R3F05Q last accessed: 2022-11-04

European Variation Archive (EVA)
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:05.943295

eva
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:05.943295

Other names: EVA, European Variation Archive (EVA), eva

The European Variation Archive is an open-access archive that accepts submission of, and provides access to, all types of genetic variation data from all species. All users are able to download any dataset, or query our study catalogue via our variation table. Access to EVA data is also provided by RESTful web services for a variety of applications, such as annotation pipelines.

Webpage:

http://www.ebi.ac.uk/eva/

Licence:

Name: EMBL-EBI Terms of Use
URL: http://www.ebi.ac.uk/about/terms-of-use

Publications:

Publications
More detailed information about this field from each metasource.

Transcriptome and genome sequencing uncovers functional variation in humans
PMID: 24037378
metasource: Fairsharing.org
version: FAIRsharing.org: EVA; European Variation Archive; DOI: https://doi.org/10.25504/FAIRsharing.6824pv; Last edited: Feb. 25, 2020, 3:03 p.m.; Last accessed: Jan 03 2022 7:05 p.m.

The European Bioinformatics Institute in 2016: Data growth and integration
PMID: 26673705
metasource: Fairsharing.org
version: FAIRsharing.org: EVA; European Variation Archive; DOI: https://doi.org/10.25504/FAIRsharing.6824pv; Last edited: Feb. 25, 2020, 3:03 p.m.; Last accessed: Jan 03 2022 7:05 p.m.

http://dx.doi.org/10.6019/tol.eva-w.2016.00001.1
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:05.943295

Transcriptome and genome sequencing uncovers functional variation in humans PubMed citations: 944.

944 articles citing: Transcriptome and genome sequencing uncovers functional variation in humans

