FAIRsharing.ekzmjp; Last edited: June 22, 2021, 11:56 a.m.; Last accessed: Jan 03 2022 7:07 p.m.

metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

ModMine
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:22.228175

metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:22.228175

Other names: ModMine

This source may no longer be available. No known URL could be resolved successfully.

modMine is an integrated web resource of data and tools to browse and search modENCODE data and experimental details, download results and access the GBrowse genome browser.

Webpage:

http://intermine.modencode.org/

Licence:

Name: LGPL-2.1

Publications: (6)

Publications
More detailed information about this field from each metasource.

Identification of functional elements and regulatory circuits by Drosophila modENCODE
PMID: 21177974
metasource: Fairsharing.org
version: FAIRsharing.org: modMine; modMine; DOI: https://doi.org/10.25504/FAIRsharing.ekzmjp; Last edited: June 22, 2021, 11:56 a.m.; Last accessed: Jan 03 2022 7:07 p.m.

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project
PMID: 21177976
metasource: Fairsharing.org
version: FAIRsharing.org: modMine; modMine; DOI: https://doi.org/10.25504/FAIRsharing.ekzmjp; Last edited: June 22, 2021, 11:56 a.m.; Last accessed: Jan 03 2022 7:07 p.m.

Unlocking the secrets of the genome
PMID: 19536255
metasource: Fairsharing.org
version: FAIRsharing.org: modMine; modMine; DOI: https://doi.org/10.25504/FAIRsharing.ekzmjp; Last edited: June 22, 2021, 11:56 a.m.; Last accessed: Jan 03 2022 7:07 p.m.

modMine: flexible access to modENCODE data
PMID: 22080565
metasource: Fairsharing.org
version: FAIRsharing.org: modMine; modMine; DOI: https://doi.org/10.25504/FAIRsharing.ekzmjp; Last edited: June 22, 2021, 11:56 a.m.; Last accessed: Jan 03 2022 7:07 p.m.

http://dx.doi.org/10.1093/nar/GKR921
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

http://dx.doi.org/10.1093/bioinformatics/bts577
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:22.228175

Identification of functional elements and regulatory circuits by Drosophila modENCODE PubMed citations: 676.

676 articles citing: Identification of functional elements and regulatory circuits by Drosophila modENCODE

