30275530
New insights into the cellular temporal response to proteostatic stress. PMID:30272558
MiPanda: A Resource for Analyzing and Visualizing Next-Generation Sequencing Transcriptomics Data. PMID:30268942
Human genes: Time to follow the roads less traveled? PMID:30256779
The synthetic histone-binding regulator protein PcTF activates interferon genes in breast cancer cells. PMID:30253781
Profiles of alternative splicing in colorectal cancer and their clinical significance: A study based on large-scale sequencing data. PMID:30243491
A differential host response to viral infection defines a subset of earlier-onset diverticulitis patients. PMID:30240468
POSTAR2: deciphering the post-transcriptional regulatory logics. PMID:30239819
Identifying core biological processes distinguishing human eye tissues with precise systems-level gene expression analyses and weighted correlation networks. PMID:30239781
The long non-coding RNA NEAT1 is elevated in polyglutamine repeat expansion diseases and protects from disease gene-dependent toxicities. PMID:30239724
Integrating hypertension phenotype and genotype with hybrid non-negative matrix factorization. PMID:30239588
New Insights Into the Long Non-coding RNA SRA: Physiological Functions and Mechanisms of Action. PMID:30238005
mRNA circularization by METTL3-eIF3h enhances translation and promotes oncogenesis. PMID:30232453
Transcriptional fates of human-specific segmental duplications in brain. PMID:30228200
Genome-wide identification of tissue-specific long non-coding RNA in three farm animal species. PMID:30227846
Enhancers active in dopamine neurons are a primary link between genetic variation and neuropsychiatric disease. PMID:30224808
Insights into the Influence of Specific Splicing Events on the Structural Organization of LRRK2. PMID:30223621
lncSLdb: a resource for long non-coding RNA subcellular localization. PMID:30219837
A combination of curcumin and oligomeric proanthocyanidins offer superior anti-tumorigenic properties in colorectal cancer. PMID:30218018
A pan-cancer atlas of cancer hallmark-associated candidate driver lncRNAs. PMID:30216655
Beyond the 3'UTR binding-microRNA-induced protein truncation via DNA binding. PMID:30214689
Refined RIP-seq protocol for epitranscriptome analysis with low input materials. PMID:30212448
The genetic basis and cell of origin of mixed phenotype acute leukaemia. PMID:30209392
Terminal exon characterization with TECtool reveals an abundance of cell-specific isoforms. PMID:30202060
Long noncoding RNA LERFS negatively regulates rheumatoid synovial aggression and proliferation. PMID:30198906
Targeting the IGF1R Pathway in Breast Cancer Using Antisense lncRNA-Mediated Promoter cis Competition. PMID:30195750
Characterisation and functional predictions of canine long non-coding RNAs. PMID:30194329
Linking prostate cancer cell AR heterogeneity to distinct castration and enzalutamide responses. PMID:30190514
ZFAS1: a novel tumor-related long non-coding RNA. PMID:30186041
Pairs of Adjacent Conserved Noncoding Elements Separated by Conserved Genomic Distances Act as Cis-Regulatory Units. PMID:30184074
Integration of gene interaction information into a reweighted random survival forest approach for accurate survival prediction and survival biomarker discovery. PMID:30181543
Discovering lncRNA mediated sponge interactions in breast cancer molecular subtypes. PMID:30180792
RibORF: Identifying Genome-Wide Translated Open Reading Frames Using Ribosome Profiling. PMID:30178897
Transcriptomic analysis reveals key lncRNAs associated with ribosomal biogenesis and epidermis differentiation in head and neck squamous cell carcinoma. PMID:30178634
Deficiency in the nuclear long noncoding RNA Charme causes myogenic defects and heart remodeling in mice. PMID:30177572
Long non-coding RNAs in the failing heart and vasculature. PMID:30175285
Molecular mechanism of activated T cells in breast cancer. PMID:30174439
ANNOgesic: a Swiss army knife for the RNA-seq based annotation of bacterial/archaeal genomes. PMID:30169674
High-affinity RNA targets of the Survival Motor Neuron protein reveal diverse preferences for sequence and structural motifs. PMID:30165668
Function of HNRNPC in breast cancer cells by controlling the dsRNA-induced interferon response. PMID:30158112
Genomic meta-analysis of the interplay between 3D chromatin organization and gene expression programs under basal and stress conditions. PMID:30157915
Mechanisms of Huangqi Decoction Granules () on Hepatitis B Cirrhosis Patients Based on RNA-Sequencing. PMID:30155678
Mapping 3D genome organization relative to nuclear compartments using TSA-Seq as a cytological ruler. PMID:30154186
The DNA methylation landscape of glioblastoma disease progression shows extensive heterogeneity in time and space. PMID:30150718
Genome-wide identification of clusters of predicted microRNA binding sites as microRNA sponge candidates. PMID:30142196
Long Non-Coding RNAs Guide the Fine-Tuning of Gene Regulation in B-Cell Development and Malignancy. PMID:30134619
Dysregulation of lncRNAs GM5524 and GM15645 involved in high‑glucose‑induced podocyte apoptosis and autophagy in diabetic nephropathy. PMID:30132544
Isoform-Level Interpretation of High-Throughput Proteomics Data Enabled by Deep Integration with RNA-seq. PMID:30125121
Alternative splicing expands the prognostic impact of KRAS in microsatellite stable primary colorectal cancer. PMID:30121958
Intron retention is a source of neoepitopes in cancer. PMID:30114007
Whole exome sequencing study identifies novel rare and common Alzheimer's-Associated variants involved in immune response and transcriptional regulation. PMID:30108311
Human proteins that interact with RNA/DNA hybrids. PMID:30108179
Risk assessment model constructed by differentially expressed lncRNAs for the prognosis of glioma. PMID:30106138
Identification of LINC01279 as a cell cycle‑associated long non‑coding RNA in endometriosis with GBA analysis. PMID:30106115
The landscape of the A-to-I RNA editome from 462 human genomes. PMID:30104667
Glucocorticoid receptor recruits to enhancers and drives activation by motif-directed binding. PMID:30097539
Curating Clinically Relevant Transcripts for the Interpretation of Sequence Variants. PMID:30096381
iMapSplice: Alleviating reference bias through personalized RNA-seq alignment. PMID:30096157
Bioinformatics-based analysis of the involvement of AC005550.3, RP11-415D17.3, and RP1-140K8.5 in homocysteine-induced vascular endothelial injury. PMID:30093949
LncFinder: an integrated platform for long non-coding RNA identification utilizing sequence intrinsic composition, structural information and physicochemical property. PMID:30084867
Detection and benchmarking of somatic mutations in cancer genomes using RNA-seq data. PMID:30083469
KDM5 histone demethylases repress immune response via suppression of STING. PMID:30080846
The Long Noncoding RNA Landscape in Amygdala Tissues from Schizophrenia Patients. PMID:30077719
Non-coding RNAs: the riddle of the transcriptome and their perspectives in cancer. PMID:30069443
Single-cell RNA-seq uncovers dynamic processes and critical regulators in mouse spermatogenesis. PMID:30061742
exoRBase: a database of circRNA, lncRNA and mRNA in human blood exosomes. PMID:30053265
Mobile elements contribute to the uniqueness of human genome with 15,000 human-specific insertions and 14 Mbp sequence increase. PMID:30052927
PausePred and Rfeet: webtools for inferring ribosome pauses and visualizing footprint density from ribosome profiling data. PMID:30049792
Functional aspects of meningeal lymphatics in ageing and Alzheimer's disease. PMID:30046111
A patient-derived xenograft pre-clinical trial reveals treatment responses and a resistance mechanism to karonudib in metastatic melanoma. PMID:30042422
Coregulation of alternative splicing by hnRNPM and ESRP1 during EMT. PMID:30042172
Comprehensive map of age-associated splicing changes across human tissues and their contributions to age-associated diseases. PMID:30026530
Photosensitivity and type I IFN responses in cutaneous lupus are driven by epidermal-derived interferon kappa. PMID:30021804
The Role of Long Non-coding RNAs in the Pathogenesis of RA, SLE, and SS. PMID:30018955
An Evolutionary Mechanism for the Generation of Competing RNA Structures Associated with Mutually Exclusive Exons. PMID:30018239
Matataki: an ultrafast mRNA quantification method for large-scale reanalysis of RNA-Seq data. PMID:30012088
Cancerin: A computational pipeline to infer cancer-associated ceRNA interaction networks. PMID:30011266
Genome-wide association study: Exploring the genetic basis for responsiveness to ketogenic dietary therapies for drug-resistant epilepsy. PMID:30009487
Comparative genomic analysis of eutherian adiponectin genes. PMID:30003153
Downregulation of lncRNA OGFRP1 inhibits hepatocellular carcinoma progression by AKT/mTOR and Wnt/β-catenin signaling pathways. PMID:29997441
Prioritization and functional assessment of noncoding variants associated with complex diseases. PMID:29996888
A deep recurrent neural network discovers complex biological rules to decipher RNA protein-coding potential. PMID:29986088
Identification of transcribed protein coding sequence remnants within lincRNAs. PMID:29986053
Mettl1/Wdr4-Mediated m7G tRNA Methylome Is Required for Normal mRNA Translation and Embryonic Stem Cell Self-Renewal and Differentiation. PMID:29983320
Loose ends: almost one in five human genes still have unresolved coding status. PMID:29982784
Clinker: visualizing fusion genes detected in RNA-seq data. PMID:29982439
Principles for targeting RNA with drug-like small molecules. PMID:29977051
Consensus molecular subtype classification of colorectal adenomas. PMID:29968252
Extracellular vesicles in DLBCL provide abundant clues to aberrant transcriptional programming and genomic alterations. PMID:29967128
Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line. PMID:29954844
Integrated pathogen load and dual transcriptome analysis of systemic host-pathogen interactions in severe malaria. PMID:29950443
COSSMO: predicting competitive alternative splice site selection using deep learning. PMID:29949959
Evidence for plant-derived xenomiRs based on a large-scale analysis of public small RNA sequencing data from human samples. PMID:29949574
Platforms for Investigating LncRNA Functions. PMID:29945466
Ribosome elongating footprints denoised by wavelet transform comprehensively characterize dynamic cellular translation events. PMID:29945224
Toward predictive R-loop computational biology: genome-scale prediction of R-loops reveals their association with complex promoter structures, G-quadruplexes and transcriptionally active enhancers. PMID:29945198
Neuronal integrity and complement control synaptic material clearance by microglia after CNS injury. PMID:29941548
Exploring the functional impact of alternative splicing on human protein isoforms using available annotation sources. PMID:29931155
Germline genetic variants were interactively associated with somatic alterations in gastric cancer. PMID:29923336
Identification of differential expressed lncRNAs in human thyroid cancer by a genome-wide analyses. PMID:29923329
Identifying autophagy gene-associated module biomarkers through construction and analysis of an autophagy-mediated ceRNA‑ceRNA interaction network in colorectal cancer. PMID:29916526
In silico read normalization using set multi-cover optimization. PMID:29912280
Integrative Analysis of Dysregulated lncRNA-Associated ceRNA Network Reveals Functional lncRNAs in Gastric Cancer. PMID:29912172
Genome-wide association study in Japanese females identifies fifteen novel skin-related trait associations. PMID:29895819
Pharmacological and genomic profiling of neurofibromatosis type 1 plexiform neurofibroma-derived schwann cells. PMID:29893754
Multi-ethnic genome-wide association study for atrial fibrillation. PMID:29892015
Identifying gene targets for brain-related traits using transcriptomic and methylomic data from blood. PMID:29891976
Comparative Annotation Toolkit (CAT)-simultaneous clade and personal genome annotation. PMID:29884752
Genome-wide association study of extreme high bone mass: Contribution of common genetic variation to extreme BMD phenotypes and potential novel BMD-associated genes. PMID:29883787
High-resolution comparative analysis of great ape genomes. PMID:29880660
Chromatin Landscape Distinguishes the Genomic Loci of Hundreds of Androgen-Receptor-Associated LincRNAs From the Loci of Non-associated LincRNAs. PMID:29875794
Comprehensive comparative analysis of 5'-end RNA-sequencing methods. PMID:29867192
Ubiquitination of ABCE1 by NOT4 in Response to Mitochondrial Damage Links Co-translational Quality Control to PINK1-Directed Mitophagy. PMID:29861391
A Deep Learning Framework for Robust and Accurate Prediction of ncRNA-Protein Interactions Using Evolutionary Information. PMID:29858068
Japanese GWAS identifies variants for bust-size, dysmenorrhea, and menstrual fever that are eQTLs for relevant protein-coding or long non-coding RNAs. PMID:29855537
Organoid Profiling Identifies Common Responders to Chemotherapy in Pancreatic Cancer. PMID:29853643
Computational analysis of ribonomics datasets identifies long non-coding RNA targets of γ-herpesviral miRNAs. PMID:29846699
From genome-wide associations to candidate causal variants by statistical fine-mapping. PMID:29844615
Identification and analysis of ribosome-associated lncRNAs using ribosome profiling data. PMID:29843593
Analysis of the androgen receptor-regulated lncRNA landscape identifies a role for ARLNC1 in prostate cancer progression. PMID:29808028
Genome-scale identification of transcription factors that mediate an inflammatory network during breast cellular transformation. PMID:29802342
Soluble inflammatory mediators induce transcriptional re-organization that is independent of dna methylation changes in cultured human chorionic villous trophoblasts. PMID:29800761
Towards a complete map of the human long non-coding RNA transcriptome. PMID:29795125
Non-coding RNAs in Various Stages of Liver Disease Leading to Hepatocellular Carcinoma: Differential Expression of miRNAs, piRNAs, lncRNAs, circRNAs, and sno/mt-RNAs. PMID:29789629
Transcriptome analysis of the adult human Klinefelter testis and cellularity-matched controls reveals disturbed differentiation of Sertoli- and Leydig cells. PMID:29789566
Variation in human chromosome 21 ribosomal RNA genes characterized by TAR cloning and long-read sequencing. PMID:29788454
LnChrom: a resource of experimentally validated lncRNA-chromatin interactions in human and mouse. PMID:29788225
Deep Surveying of the Transcriptional and Alternative Splicing Signatures for Decidual CD8+ T Cells at the First Trimester of Human Healthy Pregnancy. PMID:29780389
A long non-coding RNA signature for predicting survival in patients with colorectal cancer. PMID:29774095
GWAS4D: multidimensional analysis of context-specific regulatory variant for human complex diseases and traits. PMID:29771388
Tumor-associated intronic editing of HNRPLL generates a novel splicing variant linked to cell proliferation. PMID:29769310
Influenza Virus Mounts a Two-Pronged Attack on Host RNA Polymerase II Transcription. PMID:29768209
Prediction of enhancer-promoter interactions via natural language processing. PMID:29764360
Identification of a 5‑lncRNA signature‑based risk scoring system for survival prediction in colorectal cancer. PMID:29749517
Long intergenic non-coding RNAs have an independent impact on survival in multiple myeloma. PMID:29749396
Regulation of osteogenesis by long noncoding RNAs: An epigenetic mechanism contributing to bone formation. PMID:29745821
An integrated view of the role of miR-130b/301b miRNA cluster in prostate cancer. PMID:29744254
MALAT1: a druggable long non-coding RNA for targeted anti-cancer approaches. PMID:29739426
Optimizing exosomal RNA isolation for RNA-Seq analyses of archival sera specimens. PMID:29738525
Functional Characterization of the Osteoarthritis Genetic Risk Residing at ALDH1A2 Identifies rs12915901 as a Key Target Variant. PMID:29732726
Deciphering the roles of lncRNAs in breast development and disease. PMID:29732012
MSIQ: JOINT MODELING OF MULTIPLE RNA-SEQ SAMPLES FOR ACCURATE ISOFORM QUANTIFICATION. PMID:29731954
RNA editing in nascent RNA affects pre-mRNA splicing. PMID:29724793
Molecular mechanisms of long noncoding RNAs and their role in disease pathogenesis. PMID:29719633
The fractured landscape of RNA-seq alignment: the default in our STARs. PMID:29718481
Relapse pathway of glioblastoma revealed by single-cell molecular analysis. PMID:29718126
FOCS: a novel method for analyzing enhancer and gene activity patterns infers an extensive enhancer-promoter map. PMID:29716618
An Osteoporosis Risk SNP at 1p36.12 Acts as an Allele-Specific Enhancer to Modulate LINC00339 Expression via Long-Range Loop Formation. PMID:29706346
Bayesian nonparametric discovery of isoforms and individual specific quantification. PMID:29703885
Predicting gene structure changes resulting from genetic variants via exon definition features. PMID:29701825
An analytical framework for whole-genome sequence association studies and its implications for autism spectrum disorder. PMID:29700473
A compendium of long non-coding RNAs transcriptional fingerprint in multiple myeloma. PMID:29700321
Characterization of the enhancer and promoter landscape of inflammatory bowel disease from human colon biopsies. PMID:29695774
Identification of differential expression lncRNAs in gastric cancer using transcriptome sequencing and bioinformatics analyses. PMID:29693709
The exon-intron gene structure upstream of the initiation codon predicts translation efficiency. PMID:29684192
Mechanistic insights into anticancer properties of oligomeric proanthocyanidins from grape seeds in colorectal cancer. PMID:29684110
Distinct and Modular Organization of Protein Interacting Sites in Long Non-coding RNAs. PMID:29670884
Pan-cancer analysis of somatic mutations and transcriptomes reveals common functional gene clusters shared by multiple cancer types. PMID:29662161
Besides Pathology: Long Non-Coding RNA in Cell and Tissue Homeostasis. PMID:29657300
Rare Splice Variants in Long Non-Coding RNAs. PMID:29657294
Insights into the Function of Long Noncoding RNAs in Sepsis Revealed by Gene Co-Expression Network Analysis. PMID:29657277
Inference of the human polyadenylation code. PMID:29648582
PREDICTD PaRallel Epigenomics Data Imputation with Cloud-based Tensor Decomposition. PMID:29643364
Peripherally derived macrophages can engraft the brain independent of irradiation and maintain an identity distinct from microglia. PMID:29643186
Profiling expression of coding genes, long noncoding RNA, and circular RNA in lung adenocarcinoma by ribosomal RNA-depleted RNA sequencing. PMID:29632808
The Immune Landscape of Cancer. PMID:29628290
Recognition of the polycistronic nature of human genes is critical to understanding the genotype-phenotype relationship. PMID:29626081
iCopyDAV: Integrated platform for copy number variations-Detection, annotation and visualization. PMID:29621297
iMETHYL: an integrative database of human DNA methylation, gene expression, and genomic variation. PMID:29619235
Dynamic changes during the treatment of pancreatic cancer. PMID:29599906
Full-length mRNA sequencing uncovers a widespread coupling between transcription initiation and mRNA processing. PMID:29598823
QAPA: a new method for the systematic analysis of alternative polyadenylation from RNA-seq data. PMID:29592814
Discovery of physiological and cancer-related regulators of 3' UTR processing with KAPAC. PMID:29592812
Single-Cell Digital Lysates Generated by Phase-Switch Microfluidic Device Reveal Transcriptome Perturbation of Cell Cycle. PMID:29589910
Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes. PMID:29563166
A comprehensive catalog of predicted functional upstream open reading frames in humans. PMID:29562350
De novo mutations in regulatory elements in neurodevelopmental disorders. PMID:29562236
Comparative transcriptome profiling of the human and mouse dorsal root ganglia: an RNA-seq-based resource for pain and sensory neuroscience research. PMID:29561359
The Ever-Evolving Concept of the Gene: The Use of RNA/Protein Experimental Techniques to Understand Genome Functions. PMID:29560353
Evaluation of two main RNA-seq approaches for gene quantification in clinical RNA sequencing: polyA+ selection versus rRNA depletion. PMID:29556074
Bivalent Chromatin Domains in Glioblastoma Reveal a Subtype-Specific Signature of Glioma Stem Cells. PMID:29549165
Long non-coding RNAs regulating macrophage functions in homeostasis and disease. PMID:29548902
Genomic positional conservation identifies topological anchor point RNAs linked to developmental loci. PMID:29540241
Unveiling new interdependencies between significant DNA methylation sites, gene expression profiles and glioma patients survival. PMID:29535343
POLARIS: Polygenic LD-adjusted risk score approach for set-based analysis of GWAS data. PMID:29532500
Effects of Cadmium Exposure on DNA Methylation at Imprinting Control Regions and Genome-Wide in Mothers and Newborn Children. PMID:29529597
ChIP-ping the branches of the tree: functional genomics and the evolution of eukaryotic gene regulation. PMID:29529131
Global analysis of A-to-I RNA editing reveals association with common disease variants. PMID:29527417
The pseudogene-derived long non-coding RNA SFTA1P suppresses cell proliferation, migration, and invasion in gastric cancer. PMID:29523596
AltHapAlignR: improved accuracy of RNA-seq analyses through the use of alternative haplotypes. PMID:29514179
A large electronic-health-record-based genome-wide study of serum lipids. PMID:29507422
TERIUS: accurate prediction of lncRNA via high-throughput sequencing data representing RNA-binding protein association. PMID:29504902
Integrative analysis of omics summary data reveals putative mechanisms underlying complex traits. PMID:29500431
Discovery of coding regions in the human genome by integrated proteogenomics analysis workflow. PMID:29500430
Identification of long noncoding RNAs involved in muscle differentiation. PMID:29499054
Data Mining of Small RNA-Seq Suggests an Association Between Prostate Cancer and Altered Abundance of 5' Transfer RNA Halves in Seminal Fluid and Prostatic Tissues. PMID:29497340
Novel and Haplotype Specific MicroRNAs Encoded by the Major Histocompatibility Complex. PMID:29497078
The Role of Long Non-Coding RNAs in Hepatocarcinogenesis. PMID:29495592
PAN-cancer analysis of S-phase enriched lncRNAs identifies oncogenic drivers and biomarkers. PMID:29491376
Oligomeric proanthocyanidins (OPCs) target cancer stem-like cells and suppress tumor organoid formation in colorectal cancer. PMID:29463813
Dynamics of promoter bivalency and RNAP II pausing in mouse stem and differentiated cells. PMID:29458328
Autologous iPSC-Based Vaccines Elicit Anti-tumor Responses In Vivo. PMID:29456158
Mutation in an alternative transcript of CDKL5 in a boy with early-onset seizures. PMID:29444904
A Recurrent Mutation in Anaplastic Lymphoma Kinase with Distinct Neoepitope Conformations. PMID:29441070
The effects of death and post-mortem cold ischemia on human tissue transcriptomes. PMID:29440659
Multi-Omics Driven Assembly and Annotation of the Sandalwood (Santalum album) Genome. PMID:29440596
An epigenomic approach to identifying differential overlapping and cis-acting lncRNAs in cisplatin-resistant cancer cells. PMID:29436261
Non-coding RNAs and retroviruses. PMID:29426337
A phenotype centric benchmark of variant prioritisation tools. PMID:29423277
Small non-coding RNA profiling in human biofluids and surrogate tissues from healthy individuals: description of the diverse and most represented species. PMID:29423032
Estimating the mutational load for cardiovascular diseases in Pakistani population. PMID:29420653
Enhancer redundancy provides phenotypic robustness in mammalian development. PMID:29420474
Region-Specific Methylation Profiling in Acute Myeloid Leukemia. PMID:29405013
Long non-coding and coding RNAs characterization in Peripheral Blood Mononuclear Cells and Spinal Cord from Amyotrophic Lateral Sclerosis patients. PMID:29402919
Crosstalk between long non-coding RNAs and Wnt/β-catenin signalling in cancer. PMID:29392884
Non-coding RNA dysregulation in the amygdala region of schizophrenia patients contributes to the pathogenesis of the disease. PMID:29391398
Stop codon readthrough generates a C-terminally extended variant of the human vitamin D receptor with reduced calcitriol response. PMID:29386352
Age-Associated Decline in Thymic B Cell Expression of Aire and Aire-Dependent Self-Antigens. PMID:29386114
Shared genetic effects on chromatin and gene expression indicate a role for enhancer priming in immune response. PMID:29379200
Mitotically-Associated lncRNA (MANCR) Affects Genomic Stability and Cell Division in Aggressive Breast Cancer. PMID:29378907
Identifying and exploiting trait-relevant tissues with multiple functional annotations in genome-wide association studies. PMID:29377896
Long non-coding RNA MDC1-AS inhibits human gastric cancer cell proliferation and metastasis through an MDC1-dependent mechanism. PMID:29375682
Evidence for a Pan-Neurodegenerative Disease Response in Huntington's and Parkinson's Disease Expression Profiles. PMID:29375298
Over-expression of oncigenic pesudogene DUXAP10 promotes cell proliferation and invasion by regulating LATS1 and β-catenin in gastric cancer. PMID:29374493
Functional Classification and Experimental Dissection of Long Noncoding RNAs. PMID:29373828
Biologically active constituents of the secretome of human W8B2+ cardiac stem cells. PMID:29371689
Expression profiling of snoRNAs in normal hematopoiesis and AML. PMID:29365324
Life under the Microscope: Single-Molecule Fluorescence Highlights the RNA World. PMID:29363314
Integrated analysis of single-cell embryo data yields a unified transcriptome signature for the human pre-implantation epiblast. PMID:29361568
CCR5 Governs DNA Damage Repair and Breast Cancer Stem Cell Expansion. PMID:29358169
Ultraconserved Enhancers Are Required for Normal Development. PMID:29358049
Pan-cancer screen for mutations in non-coding elements with conservation and cancer specificity reveals correlations with expression and survival. PMID:29354286
Integrative Genomic Analysis Predicts Causative Cis-Regulatory Mechanisms of the Breast Cancer-Associated Genetic Variant rs4415084. PMID:29351903
Elucidating distinct ion channel populations on the surface of hippocampal neurons via single-particle tracking recurrence analysis. PMID:29347346
Natural antisense transcripts in diseases: From modes of action to targeted therapies. PMID:29341438
Targeting IRF3 as a YAP agonist therapy against gastric cancer. PMID:29339449
LncMAP: Pan-cancer atlas of long noncoding RNA-mediated transcriptional network perturbations. PMID:29325141
Loss-of-function variants in ADCY3 increase risk of obesity and type 2 diabetes. PMID:29311636
Novel Transcriptional Activity and Extensive Allelic Imbalance in the Human MHC Region. PMID:29311362
The Dynamic Landscape of Open Chromatin during Human Cortical Neurogenesis. PMID:29307494
HOTAIR Long Non-coding RNA: Characterizing the Locus Features by the In Silico Approaches. PMID:29307144
KIAA1109 Variants Are Associated with a Severe Disorder of Brain Development and Arthrogryposis. PMID:29290337
Genome-wide Study of Atrial Fibrillation Identifies Seven Risk Loci and Highlights Biological Pathways and Regulatory Elements Involved in Cardiac Development. PMID:29290336
Principles and methods of in-silico prioritization of non-coding regulatory variants. PMID:29288389
Clinicopathological and Prognostic Role of Long Noncoding RNA Linc00152 in Various Human Neoplasms: Evidence from Meta-Analysis. PMID:29285514
Bidirectional transcription initiation marks accessible chromatin and is not specific to enhancers. PMID:29284524
DE-kupl: exhaustive capture of biological variation in RNA-seq data through k-mer decomposition. PMID:29284518
Intergenic disease-associated regions are abundant in novel transcripts. PMID:29284497
Detection of de novo single nucleotide variants in offspring of atomic-bomb survivors close to the hypocenter by whole-genome sequencing. PMID:29279608
The Hidden Genomic and Transcriptomic Plasticity of Giant Marker Chromosomes in Cancer. PMID:29279323
Long Noncoding RNA in Cancer: Wiring Signaling Circuitry. PMID:29274663
An integrated and comparative approach towards identification, characterization and functional annotation of candidate genes for drought tolerance in sorghum (Sorghum bicolor (L.) Moench). PMID:29273003
RNA-Seq differential expression analysis: An extended review and a software tool. PMID:29267363
Genes uniquely expressed in human growth plate chondrocytes uncover a distinct regulatory network. PMID:29262782
Transcriptomic analysis of mitochondrial TFAM depletion changing cell morphology and proliferation. PMID:29259235