Transcriptome variation in human tissues revealed by long-read sequencing. PMID:35922509
Brain Proteome-Wide Association Study Identifies Candidate Genes that Regulate Protein Abundance Associated with Post-Traumatic Stress Disorder. PMID:35893077
Using population-scale transcriptomic and genomic data to map 3' UTR alternative polyadenylation quantitative trait loci. PMID:35874472
Multiplexed Visualization Method to Explore Complete Targeting Regulatory Relationships Among Circadian Genes for Insomnia Treatment. PMID:35844237
Genetic association and single-cell transcriptome analyses reveal distinct features connecting autoimmunity with cancers. PMID:35800769
Genetic dissection of the RNA polymerase II transcription cycle. PMID:35775732
Deciphering associations between three RNA splicing-related genetic variants and lung cancer risk. PMID:35773316
Approximating posteriors with high-dimensional nuisance parameters via integrated rotated Gaussian approximation. PMID:35747172
Meta-Analysis Suggests That Intron Retention Can Affect Quantification of Transposable Elements from RNA-Seq Data. PMID:35741347
Genomic architecture and functional effects of potential human inversion supergenes. PMID:35694745
Single nucleotide polymorphisms in FOXP1 and RORA of the lymphocyte activation-related pathway affect survival of lung cancer patients. PMID:35693292
GATA4 and estrogen receptor alpha bind at SNPs rs9921222 and rs10794639 to regulate AXIN1 expression in osteoblasts. PMID:35678873
Integrating 3D genomic and epigenomic data to enhance target gene discovery and drug repurposing in transcriptome-wide association studies. PMID:35672318
Regulation of HLA class I expression by non-coding gene variations. PMID:35666741
Antagonistic regulatory effects of a single cis-acting expression quantitative trait locus between transcription and translation of the MRPL43 gene. PMID:35659240
Nonsense-mediated RNA decay: an emerging modulator of malignancy. PMID:35624152
Molecular Quantitative Trait Locus Mapping in Human Complex Diseases. PMID:35587224
Multi-Cohort Transcriptomic Subtyping of B-Cell Acute Lymphoblastic Leukemia. PMID:35562965
Implication of genetic variants in primary microRNA processing sites in the risk of multiple sclerosis. PMID:35561450
Reconstruct high-resolution 3D genome structures for diverse cell-types using FLAMINGO. PMID:35551182
TNFRSF13B is a potential contributor to prostate cancer. PMID:35524261
Advances and challenges in quantitative delineation of the genetic architecture of complex traits. PMID:35492964
Powerful and robust inference of complex phenotypes' causal genes with dependent expression quantitative loci by a median-based Mendelian randomization. PMID:35460606
Transcriptome-wide association studies: a view from Mendelian randomization. PMID:35433074
The contribution of evolutionarily volatile promoters to molecular phenotypes and human trait variation. PMID:35379293
Valosin Containing Protein as a Specific Biomarker for Predicting the Development of Acute Coronary Syndrome and Its Complication. PMID:35369356
A comparison of transcriptome analysis methods with reference genome. PMID:35337265
METRO: Multi-ancestry transcriptome-wide association studies for powerful gene-trait association detection. PMID:35334221
Pervasive occurrence of splice-site-creating mutations and their possible involvement in genetic disorders. PMID:35304488
eQTL mapping using allele-specific count data is computationally feasible, powerful, and provides individual-specific estimates of genetic effects. PMID:35286297
Pan-human consensus genome significantly improves the accuracy of RNA-seq analyses. PMID:35256454
Allele-specific expression reveals genes with recurrent cis-regulatory alterations in high-risk neuroblastoma. PMID:35246212
2021 Curt Stern Award: Studying the biology of "junk". PMID:35245473
A guide for the diagnosis of rare and undiagnosed disease: beyond the exome. PMID:35220969
The molecular genetic basis of creativity: a mini review and perspectives. PMID:35217895
REL and BHLHE40 Variants Are Associated with IL-12 and IL-10 Responses and Tuberculosis Risk. PMID:35217585
Towards the Genetic Architecture of Complex Gene Expression Traits: Challenges and Prospects for eQTL Mapping in Humans. PMID:35205280
Meta-imputation of transcriptome from genotypes across multiple datasets by leveraging publicly available summary-level data. PMID:35100255
Tissue-specific multi-omics analysis of atrial fibrillation. PMID:35064145
Bacon: a comprehensive computational benchmarking framework for evaluating targeted chromatin conformation capture-specific methodologies. PMID:35063001
Single-cell sequencing reveals lineage-specific dynamic genetic regulation of gene expression during human cardiomyocyte differentiation. PMID:35061661
Adaptive eQTLs reveal the evolutionary impacts of pleiotropy and tissue-specificity while contributing to health and disease. PMID:35047867
Contribution of 3D genome topological domains to genetic risk of cancers: a genome-wide computational study. PMID:35016721
The activity of human enhancers is modulated by the splicing of their associated lncRNAs. PMID:35015755
Construction and Clinical Translation of Causal Pan-Cancer Gene Score Across Cancer Types. PMID:35003220
Detection of quantitative trait loci from RNA-seq data with or without genotypes using BaseQTL. PMID:34993494
Genetic architecture of microRNA expression and its link to complex diseases in the Japanese population. PMID:34919704
Genetically-predicted prefrontal DRD4 gene expression modulates differentiated brain responses to food cues in adolescent girls and boys. PMID:34916545
Cellular variability of nonsense-mediated mRNA decay. PMID:34893608
Evaluation of Sex-Aware PrediXcan Models for Predicting Gene Expression. PMID:34890163
miR1908-5p regulates energy homeostasis in hepatocyte models. PMID:34887471
Genetic ancestry effects on the response to viral infection are pervasive but cell type specific. PMID:34822289
Genome-wide association mapping of transcriptome variation in Mimulus guttatus indicates differing patterns of selection on cis- versus trans-acting mutations. PMID:34791192
scPower accelerates and optimizes the design of multi-sample single cell transcriptomic studies. PMID:34785648
Tapping into 5-HT3 Receptors to Modify Metabolic and Immune Responses. PMID:34769340
SARS-CoV-2 susceptibility and COVID-19 disease severity are associated with genetic variants affecting gene expression in a variety of tissues. PMID:34762851
Functional genomics data: privacy risk assessment and technological mitigation. PMID:34759381
Advances in integrative African genomics. PMID:34740451
Genetic Variants of CLEC4E and BIRC3 in Damage-Associated Molecular Patterns-Related Pathway Genes Predict Non-Small Cell Lung Cancer Survival. PMID:34692492
Evaluation of Genotype-Based Gene Expression Model Performance: A Cross-Framework and Cross-Dataset Study. PMID:34680927
Benchmarking sequencing methods and tools that facilitate the study of alternative polyadenylation. PMID:34649612
A pleiotropic ATM variant (rs1800057 C>G) is associated with risk of multiple cancers. PMID:34643693
Integrative eQTL-weighted hierarchical Cox models for SNP-set based time-to-event association studies. PMID:34627275
A sex-specific evolutionary interaction between ADCY9 and CETP. PMID:34609279
Predict long-range enhancer regulation based on protein-protein interactions between transcription factors. PMID:34570239
Gender and the Sex Hormone Estradiol Affect Multiple Sclerosis Risk Gene Expression in Epstein-Barr Virus-Infected B Cells. PMID:34566997
Unraveling Risk Genes of COVID-19 by Multi-Omics Integrative Analyses. PMID:34557504
Structural variants are a major source of gene expression differences in humans and often affect multiple nearby genes. PMID:34544830
Genome-wide functional screen of 3'UTR variants uncovers causal variants for human disease and evolution. PMID:34534445
System drift and speciation. PMID:34529267
Local adaptation and archaic introgression shape global diversity at human structural variant loci. PMID:34528508
A compendium of uniformly processed human gene expression and splicing quantitative trait loci. PMID:34493866
Genotypes of informative loci from 1000 Genomes data allude evolution and mixing of human populations. PMID:34493766
Increased risk of severe clinical course of COVID-19 in carriers of HLA-C*04:01. PMID:34490415
Evidence in disease and non-disease contexts that nonsense mutations cause altered splicing via motif disruption. PMID:34469537
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
Transcriptomic Profiling of Dromedary Camels Immunised with a MERS Vaccine Candidate. PMID:34437478
Inferring genes that escape X-Chromosome inactivation reveals important contribution of variable escape genes to sex-biased diseases. PMID:34426515
Nanopore sequencing reveals endogenous NMD-targeted isoforms in human cells. PMID:34389041
The integrative biology of genetic dominance. PMID:34382317
The molecular basis, genetic control and pleiotropic effects of local gene co-expression. PMID:34376650
Creation of a Single Cell RNASeq Meta-Atlas to Define Human Liver Immune Homeostasis. PMID:34335581
Multi-omics approach to precision medicine for immune-mediated diseases. PMID:34332645
Gaining insight into metabolic diseases from human genetic discoveries. PMID:34315631
A transcriptome-wide association study to detect novel genes for volumetric bone mineral density. PMID:34252604
ARHGEF26 enhances Salmonella invasion and inflammation in cells and mice. PMID:34242364
META-ANALYSIS OF DOLPHIN AND HUMAN PERIPHERAL BLOOD MONONUCLEAR CELLS REVEALS INFLAMMATORY SIGNATURES ASSOCIATED WITH EXPOSURE TO HIGH LEVELS OF PERFLUOROALKYL SUBSTANCES. PMID:34222538
Genetic Determinants for Bacterial Osteomyelitis: A Focused Systematic Review of Published Literature. PMID:34220937
Nonsense-mediated decay is highly stable across individuals and tissues. PMID:34216550
Genetic drivers of m6A methylation in human brain, lung, heart and muscle. PMID:34211177
Regulatory SNPs: Altered Transcription Factor Binding Sites Implicated in Complex Traits and Diseases. PMID:34208629
Brain-Specific Gene Expression and Quantitative Traits Association Analysis for Mild Cognitive Impairment. PMID:34201204
Association of genetic variants of FBXO32 and FOXO6 in the FOXO pathway with breast cancer risk. PMID:34197655
Optimizing expression quantitative trait locus mapping workflows for single-cell studies. PMID:34167583
Integrating Transcriptome-Wide Association Study and mRNA Expression Profiling Identifies Novel Genes Associated With Osteonecrosis of the Femoral Head. PMID:34163523
How Machine Learning and Statistical Models Advance Molecular Diagnostics of Rare Disorders Via Analysis of RNA Sequencing Data. PMID:34141720
Cutaneous Melanoma Classification: The Importance of High-Throughput Genomic Technologies. PMID:34123788
Positive natural selection of N6-methyladenosine on the RNAs of processed pseudogenes. PMID:34120636
Replicate sequencing libraries are important for quantification of allelic imbalance. PMID:34099647
Genetic variants of DOCK2, EPHB1 and VAV2 in the natural killer cell-related pathway are associated with non-small cell lung cancer survival. PMID:34094683
Positive Selection in Gene Regulatory Factors Suggests Adaptive Pleiotropic Changes During Human Evolution. PMID:34079582
Genetic variants of CHEK1, PRIM2 and CDK6 in the mitotic phase-related pathway are associated with nonsmall cell lung cancer survival. PMID:34058013
Diverse Molecular Mechanisms Contribute to Differential Expression of Human Duplicated Genes. PMID:34009325
Targeted RNA-seq improves efficiency, resolution, and accuracy of allele specific expression for human term placentas. PMID:34009305
MRPC: An R Package for Inference of Causal Graphs. PMID:33995486
Functional dynamic genetic effects on gene regulation are specific to particular cell types and environmental conditions. PMID:33988505
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
Meta-Analyses of Splicing and Expression Quantitative Trait Loci Identified Susceptibility Genes of Glioma. PMID:33936159
Variant to Gene Mapping to Discover New Targets for Immune Tolerance. PMID:33936046
The impact of cell type and context-dependent regulatory variants on human immune traits. PMID:33926512
Virus-derived variation in diverse human genomes. PMID:33901175
Genome-wide characterization of human minisatellite VNTRs: population-specific alleles and gene expression differences. PMID:33849068
Association of genetic variants of TMEM135 and PEX5 in the peroxisome pathway with cutaneous melanoma-specific survival. PMID:33842617
Homozygous GDF2 nonsense mutations result in a loss of circulating BMP9 and BMP10 and are associated with either PAH or an "HHT-like" syndrome in children. PMID:33834622
Variable number tandem repeats mediate the expression of proximal genes. PMID:33824302
A PDCD1 Role in the Genetic Predisposition to NAFLD-HCC? PMID:33808740
The Interaction of Human and Epstein-Barr Virus miRNAs with Multiple Sclerosis Risk Loci. PMID:33805769
Allelic Expression Imbalance Analysis Identified YAP1 Amplification in p53- Dependent Osteosarcoma. PMID:33803512
A Dual Systems Genetics Approach Identifies Common Genes, Networks, and Pathways for Type 1 and 2 Diabetes in Human Islets. PMID:33777101
Epigenetic Element-Based Transcriptome-Wide Association Study Identifies Novel Genes for Bipolar Disorder. PMID:33772305
Ethnically biased microsatellites contribute to differential gene expression and glutathione metabolism in Africans and Europeans. PMID:33765058
A single-cell atlas of the healthy breast tissues reveals clinically relevant clusters of breast epithelial cells. PMID:33763657
Genetics of osteoarthritis. PMID:33722698
Genetic association and causal inference converge on hyperglycaemia as a modifiable factor to improve lung function. PMID:33720009
Global discovery of lupus genetic risk variant allelic enhancer activity. PMID:33712590
Identification of rare and common regulatory variants in pluripotent cells using population-scale transcriptomics. PMID:33664507
The ZNF76 rs10947540 polymorphism associated with systemic lupus erythematosus risk in Chinese populations. PMID:33664275
Potentially functional variants of ERAP1, PSMF1 and NCF2 in the MHC-I-related pathway predict non-small cell lung cancer survival. PMID:33651148
Chromatin information content landscapes inform transcription factor and DNA interactions. PMID:33637709
Haplotype-resolved diverse human genomes and integrated analysis of structural variation. PMID:33632895
Applications of Community Detection Algorithms to Large Biological Datasets. PMID:33606252
Genome-wide meta-analysis, fine-mapping and integrative prioritization implicate new Alzheimer's disease risk genes. PMID:33589840
A Review of Statistical Methods for Identifying Trait-Relevant Tissues and Cell Types. PMID:33584792
OpenContami: A web-based application for detecting microbial contaminants in next-generation sequencing data. PMID:33576798
Comparative analysis of the transcriptomes of two rice subspecies during domestication. PMID:33574456
Genetic control of the human brain proteome. PMID:33571421
A versatile workflow to integrate RNA-seq genomic and transcriptomic data into mechanistic models of signaling pathways. PMID:33571195
Comparative transcriptomic analysis revealed novel potential therapeutic targets of traditional Chinese medicine (Pinggan-Qianyang decoction) on vascular remodeling in spontaneously hypertensive rats. PMID:33568194
Role of Transposable Elements in Gene Regulation in the Human Genome. PMID:33557056
Genomic Variation, Evolvability, and the Paradox of Mental Illness. PMID:33551865
Identification and analysis of splicing quantitative trait loci across multiple tissues in the human genome. PMID:33526779
IsoMiRmap-fast, deterministic, and exhaustive mining of isomiRs from short RNA-seq datasets. PMID:33471076
Detection of aberrant gene expression events in RNA sequencing data. PMID:33462443
Allele-specific alternative splicing and its functional genetic variants in human tissues. PMID:33452016
On transformative adaptive activation functions in neural networks for gene expression inference. PMID:33444316
Multi-trait transcriptome-wide association studies with probabilistic Mendelian randomization. PMID:33434493
New novel non-MHC genes were identified for cervical cancer with an integrative analysis approach of transcriptome-wide association study. PMID:33403041
Potentially functional variants of HBEGF and ITPR3 in GnRH signaling pathway genes predict survival of non-small cell lung cancer patients. PMID:33400994
Approaches to treat pulmonary arterial hypertension by targeting BMPR2: from cell membrane to nucleus. PMID:33399862
Allele-specific expression: applications in cancer and technical considerations. PMID:33383480
Systems biology in cardiovascular disease: a multiomics approach. PMID:33340009
Data structures based on k-mers for querying large collections of sequencing data sets. PMID:33328168
Approaching Shared Pathophysiology in Immune-Mediated Diseases through Functional Genomics. PMID:33317201
Probabilistic colocalization of genetic variants from complex and molecular traits: promise and limitations. PMID:33308443
Molecular and evolutionary processes generating variation in gene expression. PMID:33268840
HLA-A29 and Birdshot Uveitis: Further Down the Rabbit Hole. PMID:33262772
Single cell profiling of capillary blood enables out of clinic human immunity studies. PMID:33239690
Qtlizer: comprehensive QTL annotation of GWAS results. PMID:33235230
Associations between genetic variants of KIF5B, FMN1, and MGAT3 in the cadherin pathway and pancreatic cancer risk. PMID:33200553
Insertion variants missing in the human reference genome are widespread among human populations. PMID:33187521
Data Sanitization to Reduce Private Information Leakage from Functional Genomics. PMID:33186529
Genome-Wide Association Study of Metamizole-Induced Agranulocytosis in European Populations. PMID:33138277
Function of multiple sclerosis-protective HLA class I alleles revealed by genome-wide protein-quantitative trait loci mapping of interferon signalling. PMID:33104735
Association of Uncommon, Noncoding Variants in the APOE Region With Risk of Alzheimer Disease in Adults of European Ancestry. PMID:33090224
A unified framework for joint-tissue transcriptome-wide association and Mendelian randomization analysis. PMID:33020666
Summary-data-based Mendelian randomization prioritizes potential druggable targets for multiple sclerosis. PMID:33005893
Genetic variant effects on gene expression in human pancreatic islets and their implications for T2D. PMID:32999275
A splice acceptor variant in HLA-DRA affects the conformation and cellular localization of the class II DR alpha-chain. PMID:32986852
Fine-mapping and QTL tissue-sharing information improves the reliability of causal gene identification. PMID:32964524
Pleiotropic genomic variants at 17q21.31 associated with bone mineral density and body fat mass: a bivariate genome-wide association analysis. PMID:32963334
Bayesian Genome-wide TWAS Method to Leverage both cis- and trans-eQTL Information through Summary Statistics. PMID:32961112
Improved haplotype inference by exploiting long-range linking and allelic imbalance in RNA-seq datasets. PMID:32938926
The GTEx Consortium atlas of genetic regulatory effects across human tissues. PMID:32913098
Where Are the Disease-Associated eQTLs? PMID:32912663
A polyclonal allelic expression assay for detecting regulatory effects of transcript variants. PMID:32912286
Genetic variants of BIRC3 and NRG1 in the NLRP3 inflammasome pathway are associated with non-small cell lung cancer survival. PMID:32905523
Novel genetic variants of SYK and ITGA1 related lymphangiogenesis signaling pathway predict non-small cell lung cancer survival. PMID:32905494
On the expanding roles of tRNA fragments in modulating cell behavior. PMID:32890397
The Polygenic and Monogenic Basis of Blood Traits and Diseases. PMID:32888494
In silico identification of pseudo-exon activation events in personal genome and transcriptome data. PMID:32865117
A New ERAP2/Iso3 Isoform Expression Is Triggered by Different Microbial Stimuli in Human Cells. Could It Play a Role in the Modulation of SARS-CoV-2 Infection? PMID:32847031
Gene Expression and RNA Splicing Imputation Identifies Novel Candidate Genes Associated with Osteoporosis. PMID:32827035
On the cross-population generalizability of gene expression prediction models. PMID:32797036