Application of the 3C Method to Study the Developmental Genes in Drosophila Larvae. PMID:35910225
Neuronal activity induces glucosylceramide that is secreted via exosomes for lysosomal degradation in glia. PMID:35857503
The Chromosomal Distribution of Sex-Biased MicroRNAs in Drosophila is Nonadaptive. PMID:35809037
Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements. PMID:35789323
ChIP-Hub provides an integrative platform for exploring plant regulome. PMID:35701419
Harnessing changes in open chromatin determined by ATAC-seq to generate insulin-responsive reporter constructs. PMID:35614386
ASC proneural factors are necessary for chromatin remodeling during neuroectodermal to neuroblast fate transition to ensure the timely initiation of the neural stem cell program. PMID:35549704
Hunchback activates Bicoid in Pair1 neurons to regulate synapse number and locomotor circuit function. PMID:35512697
Exploring machine learning: a scientometrics approach using bibliometrix and VOSviewer. PMID:35434524
Multidimensional chromatin profiling of zebrafish pancreas to uncover and investigate disease-relevant enhancers. PMID:35410466
Transposable element landscapes in aging Drosophila. PMID:35239675
Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly. PMID:35239393
High Stability of the Epigenome in Drosophila Interspecific Hybrids. PMID:35143649
Episodes of Rapid Recovery of the Functional Activity of the ras85D Gene in the Evolutionary History of Phylogenetically Distant Drosophila Species. PMID:35096018
Quantifying epigenetic modulation of nucleosome breathing by high-throughput AFM imaging. PMID:35065917
Rapid Cis-Trans Coevolution Driven by a Novel Gene Retroposed from a Eukaryotic Conserved CCR4-NOT Component in Drosophila. PMID:35052398
Drosophila p53 isoforms have overlapping and distinct functions in germline genome integrity and oocyte quality control. PMID:35023826
DamID transcriptional profiling identifies the Snail/Scratch transcription factor Kahuli as an Alk target in the Drosophila visceral mesoderm. PMID:34905617
Glitazone Treatment Rescues Phenotypic Deficits in a Fly Model of Gaucher/Parkinson's Disease. PMID:34884544
Msl3 promotes germline stem cell differentiation in female Drosophila. PMID:34878097
Transposable element profiles reveal cell line identity and loss of heterozygosity in Drosophila cell culture. PMID:34849875
The Organization of Pericentromeric Heterochromatin in Polytene Chromosome 3 of the Drosophilamelanogaster Line with the Rif11; SuURES Su(var)3-906 Mutations Suppressing Underreplication. PMID:34831030
ReMap 2022: a database of Human, Mouse, Drosophila and Arabidopsis regulatory regions from an integrative analysis of DNA-binding sequencing experiments. PMID:34751401
An explainable artificial intelligence approach for decoding the enhancer histone modifications code and identification of novel enhancers in Drosophila. PMID:34749786
Inferring primase-DNA specific recognition using a data driven approach. PMID:34718733
Repression precedes independent evolutionary gains of a highly specific gene expression pattern. PMID:34706247
Pig genome functional annotation enhances the biological interpretation of complex traits and human disease. PMID:34615879
Genomic organization of the autonomous regulatory domain of eyeless locus in Drosophila melanogaster. PMID:34570231
Chromatin accessibility and regulatory vocabulary across indicine cattle tissues. PMID:34548076
Extracellular matrix protein N-glycosylation mediates immune self-tolerance in Drosophila melanogaster. PMID:34544850
Transcriptional enhancers and their communication with gene promoters. PMID:34414474
Highly contiguous assemblies of 101 drosophilid genomes. PMID:34279216
Impact of Genetic Variation in Gene Regulatory Sequences: A Population Genomics Perspective. PMID:34276769
Distinct mechanisms mediate X chromosome dosage compensation in Anopheles and Drosophila. PMID:34266874
Interactions and Feedbacks in E-Cadherin Transcriptional Regulation. PMID:34262912
The zinc finger protein CLAMP promotes long-range chromatin interactions that mediate dosage compensation of the Drosophila male X-chromosome. PMID:34187599
Evolution and genomic signatures of spontaneous somatic mutation in Drosophila intestinal stem cells. PMID:34168010
Gelsolin and dCryAB act downstream of muscle identity genes and contribute to preventing muscle splitting and branching in Drosophila. PMID:34162956
Molecular evolution and the decline of purifying selection with age. PMID:33976227
Fish-Ing for Enhancers in the Heart. PMID:33920121
A compendium and comparative epigenomics analysis of cis-regulatory elements in the pig genome. PMID:33850120
Independence of chromatin conformation and gene regulation during Drosophila dorsoventral patterning. PMID:33795866
AP-1 subunits converge promiscuously at enhancers to potentiate transcription. PMID:33674350
Unraveling the features of somatic transposition in the Drosophila intestine. PMID:33634906
Endosomal Rab GTPases regulate secretory granule maturation in Drosophila larval salivary glands. PMID:33628358
Assembly and Exploration of a Single Cell Atlas of the Drosophila Larval Ventral Cord. Identification of Rare Cell Types. PMID:33600085
Topologically associating domains and their role in the evolution of genome structure and function in Drosophila. PMID:33563719
Functional Diversification, Redundancy, and Epistasis among Paralogs of the Drosophila melanogaster Obp50a-d Gene Cluster. PMID:33560417
Transcription Factors Drive Opposite Relationships between Gene Age and Tissue Specificity in Male and Female Drosophila Gonads. PMID:33481021
White pupae phenotype of tephritids is caused by parallel mutations of a MFS transporter. PMID:33479218
NetMix: A Network-Structured Mixture Model for Reduced-Bias Estimation of Altered Subnetworks. PMID:33400606
Resilin matrix distribution, variability and function in Drosophila. PMID:33317537
Molecular and evolutionary processes generating variation in gene expression. PMID:33268840
Computational tools for geroscience. PMID:33241167
Revisiting the organization of Polycomb-repressed domains: 3D chromatin models from Hi-C compared with super-resolution imaging. PMID:33095877
Search and comparison of (epi)genomic feature patterns in multiple genome browser tracks. PMID:33076821
Interplay of pericentromeric genome organization and chromatin landscape regulates the expression of Drosophila melanogaster heterochromatic genes. PMID:33028366
A comparative analysis of chromatin accessibility in cattle, pig, and mouse tissues. PMID:33028202
Functional Transcription Factor Target Networks Illuminate Control of Epithelial Remodelling. PMID:33007944
Identification of Split-GAL4 Drivers and Enhancers That Allow Regional Cell Type Manipulations of the Drosophila melanogaster Intestine. PMID:32988987
Rosy Beginnings: Studying Peroxisomes in Drosophila. PMID:32984330
Single-cell RNA sequencing in Drosophila: Technologies and applications. PMID:32940008
Supervised enhancer prediction with epigenetic pattern recognition and targeted validation. PMID:32737473
Polymorphism and Divergence of Novel Gene Expression Patterns in Drosophila melanogaster. PMID:32737121
Perspectives on ENCODE. PMID:32728248
The Classic Lobe Eye Phenotype of Drosophila Is Caused by Transposon Insertion-Induced Misexpression of a Zinc-Finger Transcription Factor. PMID:32641295
Epigenomics and genotype-phenotype association analyses reveal conserved genetic architecture of complex traits in cattle and human. PMID:32620158
The brachyceran de novo gene PIP82, a phosphorylation target of aPKC, is essential for proper formation and maintenance of the rhabdomeric photoreceptor apical domain in Drosophila. PMID:32579558
Sequence-Independent Self-Assembly of Germ Granule mRNAs into Homotypic Clusters. PMID:32464092
Integrative analysis of reference epigenomes in 20 rice varieties. PMID:32461553
Transcriptome Analysis of Ophraella communa Male Reproductive Tract in Indirect Response to Elevated CO2 and Heat Wave. PMID:32431624
Intricate Genetic Programs Controlling Dormancy in Mycobacterium tuberculosis. PMID:32348771
Release of promoter-proximal paused Pol II in response to histone deacetylase inhibition. PMID:32297950
Genes Containing Long Introns Occupy Series of Bands and Interbands In Drosophila melanogaster polytene Chromosomes. PMID:32290448
Systematic alteration of ATAC-seq for profiling open chromatin in cryopreserved nuclei preparations from livestock tissues. PMID:32251359
The conserved regulatory basis of mRNA contributions to the early Drosophila embryo differs between the maternal and zygotic genomes. PMID:32226006
The Drosophila Y Chromosome Affects Heterochromatin Integrity Genome-Wide. PMID:32211857
Identification of a master transcription factor and a regulatory mechanism for desiccation tolerance in the anhydrobiotic cell line Pv11. PMID:32191739
The Dm-Myb Oncoprotein Contributes to Insulator Function and Stabilizes Repressive H3K27me3 PcG Domains. PMID:32160531
Hierarchical and Dynamic Regulation of Defense-Responsive Specialized Metabolism by WRKY and MYB Transcription Factors. PMID:32082343
In situ dissection of domain boundaries affect genome topology and gene transcription in Drosophila. PMID:32060283
The Drosophila MLR COMPASS complex is essential for programming cis-regulatory information and maintaining epigenetic memory during development. PMID:32052053
A native chromatin immunoprecipitation (ChIP) protocol for studying histone modifications in strawberry fruits. PMID:32025237
Genome-wide MNase hypersensitivity assay unveils distinct classes of open chromatin associated with H3K27me3 and DNA methylation in Arabidopsis thaliana. PMID:32014062
ORSO (Online Resource for Social Omics): A data-driven social network connecting scientists to genomics datasets. PMID:31978042
Large-Scale Profiling of RBP-circRNA Interactions from Public CLIP-Seq Datasets. PMID:31947823
Rho-Kinase Planar Polarization at Tissue Boundaries Depends on Phospho-regulation of Membrane Residence Time. PMID:31902655
Combinatorial interactions of the LEC1 transcription factor specify diverse developmental programs during soybean seed development. PMID:31892538
Muscle-derived Dpp regulates feeding initiation via endocrine modulation of brain dopamine biosynthesis. PMID:31831628
Faint gray bands in Drosophila melanogaster polytene chromosomes are formed by coding sequences of housekeeping genes. PMID:31820086
The Integrator Complex Attenuates Promoter-Proximal Transcription at Protein-Coding Genes. PMID:31809743
Gene activation by dCas9-CBP and the SAM system differ in target preference. PMID:31792240
Core Components of the Nuclear Pore Bind Distinct States of Chromatin and Contribute to Polycomb Repression. PMID:31784359
Bulk and Single-Cell Next-Generation Sequencing: Individualizing Treatment for Colorectal Cancer. PMID:31752125
The ENCODE Portal as an Epigenomics Resource. PMID:31751002
Super-enhancers in transcriptional regulation and genome organization. PMID:31724731
Transcriptional Silencers in Drosophila Serve a Dual Role as Transcriptional Enhancers in Alternate Cellular Contexts. PMID:31704182
Structural variants exhibit widespread allelic heterogeneity and shape variation in complex traits. PMID:31653862
Sequence and chromatin determinants of transcription factor binding and the establishment of cell type-specific binding patterns. PMID:31639474
Enhancer Dysfunction in 3D Genome and Disease. PMID:31635067
Mamo decodes hierarchical temporal gradients into terminal neuronal fate. PMID:31545163
Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci. PMID:31537640
Molecular Profiling of the Drosophila Antenna Reveals Conserved Genes Underlying Olfaction in Insects. PMID:31527046
An RNAi Screen for Genes Required for Growth of Drosophila Wing Tissue. PMID:31387856
MAPCap allows high-resolution detection and differential expression analysis of transcription start sites. PMID:31363093
The transcription factor Hey and nuclear lamins specify and maintain cell identity. PMID:31310235
A specific isoform of Pyd/ZO-1 mediates junctional remodeling and formation of slit diaphragms. PMID:31171632
Bridging the gap between reference and real transcriptomes. PMID:31159855
Innovative strategies for annotating the "relationSNP" between variants and molecular phenotypes. PMID:31114635
Identification and Conservation Analysis of Cis-Regulatory Elements in Pig Liver. PMID:31067820
Quantitative Comparison of the Anterior-Posterior Patterning System in the Embryos of Five Drosophila Species. PMID:31048401
Molecular and genetic organization of bands and interbands in the dot chromosome of Drosophila melanogaster. PMID:31041520
Genome-wide Kdm4 histone demethylase transcriptional regulation in Drosophila. PMID:31020413
A Comprehensive Drosophila melanogaster Transcription Factor Interactome. PMID:30995488
Studying alcohol use disorder using Drosophila melanogaster in the era of 'Big Data'. PMID:30992041
Dynamic control of enhancer activity drives stage-specific gene expression during flower morphogenesis. PMID:30979870
ATAC-seq reveals regional differences in enhancer accessibility during the establishment of spatial coordinates in the Drosophila blastoderm. PMID:30962180
FisherMP: fully parallel algorithm for detecting combinatorial motifs from large ChIP-seq datasets. PMID:30957858
The putative C-type lectin Schlaff ensures epidermal barrier compactness in Drosophila. PMID:30926832
Visualizing DNA folding and RNA in embryos at single-cell resolution. PMID:30886393
cRegulome: an R package for accessing microRNA and transcription factor-gene expression correlations in cancer. PMID:30867986
RECAP reveals the true statistical significance of ChIP-seq peak calls. PMID:30824903
Hierarchical Transcription Factor and Chromatin Binding Network for Wood Formation in Black Cottonwood (Populus trichocarpa). PMID:30755461
Chromatin architecture reorganization during neuronal cell differentiation in Drosophila genome. PMID:30709849
Small Segmental Duplications in Drosophila-High Rate of Emergence and Elimination. PMID:30689862
Constructing tissue-specific transcriptional regulatory networks via a Markov random field. PMID:30598101
Cell Specificity of Human Regulatory Annotations and Their Genetic Effects on Gene Expression. PMID:30593493
Pleiotropy Modulates the Efficacy of Selection in Drosophila melanogaster. PMID:30590559
Investigation of the Developmental Requirements of Drosophila HP1 and Insulator Protein Partner, HIPP1. PMID:30514714
Retrograde BMP signaling activates neuronal gene expression through widespread deployment of a conserved BMP-responsive cis-regulatory activation element. PMID:30476189
Deleterious mitochondrial DNA point mutations are overrepresented in Drosophila expressing a proofreading-defective DNA polymerase γ. PMID:30452458
CRM Discovery Beyond Model Insects. PMID:30414115
ChIP-Atlas: a data-mining suite powered by full integration of public ChIP-seq data. PMID:30413482
HP1B is a euchromatic Drosophila HP1 homolog with links to metabolism. PMID:30346969
Dense neural networks for predicting chromatin conformation. PMID:30314429
Integrative genomic analysis reveals novel regulatory mechanisms of eyeless during Drosophila eye development. PMID:30295802
Phase transitioned nuclear Oskar promotes cell division of Drosophila primordial germ cells. PMID:30260314
The interaction landscape between transcription factors and the nucleosome. PMID:30250250
Comparative Transcriptomics in Two Extreme Neopterans Reveals General Trends in the Evolution of Modern Insects. PMID:30240738
Facultative dosage compensation of developmental genes on autosomes in Drosophila and mouse embryonic stem cells. PMID:30194291
The genome-wide transcriptional regulatory landscape of ecdysone in the silkworm. PMID:30149809
Spatial regulation of expanded transcription in the Drosophila wing imaginal disc. PMID:30063727
Importance of miRNA stability and alternative primary miRNA isoforms in gene regulation during Drosophila development. PMID:30024380
Refining a steroidogenic model: an analysis of RNA-seq datasets from insect prothoracic glands. PMID:30005604
Apical and Basal Matrix Remodeling Control Epithelial Morphogenesis. PMID:29974861
DamID profiling of dynamic Polycomb-binding sites in Drosophila imaginal disc development and tumorigenesis. PMID:29871666
The importance of a halotyrosine dehalogenase for Drosophila fertility. PMID:29764939
Reduced Neuronal Transcription of Escargot, the Drosophila Gene Encoding a Snail-Type Transcription Factor, Promotes Longevity. PMID:29760717
Spermiogenesis and Male Fertility Require the Function of Suppressor of Hairy-Wing in Somatic Cyst Cells of Drosophila. PMID:29739818
Transcription start site analysis reveals widespread divergent transcription in D. melanogaster and core promoter-encoded enhancer activities. PMID:29659982
Chromatin-associated RNA sequencing (ChAR-seq) maps genome-wide RNA-to-DNA contacts. PMID:29648534
Polytene Chromosomes - A Portrait of Functional Organization of the Drosophila Genome. PMID:29606905
ChIP-ping the branches of the tree: functional genomics and the evolution of eukaryotic gene regulation. PMID:29529131
Omega Class Glutathione S-Transferase: Antioxidant Enzyme in Pathogenesis of Neurodegenerative Diseases. PMID:29435097
A maximum-entropy model for predicting chromatin contacts. PMID:29401453
Dynamic genome wide expression profiling of Drosophila head development reveals a novel role of Hunchback in retinal glia cell development and blood-brain barrier integrity. PMID:29360820
Histone H3 lysine 4 monomethylation modulates long-range chromatin interactions at enhancers. PMID:29313530
An Ichor-dependent apical extracellular matrix regulates seamless tube shape and integrity. PMID:29309404
Systematic genetic interaction studies identify histone demethylase Utx as potential target for ameliorating Huntington's disease. PMID:29281014
A conserved maternal-specific repressive domain in Zelda revealed by Cas9-mediated mutagenesis in Drosophila melanogaster. PMID:29261646
Hidden genetic variation shapes the structure of functional elements in Drosophila. PMID:29255259
IndeCut evaluates performance of network motif discovery algorithms. PMID:29236975
Zinc Detoxification: A Functional Genomics and Transcriptomics Analysis in Drosophila melanogaster Cultured Cells. PMID:29223976
Landscape and evolution of tissue-specific alternative polyadenylation across Drosophila species. PMID:29191225
CRISPR Genome Engineering for Human Pluripotent Stem Cell Research. PMID:29158838
The Encyclopedia of DNA elements (ENCODE): data portal update. PMID:29126249
Chromatin-state discovery and genome annotation with ChromHMM. PMID:29120462
High rate of translocation-based gene birth on the Drosophila Y chromosome. PMID:29078298
CBP Regulates Recruitment and Release of Promoter-Proximal RNA Polymerase II. PMID:29056321
Analysis of temporal transcription expression profiles reveal links between protein function and developmental stages of Drosophila melanogaster. PMID:29045400
Caenorhabditis elegans Dosage Compensation: Insights into Condensin-Mediated Gene Regulation. PMID:29037439
Data Resources for Human Functional Genomics. PMID:28989986
Single-molecule kinetic analysis of HP1-chromatin binding reveals a dynamic network of histone modification and DNA interactions. PMID:28985346
Gene Tagging Strategies To Assess Protein Expression, Localization, and Function in Drosophila. PMID:28978772
Rapid DNA Synthesis During Early Drosophila Embryogenesis Is Sensitive to Maternal Humpty Dumpty Protein Function. PMID:28942426
Variation in Position Effect Variegation Within a Natural Population. PMID:28931559
Multiple P450s and Variation in Neuronal Genes Underpins the Response to the Insecticide Imidacloprid in a Population of Drosophila melanogaster. PMID:28900129
Canonical and non-canonical JAK/STAT transcriptional targets may be involved in distinct and overlapping cellular processes. PMID:28893190
The Hox proteins Ubx and AbdA collaborate with the transcription pausing factor M1BP to regulate gene transcription. PMID:28871058
And yet, it moves: nuclear and chromatin dynamics of a heterochromatic double-strand break. PMID:28847828
TAF10 and TAF10b partially redundant roles during Drosophila melanogaster morphogenesis. PMID:28841365
Complex roles of myoglianin in regulating adult performance and lifespan. PMID:28837401
Rhythmic Behavior Is Controlled by the SRm160 Splicing Factor in Drosophila melanogaster. PMID:28801530
The Three-Dimensional Organization of Mammalian Genomes. PMID:28783961
High resolution temporal transcriptomics of mouse embryoid body development reveals complex expression dynamics of coding and noncoding loci. PMID:28751729
Genome-wide Single-Molecule Footprinting Reveals High RNA Polymerase II Turnover at Paused Promoters. PMID:28735898
Robust Identification of Developmentally Active Endothelial Enhancers in Zebrafish Using FANS-Assisted ATAC-Seq. PMID:28723572
A sequence level model of an intact locus predicts the location and function of nonadditive enhancers. PMID:28715438
Pervasive epigenetic effects of Drosophila euchromatic transposable elements impact their evolution. PMID:28695823
Genome-wide search for Zelda-like chromatin signatures identifies GAF as a pioneer factor in early fly development. PMID:28676122
The Arf6 activator Efa6/PSD3 confers regional specificity and modulates ethanol consumption in Drosophila and humans. PMID:28607459
mRNA quantification using single-molecule FISH in Drosophila embryos. PMID:28594816
A Short History and Description of Drosophila melanogaster Classical Genetics: Chromosome Aberrations, Forward Genetic Screens, and the Nature of Mutations. PMID:28592503
An Enhancer's Length and Composition Are Shaped by Its Regulatory Task. PMID:28588608
Modeling the cis-regulatory modules of genes expressed in developmental stages of Drosophila melanogaster. PMID:28584716
Building dialogues between clinical and biomedical research through cross-species collaborations. PMID:28579453
ADAR RNA editing below the backbone. PMID:28559490
A fast, efficient chromatin immunoprecipitation method for studying protein-DNA binding in Arabidopsis mesophyll protoplasts. PMID:28539971
Dynamic chromatin technologies: from individual molecules to epigenomic regulation in cells. PMID:28529337
Perspectives on Gene Regulatory Network Evolution. PMID:28528721
The Role of Omics in the Application of Adverse Outcome Pathways for Chemical Risk Assessment. PMID:28525648
Piwi interacts with chromatin at nuclear pores and promiscuously binds nuclear transcripts in Drosophila ovarian somatic cells. PMID:28472469
Exploring spatially adjacent TFBS-clustered regions with Hi-C data. PMID:28472433
HDAC Inhibitors Disrupt Programmed Resistance to Apoptosis During Drosophila Development. PMID:28455414
The absence of crossovers on chromosome 4 in Drosophila melanogaster: Imperfection or interesting exception? PMID:28426351
Omicseq: a web-based search engine for exploring omics datasets. PMID:28402462
High-confidence coding and noncoding transcriptome maps. PMID:28396519
Landscape of histone modifications in a sponge reveals the origin of animal cis-regulatory complexity. PMID:28395144
The developmental proteome of Drosophila melanogaster. PMID:28381612
Protein and Genetic Composition of Four Chromatin Types in Drosophila melanogaster Cell Lines. PMID:28367077
Testis-specific ATP synthase peripheral stalk subunits required for tissue-specific mitochondrial morphogenesis in Drosophila. PMID:28335714
Sex combs reduced (Scr) regulatory region of Drosophila revisited. PMID:28331962
Epigenetic and genetic alterations and their influence on gene regulation in chronic lymphocytic leukemia. PMID:28302063
Correspondence of D. melanogaster and C. elegans developmental stages revealed by alternative splicing characteristics of conserved exons. PMID:28302059