Resolving systematic errors in widely used enhancer activity assays in human cells. PMID:29256496
Beyond Transcription: Roles of Transcription Factors in Pre-mRNA Splicing. PMID:29251915
Oncogenic Role of THOR, a Conserved Cancer/Testis Long Non-coding RNA. PMID:29245011
Collaborative representation-based classification of microarray gene expression data. PMID:29236759
Genomic and Epigenomic Signatures in Ovarian Cancer Associated with Resensitization to Platinum Drugs. PMID:29229600
Age-dependent changes in mean and variance of gene expression across tissues in a twin cohort. PMID:29228364
RNAStructuromeDB: A genome-wide database for RNA structural inference. PMID:29222504
A comprehensive profile of circulating RNAs in human serum. PMID:29219730
Network analysis of pseudogene-gene relationships: from pseudogene evolution to their functional potentials. PMID:29218912
Light-focusing human micro-lenses generated from pluripotent stem cells model lens development and drug-induced cataract in vitro. PMID:29217756
Transcriptomic profiles in peripheral blood between women with unexplained recurrent implantation failure and recurrent miscarriage and the correlation with endometrium: A pilot study. PMID:29216287
LRSim: A Linked-Reads Simulator Generating Insights for Better Genome Partitioning. PMID:29213995
Ginkgo biloba extract EGb 761-induced upregulation of LincRNA-p21 inhibits colorectal cancer metastasis by associating with EZH2. PMID:29207671
Crosstalk in competing endogenous RNA network reveals the complex molecular mechanism underlying lung cancer. PMID:29207642
Microfluidic isoform sequencing shows widespread splicing coordination in the human transcriptome. PMID:29196558
circlncRNAnet: an integrated web-based resource for mapping functional networks of long or circular forms of noncoding RNAs. PMID:29194536
A multiregional proteomic survey of the postnatal human brain. PMID:29184206
Transcriptome sequencing reveals high isoform diversity in the ant Formica exsecta. PMID:29177112
Rare copy number variants identified in prune belly syndrome. PMID:29174092
Molecular and cellular reorganization of neural circuits in the human lineage. PMID:29170230
Protein complex scaffolding predicted as a prevalent function of long non-coding RNAs. PMID:29165713
Partial bisulfite conversion for unique template sequencing. PMID:29161423
Enrichment of colorectal cancer associations in functional regions: Insight for using epigenomics data in the analysis of whole genome sequence-imputed GWAS data. PMID:29161273
Long non-coding RNAs in Colorectal Cancer: Progression and Future Directions. PMID:29158793
The discovery potential of RNA processing profiles. PMID:29155959
Ensembl 2018. PMID:29155950
Modeling positional effects of regulatory sequences with spline transformations increases prediction accuracy of deep neural networks. PMID:29155928
Decoding critical long non-coding RNA in ovarian cancer epithelial-to-mesenchymal transition. PMID:29150601
Human Accelerated Regions and Other Human-Specific Sequence Variations in the Context of Evolution and Their Relevance for Brain Development. PMID:29149249
Functional annotation of structural ncRNAs within enhancer RNAs in the human genome: implications for human disease. PMID:29138457
Long noncoding RNA XIST is a prognostic factor in colorectal cancer and inhibits 5-fluorouracil-induced cell cytotoxicity through promoting thymidylate synthase expression. PMID:29137332
Arid1a Has Context-Dependent Oncogenic and Tumor Suppressor Functions in Liver Cancer. PMID:29136504
Deep RNA Sequencing Uncovers a Repertoire of Human Macrophage Long Intergenic Noncoding RNAs Modulated by Macrophage Activation and Associated With Cardiometabolic Diseases. PMID:29133519
Cis-SNPs Set Testing and PrediXcan Analysis for Gene Expression Data using Linear Mixed Models. PMID:29127305
KSRP specifies monocytic and granulocytic differentiation through regulating miR-129 biogenesis and RUNX1 expression. PMID:29127290
The Encyclopedia of DNA elements (ENCODE): data portal update. PMID:29126249
Consensus coding sequence (CCDS) database: a standardized set of human and mouse protein-coding regions supported by expert curation. PMID:29126148
MOAT: efficient detection of highly mutated regions with the Mutations Overburdening Annotations Tool. PMID:29121169
The effect of genetic variation on promoter usage and enhancer activity. PMID:29116076
Genome-wide association study identifies a novel locus for cannabis dependence. PMID:29112194
Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors. PMID:29109393
Reduced mutation rate in exons due to differential mismatch repair. PMID:29106418
High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing. PMID:29106417
Identification and Analysis of P53-Mediated Competing Endogenous RNA Network in Human Hepatocellular Carcinoma. PMID:29104512
A functional strategy to characterize expression Quantitative Trait Loci. PMID:29101457
A Long Noncoding RNA Signature That Predicts Pathological Complete Remission Rate Sensitively in Neoadjuvant Treatment of Breast Cancer. PMID:29096247
Two independent modes of chromatin organization revealed by cohesin removal. PMID:29094699
The ISB Cancer Genomics Cloud: A Flexible Cloud-Based Platform for Cancer Genomics Research. PMID:29092928
Transcription start site profiling of 15 anatomical regions of the Macaca mulatta central nervous system. PMID:29087374
Promoter-level transcriptome in primary lesions of endometrial cancer identified biomarkers associated with lymph node metastasis. PMID:29074988
Defining the location of promoter-associated R-loops at near-nucleotide resolution using bisDRIP-seq. PMID:29072160
Lnc2Meth: a manually curated database of regulatory relationships between long non-coding RNAs and DNA methylation associated with human disease. PMID:29069510
APPRIS 2017: principal isoforms for multiple gene sets. PMID:29069475
OverGeneDB: a database of 5' end protein coding overlapping genes in human and mouse genomes. PMID:29069459
Gene isoforms as expression-based biomarkers predictive of drug response in vitro. PMID:29066719
A heuristic model for computational prediction of human branch point sequence. PMID:29065858
Association analysis identifies 65 new breast cancer risk loci. PMID:29059683
dreamBase: DNA modification, RNA regulation and protein binding of expressed pseudogenes in human health and disease. PMID:29059382
CirGRDB: a database for the genome-wide deciphering circadian genes and regulators. PMID:29059379
Predicting causal variants affecting expression by using whole-genome sequencing and RNA-seq from multiple human tissues. PMID:29058714
Laser Capture and Deep Sequencing Reveals the Transcriptomic Programmes Regulating the Onset of Pancreas and Liver Differentiation in Human Embryos. PMID:29056335
LncRNAs: key players and novel insights into diabetes mellitus. PMID:29050364
A comprehensive genome-wide analysis of long noncoding RNA expression profile in hepatocellular carcinoma. PMID:29047230
RMBase v2.0: deciphering the map of RNA modifications from epitranscriptome sequencing data. PMID:29040692
Comprehensive analysis of circRNA expression profiles in humans by RAISE. PMID:29039477
A High-Resolution Genome-Wide CRISPR/Cas9 Viability Screen Reveals Structural Features and Contextual Diversity of the Human Cell-Essential Proteome. PMID:29038160
cuRRBS: simple and robust evaluation of enzyme combinations for reduced representation approaches. PMID:29036576
PLncPRO for prediction of long non-coding RNAs (lncRNAs) in plants and its application for discovery of abiotic stress-responsive lncRNAs in rice and chickpea. PMID:29036354
Integrative Analysis of Transcription Factor Combinatorial Interactions Using a Bayesian Tensor Factorization Approach. PMID:29033978
Microarray Analysis Identifies the Potential Role of Long Non-Coding RNA in Regulating Neuroinflammation during Japanese Encephalitis Virus Infection. PMID:29033949
Inference of RNA decay rate from transcriptional profiling highlights the regulatory programs of Alzheimer's disease. PMID:29030541
Single-cell gene expression analysis reveals regulators of distinct cell subpopulations among developing human neurons. PMID:29030469
Segway 2.0: Gaussian mixture models and minibatch training. PMID:29028889
Network modeling of kinase inhibitor polypharmacology reveals pathways targeted in chemical screens. PMID:29023490
The lncRNA TUG1 modulates proliferation in trophoblast cells via epigenetic suppression of RND3. PMID:29022920
Antigen receptor repertoire profiling from RNA-seq data. PMID:29020005
Data Resources for Human Functional Genomics. PMID:28989986
Exon Mapping in Long Noncoding RNAs Using Digital Filters. PMID:28989280
High-Throughput Approaches to Pinpoint Function within the Noncoding Genome. PMID:28985510
Frequent miRNA-convergent fusion gene events in breast cancer. PMID:28983113
Genome-scale detection of positive selection in nine primates predicts human-virus evolutionary conflicts. PMID:28977405
Analysis of primary microRNA loci from nascent transcriptomes reveals regulatory domains governed by chromatin architecture. PMID:28973462
Accurate and reproducible functional maps in 127 human cell types via 2D genome segmentation. PMID:28973456
DART: a fast and accurate RNA-seq mapper with a partitioning strategy. PMID:28968831
The Immune Signaling Adaptor LAT Contributes to the Neuroanatomical Phenotype of 16p11.2 BP2-BP3 CNVs. PMID:28965845
Interaction between Social/Psychosocial Factors and Genetic Variants on Body Mass Index: A Gene-Environment Interaction Analysis in a Longitudinal Setting. PMID:28961216
Pan-cancer transcriptomic analysis associates long non-coding RNAs with key mutational driver events. PMID:28959951
Human hepatic gene expression signature of non-alcoholic fatty liver disease progression, a meta-analysis. PMID:28955037
HLAProfiler utilizes k-mer profiles to improve HLA calling accuracy for rare and common alleles in RNA-seq data. PMID:28954626
Identification of hub genes involved in the development of hepatocellular carcinoma by transcriptome sequencing. PMID:28947976
Genome-Wide Interactions with Dairy Intake for Body Mass Index in Adults of European Descent. PMID:28941034
START: a system for flexible analysis of hundreds of genomic signal tracks in few lines of SQL-like queries. PMID:28938868
A novel lncRNA, LL22NC03-N64E9.1, represses KLF2 transcription through binding with EZH2 in colorectal cancer. PMID:28938648
A multidimensional blood stimulation assay reveals immune alterations underlying systemic juvenile idiopathic arthritis. PMID:28935693
CLIP-seq analysis of multi-mapped reads discovers novel functional RNA regulatory sites in the human transcriptome. PMID:28934506
5-Hydroxymethylcytosine signatures in circulating cell-free DNA as diagnostic biomarkers for human cancers. PMID:28925386
The Function and Therapeutic Potential of Long Non-coding RNAs in Cardiovascular Development and Disease. PMID:28918050
Strategies for In Vivo Screening and Mitigation of Hepatotoxicity Associated with Antisense Drugs. PMID:28918038
An Induced Pluripotent Stem Cell Patient Specific Model of Complement Factor H (Y402H) Polymorphism Displays Characteristic Features of Age-Related Macular Degeneration and Indicates a Beneficial Role for UV Light Exposure. PMID:28913923
Discriminating cirRNAs from other lncRNAs using a hierarchical extreme learning machine (H-ELM) algorithm with feature selection. PMID:28913654
Long non-coding RNA SeT and miR-155 regulate the Tnfα gene allelic expression profile. PMID:28910376
Acute doses of caffeine shift nervous system cell expression profiles toward promotion of neuronal projection growth. PMID:28904364
Catalog of Differentially Expressed Long Non-Coding RNA following Activation of Human and Mouse Innate Immune Response. PMID:28900427
Assessment of T-cell receptor repertoire and clonal expansion in peripheral T-cell lymphoma using RNA-seq data. PMID:28900149
LEF1-AS1, a long-noncoding RNA, promotes malignancy in glioblastoma. PMID:28894380
Regulation of the glucocorticoid receptor via a BET-dependent enhancer drives antiandrogen resistance in prostate cancer. PMID:28891793
Identification of high-confidence RNA regulatory elements by combinatorial classification of RNA-protein binding sites. PMID:28886744
Pulmonary endothelial cell DNA methylation signature in pulmonary arterial hypertension. PMID:28881789
Up-regulation of long non-coding RNA SPRY4-IT1 promotes tumor cell migration and invasion in lung adenocarcinoma. PMID:28881629
LncRNA ZNF503-AS1 promotes RPE differentiation by downregulating ZNF503 expression. PMID:28880276
An in-silico approach to predict and exploit synthetic lethality in cancer metabolism. PMID:28878380
Non-parametric genetic prediction of complex traits with latent Dirichlet process regression models. PMID:28878256
APOBEC3A is an oral cancer prognostic biomarker in Taiwanese carriers of an APOBEC deletion polymorphism. PMID:28878238
Atropos: specific, sensitive, and speedy trimming of sequencing reads. PMID:28875074
The Schistosoma mansoni genome encodes thousands of long non-coding RNAs predicted to be functional at different parasite life-cycle stages. PMID:28874839
Identifying DNase I hypersensitive sites as driver distal regulatory elements in breast cancer. PMID:28874753
Biology and clinical relevance of noncoding sno/scaRNAs. PMID:28869095
Spatial Clustering of de Novo Missense Mutations Identifies Candidate Neurodevelopmental Disorder-Associated Genes. PMID:28867141
Genome-wide computational analysis of potential long noncoding RNA mediated DNA:DNA:RNA triplexes in the human genome. PMID:28865451
Regulation of Noncoding Transcriptome in Developing Photoreceptors by Rod Differentiation Factor NRL. PMID:28863214
Identification of dysregulated lncRNAs profiling and metastasis-associated lncRNAs in colorectal cancer by genome-wide analysis. PMID:28857495
Noncoding RNAs in neurodegeneration. PMID:28855739
RNA-seq reveals more consistent reference genes for gene expression studies in human non-melanoma skin cancers. PMID:28852586
FANTOM5 CAGE profiles of human and mouse reprocessed for GRCh38 and GRCm38 genome assemblies. PMID:28850105
Public antibodies to malaria antigens generated by two LAIR1 insertion modalities. PMID:28847005
Two modes of targeting transposable elements by piRNA pathway in human testis. PMID:28842508
Integrated analysis of long non-coding RNAs in human gastric cancer: An in silico study. PMID:28841672
Characterization of lincRNA expression in the human retinal pigment epithelium and differentiated induced pluripotent stem cells. PMID:28837677
An integrated expression atlas of miRNAs and their promoters in human and mouse. PMID:28829439
Transcriptome analysis reveals long intergenic non-coding RNAs involved in skeletal muscle growth and development in pig. PMID:28821716
Aggregation of population-based genetic variation over protein domain homologues and its potential use in genetic diagnostics. PMID:28815929
Understanding the Role of lncRNAs in Nervous System Development. PMID:28815543
Omni-PolyA: a method and tool for accurate recognition of Poly(A) signals in human genomic DNA. PMID:28810905
Discovery of Variants Underlying Host Susceptibility to Virus Infection Using Whole-Exome Sequencing. PMID:28808973
Coding and small non-coding transcriptional landscape of tuberous sclerosis complex cortical tubers: implications for pathophysiology and treatment. PMID:28808237
Identification and characterization of a long non-coding RNA up-regulated during HIV-1 infection. PMID:28803142
Molecular pathogenesis of human prostate basal cell hyperplasia. PMID:28795417
The non-coding RNA landscape of human hematopoiesis and leukemia. PMID:28794406
Downregulation of lncRNA SDPR-AS is associated with poor prognosis in renal cell carcinoma. PMID:28790838
Long non-coding RNA and tumor hypoxia: new players ushered toward an old arena. PMID:28789687
Evaluation and comparison of computational tools for RNA-seq isoform quantification. PMID:28784092
SuperTranscripts: a data driven reference for analysis and visualisation of transcriptomes. PMID:28778180
Integrative whole-genome sequence analysis reveals roles of regulatory mutations in BCL6 and BCL2 in follicular lymphoma. PMID:28765546
Beyond mRNA: The role of non-coding RNAs in normal and aberrant hematopoiesis. PMID:28757239
High resolution temporal transcriptomics of mouse embryoid body development reveals complex expression dynamics of coding and noncoding loci. PMID:28751729
Identification of novel prostate cancer drivers using RegNetDriver: a framework for integration of genetic and epigenetic alterations with tissue-specific regulatory network. PMID:28750683
Detecting epistasis with the marginal epistasis test in genetic mapping studies of quantitative traits. PMID:28746338
Identification of four prognostic LncRNAs for survival prediction of patients with hepatocellular carcinoma. PMID:28729955
Gene expression reversal toward pre-adult levels in the aging human brain and age-related loss of cellular identity. PMID:28724976
Bioinformatics analysis to identify the critical genes, microRNAs and long noncoding RNAs in melanoma. PMID:28723760
microRNA dependent and independent deregulation of long non-coding RNAs by an oncogenic herpesvirus. PMID:28715488
Arid1b haploinsufficient mice reveal neuropsychiatric phenotypes and reversible causes of growth impairment. PMID:28695822
Strength of functional signature correlates with effect size in autism. PMID:28687074
Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis. PMID:28680106
Landscape and variation of novel retroduplications in 26 human populations. PMID:28662076
Korean Variant Archive (KOVA): a reference database of genetic variations in the Korean population. PMID:28655895
Metabolic autopsy with next generation sequencing in sudden unexpected death in infancy: Postmortem diagnosis of fatty acid oxidation disorders. PMID:28649538
A genome-wide association scan of biological processes involved in oral lichen planus and oral squamous cell carcinoma. PMID:28640079
Long Noncoding RNAs as Biomarkers in Cancer. PMID:28634418
The islet-resident macrophage is in an inflammatory state and senses microbial products in blood. PMID:28630088
Chromatin-enriched lncRNAs can act as cell-type specific activators of proximal gene transcription. PMID:28628087
Insights from Global Analyses of Long Noncoding RNAs in Breast Cancer. PMID:28616363
Pan-cancer analysis reveals technical artifacts in TCGA germline variant calls. PMID:28606096
Genetic diagnosis of Mendelian disorders via RNA sequencing. PMID:28604674
Computational prediction of lncRNA-mRNA interactionsby integrating tissue specificity in human transcriptome. PMID:28595592
A DNA methylation map of human cancer at single base-pair resolution. PMID:28581523
Long Noncoding RNA Moderates MicroRNA Activity to Maintain Self-Renewal in Embryonic Stem Cells. PMID:28579393
Research focused on microRNAs: a link between myocardial remodeling and growth during pathological processes and physical exercises. PMID:28567402
Genome annotation for clinical genomic diagnostics: strengths and weaknesses. PMID:28558813
Nucleus-Translocated ACSS2 Promotes Gene Transcription for Lysosomal Biogenesis and Autophagy. PMID:28552616
Reducing mitochondrial reads in ATAC-seq using CRISPR/Cas9. PMID:28550296
Genomic analysis of oesophageal squamous-cell carcinoma identifies alcohol drinking-related mutation signature and genomic alterations. PMID:28548104
Whole genome sequencing and imputation in isolated populations identify genetic associations with medically-relevant complex traits. PMID:28548082
The NANCI-Nkx2.1 gene duplex buffers Nkx2.1 expression to maintain lung development and homeostasis. PMID:28546511
Copy-number variants and candidate gene mutations in isolated split hand/foot malformation. PMID:28539665
Identification and Characterization of a Class of MALAT1-like Genomic Loci. PMID:28538188
A computationally constructed ceRNA interaction network based on a comparison of the SHEE and SHEEC cell lines. PMID:28536623
Prognostic and biological significance of the proangiogenic factor EGFL7 in acute myeloid leukemia. PMID:28533390
Coordinates and intervals in graph-based reference genomes. PMID:28521770
Functionally diverse human T cells recognize non-microbial antigens presented by MR1. PMID:28518056
Intranuclear and higher-order chromatin organization of the major histone gene cluster in breast cancer. PMID:28504305
Prediction of gene expression with cis-SNPs using mixed models and regularization methods. PMID:28490319
Recurrent promoter mutations in melanoma are defined by an extended context-specific mutational signature. PMID:28489852
Common genetic variation drives molecular heterogeneity in human iPSCs. PMID:28489815
Selective expression of long non-coding RNAs in a breast cancer cell progression model. PMID:28488769
The identification and functional annotation of RNA structures conserved in vertebrates. PMID:28487280
Soft Sweeps Are the Dominant Mode of Adaptation in the Human Genome. PMID:28482049
Comparative transcriptomics in human and mouse. PMID:28479595
Genome-scale measurement of off-target activity using Cas9 toxicity in high-throughput screens. PMID:28474669
Mapping the human DC lineage through the integration of high-dimensional techniques. PMID:28473638
Prognostic and biologic significance of long non-coding RNA profiling in younger adults with cytogenetically normal acute myeloid leukemia. PMID:28473620
Exploring genetic associations with ceRNA regulation in the human genome. PMID:28472449
RegulatorTrail: a web service for the identification of key transcriptional regulators. PMID:28472408
Prolonged Absence of Mechanoluminal Stimulation in Human Intestine Alters the Transcriptome and Intestinal Stem Cell Niche. PMID:28462379
RIblast: an ultrafast RNA-RNA interaction prediction system based on a seed-and-extension approach. PMID:28459942
A comprehensive analysis of cancer-driving mutations and genes in kidney cancer. PMID:28454375
Accumulation of GAS5 in exosomes is a marker of apoptosis induction. PMID:28451400
Orphan CpG islands define a novel class of highly active enhancers. PMID:28448736
A three-lncRNA expression signature associated with the prognosis of gastric cancer patients. PMID:28444881
Over-expressed long noncoding RNA HOXA11-AS promotes cell cycle progression and metastasis in gastric cancer. PMID:28441948
Normalized long read RNA sequencing in chicken reveals transcriptome complexity similar to human. PMID:28438136
Non-coding RNAs in cardiovascular diseases: diagnostic and therapeutic perspectives. PMID:28430919
Fine-mapping of lipid regions in global populations discovers ethnic-specific signals and refines previously identified lipid loci. PMID:28426890
Novel lincRNA SLINKY is a prognostic biomarker in kidney cancer. PMID:28423633
Genetic sequence-based prediction of long-range chromatin interactions suggests a potential role of short tandem repeat sequences in genome organization. PMID:28420341
Exploring the molecular pathogenesis and biomarkers of high risk oral premalignant lesions on the basis of long noncoding RNA expression profiling by serial analysis of gene expression. PMID:28418939
Runx1 stabilizes the mammary epithelial cell phenotype and prevents epithelial to mesenchymal transition. PMID:28407681
SnoVault and encodeD: A novel object-based storage system and applications to ENCODE metadata. PMID:28403240
Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly. PMID:28396521
High-confidence coding and noncoding transcriptome maps. PMID:28396519
Exploring functions of long noncoding RNAs across multiple cancers through co-expression network. PMID:28389669
De novo RNA sequence assembly during in vivo inflammatory stress reveals hundreds of unannotated lincRNAs in human blood CD14+ monocytes and in adipose tissue. PMID:28389524
Large-Scale Profiling Reveals the Influence of Genetic Variation on Gene Expression in Human Induced Pluripotent Stem Cells. PMID:28388430
Aberrant DNA Methylation in Human iPSCs Associates with MYC-Binding Motifs in a Clone-Specific Manner Independent of Genetics. PMID:28388429
LncATLAS database for subcellular localization of long noncoding RNAs. PMID:28386015
Nicotinic alpha 7 receptor expression and modulation of the lung epithelial response to lipopolysaccharide. PMID:28384302
Brain Transcriptome Sequencing of a Natural Model of Alzheimer's Disease. PMID:28373841
Chromatin-remodeling factor SMARCD2 regulates transcriptional networks controlling differentiation of neutrophil granulocytes. PMID:28369036
Exploiting Long Noncoding RNAs as Pharmacological Targets to Modulate Epigenetic Diseases. PMID:28356895
Dietary restriction protects from age-associated DNA methylation and induces epigenetic reprogramming of lipid metabolism. PMID:28351387
Dengue virus NS2B protein targets cGAS for degradation and prevents mitochondrial DNA sensing during infection. PMID:28346446
DeepBlueR: large-scale epigenomic analysis in R. PMID:28334349
QRank: a novel quantile regression tool for eQTL discovery. PMID:28334222
Network perturbation by recurrent regulatory variants in cancer. PMID:28333928
CRISPR/Cas9-mediated heterozygous knockout of the autism gene CHD8 and characterization of its transcriptional networks in cerebral organoids derived from iPS cells. PMID:28321286
Time-dependent genetic effects on gene expression implicate aging processes. PMID:28302734
The duplication mutation of Quebec platelet disorder dysregulates PLAU, but not C10orf55, selectively increasing production of normal PLAU transcripts by megakaryocytes but not granulocytes. PMID:28301587
Developing a Novel Two-Dimensional Culture System to Enrich Human Prostate Luminal Progenitors that Can Function as a Cell of Origin for Prostate Cancer. PMID:28297567
Comprehensive RNA-seq transcriptomic profiling in the malignant progression of gliomas. PMID:28291232
Fast, scalable prediction of deleterious noncoding variants from functional and population genomic data. PMID:28288115
The birth of a human-specific neural gene by incomplete duplication and gene fusion. PMID:28279197
TT-seq captures enhancer landscapes immediately after T-cell stimulation. PMID:28270558
Whole-genome sequencing identifies common-to-rare variants associated with human blood metabolites. PMID:28263315
GuideScan software for improved single and paired CRISPR guide RNA design. PMID:28263296
Defining the diverse spectrum of inversions, complex structural variation, and chromothripsis in the morbid human genome. PMID:28260531
Scalable Design of Paired CRISPR Guide RNAs for Genomic Deletion. PMID:28253259
Uncovering the roles of long non-coding RNAs in cancer stem cells. PMID:28245841
An atlas of human long non-coding RNAs with accurate 5' ends. PMID:28241135
Impacts of Neanderthal-Introgressed Sequences on the Landscape of Human Gene Expression. PMID:28235201
Evolution of Brain Active Gene Promoters in Human Lineage Towards the Increased Plasticity of Gene Regulation. PMID:28233272
CLK-dependent exon recognition and conjoined gene formation revealed with a novel small molecule inhibitor. PMID:28232751
Comparative genomic analysis of eutherian kallikrein genes. PMID:28224083
Distal CpG islands can serve as alternative promoters to transcribe genes with silenced proximal promoters. PMID:28223400
Manananggal - a novel viewer for alternative splicing events. PMID:28222683
Large-Scale Analysis of CRISPR/Cas9 Cell-Cycle Knockouts Reveals the Diversity of p53-Dependent Responses to Cell-Cycle Defects. PMID:28216383
Long Noncoding RNA LINC00673 Is Activated by SP1 and Exerts Oncogenic Properties by Interacting with LSD1 and EZH2 in Gastric Cancer. PMID:28214253
Epigenetic Landscape during Coronavirus Infection. PMID:28212305
Long noncoding AGAP2-AS1 is activated by SP1 and promotes cell proliferation and invasion in gastric cancer. PMID:28209205
Recurrently deregulated lncRNAs in hepatocellular carcinoma. PMID:28194035
Improved regulatory element prediction based on tissue-specific local epigenomic signatures. PMID:28193886
Long Noncoding RNAs: At the Intersection of Cancer and Chromatin Biology. PMID:28193769
Large-scale bioactivity analysis of the small-molecule assayed proteome. PMID:28178331
Dnmt3a restrains mast cell inflammatory responses. PMID:28167789
LocExpress: a web server for efficiently estimating expression of novel transcripts. PMID:28155723
DeepGene: an advanced cancer type classifier based on deep learning and somatic point mutations. PMID:28155641
Long noncoding RNA expression signature to predict platinum-based chemotherapeutic sensitivity of ovarian cancer patients. PMID:28154416
Whole-genome view of the consequences of a population bottleneck using 2926 genome sequences from Finland and United Kingdom. PMID:28145424
Discovery of Cancer Driver Long Noncoding RNAs across 1112 Tumour Genomes: New Candidates and Distinguishing Features. PMID:28128360
Correlated 5-Hydroxymethylcytosine (5hmC) and Gene Expression Profiles Underpin Gene and Organ-Specific Epigenetic Regulation in Adult Mouse Brain and Liver. PMID:28125731