Efficient and effective control of confounding in eQTL mapping studies through joint differential expression and Mendelian randomization analyses. PMID:32790868
Genetic variants modulate gene expression statin response in human lymphoblastoid cell lines. PMID:32787775
Detecting Allele-Specific Alternative Splicing from Population-Scale RNA-Seq Data. PMID:32781045
Using functional genomics to advance the understanding of psoriatic arthritis. PMID:32778885
Variants in SNAI1, AMDHD1 and CUBN in vitamin D pathway genes are associated with breast cancer risk: a large-scale analysis of 14 GWASs in the DRIVE study. PMID:32775008
Associations of novel variants in PIK3C3, INSR and MAP3K4 of the ATM pathway genes with pancreatic cancer risk. PMID:32775006
The regulatory genome constrains protein sequence evolution: implications for the search for disease-associated genes. PMID:32765967
Testing and controlling for horizontal pleiotropy with probabilistic Mendelian randomization in transcriptome-wide association studies. PMID:32737316
Targeting translational read-through of premature termination mutations in BMPR2 with PTC124 for pulmonary arterial hypertension. PMID:32733669
Functional fine-mapping of noncoding risk variants in amyotrophic lateral sclerosis utilizing convolutional neural network. PMID:32732921
Population variation in miRNAs and isomiRs and their impact on human immunity to infection. PMID:32731901
FANCY: fast estimation of privacy risk in functional genomics data. PMID:32726397
Neanderthal introgression reintroduced functional ancestral alleles lost in Eurasian populations. PMID:32719451
Polymorphic mobile element insertions contribute to gene expression and alternative splicing in human tissues. PMID:32718348
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
Novel genetic variants in genes of the Fc gamma receptor-mediated phagocytosis pathway predict non-small cell lung cancer survival. PMID:32676321
Genetic variation near CXCL12 is associated with susceptibility to HIV-related non-Hodgkin lymphoma. PMID:32675224
Natural Selection on Exonic SNPs Shapes Allelic Expression Imbalance (AEI) Adaptability in Lung Cancer Progression. PMID:32670357
Terminus enables the discovery of data-driven, robust transcript groups from RNA-seq data. PMID:32657377
Regulatory Nucleotide Sequence Signals for Expression of the Genes Encoding Ribosomal Proteins. PMID:32655613
Identification of genetic variants controlling RNA editing and their effect on RNA structure stabilization. PMID:32651550
Novel genetic variants of KIR3DL2 and PVR involved in immunoregulatory interactions are associated with non-small cell lung cancer survival. PMID:32642289
Maternal effects shape the alternative splicing of parental alleles in reciprocal cross hybrids of Megalobrama amblycephala × Culter alburnus. PMID:32616060
Age-of-onset information helps identify 76 genetic variants associated with allergic disease. PMID:32603359
Genetic analyses support the contribution of mRNA N6-methyladenosine (m6A) modification to human disease heritability. PMID:32601472
Predicted DRD4 prefrontal gene expression moderates snack intake and stress perception in response to the environment in adolescents. PMID:32589693
Alternative polyadenylation mediates genetic regulation of gene expression. PMID:32584258
Capturing Differential Allele-Level Expression and Genotypes of All Classical HLA Loci and Haplotypes by a New Capture RNA-Seq Method. PMID:32547543
A framework for integrating directed and undirected annotations to build explanatory models of cis-eQTL data. PMID:32516306
Molecular mechanisms of coronary disease revealed using quantitative trait loci for TCF21 binding, chromatin accessibility, and chromosomal looping. PMID:32513244
Novel Variants of ELP2 and PIAS1 in the Interferon Gamma Signaling Pathway Are Associated with Non-Small Cell Lung Cancer Survival. PMID:32493705
Expression Quantitative Trait Loci (eQTL) Mapping in Korean Patients With Crohn's Disease and Identification of Potential Causal Genes Through Integration With Disease Associations. PMID:32477412
From GWAS to Function: Using Functional Genomics to Identify the Mechanisms Underlying Complex Diseases. PMID:32477401
Integration of transcriptome-wide association study and messenger RNA expression profile to identify genes associated with osteoarthritis. PMID:32435465
Determining the impact of uncharacterized inversions in the human genome by droplet digital PCR. PMID:32424072
Twelve New Genomic Loci Associated With Bone Mineral Density. PMID:32390946
Mapping DNA interaction landscapes in psoriasis susceptibility loci highlights KLF4 as a target gene in 9q31. PMID:32366252
Population-Specific Genetic and Expression Differentiation in Europeans. PMID:32365201
Optimized Whole Genome Association Scanning for Discovery of HLA Class I-Restricted Minor Histocompatibility Antigens. PMID:32362897
On Negative Heritability and Negative Estimates of Heritability. PMID:32291292
Ribosomal RNA fragmentation into short RNAs (rRFs) is modulated in a sex- and population of origin-specific manner. PMID:32279660
A Genome-Wide Association Study Identifies Two Novel Susceptible Regions for Squamous Cell Carcinoma of the Head and Neck. PMID:32276964
APOB Genotypes and CDH13 Haplotypes in the Cholesterol-Related Pathway Genes Predict Non-Small Cell Lung Cancer Survival. PMID:32238407
Genetic variants in PDSS1 and SLC16A6 of the ketone body metabolic pathway predict cutaneous melanoma-specific survival. PMID:32232919
Analysis of mitochondrial m1A/G RNA modification reveals links to nuclear genetic variants and associated disease processes. PMID:32221480
Genetic Architecture of Gene Expression in European and African Americans: An eQTL Mapping Study in GENOA. PMID:32220292
Pervasive Differential Splicing in Marek's Disease Virus can Discriminate CVI-988 Vaccine Strain from RB-1B Very Virulent Strain in Chicken Embryonic Fibroblasts. PMID:32197378
Investigation of prediction accuracy and the impact of sample size, ancestry, and tissue in transcriptome-wide association studies. PMID:32190932
MiR&moRe2: A Bioinformatics Tool to Characterize microRNAs and microRNA-Offset RNAs from Small RNA-Seq Data. PMID:32143373
Association of microRNA biosynthesis genes XPO5 and RAN polymorphisms with cancer susceptibility: Bayesian hierarchical meta-analysis. PMID:32127945
Functional effects of variation in transcription factor binding highlight long-range gene regulation by epromoters. PMID:32112106
Regulatory sites for splicing in human basal ganglia are enriched for disease-relevant information. PMID:32098967
neoANT-HILL: an integrated tool for identification of potential neoantigens. PMID:32087727
Contribution of unfixed transposable element insertions to human regulatory variation. PMID:32075552
Potentially functional genetic variants in PLIN2, SULT2A1 and UGT1A9 genes of the ketone pathway and survival of nonsmall cell lung cancer. PMID:32072637
TypeTE: a tool to genotype mobile element insertions from whole genome resequencing data. PMID:32067044
Tumor suppressor genes and allele-specific expression: mechanisms and significance. PMID:32064050
The Progress of Multi-Omics Technologies: Determining Function in Lactic Acid Bacteria Using a Systems Level Approach. PMID:32047482
Alternative polyadenylation drives oncogenic gene expression in pancreatic ductal adenocarcinoma. PMID:32029502
Tensor decomposition of stimulated monocyte and macrophage gene expression profiles identifies neurodegenerative disease-specific trans-eQTLs. PMID:32012164
HLA-H: Transcriptional Activity and HLA-E Mobilization. PMID:32010122
Allele-Specific QTL Fine Mapping with PLASMA. PMID:32004450
A CRISPR/Cas9 genome editing pipeline in the EndoC-βH1 cell line to study genes implicated in beta cell function. PMID:31976379
A curated benchmark of enhancer-gene interactions for evaluating enhancer-target gene prediction methods. PMID:31969180
Using regulatory variants to detect gene-gene interactions identifies networks of genes linked to cell immortalisation. PMID:31953380
A practical view of fine-mapping and gene prioritization in the post-genome-wide association era. PMID:31937202
The interaction of Multiple Sclerosis risk loci with Epstein-Barr virus phenotypes implicates the virus in pathogenesis. PMID:31932685
High-Dimensional Bayesian Network Inference From Systems Genetics Data Using Genetic Node Ordering. PMID:31921278
Single-Cell Expression Variability Implies Cell Function. PMID:31861624
Transcriptome assembly from long-read RNA-seq alignments with StringTie2. PMID:31842956
KRAB-Zinc Finger Protein ZNF268a Deficiency Attenuates the Virus-Induced Pro-Inflammatory Response by Preventing IKK Complex Assembly. PMID:31835635
Using mechanistic models for the clinical interpretation of complex genomic variation. PMID:31831811
Brain Banks Spur New Frontiers in Neuropsychiatric Research and Strategies for Analysis and Validation. PMID:31811942
Differences in lipidome and metabolome organization of prefrontal cortex among human populations. PMID:31797944
Detecting, Categorizing, and Correcting Coverage Anomalies of RNA-Seq Quantification. PMID:31786209
RNA-Seq Perspectives to Improve Clinical Diagnosis. PMID:31781178
Gene Expression Value Prediction Based on XGBoost Algorithm. PMID:31781160
Common DNA sequence variation influences 3-dimensional conformation of the human genome. PMID:31779666
Impact of polymorphic transposable elements on transcription in lymphoblastoid cell lines from public data. PMID:31757210
Structural variation in the sequencing era. PMID:31729472
Novel genetic variants in HDAC2 and PPARGC1A of the CREB-binding protein pathway predict survival of non-small-cell lung cancer. PMID:31713888
Quantile regression for challenging cases of eQTL mapping. PMID:31688892
Effectiveness of integrated interpretation of exome and corresponding transcriptome data for detecting splicing variants of genes associated with autosomal recessive disorders. PMID:31687339
The impact of short tandem repeat variation on gene expression. PMID:31676866
GWAS for systemic sclerosis identifies multiple risk loci and highlights fibrotic and vasculopathy pathways. PMID:31672989
CoMM: A Collaborative Mixed Model That Integrates GWAS and eQTL Data Sets to Investigate the Genetic Architecture of Complex Traits. PMID:31662603
PGG.SNV: understanding the evolutionary and medical implications of human single nucleotide variations in diverse populations. PMID:31640808
Blood-based systems biology biomarkers for next-generation clinical trials in Alzheimer's disease . PMID:31636492
Genetic Control of Expression and Splicing in Developing Human Brain Informs Disease Mechanisms. PMID:31626773
Novel genetic variants in KIF16B and NEDD4L in the endosome-related genes are associated with nonsmall cell lung cancer survival. PMID:31618441
LnCeVar: a comprehensive database of genomic variations that disturb ceRNA network regulation. PMID:31617563
Genetic regulatory variation in populations informs transcriptome analysis in rare disease. PMID:31601707
Single cell transcriptome in aneuploidies reveals mechanisms of gene dosage imbalance. PMID:31582743
eQTL mapping of rare variant associations using RNA-seq data: An evaluation of approaches. PMID:31581212
Allele-specific NKX2-5 binding underlies multiple genetic associations with human electrocardiographic traits. PMID:31570892
Functional interpretation of genetic variants using deep learning predicts impact on chromatin accessibility and histone modification. PMID:31544924
Evolutionary and functional impact of common polymorphic inversions in the human genome. PMID:31530810
Dose and time effects of solar-simulated ultraviolet radiation on the in vivo human skin transcriptome. PMID:31529490
Identification of human genetic variants controlling circular RNA expression. PMID:31519742
A-to-I RNA editing contributes to the persistence of predicted damaging mutations in populations. PMID:31515285
Heteroplasmy concordance between mitochondrial DNA and RNA. PMID:31506522
GeneFishing to reconstruct context specific portraits of biological processes. PMID:31484776
Transcriptome Analysis of the Effects of Fasting Caecotrophy on Hepatic Lipid Metabolism in New Zealand Rabbits. PMID:31484452
Ultrarare variants drive substantial cis heritability of human gene expression. PMID:31477931
Variants in the fetal genome near pro-inflammatory cytokine genes on 2q13 associate with gestational duration. PMID:31477735
The Length of the Expressed 3' UTR Is an Intermediate Molecular Phenotype Linking Genetic Variants to Complex Diseases. PMID:31475030
Genetic variants in glutamine metabolic pathway genes predict cutaneous melanoma-specific survival. PMID:31435991
Fc Gamma Receptor Polymorphisms Modulated the Vaccine Effect on HIV-1 Risk in the HVTN 505 HIV Vaccine Trial. PMID:31434737
High-efficiency genomic editing in Epstein-Barr virus-transformed lymphoblastoid B cells using a single-stranded donor oligonucleotide strategy. PMID:31428700
Transcriptome variation in human populations and its potential application in forensics. PMID:31401728
Prospective Application of Activity-Based Proteomic Profiling in Vision Research-Potential Unique Insights into Ocular Protease Biology and Pathology. PMID:31398819
Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. PMID:31375807
Nonparametric expression analysis using inferential replicate counts. PMID:31372651
Fast and covariate-adaptive method amplifies detection power in large-scale multiple hypothesis testing. PMID:31366926
Spatial chromatin architecture alteration by structural variations in human genomes at the population scale. PMID:31362752
A Combined Transcriptomic and Genomic Analysis Identifies a Gene Signature Associated With the Response to Anti-TNF Therapy in Rheumatoid Arthritis. PMID:31312201
Single-cell RNA sequencing of a European and an African lymphoblastoid cell line. PMID:31273215
Cloudy with a Chance of Insights: Context Dependent Gene Regulation and Implications for Evolutionary Studies. PMID:31261769
TIGAR: An Improved Bayesian Tool for Transcriptomic Data Imputation Enhances Gene Mapping of Complex Traits. PMID:31230719
Genetic Variation in Human Gene Regulatory Factors Uncovers Regulatory Roles in Local Adaptation and Disease. PMID:31228201
A Deep Neural Network for Predicting and Engineering Alternative Polyadenylation. PMID:31178116
arcasHLA: high-resolution HLA typing from RNAseq. PMID:31173059
Learning Causal Biological Networks With the Principle of Mendelian Randomization. PMID:31164902
Mechanistic Characterization of RASGRP1 Variants Identifies an hnRNP-K-Regulated Transcriptional Enhancer Contributing to SLE Susceptibility. PMID:31164884
Differential analysis of combinatorial protein complexes with CompleXChange. PMID:31159772
Comprehensive Multiple eQTL Detection and Its Application to GWAS Interpretation. PMID:31123039
Model-based understanding of single-cell CRISPR screening. PMID:31110232
Detection of circular RNA expression and related quantitative trait loci in the human dorsolateral prefrontal cortex. PMID:31109370
Interferon inducible X-linked gene CXorf21 may contribute to sexual dimorphism in Systemic Lupus Erythematosus. PMID:31092820
Quantitative proteomic analyses of CD4+ and CD8+ T cells reveal differentially expressed proteins in multiple sclerosis patients and healthy controls. PMID:31080378
Integrative analysis of transcriptome-wide association study data and mRNA expression profiles identified candidate genes and pathways associated with atrial fibrillation. PMID:31065785
Genome-Wide Investigation and Functional Analysis of Sus scrofa RNA Editing Sites across Eleven Tissues. PMID:31052161
Sex-Interacting mRNA- and miRNA-eQTLs and Their Implications in Gene Expression Regulation and Disease. PMID:31024623
Amino acid signatures of HLA Class-I and II molecules are strongly associated with SLE susceptibility and autoantibody production in Eastern Asians. PMID:31022184
Expression estimation and eQTL mapping for HLA genes with a personalized pipeline. PMID:31009447
Accuracy of Gene Expression Prediction From Genotype Data With PrediXcan Varies Across and Within Continental Populations. PMID:31001318
BRB-seq: ultra-affordable high-throughput transcriptomics enabled by bulk RNA barcoding and sequencing. PMID:30999927
Genetic variants in the liver kinase B1-AMP-activated protein kinase pathway genes and pancreatic cancer risk. PMID:30997723
Dual TGFβ/BMP Pathway Inhibition Enables Expansion and Characterization of Multiple Epithelial Cell Types of the Normal and Cancerous Breast. PMID:30992305
Clinical utility of RNA sequencing to resolve unusual GNE myopathy with a novel promoter deletion. PMID:30990900
Associations of variants In the hexokinase 1 and interleukin 18 receptor regions with oxyhemoglobin saturation during sleep. PMID:30990817
Potentially functional genetic variants in the TNF/TNFR signaling pathway genes predict survival of patients with non-small cell lung cancer in the PLCO cancer screening trial. PMID:30989732
Genome-wide association and transcriptome studies identify target genes and risk loci for breast cancer. PMID:30988301
Bovine Derived in vitro Cultures Generate Heterogeneous Populations of Antigen Presenting Cells. PMID:30984187
Defining the genetic and evolutionary architecture of alternative splicing in response to infection. PMID:30975994
Three novel genetic variants in NRF2 signaling pathway genes are associated with pancreatic cancer risk. PMID:30972876
Bayesian Inference for Mixed Model-Based Genome-Wide Analysis of Expression Quantitative Trait Loci by Gibbs Sampling. PMID:30967893
An integrative U method for joint analysis of multi-level omic data. PMID:30967125
Transcriptomic analysis of fetal membranes reveals pathways involved in preterm birth. PMID:30935390
Genetic Architectures of Childhood- and Adult-Onset Asthma Are Partly Distinct. PMID:30929738
Mapping causal pathways from genetics to neuropsychiatric disorders using genome-wide imaging genetics: Current status and future directions. PMID:30864184
The metabolic network coherence of human transcriptomes is associated with genetic variation at the cadherin 18 locus. PMID:30852652
Integration of methylation QTL and enhancer-target gene maps with schizophrenia GWAS summary results identifies novel genes. PMID:30850848
Identifying Multi-Omics Causers and Causal Pathways for Complex Traits. PMID:30847004
Predictability of human differential gene expression. PMID:30846554
A statistical framework for cross-tissue transcriptome-wide association analysis. PMID:30804563
Allele specific chromatin signals, 3D interactions, and motif predictions for immune and B cell related diseases. PMID:30804403
Potential functional variants in SMC2 and TP53 in the AURORA pathway genes and risk of pancreatic cancer. PMID:30794721
Nuclear genetic regulation of the human mitochondrial transcriptome. PMID:30775970
Genetic variants in ELOVL2 and HSD17B12 predict melanoma-specific survival. PMID:30734280
A genetic variant associated with multiple sclerosis inversely affects the expression of CD58 and microRNA-548ac from the same gene. PMID:30730892
Adjusting for Principal Components of Molecular Phenotypes Induces Replicating False Positives. PMID:30692194
Intronic CNVs and gene expression variation in human populations. PMID:30677042
A statistical method for joint estimation of cis-eQTLs and parent-of-origin effects under family trio design. PMID:30666629
Characterizing the Major Structural Variant Alleles of the Human Genome. PMID:30661756
Genetic variants in RUNX3, AMD1 and MSRA in the methionine metabolic pathway and survival in nonsmall cell lung cancer patients. PMID:30650190
Fine-mapping cis-regulatory variants in diverse human populations. PMID:30650056
Functionally oriented analysis of cardiometabolic traits in a trans-ethnic sample. PMID:30624610
Genetic effects on promoter usage are highly context-specific and contribute to complex traits. PMID:30618377
Recent advances in functional genome analysis. PMID:30613379
Integration of DNA methylation patterns and genetic variation in human pediatric tissues help inform EWAS design and interpretation. PMID:30602389
Genetic variants in the calcium signaling pathway genes are associated with cutaneous melanoma-specific survival. PMID:30596980
Cell Specificity of Human Regulatory Annotations and Their Genetic Effects on Gene Expression. PMID:30593493
Constitutively Higher Level of GSTT2 in Esophageal Tissues From African Americans Protects Cells Against DNA Damage. PMID:30578782
Expression reflects population structure. PMID:30566439
Association of Genetic Variation at AQP4 Locus with Vascular Depression. PMID:30563176