Fast, scalable prediction of deleterious noncoding variants from functional and population genomic data. PMID:28288115
Network Reconstruction Reveals that Valproic Acid Activates Neurogenic Transcriptional Programs in Adult Brain Following Traumatic Injury. PMID:28271248
Molecular Population Genetics. PMID:28270526
CisMapper: predicting regulatory interactions from transcription factor ChIP-seq data. PMID:28204599
The Drosophila Gene Expression Tool (DGET) for expression analyses. PMID:28187709
Deciphering the DNA code for the function of the Drosophila polydactyl zinc finger protein Suppressor of Hairy-wing. PMID:28158673
An ensemble micro neural network approach for elucidating interactions between zinc finger proteins and their target DNA. PMID:28155662
Selecting the most appropriate time points to profile in high-throughput studies. PMID:28124972
Integration of temporal and spatial patterning generates neural diversity. PMID:28077877
Different modes of enhancer-specific regulation by Runt and Even-skipped during Drosophila segmentation. PMID:28077616
DNA Occupancy of Polymerizing Transcription Factors: A Chemical Model of the ETS Family Factor Yan. PMID:28076810
Modular combinatorial binding among human trans-acting factors reveals direct and indirect factor binding. PMID:28061806
Three-Dimensional Genome Organization and Function in Drosophila. PMID:28049701
Genome-wide assessment of sequence-intrinsic enhancer responsiveness at single-base-pair resolution. PMID:28024147
Flexible model-based clustering of mixed binary and continuous data: application to genetic regulation and cancer. PMID:27994031
Cloning and functional characterizations of an apoptogenic Hid gene in the Scuttle Fly, Megaselia scalaris (Diptera; Phoridae). PMID:27940109
FlyRNAi.org-the database of the Drosophila RNAi screening center and transgenic RNAi project: 2017 update. PMID:27924039
TFBSbank: a platform to dissect the big data of protein-DNA interaction in human and model species. PMID:27899608
Neurogenomics and the role of a large mutational target on rapid behavioral change. PMID:27825385
A transcription factor hierarchy defines an environmental stress response network. PMID:27811239
FlyBase at 25: looking to the future. PMID:27799470
Using FlyBase, a Database of Drosophila Genes and Genomes. PMID:27730573
Past Roadblocks and New Opportunities in Transcription Factor Network Mapping. PMID:27720190
Genome-wide identification of Drosophila dorso-ventral enhancers by differential histone acetylation analysis. PMID:27678375
A Variable Genetic Architecture of Melanic Evolution in Drosophila melanogaster. PMID:27638419
Genome-wide identification and characterisation of HOT regions in the human genome. PMID:27633377
Chromatin boundary elements organize genomic architecture and developmental gene regulation in Drosophila Hox clusters. PMID:27621770
Data Integration for Microarrays: Enhanced Inference for Gene Regulatory Networks. PMID:27600224
Effects of Gene Dose, Chromatin, and Network Topology on Expression in Drosophila melanogaster. PMID:27599372
Genome-Wide Ultrabithorax Binding Analysis Reveals Highly Targeted Genomic Loci at Developmental Regulators and a Potential Connection to Polycomb-Mediated Regulation. PMID:27575958
OGS2: genome re-annotation of the jewel wasp Nasonia vitripennis. PMID:27561358
Ultra-deep sequencing of ribosome-associated poly-adenylated RNA in early Drosophila embryos reveals hundreds of conserved translated sORFs. PMID:27559081
DNA replication origins-where do we begin? PMID:27542827
Genomic and expression analysis of transition proteins in Drosophila. PMID:27512614
Weak Polygenic Selection Drives the Rapid Adaptation of the Chemosensory System: Lessons from the Upstream Regions of the Major Gene Families. PMID:27503297
ORChestrating the human DNA replication program. PMID:27496327
CLIMP: Clustering Motifs via Maximal Cliques with Parallel Computing Design. PMID:27487245
Identification of Nucleolus-Associated Chromatin Domains Reveals a Role for the Nucleolus in 3D Organization of the A. thaliana Genome. PMID:27477271
Loss of function of the Drosophila Ninein-related centrosomal protein Bsg25D causes mitotic defects and impairs embryonic development. PMID:27422905
Regulation of the BMP Signaling-Responsive Transcriptional Network in the Drosophila Embryo. PMID:27379389
Reusable, extensible, and modifiable R scripts and Kepler workflows for comprehensive single set ChIP-seq analysis. PMID:27377783
The Insect Prothoracic Gland as a Model for Steroid Hormone Biosynthesis and Regulation. PMID:27320926
Chromatin Heterogeneity and Distribution of Regulatory Elements in the Late-Replicating Intercalary Heterochromatin Domains of Drosophila melanogaster Chromosomes. PMID:27300486
Experimental and Computational Considerations in the Study of RNA-Binding Protein-RNA Interactions. PMID:27256380
A multi-task graph-clustering approach for chromosome conformation capture data sets identifies conserved modules of chromosomal interactions. PMID:27233632
CHANGE POINT ANALYSIS OF HISTONE MODIFICATIONS REVEALS EPIGENETIC BLOCKS LINKING TO PHYSICAL DOMAINS. PMID:27231496
A Genetic Mosaic Screen Reveals Ecdysone-Responsive Genes Regulating Drosophila Oogenesis. PMID:27226164
Long-Term Memory in Drosophila Is Influenced by Histone Deacetylase HDAC4 Interacting with SUMO-Conjugating Enzyme Ubc9. PMID:27182943
Identification of Novel Regulators of the JAK/STAT Signaling Pathway that Control Border Cell Migration in the Drosophila Ovary. PMID:27175018
Evolution, Expression, and Function of Nonneuronal Ligand-Gated Chloride Channels in Drosophila melanogaster. PMID:27172217
The Histone Variant H3.3 Is Enriched at Drosophila Amplicon Origins but Does Not Mark Them for Activation. PMID:27172191
Genetic sources of population epigenomic variation. PMID:27156976
Nucleosome Presence at AML-1 Binding Sites Inversely Correlates with Ly49 Expression: Revelations from an Informatics Analysis of Nucleosomes and Immune Cell Transcription Factors. PMID:27124577
Evolution of Epigenetic Regulation in Vertebrate Genomes. PMID:27080453
JBrowse: a dynamic web platform for genome visualization and analysis. PMID:27072794
Drosophila polytene chromosome bands formed by gene introns. PMID:27025489
Glucocerebrosidase Deficiency in Drosophila Results in α-Synuclein-Independent Protein Aggregation and Neurodegeneration. PMID:27019408
Coding exon-structure aware realigner (CESAR) utilizes genome alignments for accurate comparative gene annotation. PMID:27016733
Genome-wide identification and developmental expression profiling of long noncoding RNAs during Drosophila metamorphosis. PMID:26996731
Principles of metadata organization at the ENCODE data coordination center. PMID:26980513
High Throughput Sequencing Identifies Misregulated Genes in the Drosophila Polypyrimidine Tract-Binding Protein (hephaestus) Mutant Defective in Spermatogenesis. PMID:26942929
Neurogenomics: An opportunity to integrate neuroscience, genomics and bioinformatics research in Africa. PMID:26937352
Bilaterian-like promoters in the highly compact Amphimedon queenslandica genome. PMID:26931148
Widespread colocalization of the Drosophila histone acetyltransferase homolog MYST5 with DREF and insulator proteins at active genes. PMID:26894919
Functional transcription factor target discovery via compendia of binding and expression profiles. PMID:26857150
Probabilistic modelling of chromatin code landscape reveals functional diversity of enhancer-like chromatin states. PMID:26841971
The Female Post-Mating Response Requires Genes Expressed in the Secondary Cells of the Male Accessory Gland in Drosophila melanogaster. PMID:26746709
Embryonic transcription is controlled by maternally defined chromatin state. PMID:26679111
DANIO-CODE: Toward an Encyclopedia of DNA Elements in Zebrafish. PMID:26671609
FIG4 regulates lysosome membrane homeostasis independent of phosphatase function. PMID:26662798
CBP binding outside of promoters and enhancers in Drosophila melanogaster. PMID:26604986
A ChIP on the shoulder? Chromatin immunoprecipitation and validation strategies for ChIP antibodies. PMID:26594335
Short linear motifs - ex nihilo evolution of protein regulation. PMID:26589632
Unique transposon landscapes are pervasive across Drosophila melanogaster genomes. PMID:26578579
Simultaneous characterization of sense and antisense genomic processes by the double-stranded hidden Markov model. PMID:26578558
BAR-SH3 sorting nexins are conserved interacting proteins of Nervous wreck that organize synapses and promote neurotransmission. PMID:26567222
Genetics on the Fly: A Primer on the Drosophila Model System. PMID:26564900
Comparative Transcriptomes and EVO-DEVO Studies Depending on Next Generation Sequencing. PMID:26543497
EMERGE: a flexible modelling framework to predict genomic regulatory elements from genomic signatures. PMID:26531828
Genome-wide identification and characterization of tissue-specific RNA editing events in D. melanogaster and their potential role in regulating alternative splicing. PMID:26512413
The TrxG Complex Mediates Cytokine Induced De Novo Enhancer Formation in Islets. PMID:26505193
Computational discovery of transcription factors associated with drug response. PMID:26503816
Single-cell epigenomics: techniques and emerging applications. PMID:26460349
Genome-Wide Detection and Analysis of Multifunctional Genes. PMID:26436655
NetBenchmark: a bioconductor package for reproducible benchmarks of gene regulatory network inference. PMID:26415849
De novo ChIP-seq analysis. PMID:26400819
An Organizational Hub of Developmentally Regulated Chromatin Loops in the Drosophila Antennapedia Complex. PMID:26391952
Optimization of next-generation sequencing transcriptome annotation for species lacking sequenced genomes. PMID:26358618
A predictive modeling approach for cell line-specific long-range regulatory interactions. PMID:26338778
Zelda is differentially required for chromatin accessibility, transcription factor binding, and gene expression in the early Drosophila embryo. PMID:26335634
Zelda overcomes the high intrinsic nucleosome barrier at enhancers during Drosophila zygotic genome activation. PMID:26335633
Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis. PMID:26319390
A Linear Mixed Model Spline Framework for Analysing Time Course 'Omics' Data. PMID:26313144
Genome-wide errant targeting by Hairy. PMID:26305409
Trans-Reactivation: A New Epigenetic Phenomenon Underlying Transcriptional Reactivation of Silenced Genes. PMID:26292210
Nonconsensus Protein Binding to Repetitive DNA Sequence Elements Significantly Affects Eukaryotic Genomes. PMID:26285121
Absence of canonical marks of active chromatin in developmentally regulated genes. PMID:26280901
DNA sequence templates adjacent nucleosome and ORC sites at gene amplification origins in Drosophila. PMID:26227968
The ecdysone receptor coactivator Taiman links Yorkie to transcriptional control of germline stem cell factors in somatic tissue. PMID:26143992
toxoMine: an integrated omics data warehouse for Toxoplasma gondii systems biology research. PMID:26130662
Mechanisms and functions of Nrf2 signaling in Drosophila. PMID:26117322
Functional annotation of HOT regions in the human genome: implications for human disease and cancer. PMID:26113264
Gene Model Annotations for Drosophila melanogaster: Impact of High-Throughput Data. PMID:26109357
Protein-DNA binding in high-resolution. PMID:26038153
Comprehensive RNA-Seq transcriptomic profiling across 11 organs, 4 ages, and 2 sexes of Fischer 344 rats. PMID:25977771
Urothelial cancer gene regulatory networks inferred from large-scale RNAseq, Bead and Oligo gene expression data. PMID:25971253
A histone modification identifies a DNA element controlling slo BK channel gene expression in muscle. PMID:25967280
Genetic Architecture of Abdominal Pigmentation in Drosophila melanogaster. PMID:25933381
Molluscs as models for translational medicine. PMID:25925630
Stepping inside the realm of epigenetic modifiers. PMID:25915083
Common binding by redundant group B Sox proteins is evolutionarily conserved in Drosophila. PMID:25887553
Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project. PMID:25854118
A genome-wide analysis of MADS-box genes in peach [Prunus persica (L.) Batsch]. PMID:25848674
cDREM: inferring dynamic combinatorial gene regulation. PMID:25844671
Pitfalls of mapping high-throughput sequencing data to repetitive sequences: Piwi's genomic targets still not identified. PMID:25805138
Integrating motif, DNA accessibility and gene expression data to build regulatory maps in an organism. PMID:25791631
Using the ENCODE Resource for Functional Annotation of Genetic Variants. PMID:25762420
Pervasive variation of transcription factor orthologs contributes to regulatory network evolution. PMID:25748510
Computational methodology for ChIP-seq analysis. PMID:25741452
Accurate inference of isoforms from multiple sample RNA-Seq data. PMID:25708199
Identifying transcriptional cis-regulatory modules in animal genomes. PMID:25704908
The Mediator complex: a central integrator of transcription. PMID:25693131
A cnidarian homologue of an insect gustatory receptor functions in developmental body patterning. PMID:25692633
An integrative analysis of TFBS-clustered regions reveals new transcriptional regulation models on the accessible chromatin landscape. PMID:25682954
Genome-wide features of neuroendocrine regulation in Drosophila by the basic helix-loop-helix transcription factor DIMMED. PMID:25634895
Neural stem cell progeny regulate stem cell death in a Notch and Hox dependent manner. PMID:25633198
Highly constrained intergenic Drosophila ultraconserved elements are candidate ncRNAs. PMID:25618141
Transcriptional control of an essential ribozyme in Drosophila reveals an ancient evolutionary divide in animals. PMID:25569672
A large-scale, in vivo transcription factor screen defines bivalent chromatin as a key property of regulatory factors mediating Drosophila wing development. PMID:25568052
Dynamic loading and redistribution of the Mcm2-7 helicase complex through the cell cycle. PMID:25555795
A hyper-dynamic nature of bivalent promoter states underlies coordinated developmental gene expression modules. PMID:25551786
Mammalian transcriptional hotspots are enriched for tissue specific enhancers near cell type specific highly expressed genes and are predicted to act as transcriptional activator hubs. PMID:25547756
Genome-wide analysis of drosophila circular RNAs reveals their structural and sequence properties and age-dependent neural accumulation. PMID:25544350
Transcriptional activation is a conserved feature of the early embryonic factor Zelda that requires a cluster of four zinc fingers for DNA binding and a low-complexity activation domain. PMID:25538246
Annotation of genomics data using bidirectional hidden Markov models unveils variations in Pol II transcription cycle. PMID:25527639
cisMEP: an integrated repository of genomic epigenetic profiles and cis-regulatory modules in Drosophila. PMID:25521507
Enhancer-core-promoter specificity separates developmental and housekeeping gene regulation. PMID:25517091
SMARTS: reconstructing disease response networks from multiple individuals using time series gene expression data. PMID:25480376
De novo prediction of cis-regulatory elements and modules through integrative analysis of a large number of ChIP datasets. PMID:25442502
Map of open and closed chromatin domains in Drosophila genome. PMID:25407537
siRNAs from an X-linked satellite repeat promote X-chromosome recognition in Drosophila melanogaster. PMID:25368194
A functional and evolutionary perspective on transcription factor binding in Arabidopsis thaliana. PMID:25361952
Characterizing the developmental transcriptome of the oriental fruit fly, Bactrocera dorsalis (Diptera: Tephritidae) through comparative genomic analysis with Drosophila melanogaster utilizing modENCODE datasets. PMID:25348373
Identifying (non-)coding RNAs and small peptides: challenges and opportunities. PMID:25345765
Two new insulator proteins, Pita and ZIPIC, target CP190 to chromatin. PMID:25342723
High-resolution digital profiling of the epigenome. PMID:25297728
Alignathon: a competitive assessment of whole-genome alignment methods. PMID:25273068
Variation in piRNA and transposable element content in strains of Drosophila melanogaster. PMID:25267446
Spermitin: a novel mitochondrial protein in Drosophila spermatids. PMID:25265054
Heritable variation of mRNA decay rates in yeast. PMID:25258386
Regulation of transcription by long noncoding RNAs. PMID:25251851
Chromatin reader L(3)mbt requires the Myb-MuvB/DREAM transcriptional regulatory complex for chromosomal recruitment. PMID:25249635
A functional insulator screen identifies NURF and dREAM components to be required for enhancer-blocking. PMID:25247414
Transcription factor networks in Drosophila melanogaster. PMID:25242320
Understanding the limits of animal models as predictors of human biology: lessons learned from the sbv IMPROVER Species Translation Challenge. PMID:25236459
The effects of purifying selection on patterns of genetic differentiation between Drosophila melanogaster populations. PMID:25227256
Buffered Qualitative Stability explains the robustness and evolvability of transcriptional networks. PMID:25182846
Insights into the epigenomic landscape of the human malaria vector Anopheles gambiae. PMID:25177345
Chromatin insulator factors involved in long-range DNA interactions and their role in the folding of the Drosophila genome. PMID:25165871
Comparative analysis of regulatory information and circuits across distant species. PMID:25164757
Comparative analysis of metazoan chromatin organization. PMID:25164756
Comparative analysis of the transcriptome across distant species. PMID:25164755
Genomics: Hiding in plain sight. PMID:25164742
Engrailed alters the specificity of synaptic connections of Drosophila auditory neurons with the giant fiber. PMID:25164665
A set of structural features defines the cis-regulatory modules of antenna-expressed genes in Drosophila melanogaster. PMID:25153327
pENCODE: a plant encyclopedia of DNA elements. PMID:25149370
MicroRNA-8 promotes robust motor axon targeting by coordinate regulation of cell adhesion molecules during synapse development. PMID:25135978
Drosophila COP9 signalosome subunit 7 interacts with multiple genomic loci to regulate development. PMID:25106867
metaseq: a Python package for integrative genome-wide analysis reveals relationships between chromatin insulators and associated nuclear mRNA. PMID:25063299
Genomic data integration for ecological and evolutionary traits in non-model organisms. PMID:25047861
Construction of mate pair full-length cDNAs libraries and characterization of transcriptional start sites and termination sites. PMID:25034687
Decoding ChIP-seq with a double-binding signal refines binding peaks to single-nucleotides and predicts cooperative interaction. PMID:25024162
Modelling epigenetic regulation of gene expression in 12 human cell types reveals combinatorial patterns of cell-type-specific genes. PMID:25014377
Combinatorial interactions are required for the efficient recruitment of pho repressive complex (PhoRC) to polycomb response elements. PMID:25010632
Diverse patterns of genomic targeting by transcriptional regulators in Drosophila melanogaster. PMID:24985916
DNA replication and transcription programs respond to the same chromatin cues. PMID:24985913
Comparison of D. melanogaster and C. elegans developmental stages, tissues, and cells by modENCODE RNA-seq data. PMID:24985912
Microsatellite repeat instability fuels evolution of embryonic enhancers in Hawaiian Drosophila. PMID:24978198
An interactive network of long non-coding RNAs facilitates the Drosophila sex determination decision. PMID:24954180
Characterizing a collective and dynamic component of chromatin immunoprecipitation enrichment profiles in yeast. PMID:24947676
Fully automated high-throughput chromatin immunoprecipitation for ChIP-seq: identifying ChIP-quality p300 monoclonal antibodies. PMID:24919486
Integrating the interactome and the transcriptome of Drosophila. PMID:24913703
Zelda potentiates morphogen activity by increasing chromatin accessibility. PMID:24909324
The mechanisms behind the therapeutic activity of BET bromodomain inhibition. PMID:24905006
Genome-scale functional characterization of Drosophila developmental enhancers in vivo. PMID:24896182
Spurious transcription factor binding: non-functional or genetically redundant? PMID:24888900
From gene action to reactive genomes. PMID:24882822
G×G×E for lifespan in Drosophila: mitochondrial, nuclear, and dietary interactions that modify longevity. PMID:24832080
Towards structural systems pharmacology to study complex diseases and personalized medicine. PMID:24830652
The Little Fly that Could: Wizardry and Artistry of Drosophila Genomics. PMID:24827974
CMT-associated mutations in glycyl- and tyrosyl-tRNA synthetases exhibit similar pattern of toxicity and share common genetic modifiers in Drosophila. PMID:24807208
Co-activation of microRNAs by Zelda is essential for early Drosophila development. PMID:24764079
Long-read sequencing of chicken transcripts and identification of new transcript isoforms. PMID:24736250
Dissection of thousands of cell type-specific enhancers identifies dinucleotide repeat motifs as general enhancer features. PMID:24714811
Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines. PMID:24714809
Sex-biased expression of microRNAs in Drosophila melanogaster. PMID:24694940
Molecular characterization and evolution of a gene family encoding both female- and male-specific reproductive proteins in Drosophila. PMID:24682282
Global quantitative modeling of chromatin factor interactions. PMID:24675896
Two enhancers control transcription of Drosophila muscleblind in the embryonic somatic musculature and in the central nervous system. PMID:24667536
Enhancer malfunction in cancer. PMID:24656127
Extreme HOT regions are CpG-dense promoters in C. elegans and humans. PMID:24653213
Comparison of sequence variants in transcriptomic control regions across 17 mouse genomes. PMID:24647628
Evolutionary conservation of the eumetazoan gene regulatory landscape. PMID:24642862
Impacts of the ubiquitous factor Zelda on Bicoid-dependent DNA binding and transcription in Drosophila. PMID:24637116
Navigating and mining modENCODE data. PMID:24636835
WIDE AWAKE mediates the circadian timing of sleep onset. PMID:24631345
Drosophila mbm is a nucleolar myc and casein kinase 2 target required for ribosome biogenesis and cell growth of central brain neuroblasts. PMID:24615015
Transcriptional enhancers: from properties to genome-wide predictions. PMID:24614317
Enhancer biology and enhanceropathies. PMID:24599251
The Zebrafish GenomeWiki: a crowdsourcing approach to connect the long tail for zebrafish gene annotation. PMID:24578356
Neuroethology of male courtship in Drosophila: from the gene to behavior. PMID:24567257
Genome methylation in D. melanogaster is found at specific short motifs and is independent of DNMT2 activity. PMID:24558263
A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages. PMID:24510058
A comparison of midline and tracheal gene regulation during Drosophila development. PMID:24465586
Evidence for site-specific occupancy of the mitochondrial genome by nuclear transcription factors. PMID:24465428
Causality in genetics: the gradient of genetic effects and back to Koch's postulates of causality. PMID:24436434
Cell lines. PMID:24434506
Late replication domains are evolutionary conserved in the Drosophila genome. PMID:24391753
Subtle changes in motif positioning cause tissue-specific effects on robustness of an enhancer's activity. PMID:24391522
Molecular neuroanatomy: a generation of progress. PMID:24388609
Time for the zebrafish ENCODE. PMID:24371190
CCAT: Combinatorial Code Analysis Tool for transcriptional regulation. PMID:24366875