Immunobiology of Long Noncoding RNAs. PMID:28125358
Lncident: A Tool for Rapid Identification of Long Noncoding RNAs Utilizing Sequence Intrinsic Composition and Open Reading Frame Information. PMID:28116287
Robust and rapid algorithms facilitate large-scale whole genome sequencing downstream analysis in an integrative framework. PMID:28115622
The Long Noncoding RNA Landscape of the Ischemic Human Left Ventricle. PMID:28115490
Tethered Oligonucleotide-Primed Sequencing, TOP-Seq: A High-Resolution Economical Approach for DNA Epigenome Profiling. PMID:28111014
Antisense transcription of the myotonic dystrophy locus yields low-abundant RNAs with and without (CAG)n repeat. PMID:28102759
Mitochondrial respiratory gene expression is suppressed in many cancers. PMID:28099114
Identification of Potential Key lncRNAs and Genes Associated with Aging Based on Microarray Data of Adipocytes from Mice. PMID:28097151
Down-Regulation of EPAS1 Transcription and Genetic Adaptation of Tibetans to High-Altitude Hypoxia. PMID:28096303
Massive Effect on LncRNAs in Human Monocytes During Fungal and Bacterial Infections and in Response to Vitamins A and D. PMID:28094339
Insertions and Deletions Target Lineage-Defining Genes in Human Cancers. PMID:28089356
RAIN: RNA-protein Association and Interaction Networks. PMID:28077569
Integrated RNA-seq and DNase-seq analyses identify phenotype-specific BMP4 signaling in breast cancer. PMID:28077088
Long noncoding RNA repertoire in chicken liver and adipose tissue. PMID:28073357
A potential prognostic lncRNA signature for predicting survival in patients with bladder urothelial carcinoma. PMID:28060759
Genome-Wide DNA Methylation Patterns Analysis of Noncoding RNAs in Temporal Lobe Epilepsy Patients. PMID:28058582
The long non-coding RNA NEAT1 is responsive to neuronal activity and is associated with hyperexcitability states. PMID:28054653
POSTAR: a platform for exploring post-transcriptional regulation coordinated by RNA-binding proteins. PMID:28053162
FEELnc: a tool for long non-coding RNA annotation and its application to the dog transcriptome. PMID:28053114
Functional Transcriptomics in Diverse Intestinal Epithelial Cell Types Reveals Robust MicroRNA Sensitivity in Intestinal Stem Cells to Microbial Status. PMID:28053090
ChimPipe: accurate detection of fusion genes and transcription-induced chimeras from RNA-seq data. PMID:28049418
Long Noncoding RNA Identification: Comparing Machine Learning Based Tools for Long Noncoding Transcripts Discrimination. PMID:28042575
Human splicing diversity and the extent of unannotated splice junctions across human RNA-seq samples on the Sequence Read Archive. PMID:28038678
Involvement of Host Non-Coding RNAs in the Pathogenesis of the Influenza Virus. PMID:28035991
Non-Coding RNAs in Lung Cancer: Contribution of Bioinformatics Analysis to the Development of Non-Invasive Diagnostic Tools. PMID:28035947
Integration of Population-Level Genotype Data with Functional Annotation Reveals Over-Representation of Long Noncoding RNAs at Ovarian Cancer Susceptibility Loci. PMID:28035019
Androgen-induced lncRNA POTEF-AS1 regulates apoptosis-related pathway to facilitate cell survival in prostate cancer cells. PMID:28032932
Targeted Sequencing of FKBP5 in Suicide Attempters with Bipolar Disorder. PMID:28030643
Down syndrome and the complexity of genome dosage imbalance. PMID:28029161
GeneBase 1.1: a tool to summarize data from NCBI gene datasets and its application to an update of human gene statistics. PMID:28025344
Genome-wide mapping of autonomous promoter activity in human cells. PMID:28024146
High-throughput interpretation of gene structure changes in human and nonhuman resequencing data, using ACE. PMID:28011790
Role of lncRNAs in Cellular Aging. PMID:27999563
Characterization of meningeal type 2 innate lymphocytes and their response to CNS injury. PMID:27994070
Using reference-free compressed data structures to analyze sequencing reads from thousands of human genomes. PMID:27986821
A cloud-based workflow to quantify transcript-expression levels in public cancer compendia. PMID:27982081
Integrating Epigenomics into the Understanding of Biomedical Insight. PMID:27980397
Large-scale mapping of mammalian transcriptomes identifies conserved genes associated with different cell states. PMID:27980097
Activin/Smad2-induced Histone H3 Lys-27 Trimethylation (H3K27me3) Reduction Is Crucial to Initiate Mesendoderm Differentiation of Human Embryonic Stem Cells. PMID:27965357
Non-CpG methylation by DNMT3B facilitates REST binding and gene silencing in developing mouse hearts. PMID:27956497
A GC-rich sequence feature in the 3' UTR directs UPF1-dependent mRNA decay in mammalian cells. PMID:27940950
Chromatin environment, transcriptional regulation, and splicing distinguish lincRNAs and mRNAs. PMID:27927715
ChIPBase v2.0: decoding transcriptional regulatory networks of non-coding RNAs and protein-coding genes from ChIP-seq data. PMID:27924033
Transcriptome and long noncoding RNA sequencing of three extracellular vesicle subtypes released from the human colon cancer LIM1863 cell line. PMID:27917920
Applications and Limitations of Mouse Models for Understanding Human Atherosclerosis. PMID:27916529
Differential variation patterns between hubs and bottlenecks in human protein-protein interaction networks. PMID:27903259
Identification of laryngeal cancer prognostic biomarkers using an inflammatory gene-related, competitive endogenous RNA network. PMID:27902487
The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog). PMID:27899670
The BIG Data Center: from deposition to integration to translation. PMID:27899658
The UCSC Genome Browser database: 2017 update. PMID:27899642
Ensembl 2017. PMID:27899575
Transcriptomic Analysis Implicates the p53 Signaling Pathway in the Establishment of HIV-1 Latency in Central Memory CD4 T Cells in an In Vitro Model. PMID:27898737
Prioritization of non-coding disease-causing variants and long non-coding RNAs in liver cancer. PMID:27895760
Discovery and genotyping of structural variation from long-read haploid genome sequence data. PMID:27895111
Simulating Next-Generation Sequencing Datasets from Empirical Mutation and Sequencing Models. PMID:27893777
SPECtre: a spectral coherence--based classifier of actively translated transcripts from ribosome profiling sequence data. PMID:27884106
Genome, transcriptome and proteome: the rise of omics data and their integration in biomedical sciences. PMID:27881428
Changes of bivalent chromatin coincide with increased expression of developmental genes in cancer. PMID:27876760
Integrative classification of human coding and noncoding genes through RNA metabolism profiles. PMID:27870833
TACO produces robust multisample transcriptome assemblies from RNA-seq. PMID:27869815
The BLUEPRINT Data Analysis Portal. PMID:27863955
Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells. PMID:27863251
An imprinted long noncoding RNA located between genes Meg8 and Meg9 in the cattle Dlk1-Dio3 domain. PMID:27858207
Global analysis of somatic structural genomic alterations and their impact on gene expression in diverse human cancers. PMID:27856756
Size distribution of function-based human gene sets and the split-merge model. PMID:27853602
Multiparameter functional diversity of human C2H2 zinc finger proteins. PMID:27852650
AnnoLnc: a web server for systematically annotating novel human lncRNAs. PMID:27852242
Integrative transcriptome network analysis of iPSC-derived neurons from schizophrenia and schizoaffective disorder patients with 22q11.2 deletion. PMID:27846841
Genome-wide association analyses using electronic health records identify new loci influencing blood pressure variation. PMID:27841878
Survey of the Heritability and Sparse Architecture of Gene Expression Traits across Human Tissues. PMID:27835642
Identification of activated enhancers and linked transcription factors in breast, prostate, and kidney tumors by tracing enhancer networks using epigenetic traits. PMID:27833659
The prognostic value of long non coding RNAs in non small cell lung cancer: A meta-analysis. PMID:27833074
A Comprehensive Characterization of the Function of LincRNAs in Transcriptional Regulation Through Long-Range Chromatin Interactions. PMID:27824113
Transcriptome analysis of distinct long non-coding RNA transcriptional fingerprints in lung adenocarcinoma and squamous cell carcinoma. PMID:27797003
Natural Selection in the Great Apes. PMID:27795229
Long non-coding RNA FOXP4-AS1 is an unfavourable prognostic factor and regulates proliferation and apoptosis in colorectal cancer. PMID:27790757
KERIS: kaleidoscope of gene responses to inflammation between species. PMID:27789704
Genetic Variants in Isolated Ebstein Anomaly Implicated in Myocardial Development Pathways. PMID:27788187
Flexible Data Analysis Pipeline for High-Confidence Proteogenomics. PMID:27786492
Transcriptome-wide effects of inverted SINEs on gene expression and their impact on RNA polymerase II activity. PMID:27782844
Divergent lncRNAs take the lead on pluripotent cell differentiation. PMID:27777936
The state of play in higher eukaryote gene annotation. PMID:27773922
Integrated Post-GWAS Analysis Sheds New Light on the Disease Mechanisms of Schizophrenia. PMID:27754856
The human-induced pluripotent stem cell initiative-data resources for cellular genetics. PMID:27733501
Novel microRNA discovery using small RNA sequencing in post-mortem human brain. PMID:27716130
Specific genomic cues regulate Cajal body assembly. PMID:27715441
Alternative Splicing May Not Be the Key to Proteome Complexity. PMID:27712956
lncScore: alignment-free identification of long noncoding RNA from assembled novel transcripts. PMID:27708423
De novo assembly and phasing of a Korean human genome. PMID:27706134
Genome-wide compendium and functional assessment of in vivo heart enhancers. PMID:27703156
Consensus Analysis of Whole Transcriptome Profiles from Two Breast Cancer Patient Cohorts Reveals Long Non-Coding RNAs Associated with Intrinsic Subtype and the Tumour Microenvironment. PMID:27685983
Long noncoding RNA (lincRNA), a new paradigm in gene expression control. PMID:27681237
Genome-wide associations for birth weight and correlations with adult disease. PMID:27680694
Laquinimod arrests experimental autoimmune encephalomyelitis by activating the aryl hydrocarbon receptor. PMID:27671624
Analysis of SOX2-Regulated Transcriptome in Glioma Stem Cells. PMID:27669421
Integrative Transcriptome Analyses of Metabolic Responses in Mice Define Pivotal LncRNA Metabolic Regulators. PMID:27667668
REVEL: An Ensemble Method for Predicting the Pathogenicity of Rare Missense Variants. PMID:27666373
Inheritable Silencing of Endogenous Genes by Hit-and-Run Targeted Epigenetic Editing. PMID:27662090
Compact and highly active next-generation libraries for CRISPR-mediated gene repression and activation. PMID:27661255
TUT-DIS3L2 is a mammalian surveillance pathway for aberrant structured non-coding RNAs. PMID:27647875
CardioTF, a database of deconstructing transcriptional circuits in the heart system. PMID:27635320
Genome-wide identification and characterisation of HOT regions in the human genome. PMID:27633377
The Tetraodon nigroviridis reference transcriptome: developmental transition, length retention and microsynteny of long non-coding RNAs in a compact vertebrate genome. PMID:27628538
Maps of context-dependent putative regulatory regions and genomic signal interactions. PMID:27625394
BmncRNAdb: a comprehensive database of non-coding RNAs in the silkworm, Bombyx mori. PMID:27623959
Sequence variation between 462 human individuals fine-tunes functional sites of RNA processing. PMID:27617755
Contribution of type W human endogenous retroviruses to the human genome: characterization of HERV-W proviral insertions and processed pseudogenes. PMID:27613107
COME: a robust coding potential calculation tool for lncRNA identification and characterization based on multiple features. PMID:27608726
rG4-seq reveals widespread formation of G-quadruplex structures in the human transcriptome. PMID:27571552
Transgenic Adipose-specific Expression of the Nuclear Receptor RORα Drives a Striking Shift in Fat Distribution and Impairs Glycemic Control. PMID:27568222
Single-nucleus RNA-seq of differentiating human myoblasts reveals the extent of fate heterogeneity. PMID:27566152
Investigation of novel LPS-induced differentially expressed long non-coding RNAs in endothelial cells. PMID:27565812
Ultra-deep sequencing of ribosome-associated poly-adenylated RNA in early Drosophila embryos reveals hundreds of conserved translated sORFs. PMID:27559081
An integrative transcriptomic atlas of organogenesis in human embryos. PMID:27557446
A molecular conundrum involving hypothalamic responses to and roles of long non-coding RNAs following food deprivation. PMID:27555291
Clonal haematopoiesis harbouring AML-associated mutations is ubiquitous in healthy adults. PMID:27546487
lncRNA expression in the auditory forebrain during postnatal development. PMID:27544636
Identification and functional analysis of long non-coding RNAs in human and mouse early embryos based on single-cell transcriptome data. PMID:27542205
Cardiometabolic risk loci share downstream cis- and trans-gene regulation across tissues and diseases. PMID:27540175
Mouse models of Down syndrome: gene content and consequences. PMID:27538963
Extension of human lncRNA transcripts by RACE coupled with long-read high-throughput sequencing (RACE-Seq). PMID:27531712
reChIP-seq reveals widespread bivalency of H3K4me3 and H3K27me3 in CD4(+) memory T cells. PMID:27530917
Modulation of long noncoding RNAs by risk SNPs underlying genetic predispositions to prostate cancer. PMID:27526323
NOTCH1 mediates a switch between two distinct secretomes during senescence. PMID:27525720
IRWRLDA: improved random walk with restart for lncRNA-disease association prediction. PMID:27517318
Prevalent Accumulation of Non-Optimal Codons through Somatic Mutations in Human Cancers. PMID:27513638
IPMiner: hidden ncRNA-protein interaction sequential pattern mining with stacked autoencoder for accurate computational prediction. PMID:27506469
Simultaneous detection and estimation of trait associations with genomic phenotypes. PMID:27496912
Comparative Transcriptome Analysis Reveals Substantial Tissue Specificity in Human Aortic Valve. PMID:27493474
Statistical Methods in Integrative Genomics. PMID:27482531
Integrative genomics analyses unveil downstream biological effectors of disease-specific polymorphisms buried in intergenic regions. PMID:27482468
A targeted sequencing study of glutamatergic candidate genes in suicide attempters with bipolar disorder. PMID:27480506
Investigating long noncoding RNAs using animal models. PMID:27479747
A Long Noncoding RNA Regulates Sister Chromatid Cohesion. PMID:27477908
FocalScan: Scanning for altered genes in cancer based on coordinated DNA and RNA change. PMID:27474725
Secondary structure impacts patterns of selection in human lncRNAs. PMID:27457204
Principles for RNA metabolism and alternative transcription initiation within closely spaced promoters. PMID:27455346
Immune DNA signature of T-cell infiltration in breast tumor exomes. PMID:27452728
TALE-directed local modulation of H3K9 methylation shapes exon recognition. PMID:27439481
Expression of evolutionarily novel genes in tumors. PMID:27437030
PETModule: a motif module based approach for enhancer target gene prediction. PMID:27436110
Identification and Classification of New Transcripts in Dorper and Small-Tailed Han Sheep Skeletal Muscle Transcriptomes. PMID:27434270
Long noncoding RNAs and Alzheimer's disease. PMID:27418812
Integrative analysis with ChIP-seq advances the limits of transcript quantification from RNA-seq. PMID:27405803
The genetic architecture of type 2 diabetes. PMID:27398621
Limits of Peripheral Blood Mononuclear Cells for Gene Expression-Based Biomarkers in Juvenile Idiopathic Arthritis. PMID:27385437
A comprehensive analysis of 3' end sequencing data sets reveals novel polyadenylation signals and the repressive role of heterogeneous ribonucleoprotein C on cleavage and polyadenylation. PMID:27382025
Distinct and shared functions of ALS-associated proteins TDP-43, FUS and TAF15 revealed by multisystem analyses. PMID:27378374
p53 induces formation of NEAT1 lncRNA-containing paraspeckles that modulate replication stress response and chemosensitivity. PMID:27376578
Identifying Centromeric RNAs Involved in Histone Dynamics In Vivo. PMID:27372766
Circulating biomarkers to monitor cancer progression and treatment. PMID:27358717
The genetic regulatory signature of type 2 diabetes in human skeletal muscle. PMID:27353450
Optimizing sgRNA position markedly improves the efficiency of CRISPR/dCas9-mediated transcriptional repression. PMID:27353328
JAK-STAT signaling in cancer: From cytokines to non-coding genome. PMID:27349799
Overexpression of long non-coding RNA HOTTIP increases chemoresistance of osteosarcoma cell by activating the Wnt/β-catenin pathway. PMID:27347346
Functional annotation of noncoding variants and prioritization of cancer-associated lncRNAs in lung cancer. PMID:27347129
Long non-coding RNAs and complex diseases: from experimental results to computational models. PMID:27345524
Androgen-induced Long Noncoding RNA (lncRNA) SOCS2-AS1 Promotes Cell Growth and Inhibits Apoptosis in Prostate Cancer Cells. PMID:27342777
The Ensembl gene annotation system. PMID:27337980
Identification of Tissue-Specific Protein-Coding and Noncoding Transcripts across 14 Human Tissues Using RNA-seq. PMID:27329541
PEDLA: predicting enhancers with a deep learning-based algorithmic framework. PMID:27329130
IntNetLncSim: an integrative network analysis method to infer human lncRNA functional similarity. PMID:27323856
FMLNCSIM: fuzzy measure-based lncRNA functional similarity calculation model. PMID:27322210
Long noncoding RNA variations in cardiometabolic diseases. PMID:27305986
Boiler: lossy compression of RNA-seq alignments using coverage vectors. PMID:27298258
Next generation sequencing technology and genomewide data analysis: Perspectives for retinal research. PMID:27297499
Long noncoding RNAs: Central to nervous system development. PMID:27296516
Emergence and Evolution of Hominidae-Specific Coding and Noncoding Genomic Sequences. PMID:27289096
Comprehensive promoter level expression quantitative trait loci analysis of the human frontal lobe. PMID:27287230
Long noncoding RNA EGOT negatively affects the antiviral response and favors HCV replication. PMID:27283940
Global transcriptome analysis for identification of interactions between coding and noncoding RNAs during human erythroid differentiation. PMID:27272188
The Ensembl Variant Effect Predictor. PMID:27268795
Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow. PMID:27250503
Insights into islet development and biology through characterization of a human iPSC-derived endocrine pancreas model. PMID:27246810
A penalized likelihood approach for robust estimation of isoform expression. PMID:27239250
An atlas of gene expression and gene co-regulation in the human retina. PMID:27235414
Long noncoding RNAs in cancer: mechanisms of action and technological advancements. PMID:27233618
Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling. PMID:27232982
Group II mGluRs suppress hyperexcitability in mouse and human nociceptors. PMID:27218869
Prediction and Quantification of Splice Events from RNA-Seq Data. PMID:27218464
Improved definition of the mouse transcriptome via targeted RNA sequencing. PMID:27197243
Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks. PMID:27197224
Upregulated long non-coding RNA AGAP2-AS1 represses LATS2 and KLF2 expression through interacting with EZH2 and LSD1 in non-small-cell lung cancer cells. PMID:27195672
Circulating long non-coding RNAs in cancer: current status and future perspectives. PMID:27189224
Discovery and validation of sub-threshold genome-wide association study loci using epigenomic signatures. PMID:27162171
Dissecting the expression relationships between RNA-binding proteins and their cognate targets in eukaryotic post-transcriptional regulatory networks. PMID:27161996
RNAex: an RNA secondary structure prediction server enhanced by high-throughput structure-probing data. PMID:27137891
IL-1 is a critical regulator of group 2 innate lymphoid cell function and plasticity. PMID:27111142
A benchmark for RNA-seq quantification pipelines. PMID:27107712
Jointly characterizing epigenetic dynamics across multiple human cell types. PMID:27095202
Candidate SNP Markers of Gender-Biased Autoimmune Complications of Monogenic Diseases Are Predicted by a Significant Change in the Affinity of TATA-Binding Protein for Human Gene Promoters. PMID:27092142
A uniform survey of allele-specific binding and expression over 1000-Genomes-Project individuals. PMID:27089393
Global molecular changes in a tibial compression induced ACL rupture model of post-traumatic osteoarthritis. PMID:27088242
Allele-Skewed DNA Modification in the Brain: Relevance to a Schizophrenia GWAS. PMID:27087318
Nucleotide excision repair is impaired by binding of transcription factors to DNA. PMID:27075101
Comprehensive analysis of lncRNA expression profiles reveals a novel lncRNA signature to discriminate nonequivalent outcomes in patients with ovarian cancer. PMID:27074572
Long Noncoding RNAs in Cancer Pathways. PMID:27070700
Whole-genome mutational landscape and characterization of noncoding and structural mutations in liver cancer. PMID:27064257
Enhancer-promoter interactions are encoded by complex genomic signatures on looping chromatin. PMID:27064255
Diagnostic and Biological Significance of KIR Expression Profile Determined by RNA-Seq in Natural Killer/T-Cell Lymphoma. PMID:27060228
Proteogenomics: Integrating Next-Generation Sequencing and Mass Spectrometry to Characterize Human Proteomic Variation. PMID:27049631
Long non-coding RNA Databases in Cardiovascular Research. PMID:27049585
Transcriptomics resources of human tissues and organs. PMID:27044256
Long-read sequence assembly of the gorilla genome. PMID:27034376
Cancer therapies activate RIG-I-like receptor pathway through endogenous non-coding RNAs. PMID:27034163
Topology based identification and comprehensive classification of four-transmembrane helix containing proteins (4TMs) in the human genome. PMID:27030248
Transcript Isoform Variation Associated with Cytosine Modification in Human Lymphoblastoid Cell Lines. PMID:27029734
ILNCSIM: improved lncRNA functional similarity calculation model. PMID:27028993
Long Intergenic Noncoding RNAs Mediate the Human Chondrocyte Inflammatory Response and Are Differentially Expressed in Osteoarthritis Cartilage. PMID:27023358
Genome-wide interaction study of brain beta-amyloid burden and cognitive impairment in Alzheimer's disease. PMID:27021820
Transcriptomic and epigenomic characterization of the developing bat wing. PMID:27019111
Hypoxia-regulated gene expression explains differences between melanoma cell line-derived xenografts and patient-derived xenografts. PMID:27009863
Mechanisms of long noncoding RNA function in development and disease. PMID:27007508
CTCF-mediated chromatin loops enclose inducible gene regulatory domains. PMID:27004515
dbWGFP: a database and web server of human whole-genome single nucleotide variants and their functional predictions. PMID:26989155
Human Knockout Carriers: Dead, Diseased, Healthy, or Improved? PMID:26988438
CLASS2: accurate and efficient splice variant annotation from RNA-seq reads. PMID:26975657
Rare loss-of-function variants in SETD1A are associated with schizophrenia and developmental disorders. PMID:26974950
RNA-binding protein IGF2BP3 targeting of oncogenic transcripts promotes hematopoietic progenitor proliferation. PMID:26974154
Constructing 3D interaction maps from 1D epigenomes. PMID:26960733
Gene expression variability in mammalian embryonic stem cells using single cell RNA-seq data. PMID:26951854
Identification and characterization of lncRNA mediated transcriptional dysregulation dictates lncRNA roles in glioblastoma. PMID:26943771
Identification of STOML2 as a putative novel asthma risk gene associated with IL6R. PMID:26932604
A Helitron transposon reconstructed from bats reveals a novel mechanism of genome shuffling in eukaryotes. PMID:26931494
Pseudo-Reference-Based Assembly of Vertebrate Transcriptomes. PMID:26927182
Changes in snoRNA and snRNA Abundance in the Human, Chimpanzee, Macaque, and Mouse Brain. PMID:26926764
An Atlas of the Human Kinome Reveals the Mutational Landscape Underlying Dysregulated Phosphorylation Cascades in Cancer. PMID:26921330
Systematic characterization of lncRNAs' cell-to-cell expression heterogeneity in glioblastoma cells. PMID:26918340
Transcriptome Analysis in Domesticated Species: Challenges and Strategies. PMID:26917953
The Role of Long Noncoding RNAs in Neurodegenerative Diseases. PMID:26910817
Genetic mutations associated with metastatic clear cell renal cell carcinoma. PMID:26908440
A Long Non-coding RNA, lncLGR, Regulates Hepatic Glucokinase Expression and Glycogen Storage during Fasting. PMID:26904944
Refined mapping of autoimmune disease associated genetic variants with gene expression suggests an important role for non-coding RNAs. PMID:26898941
Probabilistic Modeling of Imaging, Genetics and Diagnosis. PMID:26886973
Widespread RNA binding by chromatin-associated proteins. PMID:26883116
IGHV1-69 polymorphism modulates anti-influenza antibody repertoires, correlates with IGHV utilization shifts and varies by ethnicity. PMID:26880249
Tumour-specific proline vulnerability uncovered by differential ribosome codon reading. PMID:26878238
Single-cell Transcriptome Study as Big Data. PMID:26876720
SplAdder: identification, quantification and testing of alternative splicing events from RNA-Seq data. PMID:26873928
CCSI: a database providing chromatin-chromatin spatial interaction information. PMID:26868054
Distinct genomic and epigenomic features demarcate hypomethylated blocks in colon cancer. PMID:26868017
Filtering genetic variants and placing informative priors based on putative biological function. PMID:26866982
Mutation pattern is an influential factor on functional mutation rates in cancer. PMID:26865835
Curated eutherian third party data gene data sets. PMID:26862561
Genome-wide identification and characterization of long intergenic noncoding RNAs and their potential association with larval development in the Pacific oyster. PMID:26861843
Biochemical Methods To Investigate lncRNA and the Influence of lncRNA:Protein Complexes on Chromatin. PMID:26859437
ePIANNO: ePIgenomics ANNOtation tool. PMID:26859295
Redifferentiation of expanded human islet β cells by inhibition of ARX. PMID:26856418
Transcriptomic variation of pharmacogenes in multiple human tissues and lymphoblastoid cell lines. PMID:26856248
Long non-coding RNA LINC01133 represses KLF2, P21 and E-cadherin transcription through binding with EZH2, LSD1 in non small cell lung cancer. PMID:26840083
Evolutionary analysis across mammals reveals distinct classes of long non-coding RNAs. PMID:26838501
Long non-coding RNAs display higher natural expression variation than protein-coding genes in healthy humans. PMID:26821746
Comprehensive prediction of lncRNA-RNA interactions in human transcriptome. PMID:26818453
Identifying micro-inversions using high-throughput sequencing reads. PMID:26818118
Epigenomic analysis detects aberrant super-enhancer DNA methylation in human cancer. PMID:26813288
Noncoding RNAs and pancreatic cancer. PMID:26811626
Histone H3 lysine 4 acetylation and methylation dynamics define breast cancer subtypes. PMID:26783963
RNAseq analysis for the diagnosis of muscular dystrophy. PMID:26783550
cnvScan: a CNV screening and annotation tool to improve the clinical utility of computational CNV prediction from exome sequencing data. PMID:26764020
Identifying and functionally characterizing tissue-specific and ubiquitously expressed human lncRNAs. PMID:26760768
QuickRNASeq lifts large-scale RNA-seq data analyses to the next level of automation and interactive visualization. PMID:26747388
A proteogenomic approach to understand splice isoform functions through sequence and expression-based computational modeling. PMID:26740460
ELF5 isoform expression is tissue-specific and significantly altered in cancer. PMID:26738740
Global proteogenomic analysis of human MHC class I-associated peptides derived from non-canonical reading frames. PMID:26728094
In Silico Functional Annotation of Genomic Variation. PMID:26724722
Derivation of consensus inactivation status for X-linked genes from genome-wide studies. PMID:26719789
Identification of important long non-coding RNAs and highly recurrent aberrant alternative splicing events in hepatocellular carcinoma through integrative analysis of multiple RNA-Seq datasets. PMID:26711644
Differentiation of mammary tumors and reduction in metastasis upon Malat1 lncRNA loss. PMID:26701265
Non-coding yet non-trivial: a review on the computational genomics of lincRNAs. PMID:26697116