Exploring drivers of gene expression in the Cancer Genome Atlas. PMID:30561551
Identification of ANLN as a new likely pathogenic gene of branchio-otic syndrome in a three-generation Chinese family. PMID:30548429
Gene expression models based on transcription factor binding events confer insight into functional cis-regulatory variants. PMID:30541050
Genetic ancestry, admixture and health determinants in Latin America. PMID:30537949
Genome-wide study of hair colour in UK Biobank explains most of the SNP heritability. PMID:30531825
Molecular Relationships between Bronchial Asthma and Hypertension as Comorbid Diseases. PMID:30530896
A likelihood-based approach to transcriptome association analysis. PMID:30515859
Inferring Compensatory Evolution of cis- and trans-Regulatory Variation. PMID:30503570
OUTRIDER: A Statistical Method for Detecting Aberrantly Expressed Genes in RNA Sequencing Data. PMID:30503520
High-resolution genetic mapping of putative causal interactions between regions of open chromatin. PMID:30478436
Genetic analysis of isoform usage in the human anti-viral response reveals influenza-specific regulation of ERAP2 transcripts under balancing selection. PMID:30446528
Novel insights into the genetic basis of buffalo reproductive performance. PMID:30419816
Alu insertion variants alter mRNA splicing. PMID:30418605
Admixture mapping identifies novel loci for obstructive sleep apnea in Hispanic/Latino Americans. PMID:30403821
Integrative approach identifies corticosteroid response variant in diverse populations with asthma. PMID:30367910
Genomic and Phenomic Research in the 21st Century. PMID:30342790
Discovering in vivo cytokine-eQTL interactions from a lupus clinical trial. PMID:30340504
Cell-type-specific eQTL of primary melanocytes facilitates identification of melanoma susceptibility genes. PMID:30333196
Genetic Architecture of Adaptive Immune System Identifies Key Immune Regulators. PMID:30332657
Uncovering association networks through an eQTL analysis involving human miRNAs and lincRNAs. PMID:30301969
Genetic and mechanistic basis for APOBEC3H alternative splicing, retrovirus restriction, and counteraction by HIV-1 protease. PMID:30297863
Profiling the B/T cell receptor repertoire of lymphocyte derived cell lines. PMID:30285677
Genome-wide association study of developmental dysplasia of the hip identifies an association with GDF5. PMID:30273415
Potentially functional genetic variants in the complement-related immunity gene-set are associated with non-small cell lung cancer survival. PMID:30259978
Evidence GDF15 Plays a Role in Familial and Recurrent Hyperemesis Gravidarum. PMID:30258246
Personalised Medicine: The Odyssey from Hope to Practice. PMID:30248964
Genome-wide association studies and CRISPR/Cas9-mediated gene editing identify regulatory variants influencing eyebrow thickness in humans. PMID:30248107
Exome sequencing study in patients with multiple sclerosis reveals variants associated with disease course. PMID:30217166
Environmental influences on RNA processing: Biochemical, molecular and genetic regulators of cellular response. PMID:30216698
Functionally distinct ERAP1 and ERAP2 are a hallmark of HLA-A29-(Birdshot) Uveitis. PMID:30215709
Genome-wide association meta-analysis of coronary artery disease and periodontitis reveals a novel shared risk locus. PMID:30209331
Genome-Wide Expression Quantitative Trait Loci Analysis Using Mixed Models. PMID:30186313
Insights Into de novo Mutation Variation in Lithuanian Exome. PMID:30154829
Identification of expression quantitative trait loci associated with schizophrenia and affective disorders in normal brain tissue. PMID:30142156
The landscape of the A-to-I RNA editome from 462 human genomes. PMID:30104667
iMapSplice: Alleviating reference bias through personalized RNA-seq alignment. PMID:30096157
Genetic architecture of gene expression traits across diverse populations. PMID:30096133
An Atlas of Genetic Variation Linking Pathogen-Induced Cellular Traits to Human Disease. PMID:30092202
Transcriptomic population markers for human population discrimination. PMID:30086702
The Oyster River Protocol: a multi-assembler and kmer approach for de novo transcriptome assembly. PMID:30083482
De novo human genome assemblies reveal spectrum of alternative haplotypes in diverse populations. PMID:30072691
Enhancer histone-QTLs are enriched on autoimmune risk haplotypes and influence gene expression within chromatin networks. PMID:30046115
Identifying Genes Whose Mutant Transcripts Cause Dominant Disease Traits by Potential Gain-of-Function Alleles. PMID:30032986
Nuclear-Mitochondrial interactions influence susceptibility to HIV-associated neurocognitive impairment. PMID:30026132
Heritability estimation and differential analysis of count data with generalized linear mixed models in genomic sequencing studies. PMID:30020412
Genetics of trans-regulatory variation in gene expression. PMID:30014850
Normal Breast-Derived Epithelial Cells with Luminal and Intrinsic Subtype-Enriched Gene Expression Document Interindividual Differences in Their Differentiation Cascade. PMID:29997232
Insights into clonal haematopoiesis from 8,342 mosaic chromosomal alterations. PMID:29995854
An allelic variant in the intergenic region between ERAP1 and ERAP2 correlates with an inverse expression of the two genes. PMID:29991817
Genetic determinants of co-accessible chromatin regions in activated T cells across humans. PMID:29988122
Splicing heterogeneity: separating signal from noise. PMID:29986741
Comparison of methods for transcriptome imputation through application to two common complex diseases. PMID:29976976
Genomic approaches for the elucidation of genes and gene networks underlying cardiovascular traits. PMID:29934864
Analysis of sensitive information leakage in functional genomics signal profiles through genomic deletions. PMID:29934598
Grimon: graphical interface to visualize multi-omics networks. PMID:29931190
Robust imaging and gene delivery to study human lymphoblastoid cell lines. PMID:29925960
Using Gene Expression to Annotate Cardiovascular GWAS Loci. PMID:29922679
Novel genetic associations for blood pressure identified via gene-alcohol interaction in up to 570K individuals across multiple ancestries. PMID:29912962
Genomic atlas of the human plasma proteome. PMID:29875488
Intracellular Regulome Variability Along the Organ of Corti: Evidence, Approaches, Challenges, and Perspective. PMID:29868110
Genetic Modifiers of the Breast Tumor Microenvironment. PMID:29860987
Base-specific mutational intolerance near splice sites clarifies the role of nonessential splice nucleotides. PMID:29858273
Analysis of Association of Genetic Markers in the LUZP2 and FBXO40 Genes with the Normal Variability in Cognitive Performance in the Elderly. PMID:29850221
Genome-wide association study meta-analysis identifies five new loci for systemic lupus erythematosus. PMID:29848360
Landscape of Conditional eQTL in Dorsolateral Prefrontal Cortex and Co-localization with Schizophrenia GWAS. PMID:29805045
Identification of rare de novo epigenetic variations in congenital disorders. PMID:29802345
Integrative Analysis Identifies Genetic Variants Associated With Autoimmune Diseases Affecting Putative MicroRNA Binding Sites. PMID:29755505
Exploring the phenotypic consequences of tissue specific gene expression variation inferred from GWAS summary statistics. PMID:29739930
The fractured landscape of RNA-seq alignment: the default in our STARs. PMID:29718481
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
Genome-wide association analyses identify 44 risk variants and refine the genetic architecture of major depression. PMID:29700475
Human CCL3L1 copy number variation, gene expression, and the role of the CCL3L1-CCR5 axis in lung function. PMID:29682616
Analysis of 182 cerebral palsy transcriptomes points to dysregulation of trophic signalling pathways and overlap with autism. PMID:29681622
Eleven loci with new reproducible genetic associations with allergic disease risk. PMID:29679657
Complement receptor 1 gene (CR1) intragenic duplication and risk of Alzheimer's disease. PMID:29675612
Integrative Bioinformatics Approaches for Identification of Drug Targets in Hypertension. PMID:29670885
Accurate identification of RNA editing sites from primitive sequence with deep neural networks. PMID:29662087
Interactions between genetic variation and cellular environment in skeletal muscle gene expression. PMID:29659628
Single nucleotide variant counts computed from RNA sequencing and cellular traffic into human kidney allografts. PMID:29659169
Gene-level differential analysis at transcript-level resolution. PMID:29650040
New insights into the interplay between the translation machinery and nonsense-mediated mRNA decay factors. PMID:29626148
A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples. PMID:29625054
DeFine: deep convolutional neural networks accurately quantify intensities of transcription factor-DNA binding and facilitate evaluation of functional non-coding variants. PMID:29617928
IL1RN Variation Influences Both Disease Susceptibility and Response to Recombinant Human Interleukin-1 Receptor Antagonist Therapy in Systemic Juvenile Idiopathic Arthritis. PMID:29609200
Immunochip Meta-Analysis of Inflammatory Bowel Disease Identifies Three Novel Loci and Four Novel Associations in Previously Reported Loci. PMID:29584801
Glycosyltransferase genes that cause monogenic congenital disorders of glycosylation are distinct from glycosyltransferase genes associated with complex diseases. PMID:29579191
Placenta and appetite genes GDF15 and IGFBP7 are associated with hyperemesis gravidarum. PMID:29563502
UBD modifies APOL1-induced kidney disease risk. PMID:29531077
Allele-specific expression in a family quartet with autism reveals mono-to-biallelic switch and novel transcriptional processes of autism susceptibility genes. PMID:29523860
AltHapAlignR: improved accuracy of RNA-seq analyses through the use of alternative haplotypes. PMID:29514179
Gene-by-environment interactions in urban populations modulate risk phenotypes. PMID:29511166
A large electronic-health-record-based genome-wide study of serum lipids. PMID:29507422
Methods for fine-mapping with chromatin and expression data. PMID:29481575
Bias, robustness and scalability in single-cell differential expression analysis. PMID:29481549
Integrative omics for health and disease. PMID:29479082
Integrating eQTL data with GWAS summary statistics in pathway-based analysis with application to schizophrenia. PMID:29411426
Beyond Genomic Prediction: Combining Different Types of omics Data Can Improve Prediction of Hybrid Performance in Maize. PMID:29363551
GWAS in childhood acute lymphoblastic leukemia reveals novel genetic associations at chromosomes 17q12 and 8q24.21. PMID:29348612
Genetic variants in RORA and DNMT1 associated with cutaneous melanoma survival. PMID:29313974
Formidable challenges to the notion of biologically important roles for dietary small RNAs in ingesting mammals. PMID:29308096
A decade of research on the 17q12-21 asthma locus: Piecing together the puzzle. PMID:29307657
The Expanding Landscape of Alternative Splicing Variation in Human Populations. PMID:29304370
Annotation-free quantification of RNA splicing using LeafCutter. PMID:29229983
Multiplexed droplet single-cell RNA-sequencing using natural genetic variation. PMID:29227470
RetrogeneDB-a database of plant and animal retrocopies. PMID:29220443
A deep auto-encoder model for gene expression prediction. PMID:29219072
How powerful are summary-based methods for identifying expression-trait associations under different genetic architectures? PMID:29218884
Impact of regulatory variation across human iPSCs and differentiated cells. PMID:29208628
Voluntary exposure to a toxin: the genetic influence on ethanol consumption. PMID:29196862
Strawberry: Fast and accurate genome-guided transcript reconstruction and quantification from RNA-Seq. PMID:29176847
Genetic variants in the platelet-derived growth factor subunit B gene associated with pancreatic cancer risk. PMID:29168174
Cis-SNPs Set Testing and PrediXcan Analysis for Gene Expression Data using Linear Mixed Models. PMID:29127305
The effect of genetic variation on promoter usage and enhancer activity. PMID:29116076
Identification of Splicing Quantitative Trait Loci (sQTL) in Drosophila melanogaster with Developmental Lead (Pb2+) Exposure. PMID:29114259
A functional strategy to characterize expression Quantitative Trait Loci. PMID:29101457
Regulatory and evolutionary signatures of sex-biased genes on both the X chromosome and the autosomes. PMID:29096703
Structure-mediated modulation of mRNA abundance by A-to-I editing. PMID:29093448
Shared genetic origin of asthma, hay fever and eczema elucidates allergic disease biology. PMID:29083406
Human gene essentiality. PMID:29082913
Multiethnic Meta-Analysis Identifies RAI1 as a Possible Obstructive Sleep Apnea-related Quantitative Trait Locus in Men. PMID:29077507
Efficient Prioritization of Multiple Causal eQTL Variants via Sparse Polygenic Modeling. PMID:29074555
Novel genetic variants in the P38MAPK pathway gene ZAK and susceptibility to lung cancer. PMID:29071797
Sex influences eQTL effects of SLE and Sjögren's syndrome-associated genetic polymorphisms. PMID:29070082
Profiling RNA-Seq at multiple resolutions markedly increases the number of causal eQTLs in autoimmune disease. PMID:29059182
Predicting causal variants affecting expression by using whole-genome sequencing and RNA-seq from multiple human tissues. PMID:29058714
Evidence of reduced recombination rate in human regulatory domains. PMID:29058599
Controlling for Confounding Effects in Single Cell RNA Sequencing Studies Using both Control and Target Genes. PMID:29051597
A rank-based algorithm of differential expression analysis for small cell line data with statistical control. PMID:29040359
Covariate selection for association screening in multiphenotype genetic studies. PMID:29038595
PancanQTL: systematic identification of cis-eQTLs and trans-eQTLs in 33 cancer types. PMID:29036324
Mirnovo: genome-free prediction of microRNAs from small RNA sequencing data and single-cells using decision forests. PMID:29036314
New Blood Pressure-Associated Loci Identified in Meta-Analyses of 475 000 Individuals. PMID:29030403
QuASAR-MPRA: accurate allele-specific analysis for massively parallel reporter assays. PMID:29028988
Environmental perturbations lead to extensive directional shifts in RNA processing. PMID:29023442
Genetic effects on gene expression across human tissues. PMID:29022597
Quantifying the regulatory effect size of cis-acting genetic variation using allelic fold change. PMID:29021289
Enhancing GTEx by bridging the gaps between genotype, gene expression, and disease. PMID:29019975
Data Resources for Human Functional Genomics. PMID:28989986
Context-specific effects of genetic variants associated with autoimmune disease. PMID:28977443
FIRE: functional inference of genetic variants that regulate gene expression. PMID:28961785
Identification of breast cancer associated variants that modulate transcription factor binding. PMID:28957321
HLAProfiler utilizes k-mer profiles to improve HLA calling accuracy for rare and common alleles in RNA-seq data. PMID:28954626
The Epstein-Barr virus miR-BHRF1 microRNAs regulate viral gene expression in cis. PMID:28950226
Common Expression Quantitative Trait Loci Shared by Histone Genes. PMID:28929106
Natural genetic variation of the cardiac transcriptome in non-diseased donors and patients with dilated cardiomyopathy. PMID:28903782
Improved data-driven likelihood factorizations for transcript abundance estimation. PMID:28881996
Non-parametric genetic prediction of complex traits with latent Dirichlet process regression models. PMID:28878256
An xQTL map integrates the genetic architecture of the human brain's transcriptome and epigenome. PMID:28869584
Using ALoFT to determine the impact of putative loss-of-function variants in protein-coding genes. PMID:28851873
Human Retrotransposon Insertion Polymorphisms Are Associated with Health and Disease via Gene Regulatory Phenotypes. PMID:28824558
Efficient and accurate causal inference with hidden confounders from genome-transcriptome variation data. PMID:28821014
Genetic regulatory effects modified by immune activation contribute to autoimmune disease associations. PMID:28814792
Mapping the mouse Allelome reveals tissue-specific regulation of allelic expression. PMID:28806168
Genetic variants in the metzincin metallopeptidase family genes predict melanoma survival. PMID:28796414
Assessment of imprinting- and genetic variation-dependent monoallelic expression using reciprocal allele descendants between human family trios. PMID:28765567
Population and allelic variation of A-to-I RNA editing in human transcriptomes. PMID:28754146
Detecting epistasis with the marginal epistasis test in genetic mapping studies of quantitative traits. PMID:28746338
Mechanisms of Type 2 Diabetes Risk Loci. PMID:28741265
Assessment of isomiR Discrimination Using Commercial qPCR Methods. PMID:28730153
Evidence of selection on splicing-associated loci in human populations and relevance to disease loci mapping. PMID:28729732
An erythroid-specific ATP2B4 enhancer mediates red blood cell hydration and malaria susceptibility. PMID:28714864
A genomic perspective on HLA evolution. PMID:28687858
Strength of functional signature correlates with effect size in autism. PMID:28687074
Landscape and variation of novel retroduplications in 26 human populations. PMID:28662076
Fine-mapping inflammatory bowel disease loci to single-variant resolution. PMID:28658209
Effects of Type 1 Diabetes Risk Alleles on Immune Cell Gene Expression. PMID:28635624
Characterising cis-regulatory variation in the transcriptome of histologically normal and tumour-derived pancreatic tissues. PMID:28634199
Identification of sequence variants influencing immunoglobulin levels. PMID:28628107
Transcriptome sequencing identifies ANLN as a promising prognostic biomarker in bladder urothelial carcinoma. PMID:28600503
Constraints on eQTL Fine Mapping in the Presence of Multisite Local Regulation of Gene Expression. PMID:28600440
Global variation in gene expression and the value of diverse sampling. PMID:28596996
An indicator cell assay for blood-based diagnostics. PMID:28594877
Hierarchical probabilistic models for multiple gene/variant associations based on next-generation sequencing data. PMID:28575251
Frameshift indels introduced by genome editing can lead to in-frame exon skipping. PMID:28570605
A Poisson Log-Normal Model for Constructing Gene Covariation Network Using RNA-seq Data. PMID:28557607
Polygenic burdens on cell-specific pathways underlie the risk of rheumatoid arthritis. PMID:28553958
Whole-Genome Sequencing Coupled to Imputation Discovers Genetic Signals for Anthropometric Traits. PMID:28552196
Transcriptomics technologies. PMID:28545146
Gene expression variability and the analysis of large-scale RNA-seq studies with the MDSeq. PMID:28535263
Fifteen new risk loci for coronary artery disease highlight arterial-wall-specific mechanisms. PMID:28530674
Functional regression method for whole genome eQTL epistasis analysis with sequencing data. PMID:28521784
A complete tool set for molecular QTL discovery and analysis. PMID:28516912
Genetic variants in the genes encoding rho GTPases and related regulators predict cutaneous melanoma-specific survival. PMID:28510328
Associations between RNA splicing regulatory variants of stemness-related genes and racial disparities in susceptibility to prostate cancer. PMID:28510291
An independent component analysis confounding factor correction framework for identifying broad impact expression quantitative trait loci. PMID:28505156
Genetic Variants in WNT2B and BTRC Predict Melanoma Survival. PMID:28499756
Prediction of gene expression with cis-SNPs using mixed models and regularization methods. PMID:28490319
Comparative transcriptomics in human and mouse. PMID:28479595
Widespread Allelic Heterogeneity in Complex Traits. PMID:28475861
Quantification of differential gene expression by multiplexed targeted resequencing of cDNA. PMID:28474677
Exploring genetic associations with ceRNA regulation in the human genome. PMID:28472449
Methods, Tools and Current Perspectives in Proteogenomics. PMID:28456751
Multi-class computational evolution: development, benchmark evaluation and application to RNA-Seq biomarker discovery. PMID:28450890
veqtl-mapper: variance association mapping for molecular phenotypes. PMID:28449110
Genetic interplay between human longevity and metabolic pathways - a large-scale eQTL study. PMID:28421666