Spatial expression of transcription factors in Drosophila embryonic organ development. PMID:24359758
Widespread misinterpretable ChIP-seq bias in yeast. PMID:24349523
Metabolic constraint-based refinement of transcriptional regulatory networks. PMID:24348226
Dynamic regulation of transcriptional states by chromatin and transcription factors. PMID:24342920
Epigenetic landscape for initiation of DNA replication. PMID:24337246
High-resolution mapping of transcription factor binding sites on native chromatin. PMID:24336359
Effect of genetic variation in a Drosophila model of diabetes-associated misfolded human proinsulin. PMID:24281155
SND1 transcription factor-directed quantitative functional hierarchical genetic regulatory network in wood formation in Populus trichocarpa. PMID:24280390
chroGPS, a global chromatin positioning system for the functional analysis and visualization of the epigenome. PMID:24271395
Dynamic trans-acting factor colocalization in human cells. PMID:24243024
Predicting tissue specific transcription factor binding sites. PMID:24238150
Beyond the ENCODE project: using genomics and epigenomics strategies to study enhancer evolution. PMID:24218635
Human intellectual disability genes form conserved functional modules in Drosophila. PMID:24204314
JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles. PMID:24194598
Surviving an identity crisis: a revised view of chromatin insulators in the genomics era. PMID:24189492
Assessment of transcript reconstruction methods for RNA-seq. PMID:24185837
FunCoup 3.0: database of genome-wide functional coupling networks. PMID:24185702
Inducible protein traps with dominant phenotypes for functional analysis of the Drosophila genome. PMID:24172131
Long noncoding RNAs as metazoan developmental regulators. PMID:24150236
Genome of Drosophila suzukii, the spotted wing drosophila. PMID:24142924
Transcription-factor occupancy at HOT regions quantitatively predicts RNA polymerase recruitment in five human cell lines. PMID:24138567
Human genome replication proceeds through four chromatin states. PMID:24130466
Whole-genome sequencing of two North American Drosophila melanogaster populations reveals genetic differentiation and positive selection. PMID:24102956
Drosophila Kdm4 demethylases in histone H3 lysine 9 demethylation and ecdysteroid signaling. PMID:24100631
De novo prediction of DNA-binding specificities for Cys2His2 zinc finger proteins. PMID:24097433
CAST-ChIP maps cell-type-specific chromatin states in the Drosophila central nervous system. PMID:24095734
Positive and negative design for nonconsensus protein-DNA binding affinity in the vicinity of functional binding sites. PMID:24094406
Mapping human epigenomes. PMID:24074860
Extensive divergence of transcription factor binding in Drosophila embryos with highly conserved gene expression. PMID:24068946
Divergent transcriptional regulatory logic at the intersection of tissue growth and developmental patterning. PMID:24039600
Mapping yeast transcriptional networks. PMID:24018767
Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis. PMID:24002785
Reconstructing dynamic microRNA-regulated interaction networks. PMID:23986498
Identification of transcription factor binding sites from ChIP-seq data at high resolution. PMID:23980024
The Drosophila enhancer of split gene complex: architecture and coordinate regulation by notch, cohesin, and polycomb group proteins. PMID:23979932
Analysis of insulator proteins binding in reporter genetic constructs transfected into Drosophila S2 cells. PMID:23975400
Sustained-input switches for transcription factors and microRNAs are central building blocks of eukaryotic gene circuits. PMID:23972209
Computational identification of diverse mechanisms underlying transcription factor-DNA occupancy. PMID:23935523
Cellular resolution models for even skipped regulation in the entire Drosophila embryo. PMID:23930223
The insulator protein Suppressor of Hairy-wing is an essential transcriptional repressor in the Drosophila ovary. PMID:23884443
Effective blocking of the white enhancer requires cooperation between two main mechanisms suggested for the insulator function. PMID:23861668
Highly parallel assays of tissue-specific enhancers in whole Drosophila embryos. PMID:23852450
Genome-wide identification of chromatin transitional regions reveals diverse mechanisms defining the boundary of facultative heterochromatin. PMID:23840609
Dido3 PHD modulates cell differentiation and division. PMID:23831028
Multiscale modeling of the causal functional roles of nsSNPs in a genome-wide association study: application to hypoxia. PMID:23819581
Understanding the regulatory and transcriptional complexity of the genome through structure. PMID:23817049
Ionotropic glutamate receptors IR64a and IR8a form a functional odorant receptor complex in vivo in Drosophila. PMID:23804096
Transcriptional regulation of gene expression in C. elegans. PMID:23801596
Temporal patterning of Drosophila medulla neuroblasts controls neural fates. PMID:23783517
Transcriptional response of honey bee larvae infected with the bacterial pathogen Paenibacillus larvae. PMID:23762370
Investigation of dmyc Promoter and Regulatory Regions. PMID:23761963
A meta-analysis of the genomic and transcriptomic composition of complex life. PMID:23759593
Drosophila functional elements are embedded in structurally constrained sequences. PMID:23750124
Side effects: substantial non-neutral evolution flanking regulatory sites. PMID:23737755
A synthetic biology approach to the development of transcriptional regulatory models and custom enhancer design. PMID:23732772
Receptor tyrosine kinases in Drosophila development. PMID:23732470
Machine learning and genome annotation: a match meant to be? PMID:23731483
Mutations within lncRNAs are effectively selected against in fruitfly but not in human. PMID:23710818
[Regulation of DNA replication timing]. PMID:23705493
Extensive polymerase pausing during Drosophila axis patterning enables high-level and pliable transcription. PMID:23699410
The majority of primate-specific regulatory sequences are derived from transposable elements. PMID:23675311
A statistical framework for power calculations in ChIP-seq experiments. PMID:23665773
The impact of trans-regulation on the evolutionary rates of metazoan proteins. PMID:23658220
UpSET-ting the balance: modulating open chromatin features in metazoan genomes. PMID:23649046
New properties of Drosophila scs and scs' insulators. PMID:23638134
Insulators target active genes to transcription factories and polycomb-repressed genes to polycomb bodies. PMID:23637616
Fundamental differences in endoreplication in mammals and Drosophila revealed by analysis of endocycling and endomitotic cells. PMID:23613587
Interplay between chromatin state, regulator binding, and regulatory motifs in six human cell types. PMID:23595227
Visualizing time-related data in biology, a review. PMID:23585583
The Drosophila over compensating males gene genetically inhibits dosage compensation in males. PMID:23565249
Following the 'tracks': Tramtrack69 regulates epithelial tube expansion in the Drosophila ovary through Paxillin, Dynamin, and the homeobox protein Mirror. PMID:23545328
Cancer bioinformatics: detection of chromatin states, SNP-containing motifs, and functional enrichment modules. PMID:23544450
Integrative analysis of C. elegans modENCODE ChIP-seq data sets to infer gene regulatory interactions. PMID:23531767
Deep sequencing reveals complex mechanisms of diapause preparation in the invasive mosquito, Aedes albopictus. PMID:23516243
Global analysis of Drosophila Cys₂-His₂ zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants. PMID:23471540
The BEN domain is a novel sequence-specific DNA-binding domain conserved in neural transcriptional repressors. PMID:23468431
Current trends in the development and application of molecular technologies for cancer epigenetics. PMID:23467485
Regulation of nucleosome dynamics by histone modifications. PMID:23463310
Insertion mutants in Drosophila melanogaster Hsc20 halt larval growth and lead to reduced iron-sulfur cluster enzyme activities and impaired iron homeostasis. PMID:23444034
New insights from existing sequence data: generating breakthroughs without a pipette. PMID:23438857
Sex-biased networks and nodes of sexually antagonistic conflict in Drosophila. PMID:23431497
Genome-Level Analysis of Selective Constraint without Apparent Sequence Conservation. PMID:23418180
Inference of natural selection from interspersed genomic elements based on polymorphism and divergence. PMID:23386628
High-throughput sequencing for biology and medicine. PMID:23340846
Genome-wide screens for in vivo Tinman binding sites identify cardiac enhancers with diverse functional architectures. PMID:23326246
Teaching the fundamentals of biological data integration using classroom games. PMID:23300402
Structure-based whole-genome realignment reveals many novel noncoding RNAs. PMID:23296921
The border between the ultrabithorax and abdominal-A regulatory domains in the Drosophila bithorax complex. PMID:23288934
A polycomb group protein is retained at specific sites on chromatin in mitosis. PMID:23284300
Population Genomics of sub-saharan Drosophila melanogaster: African diversity and non-African admixture. PMID:23284287
The comprehensive epigenome map of piRNA clusters. PMID:23258708
Predicting spatial and temporal gene expression using an integrative model of transcription factor occupancy and chromatin state. PMID:23236268
Epigenetic regulation of planarian stem cells by the SET1/MLL family of histone methyltransferases. PMID:23235145
CBS: an open platform that integrates predictive methods and epigenetics information to characterize conserved regulatory features in multiple Drosophila genomes. PMID:23228284
Drosophila protein interaction map (DPiM): a paradigm for metazoan protein complex interactions. PMID:23222005
Cell-type specific cis-regulatory networks: insights from Hox transcription factors. PMID:23221502
Gene set control analysis predicts hematopoietic control mechanisms from genome-wide transcription factor binding data. PMID:23220237
Histone lysine methylation dynamics: establishment, regulation, and biological impact. PMID:23200123
Ash2 acts as an ecdysone receptor coactivator by stabilizing the histone methyltransferase Trr. PMID:23197473
Genomic variation and its impact on gene expression in Drosophila melanogaster. PMID:23189034
UpSET recruits HDAC complexes and restricts chromatin accessibility and acetylation at promoter regions. PMID:23177352
Identification of gene expression changes associated with long-term memory of courtship rejection in Drosophila males. PMID:23173095
The relationship between long-range chromatin occupancy and polymerization of the Drosophila ETS family transcriptional repressor Yan. PMID:23172856
Captured segment exchange: a strategy for custom engineering large genomic regions in Drosophila melanogaster. PMID:23150604
A graphical modelling approach to the dissection of highly correlated transcription factor binding site profiles. PMID:23144600
Interpreting noncoding genetic variation in complex traits and human disease. PMID:23138309
Genomic occupancy of the transcriptional co-activators p300 and CBP. PMID:23131664
Linking the signaling cascades and dynamic regulatory networks controlling stress responses. PMID:23064748
The chromatin insulator CTCF and the emergence of metazoan diversity. PMID:23045651
Enrichment of HP1a on Drosophila chromosome 4 genes creates an alternate chromatin structure critical for regulation in this heterochromatic domain. PMID:23028361
Interpreting the regulatory genome: the genomics of transcription factor function in Drosophila melanogaster. PMID:23023663
Transcription termination between polo and snap, two closely spaced tandem genes of D. melanogaster. PMID:22992452
P-value-based regulatory motif discovery using positional weight matrices. PMID:22990209
Chromatin signature discovery via histone modification profile alignments. PMID:22989711
Circuitry and dynamics of human transcription factor regulatory networks. PMID:22959076
Regulatory RNAs in the light of Drosophila genomics. PMID:22956639
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. PMID:22955991
The chromatin fingerprint of gene enhancer elements. PMID:22952241
Genome-wide epigenetic data facilitate understanding of disease susceptibility association studies. PMID:22952232
The histone acetyltransferases CBP and Chameau integrate developmental and DNA replication programs in Drosophila ovarian follicle cells. PMID:22951641
Analysis of variation at transcription factor binding sites in Drosophila and humans. PMID:22950968
Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors. PMID:22950945
Deciphering the transcriptional regulation of microRNA genes in humans with ACTLocater. PMID:22941648
A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals. PMID:22940246
ncDNA and drift drive binding site accumulation. PMID:22935101
Disentangling the many layers of eukaryotic transcriptional regulation. PMID:22934649
H3K9 and H3K14 acetylation co-occur at many gene regulatory elements, while H3K14ac marks a subset of inactive inducible promoters in mouse embryonic stem cells. PMID:22920947
An atlas of the Epstein-Barr virus transcriptome and epigenome reveals host-virus regulatory interactions. PMID:22901543
DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data. PMID:22897824
The BEAF-32 insulator coordinates genome organization and function during the evolution of Drosophila species. PMID:22895281
Dissecting sources of quantitative gene expression pattern divergence between Drosophila species. PMID:22893002
Ectopic assembly of heterochromatin in Drosophila melanogaster triggered by transposable elements. PMID:22891327
Modeling dilated cardiomyopathies in Drosophila. PMID:22863366
Cell type-specific genomics of Drosophila neurons. PMID:22855560
Studying and modelling dynamic biological processes using time-series gene expression data. PMID:22805708
The cis-regulatory code of Hox function in Drosophila. PMID:22781127
A map of the cis-regulatory sequences in the mouse genome. PMID:22763441
HP1a targets the Drosophila KDM4A demethylase to a subset of heterochromatic genes to regulate H3K36me3 levels. PMID:22761891
Preferential genome targeting of the CBP co-activator by Rel and Smad proteins in early Drosophila melanogaster embryos. PMID:22737084
i-cisTarget: an integrative genomics method for the prediction of regulatory features and cis-regulatory modules. PMID:22718975
Genomic approaches towards finding cis-regulatory modules in animals. PMID:22705667
Biclustering of linear patterns in gene expression data. PMID:22697238
Global patterns of tissue-specific alternative polyadenylation in Drosophila. PMID:22685694
Genomic variation in natural populations of Drosophila melanogaster. PMID:22673804
Genomic dark matter: the reliability of short read mapping illustrated by the genome mappability score. PMID:22668792
Cis-acting polymorphisms affect complex traits through modifications of microRNA regulation pathways. PMID:22606281
Sequence-specific targeting of dosage compensation in Drosophila favors an active chromatin context. PMID:22570616
The transcriptional programme controlled by Runx1 during early embryonic blood development. PMID:22554697
HOT DNAs: a novel class of developmental enhancers. PMID:22549952
Reshaping of global gene expression networks and sex-biased gene expression by integration of a young gene. PMID:22543869
Roles for microRNAs in conferring robustness to biological processes. PMID:22541426
Systematic evaluation of factors influencing ChIP-seq fidelity. PMID:22522655
HOT regions function as patterned developmental enhancers and have a distinct cis-regulatory signature. PMID:22499593
Spatial proximity and similarity of the epigenetic state of genome domains. PMID:22496774
Phenotypic plasticity of the Drosophila transcriptome. PMID:22479193
Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks. PMID:22456606
Expression and characterization of Drosophila signal peptide peptidase-like (sppL), a gene that encodes an intramembrane protease. PMID:22439002
Sequence signatures involved in targeting the Male-Specific Lethal complex to X-chromosomal genes in Drosophila melanogaster. PMID:22424303
H2B monoubiquitylation is a 5'-enriched active transcription mark and correlates with exon-intron structure in human cells. PMID:22421545
Molecular analysis of enhancer RNAs and chromatin modifications in the region of their synthesis in Drosophila cells possessing genetic constructs. PMID:22419084
Probabilistic inference for nucleosome positioning with MNase-based or sonicated short-read data. PMID:22393380
ChromHMM: automating chromatin-state discovery and characterization. PMID:22373907
Segmental duplication, microinversion, and gene loss associated with a complex inversion breakpoint region in Drosophila. PMID:22328714
Evaluation of the role of functional constraints on the integrity of an ultraconserved region in the genus Drosophila. PMID:22319453
Evolutionary conservation of histone modifications in mammals. PMID:22319170
The Drosophila melanogaster Genetic Reference Panel. PMID:22318601
Gene alterations at Drosophila inversion breakpoints provide prima facie evidence for natural selection as an explanation for rapid chromosomal evolution. PMID:22296923
TranscriptomeBrowser 3.0: introducing a new compendium of molecular interactions and a new visualization tool for the study of gene regulatory networks. PMID:22292669
AU-rich element-mediated mRNA decay can occur independently of the miRNA machinery in mouse embryonic fibroblasts and Drosophila S2-cells. PMID:22253700
The TAGteam motif facilitates binding of 21 sequence-specific transcription factors in the Drosophila embryo. PMID:22247430
Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development. PMID:22231485
A highly efficient and effective motif discovery method for ChIP-seq/ChIP-chip data using positional information. PMID:22228832
Tramtrack is genetically upstream of genes controlling tracheal tube size in Drosophila. PMID:22216153
Evolution of biological interaction networks: from models to real data. PMID:22204388
Cis-regulatory elements: molecular mechanisms and evolutionary processes underlying divergence. PMID:22143240
A vision for a biomedical cloud. PMID:22142244
The epigenome in early vertebrate development. PMID:22139962
Sparse linear modeling of next-generation mRNA sequencing (RNA-Seq) data for isoform discovery and abundance estimation. PMID:22135461
FlyBase 101--the basics of navigating FlyBase. PMID:22127867
Construction and analysis of an integrated regulatory network derived from high-throughput sequencing data. PMID:22125477
Emerging biomedical applications of synthetic biology. PMID:22124480
MitoMiner: a data warehouse for mitochondrial proteomics data. PMID:22121219
Clustered ChIP-Seq-defined transcription factor binding sites and histone modifications map distinct classes of regulatory elements. PMID:22115494
High-resolution mapping of open chromatin in the rice genome. PMID:22110044
Studying synthetic lethal interactions in the zebrafish system: insight into disease genes and mechanisms. PMID:22107871
Widespread generation of alternative UTRs contributes to sex-specific RNA binding by UNR. PMID:22101243
modMine: flexible access to modENCODE data. PMID:22080565
TIP: a probabilistic method for identifying transcription factor target genes from ChIP-seq binding profiles. PMID:22039215
Temporal coordination of gene networks by Zelda in the early Drosophila embryo. PMID:22028675
Zelda binding in the early Drosophila melanogaster embryo marks regions subsequently activated at the maternal-to-zygotic transition. PMID:22028662
Behavior-specific changes in transcriptional modules lead to distinct and predictable neurogenomic states. PMID:21960440
Flickin' the ubiquitin switch: the role of H2B ubiquitylation in development. PMID:21937884
Dissecting the transcriptional regulatory properties of human chromosome 16 highly conserved non-coding regions. PMID:21935474
Drosophila, genetic screens, and cardiac function. PMID:21921272
Drosophila P elements preferentially transpose to replication origins. PMID:21896744
Neural-specific elongation of 3' UTRs during Drosophila development. PMID:21896737
Making sense of chromatin states. PMID:21878916
Pol III binding in six mammals shows conservation among amino acid isotypes despite divergence among tRNA genes. PMID:21873999
The modENCODE Data Coordination Center: lessons in harvesting comprehensive experimental details. PMID:21856757
Molecular genetic analyses of polytene chromosome region 72A-D in Drosophila melanogaster reveal a gene desert in 72D. PMID:21853143
RNAi-independent role for Argonaute2 in CTCF/CP190 chromatin insulator function. PMID:21852534
Synthetic spike-in standards for RNA-seq experiments. PMID:21816910
Automatic annotation of spatial expression patterns via sparse Bayesian factor models. PMID:21814502
Membrane protein insertion at the endoplasmic reticulum. PMID:21801011
The future of model organisms in human disease research. PMID:21765459
Post-transcription initiation function of the ubiquitous SAGA complex in tissue-specific gene activation. PMID:21764853
Drosophila RNAi screening in a postgenomic world. PMID:21752787
RNA-Seq unleashed. PMID:21747384
Drosophila glutamate receptor mRNA expression and mRNP particles. PMID:21743295
Mirtrons: microRNA biogenesis via splicing. PMID:21712066
Heterochromatin boundaries are hotspots for de novo kinetochore formation. PMID:21685892
PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions. PMID:21685081
The role of the Suppressor of Hairy-wing insulator protein in Drosophila oogenesis. PMID:21651900
Reconstructing regulatory network transitions. PMID:21632251
Genome Surveyor 2.0: cis-regulatory analysis in Drosophila. PMID:21593125
Genome-wide analysis of simultaneous GATA1/2, RUNX1, FLI1, and SCL binding in megakaryocytes identifies hematopoietic regulators. PMID:21571218
Strategic approaches to unraveling genetic causes of cardiovascular diseases. PMID:21566222
Chromatin: constructing the big picture. PMID:21527910
The Drosophila gene disruption project: progress using transposons with distinctive site specificities. PMID:21515576
Adipogenic hotspots: where the action is. PMID:21505519
Integrative epigenomic mapping defines four main chromatin states in Arabidopsis. PMID:21487388
What makes flies and worms tick. PMID:21473021
DNA shape, genetic codes, and evolution. PMID:21439813
Molecular biology: A fly in the face of genomics. PMID:21430772
Defining the replication program through the chromatin landscape. PMID:21417598
The molecular basis of making spiral ganglion neurons and connecting them to hair cells of the organ of Corti. PMID:21414397
RNA templating the epigenome: long noncoding RNAs as molecular scaffolds. PMID:21393997
A modENCODE snapshot. PMID:21390030
Genotyping gastric cancer. PMID:21373953
Nucleosomes in the neighborhood: new roles for chromatin modifications in replication origin control. PMID:21364325
Transcriptional regulation of haematopoietic transcription factors. PMID:21345252
Charting a course for genomic medicine from base pairs to bedside. PMID:21307933
Genomes: the truth is in there. PMID:21283113
Operating on chromatin, a colorful language where context matters. PMID:21272588
Dissecting the molecular basis of organ of Corti development: Where are we now? PMID:21256948
Functional genomics: the modENCODE guide to the genome. PMID:21245826
Comprehensive analysis of the chromatin landscape in Drosophila melanogaster. PMID:21179089
Chromatin signatures of the Drosophila replication program. PMID:21177973
Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin. PMID:21177972
The transcriptional diversity of 25 Drosophila cell lines. PMID:21177962
Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project PubMed citations: 564.