Forward Individualized Medicine from Personal Genomes to Interactomes. PMID:26696898
Obesity-related known and candidate SNP markers can significantly change affinity of TATA-binding protein for human gene promoters. PMID:26694100
Long noncoding RNAs in cancer: from function to translation. PMID:26693181
Decreased long noncoding RNA MIR31HG is correlated with poor prognosis and contributes to cell proliferation in gastric cancer. PMID:26692098
Stress and glucocorticoid receptor transcriptional programming in time and space: Implications for the brain-gut axis. PMID:26690871
Ensembl 2016. PMID:26687719
Many lncRNAs, 5'UTRs, and pseudogenes are translated and some are likely to express functional proteins. PMID:26687005
Comprehensive Identification of Long Non-coding RNAs in Purified Cell Types from the Brain Reveals Functional LncRNA in OPC Fate Determination. PMID:26683846
A human haploid gene trap collection to study lncRNAs with unusual RNA biology. PMID:26670263
Unique features of long non-coding RNA biogenesis and function. PMID:26666209
Rare copy number variants implicated in posterior urethral valves. PMID:26663319
Detecting actively translated open reading frames in ribosome profiling data. PMID:26657557
proBAMsuite, a Bioinformatics Framework for Genome-Based Representation and Analysis of Proteomics Data. PMID:26657539
The domain structure and distribution of Alu elements in long noncoding RNAs and mRNAs. PMID:26654912
Comparative genomic analysis of eutherian tumor necrosis factor ligand genes. PMID:26646413
Integrating Diverse Types of Genomic Data to Identify Genes that Underlie Adverse Pregnancy Phenotypes. PMID:26641094
RNA Sequence Analysis of Human Huntington Disease Brain Reveals an Extensive Increase in Inflammatory and Developmental Gene Expression. PMID:26636579
The Role of H3K4me3 in Transcriptional Regulation Is Altered in Huntington's Disease. PMID:26636336
LncRNA-HIT Functions as an Epigenetic Regulator of Chondrogenesis through Its Recruitment of p100/CBP Complexes. PMID:26633036
ADMIRE: analysis and visualization of differential methylation in genomic regions using the Infinium HumanMethylation450 Assay. PMID:26628921
Transcript Expression Data from Human Islets Links Regulatory Signals from Genome-Wide Association Studies for Type 2 Diabetes and Glycemic Traits to Their Downstream Effectors. PMID:26624892
Variable reproducibility in genome-scale public data: A case study using ENCODE ChIP sequencing resource. PMID:26619763
Towards improved genome-scale metabolic network reconstructions: unification, transcript specificity and beyond. PMID:26615025
DIANA-LncBase v2: indexing microRNA targets on non-coding transcripts. PMID:26612864
Cancer RNA-Seq Nexus: a database of phenotype-specific transcriptome profiling in cancer cells. PMID:26602695
RNA sequencing of transcriptomes in human brain regions: protein-coding and non-coding RNAs, isoforms and alleles. PMID:26597164
The UCSC Genome Browser database: 2016 update. PMID:26590259
deepBase v2.0: identification, expression, evolution and function of small RNAs, LncRNAs and circular RNAs from deep-sequencing data. PMID:26590255
Inferring Selective Constraint from Population Genomic Data Suggests Recent Regulatory Turnover in the Human Brain. PMID:26590212
Identification of global regulators of T-helper cell lineage specification. PMID:26589177
A Dual Model for Prioritizing Cancer Mutations in the Non-coding Genome Based on Germline and Somatic Events. PMID:26588488
CpG island erosion, polycomb occupancy and sequence motif enrichment at bivalent promoters in mammalian embryonic stem cells. PMID:26582124
Death of a dogma: eukaryotic mRNAs can code for more than one protein. PMID:26578573
KATZLDA: KATZ measure for the lncRNA-disease association prediction. PMID:26577439
Distinguishing the immunostimulatory properties of noncoding RNAs expressed in cancer cells. PMID:26575629
Meta-Analysis of DNA Tumor-Viral Integration Site Selection Indicates a Role for Repeats, Gene Expression and Epigenetics. PMID:26569308
The pig X and Y Chromosomes: structure, sequence, and evolution. PMID:26560630
Union Exon Based Approach for RNA-Seq Gene Quantification: To Be or Not to Be? PMID:26559532
dbNSFP v3.0: A One-Stop Database of Functional Predictions and Annotations for Human Nonsynonymous and Splice-Site SNVs. PMID:26555599
DASHR: database of small human noncoding RNAs. PMID:26553799
Full-length single-cell RNA-seq applied to a viral human cancer: applications to HPV expression and splicing analysis in HeLa S3 cells. PMID:26550473
A potential prognostic long non-coding RNA signature to predict metastasis-free survival of breast cancer patients. PMID:26549855
Long noncoding RNAs in T lymphocytes. PMID:26538526
Using Population Genetics to Interrogate the Monogenic Nephrotic Syndrome Diagnosis in a Case Cohort. PMID:26534921
Differential expression analysis of human endogenous retroviruses based on ENCODE RNA-seq data. PMID:26530187
The Clinical Relevance of Long Non-Coding RNAs in Cancer. PMID:26516918
How to Use SNP_TATA_Comparator to Find a Significant Change in Gene Expression Caused by the Regulatory SNP of This Gene's Promoter via a Change in Affinity of the TATA-Binding Protein for This Promoter. PMID:26516624
Multiple SNP Set Analysis for Genome-Wide Association Studies Through Bayesian Latent Variable Selection. PMID:26515609
CAGE profiling of ncRNAs in hepatocellular carcinoma reveals widespread activation of retroviral LTR promoters in virus-induced tumors. PMID:26510915
Genetics of RA susceptibility, what comes next? PMID:26509058
Protective alleles and modifier variants in human health and disease. PMID:26503796
Discovery and characterization of Alu repeat sequences via precise local read assembly. PMID:26503250
Promoter-like epigenetic signatures in exons displaying cell type-specific splicing. PMID:26498677
Evidence of Extensive Alternative Splicing in Post Mortem Human Brain HTT Transcription by mRNA Sequencing. PMID:26496077
The potential clinical impact of the release of two drafts of the human proteome. PMID:26496066
DECKO: Single-oligo, dual-CRISPR deletion of genomic elements including long non-coding RNAs. PMID:26493208
Cancer Specific Long Noncoding RNAs Show Differential Expression Patterns and Competing Endogenous RNA Potential in Hepatocellular Carcinoma. PMID:26492393
CRISPR/Cas9-mediated heterozygous knockout of the autism gene CHD8 and characterization of its transcriptional networks in neurodevelopment. PMID:26491539
Third party annotation gene data set of eutherian lysozyme genes. PMID:26484105
Dynamic expression of long noncoding RNAs and repeat elements in synaptic plasticity. PMID:26483626
Identification of linc-NeD125, a novel long non coding RNA that hosts miR-125b-1 and negatively controls proliferation of human neuroblastoma cells. PMID:26480000
Multiple breast cancer risk variants are associated with differential transcript isoform expression in tumors. PMID:26472073
Genome-wide DNA methylome reveals the dysfunction of intronic microRNAs in major psychosis. PMID:26462620
lncRScan-SVM: A Tool for Predicting Long Non-Coding RNAs Using Support Vector Machine. PMID:26437338
Discovery of four recessive developmental disorders using probabilistic genotype and phenotype matching among 4,125 families. PMID:26437029
Alternative Splicing QTLs in European and African Populations. PMID:26430802
Linking RNA biology to lncRNAs. PMID:26430155
Single-Molecule Sequencing Reveals Estrogen-Regulated Clinically Relevant lncRNAs in Breast Cancer. PMID:26426411
Transcriptome sequencing and analysis of major genes involved in calcium signaling pathways in pear plants (Pyrus calleryana Decne.). PMID:26424153
Rare Variants in PLD3 Do Not Affect Risk for Early-Onset Alzheimer Disease in a European Consortium Cohort. PMID:26411346
Extracellular vesicle-mediated transfer of processed and functional RNY5 RNA. PMID:26392588
BIDCHIPS: bias decomposition and removal from ChIP-seq data clarifies true binding signal and its functional correlates. PMID:26388941
Using mixtures of biological samples as process controls for RNA-sequencing experiments. PMID:26383878
A survey of tandem repeat instabilities and associated gene expression changes in 35 colorectal cancers. PMID:26376692
Devising a Consensus Framework for Validation of Novel Human Coding Loci. PMID:26367542
Regulatory RNAs and control of epigenetic mechanisms: expectations for cognition and cognitive dysfunction. PMID:26366811
Co-LncRNA: investigating the lncRNA combinatorial effects in GO annotations and KEGG pathways based on human RNA-Seq data. PMID:26363020
Identification and validation of potential prognostic lncRNA biomarkers for predicting survival in patients with multiple myeloma. PMID:26362431
Targeted deep sequencing identifies rare loss-of-function variants in IFNGR1 for risk of atopic dermatitis complicated by eczema herpeticum. PMID:26343451
Tracking Distinct RNA Populations Using Efficient and Reversible Covalent Chemistry. PMID:26340425
Comparison of stranded and non-stranded RNA-seq transcriptome profiling and investigation of gene overlap. PMID:26334759
Allele-Selective Transcriptome Recruitment to Polysomes Primed for Translation: Protein-Coding and Noncoding RNAs, and RNA Isoforms. PMID:26331722
Integration of extracellular RNA profiling data using metadata, biomedical ontologies and Linked Data technologies. PMID:26320941
Architectural and Functional Commonalities between Enhancers and Promoters. PMID:26317464
LARVA: an integrative framework for large-scale analysis of recurrent variants in noncoding annotations. PMID:26304545
Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions. PMID:26300125
Aberrant RNA splicing in cancer; expression changes and driver mutations of splicing factor genes. PMID:26300000
Integrative analysis of RNA, translation, and protein levels reveals distinct regulatory variation across humans. PMID:26297486
Bioinformatics Methods and Tools to Advance Clinical Care. Findings from the Yearbook 2015 Section on Bioinformatics and Translational Informatics. PMID:26293864
Prediction of Causal Candidate Genes in Coronary Artery Disease Loci. PMID:26293461
Evolution of the unspliced transcriptome. PMID:26289325
Read clouds uncover variation in complex regions of the human genome. PMID:26286554
piRNAs derived from ancient viral processed pseudogenes as transgenerational sequence-specific immune memory in mammals. PMID:26283688
Systematic chromatin state comparison of epigenomes associated with diverse properties including sex and tissue type. PMID:26282110
Predicting lncRNA-disease associations and constructing lncRNA functional similarity network based on the information of miRNA. PMID:26278472
Generalised Anxiety Disorder--A Twin Study of Genetic Architecture, Genome-Wide Association and Differential Gene Expression. PMID:26274327
An Association Rule Mining Approach to Discover lncRNAs Expression Patterns in Cancer Datasets. PMID:26273587
Predicting effective microRNA target sites in mammalian mRNAs. PMID:26267216
Next-generation analysis of gene expression regulation--comparing the roles of synthesis and degradation. PMID:26259698
A gene-based association method for mapping traits using reference transcriptome data. PMID:26258848
Genome-wide association between YAP/TAZ/TEAD and AP-1 at enhancers drives oncogenic growth. PMID:26258633
Nuclear Fractionation Reveals Thousands of Chromatin-Tethered Noncoding RNAs Adjacent to Active Genes. PMID:26257179
The use of exome capture RNA-seq for highly degraded RNA with application to clinical cancer sequencing. PMID:26253700
Comprehensive assembly of novel transcripts from unmapped human RNA-Seq data and their association with cancer. PMID:26253570
Paradigm shifts in genomics through the FANTOM projects. PMID:26253466
A reanalysis of mouse ENCODE comparative gene expression data. PMID:26236466
Integrated analysis of mRNA and miRNA expression in response to interleukin-6 in hepatocytes. PMID:26217794
BayesPI-BAR: a new biophysical model for characterization of regulatory sequence variations. PMID:26202972
Comparative assessment of methods for the computational inference of transcript isoform abundance from RNA-seq data. PMID:26201343
Low-frequency germline variants across 6p22.2-6p21.33 are associated with non-obstructive azoospermia in Han Chinese men. PMID:26199320
Creating reference gene annotation for the mouse C57BL6/J genome assembly. PMID:26187010
Data quality aware analysis of differential expression in RNA-seq with NOISeq R/Bioc package. PMID:26184878
A potential signature of eight long non-coding RNAs predicts survival in patients with non-small cell lung cancer. PMID:26183581
Small RNA deep sequencing discriminates subsets of extracellular vesicles released by melanoma cells--Evidence of unique microRNA cargos. PMID:26176991
Drosophila and Caenorhabditis elegans as Discovery Platforms for Genes Involved in Human Alcohol Use Disorder. PMID:26173477
MicroRNA Profiling of Neurons Generated Using Induced Pluripotent Stem Cells Derived from Patients with Schizophrenia and Schizoaffective Disorder, and 22q11.2 Del. PMID:26173148
RNA editing differently affects protein-coding genes in D. melanogaster and H. sapiens. PMID:26169954
A semi-supervised approach uncovers thousands of intragenic enhancers differentially activated in human cells. PMID:26169177
Long non-coding RNAs in innate and adaptive immunity. PMID:26166759
Revealing Missing Human Protein Isoforms Based on Ab Initio Prediction, RNA-seq and Proteomics. PMID:26156868
Recessive mutations in POLR1C cause a leukodystrophy by impairing biogenesis of RNA polymerase III. PMID:26151409
Comparison of Gene Coexpression Profiles and Construction of Conserved Gene Networks to Find Functional Modules. PMID:26147120
Discovery and Fine-Mapping of Glycaemic and Obesity-Related Trait Loci Using High-Density Imputation. PMID:26132169
Human bone marrow- and adipose-mesenchymal stem cells secrete exosomes enriched in distinctive miRNA and tRNA species. PMID:26129847
Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction. PMID:26110515
Gene Model Annotations for Drosophila melanogaster: Impact of High-Throughput Data. PMID:26109357
Comparison of RNA-seq and microarray-based models for clinical endpoint prediction. PMID:26109056
SIRT1 affects DNA methylation of polycomb group protein target genes, a hotspot of the epigenetic shift observed in ageing. PMID:26104761
Dysregulated transcription across diverse cancer types reveals the importance of RNA-binding protein in carcinogenesis. PMID:26100984
Possible Human Papillomavirus 38 Contamination of Endometrial Cancer RNA Sequencing Samples in The Cancer Genome Atlas Database. PMID:26085148
Single-cell mRNA sequencing identifies subclonal heterogeneity in anti-cancer drug responses of lung adenocarcinoma cells. PMID:26084335
Natural variability of minimotifs in 1092 people indicates that minimotifs are targets of evolution. PMID:26068475
Constructing lncRNA functional similarity network based on lncRNA-disease associations and disease semantic similarity. PMID:26061969
Alternatively Spliced Homologous Exons Have Ancient Origins and Are Highly Expressed at the Protein Level. PMID:26061177
A general concept for consistent documentation of computational analyses. PMID:26055099
Recurrent somatic mutations in regulatory regions of human cancer genomes. PMID:26053494
Non-coding RNAs: Epigenetic regulators of bone development and homeostasis. PMID:26039869
RNA biomarkers to facilitate the identification of aggressive prostate cancer. PMID:26022941
JAFFA: High sensitivity transcriptome-focused fusion gene detection. PMID:26019724
Systematic transcriptome analysis reveals tumor-specific isoforms for ovarian cancer diagnosis and therapy. PMID:26015570
Spatial genomic heterogeneity within localized, multifocal prostate cancer. PMID:26005866
StarScan: a web server for scanning small RNA targets from degradome sequencing data. PMID:25990732
APPRIS WebServer and WebServices. PMID:25990727
Comprehensive transcriptome analysis using synthetic long-read sequencing reveals molecular co-association of distant splicing events. PMID:25985263
Seq2pathway: an R/Bioconductor package for pathway analysis of next-generation sequencing data. PMID:25979472
Longitudinal epigenetic and gene expression profiles analyzed by three-component analysis reveal down-regulation of genes involved in protein translation in human aging. PMID:25977295
Recursive splicing in long vertebrate genes. PMID:25970246
Human genomics. The human transcriptome across tissues and individuals. PMID:25954002
Human genomics. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans. PMID:25954001
Initial description of primate-specific cystine-knot Prometheus genes and differential gene expansions of D-dopachrome tautomerase genes. PMID:25941635
Enhanced meta-analysis and replication studies identify five new psoriasis susceptibility loci. PMID:25939698
Low-frequency coding variants at 6p21.33 and 20q11.21 are associated with lung cancer risk in Chinese populations. PMID:25937444
A cluster of noncoding RNAs activates the ESR1 locus during breast cancer adaptation. PMID:25923108
Genetic code evolution reveals the neutral emergence of mutational robustness, and information as an evolutionary constraint. PMID:25919033
Inosine modifications in human tRNAs are incorporated at the precursor tRNA level. PMID:25916855
Cross-population joint analysis of eQTLs: fine mapping and functional annotation. PMID:25906321
ZNF804A Transcriptional Networks in Differentiating Neurons Derived from Induced Pluripotent Stem Cells of Human Origin. PMID:25905630
Expression and functions of long noncoding RNAs during human T helper cell differentiation. PMID:25903499
Long non-coding RNA discovery across the genus anopheles reveals conserved secondary structures within and beyond the Gambiae complex. PMID:25903279
Characterization and identification of hidden rare variants in the human genome. PMID:25903059
Applying the new genomics to alcohol dependence. PMID:25896098
Proteogenomics analysis reveals specific genomic orientations of distal regulatory regions composed by non-canonical histone variants. PMID:25878728
The Landscape of long noncoding RNA classification. PMID:25869999
Targeting the schizophrenia genome: a fast track strategy from GWAS to clinic. PMID:25869805
RNA imaging. Spatially resolved, highly multiplexed RNA profiling in single cells. PMID:25858977
miRGate: a curated database of human, mouse and rat miRNA-mRNA targets. PMID:25858286
Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project. PMID:25854118
Transcript and protein expression decoupling reveals RNA binding proteins and miRNAs as potential modulators of human aging. PMID:25853883
Transposon mutagenesis identifies genetic drivers of Braf(V600E) melanoma. PMID:25848750
The lncRNA DEANR1 facilitates human endoderm differentiation by activating FOXA2 expression. PMID:25843708
Disease-Associated Single-Nucleotide Polymorphisms From Noncoding Regions in Juvenile Idiopathic Arthritis Are Located Within or Adjacent to Functional Genomic Elements of Human Neutrophils and CD4+ T Cells. PMID:25833190
A thesaurus of genetic variation for interrogation of repetitive genomic regions. PMID:25820428
Re-annotation of presumed noncoding disease/trait-associated genetic variants by integrative analyses. PMID:25819875
SCAN database: facilitating integrative analyses of cytosine modification and expression QTL. PMID:25818895
Predicting the functions of long noncoding RNAs using RNA-seq based on Bayesian network. PMID:25815337
Immunoglobulin transcript sequence and somatic hypermutation computation from unselected RNA-seq reads in chronic lymphocytic leukemia. PMID:25787252
Transcriptome sequencing reveals potential mechanism of cryptic 3' splice site selection in SF3B1-mutated cancers. PMID:25768983
A comprehensive evaluation of ensembl, RefSeq, and UCSC annotations in the context of RNA-seq read mapping and gene quantification. PMID:25765860
GASS: genome structural annotation for Eukaryotes based on species similarity. PMID:25764973
Using the ENCODE Resource for Functional Annotation of Genetic Variants. PMID:25762420
Designing optogenetically controlled RNA for regulating biological systems. PMID:25758022
Systematic identification and characterization of long intergenic non-coding RNAs in fetal porcine skeletal muscle development. PMID:25753296
Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing. PMID:25751143
Interferon-alpha competing endogenous RNA network antagonizes microRNA-1270. PMID:25746225
Prognostic impact of HOTAIR expression is restricted to ER-negative breast cancers. PMID:25739705
Most highly expressed protein-coding genes have a single dominant isoform. PMID:25732134
A survey of imprinted gene expression in mouse trophoblast stem cells. PMID:25711832
LncRNA2Function: a comprehensive resource for functional investigation of human lncRNAs based on RNA-seq data. PMID:25707511
Genome-Wide Identification and Classification of MicroRNAs Derived from Repetitive Elements. PMID:25705168
Oncotator: cancer variant annotation tool. PMID:25703262
Spatiotemporal 16p11.2 protein network implicates cortical late mid-fetal brain development and KCTD13-Cul3-RhoA pathway in psychiatric diseases. PMID:25695269
Epigenomic footprints across 111 reference epigenomes reveal tissue-specific epigenetic regulation of lincRNAs. PMID:25691256
Novel long non-coding RNAs are specific diagnostic and prognostic markers for prostate cancer. PMID:25686826
An integrative analysis of TFBS-clustered regions reveals new transcriptional regulation models on the accessible chromatin landscape. PMID:25682954
Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell-type-specific expression. PMID:25677182
Integrating transcriptomics and proteomics to show that tanshinone IIA suppresses cell growth by blocking glucose metabolism in gastric cancer cells. PMID:25652794
Discovery of Protein-lncRNA Interactions by Integrating Large-Scale CLIP-Seq and RNA-Seq Datasets. PMID:25642422
An Island-Based Approach for Differential Expression Analysis. PMID:25632406
Correlation of circular RNA abundance with proliferation--exemplified with colorectal and ovarian cancer, idiopathic lung fibrosis, and normal human tissues. PMID:25624062
Long Non-Coding RNA BST2/BISPR is Induced by IFN and Regulates the Expression of the Antiviral Factor Tetherin. PMID:25620967
3USS: a web server for detecting alternative 3'UTRs from RNA-seq experiments. PMID:25617413
The landscape of long noncoding RNAs in the human transcriptome. PMID:25599403
A method for calculating probabilities of fitness consequences for point mutations across the human genome. PMID:25599402
Kleat: cleavage site analysis of transcriptomes. PMID:25592595
Identifying mutation specific cancer pathways using a structurally resolved protein interaction network. PMID:25592571
Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression. PMID:25582907
A long non-coding RNA links calreticulin-mediated immunogenic cell removal to RB1 transcription. PMID:25579178
Transposable elements modulate human RNA abundance and splicing via specific RNA-protein interactions. PMID:25572935
Genome-wide discovery of human splicing branchpoints. PMID:25561518
Long non-coding RNAs as regulators of the endocrine system. PMID:25560704
Biased allelic expression in human primary fibroblast single cells. PMID:25557783
Uncapped 5' ends of mRNAs targeted by cytoplasmic capping map to the vicinity of downstream CAGE tags. PMID:25541487
Uncovering RNA Editing Sites in Long Non-Coding RNAs. PMID:25538940
Recombinant renewable polyclonal antibodies. PMID:25530082
Systems genomics evaluation of the SH-SY5Y neuroblastoma cell line as a model for Parkinson's disease. PMID:25528190
Long non-coding RNA normalisers in human brain tissue. PMID:25528156
Annotation of genomics data using bidirectional hidden Markov models unveils variations in Pol II transcription cycle. PMID:25527639
Genome-wide analysis of the human p53 transcriptional network unveils a lncRNA tumour suppressor signature. PMID:25524025
Comprehensive discovery of DNA motifs in 349 human cells and tissues reveals new features of motifs. PMID:25505144
Computational approaches to interpreting genomic sequence variation. PMID:25473426
Proteome sequencing goes deep. PMID:25461719
Gene-gene and gene-environment interactions detected by transcriptome sequence analysis in twins. PMID:25436857
The RCSB Protein Data Bank: views of structural biology for basic and applied research and education. PMID:25428375
The UCSC Genome Browser database: 2015 update. PMID:25428374
Expression profiles of long non-coding RNAs located in autoimmune disease-associated regions reveal immune cell-type specificity. PMID:25419237
Population genetic simulations of complex phenotypes with implications for rare variant association tests. PMID:25417809
Type I Interferon Regulates the Expression of Long Non-Coding RNAs. PMID:25414701
Comparison of the transcriptional landscapes between human and mouse tissues. PMID:25413365
Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution. PMID:25411453
RADIA: RNA and DNA integrated analysis for somatic mutation detection. PMID:25405470
Human nonsense-mediated RNA decay initiates widely by endonucleolysis and targets snoRNA host genes. PMID:25403180
LncRNAWiki: harnessing community knowledge in collaborative curation of human long non-coding RNAs. PMID:25399417
Splicing mutation analysis reveals previously unrecognized pathways in lymph node-invasive breast cancer. PMID:25394353
Genetic associations of nonsynonymous exonic variants with psychophysiological endophenotypes. PMID:25387709
Systems biology approaches for studying the pathogenesis of non-alcoholic fatty liver disease. PMID:25386055
Systematic analysis of noncoding somatic mutations and gene expression alterations across 14 tumor types. PMID:25383969
Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers. PMID:25383968
A stationary wavelet entropy-based clustering approach accurately predicts gene expression. PMID:25383910
Transcriptome analysis of the human corneal endothelium. PMID:25377225
24-hour rhythms of DNA methylation and their relation with rhythms of RNA expression in the human dorsolateral prefrontal cortex. PMID:25375876
Megabase-scale deletion using CRISPR/Cas9 to generate a fully haploid human cell line. PMID:25373145
Small and Long Regulatory RNAs in the Immune System and Immune Diseases. PMID:25368617
Understanding gene regulatory mechanisms by integrating ChIP-seq and RNA-seq data: statistical solutions to biological problems. PMID:25364758
Genenames.org: the HGNC resources in 2015. PMID:25361968
Transdifferentiation of human fibroblasts to endothelial cells: role of innate immunity. PMID:25359165
Proteogenomics: concepts, applications and computational strategies. PMID:25357241
Ensembl 2015. PMID:25352552
RNAcentral: an international database of ncRNA sequences. PMID:25352543
SeAMotE: a method for high-throughput motif discovery in nucleic acid sequences. PMID:25341390
lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs. PMID:25332394
VAS: a convenient web portal for efficient integration of genomic features with millions of genetic variants. PMID:25306238
MUSIC: identification of enriched regions in ChIP-Seq experiments using a mappability-corrected multiscale signal processing framework. PMID:25292436
Promoter analysis reveals globally differential regulation of human long non-coding RNA and protein-coding genes. PMID:25275320
Distinct structural transitions of chromatin topological domains correlate with coordinated hormone-induced gene regulation. PMID:25274727
FunSeq2: a framework for prioritizing noncoding regulatory variants in cancer. PMID:25273974
Long non-coding RNAs differentially expressed between normal versus primary breast tumor tissues disclose converse changes to breast cancer-related protein-coding genes. PMID:25264628
Long non-coding RNAs and control of gene expression in the immune system. PMID:25262537
lincRNA-RoR and miR-145 regulate invasion in triple-negative breast cancer via targeting ARF6. PMID:25253741
High-resolution transcriptome analysis with long-read RNA sequencing. PMID:25251678
PLEK: a tool for predicting long non-coding RNAs and messenger RNAs based on an improved k-mer scheme. PMID:25239089
Long non-coding RNAs as a source of new peptides. PMID:25233276
LncRBase: an enriched resource for lncRNA information. PMID:25233092
Novel copy-number variants in a population-based investigation of classic heterotaxy. PMID:25232849
Resetting transcription factor control circuitry toward ground-state pluripotency in human. PMID:25215486
The landscape of kinase fusions in cancer. PMID:25204415
Global genomic and transcriptomic analysis of human pancreatic islets reveals novel genes influencing glucose metabolism. PMID:25201977
Mutational analysis of genes coding for cell surface proteins in colorectal cancer cell lines reveal novel altered pathways, druggable mutations and mutated epitopes for targeted therapy. PMID:25193853