Regulatory network of GATA3 in pediatric acute lymphoblastic leukemia. PMID:28415601
Predictive long-range allele-specific mapping of regulatory variants and target transcripts. PMID:28406955
Omicseq: a web-based search engine for exploring omics datasets. PMID:28402462
Genetic variants of PTPN2 are associated with lung cancer risk: a re-analysis of eight GWASs in the TRICL-ILCCO consortium. PMID:28400551
Population- and individual-specific regulatory variation in Sardinia. PMID:28394350
Large-Scale Profiling Reveals the Influence of Genetic Variation on Gene Expression in Human Induced Pluripotent Stem Cells. PMID:28388430
Functional variants in DCAF4 associated with lung cancer risk in European populations. PMID:28383684
Evolutionary and polymorphism analyses reveal the central role of BTN3A2 in the concerted evolution of the BTN3 gene family. PMID:28382515
Genome-wide association analysis for chronic venous disease identifies EFEMP1 and KCNH8 as susceptibility loci. PMID:28374850
Differential expression analysis for RNAseq using Poisson mixed models. PMID:28369632
Enhanced methods to detect haplotypic effects on gene expression. PMID:28369161
The impact of structural variation on human gene expression. PMID:28369037
A computational method for estimating the PCR duplication rate in DNA and RNA-seq experiments. PMID:28361665
Functional Architectures of Local and Distal Regulation of Gene Expression in Multiple Human Tissues. PMID:28343628
Identification of genetic variants affecting vitamin D receptor binding and associations with autoimmune disease. PMID:28335003
cepip: context-dependent epigenomic weighting for prioritization of regulatory variants and disease-associated genes. PMID:28302177
Screening for interaction effects in gene expression data. PMID:28301596
Genome-wide associations of CD46 and IFI44L genetic variants with neutralizing antibody response to measles vaccine. PMID:28289848
Large-Scale trans-eQTLs Affect Hundreds of Transcripts and Mediate Patterns of Transcriptional Co-regulation. PMID:28285767
Shared regulatory sites are abundant in the human genome and shed light on genome evolution and disease pleiotropy. PMID:28282383
Salmon provides fast and bias-aware quantification of transcript expression. PMID:28263959
Effects of multiple genetic loci on the pathogenesis from serum urate to gout. PMID:28252667
Playing hide and seek with repeats in local and global de novo transcriptome assembly of short RNA-seq reads. PMID:28250805
Individualized Breast Cancer Characterization through Single-Cell Analysis of Tumor and Adjacent Normal Cells. PMID:28249895
OSBPL10, RXRA and lipid metabolism confer African-ancestry protection against dengue haemorrhagic fever in admixed Cubans. PMID:28241052
Connecting genetic risk to disease end points through the human blood plasma proteome. PMID:28240269
Integrating Gene Expression with Summary Association Statistics to Identify Genes Associated with 30 Complex Traits. PMID:28238358
BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes. PMID:28235418
Single nucleotide polymorphism discovery in bovine liver using RNA-seq technology. PMID:28234981
Population and clinical genetics of human transposable elements in the (post) genomic era. PMID:28228978
Accurate eQTL prioritization with an ensemble-based framework. PMID:28224684
MINTmap: fast and exhaustive profiling of nuclear and mitochondrial tRNA fragments from short RNA-seq data. PMID:28220888
Predicting gene expression in massively parallel reporter assays: A comparative study. PMID:28220625
Limited statistical evidence for shared genetic effects of eQTLs and autoimmune-disease-associated loci in three major immune-cell types. PMID:28218759
Threshold-seq: a tool for determining the threshold in short RNA-seq datasets. PMID:28203700
ulfasQTL: an ultra-fast method of composite splicing QTL analysis. PMID:28198669
Promoter shape varies across populations and affects promoter evolution and expression noise. PMID:28191888
A Genomewide Association Study Identifies Two Sex-Specific Loci, at SPTB and IZUMO3, Influencing Pediatric Bone Mineral Density at Multiple Skeletal Sites. PMID:28181694
Epistasis and destabilizing mutations shape gene expression variability in humans via distinct modes of action. PMID:28171656
Conditional eQTL analysis reveals allelic heterogeneity of gene expression. PMID:28165122
Accurately annotate compound effects of genetic variants using a context-sensitive framework. PMID:28158838
Pathway-analysis of published genome-wide association studies of lung cancer: A potential role for the CYP4F3 locus. PMID:28150878
Genetic variant rs763361 regulates multiple sclerosis CD226 gene expression. PMID:28137889
Genetic variant rs763361 regulates multiple sclerosis CD226 gene expression. PMID:28137889
Evaluation of 10 SLE susceptibility loci in Asian populations, which were initially identified in European populations. PMID:28128292
Introducing COCOS: codon consequence scanner for annotating reading frame changes induced by stop-lost and frame shift variants. PMID:28122779
Predicting enhancer activity and variant impact using gkm-SVM. PMID:28120510
Genome-wide association analysis of chronic lymphocytic leukaemia, Hodgkin lymphoma and multiple myeloma identifies pleiotropic risk loci. PMID:28112199
Non-Coding Loss-of-Function Variation in Human Genomes. PMID:28076858
Expression quantitative trait loci for PI3K/AKT pathway. PMID:28072738
Mapping eQTLs with RNA-seq reveals novel susceptibility genes, non-coding RNAs and alternative-splicing events in systemic lupus erythematosus. PMID:28062664
Survey of 800+ data sets from human tissue and body fluid reveals xenomiRs are likely artifacts. PMID:28062594
Molecular mechanisms underlying noncoding risk variations in psychiatric genetic studies. PMID:28044063
A Genome-wide Association Study Identifies Risk Alleles in Plasminogen and P4HA2 Associated with Giant Cell Arteritis. PMID:28041642
The incredible complexity of RNA splicing. PMID:28038679
Human splicing diversity and the extent of unannotated splice junctions across human RNA-seq samples on the Sequence Read Archive. PMID:28038678
Strong cis-acting expression quantitative trait loci for the genes encoding SNHG5 and PEX6. PMID:28033303
Down syndrome and the complexity of genome dosage imbalance. PMID:28029161
Analysis of Transcriptional Variability in a Large Human iPSC Library Reveals Genetic and Non-genetic Determinants of Heterogeneity. PMID:28017796
High-throughput interpretation of gene structure changes in human and nonhuman resequencing data, using ACE. PMID:28011790
Human population-specific gene expression and transcriptional network modification with polymorphic transposable elements. PMID:27998931
Evidence of Recent Intricate Adaptation in Human Populations. PMID:27992444
Genome-wide association study of primary sclerosing cholangitis identifies new risk loci and quantifies the genetic relationship with inflammatory bowel disease. PMID:27992413
TMEM258 Is a Component of the Oligosaccharyltransferase Complex Controlling ER Stress and Intestinal Inflammation. PMID:27974209
Identification of context-dependent expression quantitative trait loci in whole blood. PMID:27918533
Genetic variants in the integrin signaling pathway genes predict cutaneous melanoma survival. PMID:27914105
Genetic Overlap Between Attention-Deficit/Hyperactivity Disorder and Bipolar Disorder: Evidence From Genome-wide Association Study Meta-analysis. PMID:27890468
variancePartition: interpreting drivers of variation in complex gene expression studies. PMID:27884101
Genome, transcriptome and proteome: the rise of omics data and their integration in biomedical sciences. PMID:27881428
Non-coding RNAs match the deleted genomic regions in humans. PMID:27853310
The roles of RNA processing in translating genotype to phenotype. PMID:27847391
Archaic Hominin Admixture Facilitated Adaptation to Out-of-Africa Environments. PMID:27839976
Autoimmune risk variants in ERAP2 are associated with gene-expression levels in thymus. PMID:27829666
Ancient Out-of-Africa Mitochondrial DNA Variants Associate with Distinct Mitochondrial Gene Expression Patterns. PMID:27812116
Susceptibility loci of CNOT6 in the general mRNA degradation pathway and lung cancer risk-A re-analysis of eight GWASs. PMID:27805284
Evaluation of computational programs to predict HLA genotypes from genomic sequencing data. PMID:27802932
Small RNA Sequencing in Cells and Exosomes Identifies eQTLs and 14q32 as a Region of Active Export. PMID:27799337
Capture Hi-C identifies a novel causal gene, IL20RA, in the pan-autoimmune genetic susceptibility region 6q23. PMID:27799070
A prior-based integrative framework for functional transcriptional regulatory network inference. PMID:27794550
A statistical approach for identifying differential distributions in single-cell RNA-seq experiments. PMID:27782827
Genetic Adaptation and Neandertal Admixture Shaped the Immune System of Human Populations. PMID:27768888
Discovering Single Nucleotide Polymorphisms Regulating Human Gene Expression Using Allele Specific Expression from RNA-seq Data. PMID:27765809
Genome-wide identification of expression quantitative trait loci for human telomerase. PMID:27759658
Roar: detecting alternative polyadenylation with standard mRNA sequencing libraries. PMID:27756200
Simul-seq: combined DNA and RNA sequencing for whole-genome and transcriptome profiling. PMID:27723755
Flexible expressed region analysis for RNA-seq with derfinder. PMID:27694310
Uncoupling of mucosal gene regulation, mRNA splicing and adherent microbiota signatures in inflammatory bowel disease. PMID:27694142
Pseudoexons provide a mechanism for allele-specific expression of APC in familial adenomatous polyposis. PMID:27683109
Genome-wide associations for birth weight and correlations with adult disease. PMID:27680694
Modeling of RNA-seq fragment sequence bias reduces systematic errors in transcript abundance estimation. PMID:27669167
Discovery and refinement of genetic loci associated with cardiometabolic risk using dense imputation maps. PMID:27668658
Analysis of Genome-Wide Monoallelic Expression Patterns in Three Major Cell Types of Mouse Visual Cortex Using Laser Capture Microdissection. PMID:27662371
Translational plasticity facilitates the accumulation of nonsense genetic variants in the human population. PMID:27646533
Modeling disease risk through analysis of physical interactions between genetic variants within chromatin regulatory circuitry. PMID:27643537
Immunoseq: the identification of functionally relevant variants through targeted capture and sequencing of active regulatory regions in human immune cells. PMID:27624058
Hypothalamic transcriptomes of 99 mouse strains reveal trans eQTL hotspots, splicing QTLs and novel non-coding genes. PMID:27623010
A haplotype-based normalization technique for the analysis and detection of allele specific expression. PMID:27618913
The rules and impact of nonsense-mediated mRNA decay in human cancers. PMID:27618451
Sequence variation between 462 human individuals fine-tunes functional sites of RNA processing. PMID:27617755
Rare variant phasing and haplotypic expression from RNA sequencing with phASER. PMID:27605262
Rail-RNA: scalable analysis of RNA-seq splicing and coverage. PMID:27592709
Discrepancies between human DNA, mRNA and protein reference sequences and their relation to single nucleotide variants in the human population. PMID:27589963
Cardiometabolic risk loci share downstream cis- and trans-gene regulation across tissues and diseases. PMID:27540175
CRISPR/Cas9 mediated genome editing in ES cells and its application for chimeric analysis in mice. PMID:27530713
Literature-Informed Analysis of a Genome-Wide Association Study of Gestational Age in Norwegian Women and Children Suggests Involvement of Inflammatory Pathways. PMID:27490719
Emergence of a Homo sapiens-specific gene family and chromosome 16p11.2 CNV susceptibility. PMID:27487209
Selected heterozygosity at cis-regulatory sequences increases the expression homogeneity of a cell population in humans. PMID:27468897
Integrating Epigenomic Elements and GWASs Identifies BDNF Gene Affecting Bone Mineral Density and Osteoporotic Fracture Risk. PMID:27465306
SNP calling from RNA-seq data without a reference genome: identification, quantification, differential analysis and impact on the protein sequence. PMID:27458203
Applications of the 1000 Genomes Project resources. PMID:27436001
Consensus Genome-Wide Expression Quantitative Trait Loci and Their Relationship with Human Complex Trait Disease. PMID:27428252
Genome-wide association meta-analyses identified 1q43 and 2q32.2 for hip Ward's triangle areal bone mineral density. PMID:27397699
Fine-Mapping of Common Genetic Variants Associated with Colorectal Tumor Risk Identified Potential Functional Variants. PMID:27379672
The genetic regulatory signature of type 2 diabetes in human skeletal muscle. PMID:27353450
Exome Genotyping Identifies Pleiotropic Variants Associated with Red Blood Cell Traits. PMID:27346685
RapMap: a rapid, sensitive and accurate tool for mapping RNA-seq reads to transcriptomes. PMID:27307617
Boiler: lossy compression of RNA-seq alignments using coverage vectors. PMID:27298258
Principles of microRNA Regulation Revealed Through Modeling microRNA Expression Quantitative Trait Loci. PMID:27260304
Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay. PMID:27259153
Chromosomal contacts connect loci associated with autism, BMI and head circumference phenotypes. PMID:27240531
Efficient Integrative Multi-SNP Association Analysis via Deterministic Approximation of Posteriors. PMID:27236919
Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling. PMID:27232982
Transcriptome-Wide Analysis Reveals Modulation of Human Macrophage Inflammatory Phenotype Through Alternative Splicing. PMID:27230130
Prediction and Quantification of Splice Events from RNA-Seq Data. PMID:27218464
Coregulation of tandem duplicate genes slows evolution of subfunctionalization in mammals. PMID:27199432
Impact of the X Chromosome and sex on regulatory variation. PMID:27197214
Selection and explosive growth alter genetic architecture and hamper the detection of causal rare variants. PMID:27197206
A splice variant in the ACSL5 gene relates migraine with fatty acid activation in mitochondria. PMID:27189022
Multivariate eQTL mapping uncovers functional variation on the X-chromosome associated with complex disease traits. PMID:27155841
MINTbase: a framework for the interactive exploration of mitochondrial and nuclear tRNA fragments. PMID:27153631
A Common Polymorphism in HIBCH Influences Methylmalonic Acid Concentrations in Blood Independently of Cobalamin. PMID:27132595
RNA splicing is a primary link between genetic variation and disease. PMID:27126046
A benchmark for RNA-seq quantification pipelines. PMID:27107712
A uniform survey of allele-specific binding and expression over 1000-Genomes-Project individuals. PMID:27089393
Pooled ChIP-Seq Links Variation in Transcription Factor Binding to Complex Disease Risk. PMID:27087447
Allelic imbalance of multiple sclerosis susceptibility genes IKZF3 and IQGAP1 in human peripheral blood. PMID:27080863
RNA-seq analysis for detecting quantitative trait-associated genes. PMID:27071914
Allelic Imbalance in Regulation of ANRIL through Chromatin Interaction at 9p21 Endometriosis Risk Locus. PMID:27055116
Near-optimal probabilistic RNA-seq quantification. PMID:27043002
FCGR2C Polymorphisms Associated with HIV-1 Vaccine Protection Are Linked to Altered Gene Expression of Fc-γ Receptors in Human B Cells. PMID:27015273
Variation at 2q35 (PNKD and TMBIM1) influences colorectal cancer risk and identifies a pleiotropic effect with inflammatory bowel disease. PMID:27005424
Allele-specific transcription factor binding to common and rare variants associated with disease and gene expression. PMID:26993500
Network-Based Identification and Prioritization of Key Regulators of Coronary Artery Disease Loci. PMID:26966275
Identifying genetic modulators of the connectivity between transcription factors and their transcriptional targets. PMID:26966232
Germline genetics of cancer of unknown primary (CUP) and its specific subtypes. PMID:26959888
Testing for association between RNA-Seq and high-dimensional data. PMID:26951498
Quantitative Trait Loci Identify Functional Noncoding Variation in Cancer. PMID:26938653
Identification of STOML2 as a putative novel asthma risk gene associated with IL6R. PMID:26932604
G72 primate-specific gene: a still enigmatic element in psychiatric disorders. PMID:26914235
Modelling local gene networks increases power to detect trans-acting genetic effects on gene expression. PMID:26911988
Autoimmune diseases - connecting risk alleles with molecular traits of the immune system. PMID:26907721
Natural variation in non-coding regions underlying phenotypic diversity in budding yeast. PMID:26898953
From Loci to Biology: Functional Genomics of Genome-Wide Association for Coronary Disease. PMID:26892960
Alternative splicing modulated by genetic variants demonstrates accelerated evolution regulated by highly conserved proteins. PMID:26888265
Gene control of tyrosine kinase TIE2 and vascular manifestations of infections. PMID:26884170
Regulatory polymorphisms modulate the expression of HLA class II molecules and promote autoimmunity. PMID:26880555
Gene expression inference with deep learning. PMID:26873929
A variant at 9p21.3 functionally implicates CDKN2B in paediatric B-cell precursor acute lymphoblastic leukaemia aetiology. PMID:26868379
Selective amplification and sequencing of cyclic phosphate-containing RNAs by the cP-RNA-seq method. PMID:26866791
Analysing multiple types of molecular profiles simultaneously: connecting the needles in the haystack. PMID:26860128
Integrative approaches for large-scale transcriptome-wide association studies. PMID:26854917
Quantification of private information leakage from phenotype-genotype data: linking attacks. PMID:26828419
Long non-coding RNAs display higher natural expression variation than protein-coding genes in healthy humans. PMID:26821746
A survey of best practices for RNA-seq data analysis. PMID:26813401
Genetic Variation, Not Cell Type of Origin, Underlies the Majority of Identifiable Regulatory Differences in iPSCs. PMID:26812582
Autoimmune vitiligo is associated with gain-of-function by a transcriptional regulator that elevates expression of HLA-A*02:01 in vivo. PMID:26787886
Role of non-coding sequence variants in cancer. PMID:26781813
Genetic variants in ABCG1 are associated with survival of nonsmall-cell lung cancer patients. PMID:26757251
An Efficient Multiple-Testing Adjustment for eQTL Studies that Accounts for Linkage Disequilibrium between Variants. PMID:26749306
Introgression of Neandertal- and Denisovan-like Haplotypes Contributes to Adaptive Variation in Human Toll-like Receptors. PMID:26748514
A spectral approach integrating functional genomic annotations for coding and noncoding variants. PMID:26727659
Fast and efficient QTL mapper for thousands of molecular phenotypes. PMID:26708335
Postmortem human brain genomics in neuropsychiatric disorders--how far can we go? PMID:26685806
Metagenomics: Retrospect and Prospects in High Throughput Age. PMID:26664751
HaploReg v4: systematic mining of putative causal variants, cell types, regulators and target genes for human complex traits and disease. PMID:26657631
Fine-mapping cellular QTLs with RASQUAL and ATAC-seq. PMID:26656845
Genetic Determinants of RNA Editing Levels of ADAR Targets in Drosophila melanogaster. PMID:26656153
Abundant contribution of short tandem repeats to gene expression variation in humans. PMID:26642241
PExFInS: An Integrative Post-GWAS Explorer for Functional Indels and SNPs. PMID:26612672
Identification of candidate genes for prostate cancer-risk SNPs utilizing a normal prostate tissue eQTL data set. PMID:26611117
Association mapping reveals the role of purifying selection in the maintenance of genomic variation in gene expression. PMID:26604315
Variability in Humoral Immunity to Measles Vaccine: New Developments. PMID:26602762
Total Binding Affinity Profiles of Regulatory Regions Predict Transcription Factor Binding and Gene Expression in Human Cells. PMID:26599758
Genome-wide patterns of selection in 230 ancient Eurasians. PMID:26595274
Discover hidden splicing variations by mapping personal transcriptomes to personal genomes. PMID:26578562
Circulating microbial RNA and health. PMID:26576508
Functional implications of disease-specific variants in loci jointly associated with coeliac disease and rheumatoid arthritis. PMID:26546613