564 articles citing: Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project

A metabolic regulatory network for the Caenorhabditis elegans intestine. PMID:35847555
Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements. PMID:35789323
ChIP-Hub provides an integrative platform for exploring plant regulome. PMID:35701419
Nematode chromosomes. PMID:35323874
The zinc-finger transcription factor LSL-1 is a major regulator of the germline transcriptional program in Caenorhabditis elegans. PMID:35262739
Nervous system-wide analysis of Hox regulation of terminal neuronal fate specification in Caenorhabditis elegans. PMID:35226663
Deficiency in RCAT-1 Function Causes Dopamine Metabolism Related Behavioral Disorders in Caenorhabditis elegans. PMID:35216508
Balancing Selection of the Intracellular Pathogen Response in Natural Caenorhabditis elegans Populations. PMID:35174100
WormBase in 2022-data, processes, and tools for analyzing Caenorhabditis elegans. PMID:35134929
Status of diagnosis and treatment of esophageal cancer and non-coding RNA correlation research: a narrative review. PMID:35116309
Virtual Gene Concept and a Corresponding Pragmatic Research Program in Genetical Data Science. PMID:35052043
Accessible Region Conformation Capture (ARC-C) gives high-resolution insights into genome architecture and regulation. PMID:34933938
Genome-wide characterization, evolution, structure, and expression analysis of the F-box genes in Caenorhabditis. PMID:34895149
Master lineage transcription factors anchor trans mega transcriptional complexes at highly accessible enhancer sites to promote long-range chromatin clustering and transcription of distal target genes. PMID:34850122
daf-16/FOXO blocks adult cell fate in Caenorhabditis elegans dauer larvae via lin-41/TRIM71. PMID:34780472
Introns control stochastic allele expression bias. PMID:34764277
Pig genome functional annotation enhances the biological interpretation of complex traits and human disease. PMID:34615879
Identification of essential genes in Caenorhabditis elegans through whole-genome sequencing of legacy mutant collections. PMID:34550348
Chromatin accessibility and regulatory vocabulary across indicine cattle tissues. PMID:34548076
BLMP-1 promotes developmental cell death in C. elegans by timely repression of ced-9 transcription. PMID:34541605
Reciprocal interactions between transforming growth factor beta signaling and collagens: Insights from Caenorhabditis elegans. PMID:34537996
Virus infection modulates male sexual behaviour in Caenorhabditis elegans. PMID:34534386
Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review. PMID:34439912
Polymer Modeling of 3D Epigenome Folding: Application to Drosophila. PMID:34415542
Transcriptional enhancers and their communication with gene promoters. PMID:34414474
Comparative Analysis of Promoters and Enhancers in the Pituitary Glands of the Bama Xiang and Large White Pigs. PMID:34367256
AnnoMiner is a new web-tool to integrate epigenetics, transcription factor occupancy and transcriptomics data to predict transcriptional regulators. PMID:34326396
Regulation of UNC-40/DCC and UNC-6/Netrin by DAF-16 promotes functional rewiring of the injured axon. PMID:34109380
The Chromatin Accessibility Landscape of Adult Rat. PMID:34108989
Fish-Ing for Enhancers in the Heart. PMID:33920121
Single-cell dynamics of chromatin activity during cell lineage differentiation in Caenorhabditis elegans embryos. PMID:33900055
A compendium and comparative epigenomics analysis of cis-regulatory elements in the pig genome. PMID:33850120
Comparative genomics of Chlamydomonas. PMID:33793842
A novel allele of SIR2 reveals a heritable intermediate state of gene silencing. PMID:33713126
AP-1 subunits converge promiscuously at enhancers to potentiate transcription. PMID:33674350
Extensive non-redundancy in a recently duplicated developmental gene family. PMID:33648446
Gametes deficient for Pot1 telomere binding proteins alter levels of telomeric foci for multiple generations. PMID:33542458
The Snail transcription factor CES-1 regulates glutamatergic behavior in C. elegans. PMID:33529210
Expression pattern determines regulatory logic. PMID:33395445
A primer for generating and using transcriptome data and gene sets. PMID:33361089
To mock or not: a comprehensive comparison of mock IP and DNA input for ChIP-seq. PMID:33347581
The computational approaches of lncRNA identification based on coding potential: Status quo and challenges. PMID:33304463
Evidence of widespread, independent sequence signature for transcription factor cobinding. PMID:33303494
Alternative splicing in endothelial cells: novel therapeutic opportunities in cancer angiogenesis. PMID:33287867
Molecular and evolutionary processes generating variation in gene expression. PMID:33268840
Computational tools for geroscience. PMID:33241167
A map of cis-regulatory elements and 3D genome structures in zebrafish. PMID:33239788
Genomic and transcriptomic variation defines the chromosome-scale assembly of Haemonchus contortus, a model gastrointestinal worm. PMID:33168940
Single-cell RNA profiling links ncRNAs to spatiotemporal gene expression during C. elegans embryogenesis. PMID:33139759
Global regulatory features of alternative splicing across tissues and within the nervous system of C. elegans. PMID:33127752
Distinctive regulatory architectures of germline-active and somatic genes in C. elegans. PMID:33093068
A comparative analysis of chromatin accessibility in cattle, pig, and mouse tissues. PMID:33028202
Ancestral function of Inhibitors-of-kappaB regulates Caenorhabditis elegans development. PMID:32999373
Characterizing a strong pan-muscular promoter (Pmlc-1) as a fluorescent co-injection marker to select for single-copy insertions. PMID:32908967
Alternative splicing of coq-2 controls the levels of rhodoquinone in animals. PMID:32744503
Perspectives on ENCODE. PMID:32728248
Occupancy maps of 208 chromatin-associated proteins in one human cell type. PMID:32728244
The SEM-4 Transcription Factor Is Required for Regulation of the Oxidative Stress Response in Caenorhabditis elegans. PMID:32718932
The Nuclear Lamina: Protein Accumulation and Disease. PMID:32630170
Maternal effects shape the alternative splicing of parental alleles in reciprocal cross hybrids of Megalobrama amblycephala × Culter alburnus. PMID:32616060
Loss of dpy-2 and dpy-9 has stage-specific effects on DBL-1 pathway signaling. PMID:32550453
Integrative analysis of reference epigenomes in 20 rice varieties. PMID:32461553
Degradation of the Repetitive Genomic Landscape in a Close Relative of Caenorhabditis elegans. PMID:32359146
ngn-1/neurogenin Activates Transcription of Multiple Terminal Selector Transcription Factors in the Caenorhabditis elegans Nervous System. PMID:32273286
Systematic alteration of ATAC-seq for profiling open chromatin in cryopreserved nuclei preparations from livestock tissues. PMID:32251359
Cuticle Collagen Expression Is Regulated in Response to Environmental Stimuli by the GATA Transcription Factor ELT-3 in Caenorhabditis elegans. PMID:32229533
Completing the ENCODE3 compendium yields accurate imputations across a variety of assays and human biosamples. PMID:32228713
GLP-1 Notch-LAG-1 CSL control of the germline stem cell fate is mediated by transcriptional targets lst-1 and sygl-1. PMID:32196486
Learning causal networks using inducible transcription factors and transcriptome-wide time series. PMID:32181581
The Hox Gene egl-5 Acts as a Terminal Selector for VD13 Development via Wnt Signaling. PMID:32138237
Chromosome-Level Assembly of the Caenorhabditis remanei Genome Reveals Conserved Patterns of Nematode Genome Organization. PMID:32111628
A spontaneous complex structural variant in rcan-1 increases exploratory behavior and laboratory fitness of Caenorhabditis elegans. PMID:32092052
Hierarchical and Dynamic Regulation of Defense-Responsive Specialized Metabolism by WRKY and MYB Transcription Factors. PMID:32082343
Direct full-length RNA sequencing reveals unexpected transcriptome complexity during Caenorhabditis elegans development. PMID:32024662
The full-length transcriptome of C. elegans using direct RNA sequencing. PMID:32024661
ORSO (Online Resource for Social Omics): A data-driven social network connecting scientists to genomics datasets. PMID:31978042
New Roles for the Heterochronic Transcription Factor LIN-29 in Cuticle Maintenance and Lipid Metabolism at the Larval-to-Adult Transition in Caenorhabditis elegans. PMID:31974205
Transcription-independent TFIIIC-bound sites cluster near heterochromatin boundaries within lamina-associated domains in C. elegans. PMID:31918747
Combinatorial interactions of the LEC1 transcription factor specify diverse developmental programs during soybean seed development. PMID:31892538
SLC17A6/7/8 Vesicular Glutamate Transporter Homologs in Nematodes. PMID:31776169
The ENCODE Portal as an Epigenomics Resource. PMID:31751002
The C. elegans 3' UTRome v2 resource for studying mRNA cleavage and polyadenylation, 3'-UTR biology, and miRNA targeting. PMID:31744903
Genetic interactions between the DBL-1/BMP-like pathway and dpy body size-associated genes in Caenorhabditis elegans. PMID:31693440
WormBase: a modern Model Organism Information Resource. PMID:31642470
Selection and gene flow shape niche-associated variation in pheromone response. PMID:31548647
Distinct functions and temporal regulation of methylated histone H3 during early embryogenesis. PMID:31540912
C. elegans synMuv B proteins regulate spatial and temporal chromatin compaction during development. PMID:31515206
Molecular evolution across developmental time reveals rapid divergence in early embryogenesis. PMID:31388446
The transcription factor Hey and nuclear lamins specify and maintain cell identity. PMID:31310235
The demethylase NMAD-1 regulates DNA replication and repair in the Caenorhabditis elegans germline. PMID:31283754
Fast genetic mapping of complex traits in C. elegans using millions of individuals in bulk. PMID:31213597
The regulatory control of Cebpa enhancers and silencers in the myeloid and red-blood cell lineages. PMID:31181110
Bridging the gap between reference and real transcriptomes. PMID:31159855
Binding of an X-Specific Condensin Correlates with a Reduction in Active Histone Modifications at Gene Regulatory Elements. PMID:31123040
HOT or not: examining the basis of high-occupancy target regions. PMID:31114922
Innovative strategies for annotating the "relationSNP" between variants and molecular phenotypes. PMID:31114635
An in-silico approach for discovery of microRNA-TF regulation of DISC1 interactome mediating neuronal migration. PMID:31098296
Identification and Conservation Analysis of Cis-Regulatory Elements in Pig Liver. PMID:31067820
FisherMP: fully parallel algorithm for detecting combinatorial motifs from large ChIP-seq datasets. PMID:30957858
The Long Non-Coding RNA lep-5 Promotes the Juvenile-to-Adult Transition by Destabilizing LIN-28. PMID:30956008
HSP-4/BiP expression in secretory cells is regulated by a developmental program and not by the unfolded protein response. PMID:30908491
H3K9me3 is required for inheritance of small RNAs that target a unique subset of newly evolved genes. PMID:30869075
Meta-analysis suggests evidence of novel stress-related pathway components in Orsay virus - Caenorhabditis elegans viral model. PMID:30867481
A DNA repair protein and histone methyltransferase interact to promote genome stability in the Caenorhabditis elegans germ line. PMID:30794539
Global transcriptional regulation of innate immunity by ATF-7 in C. elegans. PMID:30789901
Identification of functional long non-coding RNAs in C. elegans. PMID:30777050
DAF-16 stabilizes the aging transcriptome and is activated in mid-aged Caenorhabditis elegans to cope with internal stress. PMID:30773782
Hierarchical Transcription Factor and Chromatin Binding Network for Wood Formation in Black Cottonwood (Populus trichocarpa). PMID:30755461
Heterochromatic foci and transcriptional repression by an unstructured MET-2/SETDB1 co-factor LIN-65. PMID:30737265
Transcription-driven chromatin repression of Intragenic transcription start sites. PMID:30707695
Electron microscopy snapshots of single particles from single cells. PMID:30541924
Genomic identification and functional analysis of essential genes in Caenorhabditis elegans. PMID:30514206
MRG-1/MRG15 Is a Barrier for Germ Cell to Neuron Reprogramming in Caenorhabditis elegans. PMID:30425042
ChIP-Atlas: a data-mining suite powered by full integration of public ChIP-seq data. PMID:30413482
Chromatin accessibility dynamics across C. elegans development and ageing. PMID:30362940
BMP Signaling Determines Body Size via Transcriptional Regulation of Collagen Genes in Caenorhabditis elegans. PMID:30274988
Alternative splicing links histone modifications to stem cell fate decision. PMID:30217220
Developmental Constraints on Genome Evolution in Four Bilaterian Model Species. PMID:30137380
Caenorhabditis elegans as an emerging model system in environmental epigenetics. PMID:30091255
Effects of liquid cultivation on gene expression and phenotype of C. elegans. PMID:30064382
SL-quant: a fast and flexible pipeline to quantify spliced leader trans-splicing events from RNA-seq data. PMID:30010768
Opposing roles of microRNA Argonautes during Caenorhabditis elegans aging. PMID:29927939
Function, dynamics and evolution of network motif modules in integrated gene regulatory networks of worm and plant. PMID:29873777
Using WormBase: A Genome Biology Resource for Caenorhabditis elegans and Related Nematodes. PMID:29761466
Regulation of C. elegans L4 cuticle collagen genes by the heterochronic protein LIN-29. PMID:29604168
Combined flow cytometry and high-throughput image analysis for the study of essential genes in Caenorhabditis elegans. PMID:29598825
A Strategy To Isolate Modifiers of Caenorhabditis elegans Lethal Mutations: Investigating the Endoderm Specifying Ability of the Intestinal Differentiation GATA Factor ELT-2. PMID:29593072
A transcription factor collective defines the HSN serotonergic neuron regulatory landscape. PMID:29553368
ChIP-ping the branches of the tree: functional genomics and the evolution of eukaryotic gene regulation. PMID:29529131
Effect of the diet type and temperature on the C. elegans transcriptome. PMID:29515753
Proliferation of Regulatory DNA Elements Derived from Transposable Elements in the Maize Genome. PMID:29463772
Repressive Chromatin in Caenorhabditis elegans: Establishment, Composition, and Function. PMID:29378810
Genomic Identification and Functional Characterization of Essential Genes in Caenorhabditis elegans. PMID:29339407
Rapid genome shrinkage in a self-fertile nematode reveals sperm competition proteins. PMID:29302007
The ModERN Resource: Genome-Wide Binding Profiles for Hundreds of Drosophila and Caenorhabditis elegans Transcription Factors. PMID:29284660
Nuclear receptors in cancer - uncovering new and evolving roles through genomic analysis. PMID:29279606
Conserved noncoding transcription and core promoter regulatory code in early Drosophila development. PMID:29260710
HOP-1 Presenilin Deficiency Causes a Late-Onset Notch Signaling Phenotype That Affects Adult Germline Function in Caenorhabditis elegans. PMID:29242286
Regulation of Crossover Frequency and Distribution during Meiotic Recombination. PMID:29222342
FMRFamide-like peptides expand the behavioral repertoire of a densely connected nervous system. PMID:29167374
Chromatin accessibility dynamics reveal novel functional enhancers in C. elegans. PMID:29141961
The Encyclopedia of DNA elements (ENCODE): data portal update. PMID:29126249
Evaluation of Sox2 binding affinities for distinct DNA patterns using steered molecular dynamics simulation. PMID:29123983
The Substrates of Nonsense-Mediated mRNA Decay in Caenorhabditis elegans. PMID:29122854
A microRNA feedback loop regulates global microRNA abundance during aging. PMID:29114017
Genome-wide discovery of active regulatory elements and transcription factor footprints in Caenorhabditis elegans using DNase-seq. PMID:29074739
Comparative Transcriptomics of Steinernema and Caenorhabditis Single Embryos Reveals Orthologous Gene Expression Convergence during Late Embryogenesis. PMID:29048526
Caenorhabditis elegans Dosage Compensation: Insights into Condensin-Mediated Gene Regulation. PMID:29037439
Deep learning of the splicing (epi)genetic code reveals a novel candidate mechanism linking histone modifications to ESC fate decision. PMID:29036709
BINDING SITE ANALYSIS OF THE CAENORHABDITIS ELEGANS NR4A NUCLEAR RECEPTOR NHR-6 DURING DEVELOPMENT. PMID:29026837
Data Resources for Human Functional Genomics. PMID:28989986
Comprehensive single-cell transcriptional profiling of a multicellular organism. PMID:28818938
Intricate and Cell Type-Specific Populations of Endogenous Circular DNA (eccDNA) in Caenorhabditis elegans and Homo sapiens. PMID:28801508
Increased mitochondrial fusion allows the survival of older animals in diverse C. elegans longevity pathways. PMID:28769038
Ras/MAPK Modifier Loci Revealed by eQTL in Caenorhabditis elegans. PMID:28751501
Robust Identification of Developmentally Active Endothelial Enhancers in Zebrafish Using FANS-Assisted ATAC-Seq. PMID:28723572
Spatiotemporal expression profiling of long intervening noncoding RNAs in Caenorhabditis elegans. PMID:28701691
Trans-splicing enhances translational efficiency in C. elegans. PMID:28684554
Contribution of trans regulatory eQTL to cryptic genetic variation in C. elegans. PMID:28662696
Caenorhabditis elegans CES-1 Snail Represses pig-1 MELK Expression To Control Asymmetric Cell Division. PMID:28652378
The Oxidative Stress Response in Caenorhabditis elegans Requires the GATA Transcription Factor ELT-3 and SKN-1/Nrf2. PMID:28600327
Building dialogues between clinical and biomedical research through cross-species collaborations. PMID:28579453
Cooperation between a hierarchical set of recruitment sites targets the X chromosome for dosage compensation. PMID:28562241
Superresolution microscopy reveals the three-dimensional organization of meiotic chromosome axes in intact Caenorhabditis elegans tissue. PMID:28559338
C. elegans DAF-16/FOXO interacts with TGF-ß/BMP signaling to induce germline tumor formation via mTORC1 activation. PMID:28549065
Exploring spatially adjacent TFBS-clustered regions with Hi-C data. PMID:28472433
Omicseq: a web-based search engine for exploring omics datasets. PMID:28402462
High-confidence coding and noncoding transcriptome maps. PMID:28396519
Landscape of histone modifications in a sponge reveals the origin of animal cis-regulatory complexity. PMID:28395144
Alternative Polyadenylation Directs Tissue-Specific miRNA Targeting in Caenorhabditis elegans Somatic Tissues. PMID:28348061
Evolutionary insights into T-type Ca2+ channel structure, function, and ion selectivity from the Trichoplax adhaerens homologue. PMID:28330839
Identification of an RNA Polymerase III Regulator Linked to Disease-Associated Protein Aggregation. PMID:28306505
Correspondence of D. melanogaster and C. elegans developmental stages revealed by alternative splicing characteristics of conserved exons. PMID:28302059
Fast, scalable prediction of deleterious noncoding variants from functional and population genomic data. PMID:28288115
CisMapper: predicting regulatory interactions from transcription factor ChIP-seq data. PMID:28204599
Recurrently deregulated lncRNAs in hepatocellular carcinoma. PMID:28194035
Effect of mutation mechanisms on variant composition and distribution in Caenorhabditis elegans. PMID:28135268
Sex-specific chromatin landscapes in an ultra-compact chordate genome. PMID:28115992
GExplore 1.4: An expanded web interface for queries on Caenorhabditis elegans protein and gene function. PMID:28090394