Transcriptome sequencing of a large human family identifies the impact of rare noncoding variants. PMID:25192044
Advances in translational biomedicine from systems approaches. PMID:25177342
Frameshift alignment: statistics and post-genomic applications. PMID:25172925
The architecture of a scrambled genome reveals massive levels of genomic rearrangement during development. PMID:25171416
Ribosome profiling reveals pervasive translation outside of annotated protein-coding genes. PMID:25159147
A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium. PMID:25150838
Identification of genetic variants associated with alternative splicing using sQTLseekeR. PMID:25140736
Tandem RNA chimeras contribute to transcriptome diversity in human population and are associated with intronic genetic variants. PMID:25133550
Long noncoding RNA associated-competing endogenous RNAs in gastric cancer. PMID:25124853
Complex interactions of transcription factors in mediating cytokine biology in T cells. PMID:25123282
Negative regulation of the interferon response by an interferon-induced long non-coding RNA. PMID:25122750
Down-regulation of long non-coding RNA GAS5 is associated with the prognosis of hepatocellular carcinoma. PMID:25120813
Transcriptome sequencing reveals altered long intergenic non-coding RNAs in lung cancer. PMID:25116943
Alternative forms of Y-box binding protein 1 and YB-1 mRNA. PMID:25116735
Identification of copy number variants from exome sequence data. PMID:25102989
Genome-wide mapping and characterization of Notch-regulated long noncoding RNAs in acute leukemia. PMID:25083870
SNP@lincTFBS: an integrated database of polymorphisms in human LincRNA transcription factor binding sites. PMID:25075616
Whole-genome bisulfite sequencing of multiple individuals reveals complementary roles of promoter and gene body methylation in transcriptional regulation. PMID:25074712
A wavelet approach to detect enriched regions and explore epigenomic landscapes. PMID:25072902
Missing genetic risk in neural tube defects: can exome sequencing yield an insight? PMID:25044326
Construction of mate pair full-length cDNAs libraries and characterization of transcriptional start sites and termination sites. PMID:25034687
Data integration in the era of omics: current and future challenges. PMID:25032990
Identification and characterization of long intergenic non-coding RNAs related to mouse liver development. PMID:25012394
Exploring the stability of long intergenic non-coding RNA in K562 cells by comparative studies of RNA-Seq datasets. PMID:24996425
Coherent somatic mutation in autoimmune disease. PMID:24988487
The effect of homozygous deletion of the BBOX1 and Fibin genes on carnitine level and acyl carnitine profile. PMID:24986124
EZH2-mediated epigenetic suppression of long noncoding RNA SPRY4-IT1 promotes NSCLC cell proliferation and metastasis by affecting the epithelial-mesenchymal transition. PMID:24967960
Defining a personal, allele-specific, and single-molecule long-read transcriptome. PMID:24961374
The emerging era of genomic data integration for analyzing splice isoform function. PMID:24951248
Choice of transcripts and software has a large effect on variant annotation. PMID:24944579
Multiple evidence strands suggest that there may be as few as 19,000 human protein-coding genes. PMID:24939910
Long non-coding RNA-dependent transcriptional regulation in neuronal development and disease. PMID:24936207
Human 45,X fibroblast transcriptome reveals distinct differentially expressed genes including long noncoding RNAs potentially associated with the pathophysiology of Turner syndrome. PMID:24932682
Dicer-microRNA-Myc circuit promotes transcription of hundreds of long noncoding RNAs. PMID:24929436
Capture and Amplification by Tailing and Switching (CATS). An ultrasensitive ligation-independent method for generation of DNA libraries for deep sequencing from picogram amounts of DNA and RNA. PMID:24922482
Analysis and expansion of the eosinophilic esophagitis transcriptome by RNA sequencing. PMID:24920534
Structured RNAs and synteny regions in the pig genome. PMID:24917120
Genome-wide identification of long intergenic noncoding RNA genes and their potential association with domestication in pigs. PMID:24891613
Computational approaches for isoform detection and estimation: good and bad news. PMID:24885830
Genetic distance as an alternative to physical distance for definition of gene units in association studies. PMID:24884992
Integrative transcriptome meta-analysis reveals widespread sex-biased gene expression at the human fetal-maternal interface. PMID:24867328
Deep sequencing of HIV-infected cells: insights into nascent transcription and host-directed therapy. PMID:24850744
A Bayesian method to incorporate hundreds of functional characteristics with association evidence to improve variant prioritization. PMID:24844982
Long non-coding RNAs in stem cells and cancer. PMID:24829860
Global view of enhancer-promoter interactome in human cells. PMID:24821768
Realistic artificial DNA sequences as negative controls for computational genomics. PMID:24803667
Using common variants to indicate cancer genes. PMID:24798945
A comprehensive resequence-analysis of 250 kb region of 8q24.21 in men of African ancestry. PMID:24783269
Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance. PMID:24777452
Genetic interactions affecting human gene expression identified by variance association mapping. PMID:24771767
Multi-ethnic fine-mapping of 14 central adiposity loci. PMID:24760767
Guidelines for investigating causality of sequence variants in human disease. PMID:24759409
Heat shock alters the expression of schizophrenia and autism candidate genes in an induced pluripotent stem cell model of the human telencephalon. PMID:24736721
TF2LncRNA: identifying common transcription factors for a list of lncRNA genes from ChIP-Seq data. PMID:24729968
Improved annotation of 3' untranslated regions and complex loci by combination of strand-specific direct RNA sequencing, RNA-Seq and ESTs. PMID:24722185
A short guide to long non-coding RNA gene nomenclature. PMID:24716852
Evidence for the biogenesis of more than 1,000 novel human microRNAs. PMID:24708865
Identification and characterization of alternative splicing in parasitic nematode transcriptomes. PMID:24690220
The retrovirus HERVH is a long noncoding RNA required for human embryonic stem cell identity. PMID:24681886
Diversity and dynamics of the Drosophila transcriptome. PMID:24670639
Effects of cytosine methylation on transcription factor binding sites. PMID:24669864
Long non-coding RNA and alternative splicing modulations in Parkinson's leukocytes identified by RNA sequencing. PMID:24651478
Genome-guided transcript assembly by integrative analysis of RNA sequence data. PMID:24633242
The challenges and importance of structural variation detection in livestock. PMID:24600474
MARIS: method for analyzing RNA following intracellular sorting. PMID:24594682
Cell cycle, oncogenic and tumor suppressor pathways regulate numerous long and macro non-protein-coding RNAs. PMID:24594072
AnaLysis of Expression on human chromosome 21, ALE-HSA21: a pilot integrated web resource. PMID:24573881
Exome-based mapping and variant prioritization for inherited Mendelian disorders. PMID:24560519
The master regulator of the cellular stress response (HSF1) is critical for orthopoxvirus infection. PMID:24516381
Differentiated human stem cells resemble fetal, not adult, β cells. PMID:24516164
A pan-cancer analysis of transcriptome changes associated with somatic mutations in U2AF1 reveals commonly altered splicing events. PMID:24498085
The cleverSuite approach for protein characterization: predictions of structural properties, solubility, chaperone requirements and RNA-binding abilities. PMID:24493033
bwtool: a tool for bigWig files. PMID:24489365
Functional annotation of noncoding sequence variants. PMID:24487584
Combinatorial epigenetic patterns as quantitative predictors of chromatin biology. PMID:24472558
Exon identity crisis: disease-causing mutations that disrupt the splicing code. PMID:24456648
A survey of software for genome-wide discovery of differential splicing in RNA-Seq data. PMID:24447644
Single molecule fluorescence approaches shed light on intracellular RNAs. PMID:24417544
Revisiting the thrifty gene hypothesis via 65 loci associated with susceptibility to type 2 diabetes. PMID:24412096
Dissecting the expression landscape of RNA-binding proteins in human cancers. PMID:24410894
Constitutive patterns of gene expression regulated by RNA-binding proteins. PMID:24401680
Sebnif: an integrated bioinformatics pipeline for the identification of novel large intergenic noncoding RNAs (lincRNAs)--application in human skeletal muscle cells. PMID:24400097
CGAT: computational genomics analysis toolkit. PMID:24395753
Extensive localization of long noncoding RNAs to the cytosol and mono- and polyribosomal complexes. PMID:24393600
Genomics of alternative splicing: evolution, development and pathophysiology. PMID:24378600
Feature-based classification of amino acid substitutions outside conserved functional protein domains. PMID:24348198
Comparative genomic analysis of eutherian ribonuclease A genes. PMID:24337645
Long non-coding RNAs and chromatin modifiers: their place in the epigenetic code. PMID:24335342
Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments. PMID:24335146
Transparency tools in gene patenting for informing policy and practice. PMID:24316644
The Vertebrate Genome Annotation browser 10 years on. PMID:24316575
DPRP: a database of phenotype-specific regulatory programs derived from transcription factor binding data. PMID:24302579
From single-cell to cell-pool transcriptomes: stochasticity in gene expression and RNA splicing. PMID:24299736
starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data. PMID:24297251
Genetic associations with 25-hydroxyvitamin D deficiency in HIV-1-infected youth: fine-mapping for the GC/DBP gene that encodes the vitamin D-binding protein. PMID:24294218
Chromatin signatures at transcriptional start sites separate two equally populated yet distinct classes of intergenic long noncoding RNAs. PMID:24289259
Locus Reference Genomic: reference sequences for the reporting of clinically relevant sequence variants. PMID:24285302
Expression and phosphorylation of the AS160_v2 splice variant supports GLUT4 activation and the Warburg effect in multiple myeloma. PMID:24280290
The UCSC Genome Browser database: 2014 update. PMID:24270787
Genetic and epigenetic regulation of human lincRNA gene expression. PMID:24268656
Comprehensive analysis of long non-coding RNAs in ovarian cancer reveals global patterns and targeted DNA amplification. PMID:24265805
Systematically differentiating functions for alternatively spliced isoforms through integrating RNA-seq data. PMID:24244129
Identification of novel transcripts and noncoding RNAs in bovine skin by deep next generation sequencing. PMID:24225384
Many human accelerated regions are developmental enhancers. PMID:24218637
Current status and new features of the Consensus Coding Sequence database. PMID:24217909
Regulatory Roles for Long ncRNA and mRNA. PMID:24216986
Finding the active genes in deep RNA-seq gene expression studies. PMID:24215113
SelenoDB 2.0: annotation of selenoprotein genes in animals and their genetic diversity in humans. PMID:24194593
Coupling transcription factor occupancy to nucleosome architecture with DNase-FLASH. PMID:24185839
Assessment of transcript reconstruction methods for RNA-seq. PMID:24185837
A genome-wide association study of prostate cancer in West African men. PMID:24185611
Large-scale mass spectrometric detection of variant peptides resulting from nonsynonymous nucleotide differences. PMID:24175627
Functional transcriptomics in the post-ENCODE era. PMID:24172201
Integrating and mining the chromatin landscape of cell-type specificity using self-organizing maps. PMID:24170599
Transcriptome interrogation of human myometrium identifies differentially expressed sense-antisense pairs of protein-coding and long non-coding RNA genes in spontaneous labor at term. PMID:24168098
Long non-coding RNA HOTAIR in carcinogenesis and metastasis. PMID:24165275
Gene regulation by non-coding RNAs. PMID:24164576
An emerging role for long non-coding RNA dysregulation in neurological disorders. PMID:24129177
A single-molecule long-read survey of the human transcriptome. PMID:24108091
Transcriptome comparison of human neurons generated using induced pluripotent stem cells derived from dental pulp and skin fibroblasts. PMID:24098394
Extensive divergence of transcription factor binding in Drosophila embryos with highly conserved gene expression. PMID:24068946
Transcriptome and genome sequencing uncovers functional variation in humans. PMID:24037378
Analysis of variable retroduplications in human populations suggests coupling of retrotransposition to cell division. PMID:24026178
Noncoding RNA in oncogenesis: a new era of identifying key players. PMID:24013378
Principles of self-organization in biological pathways: a hypothesis on the autogenous association of alpha-synuclein. PMID:24003031
Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis. PMID:24002785
Web Apollo: a web-based genomic annotation editing platform. PMID:24000942
Finding the lost treasures in exome sequencing data. PMID:23972387
Transcriptomic signatures in cartilage ageing. PMID:23971731
A model-based analysis of GC-biased gene conversion in the human and chimpanzee genomes. PMID:23966869
Identification of the missing pluripotency mediator downstream of leukaemia inhibitory factor. PMID:23942233
Genistein inhibits prostate cancer cell growth by targeting miR-34a and oncogenic HOTAIR. PMID:23936419
Autosomal dominant diabetes arising from a Wolfram syndrome 1 mutation. PMID:23903355
Computational approaches to identify functional genetic variants in cancer genomes. PMID:23900255
Detecting and comparing non-coding RNAs in the high-throughput era. PMID:23887659
Transcription factor binding profiles reveal cyclic expression of human protein-coding genes and non-coding RNAs. PMID:23874175
Assessing association between protein truncating variants and quantitative traits. PMID:23860716
dbNSFP v2.0: a database of human non-synonymous SNVs and their functional predictions and annotations. PMID:23843252
Chromatin-bound RNA and the neurobiology of psychiatric disease. PMID:23831425
Dissecting the Characteristics and Dynamics of Human Protein Complexes at Transcriptome Cascade Using RNA-Seq Data. PMID:23824284
Pervasive transcription of the human genome produces thousands of previously unidentified long intergenic noncoding RNAs. PMID:23818866
Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene. PMID:23815980
Food, nutrigenomics, and neurodegeneration--neuroprotection by what you eat! PMID:23813102
Analysis of long non-coding RNA expression profiles in gastric cancer. PMID:23801869
Separating homeologs by phasing in the tetraploid wheat transcriptome. PMID:23800085
A probabilistic approach to learn chromatin architecture and accurate inference of the NF-κB/RelA regulatory network using ChIP-Seq. PMID:23771139
The non-obese diabetic mouse sequence, annotation and variation resource: an aid for investigating type 1 diabetes. PMID:23729657
A brief review on the Human Encyclopedia of DNA Elements (ENCODE) project. PMID:23722115
A statistical framework for power calculations in ChIP-seq experiments. PMID:23665773
Transposable elements are major contributors to the origin, diversification, and regulation of vertebrate long noncoding RNAs. PMID:23637635
Discovery and mass spectrometric analysis of novel splice-junction peptides using RNA-Seq. PMID:23629695
Genomics and proteomics in solving brain complexity. PMID:23615871
Peppy: proteogenomic search software. PMID:23614390
Conserved expression of natural antisense transcripts in mammals. PMID:23577827
Comprehensive characterization of human genome variation by high coverage whole-genome sequencing of forty four Caucasians. PMID:23577066
A new method for stranded whole transcriptome RNA-seq. PMID:23557989
Epigenetics in Friedreich's Ataxia: Challenges and Opportunities for Therapy. PMID:23533785
Long noncoding RNAs: new players in the molecular mechanism for maintenance and differentiation of pluripotent stem cells. PMID:23528033
Genomic and epigenomic insights into nutrition and brain disorders. PMID:23503168
Transcriptional regulation and its misregulation in disease. PMID:23498934
Non-Coding RNAs: Functional Aspects and Diagnostic Utility in Oncology. PMID:23455466
Accurate identification and analysis of human mRNA isoforms using deep long read sequencing. PMID:23450794
Incorporating the human gene annotations in different databases significantly improved transcriptomic and genetic analyses. PMID:23431329
Inference of natural selection from interspersed genomic elements based on polymorphism and divergence. PMID:23386628
Predicting cell types and genetic variations contributing to disease by combining GWAS and epigenetic data. PMID:23382893
Regulatory mechanisms of long noncoding RNAs in vertebrate central nervous system development and function. PMID:23337534
DIANA-LncBase: experimentally verified and computationally predicted microRNA targets on long non-coding RNAs. PMID:23193281
ENCODE data in the UCSC Genome Browser: year 5 update. PMID:23193274
APPRIS: annotation of principal and alternative splice isoforms. PMID:23161672
Uniting ENCODE with genome-wide proteomics. PMID:23138303
A fish-specific transposable element shapes the repertoire of p53 target genes in zebrafish. PMID:23118857
STAR: ultrafast universal RNA-seq aligner. PMID:23104886
Differentially expressed, variant U1 snRNAs regulate gene expression in human cells. PMID:23070852
Annotation of functional variation in personal genomes using RegulomeDB. PMID:22955989
The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. PMID:22955988
Linking disease associations with regulatory information in the human genome. PMID:22955986
Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements. PMID:22955985
Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome. PMID:22955982
Understanding transcriptional regulation by integrative analysis of transcription factor binding data. PMID:22955978
Toward mapping the biology of the genome. PMID:22955973
What does our genome encode? PMID:22955972
Decoding the human genome. PMID:22955971
The long-range interaction landscape of gene promoters. PMID:22955621
Landscape of transcription in human cells. PMID:22955620
The accessible chromatin landscape of the human genome. PMID:22955617
An integrated encyclopedia of DNA elements in the human genome. PMID:22955616
The GENCODE pseudogene resource. PMID:22951037
The Ensembl Variant Effect Predictor PubMed citations: 2021.

2021 articles citing: The Ensembl Variant Effect Predictor

Clinical and genotypic analysis in determining dystonia non-motor phenotypic heterogeneity: a UK Biobank study. PMID:35925398
Transcriptome variation in human tissues revealed by long-read sequencing. PMID:35922509
Mutations in SORL1 and MTHFDL1 possibly contribute to the development of Alzheimer's disease in a multigenerational Colombian Family. PMID:35905044
Rare loss of function variants in the hepatokine gene INHBE protect from abdominal obesity. PMID:35896531
Whole Exome Sequencing Enhanced Imputation Identifies 85 Metabolite Associations in the Alpine CHRIS Cohort. PMID:35888728
Large-Scale Multi-Omics Studies Provide New Insights into Blood Pressure Regulation. PMID:35886906
Functional Genomics Analysis to Disentangle the Role of Genetic Variants in Major Depression. PMID:35886042
Phenotypic and Genotypic Spectrum of Early-Onset Developmental and Epileptic Encephalopathies-Data from a Romanian Cohort. PMID:35886038
Genome-Wide Analysis Identifies Candidate Genes Encoding Feather Color in Ducks. PMID:35886032
Exploring the Mutational Landscape of Isolated Congenital Heart Defects: An Exome Sequencing Study Using Cardiac DNA. PMID:35885997
Dynamic Features of Chromosomal Instability during Culture of Induced Pluripotent Stem Cells. PMID:35885940
Tracking Clonal Evolution of Multiple Myeloma Using Targeted Next-Generation DNA Sequencing. PMID:35884979
Uncovering the Contribution of Moderate-Penetrance Susceptibility Genes to Breast Cancer by Whole-Exome Sequencing and Targeted Enrichment Sequencing of Candidate Genes in Women of European Ancestry. PMID:35884425
Nisin Mutant Prevention Concentration and the Role of Subinhibitory Concentrations on Resistance Development by Diabetic Foot Staphylococci. PMID:35884226
A systematic analysis of splicing variants identifies new diagnoses in the 100,000 Genomes Project. PMID:35883178
Somatic DNA Damage Response and Homologous Repair Gene Alterations and Its Association With Tumor Variant Burden in Breast Cancer Patients With Occupational Exposure to Pesticides. PMID:35875117
Unravelling genetic variants of a swedish family with high risk of prostate cancer. PMID:35870994
PROM1, CXCL8, RUNX1, NAV1 and TP73 genes as independent markers predictive of prognosis or response to treatment in two cohorts of high-grade serous ovarian cancer patients. PMID:35867729
Integrative Genomic and Transcriptomic Analysis of Primary Malignant Gliomas Revealed Different Patterns Between Grades and Somatic Mutations Related to Glioblastoma Prognosis. PMID:35865002
Genetic evidence of tri-genealogy hypothesis on the origin of ethnic minorities in Yunnan. PMID:35864541
Pan-cancer analyses of synonymous mutations based on tissue-specific codon optimality. PMID:35860410
The sequences of 150,119 genomes in the UK Biobank. PMID:35859178
Next-generation sequencing reveals novel variants and large deletion in FANCA gene in Polish family with Fanconi anemia. PMID:35854323
Targeting Mre11 overcomes platinum resistance and induces synthetic lethality in XRCC1 deficient epithelial ovarian cancers. PMID:35853939
Immuno-Modulatory Effects of Intervertebral Disc Cells. PMID:35846355
Tumor treating fields affect mesothelioma cell proliferation by exerting histotype-dependent cell cycle checkpoint activations and transcriptional modulations. PMID:35840560
Genome-wide analyses of 200,453 individuals yield new insights into the causes and consequences of clonal hematopoiesis. PMID:35835912
Heterogeneous Distribution of Genetic Mutations in Myosin Binding Protein-C Paralogs. PMID:35832193
Meiotic drive in house mice: mechanisms, consequences, and insights for human biology. PMID:35829972
Functional landscapes of POLE and POLD1 mutations in checkpoint blockade-dependent antitumor immunity. PMID:35817971
Analysis of the docking property of host variants of hACE2 for SARS-CoV-2 in a large cohort. PMID:35816517
Decoding RNA Editing Sites Through Transcriptome Analysis in Rice Under Alkaline Stress. PMID:35812946
Dissecting Generalizability and Actionability of Disease-Associated Genes From 20 Worldwide Ethnolinguistic Cultural Groups. PMID:35812734
The contribution of common regulatory and protein-coding TYR variants to the genetic architecture of albinism. PMID:35803923
Patient-derived renal cell carcinoma organoids for personalized cancer therapy. PMID:35802820
A Molecularly Characterized Preclinical Platform of Subcutaneous Renal Cell Carcinoma (RCC) Patient-Derived Xenograft Models to Evaluate Novel Treatment Strategies. PMID:35800063
Gut microbiota composition in colorectal cancer patients is genetically regulated. PMID:35794137
Baseline and post-treatment biomarkers of resistance to anti-PD-1 therapy in acral and mucosal melanoma: an observational study. PMID:35793874
Local and systemic immune profiles of human pancreatic ductal adenocarcinoma revealed by single-cell mass cytometry. PMID:35793870
Deciphering associations between three RNA splicing-related genetic variants and lung cancer risk. PMID:35773316
A genome-wide cross-trait analysis identifies shared loci and causal relationships of type 2 diabetes and glycaemic traits with polycystic ovary syndrome. PMID:35771237
Investigating the characteristics of genes and variants associated with self-reported hearing difficulty in older adults in the UK Biobank. PMID:35761239
Common genetic variation associated with Mendelian disease severity revealed through cryptic phenotype analysis. PMID:35760791
Whole Genome Analysis of Dizygotic Twins With Autism Reveals Prevalent Transposon Insertion Within Neuronal Regulatory Elements: Potential Implications for Disease Etiology and Clinical Assessment. PMID:35759154
Computational cancer neoantigen prediction: current status and recent advances. PMID:35755950
Calculating genetic risk for dysfunction in pleiotropic biological processes using whole exome sequencing data. PMID:35751013
Microbiome-associated human genetic variants impact phenome-wide disease risk. PMID:35749358
Transcription factor retention through multiple polyploidization steps in wheat. PMID:35748743
Genomic Analysis of Waterpipe Smoke-Induced Lung Tumor Autophagy and Plasticity. PMID:35743294
mGWAS-Explorer: Linking SNPs, Genes, Metabolites, and Diseases for Functional Insights. PMID:35736459
Single-nucleus profiling of human dilated and hypertrophic cardiomyopathy. PMID:35732739
QTL-mapping in the obese Berlin Fat Mouse identifies additional candidate genes for obesity and fatty liver disease. PMID:35729251
Presence of rare potential pathogenic variants in subjects under 65 years old with very severe or fatal COVID-19. PMID:35725860
Germline variants of ATG7 in familial cholangiocarcinoma alter autophagy and p62. PMID:35725745
SNPs, short tandem repeats, and structural variants are responsible for differential gene expression across C57BL/6 and C57BL/10 substrains. PMID:35720252
Using genomics to understand the mechanisms of virulence and drug resistance in fungal pathogens. PMID:35713390
Contribution of Helicobacter pylori to the Inflammatory Complications of Common Variable Immunodeficiency. PMID:35711410
Reanalysis of exome negative patients with rare disease: a pragmatic workflow for diagnostic applications. PMID:35710456
Recessive inborn errors of type I IFN immunity in children with COVID-19 pneumonia. PMID:35708626
Genetic subtypes of smoldering multiple myeloma are associated with distinct pathogenic phenotypes and clinical outcomes. PMID:35705541
Systematic Review of Cerebral Phenotypes Associated With Monogenic Cerebral Small-Vessel Disease. PMID:35699195
Genomic architecture and functional effects of potential human inversion supergenes. PMID:35694745
Rare Variants in Inborn Errors of Immunity Genes Associated With Covid-19 Severity. PMID:35694544
Fine Mapping of a Major Backfat QTL Reveals a Causal Regulatory Variant Affecting the CCND2 Gene. PMID:35692822
Multiomic analysis reveals cell-type-specific molecular determinants of COVID-19 severity. PMID:35690068
Genome-wide association study across five cohorts identifies five novel loci associated with idiopathic pulmonary fibrosis. PMID:35688625
Allelic expression imbalance of PIK3CA mutations is frequent in breast cancer and prognostically significant. PMID:35676284
Enhanced BRAF engagement by NRAS mutants capable of promoting melanoma initiation. PMID:35672316
Exome Sequencing Data Analysis and a Case-Control Study in Mexican Population Reveals Lipid Trait Associations of New and Known Genetic Variants in Dyslipidemia-Associated Loci. PMID:35669185
The drug-induced phenotypic landscape of colorectal cancer organoids. PMID:35668108
Repeated Winning and Losing Experiences in Chronic Social Conflicts Are Linked to RNA Editing Pattern Difference. PMID:35664469
Pharmacokinetics and Genetic Factors of Atorvastatin in Healthy Korean Subjects. PMID:35664336
A Role for Gene-Environment Interactions in Autism Spectrum Disorder Is Supported by Variants in Genes Regulating the Effects of Exposure to Xenobiotics. PMID:35663546
Rare and population-specific functional variation across pig lines. PMID:35659233
CI-SpliceAI-Improving machine learning predictions of disease causing splicing variants using curated alternative splice sites. PMID:35657932
A Paradigm Shift in the Combination Changes of SARS-CoV-2 Variants and Increased Spread of Delta Variant (B.1.617.2) across the World. PMID:35656100
MHC class II molecules on pancreatic cancer cells indicate a potential for neo-antigen-based immunotherapy. PMID:35655709
Combined exome and transcriptome sequencing of non-muscle-invasive bladder cancer: associations between genomic changes, expression subtypes, and clinical outcomes. PMID:35655252
A multiancestry genome-wide association study of unexplained chronic ALT elevation as a proxy for nonalcoholic fatty liver disease with histological and radiological validation. PMID:35654975
How does re-classification of variants of unknown significance (VUS) impact the management of patients at risk for hereditary breast cancer? PMID:35641994
Annotation Query (AnnoQ): an integrated and interactive platform for large-scale genetic variant annotation. PMID:35640593
OmicsNet 2.0: a web-based platform for multi-omics integration and network visual analytics. PMID:35639733