Meta-analysis identifies seven susceptibility loci involved in the atopic march. PMID:26542096
Genetic Variants on Chromosome 1p13.3 Are Associated with Non-ST Elevation Myocardial Infarction and the Expression of DRAM2 in the Finnish Population. PMID:26509668
Inter-population Differences in Retrogene Loss and Expression in Humans. PMID:26474060
Multiple breast cancer risk variants are associated with differential transcript isoform expression in tumors. PMID:26472073
Bayesian integration of genetics and epigenetics detects causal regulatory SNPs underlying expression variability. PMID:26456756
Intron retention is a widespread mechanism of tumor-suppressor inactivation. PMID:26437032
An integrated map of structural variation in 2,504 human genomes. PMID:26432246
Alternative Splicing QTLs in European and African Populations. PMID:26430802
Genomic approaches for understanding the genetics of complex disease. PMID:26430153
Functional genomics bridges the gap between quantitative genetics and molecular biology. PMID:26430152
Functional Impact and Evolution of a Novel Human Polymorphic Inversion That Disrupts a Gene and Creates a Fusion Transcript. PMID:26427027
Genome-wide association study identifies multiple susceptibility loci for glioma. PMID:26424050
Enabling research with human embryonic and fetal tissue resources. PMID:26395135
Omic personality: implications of stable transcript and methylation profiles for personalized medicine. PMID:26391122
Complexity and diversity of F8 genetic variations in the 1000 genomes. PMID:26383047
Tools and best practices for data processing in allelic expression analysis. PMID:26381377
Genetic mapping uncovers cis-regulatory landscape of RNA editing. PMID:26373807
Identification of Genes Whose Expression Profile Is Associated with Non-Progression towards AIDS Using eQTLs. PMID:26367535
WASP: allele-specific software for robust molecular quantitative trait locus discovery. PMID:26366987
Genome-wide association analyses based on whole-genome sequencing in Sardinia provide insights into regulation of hemoglobin levels. PMID:26366553
Molecular Characterization of the NLRC4 Expression in Relation to Interleukin-18 Levels. PMID:26362438
A comprehensive catalogue of the coding and non-coding transcripts of the human inner ear. PMID:26341477
Regulatory Divergence of Transcript Isoforms in a Mammalian Model System. PMID:26339903
Allele-Selective Transcriptome Recruitment to Polysomes Primed for Translation: Protein-Coding and Noncoding RNAs, and RNA Isoforms. PMID:26331722
Dissecting tRNA-derived fragment complexities using personalized transcriptomes reveals novel fragment classes and unexpected dependencies. PMID:26325506
Allelic variation in CRHR1 predisposes to panic disorder: evidence for biased fear processing. PMID:26324098
Natural Selection at the Brush-Border: Adaptations to Carbohydrate Diets in Humans and Other Mammals. PMID:26319403
Ethnicity-Dependent and -Independent Heterogeneity in Healthy Normal Breast Hierarchy Impacts Tumor Characterization. PMID:26311223
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
Pathway analysis for RNA-Seq data using a score-based approach. PMID:26259845
Genome-wide analysis of the genetic regulation of gene expression in human neutrophils. PMID:26259071
A gene-based association method for mapping traits using reference transcriptome data. PMID:26258848
Prediction of human population responses to toxic compounds by a collaborative competition. PMID:26258538
Extensive allele-specific translational regulation in hybrid mice. PMID:26253569
Transcriptional profiling of macrophages derived from monocytes and iPS cells identifies a conserved response to LPS and novel alternative transcription. PMID:26224331
Designing alternative splicing RNA-seq studies. Beyond generic guidelines. PMID:26220961
Long-Range Modulation of PAG1 Expression by 8q21 Allergy Risk Variants. PMID:26211970
Populational landscape of INDELs affecting transcription factor-binding sites in humans. PMID:26194008
Genomic modulators of gene expression in human neutrophils. PMID:26151758
Disentangling the Effects of Colocalizing Genomic Annotations to Functionally Prioritize Non-coding Variants within Complex-Trait Loci. PMID:26140449
Predominant contribution of cis-regulatory divergence in the evolution of mouse alternative splicing. PMID:26134616
Expression quantitative trait locus analysis for translational medicine. PMID:26110023
Massively parallel quantification of the regulatory effects of noncoding genetic variation in a human cohort. PMID:26084464
Ancestral alleles in the human genome based on population sequencing data. PMID:26020928
Variants in ELL2 influencing immunoglobulin levels associate with multiple myeloma. PMID:26007630
Genome-wide patterns and properties of de novo mutations in humans. PMID:25985141
Comprehensively evaluating cis-regulatory variation in the human prostate transcriptome by using gene-level allele-specific expression. PMID:25983244
Recommendations for Accurate Resolution of Gene and Isoform Allele-Specific Expression in RNA-Seq Data. PMID:25965996
Polymorphism at 19q13.41 Predicts Breast Cancer Survival Specifically after Endocrine Therapy. PMID:25964295
Cell Specific eQTL Analysis without Sorting Cells. PMID:25955312
Calling genotypes from public RNA-sequencing data enables identification of genetic variants that affect gene-expression levels. PMID:25954321
Human genomics. Effect of predicted protein-truncating genetic variants on the human transcriptome. PMID:25954003
Human genomics. The human transcriptome across tissues and individuals. PMID:25954002
The landscape of genomic imprinting across diverse adult human tissues. PMID:25953952
A pooling-based approach to mapping genetic variants associated with DNA methylation. PMID:25910490
Identification of recurrent regulated alternative splicing events across human solid tumors. PMID:25908786
Cross-population joint analysis of eQTLs: fine mapping and functional annotation. PMID:25906321
Natural variation of gene models in Drosophila melanogaster. PMID:25888292
Evaluating intra- and inter-individual variation in the human placental transcriptome. PMID:25887593
Integrative network analysis reveals molecular mechanisms of blood pressure regulation. PMID:25882670
Splice-shifting oligonucleotide (SSO) mediated blocking of an exonic splicing enhancer (ESE) created by the prevalent c.903+469T>C MTRR mutation corrects splicing and restores enzyme activity in patient cells. PMID:25878036
RNA Sequencing and Analysis. PMID:25870306
An integrated network of microRNA and gene expression in ovarian cancer. PMID:25860109
Genetic variation and alternative splicing. PMID:25850059
Recent positive selection has acted on genes encoding proteins with more interactions within the whole human interactome. PMID:25840415
Sensitivity of quantitative traits to mutational effects and number of loci. PMID:25840144
Uncovering RNA binding proteins associated with age and gender during liver maturation. PMID:25824884
Assessing allele-specific expression across multiple tissues from RNA-seq read data. PMID:25819081
Origins and impacts of new mammalian exons. PMID:25801031
Sensitive detection of chromatin-altering polymorphisms reveals autoimmune disease mechanisms. PMID:25799442
Identification of active transcriptional regulatory elements from GRO-seq data. PMID:25799441
Mapping Bias Overestimates Reference Allele Frequencies at the HLA Genes in the 1000 Genomes Project Phase I Data. PMID:25787242
Ballgown bridges the gap between transcriptome assembly and expression analysis. PMID:25748911
Mapping Splicing Quantitative Trait Loci in RNA-Seq. PMID:25733796
The genetic architecture of gene expression levels in wild baboons. PMID:25714927
Integrative analysis of haplotype-resolved epigenomes across human tissues. PMID:25693566
Impact of allele-specific peptides in proteome quantification. PMID:25676416
Vision from next generation sequencing: multi-dimensional genome-wide analysis for producing gene regulatory networks underlying retinal development, aging and disease. PMID:25668385
Multi-omic data analysis using Galaxy. PMID:25658277
Genomic variation. Impact of regulatory variation from RNA to protein. PMID:25657249
The role of Abcb5 alleles in susceptibility to haloperidol-induced toxicity in mice and humans. PMID:25647612
Defining the biological bases of individual differences in musicality. PMID:25646515
ZNF143 provides sequence specificity to secure chromatin interactions at gene promoters. PMID:25645053
Tissue-specific effects of genetic and epigenetic variation on gene regulation and splicing. PMID:25634236
Huntington's disease biomarker progression profile identified by transcriptome sequencing in peripheral blood. PMID:25626709
Large multiallelic copy number variations in humans. PMID:25621458
Aberrant gene expression in humans. PMID:25617623
ST13 polymorphisms and their effect on exacerbations in steroid-treated asthmatic children and young adults. PMID:25616159
Analysis of genome-wide RNA-sequencing data suggests age of the CEPH/Utah (CEU) lymphoblastoid cell lines systematically biases gene expression profiles. PMID:25609584
Genome-wide meta-analysis in alopecia areata resolves HLA associations and reveals two new susceptibility loci. PMID:25608926
A method for calculating probabilities of fitness consequences for point mutations across the human genome. PMID:25599402
Personalized medicine: from genotypes, molecular phenotypes and the quantified self, towards improved medicine. PMID:25592594
Integrative genome-wide analysis of the determinants of RNA splicing in kidney renal clear cell carcinoma. PMID:25592567
Effects of copy number variable regions on local gene expression in white blood cells of Mexican Americans. PMID:25585699
Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression. PMID:25582907
Methods of integrating data to uncover genotype-phenotype interactions. PMID:25582081
Multi-ethnic analysis reveals soluble L-selectin may be post-transcriptionally regulated by 3'UTR polymorphism: the Multi-Ethnic Study of Atherosclerosis (MESA). PMID:25576479
The genetic and mechanistic basis for variation in gene regulation. PMID:25569255
Insight in genome-wide association of metabolite quantitative traits by exome sequence analyses. PMID:25569235
Biased allelic expression in human primary fibroblast single cells. PMID:25557783
Generation of genomic deletions in mammalian cell lines via CRISPR/Cas9. PMID:25549070
Profile of differential promoter activity by nucleotide substitution at GWAS signals for multiple sclerosis. PMID:25526461
RNA splicing. The human splicing code reveals new insights into the genetic determinants of disease. PMID:25525159
Determining the quality and complexity of next-generation sequencing data without a reference genome. PMID:25514851
Genome-wide association study and admixture mapping reveal new loci associated with total IgE levels in Latinos. PMID:25488688
The 7p15.3 (rs4487645) association for multiple myeloma shows strong allele-specific regulation of the MYC-interacting gene CDCA7L in malignant plasma cells. PMID:25480495
QuASAR: quantitative allele-specific analysis of reads. PMID:25480375
Gene age predicts the strength of purifying selection acting on gene expression variation in humans. PMID:25480033
Approaches for establishing the function of regulatory genetic variants involved in disease. PMID:25473428
Transcription restores DNA repair to heterochromatin, determining regional mutation rates in cancer genomes. PMID:25456125
Sleeping Beauty transposon system for genetic etiological research and gene therapy of cancers. PMID:25455252
Mapping Splicing Quantitative Trait Loci in RNA-Seq. PMID:25452687
Partitioning heritability of regulatory and cell-type-specific variants across 11 common diseases. PMID:25439723
Gene-gene and gene-environment interactions detected by transcriptome sequence analysis in twins. PMID:25436857
Alternative splicing at GYNNGY 5' splice sites: more noise, less regulation. PMID:25428370
The BioGRID interaction database: 2015 update. PMID:25428363
Genetic variation in human DNA replication timing. PMID:25416942
Microbial contamination in next generation sequencing: implications for sequence-based analysis of clinical samples. PMID:25412476
Quantitative genetics of CTCF binding reveal local sequence effects and different modes of X-chromosome association. PMID:25411781
Association of the PDE3A-SLCO1C1 locus with the response to anti-TNF agents in psoriasis. PMID:25403996
Whole-genome sequencing to understand the genetic architecture of common gene expression and biomarker phenotypes. PMID:25378555
The eSNV-detect: a computational system to identify expressed single nucleotide variants from transcriptome sequencing data. PMID:25352556
Common variants associated with general and MMR vaccine-related febrile seizures. PMID:25344690
Genetic influences on translation in yeast. PMID:25340754
Allelic expression mapping across cellular lineages to establish impact of non-coding SNPs. PMID:25326100
Explicit DNase sequence bias modeling enables high-resolution transcription factor footprint detection. PMID:25294828
svaseq: removing batch effects and other unwanted noise from sequencing data. PMID:25294822
Variation and genetic control of gene expression in primary immunocytes across inbred mouse strains. PMID:25267973
The role of the interactome in the maintenance of deleterious variability in human populations. PMID:25261458
High-resolution transcriptome analysis with long-read RNA sequencing. PMID:25251678
Allelic mapping bias in RNA-sequencing is not a major confounder in eQTL studies. PMID:25239376
RNA-Seq alignment to individualized genomes improves transcript abundance estimates in multiparent populations. PMID:25236449
Methylation QTLs are associated with coordinated changes in transcription factor binding, histone modifications, and gene expression levels. PMID:25233095
Novel distal eQTL analysis demonstrates effect of population genetic architecture on detecting and interpreting associations. PMID:25230953
IsomiR expression profiles in human lymphoblastoid cell lines exhibit population and gender dependencies. PMID:25229428
Understanding susceptibility to breast cancer metastasis: the genetic approach. PMID:25214894
Intersection of population variation and autoimmunity genetics in human T cell activation. PMID:25214635
Co-regulated transcripts associated to cooperating eSNPs define Bi-fan motifs in human gene networks. PMID:25210734
Expression QTL-based analyses reveal the mechanisms underlying colorectal cancer predisposition. PMID:25201067
Transcriptome sequencing of a large human family identifies the impact of rare noncoding variants. PMID:25192044
A regulatory polymorphism in HAVCR2 modulates susceptibility to HIV-1 infection. PMID:25180498
Dissecting complex traits using the Drosophila Synthetic Population Resource. PMID:25175100
RNA-Seq reveals novel transcriptional reorganization in human alcoholic brain. PMID:25172479
Genetics of gene expression in CNS. PMID:25172476
MIRPIPE: quantification of microRNAs in niche model organisms. PMID:25165094
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
Transcriptome sequencing from diverse human populations reveals differentiated regulatory architecture. PMID:25121757
Missing heritability of common diseases and treatments outside the protein-coding exome. PMID:25107510
Downregulation of the acetyl-CoA metabolic network in adipose tissue of obese diabetic individuals and recovery after weight loss. PMID:25099943
Putative cis-regulatory drivers in colorectal cancer. PMID:25079323
Distribution and medical impact of loss-of-function variants in the Finnish founder population. PMID:25078778
Genetics of gene expression in immunity to infection. PMID:25078545
MicroRNA-138 is a potential regulator of memory performance in humans. PMID:25071529
MicroRNA-138 is a potential regulator of memory performance in humans. PMID:25071529
Analysis of stop-gain and frameshift variants in human innate immunity genes. PMID:25058640
Integrative genomics reveals novel molecular pathways and gene networks for coronary artery disease. PMID:25033284
Gene expression profiling of the response to interferon beta in Epstein-Barr-transformed and primary B cells of patients with multiple sclerosis. PMID:25025430
Single nucleotide polymorphisms with cis-regulatory effects on long non-coding transcripts in human primary monocytes. PMID:25025429
Cis and trans effects of human genomic variants on gene expression. PMID:25010687
Adipose tissue CIDEA is associated, independently of weight variation, to change in insulin resistance during a longitudinal weight control dietary program in obese individuals. PMID:24983748
Cancer affects microRNA expression, release, and function in cardiac and skeletal muscle. PMID:24980554
Allele-specific expression and eQTL analysis in mouse adipose tissue. PMID:24927774
Genetic studies of Crohn's disease: past, present and future. PMID:24913378
Characterization of genomic deletion efficiency mediated by clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 nuclease system in mammalian cells. PMID:24907273
A tour through the transcriptional landscape of platelets. PMID:24904119
Genetic background drives transcriptional variation in human induced pluripotent stem cells. PMID:24901476
Inference of high resolution HLA types using genome-wide RNA or DNA sequencing reads. PMID:24884790
Genome-wide interaction studies reveal sex-specific asthma risk alleles. PMID:24824216
A symbiotic liaison between the genetic and epigenetic code. PMID:24822056
Genetic dissection of the Drosophila melanogaster female head transcriptome reveals widespread allelic heterogeneity. PMID:24810915
Evolution at protein ends: major contribution of alternative transcription initiation and termination to the transcriptome and proteome diversity in mammals. PMID:24792168
Polarization of the effects of autoimmune and neurodegenerative risk alleles in leukocytes. PMID:24786080
Determining effects of non-synonymous SNPs on protein-protein interactions using supervised and semi-supervised learning. PMID:24784581
Genetic interactions affecting human gene expression identified by variance association mapping. PMID:24771767
Determining causality and consequence of expression quantitative trait loci. PMID:24770875
Principles and methods of integrative genomic analyses in cancer. PMID:24759209
Expression quantitative trait analyses to identify causal genetic variants for type 2 diabetes susceptibility. PMID:24748924
Domains of genome-wide gene expression dysregulation in Down's syndrome. PMID:24740065
Reading and language disorders: the importance of both quantity and quality. PMID:24705331
Joint analysis of functional genomic data and genome-wide association studies of 18 human traits. PMID:24702953
Unlocking the treasure trove: from genes to schizophrenia biology. PMID:24674812
Tempo and mode of regulatory evolution in Drosophila. PMID:24567308
A cis-eQTL of HLA-DRB1 and a frameshift mutation of MICA contribute to the pattern of association of HLA alleles with cervical cancer. PMID:24520070
High risk population isolate reveals low frequency variants predisposing to intracranial aneurysms. PMID:24497844
A genomic portrait of the genetic architecture and regulatory impact of microRNA expression in response to infection. PMID:24482540
Exon identity crisis: disease-causing mutations that disrupt the splicing code. PMID:24456648
Diversity of human tRNA genes from the 1000-genomes project. PMID:24448271
Causality in genetics: the gradient of genetic effects and back to Koch's postulates of causality. PMID:24436434
Genetics of single-cell protein abundance variation in large yeast populations. PMID:24402228
Progress in genomics according to bingo: 2013 edition. PMID:24367899
PennSeq: accurate isoform-specific gene expression quantification in RNA-Seq by modeling non-uniform read distribution. PMID:24362841
Personalized medicine: from genotypes and molecular phenotypes towards therapy- session introduction. PMID:24297549
Systems genetics approaches to understand complex traits. PMID:24296534
Finding the active genes in deep RNA-seq gene expression studies. PMID:24215113
Beyond GWASs: illuminating the dark road from association to function. PMID:24210251
Editors' pick: transcriptomes of 1000 genomes. PMID:24139098
Coordinated effects of sequence variation on DNA binding, chromatin structure, and transcription. PMID:24136355
Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories. PMID:24037425
The European Bioinformatics Institute in 2016: Data growth and integration PubMed citations: 37.