Modular combinatorial binding among human trans-acting factors reveals direct and indirect factor binding. PMID:28061806
Cell Biology of the Caenorhabditis elegans Nucleus. PMID:28049702
The Lipocalin LPR-1 Cooperates with LIN-3/EGF Signaling To Maintain Narrow Tube Integrity in Caenorhabditis elegans. PMID:28040739
A Differentiation Transcription Factor Establishes Muscle-Specific Proteostasis in Caenorhabditis elegans. PMID:28036392
Spatiotemporal coupling and decoupling of gene transcription with DNA replication origins during embryogenesis in C. elegans. PMID:28009254
A Network of Chromatin Factors Is Regulating the Transition to Postembryonic Development in Caenorhabditis elegans. PMID:28007841
Integrating transcriptomic and proteomic data for accurate assembly and annotation of genomes. PMID:28003436
ChIPBase v2.0: decoding transcriptional regulatory networks of non-coding RNAs and protein-coding genes from ChIP-seq data. PMID:27924033
Developmental Wiring of Specific Neurons Is Regulated by RET-1/Nogo-A in Caenorhabditis elegans. PMID:27821431
A transcription factor hierarchy defines an environmental stress response network. PMID:27811239
Enhancer Sharing Promotes Neighborhoods of Transcriptional Regulation Across Eukaryotes. PMID:27799341
Stable Caenorhabditis elegans chromatin domains separate broadly expressed and developmentally regulated genes. PMID:27791097
A gene-centered C. elegans protein-DNA interaction network provides a framework for functional predictions. PMID:27777270
Gene Function Prediction Based on Developmental Transcriptomes of the Two Sexes in C. elegans. PMID:27732864
A Surveillance System Ensures Crossover Formation in C. elegans. PMID:27720619
Past Roadblocks and New Opportunities in Transcription Factor Network Mapping. PMID:27720190
E2F coregulates an essential HSF developmental program that is distinct from the heat-shock response. PMID:27688402
Genome-wide identification and characterisation of HOT regions in the human genome. PMID:27633377
Maps of context-dependent putative regulatory regions and genomic signal interactions. PMID:27625394
COME: a robust coding potential calculation tool for lncRNA identification and characterization based on multiple features. PMID:27608726
Tissue- and Time-Specific Expression of Otherwise Identical tRNA Genes. PMID:27560950
First insights into the nature and evolution of antisense transcription in nematodes. PMID:27549405
DNA replication origins-where do we begin? PMID:27542827
The time-resolved transcriptome of C. elegans. PMID:27531719
Genomic and expression analysis of transition proteins in Drosophila. PMID:27512614
DLK-1, SEK-3 and PMK-3 Are Required for the Life Extension Induced by Mitochondrial Bioenergetic Disruption in C. elegans. PMID:27420916
Microsporidia Intracellular Development Relies on Myc Interaction Network Transcription Factors in the Host. PMID:27402359
Hitting two birds with one stone: The unforeseen consequences of nested gene knockouts in Caenorhabditis elegans. PMID:27386165
Regulation of UNC-130/FOXD-mediated mesodermal patterning in C. elegans. PMID:27341757
BLIMP-1/BLMP-1 and Metastasis-Associated Protein Regulate Stress Resistant Development in Caenorhabditis elegans. PMID:27334271
Dopamine signaling promotes the xenobiotic stress response and protein homeostasis. PMID:27261197
Experimental and Computational Considerations in the Study of RNA-Binding Protein-RNA Interactions. PMID:27256380
IGF2BP3 Modulates the Interaction of Invasion-Associated Transcripts with RISC. PMID:27210763
Genetic sources of population epigenomic variation. PMID:27156976
CUL2 overexpression driven by CUL2/E2F1/miR-424 regulatory loop promotes HPV16 E7 induced cervical carcinogenesis. PMID:27153550
Comparative genomic analysis of upstream miRNA regulatory motifs in Caenorhabditis. PMID:27140965
Evolution of Epigenetic Regulation in Vertebrate Genomes. PMID:27080453
JBrowse: a dynamic web platform for genome visualization and analysis. PMID:27072794
Deactivation of the GATA Transcription Factor ELT-2 Is a Major Driver of Normal Aging in C. elegans. PMID:27070429
Coding exon-structure aware realigner (CESAR) utilizes genome alignments for accurate comparative gene annotation. PMID:27016733
Meiotic recombination and the crossover assurance checkpoint in Caenorhabditis elegans. PMID:27013114
Mondo complexes regulate TFEB via TOR inhibition to promote longevity in response to gonadal signals. PMID:27001890
Principles of metadata organization at the ENCODE data coordination center. PMID:26980513
Constructing 3D interaction maps from 1D epigenomes. PMID:26960733
Enhancers as non-coding RNA transcription units: recent insights and future perspectives. PMID:26948815
The analysis of novel distal Cebpa enhancers and silencers using a transcriptional model reveals the complex regulatory logic of hematopoietic lineage specification. PMID:26945717
Neurogenomics: An opportunity to integrate neuroscience, genomics and bioinformatics research in Africa. PMID:26937352
Pseudo-Reference-Based Assembly of Vertebrate Transcriptomes. PMID:26927182
Overlapping cell population expression profiling and regulatory inference in C. elegans. PMID:26926147
Mutagenesis of GATA motifs controlling the endoderm regulator elt-2 reveals distinct dominant and secondary cis-regulatory elements. PMID:26896592
Single-cell Transcriptome Study as Big Data. PMID:26876720
Functional transcription factor target discovery via compendia of binding and expression profiles. PMID:26857150
Probabilistic modelling of chromatin code landscape reveals functional diversity of enhancer-like chromatin states. PMID:26841971
All the microbiology nematodes can teach us. PMID:26839382
A transgenerational role of the germline nuclear RNAi pathway in repressing heat stress-induced transcriptional activation in C. elegans. PMID:26779286
Embryonic transcription is controlled by maternally defined chromatin state. PMID:26679111
The Inflammatory Transcription Factors NFκB, STAT1 and STAT3 Drive Age-Associated Transcriptional Changes in the Human Kidney. PMID:26678048
DANIO-CODE: Toward an Encyclopedia of DNA Elements in Zebrafish. PMID:26671609
Membrane-associated collagens with interrupted triple-helices (MACITs): evolution from a bilaterian common ancestor and functional conservation in C. elegans. PMID:26667623
High-resolution mapping of H4K16 and H3K23 acetylation reveals conserved and unique distribution patterns in Arabidopsis and rice. PMID:26646900
A ChIP on the shoulder? Chromatin immunoprecipitation and validation strategies for ChIP antibodies. PMID:26594335
Short linear motifs - ex nihilo evolution of protein regulation. PMID:26589632
Cell nonautonomous activation of flavin-containing monooxygenase promotes longevity and health span. PMID:26586189
Comparative Transcriptomes and EVO-DEVO Studies Depending on Next Generation Sequencing. PMID:26543497
H3K23me2 is a new heterochromatic mark in Caenorhabditis elegans. PMID:26476455
Identification of Predictive Cis-Regulatory Elements Using a Discriminative Objective Function and a Dynamic Search Space. PMID:26465884
Single-cell epigenomics: techniques and emerging applications. PMID:26460349
New links between protein N-terminal acetylation, dauer diapause, and the insulin/IGF-1 signaling pathway in Caenorhabditis elegans. PMID:26435887
Getting Down to Specifics: Profiling Gene Expression and Protein-DNA Interactions in a Cell Type-Specific Manner. PMID:26410031
Comparative genomics of Steinernema reveals deeply conserved gene regulatory networks. PMID:26392177
Hepatic Bmal1 Regulates Rhythmic Mitochondrial Dynamics and Promotes Metabolic Fitness. PMID:26365180
Extensive identification and analysis of conserved small ORFs in animals. PMID:26364619
Inhibition of elongin C promotes longevity and protein homeostasis via HIF-1 in C. elegans. PMID:26361075
Zelda is differentially required for chromatin accessibility, transcription factor binding, and gene expression in the early Drosophila embryo. PMID:26335634
Genome-wide errant targeting by Hairy. PMID:26305409
Trans-Reactivation: A New Epigenetic Phenomenon Underlying Transcriptional Reactivation of Silenced Genes. PMID:26292210
FlyVar: a database for genetic variation in Drosophila melanogaster. PMID:26289428
Nonconsensus Protein Binding to Repetitive DNA Sequence Elements Significantly Affects Eukaryotic Genomes. PMID:26285121
Absence of canonical marks of active chromatin in developmentally regulated genes. PMID:26280901
An Interactive Database for the Assessment of Histone Antibody Specificity. PMID:26212453
Lipid-mediated regulation of SKN-1/Nrf in response to germ cell absence. PMID:26196144
Metazoan tRNA introns generate stable circular RNAs in vivo. PMID:26194134
Enrichment of H3K9me2 on Unsynapsed Chromatin in Caenorhabditis elegans Does Not Target de Novo Sites. PMID:26156747
Predominant contribution of cis-regulatory divergence in the evolution of mouse alternative splicing. PMID:26134616
Tinkering signaling pathways by gain and loss of protein isoforms: the case of the EDA pathway regulator EDARADD. PMID:26134525
Integrative Analysis Reveals Regulatory Programs in Endometriosis. PMID:26134036
Visualization and dissemination of multidimensional proteomics data comparing protein abundance during Caenorhabditis elegans development. PMID:26133526
toxoMine: an integrated omics data warehouse for Toxoplasma gondii systems biology research. PMID:26130662
Functional annotation of HOT regions in the human genome: implications for human disease and cancer. PMID:26113264
Systems-level quantification of division timing reveals a common genetic architecture controlling asynchrony and fate asymmetry. PMID:26063786
Protein-DNA binding in high-resolution. PMID:26038153
The Developmental Intestinal Regulator ELT-2 Controls p38-Dependent Immune Responses in Adult C. elegans. PMID:26016853
Comprehensive RNA-Seq transcriptomic profiling across 11 organs, 4 ages, and 2 sexes of Fischer 344 rats. PMID:25977771
Molluscs as models for translational medicine. PMID:25925630
Mapping and analysis of Caenorhabditis elegans transcription factor sequence specificities. PMID:25905672
An approach for determining and measuring network hierarchy applied to comparing the phosphorylome and the regulome. PMID:25880651
ClusTrack: feature extraction and similarity measures for clustering of genome-wide data sets. PMID:25879845
Spatial reconstruction of single-cell gene expression data. PMID:25867923
Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project. PMID:25854118
The GATA factor elt-1 regulates C. elegans developmental timing by promoting expression of the let-7 family microRNAs. PMID:25816370
Genome-wide profiling of the C. elegans dsRNAome. PMID:25805852
Using the ENCODE Resource for Functional Annotation of Genetic Variants. PMID:25762420
Wash interacts with lamin and affects global nuclear organization. PMID:25754639
Computational methodology for ChIP-seq analysis. PMID:25741452
The genome and transcriptome of the zoonotic hookworm Ancylostoma ceylanicum identify infection-specific gene families. PMID:25730766
Important biological information uncovered in previously unaligned reads from chromatin immunoprecipitation experiments (ChIP-Seq). PMID:25727450
Multiple cis elements and GATA factors regulate a cuticle collagen gene in Caenorhabditis elegans. PMID:25711168
Identifying transcriptional cis-regulatory modules in animal genomes. PMID:25704908
The Mediator complex: a central integrator of transcription. PMID:25693131
An integrative analysis of TFBS-clustered regions reveals new transcriptional regulation models on the accessible chromatin landscape. PMID:25682954
Regulatory roles of RNA binding proteins in the nervous system of C. elegans. PMID:25628531
Comparative RNA-Seq analysis reveals pervasive tissue-specific alternative polyadenylation in Caenorhabditis elegans intestine and muscles. PMID:25601023
Mammalian transcriptional hotspots are enriched for tissue specific enhancers near cell type specific highly expressed genes and are predicted to act as transcriptional activator hubs. PMID:25547756
Conditional mutual inclusive information enables accurate quantification of associations in gene regulatory networks. PMID:25539927
A common set of distinct features that characterize noncoding RNAs across multiple species. PMID:25505163
Physiological roles for mafr-1 in reproduction and lipid homeostasis. PMID:25497095
Deciphering miRNA transcription factor feed-forward loops to identify drug repurposing candidates for cystic fibrosis. PMID:25484921
Regulation of C. elegans neuronal differentiation by the ZEB-family factor ZAG-1 and the NK-2 homeodomain factor CEH-28. PMID:25474681
De novo prediction of cis-regulatory elements and modules through integrative analysis of a large number of ChIP datasets. PMID:25442502
The C. elegans SNAPc component SNPC-4 coats piRNA domains and is globally required for piRNA abundance. PMID:25373775
Isolation of specific neurons from C. elegans larvae for gene expression profiling. PMID:25372608
A functional and evolutionary perspective on transcription factor binding in Arabidopsis thaliana. PMID:25361952
The DAF-16 FOXO transcription factor regulates natc-1 to modulate stress resistance in Caenorhabditis elegans, linking insulin/IGF-1 signaling to protein N-terminal acetylation. PMID:25330323
Profiling the transcription factor regulatory networks of human cell types. PMID:25300490
High-resolution digital profiling of the epigenome. PMID:25297728
Translational control of the oogenic program by components of OMA ribonucleoprotein particles in Caenorhabditis elegans. PMID:25261697
Heritable variation of mRNA decay rates in yeast. PMID:25258386
MicroRNAs mediate dietary-restriction-induced longevity through PHA-4/FOXA and SKN-1/Nrf transcription factors. PMID:25242029
Understanding the limits of animal models as predictors of human biology: lessons learned from the sbv IMPROVER Species Translation Challenge. PMID:25236459
Genome-wide map of regulatory interactions in the human genome. PMID:25228660
Creating and validating cis-regulatory maps of tissue-specific gene expression regulation. PMID:25200088
Buffered Qualitative Stability explains the robustness and evolvability of transcriptional networks. PMID:25182846
RNA-Seq reveals novel transcriptional reorganization in human alcoholic brain. PMID:25172479
Comparative analysis of regulatory information and circuits across distant species. PMID:25164757
Comparative analysis of metazoan chromatin organization. PMID:25164756
Comparative analysis of the transcriptome across distant species. PMID:25164755
Regulatory analysis of the C. elegans genome with spatiotemporal resolution. PMID:25164749
Genomics: Hiding in plain sight. PMID:25164742
pENCODE: a plant encyclopedia of DNA elements. PMID:25149370
Competence for chemical reprogramming of sexual fate correlates with an intersexual molecular signature in Caenorhabditis elegans. PMID:25146970
Absence of a simple code: how transcription factors read the genome. PMID:25129887
Modeling epigenome folding: formation and dynamics of topologically associated chromatin domains. PMID:25092923
A new dataset of spermatogenic vs. oogenic transcriptomes in the nematode Caenorhabditis elegans. PMID:25060624
Crossover recombination mediated by HIM-18/SLX4-associated nucleases. PMID:25057454
Genomic data integration for ecological and evolutionary traits in non-model organisms. PMID:25047861
The comprehensive transcriptional analysis in Caenorhabditis elegans by integrating ChIP-seq and gene expression data. PMID:25023089
Comparison of D. melanogaster and C. elegans developmental stages, tissues, and cells by modENCODE RNA-seq data. PMID:24985912
Global characterization of the oocyte-to-embryo transition in Caenorhabditis elegans uncovers a novel mRNA clearance mechanism. PMID:24957527
Characterizing a collective and dynamic component of chromatin immunoprecipitation enrichment profiles in yeast. PMID:24947676
Fully automated high-throughput chromatin immunoprecipitation for ChIP-seq: identifying ChIP-quality p300 monoclonal antibodies. PMID:24919486
A pair of RNA-binding proteins controls networks of splicing events contributing to specialization of neural cell types. PMID:24910101
Paternal RNA contributions in the Caenorhabditis elegans zygote. PMID:24894551
Bioinformatic and proteomic analysis of bulk histones reveals PTM crosstalk and chromatin features. PMID:24894457
Spurious transcription factor binding: non-functional or genetically redundant? PMID:24888900
Multiple transcription factors directly regulate Hox gene lin-39 expression in ventral hypodermal cells of the C. elegans embryo and larva, including the hypodermal fate regulators LIN-26 and ELT-6. PMID:24885717
High-throughput capturing and characterization of mutations in essential genes of Caenorhabditis elegans. PMID:24884423
The influences of PRG-1 on the expression of small RNAs and mRNAs. PMID:24884413
RNA polymerase II transcription elongation and Pol II CTD Ser2 phosphorylation: A tail of two kinases. PMID:24879308
Worm variation made accessible: Take your shopping cart to store, link, and investigate! PMID:24843834
Towards structural systems pharmacology to study complex diseases and personalized medicine. PMID:24830652
The Little Fly that Could: Wizardry and Artistry of Drosophila Genomics. PMID:24827974
Loss-of-function of β-catenin bar-1 slows development and activates the Wnt pathway in Caenorhabditis elegans. PMID:24819947
Long-read sequencing of chicken transcripts and identification of new transcript isoforms. PMID:24736250
Holocentromeres are dispersed point centromeres localized at transcription factor hotspots. PMID:24714495
Evidence for the biogenesis of more than 1,000 novel human microRNAs. PMID:24708865
MUT-14 and SMUT-1 DEAD box RNA helicases have overlapping roles in germline RNAi and endogenous siRNA formation. PMID:24684932
Enhancer malfunction in cancer. PMID:24656127
Extreme HOT regions are CpG-dense promoters in C. elegans and humans. PMID:24653213
Defects in the C. elegans acyl-CoA synthase, acs-3, and nuclear hormone receptor, nhr-25, cause sensitivity to distinct, but overlapping stresses. PMID:24651852
Comparison of sequence variants in transcriptomic control regions across 17 mouse genomes. PMID:24647628
Evolutionary conservation of the eumetazoan gene regulatory landscape. PMID:24642862
Proteolytic processing of the extracellular scaffolding protein LEV-9 is required for clustering acetylcholine receptors. PMID:24619422
The Zebrafish GenomeWiki: a crowdsourcing approach to connect the long tail for zebrafish gene annotation. PMID:24578356
Use of an activated beta-catenin to identify Wnt pathway target genes in caenorhabditis elegans, including a subset of collagen genes expressed in late larval development. PMID:24569038
Nuclear RNAi contributes to the silencing of off-target genes and repetitive sequences in Caenorhabditis elegans. PMID:24532782
Increased sensitivity and accuracy of a single-stranded DNA splint-mediated ligation assay (sPAT) reveals poly(A) tail length dynamics of developmentally regulated mRNAs. PMID:24526206
A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages. PMID:24510058
Transcriptional control of a whole chromosome: emerging models for dosage compensation. PMID:24500429
Genome-wide analysis links emerin to neuromuscular junction activity in Caenorhabditis elegans. PMID:24490688
Pol II docking and pausing at growth and stress genes in C. elegans. PMID:24485661
A rapid and massive gene expression shift marking adolescent transition in C. elegans. PMID:24468752
Evidence for site-specific occupancy of the mitochondrial genome by nuclear transcription factors. PMID:24465428