Comprehensive genomic and tumour immune profiling reveals potential therapeutic targets in malignant pleural mesothelioma. PMID:35637530
In utero origin of myelofibrosis presenting in adult monozygotic twins. PMID:35637336
Technical Performance of a 430-Gene Preventative Genomics Assay to Identify Multiple Variant Types Associated with Adult-Onset Monogenic Conditions, Susceptibility Loci, and Pharmacogenetic Insights. PMID:35629091
Effects of Multi-Omics Characteristics on Identification of Driver Genes Using Machine Learning Algorithms. PMID:35627101
Genetic variants associated with two major bovine milk fatty acids offer opportunities to breed for altered milk fat composition. PMID:35619070
Genetic changes associated with relapse in favorable histology Wilms tumor: A Children's Oncology Group AREN03B2 study. PMID:35617957
Genomic Evolution and Personalized Therapy of an Infantile Fibrosarcoma Harboring an NTRK Oncogenic Fusion. PMID:35613412
Fine mapping and candidate gene analysis of a dravet syndrome modifier locus on mouse chromosome 11. PMID:35606653
Allelic Variation in Zmfatb Gene Defines Variability for Fatty Acids Composition Among Diverse Maize Genotypes. PMID:35600823
The Value of Rare Genetic Variation in the Prediction of Common Obesity in European Ancestry Populations. PMID:35592775
DNA sequence features underlying large-scale duplications and deletions in human. PMID:35590085
Integration of rare expression outlier-associated variants improves polygenic risk prediction. PMID:35588732
Refinements and considerations for trio whole-genome sequence analysis when investigating Mendelian diseases presenting in early childhood. PMID:35586607
Breast cancer risks associated with missense variants in breast cancer susceptibility genes. PMID:35585550
Feasibility of whole genome and transcriptome profiling in pediatric and young adult cancers. PMID:35585047
PWWP2B promotes DNA end resection and homologous recombination. PMID:35582821
Impact of natural selection on global patterns of genetic variation and association with clinical phenotypes at genes involved in SARS-CoV-2 infection. PMID:35580180
Genome-Wide Genomic and Functional Association Study for Workability and Calving Traits in Holstein Cattle. PMID:35565554
The Thousand Polish Genomes-A Database of Polish Variant Allele Frequencies. PMID:35562925
Brain Epitranscriptomic Analysis Revealed Altered A-to-I RNA Editing in Septic Patients. PMID:35559016
Exome sequencing of hepatocellular carcinoma in lemurs identifies potential cancer drivers: A pilot study. PMID:35557512
TMC-SNPdb 2.0: an ethnic-specific database of Indian germline variants. PMID:35551364
Unlocking the functional potential of polyploid yeasts. PMID:35545616
Association of Pathogenic DNA Variants Predisposing to Cardiomyopathy With Cardiovascular Disease Outcomes and All-Cause Mortality. PMID:35544052
Identification of biomarkers of response to preoperative talazoparib monotherapy in treatment naïve gBRCA+ breast cancers. PMID:35538088
Identification of heritable rare variants associated with early-stage lung adenocarcinoma risk. PMID:35529798
Lymph node colonization induces tumor-immune tolerance to promote distant metastasis. PMID:35525247
Data Mining, Quality and Management in the Life Sciences. PMID:35507257
Gene-based whole genome sequencing meta-analysis of 250 circulating proteins in three isolated European populations. PMID:35504531
Massively parallel sequencing uncovered disease-associated variant spectra of glucose-6-phosphate dehydrogenase deficiency, phenylketonuria and galactosemia in Vietnamese pregnant women. PMID:35502621
Plasma proteome analyses in individuals of European and African ancestry identify cis-pQTLs and models for proteome-wide association studies. PMID:35501419
Genetic analysis of the PCSK9 locus in psychological, psychiatric, metabolic and cardiovascular traits in UK Biobank. PMID:35501368
Integrative genomic analysis reveals low T-cell infiltration as the primary feature of tobacco use in HPV-positive oropharyngeal cancer. PMID:35494251
Balancing selection at the human salivary agglutinin gene (DMBT1) driven by host-microbe interactions. PMID:35494225
The Polymorphism and Expression of EGFL7 and miR-126 Are Associated With NSCLC Susceptibility. PMID:35494025
Rare coding variants in DNA damage repair genes associated with timing of natural menopause. PMID:35493704
Comparative Analysis and Data Provenance for 1,113 Bacterial Genome Assemblies. PMID:35491842
Comprehensive profiling of 1015 patients' exomes reveals genomic-clinical associations in colorectal cancer. PMID:35487942
Identification of a new splice-acceptor mutation in HFM1 and functional analysis through molecular docking in nonobstructive azoospermia. PMID:35486194
Role of testis‑specific serine kinase 1B in undiagnosed male infertility. PMID:35485285
Computational and experimental methods for classifying variants of unknown clinical significance. PMID:35483875
Genetic and environmental determinants of diastolic heart function. PMID:35479509
A recurrent ZP1 variant is responsible for oocyte maturation defect with degenerated oocytes in infertile females. PMID:35460069
Robust Mutation Profiling of SARS-CoV-2 Variants from Multiple Raw Illumina Sequencing Data with Cloud Workflow. PMID:35456492
Predominant Founder Effect among Recurrent Pathogenic Variants for an X-Linked Disorder. PMID:35456481
Case Report: A Detailed Phenotypic Description of Patients and Relatives with Combined Central Hypothyroidism and Growth Hormone Deficiency Carrying IGSF1 Mutations. PMID:35456429
New Insights on Gene by Environmental Effects of Drugs of Abuse in Animal Models Using GeneNetwork. PMID:35456420
The Impact of Genetic Polymorphisms in Glutamate-Cysteine Ligase, a Key Enzyme of Glutathione Biosynthesis, on Ischemic Stroke Risk and Brain Infarct Size. PMID:35455093
A locus conferring tolerance to Theileria infection in African cattle. PMID:35446841
Astroblastomas exhibit radial glia stem cell lineages and differential expression of imprinted and X-inactivation escape genes. PMID:35440587
Epigenetic and genomic profiling of chordoid meningioma: implications for clinical management. PMID:35440040
Case Report: Exome and RNA Sequencing Identify a Novel de novo Missense Variant in HNRNPK in a Chinese Patient With Au-Kline Syndrome. PMID:35422839
Genome-Wide Association Study of Campylobacter-Positive Diarrhea Identifies Genes Involved in Toxin Processing and Inflammatory Response. PMID:35420468
Mutation rate of SARS-CoV-2 and emergence of mutators during experimental evolution. PMID:35419205
Comparative Analysis of Differentially Mutated Genes in Non-Muscle and Muscle-Invasive Bladder Cancer in the Chinese Population by Whole Exome Sequencing. PMID:35419031
Exome sequencing in bipolar disorder identifies AKAP11 as a risk gene shared with schizophrenia. PMID:35410376
Lineage Conversion in Pediatric B-Cell Precursor Acute Leukemia under Blinatumomab Therapy. PMID:35409391
Deciphering Haplotypic Variation and Gene Expression Dynamics Associated with Nutritional and Cooking Quality in Rice. PMID:35406707
One Health and Cattle Genetic Resources: Mining More than 500 Cattle Genomes to Identify Variants in Candidate Genes Potentially Affecting Coronavirus Infections. PMID:35405828
Proof-of-Concept Pilot Study on Comprehensive Spatiotemporal Intra-Patient Heterogeneity for Colorectal Cancer With Liver Metastasis. PMID:35402285
The first successful treatment and genetic sequencing of primary hepatic adenosarcoma with sarcomatous overgrowth: a case report. PMID:35400213
Integrated genomic analyses identify high-risk factors and actionable targets in T-cell acute lymphoblastic leukemia. PMID:35399540
The Genomic Landscape of Early-Stage Ovarian High-Grade Serous Carcinoma. PMID:35398881
Meta-analysis of genome-wide association studies identifies ancestry-specific associations underlying circulating total tau levels. PMID:35396452
Germline variants in tumor suppressor FBXW7 lead to impaired ubiquitination and a neurodevelopmental syndrome. PMID:35395208
Identification of genetic effects underlying type 2 diabetes in South Asian and European populations. PMID:35393509
Phase 1b study of berzosertib and cisplatin in patients with advanced triple-negative breast cancer. PMID:35393425
A joint NCBI and EMBL-EBI transcript set for clinical genomics and research. PMID:35388217
Common and Rare 5'UTR Variants Altering Upstream Open Reading Frames in Cardiovascular Genomics. PMID:35387445
In-Silico and In-Vitro Analysis of Human SOS1 Protein Causing Noonan Syndrome - A Novel Approach to Explore the Molecular Pathways. PMID:35386434
Genome-Wide Association Study of Alzheimer's Disease Brain Imaging Biomarkers and Neuropsychological Phenotypes in the European Medical Information Framework for Alzheimer's Disease Multimodal Biomarker Discovery Dataset. PMID:35386118
Neutralizing antibody response against the B.1.617.2 (delta) and the B.1.1.529 (omicron) variants after a third mRNA SARS-CoV-2 vaccine dose in kidney transplant recipients. PMID:35384272
RNA sequencing role and application in clinical diagnostic. PMID:35382420
Analyzing human knockouts to validate GPR151 as a therapeutic target for reduction of body mass index. PMID:35381001
Harmonizing model organism data in the Alliance of Genome Resources. PMID:35380658
Exome sequencing of individuals with Huntington's disease implicates FAN1 nuclease activity in slowing CAG expansion and disease onset. PMID:35379994
Clinical implementation of RNA sequencing for Mendelian disease diagnostics. PMID:35379322
Precise in vivo functional analysis of DNA variants with base editing using ACEofBASEs target prediction. PMID:35373735
Multi-Omics Investigations Revealed Underlying Molecular Mechanisms Associated With Tumor Stiffness and Identified Sunitinib as a Potential Therapy for Reducing Stiffness in Pituitary Adenomas. PMID:35372359
Therapeutic and immunomodulatory potential of pazopanib in malignant phyllodes tumor. PMID:35365682
Identification and Management of Pathogenic Variants in BRCA1, BRCA2, and PALB2 in a Tumor-Only Genomic Testing Program. PMID:35363308
Case Report: Preimplantation Genetic Testing for Meckel Syndrome Induced by Novel Compound Heterozygous Mutations of MKS1. PMID:35360848
Ultrasensitive profiling of UV-induced mutations identifies thousands of subclinical facial tumors in tuberous sclerosis complex. PMID:35358092
A complete reference genome improves analysis of human genetic variation. PMID:35357935
Novel genes bearing mutations in rare cases of early-onset ataxia with cerebellar hypoplasia. PMID:35351988
Runs of Homozygosity Uncover Potential Functional-Altering Mutation Associated With Body Weight and Length in Two Duroc Pig Lines. PMID:35350434
Genomic diversity and post-admixture adaptation in the Uyghurs. PMID:35350227
Genetic variants of the hypoxia-inducible factor 3 alpha subunit (Hif3a) gene in the Fat and Lean mouse selection lines. PMID:35347545
Distinct genomic landscape of Chinese pediatric acute myeloid leukemia impacts clinical risk classification. PMID:35347147
Nasal airway transcriptome-wide association study of asthma reveals genetically driven mucus pathobiology. PMID:35347136
Genome-wide association studies of metabolites in Finnish men identify disease-relevant loci. PMID:35347128
Findings from precision oncology in the clinic: rare, novel variants are a significant contributor to scaling molecular diagnostics. PMID:35346197
Computational Analysis of the Potential Impact of MTC Complex Missenses SNPs Associated with Male Infertility. PMID:35342767
Hypothalamic Irak4 is a genetically controlled regulator of hypoglycemia-induced glucagon secretion. PMID:35339728
Genetic regulation of post-translational modification of two distinct proteins. PMID:35332118
A Homozygous Deep Intronic Variant Causes Von Willebrand Factor Deficiency and Lack of Endothelial-Specific Secretory Organelles, Weibel-Palade Bodies. PMID:35328514
Identification of Genetic Risk Factors of Severe COVID-19 Using Extensive Phenotypic Data: A Proof-of-Concept Study in a Cohort of Russian Patients. PMID:35328087
Gene Variants Involved in Nonsense-Mediated mRNA Decay Suggest a Role in Autism Spectrum Disorder. PMID:35327467
Comprehensive Analyses of Bone and Cartilage Transcriptomes Evince Ion Transport, Inflammation and Cartilage Development-Related Genes Involved in Chickens' Femoral Head Separation. PMID:35327184
Significant sparse polygenic risk scores across 813 traits in UK Biobank. PMID:35324888
Reduced reproductive success is associated with selective constraint on human genes. PMID:35322230
Genome-Wide Association Study Identifies Genetic Loci Associated With Fat Cell Number and Overlap With Genetic Risk Loci for Type 2 Diabetes. PMID:35320353
Characterization of the genetic architecture of infant and early childhood body mass index. PMID:35315439
A Novel Osteochondrodysplasia With Empty Sella Associates With a TBX2 Variant. PMID:35311234
The GA4GH Variation Representation Specification: A computational framework for variation representation and federated identification. PMID:35311178
Cancer Neoantigens: Challenges and Future Directions for Prediction, Prioritization, and Validation. PMID:35311072
NeoScore Integrates Characteristics of the Neoantigen:MHC Class I Interaction and Expression to Accurately Prioritize Immunogenic Neoantigens. PMID:35304420
RAREsim: A simulation method for very rare genetic variants. PMID:35298919
Positive selection acts on regulatory genetic variants in populations of European ancestry that affect ALDH2 gene expression. PMID:35296751
Identification and characterisation of spontaneous mutations causing deafness from a targeted knockout programme. PMID:35296311
Contribution of NOTCH1 genetic variants to bicuspid aortic valve and other congenital lesions. PMID:35288444
Genome-wide investigation and functional analysis of RNA editing sites in wheat. PMID:35275970
Deciphering the Retinal Epigenome during Development, Disease and Reprogramming: Advancements, Challenges and Perspectives. PMID:35269428
Integrative genetic and immune cell analysis of plasma proteins in healthy donors identifies novel associations involving primary immune deficiency genes. PMID:35264221
Assessment of linkage disequilibrium patterns between structural variants and single nucleotide polymorphisms in three commercial chicken populations. PMID:35264116
A 1-bp deletion in bovine QRICH2 causes low sperm count and immotile sperm with multiple morphological abnormalities. PMID:35255804
Epilepsy Genetics and Precision Medicine in Adults: A New Landscape for Developmental and Epileptic Encephalopathies. PMID:35250806
RASGRF1 Fusions Activate Oncogenic RAS Signaling and Confer Sensitivity to MEK Inhibition. PMID:35247929
A comprehensive WGS-based pipeline for the identification of new candidate genes in inherited retinal dystrophies. PMID:35246562
Allele-specific expression reveals genes with recurrent cis-regulatory alterations in high-risk neuroblastoma. PMID:35246212
Tertiary lymphoid structure and decreased CD8+ T cell infiltration in minimally invasive adenocarcinoma. PMID:35243243
Genome-Wide Association Study-Guided Exome Rare Variant Burden Analysis Identifies IL1R1 and CD3E as Potential Autoimmunity Risk Genes for Celiac Disease. PMID:35237542
Fibrillar Collagen Variants in Spontaneous Coronary Artery Dissection. PMID:35234813
TADA-a machine learning tool for functional annotation-based prioritisation of pathogenic CNVs. PMID:35232478
Computational Resources for the Interpretation of Variations in Cancer. PMID:35230689
Somatic and Germline Variant Calling from Next-Generation Sequencing Data. PMID:35230682
GWAS in people of Middle Eastern descent reveals a locus protective of kidney function-a cross-sectional study. PMID:35227251
Comparison of multiple imputation algorithms and verification using whole-genome sequencing in the CMUH genetic biobank. PMID:35223420
A human breast cancer-derived xenograft and organoid platform for drug discovery and precision oncology. PMID:35221336
The Molecular Tumor Board Portal supports clinical decisions and automated reporting for precision oncology. PMID:35221333
PacBio long-read amplicon sequencing enables scalable high-resolution population allele typing of the complex CYP2D6 locus. PMID:35217695
Characterizing mobile element insertions in 5675 genomes. PMID:35212372
Exploring the relevance of NUP93 variants in steroid-resistant nephrotic syndrome using next generation sequencing and a fly kidney model. PMID:35211795
Discovery of an unusually high number of de novo mutations in sperm of older men using duplex sequencing. PMID:35210354
SWAAT Bioinformatics Workflow for Protein Structure-Based Annotation of ADME Gene Variants. PMID:35207751
A Case of Severe Left-Ventricular Noncompaction Associated with Splicing Altering Variant in the FHOD3 Gene. PMID:35205353
Genomic Hatchery Introgression in Brown Trout (Salmo trutta L.): Development of a Diagnostic SNP Panel for Monitoring the Impacted Mediterranean Rivers. PMID:35205298
Chemerin Impact on Alternative mRNA Transcription in the Porcine Luteal Cells. PMID:35203364
Genetic associations of protein-coding variants in human disease. PMID:35197637
Integrative molecular and clinical profiling of acral melanoma links focal amplification of 22q11.21 to metastasis. PMID:35197475
Genomic characterization of the world's longest selection experiment in mouse reveals the complexity of polygenic traits. PMID:35189878
Cancer/Testis Antigen 55 is required for cancer cell proliferation and mitochondrial DNA maintenance. PMID:35189384
EBF1 nuclear repositioning instructs chromatin refolding to promote therapy resistance in T leukemic cells. PMID:35182476
Genomics4RD: An integrated platform to share Canadian deep-phenotype and multiomic data for international rare disease gene discovery. PMID:35181971
Evaluating the detection ability of a range of epistasis detection methods on simulated data for pure and impure epistatic models. PMID:35180244
The RD-Connect Genome-Phenome Analysis Platform: Accelerating diagnosis, research, and gene discovery for rare diseases. PMID:35178824
An Alu insertion map of the Indian population: identification and analysis in 1021 genomes of the IndiGen project. PMID:35178516
Analysis of rare genetic variation underlying cardiometabolic diseases and traits among 200,000 individuals in the UK Biobank. PMID:35177841
BrewerIX enables allelic expression analysis of imprinted and X-linked genes from bulk and single-cell transcriptomes. PMID:35177756
Dihydroceramide- and ceramide-profiling provides insights into human cardiometabolic disease etiology. PMID:35177612
Spatiotemporal dynamics of clonal selection and diversification in normal endometrial epithelium. PMID:35177608
Whole-genome analysis of human embryonic stem cells enables rational line selection based on genetic variation. PMID:35176222
Transcriptome-wide association study of coronary artery disease identifies novel susceptibility genes. PMID:35175464
The S100A7 nuclear interactors in autoimmune diseases: a coevolutionary study in mammals. PMID:35174412
Whole-exome sequencing improves the diagnosis and care of men with non-obstructive azoospermia. PMID:35172124
Compound heterozygous variants in OTULIN are associated with fulminant atypical late-onset ORAS. PMID:35170849
Large-scale association study on daily weight gain in pigs reveals overlap of genetic factors for growth in humans. PMID:35168569
Neurodevelopmental Syndrome with Intellectual Disability, Speech Impairment, and Quadrupedia Is Associated with Glutamate Receptor Delta 2 Gene Defect. PMID:35159210
Rare Occurrence of Aristolochic Acid Mutational Signatures in Oro-Gastrointestinal Tract Cancers. PMID:35158844
Contribution of common and rare genetic variants in CEP72 on vincristine-induced peripheral neuropathy in brain tumour patients. PMID:35150001
Genome Nexus: A Comprehensive Resource for the Annotation and Interpretation of Genomic Variants in Cancer. PMID:35148171
An effector index to predict target genes at GWAS loci. PMID:35147782
Hybridization underlies localized trait evolution in cavefish. PMID:35146393
High male specific contribution of the X-chromosome to individual global recombination rate in dairy cattle. PMID:35144552
DECIPHER: Supporting the interpretation and sharing of rare disease phenotype-linked variant data to advance diagnosis and research. PMID:35143074
Mapping clustered mutations in cancer reveals APOBEC3 mutagenesis of ecDNA. PMID:35140399
Zebrafish patient-derived xenograft models predict lymph node involvement and treatment outcome in non-small cell lung cancer. PMID:35139880
Transcriptome-wide association study in UK Biobank Europeans identifies associations with blood cell traits. PMID:35138379
Genetic load: genomic estimates and applications in non-model animals. PMID:35136196
WormBase in 2022-data, processes, and tools for analyzing Caenorhabditis elegans. PMID:35134929
CYP2C8, CYP2C9, and CYP2C19 Characterization Using Next-Generation Sequencing and Haplotype Analysis: A GeT-RM Collaborative Project. PMID:35134542
Prioritization of putatively detrimental variants in euploid miscarriages. PMID:35132093
Genome-wide association meta-analysis identifies 29 new acne susceptibility loci. PMID:35132056
Integrative Genomic Analyses of 1,145 Patient Samples Reveal New Biomarkers in Esophageal Squamous Cell Carcinoma. PMID:35127817
Multiregion sequencing of sarcomatoid renal cell carcinoma arising from autosomal dominant polycystic kidney disease. PMID:35122417
Targeting purine synthesis in ASS1-expressing tumors enhances the response to immune checkpoint inhibitors. PMID:35121952
Leveraging deep phenotyping from health check-up cohort with 10,000 Korean individuals for phenome-wide association study of 136 traits. PMID:35121771
Population-level deficit of homozygosity unveils CPSF3 as an intellectual disability syndrome gene. PMID:35121750
Comprehensive variant calling from whole-genome sequencing identifies a complex inversion that disrupts ZFPM2 in familial congenital diaphragmatic hernia. PMID:35119225
Exploration of the genomic landscape of a long-term surviving stage III colorectal cancer patient identifies recurrent and rare mutations: a case report. PMID:35117655
Computational Prediction of the Pathogenic Status of Cancer-Specific Somatic Variants. PMID:35116056
Genome-wide analysis of 102,084 migraine cases identifies 123 risk loci and subtype-specific risk alleles. PMID:35115687
An ultra-rare case of immunoskeletal dysplasia with neurodevelopmental abnormalities in an Indian patient with homozygous c.953C > T variant in EXTL3 gene: a case report. PMID:35114981
Inhibition of BCL2A1 by STAT5 inactivation overcomes resistance to targeted therapies of FLT3-ITD/D835 mutant AML. PMID:35114569
Fast neutron mutagenesis in soybean enriches for small indels and creates frameshift mutations. PMID:35100358
Role of IGF2 in the Study of Development and Evolution of Prostate Cancer. PMID:35095996
Heritability of social behavioral phenotypes and preliminary associations with autism spectrum disorder risk genes in rhesus macaques: A whole exome sequencing study. PMID:35092647
Variant interpretation: UCSC Genome Browser Recommended Track Sets. PMID:35088925
An evaluation of pipelines for DNA variant detection can guide a reanalysis protocol to increase the diagnostic ratio of genetic diseases. PMID:35087072
Endosomal cargo recycling mediated by Gpa1 and phosphatidylinositol 3-kinase is inhibited by glucose starvation. PMID:35080991
Variant pathogenic prediction by locus variability: the importance of the current picture of evolution. PMID:35079159
Coding and regulatory variants are associated with serum protein levels and disease. PMID:35079000
A genome-wide association study of serum proteins reveals shared loci with common diseases. PMID:35078996
Parallel functional assessment of m6A sites in human endodermal differentiation with base editor screens. PMID:35078991
Recessive variants in COL25A1 gene as novel cause of arthrogryposis multiplex congenita with ocular congenital cranial dysinnervation disorder. PMID:35077597
Population-Based Penetrance of Deleterious Clinical Variants. PMID:35076666
Mitochondrial DNA variation across 56,434 individuals in gnomAD. PMID:35074858
Comprehensive assessment of germline pathogenic variant detection in tumor-only sequencing. PMID:35074424
Non-additive QTL mapping of lactation traits in 124,000 cattle reveals novel recessive loci. PMID:35073835
The structural coverage of the human proteome before and after AlphaFold. PMID:35073311
Pathogenic Variant Profile of Hereditary Cancer Syndromes in a Vietnamese Cohort. PMID:35070997
Alzheimer's Disease Variant Portal: A Catalog of Genetic Findings for Alzheimer's Disease. PMID:35068457
Tissue-specific multi-omics analysis of atrial fibrillation. PMID:35064145
Genome-Wide Analysis of Disordered Eating Behavior in the Mexican Population. PMID:35057575
Clin.iobio: A Collaborative Diagnostic Workflow to Enable Team-Based Precision Genomics. PMID:35055388
Canine Oral Melanoma Genomic and Transcriptomic Study Defines Two Molecular Subgroups with Different Therapeutical Targets. PMID:35053440
Phenotypic Heterogeneity among GBA p.R202X Carriers in Lewy Body Spectrum Disorders. PMID:35052839
Cyanogenesis in the Sorghum Genus: From Genotype to Phenotype. PMID:35052482
Thirteen Independent Genetic Loci Associated with Preserved Processing Speed in a Study of Cognitive Resilience in 330,097 Individuals in the UK Biobank. PMID:35052462
Diagnostic Yield and Economic Implications of Whole-Exome Sequencing for ASD Diagnosis in Israel. PMID:35052376
Genetic Dissection of Temperament Personality Traits in Italian Isolates. PMID:35052345
Landscape of driver gene events, biomarkers, and druggable targets identified by whole-genome sequencing of glioblastomas. PMID:35047820
Genome-wide identification of the genetic basis of amyotrophic lateral sclerosis. PMID:35045337
Germline sequence variants contributing to cancer susceptibility in South African breast cancer patients of African ancestry. PMID:35039564
Integration of tumour sequencing and case-control data to assess pathogenicity of RAD51C missense variants in familial breast cancer. PMID:35039523
ClinGen Variant Curation Interface: a variant classification platform for the application of evidence criteria from ACMG/AMP guidelines. PMID:35039090
Historical museum samples enable the examination of divergent and parallel evolution during invasion. PMID:35038768
Scripting Analyses of Genomes in Ensembl Plants. PMID:35037199
Peptide ancestry informative markers in uterine neoplasms from women of European, African, and Asian ancestry. PMID:35036865
Aristotle: stratified causal discovery for omics data. PMID:35033007
StrVCTVRE: A supervised learning method to predict the pathogenicity of human genome structural variants. PMID:35032432
Transcriptional programs regulating neuronal differentiation are disrupted in DLG2 knockout human embryonic stem cells and enriched for schizophrenia and related disorders risk variants. PMID:35031607
From azoospermia to macrozoospermia, a phenotypic continuum due to mutations in the ZMYND15 gene. PMID:35017390
Genomic landscape of TCRαβ and TCRγδ T-large granular lymphocyte leukemia. PMID:35015834
Phenotypic spectrum of patients with mutations in CHD7: clinical implications of endocrinological findings. PMID:35015700
SorghumBase: a web-based portal for sorghum genetic information and community advancement. PMID:35015132
A de novo paradigm for male infertility. PMID:35013161
Comprehensive Molecular Landscape of Cetuximab Resistance in Head and Neck Cancer Cell Lines. PMID:35011716
Combined Use of Whole Exome Sequencing and CRISPR/Cas9 to Study the Etiology of Non-Obstructive Azoospermia: Demonstration of the Dispensable Role of the Testis-Specific Genes C1orf185 and CCT6B. PMID:35011680
Whole-Exome Sequencing of HPV Positive Tonsillar and Base of Tongue Squamous Cell Carcinomas Reveals a Global Mutational Pattern along with Relapse-Specific Somatic Variants. PMID:35008243
Proteomic identification of proliferation and progression markers in human polycythemia vera stem and progenitor cells. PMID:35008095
RAD50 deficiency is a predictor of platinum sensitivity in sporadic epithelial ovarian cancers. PMID:35006434
A network-based integration for understanding racial disparity in prostate cancer. PMID:34998235
SOD1 mutations associated with amyotrophic lateral sclerosis analysis of variant severity. PMID:34996976
Characterization of non-specific lipid transfer protein (nsLtp) gene families in the Brassica napus pangenome reveals abundance variation. PMID:34996379
Genomic predictors of response to PD-1 inhibition in children with germline DNA replication repair deficiency. PMID:34992263
Hepatocellular carcinoma patients with high circulating cytotoxic T cells and intra-tumoral immune signature benefit from pembrolizumab: results from a single-arm phase 2 trial. PMID:34986867