37 articles citing: The European Bioinformatics Institute in 2016: Data growth and integration

Galbase: a comprehensive repository for integrating chicken multi-omics data. PMID:35549894
Murine allele and transgene symbols: ensuring unique, concise, and informative nomenclature. PMID:34389871
ELIXIR-EXCELERATE: establishing Europe's data infrastructure for the life science research of the future. PMID:33565128
The reuse of public datasets in the life sciences: potential risks and rewards. PMID:33024631
The Biological Significance of Multi-copy Regions and Their Impact on Variant Discovery. PMID:32827758
An open-source GIS-enabled lookup service for Nagoya Protocol party information. PMID:32283554
Novel phylogenetic methods are needed for understanding gene function in the era of mega-scale genome sequencing. PMID:31943056
A Vision for Development and Utilization of High-Throughput Phenotyping and Big Data Analytics in Livestock. PMID:31921279
MiST 3.0: an updated microbial signal transduction database with an emphasis on chemosensory systems. PMID:31754718
geneHummus: an R package to define gene families and their expression in legumes and beyond. PMID:31319791
Drug prioritization using the semantic properties of a knowledge graph. PMID:31000794
The EMBL-EBI search and sequence analysis tools APIs in 2019. PMID:30976793
How to Develop a Drug Target Ontology: KNowledge Acquisition and Representation Methodology (KNARM). PMID:30848456
Colombia, an unknown genetic diversity in the era of Big Data. PMID:30537922
The European Bioinformatics Institute in 2018: tools, infrastructure and training. PMID:30445657
IMG/VR v.2.0: an integrated data management and analysis system for cultivated and environmental viral genomes. PMID:30407573
The European Nucleotide Archive in 2018. PMID:30395270
Secure large-scale genome data storage and query. PMID:30337067
BTW-Bioinformatics Through Windows: an easy-to-install package to analyze marker gene data. PMID:30083449
An Artificial Neural Network Integrated Pipeline for Biomarker Discovery Using Alzheimer's Disease as a Case Study. PMID:29977480
Data distribution in public veterinary service: health and safety challenges push for context-aware systems. PMID:29273034
The European Bioinformatics Institute in 2017: data coordination and integration. PMID:29186510
Establishing a distributed national research infrastructure providing bioinformatics support to life science researchers in Australia. PMID:29106479
Genome Variation Map: a data repository of genome variations in BIG Data Center. PMID:29069473
A Review of Recent Advances in Translational Bioinformatics: Bridges from Biology to Medicine. PMID:29063562
From chromatogram to analyte to metabolite. How to pick horses for courses from the massive web resources for mass spectral plant metabolomics. PMID:28520864
Toxic Electrophiles Induce Expression of the Multidrug Efflux Pump MexEF-OprN in Pseudomonas aeruginosa through a Novel Transcriptional Regulator, CmrA. PMID:28507116
GSA: Genome Sequence Archive<sup/> PMID:28387199
"Big Data" for Breast Cancer: Where to look and what you will find. PMID:28164152
Global open data management in metabolomics. PMID:28092796
Controlling new knowledge: Genomic science, governance and the politics of bioinformatics. PMID:28056721
VaProS: a database-integration approach for protein/genome information retrieval. PMID:28012137
WormBase ParaSite - a comprehensive resource for helminth genomics. PMID:27899279
Genome, transcriptome and proteome: the rise of omics data and their integration in biomedical sciences. PMID:27881428
IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses. PMID:27799466
Using Big Data to Discover Diagnostics and Therapeutics for Gastrointestinal and Liver Diseases. PMID:27773806
Patterns of database citation in articles and patents indicate long-term scientific and industry value of biological data resources. PMID:27092246
http://dx.doi.org/10.6019/tol.eva-w.2016.00001.1