Trichinella spiralis, potential model nematode for epigenetics and its implication in metazoan parasitism. PMID:24454291
Pancreatic islet enhancer clusters enriched in type 2 diabetes risk-associated variants. PMID:24413736
Molecular neuroanatomy: a generation of progress. PMID:24388609
Time for the zebrafish ENCODE. PMID:24371190
Spatial expression of transcription factors in Drosophila embryonic organ development. PMID:24359758
Widespread misinterpretable ChIP-seq bias in yeast. PMID:24349523
C. elegans epigenetic regulation in development and aging. PMID:24326118
Computational identification and analysis of orphan assembly-line polyketide synthases. PMID:24301183
SND1 transcription factor-directed quantitative functional hierarchical genetic regulatory network in wood formation in Populus trichocarpa. PMID:24280390
chroGPS, a global chromatin positioning system for the functional analysis and visualization of the epigenome. PMID:24271395
RNA-binding protein GLD-1/quaking genetically interacts with the mir-35 and the let-7 miRNA pathways in Caenorhabditis elegans. PMID:24258276
Dynamic trans-acting factor colocalization in human cells. PMID:24243024
Predicting tissue specific transcription factor binding sites. PMID:24238150
Beyond the ENCODE project: using genomics and epigenomics strategies to study enhancer evolution. PMID:24218635
Discover context-specific combinatorial transcription factor interactions by integrating diverse ChIP-Seq data sets. PMID:24217919
WormQTLHD--a web database for linking human disease to natural variation data in C. elegans. PMID:24217915
Coordination of cell proliferation and cell fate determination by CES-1 snail. PMID:24204299
JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles. PMID:24194598
FunCoup 3.0: database of genome-wide functional coupling networks. PMID:24185702
C. elegans nuclear receptor NHR-6 functionally interacts with the jun-1 transcription factor during spermatheca development. PMID:24178943
A multitasking Argonaute: exploring the many facets of C. elegans CSR-1. PMID:24178449
Crossover heterogeneity in the absence of hotspots in Caenorhabditis elegans. PMID:24172135
Homeland security in the C. elegans germ line: insights into the biogenesis and function of piRNAs. PMID:24149573
Mated progeny production is a biomarker of aging in Caenorhabditis elegans. PMID:24142929
Transcription-factor occupancy at HOT regions quantitatively predicts RNA polymerase recruitment in five human cell lines. PMID:24138567
Human genome replication proceeds through four chromatin states. PMID:24130466
Genome-wide analysis of condensin binding in Caenorhabditis elegans. PMID:24125077
Collaborative regulation of development but independent control of metabolism by two epidermis-specific transcription factors in Caenorhabditis elegans. PMID:24097988
Positive and negative design for nonconsensus protein-DNA binding affinity in the vicinity of functional binding sites. PMID:24094406
Alternative Splicing Regulation of Cancer-Related Pathways in Caenorhabditis elegans: An In Vivo Model System with a Powerful Reverse Genetics Toolbox. PMID:24069034
Transcription factor binding to Caenorhabditis elegans first introns reveals lack of redundancy with gene promoters. PMID:24068555
Toward 959 nematode genomes. PMID:24058822
WormBase: Annotating many nematode genomes. PMID:24058818
TRA-1 ChIP-seq reveals regulators of sexual differentiation and multilevel feedback in nematode sex determination. PMID:24046365
Dampening of expression oscillations by synchronous regulation of a microRNA and its target. PMID:24036951
Mapping yeast transcriptional networks. PMID:24018767
Engineering the Caenorhabditis elegans genome using Cas9-triggered homologous recombination. PMID:23995389
Endogenous nuclear RNAi mediates behavioral adaptation to odor. PMID:23993094
Cellular resolution models for even skipped regulation in the entire Drosophila embryo. PMID:23930223
Interplay between structure-specific endonucleases for crossover control during Caenorhabditis elegans meiosis. PMID:23874210
jMOSAiCS: joint analysis of multiple ChIP-seq datasets. PMID:23844871
The ZFP-1(AF10)/DOT-1 complex opposes H2B ubiquitination to reduce Pol II transcription. PMID:23806335
Proteogenomic database construction driven from large scale RNA-seq data. PMID:23802565
Transcriptional regulation of gene expression in C. elegans. PMID:23801596
The million mutation project: a new approach to genetics in Caenorhabditis elegans. PMID:23800452
Extensive rewiring and complex evolutionary dynamics in a C. elegans multiparameter transcription factor network. PMID:23791784
RSR-2, the Caenorhabditis elegans ortholog of human spliceosomal component SRm300/SRRM2, regulates development by influencing the transcriptional machinery. PMID:23754964
Machine learning and genome annotation: a match meant to be? PMID:23731483
The C. elegans gene pan-1 encodes novel transmembrane and cytoplasmic leucine-rich repeat proteins and promotes molting and the larva to adult transition. PMID:23682709
A statistical framework for power calculations in ChIP-seq experiments. PMID:23665773
Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data. PMID:23657480
The transcription start site landscape of C. elegans. PMID:23636945
DAF-16 employs the chromatin remodeller SWI/SNF to promote stress resistance and longevity. PMID:23604319
Computational solutions for omics data. PMID:23594911
The landscape of RNA polymerase II transcription initiation in C. elegans reveals promoter and enhancer architectures. PMID:23550086
Integrative analysis of C. elegans modENCODE ChIP-seq data sets to infer gene regulatory interactions. PMID:23531767
Molecular hyperdiversity and evolution in very large populations. PMID:23506466
Comparative genomics and functional study of lipid metabolic genes in Caenorhabditis elegans. PMID:23496871
Oct4 switches partnering from Sox2 to Sox17 to reinterpret the enhancer code and specify endoderm. PMID:23474895
Roles of the developmental regulator unc-62/Homothorax in limiting longevity in Caenorhabditis elegans. PMID:23468654
Regulation of nucleosome dynamics by histone modifications. PMID:23463310
Promoter- and RNA polymerase II-dependent hsp-16 gene association with nuclear pores in Caenorhabditis elegans. PMID:23460676
New insights from existing sequence data: generating breakthroughs without a pipette. PMID:23438857
A compendium of Caenorhabditis elegans RNA binding proteins predicts extensive regulation at multiple levels. PMID:23390605
Inference of natural selection from interspersed genomic elements based on polymorphism and divergence. PMID:23386628
High-throughput sequencing reveals extraordinary fluidity of miRNA, piRNA, and siRNA pathways in nematodes. PMID:23363624
Centromere-like regions in the budding yeast genome. PMID:23349633
Tissue-specific direct targets of Caenorhabditis elegans Rb/E2F dictate distinct somatic and germline programs. PMID:23347407
High-throughput sequencing for biology and medicine. PMID:23340846
The Caenorhabditis elegans homeobox gene ceh-19 is required for MC motorneuron function. PMID:23315936
The RNA Pol II elongation factor Ell3 marks enhancers in ES cells and primes future gene activation. PMID:23273992
The GATA transcription factor egl-27 delays aging by promoting stress resistance in Caenorhabditis elegans. PMID:23271974
The comprehensive epigenome map of piRNA clusters. PMID:23258708
Embryonic priming of a miRNA locus predetermines postmitotic neuronal left/right asymmetry in C. elegans. PMID:23201143
Histone lysine methylation dynamics: establishment, regulation, and biological impact. PMID:23200123
WormQTL--public archive and analysis web portal for natural variation data in Caenorhabditis spp. PMID:23180786
ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data. PMID:23161675
The expanding scope of DNA sequencing. PMID:23138308
Binary Interval Search: a scalable algorithm for counting interval intersections. PMID:23129298
Chromatin signature discovery via histone modification profile alignments. PMID:22989711
RNA sequencing reveals a diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development. PMID:22960373
Circuitry and dynamics of human transcription factor regulatory networks. PMID:22959076
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. PMID:22955991
Genome-wide in silico prediction of gene expression. PMID:22954627
The chromatin fingerprint of gene enhancer elements. PMID:22952241
Genome-wide epigenetic data facilitate understanding of disease susceptibility association studies. PMID:22952232
Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors. PMID:22950945
Deciphering the transcriptional regulation of microRNA genes in humans with ACTLocater. PMID:22941648
A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals. PMID:22940246
ncDNA and drift drive binding site accumulation. PMID:22935101
Regulatory elements of Caenorhabditis elegans ribosomal protein genes. PMID:22928635
SLX-1 is required for maintaining genomic integrity and promoting meiotic noncrossovers in the Caenorhabditis elegans germline. PMID:22927825
A genome-scale resource for in vivo tag-based protein function exploration in C. elegans. PMID:22901814
An atlas of the Epstein-Barr virus transcriptome and epigenome reveals host-virus regulatory interactions. PMID:22901543
Germ cell specification. PMID:22872473
Evidence for sequence biases associated with patterns of histone methylation. PMID:22857523
One Hand Clapping: detection of condition-specific transcription factor interactions from genome-wide gene activity data. PMID:22844089
A survey of putative secreted and transmembrane proteins encoded in the C. elegans genome. PMID:22823938
Studying and modelling dynamic biological processes using time-series gene expression data. PMID:22805708
Cohesin regulates tissue-specific expression by stabilizing highly occupied cis-regulatory modules. PMID:22780989
Nonspecific protein-DNA binding is widespread in the yeast genome. PMID:22768944
A map of the cis-regulatory sequences in the mouse genome. PMID:22763441
Poly-acetylated chromatin signatures are preferred epitopes for site-specific histone H4 acetyl antibodies. PMID:22761995
Transcription factor redundancy and tissue-specific regulation: evidence from functional and physical network connectivity. PMID:22730465
Divergent gene expression in the conserved dauer stage of the nematodes Pristionchus pacificus and Caenorhabditis elegans. PMID:22712530
Long noncoding RNAs in C. elegans. PMID:22707570
Genomic approaches towards finding cis-regulatory modules in animals. PMID:22705667
Biclustering of linear patterns in gene expression data. PMID:22697238
Inferring direct DNA binding from ChIP-seq. PMID:22610855
Cis-acting polymorphisms affect complex traits through modifications of microRNA regulation pathways. PMID:22606281
Finding a balance: how diverse dosage compensation strategies modify histone h4 to regulate transcription. PMID:22567401
HOT DNAs: a novel class of developmental enhancers. PMID:22549952
Regulation of chromatin structure by long noncoding RNAs: focus on natural antisense transcripts. PMID:22541732
Roles for microRNAs in conferring robustness to biological processes. PMID:22541426
Conserved Motifs and Prediction of Regulatory Modules in Caenorhabditis elegans. PMID:22540038
Nutritional control of mRNA isoform expression during developmental arrest and recovery in C. elegans. PMID:22539650
PIWI associated siRNAs and piRNAs specifically require the Caenorhabditis elegans HEN1 ortholog henn-1. PMID:22536158
Multidimensional regulation of gene expression in the C. elegans embryo. PMID:22508763
HOT regions function as patterned developmental enhancers and have a distinct cis-regulatory signature. PMID:22499593
Transcriptome analysis reveals strain-specific and conserved stemness genes in Schmidtea mediterranea. PMID:22496805
Spatial proximity and similarity of the epigenetic state of genome domains. PMID:22496774
Causes and consequences of the evolution of reproductive mode in Caenorhabditis nematodes. PMID:22480920
Combinatorial complexity in chromatin structure and function: revisiting the histone code. PMID:22440480
Organotellurium and organoselenium compounds attenuate Mn-induced toxicity in Caenorhabditis elegans by preventing oxidative stress. PMID:22406322
Genomic analysis of the hydrocarbon-producing, cellulolytic, endophytic fungus Ascocoryne sarcoides. PMID:22396667
Insulin/IGF-1 and hypoxia signaling act in concert to regulate iron homeostasis in Caenorhabditis elegans. PMID:22396654
Caenorhabditis elegans dosage compensation regulates histone H4 chromatin state on X chromosomes. PMID:22393255
A differential sequencing-based analysis of the C. elegans noncoding transcriptome. PMID:22345127
Evolutionary conservation of histone modifications in mammals. PMID:22319170
Fast, sensitive discovery of conserved genome-wide motifs. PMID:22300316
TranscriptomeBrowser 3.0: introducing a new compendium of molecular interactions and a new visualization tool for the study of gene regulatory networks. PMID:22292669
Tempo and mode in evolution of transcriptional regulation. PMID:22291600
Quantitative analysis of the chromatin proteome in disease reveals remodeling principles and identifies high mobility group protein B2 as a regulator of hypertrophic growth. PMID:22270000
The TAGteam motif facilitates binding of 21 sequence-specific transcription factors in the Drosophila embryo. PMID:22247430
IQSeq: integrated isoform quantification analysis based on next-generation sequencing. PMID:22238592
A highly efficient and effective motif discovery method for ChIP-seq/ChIP-chip data using positional information. PMID:22228832
A regulatory cascade of three transcription factors in a single specific neuron, DVC, in Caenorhabditis elegans. PMID:22207033
Evolution of biological interaction networks: from models to real data. PMID:22204388
An HNF4α-miRNA inflammatory feedback circuit regulates hepatocellular oncogenesis. PMID:22153071
In vivo and transcriptome-wide identification of RNA binding protein target sites. PMID:22152485
Cis-regulatory elements: molecular mechanisms and evolutionary processes underlying divergence. PMID:22143240
The epigenome in early vertebrate development. PMID:22139962
Sparse linear modeling of next-generation mRNA sequencing (RNA-Seq) data for isoform discovery and abundance estimation. PMID:22135461
Construction and analysis of an integrated regulatory network derived from high-throughput sequencing data. PMID:22125477
High-resolution mapping of open chromatin in the rice genome. PMID:22110044
The ERI-6/7 helicase acts at the first stage of an siRNA amplification pathway that targets recent gene duplications. PMID:22102828
Filarial and Wolbachia genomics. PMID:22098559
modMine: flexible access to modENCODE data. PMID:22080565
WormBase 2012: more genomes, more data, new website. PMID:22067452
Allelic methylation levels of the noncoding VTRNA2-1 located on chromosome 5q31.1 predict outcome in AML. PMID:22058117
TIP: a probabilistic method for identifying transcription factor target genes from ChIP-seq binding profiles. PMID:22039215
Evidence for compensatory upregulation of expressed X-linked genes in mammals, Caenorhabditis elegans and Drosophila melanogaster. PMID:22019781
Transgenerational epigenetic inheritance of longevity in Caenorhabditis elegans. PMID:22012258
Regulation of DCC localization by HTZ-1/H2A.Z and DPY-30 does not correlate with H3K4 methylation levels. PMID:21998734
A conserved PHD finger protein and endogenous RNAi modulate insulin signaling in Caenorhabditis elegans. PMID:21980302
The early bird catches the worm: new technologies for the Caenorhabditis elegans toolkit. PMID:21969037
Seeing elegance in gene regulatory networks of the worm. PMID:21963133
Modeling the relative relationship of transcription factor binding and histone modifications to gene expression levels in mouse embryonic stem cells. PMID:21926158
Functional consequences of developmentally regulated alternative splicing. PMID:21921927
Distant cis-regulatory elements in human skeletal muscle differentiation. PMID:21907276
Making sense of chromatin states. PMID:21878916
Pol III binding in six mammals shows conservation among amino acid isotypes despite divergence among tRNA genes. PMID:21873999
Caenorhabditis elegans UCP4 protein controls complex II-mediated oxidative phosphorylation through succinate transport. PMID:21862587
The modENCODE Data Coordination Center: lessons in harvesting comprehensive experimental details. PMID:21856757
Synthetic spike-in standards for RNA-seq experiments. PMID:21816910
Membrane protein insertion at the endoplasmic reticulum. PMID:21801011
Structural and functional evaluation of C. elegans filamins FLN-1 and FLN-2. PMID:21799850
The future of model organisms in human disease research. PMID:21765459
RNA-Seq unleashed. PMID:21747384
OrthoList: a compendium of C. elegans genes with human orthologs. PMID:21647448
Systematic bias in high-throughput sequencing data and its correction by BEADS. PMID:21646344
Reconstructing regulatory network transitions. PMID:21632251
Strategic approaches to unraveling genetic causes of cardiovascular diseases. PMID:21566222
PeakRanger: a cloud-enabled peak caller for ChIP-seq data. PMID:21554709
RNA structure and the mechanisms of alternative splicing. PMID:21530232
Chromatin: constructing the big picture. PMID:21527910
Nematodes: the worm and its relatives. PMID:21526226
Adipogenic hotspots: where the action is. PMID:21505519
Integrative epigenomic mapping defines four main chromatin states in Arabidopsis. PMID:21487388
What makes flies and worms tick. PMID:21473021
DNA shape, genetic codes, and evolution. PMID:21439813
A cis-regulatory map of the Drosophila genome. PMID:21430782
Molecular biology: A fly in the face of genomics. PMID:21430772
Networking in a global world: establishing functional connections between neural splicing regulators and their target transcripts. PMID:21415141
A modENCODE snapshot. PMID:21390030
The Caenorhabditis elegans intermediate-size transcriptome shows high degree of stage-specific expression. PMID:21378118
Genotyping gastric cancer. PMID:21373953
An MLL/COMPASS subunit functions in the C. elegans dosage compensation complex to target X chromosomes for transcriptional regulation of gene expression. PMID:21363964
Locking the genome: nuclear organization and cell fate. PMID:21345665
Charting a course for genomic medicine from base pairs to bedside. PMID:21307933
The C. elegans SoxC protein SEM-2 opposes differentiation factors to promote a proliferative blast cell fate in the postembryonic mesoderm. PMID:21307099
Operating on chromatin, a colorful language where context matters. PMID:21272588
Measuring the evolutionary rewiring of biological networks. PMID:21253555
Functional genomics: the modENCODE guide to the genome. PMID:21245826
Comprehensive analysis of the chromatin landscape in Drosophila melanogaster. PMID:21179089
Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin. PMID:21177972
Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data. PMID:21177971
A spatial and temporal map of C. elegans gene expression. PMID:21177967
High nucleosome occupancy is encoded at X-linked gene promoters in C. elegans. PMID:21177966
Broad chromosomal domains of histone modification patterns in C. elegans. PMID:21177964
Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans. PMID:21177963
A global analysis of C. elegans trans-splicing. PMID:21177958
Caenorhabditis elegans chromosome arms are anchored to the nuclear membrane via discontinuous association with LEM-2. PMID:21176223
Unlocking the secrets of the genome PubMed citations: 482.