Evaluation of CRISPR gene-editing tools in zebrafish. PMID:34986794
Clinical and genetic investigation of ichthyosis in familial and sporadic cases in south of Tunisia: genotype-phenotype correlation. PMID:34983512
Genetic analysis of a malignant meningioma and associated metastases. PMID:34981192
Interpreting ciliopathy-associated missense variants of uncertain significance (VUS) in Caenorhabditis elegans. PMID:34964473
The mitochondrial DNA constitution shaping T-cell immunity in patients with rectal cancer at high risk of metastatic progression. PMID:34961902
Machine learning enables new insights into genetic contributions to liver fat accumulation. PMID:34957434
Genomic analyses of the metastasis-derived prostate cancer cell lines LNCaP, VCaP, and PC3-AR. PMID:34951700
Whole Exome Sequencing-Based Identification of a Novel Gene Involved in Root Hair Development in Barley (Hordeum vulgare L.). PMID:34948205
Exome Sequencing Reveals Novel Variants and Expands the Genetic Landscape for Congenital Microcephaly. PMID:34946966
Novel In-Frame Deletion in HTRA1 Gene, Responsible for Stroke at a Young Age and Dementia-A Case Study. PMID:34946904
Variant Selection and Interpretation: An Example of Modified VarSome Classifier of ACMG Guidelines in the Diagnostic Setting. PMID:34946832
Evidence for the Association between the Intronic Haplotypes of Ionotropic Glutamate Receptors and First-Episode Schizophrenia. PMID:34945722
Pan-Genomic Sequencing Reveals Actionable CDKN2A/2B Deletions and Kataegis in Anaplastic Thyroid Carcinoma. PMID:34944959
New Variants of the Cytochrome P450 2R1 (CYP2R1) Gene in Individuals with Severe Vitamin D-Activating Enzyme 25(OH)D Deficiency. PMID:34944511
A Functional Precision Medicine Pipeline Combines Comparative Transcriptomics and Tumor Organoid Modeling to Identify Bespoke Treatment Strategies for Glioblastoma. PMID:34943910
Genetic Connections and Convergent Evolution of Tropical Indigenous Peoples in Asia. PMID:34940850
Neoadjuvant immunotherapy with nivolumab and ipilimumab induces major pathological responses in patients with head and neck squamous cell carcinoma. PMID:34937871
Rare coding variants in 35 genes associate with circulating lipid levels-A multi-ancestry analysis of 170,000 exomes. PMID:34932938
Validation of HER2 Status in Whole Genome Sequencing Data of Breast Cancers with the Ploidy-Corrected Copy Number Approach. PMID:34932189
Comprehensive multiomic characterization of human papillomavirus-driven recurrent respiratory papillomatosis reveals distinct molecular subtypes. PMID:34931021
Genome-wide association and functional interrogation identified a variant at 3p26.1 modulating ovarian cancer survival among Chinese women. PMID:34930913
cbpManager: a web application to streamline the integration of clinical and genomic data in cBioPortal to support the Molecular Tumor Board. PMID:34930224
Genetic analysis of four consanguineous multiplex families with inflammatory bowel disease. PMID:34925849
De novo pathogenic variant in SETX causes a rapidly progressive neurodegenerative disorder of early childhood-onset with severe axonal polyneuropathy. PMID:34922620
Design and performance of a bovine 200 k SNP chip developed for endangered German Black Pied cattle (DSN). PMID:34922441
Prioritising positively selected variants in whole-genome sequencing data using FineMAV. PMID:34922440
The Dawn of next generation DNA sequencing in myelodysplastic syndromes- experience from Pakistan. PMID:34915860
Patient-Derived Upper Tract Urothelial Carcinoma Organoids as a Platform for Drug Screening. PMID:34914855
Oral Squamous Cell Carcinoma in Young Patients Show Higher Rates of EGFR Amplification: Implications for Novel Personalized Therapy. PMID:34912708
Genomic signatures of pre-resistance in Mycobacterium tuberculosis. PMID:34911948
Biallelic mutations in calcium release activated channel regulator 2A (CRACR2A) cause a primary immunodeficiency disorder. PMID:34908525
The importance of automation in genetic diagnosis: Lessons from analyzing an inherited retinal degeneration cohort with the Mendelian Analysis Toolkit (MATK). PMID:34906470
Accurate Prediction of Protein Sequences for Proteogenomics Data Integration. PMID:34905178
Clinical presentation, treatment, and genetic and histopathological analysis of juvenile cataracts and secondary glaucoma in a rhesus macaque (Macaca mulatta). PMID:34897697
NLR diversity and candidate fusiform rust resistance genes in loblolly pine. PMID:34897455
The genomic basis of high-elevation adaptation in wild house mice (Mus musculus domesticus) from South America. PMID:34897431
The power of genetic diversity in genome-wide association studies of lipids. PMID:34887591
Tumor Mutation Burden, Expressed Neoantigens and the Immune Microenvironment in Diffuse Gliomas. PMID:34885201
BTK and PI3K Inhibitors Reveal Synergistic Inhibitory Anti-Tumoral Effects in Canine Diffuse Large B-Cell Lymphoma Cells. PMID:34884478
Non-genetic determinants of malignant clonal fitness at single-cell resolution. PMID:34880496
Computational analysis of cancer genome sequencing data. PMID:34880424
Targeted analysis of genomic regions enriched in African ancestry reveals novel classical HLA alleles associated with asthma in Southwestern Europeans. PMID:34880287
Identification of Rare Loss-of-Function Genetic Variation Regulating Body Fat Distribution. PMID:34875679
Multi-omic machine learning predictor of breast cancer therapy response. PMID:34875674
Steroid-sensitive nephrotic syndrome candidate gene CLVS1 regulates podocyte oxidative stress and endocytosis. PMID:34874915
Whole-exome sequencing, EGFR amplification and infiltration patterns in human glioblastoma. PMID:34873478
Sequencing-based genome-wide association studies reporting standards. PMID:34870259
A functionally impaired missense variant identified in French Canadian families implicates FANCI as a candidate ovarian cancer-predisposing gene. PMID:34861889
Large-scale integration of the plasma proteome with genetics and disease. PMID:34857953
Mapping the serum proteome to neurological diseases using whole genome sequencing. PMID:34857772
A comprehensive genome-wide scan detects genomic regions related to local adaptation and climate resilience in Mediterranean domestic sheep. PMID:34856922
SCOPe: improvements to the structural classification of proteins - extended database to facilitate variant interpretation and machine learning. PMID:34850923
Genomic evidence for inbreeding depression and purging of deleterious genetic variation in Indian tigers. PMID:34848534
A 3D structural SARS-CoV-2-human interactome to explore genetic and drug perturbations. PMID:34845387
Deep learning enables genetic analysis of the human thoracic aorta. PMID:34837083
PharmVIP: A Web-Based Tool for Pharmacogenomic Variant Analysis and Interpretation. PMID:34834582
Genomic and Transcriptomic Profiling of Brain Metastases. PMID:34830758
Poking COVID-19: Insights on Genomic Constraints among Immune-Related Genes between Qatari and Italian Populations. PMID:34828448
Genomewide Association Analyses of Lactation Persistency and Milk Production Traits in Holstein Cattle Based on Imputed Whole-Genome Sequence Data. PMID:34828436
Genetic and Bioinformatic Strategies to Improve Diagnosis in Three Inherited Bleeding Disorders in Bogotá, Colombia. PMID:34828413
A Missense Variant in the Bardet-Biedl Syndrome 2 Gene (BBS2) Leads to a Novel Syndromic Retinal Degeneration in the Shetland Sheepdog. PMID:34828377
First DNA Sequencing in Beninese Indigenous Cattle Breeds Captures New Milk Protein Variants. PMID:34828308
Genetic diversity of 'Very Important Pharmacogenes' in two South-Asian populations. PMID:34824904
Non-coding regulatory elements: Potential roles in disease and the case of epilepsy. PMID:34820881
Synergistic insights into human health from aptamer- and antibody-based proteomic profiling. PMID:34819519
Rare germline variants in the AXIN2 gene in families with colonic polyposis and colorectal cancer. PMID:34817745
Annotating and prioritizing genomic variants using the Ensembl Variant Effect Predictor-A tutorial. PMID:34816521
Mutation saturation for fitness effects at human CpG sites. PMID:34806592
Mitotic Errors Promote Genomic Instability and Leukemia in a Novel Mouse Model of Fanconi Anemia. PMID:34804941
Case Report: Reactive Lymphohistiocytic Proliferation in Infant With a Novel Nonsense Variant of IL2RG Who Received BCG Vaccine. PMID:34796149
Associations Between the Purinergic Receptor P2X7 and Leprosy Disease. PMID:34795692
Comprehensive molecular-genetic analysis of mid-frequency sensorineural hearing loss. PMID:34795337
Whole genome sequencing and in vitro splice assays reveal genetic causes for inherited retinal diseases. PMID:34795310
Ensembl Genomes 2022: an expanding genome resource for non-vertebrates. PMID:34791415
Ensembl 2022. PMID:34791404
Transmission distortion and genetic incompatibilities between alleles in a multigenerational mouse advanced intercross line. PMID:34791189
Soluble guanylate cyclase signalling mediates etoposide resistance in progressing small cell lung cancer. PMID:34789728
The global carrier frequency and genetic prevalence of Upshaw-Schulman syndrome. PMID:34789164
De novo FZR1 loss-of-function variants cause developmental and epileptic encephalopathies. PMID:34788397
Rare variant analysis in eczema identifies exonic variants in DUSP1, NOTCH4 and SLC9A4. PMID:34785669
Short NK- and Naïve T-Cell Telomere Length Is Associated with Thyroid Cancer in Childhood Cancer Survivors: A Report from the Childhood Cancer Survivor Study. PMID:34782395
IRF7 and RNH1 are modifying factors of HIV-1 reservoirs: a genome-wide association analysis. PMID:34781942
A Study on the Genetics of Primary Ciliary Dyskinesia. PMID:34768622
PD-1 antibody camrelizumab for Epstein-Barr virus-positive metastatic gastric cancer: a single-arm, open-label, phase 2 trial. PMID:34765307
Identification of discriminative gene-level and protein-level features associated with pathogenic gain-of-function and loss-of-function variants. PMID:34762822
Cancer drivers and clonal dynamics in acute lymphoblastic leukaemia subtypes. PMID:34753926
Integrative analysis of the plasma proteome and polygenic risk of cardiometabolic diseases. PMID:34750571
VPMBench: a test bench for variant prioritization methods. PMID:34749640
Predicting novel candidate human obesity genes and their site of action by systematic functional screening in Drosophila. PMID:34748544
Pairwise effects between lipid GWAS genes modulate lipid plasma levels and cellular uptake. PMID:34741066
Advances in integrative African genomics. PMID:34740451
Low neoantigen expression and poor T-cell priming underlie early immune escape in colorectal cancer. PMID:34738089
MC3R links nutritional state to childhood growth and the timing of puberty. PMID:34732894
Gene-level analysis of rare variants in 379,066 whole exome sequences identifies an association of GIGYF1 loss of function with type 2 diabetes. PMID:34732801
Placenta mediates the effect of maternal hypertension polygenic score on offspring birth weight: a study of birth cohort with fetal growth velocity data. PMID:34732167
Allele-specific genomic data elucidate the role of somatic gain and copy-number neutral loss of heterozygosity in cancer. PMID:34731645
Merkel cell polyomavirus-negative Merkel cell carcinoma is associated with JAK-STAT and MEK-ERK pathway activation. PMID:34724284
Analysis of 200,000 Exome-Sequenced UK Biobank Subjects Implicates Genes Involved in Increased and Decreased Risk of Hypertension. PMID:34722352
The Extent and Impact of Variation in ADME Genes in Sub-Saharan African Populations. PMID:34721006
The European Variation Archive: a FAIR resource of genomic variation for all species. PMID:34718739
Exome-Wide Pan-Cancer Analysis of Germline Variants in 8,719 Individuals Finds Little Evidence of Rare Variant Associations. PMID:34718237
Detection of PKD1 and PKD2 Somatic Variants in Autosomal Dominant Polycystic Kidney Cyst Epithelial Cells by Whole-Genome Sequencing. PMID:34716216
Genetic structure of immunologically associated candidate genes suggests arctic rabies variants exert differential selection in arctic fox populations. PMID:34714859
An open approach to systematically prioritize causal variants and genes at all published human GWAS trait-associated loci. PMID:34711957
Whole-exome analysis in Tunisian Imazighen and Arabs shows the impact of demography in functional variation. PMID:34702931
Narrow mutational signatures drive acquisition of multidrug resistance in the fungal pathogen Candida glabrata. PMID:34699784
Mouse Genome Informatics (MGI): latest news from MGD and GXD. PMID:34698891
Genomic Epidemiology of SARS-CoV-2 in Pakistan. PMID:34695600
Prioritizing natural-selection signals from the deep-sequencing genomic data suggests multi-variant adaptation in Tibetan highlanders. PMID:34691999
Targeted Sequencing of 242 Clinically Important Genes in the Russian Population From the Ivanovo Region. PMID:34691145
Identification of four novel QTL linked to the metabolic syndrome in the Berlin Fat Mouse. PMID:34689180
The flashfm approach for fine-mapping multiple quantitative traits. PMID:34686674
Congenital X-linked neutropenia with myelodysplasia and somatic tetraploidy due to a germline mutation in SEPT6. PMID:34677878
The intronic branch point sequence is under strong evolutionary constraint in the bovine and human genome. PMID:34675361
A multiethnic whole genome sequencing study to identify novel loci for bone mineral density. PMID:34673960
Profile of esophageal squamous cell carcinoma mutations in Brazilian patients. PMID:34663841
From GWAS to Gene: Transcriptome-Wide Association Studies and Other Methods to Functionally Understand GWAS Discoveries. PMID:34659337
Gene.iobio: an interactive web tool for versatile, clinically-driven variant interrogation and prioritization. PMID:34645894
Artificial intelligence enables comprehensive genome interpretation and nomination of candidate diagnoses for rare genetic diseases. PMID:34645491
TIGER: The gene expression regulatory variation landscape of human pancreatic islets. PMID:34644572
Liquid Biopsy in Gastric Cancer: Analysis of Somatic Cancer Tissue Mutations in Plasma Cell-Free DNA for Predicting Disease State and Patient Survival. PMID:34644276
WDR37 syndrome: identification of a distinct new cluster of disease-associated variants and functional analyses of mutant proteins. PMID:34642815
Thousands of Qatari genomes inform human migration history and improve imputation of Arab haplotypes. PMID:34642339
Whole-exome sequencing identified first homozygous frameshift variant in the COLEC10 gene in an Iranian patient causing 3MC syndrome type 3. PMID:34636477
Three chromosome-level duck genome assemblies provide insights into genomic variation during domestication. PMID:34635656
The genetic impact of an Ebola outbreak on a wild gorilla population. PMID:34635054
SomaMutDB: a database of somatic mutations in normal human tissues. PMID:34634815
The Ensembl COVID-19 resource: ongoing integration of public SARS-CoV-2 data. PMID:34634797
Whole-exome sequencing reveals a role of HTRA1 and EGFL8 in brain white matter hyperintensities. PMID:34626176
HIF-1α Pulmonary Phenotype Wide Association Study Unveils a Link to Inflammatory Airway Conditions. PMID:34621299
A systematic analysis of genetic interactions and their underlying biology in childhood cancer. PMID:34615983
Polygenic basis and biomedical consequences of telomere length variation. PMID:34611362
Characterization of the Genomic and Immunologic Diversity of Malignant Brain Tumors through Multisector Analysis. PMID:34610950
Long term follow-up of a phase II study of cladribine with concurrent rituximab with hairy cell leukemia variant. PMID:34607348
Case Report: Two Newly Diagnosed Patients With KBG Syndrome-Two Different Molecular Changes. PMID:34604130
Privacy-preserving storage of sequenced genomic data. PMID:34600465
Targeted exome analysis of Russian patients with hypertrophic cardiomyopathy. PMID:34598319
Gene-based mapping of trehalose biosynthetic pathway genes reveals association with source- and sink-related yield traits in a spring wheat panel. PMID:34594548
A cross-population atlas of genetic associations for 220 human phenotypes. PMID:34594039
Rare, Damaging DNA Variants in CORIN and Risk of Coronary Artery Disease: Insights From Functional Genomics and Large-Scale Sequencing Analyses. PMID:34592835
Regional TMPRSS2 V197M Allele Frequencies Are Correlated with COVID-19 Case Fatality Rates. PMID:34588322
Multiple variants in XDH and MOCOS underlie xanthine urolithiasis in dogs. PMID:34584846
Mutant collagen COL11A1 enhances cancerous invasion. PMID:34584216
An enhanced variant effect predictor based on a deep generative model and the Born-Again Networks. PMID:34580383
Integrated genomics point to immune vulnerabilities in pleural mesothelioma. PMID:34580349
High Rate of Mutational Events in SARS-CoV-2 Genomes across Brazilian Geographical Regions, February 2020 to June 2021. PMID:34578387
Common and Unique Genetic Background between Attention-Deficit/Hyperactivity Disorder and Excessive Body Weight. PMID:34573389
Real-World Evaluation of Universal Germline Screening for Cancer Treatment-Relevant Pharmacogenes. PMID:34572750
Aqueous Humor as a Liquid Biopsy for Retinoblastoma: Clear Corneal Paracentesis and Genomic Analysis. PMID:34570090
iPSC culture expansion selects against putatively actionable mutations in the mitochondrial genome. PMID:34560000
SNP prioritization in targeted sequencing data associated with humoral immune responses in chicken. PMID:34551372
Distinct clinical characteristics of DUX4- and PAX5-altered childhood B-lymphoblastic leukemia. PMID:34547766
Rare and de novo variants in 827 congenital diaphragmatic hernia probands implicate LONP1 as candidate risk gene. PMID:34547244
Variance-component-based meta-analysis of gene-environment interactions for rare variants. PMID:34544119
A Roadmap to Gene Discoveries and Novel Therapies in Monogenic Low and High Bone Mass Disorders. PMID:34539568
SmProt: A Reliable Repository with Comprehensive Annotation of Small Proteins Identified from Ribosome Profiling. PMID:34536568
PIGG defines the Emm blood group system. PMID:34535746
A survey of RNA editing at single-cell resolution links interneurons to schizophrenia and autism. PMID:34535545
Genome-wide functional screen of 3'UTR variants uncovers causal variants for human disease and evolution. PMID:34534445
Genetic differentiation of mainland-island sheep of Greece: Implications for identifying candidate genes for long-term local adaptation. PMID:34529728
A modified fluctuation assay reveals a natural mutator phenotype that drives mutation spectrum variation within Saccharomyces cerevisiae. PMID:34523420
Integrated protocol for exitron and exitron-derived neoantigen identification using human RNA-seq data with ScanExitron and ScanNeo. PMID:34522901
The LOVD3 platform: efficient genome-wide sharing of genetic variants. PMID:34521998
Multi-region exome sequencing reveals the intratumoral heterogeneity of surgically resected small cell lung cancer. PMID:34521849
Rare variants in the endocytic pathway are associated with Alzheimer's disease, its related phenotypes, and functional consequences. PMID:34516545
Levodopa-responsive dystonia caused by biallelic PRKN exon inversion invisible to exome sequencing. PMID:34514401
Scalable analysis of multi-modal biomedical data. PMID:34508579
Exploring the Genomic Landscape of Cancer Patient Cohorts with GenVisR. PMID:34506690
Differential whole-genome doubling and homologous recombination deficiencies across breast cancer subtypes from the Taiwanese population. PMID:34504292
Schizophrenia, autism spectrum disorders and developmental disorders share specific disruptive coding mutations. PMID:34504065
A genome-wide scan to identify signatures of selection in two Iranian indigenous chicken ecotypes. PMID:34503452
Mutational landscape of marginal zone B-cell lymphomas of various origin: organotypic alterations and diagnostic potential for assignment of organ origin. PMID:34494161
Molecular profiling of advanced solid tumours. The impact of experimental molecular-matched therapies on cancer patient outcomes in early-phase trials: the MAST study. PMID:34493820
Detection of mobile elements insertions for routine clinical diagnostics in targeted sequencing data. PMID:34491624
iSheep: an Integrated Resource for Sheep Genome, Variant and Phenotype. PMID:34490043
Case Report: A Case of Leukocyte Adhesion Deficiency, Type III Presenting With Impaired Platelet Function, Lymphocytosis and Granulocytosis. PMID:34485203
Targeted whole exome sequencing and Drosophila modelling to unveil the molecular basis of primary ovarian insufficiency. PMID:34480478
Autophagy promotes growth of tumors with high mutational burden by inhibiting a T-cell immune response. PMID:34476408
Prospects and challenges of cancer systems medicine: from genes to disease networks. PMID:34471925
TSNAD v2.0: A one-stop software solution for tumor-specific neoantigen detection. PMID:34471496
Comprehensive molecular profiling to predict clinical outcomes in pancreatic cancer. PMID:34471425
Full-length isoform transcriptome of the developing human brain provides further insights into autism. PMID:34469739
Building a Chinese pan-genome of 486 individuals. PMID:34462542
Dual PD-L1 and TGF-b blockade in patients with recurrent respiratory papillomatosis. PMID:34462327
Evidence for and localization of proposed causative variants in cattle and pig genomes. PMID:34461824
A Missense Mutation in the MYBPH Gene Is Associated With Abdominal Fat Traits in Meat-Type Chickens. PMID:34456973
SMAD4 is critical in suppression of BRAF-V600E serrated tumorigenesis. PMID:34453124
The PEMDAC phase 2 study of pembrolizumab and entinostat in patients with metastatic uveal melanoma. PMID:34453044
Pan-cancer analysis of longitudinal metastatic tumors reveals genomic alterations and immune landscape dynamics associated with pembrolizumab sensitivity. PMID:34446728
A Genome-Wide Association Study on Liver Stiffness Changes during Hepatitis C Virus Infection Cure. PMID:34441435
Variants Affecting the C-Terminal Tail of UNC93B1 Are Not a Common Risk Factor for Systemic Lupus Erythematosus. PMID:34440442
Whole-Genome Sequencing Improves the Diagnosis of DFNB1 Monoallelic Patients. PMID:34440441
Wide Fontanels, Delayed Speech Development and Hoarse Voice as Useful Signs in the Diagnosis of KBG Syndrome: A Clinical Description of 23 Cases with Pathogenic Variants Involving the ANKRD11 Gene or Submicroscopic Chromosomal Rearrangements of 16q24.3. PMID:34440431
Hearing Function: Identification of New Candidate Genes Further Explaining the Complexity of This Sensory Ability. PMID:34440402
Genome-Wide Association Study Using Whole-Genome Sequence Data for Fertility, Health Indicator, and Endoparasite Infection Traits in German Black Pied Cattle. PMID:34440337
agReg-SNPdb: A Database of Regulatory SNPs for Agricultural Animal Species. PMID:34440019
Shared Genetic Background between Parkinson's Disease and Schizophrenia: A Two-Sample Mendelian Randomization Study. PMID:34439661
MET Mutation Is a Potential Therapeutic Target for Advanced Endometrial Cancer. PMID:34439385
High-throughput screening and genome-wide analyses of 44 anticancer drugs in the 1000 Genomes cell lines reveals an association of the NQO1 gene with the response of multiple anticancer drugs. PMID:34437536
Identification of Key Genes Mutations Associated With the Radiosensitivity by Whole Exome Sequencing in Pancreatic Cancer. PMID:34434896
Frequency of Heterozygous Parkin (PRKN) Variants and Penetrance of Parkinson's Disease Risk Markers in the Population-Based CHRIS Cohort. PMID:34434164
A clinically applicable integrative molecular classification of meningiomas. PMID:34433969
Current gene panels account for nearly all homologous recombination repair-associated multiple-case breast cancer families. PMID:34433815
Predicting functional consequences of mutations using molecular interaction network features. PMID:34432150
A global map of associations between types of protein posttranslational modifications and human genetic diseases. PMID:34430807
Comprehensive characterization of 536 patient-derived xenograft models prioritizes candidatesfor targeted treatment. PMID:34429404
Multidimensional Approach Assessing the Role of Interleukin 1 Beta in Mesial Temporal Lobe Epilepsy. PMID:34421794
The MURAL collection of prostate cancer patient-derived xenografts enables discovery through preclinical models of uro-oncology. PMID:34413304
X-linked recessive TLR7 deficiency in ~1% of men under 60 years old with life-threatening COVID-19. PMID:34413140
Delaying or delivering: identification of novel NAM-1 alleles that delay senescence to extend wheat grain fill duration. PMID:34405865
The ABCC4 gene is associated with pyometra in golden retriever dogs. PMID:34404837
Genomics pipelines to investigate susceptibility in whole genome and exome sequenced data for variant discovery, annotation, prediction and genotyping. PMID:34395068
Tunisian Maturity-Onset Diabetes of the Young: A Short Review and a New Molecular and Clinical Investigation. PMID:34393998
A novel compound heterozygous leptin receptor mutation causes more severe obesity than in Leprdb/db mice. PMID:34390703
Positive predictive value highlights four novel candidates for actionable genetic screening from analysis of 220,000 clinicogenomic records. PMID:34385667
Overcoming microenvironmental resistance to PD-1 blockade in genetically engineered lung cancer models. PMID:34380768
Biallelic truncating variants in ATP9A cause a novel neurodevelopmental disorder involving postnatal microcephaly and failure to thrive. PMID:34379057
Bisection of the X chromosome disrupts the initiation of chromosome silencing during meiosis in Caenorhabditis elegans. PMID:34376665
Pathogenic nsSNPs that increase the risks of cancers among the Orang Asli and Malays. PMID:34373545
A novel machine learning-based approach for the computational functional assessment of pharmacogenomic variants. PMID:34372920
Fifteen Years of the Australian Imaging, Biomarkers and Lifestyle (AIBL) Study: Progress and Observations from 2,359 Older Adults Spanning the Spectrum from Cognitive Normality to Alzheimer's Disease. PMID:34368630
Mutational patterns and clonal evolution from diagnosis to relapse in pediatric acute lymphoblastic leukemia. PMID:34362951
Exploiting genomic synteny in Felidae: cross-species genome alignments and SNV discovery can aid conservation management. PMID:34362297
Single Nucleotide Polymorphism Induces Divergent Dynamic Patterns in CYP3A5: A Microsecond Scale Biomolecular Simulation of Variants Identified in Sub-Saharan African Populations. PMID:34360551
A proteogenomic portrait of lung squamous cell carcinoma. PMID:34358469
The CD155/TIGIT axis promotes and maintains immune evasion in neoantigen-expressing pancreatic cancer. PMID:34358448
Targeting mitotic exit in solid tumors. PMID:34354869
Genetic insights into biological mechanisms governing human ovarian ageing. PMID:34349265
A case of Fibrodysplasia Ossificans Progressiva associated with a novel variant of the ACVR1 gene. PMID:34347384
Interaction with the CCT chaperonin complex limits APOBEC3A cytidine deaminase cytotoxicity. PMID:34347354
The effects of genotype on inflammatory response in hippocampal progenitor cells: A computational approach. PMID:34345870
SorGSD: updating and expanding the sorghum genome science database with new contents and tools. PMID:34344425
Impact of natural selection on global patterns of genetic variation, and association with clinical phenotypes, at genes involved in SARS-CoV-2 infection. PMID:34341784
BinomiRare: A robust test for association of a rare genetic variant with a binary outcome for mixed models and any case-control proportion. PMID:34337551
MLPA followed by target-NGS to detect mutations in the dystrophin gene of Peruvian patients suspected of DMD/DMB. PMID:34327855
Careful feature selection is key in classification of Alzheimer's disease patients based on whole-genome sequencing data. PMID:34327330
Detection of genomic regions associated malformations in newborn piglets: a machine-learning approach. PMID:34327051
Large scale clinical exome sequencing uncovers the scope and severity of skin disorders associated with MC1R genetic variants. PMID:34326492
The genomic landscape of 85 advanced neuroendocrine neoplasms reveals subtype-heterogeneity and potential therapeutic targets. PMID:34326338
The role of neutral and adaptive genomic variation in population diversification and speciation in two ground squirrel species of conservation concern. PMID:34324748
Profiling of hepatocellular carcinoma neoantigens reveals immune microenvironment and clonal evolution related patterns. PMID:34321833
Efficacy of computational predictions of the functional effect of idiosyncratic pharmacogenetic variants. PMID:34316407