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dna structural variation
metasource: Fairsharing.org
version: FAIRsharing.org: EVA; European Variation Archive; DOI: https://doi.org/10.25504/FAIRsharing.6824pv; Last edited: Feb. 25, 2020, 3:03 p.m.; Last accessed: Jan 03 2022 7:05 p.m.

genetic polymorphism
metasource: Fairsharing.org
version: FAIRsharing.org: EVA; European Variation Archive; DOI: https://doi.org/10.25504/FAIRsharing.6824pv; Last edited: Feb. 25, 2020, 3:03 p.m.; Last accessed: Jan 03 2022 7:05 p.m.

genotype
metasource: Fairsharing.org
version: FAIRsharing.org: EVA; European Variation Archive; DOI: https://doi.org/10.25504/FAIRsharing.6824pv; Last edited: Feb. 25, 2020, 3:03 p.m.; Last accessed: Jan 03 2022 7:05 p.m.

sequence variant
metasource: Fairsharing.org
version: FAIRsharing.org: EVA; European Variation Archive; DOI: https://doi.org/10.25504/FAIRsharing.6824pv; Last edited: Feb. 25, 2020, 3:03 p.m.; Last accessed: Jan 03 2022 7:05 p.m.

sequencing
metasource: Fairsharing.org
version: FAIRsharing.org: EVA; European Variation Archive; DOI: https://doi.org/10.25504/FAIRsharing.6824pv; Last edited: Feb. 25, 2020, 3:03 p.m.; Last accessed: Jan 03 2022 7:05 p.m.

dna sequences
metasource: re3data.org
version: re3data.org: European Variation Archive; editing status 2021-09-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3F05Q last accessed: 2022-11-04

ga4gh
metasource: re3data.org
version: re3data.org: European Variation Archive; editing status 2021-09-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3F05Q last accessed: 2022-11-04

global alliance for genomic and health
metasource: re3data.org
version: re3data.org: European Variation Archive; editing status 2021-09-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3F05Q last accessed: 2022-11-04

genomics
metasource: re3data.org
version: re3data.org: European Variation Archive; editing status 2021-09-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3F05Q last accessed: 2022-11-04

metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:05.943295

genetics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:05.943295

genetic variation
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:05.943295

dna structural variation polymorphism genotype sequence variant sequencing dna sequences ga4gh global alliance for genomic and health genomics genetics genetic variation

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Human Genetic Variation Database

The European Bioinformatics Institute Tools

The European Genome-phenome Archive

European Nucleotide Archive

BioStudies

Database of genomic structural VARiation

Database of Genomic Variants archive (DGVa)

European Genome-phenome Archive (EGA)

Pharmacogenomics Knowledge Base

MGnify

BioImage Archive

Database of Genomic Variants

IMGT database of human MHC

gnomAD

BioSamples at the European Bioinformatics Institute

PhenoModifier

IPD - Immuno Polymorphism Database

Genome Variation Map

China National GeneBank DataBase

UniSave