GWAS of serum ALT and AST reveals an association of SLC30A10 Thr95Ile with hypermanganesemia symptoms. PMID:34315874
Multiethnic Prediction of Nicotine Biomarkers and Association With Nicotine Dependence. PMID:34313775
Recent ultra-rare inherited variants implicate new autism candidate risk genes. PMID:34312540
Watch Out for a Second SNP: Focus on Multi-Nucleotide Variants in Coding Regions and Rescued Stop-Gained. PMID:34306009
The clinical importance of tandem exon duplication-derived substitutions. PMID:34302486
G6PD distribution in sub-Saharan Africa and potential risks of using chloroquine/hydroxychloroquine based treatments for COVID-19. PMID:34302047
Effect of the Electromagnetic Field (EMF) Radiation on Transcriptomic Profile of Pig Myometrium during the Peri-Implantation Period-An In Vitro Study. PMID:34298942
Genomic Analysis of Response to Neoadjuvant Chemotherapy in Esophageal Adenocarcinoma. PMID:34298611
Comparative Analysis of Mammal Genomes Unveils Key Genomic Variability for Human Life Span. PMID:34297086
Comparison of the oncogenomic landscape of canine and feline hemangiosarcoma shows novel parallels with human angiosarcoma. PMID:34296746
Hearing difficulty is linked to Alzheimer's disease by common genetic vulnerability, not shared genetic architecture. PMID:34294723
Impact of Tenascin-C on Radiotherapy in a Novel Syngeneic Oral Squamous Cell Carcinoma Model With Spontaneous Dissemination to the Lymph Nodes. PMID:34290694
Prevalence of cancer susceptibility variants in patients with multiple Lynch syndrome related cancers. PMID:34285288
Case Report: Pansynostosis, Chiari I Malformation and Syringomyelia in a Child With Frontometaphyseal Dysplasia 1. PMID:34277511
Clinical evaluation of RB1 genetic testing reveals novel mutations in Vietnamese patients with retinoblastoma. PMID:34277001
The mutational profile of immune surveillance genes in diagnostic and refractory/relapsed DLBCLs. PMID:34275438
Genomic and pleiotropic analyses of resting QT interval identifies novel loci and overlap with atrial electrical disorders. PMID:34274964
An overview of germline variations in genes of primary immunodeficiences through integrative analysis of ClinVar, HGMD® and dbSNP databases. PMID:34272616
Discovery and prioritization of variants and genes for kidney function in >1.2 million individuals. PMID:34272381
Secondary resistance to anti-EGFR therapy by transcriptional reprogramming in patient-derived colorectal cancer models. PMID:34271981
Deploying new generation sequencing for the study of flesh color depletion in Atlantic Salmon (Salmo salar). PMID:34271869
Effective variant filtering and expected candidate variant yield in studies of rare human disease. PMID:34267211
Genome-Wide Detection of Structural Variations Reveals New Regions Associated with Domestication in Small Ruminants. PMID:34264322
RNA-Seq Data for Reliable SNP Detection and Genotype Calling: Interest for Coding Variant Characterization and Cis-Regulation Analysis by Allele-Specific Expression in Livestock Species. PMID:34262593
Association of Coding Variants in Hydroxysteroid 17-beta Dehydrogenase 14 (HSD17B14) with Reduced Progression to End Stage Kidney Disease in Type 1 Diabetes. PMID:34261756
Bi-allelic truncating variants in CFAP206 cause male infertility in human and mouse. PMID:34255152
A computational and structural analysis of germline and somatic variants affecting the DDR mechanism, and their impact on human diseases. PMID:34253785
The role of genetic polymorphisms in endolysosomal ion channels TPC2 and P2RX4 in cancer pathogenesis, prognosis, and diagnosis: a genetic association in the UK Biobank. PMID:34253731
Repeated evolution of circadian clock dysregulation in cavefish populations. PMID:34252077
Synchronous, Yet Genomically Distinct, GIST Offer New Insights Into Precise Targeting of Tumor Driver Mutations. PMID:34250403
South African Buffalo-Derived Theileria parva Is Distinct From Other Buffalo and Cattle-Derived T. parva. PMID:34249088
Genomic analyses of high-grade neuroendocrine gynecological malignancies reveal a unique mutational landscape and therapeutic vulnerabilities. PMID:34245124
Novel PRMT7 mutation in a rare case of dysmorphism and intellectual disability. PMID:34244600
Genetic Analysis of Functional Rare Germline Variants across Nine Cancer Types from an Electronic Health Record Linked Biobank. PMID:34244158
Mapping the human genetic architecture of COVID-19. PMID:34237774
Novel Gene Mutations Regulating Immune Responses in Autoimmune Polyglandular Syndrome With an Atypical Course. PMID:34235359
The first insight into the genetic structure of the population of modern Serbia. PMID:34234178
GIGYF1 loss of function is associated with clonal mosaicism and adverse metabolic health. PMID:34234147
Impact of natural selection on global patterns of genetic variation, and association with clinical phenotypes, at genes involved in SARS-CoV-2 infection. PMID:34230933
Oncogenic cooperation between TCF7-SPI1 and NRAS(G12D) requires β-catenin activity to drive T-cell acute lymphoblastic leukemia. PMID:34230493
Genetic epidemiology approach to estimating birth incidence and current disease prevalence for rhizomelic chondrodysplasia punctata. PMID:34229749
Whole-exome imputation within UK Biobank powers rare coding variant association and fine-mapping analyses. PMID:34226706
Admixture Has Shaped Romani Genetic Diversity in Clinically Relevant Variants. PMID:34220960
Pooled Sequencing Analysis of Geese (Anser cygnoides) Reveals Genomic Variations Associated With Feather Color. PMID:34220935
Admixture mapping reveals the association between Native American ancestry at 3q13.11 and reduced risk of Alzheimer's disease in Caribbean Hispanics. PMID:34217363
Targeted long-read sequencing identifies missing disease-causing variation. PMID:34216551
Identification of novel and rare variants associated with handgrip strength using whole genome sequence data from the NHLBI Trans-Omics in Precision Medicine (TOPMed) Program. PMID:34214102
A Homozygous Deep Intronic Mutation Alters the Splicing of Nebulin Gene in a Patient With Nemaline Myopathy. PMID:34211429
UVB mutagenesis differs in Nras- and Braf-mutant mouse models of melanoma. PMID:34210801
Deleterious Mutations in the TPO Gene Associated with Familial Thyroid Follicular Cell Carcinoma in Dutch German Longhaired Pointers. PMID:34209805
CD74 and CD44 Expression on CTCs in Cancer Patients with Brain Metastasis. PMID:34209696
Identification of Novel Mutations in Colorectal Cancer Patients Using AmpliSeq Comprehensive Cancer Panel. PMID:34207827
Single Nucleotide Polymorphisms in Genes Encoding Toll-Like Receptors 7 and 8 and Their Association with Proviral Load of SRLVs in Goats of Polish Carpathian Breed. PMID:34206971
Identifying Cancer Drivers Using DRIVE: A Feature-Based Machine Learning Model for a Pan-Cancer Assessment of Somatic Missense Mutations. PMID:34205004
Bioinformatics Accelerates the Major Tetrad: A Real Boost for the Pharmaceutical Industry. PMID:34201152
Two novel variants in DYRK1B causative of AOMS3: expanding the clinical spectrum. PMID:34193236
Broadening INPP5E phenotypic spectrum: detection of rare variants in syndromic and non-syndromic IRD. PMID:34188062
A trans locus causes a ribosomopathy in hypertrophic hearts that affects mRNA translation in a protein length-dependent fashion. PMID:34183069
Whole-Exome Sequencing Analysis of Human Semen Quality in Russian Multiethnic Population. PMID:34178030
Immunogenomic profiling and pathological response results from a clinical trial of docetaxel and carboplatin in triple-negative breast cancer. PMID:34173924
The AML microenvironment catalyzes a stepwise evolution to gilteritinib resistance. PMID:34171263
Whole-genome Sequencing of Follicular Thyroid Carcinomas Reveal Recurrent Mutations in MicroRNA Processing Subunit DGCR8. PMID:34171097
DIVIS: Integrated and Customizable Pipeline for Cancer Genome Sequencing Analysis and Interpretation. PMID:34168993
Association of mitochondrial variants and haplogroups identified by whole exome sequencing with Alzheimer's disease. PMID:34152079
Oligogenic Inheritance of Monoallelic TRIP11, FKBP10, NEK1, TBX5, and NBAS Variants Leading to a Phenotype Similar to Odontochondrodysplasia. PMID:34149817
Establishment and characterization of immortalized human breast cancer cell lines from breast cancer patient-derived xenografts (PDX). PMID:34145270
Genome Scan for Variable Genes Involved in Environmental Adaptations of Nubian Ibex. PMID:34142199
Prioritizing the Role of Major Lipoproteins and Subfractions as Risk Factors for Peripheral Artery Disease. PMID:34139859
Whole-exome sequencing reveals insights into genetic susceptibility to Congenital Zika Syndrome. PMID:34125832
High-Throughput Imaging Assay for Drug Screening of 3D Prostate Cancer Organoids. PMID:34111999
Determinants of penetrance and variable expressivity in monogenic metabolic conditions across 77,184 exomes. PMID:34108472
Genome-wide association analysis of adaptation to oxygen stress in Nile tilapia (Oreochromis niloticus). PMID:34107887
Genome wide study of tardive dyskinesia in schizophrenia. PMID:34103471
Systems genetics in diversity outbred mice inform BMD GWAS and identify determinants of bone strength. PMID:34099702
Leveraging supervised learning for functionally informed fine-mapping of cis-eQTLs identifies an additional 20,913 putative causal eQTLs. PMID:34099641
Mitochondrial genome copy number measured by DNA sequencing in human blood is strongly associated with metabolic traits via cell-type composition differences. PMID:34099068
CRISPR/Cas9-mediated correction of MITF homozygous point mutation in a Waardenburg syndrome 2A pig model. PMID:34094716
Transcriptome-Wide Identification of G-to-A RNA Editing in Chronic Social Defeat Stress Mouse Models. PMID:34093668
Genome-wide association study on blood pressure traits in the Iranian population suggests ZBED9 as a new locus for hypertension. PMID:34083597
Whole-Exome Sequencing Reveals Rare Germline Mutations in Patients With Hemifacial Microsomia. PMID:34079577
Eleven genomic loci affect plasma levels of chronic inflammation marker soluble urokinase-type plasminogen activator receptor. PMID:34079037
Solving patients with rare diseases through programmatic reanalysis of genome-phenome data. PMID:34075210
High Concordance of Genomic Profiles between Primary and Metastatic Colorectal Cancer. PMID:34074070
Prognostic Genetic Biomarkers Based on Oncogenic Signaling Pathways for Outcome Prediction in Patients with Oral Cavity Squamous Cell Carcinoma. PMID:34070941
Genotype and Trait Specific Responses to Rapamycin Intake in Drosophila melanogaster. PMID:34065203
An in vitro model of tumor heterogeneity resolves genetic, epigenetic, and stochastic sources of cell state variability. PMID:34061819
Detection of Disease-Causing SNVs/Indels and CNVs in Single Test Based on Whole Exome Sequencing: A Retrospective Case Study in Epileptic Encephalopathies. PMID:34055682
Association of CASR, CALCR, and ORAI1 Genes Polymorphisms With the Calcium Urolithiasis Development in Russian Population. PMID:34054913
MTR3D: identifying regions within protein tertiary structures under purifying selection. PMID:34050760
Towards population-scale long-read sequencing. PMID:34050336
snpXplorer: a web application to explore human SNP-associations and annotate SNP-sets. PMID:34048563
Novel loci and Mapuche genetic ancestry are associated with pubertal growth traits in Chilean boys. PMID:34047840
Comprehensive phenotypic and functional analysis of dominant and recessive FOXE3 alleles in ocular developmental disorders. PMID:34046667
Assessing the functional relevance of splice isoforms. PMID:34046593
Natural variants suppress mutations in hundreds of essential genes. PMID:34042294
Mutations in MT-ATP6 are a frequent cause of adult-onset spinocerebellar ataxia. PMID:34037856
Association of FAAH p.Pro129Thr and COMT p.Ala72Ser with schizophrenia and comorbid substance use through next-generation sequencing: an exploratory analysis. PMID:34037083
Impact of a 40-Gene Targeted Panel Test on Physician Decision Making for Patients With Acute Myeloid Leukemia. PMID:34036230
Infant inhibited temperament in primates predicts adult behavior, is heritable, and is associated with anxiety-relevant genetic variation. PMID:34035480
Whole-Exome Sequencing of Radiation-Induced Thymic Lymphoma in Mouse Models Identifies Notch1 Activation as a Driver of p53 Wild-Type Lymphoma. PMID:34035082
Impact of rare and common genetic variation in the interleukin-1 pathway on human cytokine responses. PMID:34034819
Anti-PD-1 in Combination With Trametinib Suppresses Tumor Growth and Improves Survival of Intrahepatic Cholangiocarcinoma in Mice. PMID:34033968
An international genome-wide meta-analysis of primary biliary cholangitis: Novel risk loci and candidate drugs. PMID:34033851
Predicting MHC I restricted T cell epitopes in mice with NAP-CNB, a novel online tool. PMID:34031450
Molecular landscape and subtype-specific therapeutic response of nasopharyngeal carcinoma revealed by integrative pharmacogenomics. PMID:34031426
Rare Missense Functional Variants at COL4A1 and COL4A2 in Sporadic Intracerebral Hemorrhage. PMID:34031201
Standing genetic variation in laboratory populations of insecticide-susceptible Phlebotomus papatasi and Lutzomyia longipalpis (Diptera: Psychodidae: Phlebotominae) for the evolution of resistance. PMID:34025765
Combination of Immunotherapy and Radiotherapy for Recurrent Malignant Gliomas: Results From a Prospective Study. PMID:34025640
Causal effect of alcohol use on the risk of end-stage kidney disease and related comorbidities: a Mendelian randomization study. PMID:34024088
Non-coding region variants upstream of MEF2C cause severe developmental disorder through three distinct loss-of-function mechanisms. PMID:34022131
Genetic Origins and Sex-Biased Admixture of the Huis. PMID:34021754
Characterizing the molecular and immune landscape of canine bladder cancer. PMID:34021685
GWAS of allometric body-shape indices in UK Biobank identifies loci suggesting associations with morphogenesis, organogenesis, adrenal cell renewal and cancer. PMID:34021172
Chemically defined and xeno-free culture condition for human extended pluripotent stem cells. PMID:34021145
Unique evolutionary trajectories of breast cancers with distinct genomic and spatial heterogeneity. PMID:34011996
Investigating the impact of reference assembly choice on genomic analyses in a cattle breed. PMID:34011274
Decreased ATM Function Causes Delayed DNA Repair and Apoptosis in Common Variable Immunodeficiency Disorders. PMID:34009545
Bintrafusp Alfa, a Bifunctional Fusion Protein Targeting TGF-β and PD-L1, in Patients with Esophageal Adenocarcinoma: Results from a Phase 1 Cohort. PMID:34009501
Targeted RNA-seq improves efficiency, resolution, and accuracy of allele specific expression for human term placentas. PMID:34009305
Genetic pleiotropy of ERCC6 loss-of-function and deleterious missense variants links retinal dystrophy, arrhythmia, and immunodeficiency in diverse ancestries. PMID:34005834
Reproductive history determines Erbb2 locus amplification, WNT signalling and tumour phenotype in a murine breast cancer model. PMID:34003256
Mutations in HID1 Cause Syndromic Infantile Encephalopathy and Hypopituitarism. PMID:33999436
Accessing Livestock Resources in Ensembl. PMID:33995484
A genetic screen for regulators of muscle morphogenesis in Drosophila. PMID:33993253
Plasma Metabolomic Signatures of Chronic Obstructive Pulmonary Disease and the Impact of Genetic Variants on Phenotype-Driven Modules. PMID:33987620
Whole-exome sequencing identifies somatic mutations associated with lung cancer metastasis to the brain. PMID:33987392
A founder mutation in the PLPBP gene in families from Saguenay-Lac-St-Jean region affected by a pyridoxine-dependent epilepsy. PMID:33977028
Identification of missense MAB21L1 variants in microphthalmia and aniridia. PMID:33973683
Novel functional sequences uncovered through a bovine multiassembly graph. PMID:33972446
Rare variant analysis of 4241 pulmonary arterial hypertension cases from an international consortium implicates FBLN2, PDGFD, and rare de novo variants in PAH. PMID:33971972
Knowledge bases and software support for variant interpretation in precision oncology. PMID:33971666
DNMT3A haploinsufficiency causes dichotomous DNA methylation defects at enhancers in mature human immune cells. PMID:33970190
Variants in GCNA, X-linked germ-cell genome integrity gene, identified in men with primary spermatogenic failure. PMID:33963445
Matrilineal analysis of mutations in the DMD gene in a multigenerational South Indian cohort using DMD gene panel sequencing. PMID:33960727
Microdeletion of 9q22.3: A patient with minimal deletion size associated with a severe phenotype. PMID:33960642
Accelerating Medicines Partnership: Parkinson's Disease. Genetic Resource. PMID:33960523
CDX2 expression in the hematopoietic lineage promotes leukemogenesis via TGFβ inhibition. PMID:33960108
Limited haplotype diversity underlies polygenic trait architecture across 70 years of wheat breeding. PMID:33957956
Systematic interrogation of mutation groupings reveals divergent downstream expression programs within key cancer genes. PMID:33957863
A natural knockout of the MYO7A gene leads to pre-weaning mortality in pigs. PMID:33955556
Copy number signature analysis tool and its application in prostate cancer reveals distinct mutational processes and clinical outcomes. PMID:33945534
A web-based survey on various symptoms of computer vision syndrome and the genetic understanding based on a multi-trait genome-wide association study. PMID:33941792
Single nucleotide polymorphism array-based signature of low hypodiploidy in acute lymphoblastic leukemia. PMID:33938069
Predicting Ovarian/Breast Cancer Pathogenic Risks of Human BRCA1 Gene Variants of Unknown Significance. PMID:33937409
An Integrated Genomic, Proteomic, and Immunopeptidomic Approach to Discover Treatment-Induced Neoantigens. PMID:33936100
Disparities in COVID-19 severities and casualties across ethnic groups around the globe and patterns of ACE2 and PIR variants. PMID:33933634
Common Variation in Cytoskeletal Genes is Associated with Conotruncal Heart Defects. PMID:33925651
Comorbidities and Susceptibility to COVID-19: A Generalized Gene Set Data Mining Approach. PMID:33924631
Application of Genome Sequencing from Blood to Diagnose Mitochondrial Diseases. PMID:33924034
TILLING-by-Sequencing+ to Decipher Oil Biosynthesis Pathway in Soybeans: A New and Effective Platform for High-Throughput Gene Functional Analysis. PMID:33921707
Novel Compound Heterozygous Mutation in TRAPPC9 Gene: The Relevance of Whole Genome Sequencing. PMID:33921338
Compound Haplotype Variants in CFH and CD46 Genes Determine Clinical Outcome of Atypical Hemolytic Uremic Syndrome (aHUS)-A Series of Cases from a Single Family. PMID:33920896
Evolutionary Trajectories and Genomic Divergence in Localized Breast Cancers after Ipsilateral Breast Tumor Recurrence. PMID:33920370
Genetic Analysis Reveals Rare Variants in T-Cell Response Gene MR1 Associated with Poor Overall Survival after Urothelial Cancer Diagnosis. PMID:33919687
Clinicopathologic Profile of Breast Cancer in Germline ATM and CHEK2 Mutation Carriers. PMID:33919281
Genetic Regulation of Biomarkers as Stress Proxies in Dairy Cows. PMID:33917627
Tumor Signature Analysis Implicates Hereditary Cancer Genes in Endometrial Cancer Development. PMID:33917078
Variants at the ASIP locus contribute to coat color darkening in Nellore cattle. PMID:33910501
Pathogenic missense protein variants affect different functional pathways and proteomic features than healthy population variants. PMID:33909605
Molecular Parallelism Underlies Convergent Highland Adaptation of Maize Landraces. PMID:33905497
Linkage of Alzheimer disease families with Puerto Rican ancestry identifies a chromosome 9 locus. PMID:33902942
The Clinical Implications of Tumor Mutational Burden in Osteosarcoma. PMID:33898301
Heterogeneity of a dwarf phenotype in Dutch traditional chicken breeds revealed by genomic analyses. PMID:33897823
Investigation of Association of Rare, Functional Genetic Variants With Heavy Drinking and Problem Drinking in Exome Sequenced UK Biobank Participants. PMID:33893496
Genomic profile of advanced breast cancer in circulating tumour DNA. PMID:33893289
Integrated Genomic Analysis Identifies Driver Genes and Cisplatin-Resistant Progenitor Phenotype in Pediatric Liver Cancer. PMID:33893148
A worldwide map of swine short tandem repeats and their associations with evolutionary and environmental adaptations. PMID:33892623
Comprehensive Study of Germline Mutations and Double-Hit Events in Esophageal Squamous Cell Cancer. PMID:33889545
Characterization of a haplotype-reference panel for genotyping by low-pass sequencing in Swiss Large White pigs. PMID:33882824
Genetics of HLA Peptide Presentation and Impact on Outcomes in HLA-Matched Allogeneic Hematopoietic Cell Transplantation. PMID:33882342
Pharmacogene Sequencing of a Gabonese Population with Severe Plasmodium falciparum Malaria Reveals Multiple Novel Variants with Putative Relevance for Antimalarial Treatment. PMID:33875422
Systematic identification of A-to-I RNA editing in zebrafish development and adult organs. PMID:33872356
The copy number variation and stroke (CaNVAS) risk and outcome study. PMID:33872305
Inferring Adaptive Codon Preference to Understand Sources of Selection Shaping Codon Usage Bias. PMID:33871580
Microsecond-timescale MD simulation of EGFR minor mutation predicts the structural flexibility of EGFR kinase core that reflects EGFR inhibitor sensitivity. PMID:33863983
Multi-omic analyses in Abyssinian cats with primary renal amyloid deposits. PMID:33863921
A Rare Autosomal Dominant Variant in Regulator of Calcineurin Type 1 (RCAN1) Gene Confers Enhanced Calcineurin Activity and May Cause FSGS. PMID:33863784
A pan-cancer transcriptome analysis of exitron splicing identifies novel cancer driver genes and neoepitopes. PMID:33861991
Case Report: Novel Likely Pathogenic ACTN2 Variant Causing Heterogeneous Phenotype in a Korean Family With Left Ventricular Non-compaction. PMID:33859969
The mode of expression divergence in Drosophila fat body is infection-specific. PMID:33858842
Impact of clinical targeted sequencing on endocrine responsiveness in estrogen receptor-positive, HER2-negative metastatic breast cancer. PMID:33854152
Bioinformatic strategies for the analysis of genomic aberrations detected by targeted NGS panels with clinical application. PMID:33850640
Tissue-specific cell-free DNA degradation quantifies circulating tumor DNA burden. PMID:33850132
Identifying therapeutic drug targets using bidirectional effect genes. PMID:33850126
Phase II Multicenter Study of Enzalutamide in Metastatic Castration-Resistant Prostate Cancer to Identify Mechanisms Driving Resistance. PMID:33849963
Human ACE2 receptor polymorphisms and altered susceptibility to SARS-CoV-2. PMID:33846513
Exploring a Region on Chromosome 8p23.1 Displaying Positive Selection Signals in Brazilian Admixed Populations: Additional Insights Into Predisposition to Obesity and Related Disorders. PMID:33841501
Bintrafusp Alfa, a Bifunctional Fusion Protein Targeting TGFβ and PD-L1, in Patients with Esophageal Squamous Cell Carcinoma: Results from a Phase 1 Cohort in Asia. PMID:33840050
Reprogramming enriches for somatic cell clones with small-scale mutations in cancer-associated genes. PMID:33831558
The role of a mechanistic host in maintaining arctic rabies variant distributions: Assessment of functional genetic diversity in Alaskan red fox (Vulpes vulpes). PMID:33831031
Genome-wide enhancer maps link risk variants to disease genes. PMID:33828297
Genetic variability in COVID-19-related genes in the Brazilian population. PMID:33824725
Common genetic variants and pathways in diabetes and associated complications and vulnerability of populations with different ethnic origins. PMID:33820928
Genome-Wide Association Identifies Risk Pathways for SAPHO Syndrome. PMID:33816493
Exome-Wide Search for Genes Associated With Central Nervous System Inflammatory Demyelinating Diseases Following CHIKV Infection: The Tip of the Iceberg. PMID:33815474
Tumor genomic, transcriptomic, and immune profiling characterizes differential response to first-line platinum chemotherapy in high grade serous ovarian cancer. PMID:33811746
Detection of loci exhibiting pleiotropic effects on body weight and egg number in female broilers. PMID:33811218
Detection of Rare Germline Variants in the Genomes of Patients with B-Cell Neoplasms. PMID:33809641
Multivariate Analysis Identifies Eight Novel Loci Associated with Meat Productivity Traits in Sheep. PMID:33806625
Combined Genome, Transcriptome and Metabolome Analysis in the Diagnosis of Childhood Cerebellar Ataxia. PMID:33804237
Phenotypic Diversity of Cardiomyopathy Caused by an MYBPC3 Frameshift Mutation in a Korean Family: A Case Report. PMID:33803538
Progressive myoclonus epilepsies-Residual unsolved cases have marked genetic heterogeneity including dolichol-dependent protein glycosylation pathway genes. PMID:33798445
Muscle allele-specific expression QTLs may affect meat quality traits in Bos indicus. PMID:33795794
A novel age-informed approach for genetic association analysis in Alzheimer's disease. PMID:33794991
A domestic cat whole exome sequencing resource for trait discovery. PMID:33785770
Model-based assessment of replicability for genome-wide association meta-analysis. PMID:33785739
Autosomal recessive loci contribute significantly to quantitative variation of male fertility in a dairy cattle population. PMID:33784962
Demographic History, Adaptation, and NRAP Convergent Evolution at Amino Acid Residue 100 in the World Northernmost Cattle from Siberia. PMID:33784744
How array design creates SNP ascertainment bias. PMID:33784304
Comprehensive comparative genomic and microsatellite analysis of SARS, MERS, BAT-SARS, and COVID-19 coronaviruses. PMID:33782990
Gain-of-function variants in SYK cause immune dysregulation and systemic inflammation in humans and mice. PMID:33782605
A common 1.6 mb Y-chromosomal inversion predisposes to subsequent deletions and severe spermatogenic failure in humans. PMID:33781384
Loss of TANGO1 Leads to Absence of Bone Mineralization. PMID:33778321
OncoGEMINI: software for investigating tumor variants from multiple biopsies with integrated cancer annotations. PMID:33771218
Potential Impact of DPYD Variation on Fluoropyrimidine Drug Response in sub-Saharan African Populations. PMID:33767731
Inborn errors of immunity-recent advances in research on the pathogenesis. PMID:33766139
In silico candidate variant and gene identification using inbred mouse strains. PMID:33763305
Genome-wide association study of psychiatric and substance use comorbidity in Mexican individuals. PMID:33762635
Identification of deleterious recessive haplotypes and candidate deleterious recessive mutations in Japanese Black cattle. PMID:33758295
Identification of resistance loci against new pathotypes of Plasmodiophora brassicae in Brassica napus based on genome-wide association mapping. PMID:33758222
R-locus for roaned coat is associated with a tandem duplication in an intronic region of USH2A in dogs and also contributes to Dalmatian spotting. PMID:33755696
A first-generation pediatric cancer dependency map. PMID:33753930
Triple-negative breast lobular carcinoma: a luminal androgen receptor carcinoma with specific ESRRA mutations. PMID:33753865
Variants in ACE2 and TMPRSS2 Genes Are Not Major Determinants of COVID-19 Severity in UK Biobank Subjects. PMID:33752217
Sequencing at lymphoid neoplasm susceptibility loci maps six myeloma risk genes. PMID:33751038
A drought-responsive rice amidohydrolase is the elusive plant guanine deaminase with the potential to modulate the epigenome. PMID:33749847
Remus: A Web Application for Prioritization of Regulatory Regions and Variants in Monogenic Diseases. PMID:33747049
Spectrum of splicing variants in disease genes and the ability of RNA analysis to reduce uncertainty in clinical interpretation. PMID:33743207
Genome-wide association study suggests that variation at the RCOR1 locus is associated with tinnitus in UK Biobank. PMID:33742053
Mutational profiles of marker genes of cervical carcinoma in Bangladeshi patients. PMID:33736612
Global proteomic analysis of extracellular matrix in mouse and human brain highlights relevance to cerebrovascular disease. PMID:33730931
High mutation burden in the checkpoint and micro-RNA processing genes in myelodysplastic syndrome. PMID:33730109
Gene variants of coagulation related proteins that interact with SARS-CoV-2. PMID:33730015
Natural human knockouts and Mendelian disorders: deep phenotyping in Italian isolates. PMID:33727708
Integration of whole genome sequencing into a healthcare setting: high diagnostic rates across multiple clinical entities in 3219 rare disease patients. PMID:33726816
Infertility due to defective sperm flagella caused by an intronic deletion in DNAH17 that perturbs splicing.