482 articles citing: Unlocking the secrets of the genome

The E3 ligase Thin controls homeostatic plasticity through neurotransmitter release repression. PMID:35796533
Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements. PMID:35789323
Endomitosis controls tissue-specific gene expression during development. PMID:35609035
Single-Cell Analysis of the Transcriptome and Epigenome. PMID:35604552
Transposon activity, local duplications and propagation of structural variants across haplotypes drive the evolution of the Drosophila S2 cell line. PMID:35392795
Chinmo is the larval member of the molecular trinity that directs Drosophila metamorphosis. PMID:35377802
Domesticated LTR-Retrotransposon gag-Related Gene (Gagr) as a Member of the Stress Response Network in Drosophila. PMID:35330115
Divergent regulatory roles of NuRD chromatin remodeling complex subunits GATAD2 and CHD4 in Caenorhabditis elegans. PMID:35323946
Drosophila carrying epilepsy-associated variants in the vitamin B6 metabolism gene PNPO display allele- and diet-dependent phenotypes. PMID:35217610
Deficiency in RCAT-1 Function Causes Dopamine Metabolism Related Behavioral Disorders in Caenorhabditis elegans. PMID:35216508
Targeted DamID in C. elegans reveals a direct role for LIN-22 and NHR-25 in antagonizing the epidermal stem cell fate. PMID:35119932
Evidence of the Physical Interaction between Rpl22 and the Transposable Element Doc5, a Heterochromatic Transposon of Drosophila melanogaster. PMID:34946947
Pregnancy, preeclampsia and maternal aging: From epidemiology to functional genomics. PMID:34871806
Histone variant H2A.Z regulates zygotic genome activation. PMID:34853314
The SAGA core module is critical during Drosophila oogenesis and is broadly recruited to promoters. PMID:34807910
Temporal inhibition of chromatin looping and enhancer accessibility during neuronal remodeling. PMID:34737269
Characterization of the Zebrafish Cell Landscape at Single-Cell Resolution. PMID:34660600
Deletion of a putative HDA-1 binding site in the hlh-2 promoter eliminates expression in C. elegans dorsal uterine cells. PMID:34514358
Region-specific H3K9me3 gain in aged somatic tissues in Caenorhabditis elegans. PMID:34506495
Homeotic Genes: Clustering, Modularity, and Diversity. PMID:34458272
Non-Rodent Genetic Animal Models for Studying Tauopathy: Review of Drosophila, Zebrafish, and C. elegans Models. PMID:34445171
The neuroblast timer gene nubbin exhibits functional redundancy with gap genes to regulate segment identity in Tribolium. PMID:34351412
An actin-related protein that is most highly expressed in Drosophila testes is critical for embryonic development. PMID:34282725
Stem Cells and Innate Immunity in Aquatic Invertebrates: Bridging Two Seemingly Disparate Disciplines for New Discoveries in Biology. PMID:34276677
Automated generation of context-specific gene regulatory networks with a weighted approach in Drosophila melanogaster. PMID:34123358
Regulation of UNC-40/DCC and UNC-6/Netrin by DAF-16 promotes functional rewiring of the injured axon. PMID:34109380
Accelerated cell cycles enable organ regeneration under developmental time constraints in the Drosophila hindgut. PMID:34019841
MOCCA: a flexible suite for modelling DNA sequence motif occurrence combinatorics. PMID:33962556
HIM-17 regulates the position of recombination events and GSP-1/2 localization to establish short arm identity on bivalents in meiosis. PMID:33883277
A machine learning framework for the prediction of chromatin folding in Drosophila using epigenetic features. PMID:33816958
Genome-wide RNAi screen for regulators of UPRmt in Caenorhabditis elegans mutants with defects in mitochondrial fusion. PMID:33784383
Biological impact of mutually exclusive exon switching. PMID:33651795
The Krüppel-like factor Cabut has cell cycle regulatory properties similar to E2F1. PMID:33558234
Single-cell transcriptomes of developing and adult olfactory receptor neurons in Drosophila. PMID:33555999
In-silico definition of the Drosophila melanogaster matrisome. PMID:33543012
The negative elongation factor NELF promotes induced transcriptional response of Drosophila ecdysone-dependent genes. PMID:33420323
Order and stochasticity in the folding of individual Drosophila genomes. PMID:33397980
A primer for generating and using transcriptome data and gene sets. PMID:33361089
Nucleosome Positioning around Transcription Start Site Correlates with Gene Expression Only for Active Chromatin State in Drosophila Interphase Chromosomes. PMID:33291385
A context-dependent bifurcation in the Pointed transcriptional effector network contributes specificity and robustness to retinal cell fate acquisition. PMID:33253156
μDamID: A Microfluidic Approach for Joint Imaging and Sequencing of Protein-DNA Interactions in Single Cells. PMID:33099405
Proteomic analysis of Drosophila CLOCK complexes identifies rhythmic interactions with SAGA and Tip60 complex component NIPPED-A. PMID:33087840
Learning Retention Mechanisms and Evolutionary Parameters of Duplicate Genes from Their Expression Data. PMID:33045078
Insulin and Leptin/Upd2 Exert Opposing Influences on Synapse Number in Fat-Sensing Neurons. PMID:32976758
Analysis of Gal4 Expression Patterns in Adult Drosophila Females. PMID:32917721
Stable unmethylated DNA demarcates expressed genes and their cis-regulatory space in plant genomes. PMID:32879011
Interpretation of psychiatric genome-wide association studies with multispecies heterogeneous functional genomic data integration. PMID:32791514
Partitiviruses Infecting Drosophila melanogaster and Aedes aegypti Exhibit Efficient Biparental Vertical Transmission. PMID:32759315
Mapping a mammalian adult adrenal gland hierarchy across species by microwell-seq. PMID:32743779
A Meta-Analysis of Wolbachia Transcriptomics Reveals a Stage-Specific Wolbachia Transcriptional Response Shared Across Different Hosts. PMID:32718933
Abnormal Social Interactions in a Drosophila Mutant of an Autism Candidate Gene: Neuroligin 3. PMID:32610435
Rapid Homeostatic Turnover of Embryonic ECM during Tissue Morphogenesis. PMID:32585131
Prime time for primate functional genomics. PMID:32544775
Evolutionarily conserved transcription factors drive the oxidative stress response in Drosophila. PMID:32532866
Comparative Transcriptomics across Nematode Life Cycles Reveal Gene Expression Conservation and Correlated Evolution in Adjacent Developmental Stages. PMID:32467980
Ten-eleven translocation proteins and their role beyond DNA demethylation - what we can learn from the fly. PMID:32419604
Construction of a human cell landscape at single-cell level. PMID:32214235
*-DCC: A platform to collect, annotate, and explore a large variety of sequencing experiments. PMID:32170312
Lamina-Dependent Stretching and Unconventional Chromosome Compartments in Early C. elegans Embryos. PMID:32105612
Meta-analysis of honey bee neurogenomic response links Deformed wing virus type A to precocious behavioral maturation. PMID:32080242
"What You Need, Baby, I Got It": Transposable Elements as Suppliers of Cis-Operating Sequences in Drosophila. PMID:32028630
Population Genomics on the Fly: Recent Advances in Drosophila. PMID:31975175
Transcriptome-wide-scale-predicted dsRNAs potentially involved in RNA homoeostasis are remarkably excluded from genes with no/very low expression in all developmental stages. PMID:31971862
ManiNetCluster: a novel manifold learning approach to reveal the functional links between gene networks. PMID:31888454
Structural and Functional Dissection of the 5' Region of the Notch Gene in Drosophila melanogaster. PMID:31842424
New developments on the Encyclopedia of DNA Elements (ENCODE) data portal. PMID:31713622
Transcriptional Silencers in Drosophila Serve a Dual Role as Transcriptional Enhancers in Alternate Cellular Contexts. PMID:31704182
A Burst of Genetic Innovation in Drosophila Actin-Related Proteins for Testis-Specific Function. PMID:31697328
Genetic interactions between the DBL-1/BMP-like pathway and dpy body size-associated genes in Caenorhabditis elegans. PMID:31693440
SEA version 3.0: a comprehensive extension and update of the Super-Enhancer archive. PMID:31667506
A secreted microRNA disrupts autophagy in distinct tissues of Caenorhabditis elegans upon ageing. PMID:31645592
Model system identification of novel congenital heart disease gene candidates: focus on RPL13. PMID:31625562
Hi-C guided assemblies reveal conserved regulatory topologies on X and autosomes despite extensive genome shuffling. PMID:31601616
Patterns and Constraints in the Evolution of Sperm Individualization Genes in Insects, with an Emphasis on Beetles. PMID:31590243
Vitellogenins - Yolk Gene Function and Regulation in Caenorhabditis elegans. PMID:31551797
Drosophila ClC-a is required in glia of the stem cell niche for proper neurogenesis and wiring of neural circuits. PMID:31479171
DNA sequence models of genome-wide Drosophila melanogaster Polycomb binding sites improve generalization to independent Polycomb Response Elements. PMID:31340029
Correlations Between LC-MS/MS-Detected Glycomics and NMR-Detected Metabolomics in Caenorhabditis elegans Development. PMID:31316996
Genome-Wide Association Analysis of Anoxia Tolerance in Drosophila melanogaster. PMID:31311780
Identifying loci with breeding potential across temperate and tropical adaptation via EigenGWAS and EnvGWAS. PMID:31287919
Inferring Interaction Networks From Multi-Omics Data. PMID:31249591
Interplay between small RNA pathways shapes chromatin landscapes in C. elegans. PMID:31216042
The NCATS BioPlanet - An Integrated Platform for Exploring the Universe of Cellular Signaling Pathways for Toxicology, Systems Biology, and Chemical Genomics. PMID:31133849
Active chromatin marks drive spatial sequestration of heterochromatin in C. elegans nuclei. PMID:31118512
HOT or not: examining the basis of high-occupancy target regions. PMID:31114922
Mitochondrial fragmentation drives selective removal of deleterious mtDNA in the germline. PMID:31092924
Two modes of transvection at the eyes absent gene of Drosophila demonstrate plasticity in transcriptional regulatory interactions in cis and in trans. PMID:31075100
Applications of ENCODE data to Systematic Analyses via Data Integration. PMID:31011690
ATAC-seq reveals regional differences in enhancer accessibility during the establishment of spatial coordinates in the Drosophila blastoderm. PMID:30962180
Association of Human FOS Promoter Variants with the Occurrence of Knee-Osteoarthritis in a Case Control Association Study. PMID:30893847
Loss of a proteostatic checkpoint in intestinal stem cells contributes to age-related epithelial dysfunction. PMID:30837466
A splice-site variant in the lncRNA gene RP1-140A9.1 cosegregates in the large Volkmann cataract family. PMID:30820140
Sperm-Leucylaminopeptidases are required for male fertility as structural components of mitochondrial paracrystalline material in Drosophila melanogaster sperm. PMID:30802236
Maternal Ribosomes Are Sufficient for Tissue Diversification during Embryonic Development in C. elegans. PMID:30799226
Heme peroxidase HPX-2 protects Caenorhabditis elegans from pathogens. PMID:30695063
Small Segmental Duplications in Drosophila-High Rate of Emergence and Elimination. PMID:30689862
Drosophila ML-DmD17-c3 cells respond robustly to Dpp and exhibit complex transcriptional feedback on BMP signaling components. PMID:30669963
Integrating Selection Mapping With Genetic Mapping and Functional Genomics. PMID:30619447
Reveal cell type-specific regulatory elements and their characterized histone code classes via a hidden Markov model. PMID:30598107
Drosophila Sister-of-Sex-lethal reinforces a male-specific gene expression pattern by controlling Sex-lethal alternative splicing. PMID:30590805
CHRAC/ACF contribute to the repressive ground state of chromatin. PMID:30456345
Epithelial Shaping by Diverse Apical Extracellular Matrices Requires the Nidogen Domain Protein DEX-1 in Caenorhabditis elegans. PMID:30409789
Epidermal Remodeling in Caenorhabditis elegans Dauers Requires the Nidogen Domain Protein DEX-1. PMID:30409788
SLIC-CAGE: high-resolution transcription start site mapping using nanogram-levels of total RNA. PMID:30404778
Allele-specific expression elucidates cis-regulatory logic. PMID:30383744
Determinants of promoter and enhancer transcription directionality in metazoans. PMID:30367057
Selective interactions between diverse STEs organize the ANT-C Hox cluster. PMID:30310129
Quantitative Proteomics Identification of Seminal Fluid Proteins in Male Drosophila melanogaster. PMID:30287546
Chromatin conformation and transcriptional activity are permissive regulators of DNA replication initiation in Drosophila. PMID:30279224
4C-seq characterization of Drosophila BEAF binding regions provides evidence for highly variable long-distance interactions between active chromatin. PMID:30248133
Comparative Transcriptomics in Two Extreme Neopterans Reveals General Trends in the Evolution of Modern Insects. PMID:30240738
GDAP2 mutations implicate susceptibility to cellular stress in a new form of cerebellar ataxia. PMID:30084953
Pooled genome-wide CRISPR screening for basal and context-specific fitness gene essentiality in Drosophila cells. PMID:30051818
aaquetzalli is required for epithelial cell polarity and neural tissue formation in Drosophila. PMID:29942698
A Fly's Eye View of Natural and Drug Reward. PMID:29720947
Similarity in replication timing between polytene and diploid cells is associated with the organization of the Drosophila genome. PMID:29659604
pDHS-ELM: computational predictor for plant DNase I hypersensitive sites based on extreme learning machines. PMID:29594496
Integrating ChIP-seq with other functional genomics data. PMID:29579165
Early experiences mediate distinct adult gene expression and reproductive programs in Caenorhabditis elegans. PMID:29447162
Re-Arrangements in the Cytoplasmic Distribution of Small RNAs Following the Maternal-to-Zygotic Transition in Drosophila Embryos. PMID:29439397
Chinmo prevents transformer alternative splicing to maintain male sex identity. PMID:29389999
Dynamic genome wide expression profiling of Drosophila head development reveals a novel role of Hunchback in retinal glia cell development and blood-brain barrier integrity. PMID:29360820
Knockdown of wfs1, a fly homolog of Wolfram syndrome 1, in the nervous system increases susceptibility to age- and stress-induced neuronal dysfunction and degeneration in Drosophila. PMID:29357349
High-resolution TADs reveal DNA sequences underlying genome organization in flies. PMID:29335486
Evidence for a hierarchical transcriptional circuit in Drosophila male germline involving testis-specific TAF and two gene-specific transcription factors, Mod and Acj6. PMID:29235675
A Moving Source of Matrix Components Is Essential for De Novo Basement Membrane Formation. PMID:29129537
Enhanced chromatin accessibility of the dosage compensated Drosophila male X-chromosome requires the CLAMP zinc finger protein. PMID:29077765
WormBase 2017: molting into a new stage. PMID:29069413
Generalized correlation measure using count statistics for gene expression data with ordered samples. PMID:29040382
Extracellular NME proteins: a player or a bystander? PMID:29035383
Accounting for GC-content bias reduces systematic errors and batch effects in ChIP-seq data. PMID:29025895
Comparative analysis of miRNA expression during the development of insects of different metamorphosis modes and germ-band types. PMID:29020923
Silencing of Repetitive DNA Is Controlled by a Member of an Unusual Caenorhabditis elegans Gene Family. PMID:28801529
Deleterious Consequences of UDP-Galactopyranose Mutase Inhibition for Nematodes. PMID:28732158
Mapping genome-wide transcription-factor binding sites using DAP-seq. PMID:28726847
Trans-splicing enhances translational efficiency in C. elegans. PMID:28684554
FlyExpress 7: An Integrated Discovery Platform To Study Coexpressed Genes Using in Situ Hybridization Images in Drosophila. PMID:28667017
EDEM Function in ERAD Protects against Chronic ER Proteinopathy and Age-Related Physiological Decline in Drosophila. PMID:28633019
Integrated analysis and transcript abundance modelling of H3K4me3 and H3K27me3 in developing secondary xylem. PMID:28611454
Genomic signatures of local adaptation in the Drosophila immune response. PMID:28586288
Challenges and progress in interpretation of non-coding genetic variants associated with human disease. PMID:28581336
SLC46 Family Transporters Facilitate Cytosolic Innate Immune Recognition of Monomeric Peptidoglycans. PMID:28539433
Blocking promiscuous activation at cryptic promoters directs cell type-specific gene expression. PMID:28522526
A Drosophila model for developmental nicotine exposure. PMID:28498868
Alcohol-Induced Neuroadaptation Is Orchestrated by the Histone Acetyltransferase CBP. PMID:28442993
VAMP3/Syb and YKT6 are required for the fusion of constitutive secretory carriers with the plasma membrane. PMID:28403141
Sex combs reduced (Scr) regulatory region of Drosophila revisited. PMID:28331962
Atrophin controls developmental signaling pathways via interactions with Trithorax-like. PMID:28327288
Correspondence of D. melanogaster and C. elegans developmental stages revealed by alternative splicing characteristics of conserved exons. PMID:28302059
Simultaneous Transcriptional and Epigenomic Profiling from Specific Cell Types within Heterogeneous Tissues In Vivo. PMID:28122230
A Network of Chromatin Factors Is Regulating the Transition to Postembryonic Development in Caenorhabditis elegans. PMID:28007841
LTR-mediated retroposition as a mechanism of RNA-based duplication in metazoans. PMID:27934698
Simultaneous dimension reduction and adjustment for confounding variation. PMID:27930330
Establishment and maintenance of heritable chromatin structure during early Drosophila embryogenesis. PMID:27879204
Systematic comparison of monoclonal versus polyclonal antibodies for mapping histone modifications by ChIP-seq. PMID:27826357
RNA-binding profiles of Drosophila CPEB proteins Orb and Orb2. PMID:27791065
An RNAi Screen To Identify Protein Phosphatases That Function Within the Drosophila Circadian Clock. PMID:27784754
Phased diploid genome assembly with single-molecule real-time sequencing. PMID:27749838
Bayesian Correlation Analysis for Sequence Count Data. PMID:27701449
LMethyR-SVM: Predict Human Enhancers Using Low Methylated Regions based on Weighted Support Vector Machines. PMID:27662487
Fine-tuning of chromatin composition and Polycomb recruitment by two Mi2 homologues during C. elegans early embryonic development. PMID:27651832
CardioTF, a database of deconstructing transcriptional circuits in the heart system. PMID:27635320
Chromatin boundary elements organize genomic architecture and developmental gene regulation in Drosophila Hox clusters. PMID:27621770
Repeated Duplication of Argonaute2 Is Associated with Strong Selection and Testis Specialization in Drosophila. PMID:27535930
Cross-species Conservation of context-specific networks. PMID:27531214
Transcription factors GAF and HSF act at distinct regulatory steps to modulate stress-induced gene activation. PMID:27492368
Transcriptional control of non-apoptotic developmental cell death in C. elegans. PMID:27472063
The Landscape of A-to-I RNA Editome Is Shaped by Both Positive and Purifying Selection. PMID:27467689
Formation of a Polycomb-Domain in the Absence of Strong Polycomb Response Elements. PMID:27466807
AGOUTI: improving genome assembly and annotation using transcriptome data. PMID:27435057
Heat*seq: an interactive web tool for high-throughput sequencing experiment comparison with public data. PMID:27378302
Genomic and Transcriptomic Associations Identify a New Insecticide Resistance Phenotype for the Selective Sweep at the Cyp6g1 Locus of Drosophila melanogaster. PMID:27317781
Chromatin Heterogeneity and Distribution of Regulatory Elements in the Late-Replicating Intercalary Heterochromatin Domains of Drosophila melanogaster Chromosomes. PMID:27300486
Combinatorial Gene Regulatory Functions Underlie Ultraconserved Elements in Drosophila. PMID:27247329
flyDIVaS: A Comparative Genomics Resource for Drosophila Divergence and Selection. PMID:27226167
DIANA-mirExTra v2.0: Uncovering microRNAs and transcription factors with crucial roles in NGS expression data. PMID:27207881
Comparative Expression Dynamics of Intergenic Long Noncoding RNAs in the Genus Drosophila. PMID:27189981
An ancient yet flexible cis-regulatory architecture allows localized Hedgehog tuning by patched/Ptch1. PMID:27146892
Architectural proteins Pita, Zw5,and ZIPIC contain homodimerization domain and support specific long-range interactions in Drosophila. PMID:27137890
GATA transcription factors as tissue-specific master regulators for induced responses. PMID:27123374
Abnormal Osmotic Avoidance Behavior in C. elegans Is Associated with Increased Hypertonic Stress Resistance and Improved Proteostasis. PMID:27111894
Enhancer-promoter interactions are encoded by complex genomic signatures on looping chromatin. PMID:27064255
The Genetic Architecture of Natural Variation in Recombination Rate in Drosophila melanogaster. PMID:27035832
Classification of Promoters Based on the Combination of Core Promoter Elements Exhibits Different Histone Modification Patterns. PMID:27003446
Bioinformatic analyses of sense and antisense expression from terminal inverted repeat transposons in Drosophila somatic cells. PMID:26986720
Snoo and Dpp Act as Spatial and Temporal Regulators Respectively of Adult Progenitor Cells in the Drosophila Trachea. PMID:26942411
The Neuronal Kinesin UNC-104/KIF1A Is a Key Regulator of Synaptic Aging and Insulin Signaling-Regulated Memory. PMID:26877087
The histone demethylase dKDM5/LID interacts with the SIN3 histone deacetylase complex and shares functional similarities with SIN3. PMID:26848313
NEAT: a framework for building fully automated NGS pipelines and analyses. PMID:26830846
DNMT3L enables accumulation and inheritance of epimutations in transgenic Drosophila. PMID:26795243
Quantification of gene-specific methylation of DNMT3B and MTHFR using sequenom EpiTYPER®. PMID:26759827
Genome-Wide Analysis Reveals Novel Regulators of Growth in Drosophila melanogaster. PMID:26751788
The Female Post-Mating Response Requires Genes Expressed in the Secondary Cells of the Male Accessory Gland in Drosophila melanogaster. PMID:26746709
TrpA1 Regulates Defecation of Food-Borne Pathogens under the Control of the Duox Pathway. PMID:26726767
Don't pull the plug! the Drosophila mating plug preserves fertility. PMID:26695093
The Ski2-family helicase Obelus regulates Crumbs alternative splicing and cell polarity. PMID:26644515
Effects of DNA Methylation and Chromatin State on Rates of Molecular Evolution in Insects. PMID:26637432
The Gas2 family protein Pigs is a microtubule +TIP that affects cytoskeleton organisation. PMID:26585311
SEA: a super-enhancer archive. PMID:26578594
Genetics on the Fly: A Primer on the Drosophila Model System. PMID:26564900
Linking Genes to Cardiovascular Diseases: Gene Action and Gene-Environment Interactions. PMID:26545598
The evolutionary landscape of intergenic trans-splicing events in insects. PMID:26521696
Active chromatin and transcription play a key role in chromosome partitioning into topologically associating domains. PMID:26518482
Genome-wide identification and characterization of tissue-specific RNA editing events in D. melanogaster and their potential role in regulating alternative splicing. PMID:26512413
Early-late genes of the ecdysone cascade as models for transcriptional studies. PMID:26506480
Trithorax regulates systemic signaling during Drosophila imaginal disc regeneration. PMID:26487779
The Central Region of the Drosophila Co-repressor Groucho as a Regulatory Hub. PMID:26483546
H3K23me2 is a new heterochromatic mark in Caenorhabditis elegans. PMID:26476455
Reconstruction of composite regulator-target splicing networks from high-throughput transcriptome data. PMID:26449793
Polarized Rac-dependent protrusions drive epithelial intercalation in the embryonic epidermis of C. elegans. PMID:26395474
REC-1 and HIM-5 distribute meiotic crossovers and function redundantly in meiotic double-strand break formation in Caenorhabditis elegans. PMID:26385965
A convex formulation for joint RNA isoform detection and quantification from multiple RNA-seq samples. PMID:26286719
Gene Model Annotations for Drosophila melanogaster: Impact of High-Throughput Data. PMID:26109357
Drosophila sodium channel mutations: Contributions to seizure-susceptibility. PMID:26093037
In vivo characterization of the Drosophila mRNA 3' end processing core cleavage complex. PMID:26081560
Probing long-range interactions by extracting free energies from genome-wide chromosome conformation capture data. PMID:26001583
MicroRNA-Dependent Transcriptional Silencing of Transposable Elements in Drosophila Follicle Cells. PMID:25993106
Comprehensive RNA-Seq transcriptomic profiling across 11 organs, 4 ages, and 2 sexes of Fischer 344 rats. PMID:25977771
High-resolution profiling of Drosophila replication start sites reveals a DNA shape and chromatin signature of metazoan origins. PMID:25921534
ATP synthase promotes germ cell differentiation independent of oxidative phosphorylation. PMID:25915123
An automated method for efficient, accurate and reproducible construction of RNA-seq libraries. PMID:25879881
Wormpath: searching for molecular interaction networks in Caenorhabditis elegans. PMID:25866556
Conservation of transcription factor binding specificities across 600 million years of bilateria evolution. PMID:25779349
The complex contributions of genetics and nutrition to immunity in Drosophila melanogaster. PMID:25764027
Using the ENCODE Resource for Functional Annotation of Genetic Variants. PMID:25762420
Condensin II Regulates Interphase Chromatin Organization Through the Mrg-Binding Motif of Cap-H2. PMID:25758823
Evolution of an epigenetic gene ensemble within the genus Anopheles. PMID:25724208
Base-resolution methylation patterns accurately predict transcription factor bindings in vivo. PMID:25722376
acal is a long non-coding RNA in JNK signaling in epithelial shape changes during drosophila dorsal closure. PMID:25710168
bHLH proteins involved in Drosophila neurogenesis are mutually regulated at the level of stability. PMID:25694512
Proximity ligation assays of protein and RNA interactions in the male-specific lethal complex on Drosophila melanogaster polytene chromosomes. PMID:25694028
A novel statistical method for quantitative comparison of multiple ChIP-seq datasets. PMID:25682068
Regulation of mechanosensation in C. elegans through ubiquitination of the MEC-4 mechanotransduction channel. PMID:25653375
Recent insights into Groucho co-repressor recruitment and function. PMID:25603281
Parallel functional changes in independent testis-specific duplicates of Aldehyde dehydrogenase in Drosophila. PMID:25564519
Genomics of ecological adaptation in cactophilic Drosophila. PMID:25552534
Association mapping across numerous traits reveals patterns of functional variation in maize. PMID:25474422
Collaboration between mitochondria and the nucleus is key to long life in Caenorhabditis elegans. PMID:25450327
De novo prediction of cis-regulatory elements and modules through integrative analysis of a large number of ChIP datasets. PMID:25442502
Non-referenced genome assembly from epigenomic short-read data. PMID:25437048
FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations. PMID:25398896
Tethering of SUUR and HP1 proteins results in delayed replication of euchromatic regions in Drosophila melanogaster polytene chromosomes. PMID:25398563
In silico pooling of ChIP-seq control experiments. PMID:25380244
siRNAs from an X-linked satellite repeat promote X-chromosome recognition in Drosophila melanogaster. PMID:25368194
Global analysis of transcription factor-binding sites in yeast using ChIP-Seq. PMID:25213249
Whole-genome expression analysis in the third instar larval midgut of Drosophila melanogaster. PMID:25193493
Evidence for deep regulatory similarities in early developmental programs across highly diverged insects. PMID:25173756
The Groucho co-repressor is primarily recruited to local target sites in active chromatin to attenuate transcription. PMID:25165826
Genomics: Hiding in plain sight. PMID:25164742
Wisdom from the fly. PMID:25161083
Functional specialization among members of Knickkopf family of proteins in insect cuticle organization. PMID:25144557
A view through a chromatin loop: insights into the ecdysone activation of early genes in Drosophila. PMID:25143532
Phylogenetic analyses and characterization of RNase X25 from Drosophila melanogaster suggest a conserved housekeeping role and additional functions for RNase T2 enzymes in protostomes. PMID:25133712
SIN3 is critical for stress resistance and modulates adult lifespan. PMID:25133314
metaseq: a Python package for integrative genome-wide analysis reveals relationships between chromatin insulators and associated nuclear mRNA. PMID:25063299
Data integration in the era of omics: current and future challenges. PMID:25032990
A novel dataset for identifying sex-biased genes in Drosophila. PMID:25031657
Comparative validation of the D. melanogaster modENCODE transcriptome annotation. PMID:24985915
Comparison of D. melanogaster and C. elegans developmental stages, tissues, and cells by modENCODE RNA-seq data. PMID:24985912
Altering the sex determination pathway in Drosophila fat body modifies sex-specific stress responses. PMID:24789992
Dynamic regulation of genetic pathways and targets during aging in Caenorhabditis elegans. PMID:24739375
The four aldehyde oxidases of Drosophila melanogaster have different gene expression patterns and enzyme substrate specificities. PMID:24737760
The Caenorhabditis elegans Myc-Mondo/Mad complexes integrate diverse longevity signals. PMID:24699255
Ancient association between cation leak channels and Mid1 proteins is conserved in fungi and animals. PMID:24639627
Navigating and mining modENCODE data. PMID:24636835
PolyaPeak: detecting transcription factor binding sites from ChIP-seq using peak shape information. PMID:24608116
Genome-wide analysis of regulation of gene expression and H3K9me2 distribution by JIL-1 kinase mediated histone H3S10 phosphorylation in Drosophila. PMID:24598257
SPIC: a novel similarity metric for comparing transcription factor binding site motifs based on information contents. PMID:24564945
A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages. PMID:24510058
Combinatorial modeling of chromatin features quantitatively predicts DNA replication timing in Drosophila. PMID:24465194
Tau promotes neurodegeneration through global chromatin relaxation. PMID:24464041
Competition within Introns: Splicing Wins over Polyadenylation via a General Mechanism. PMID:24455183
Insulin/IGF1 signaling inhibits age-dependent axon regeneration. PMID:24440228
Neprilysins: an evolutionarily conserved family of metalloproteases that play important roles in reproduction in Drosophila. PMID:24395329
Alcohol-induced histone acetylation reveals a gene network involved in alcohol tolerance. PMID:24348266
chroGPS, a global chromatin positioning system for the functional analysis and visualization of the epigenome. PMID:24271395
The dynamic architectural and epigenetic nuclear landscape: developing the genomic almanac of biology and disease. PMID:24242872
A p53 enhancer region regulates target genes through chromatin conformations in cis and in trans. PMID:24240233
Coordination of cell proliferation and cell fate determination by CES-1 snail. PMID:24204299
The Drosophila eve insulator Homie promotes eve expression and protects the adjacent gene from repression by polycomb spreading. PMID:24204298
WormBase: Annotating many nematode genomes. PMID:24058818
Functional genetics in the post-genomics era: building a better roadmap in Drosophila. PMID:24019096
Functional genetics in the post-genomics era: building a better roadmap in Drosophila. PMID:24018766
Efficient alignment of RNA secondary structures using sparse dynamic programming. PMID:24011432
MITIE: Simultaneous RNA-Seq-based transcript identification and quantification in multiple samples. PMID:23980025
Identification of transcription factor binding sites from ChIP-seq data at high resolution. PMID:23980024
Discovery of cell-type specific regulatory elements in the human genome using differential chromatin modification analysis. PMID:23945931
Computational identification of diverse mechanisms underlying transcription factor-DNA occupancy. PMID:23935523
Pleiohomeotic interacts with the core transcription elongation factor Spt5 to regulate gene expression in Drosophila. PMID:23894613
Cloud-based uniform ChIP-Seq processing tools for modENCODE and ENCODE. PMID:23875683
Neurodegeneration in drop-dead mutant drosophila melanogaster is associated with the respiratory system but not with Hypoxia. PMID:23874488
Widespread evidence of cooperative DNA binding by transcription factors in Drosophila development. PMID:23847101
Multiplexed Illumina sequencing libraries from picogram quantities of DNA. PMID:23837789
CpG islands under selective pressure are enriched with H3K4me3, H3K27ac and H3K36me3 histone modifications. PMID:23837650
Modeling exon expression using histone modifications. PMID:23825663
Deregulation of the protocadherin gene FAT1 alters muscle shapes: implications for the pathogenesis of facioscapulohumeral dystrophy. PMID:23785297
Chromatin and epigenetic features of long-range gene regulation. PMID:23766291
Global Mapping of Transcription Factor Binding Sites by Sequencing Chromatin Surrogates: a Perspective on Experimental Design, Data Analysis, and Open Problems. PMID:23762209
A synthetic biology approach to the development of transcriptional regulatory models and custom enhancer design. PMID:23732772
The secretory pathway calcium ATPase PMR-1/SPCA1 has essential roles in cell migration during Caenorhabditis elegans embryonic development. PMID:23696750
Integrative genomic analysis of CREB defines a critical role for transcription factor networks in mediating the fed/fasted switch in liver. PMID:23682854
Holo-TFIID controls the magnitude of a transcription burst and fine-tuning of transcription. PMID:23610421
Insulator protein Su(Hw) recruits SAGA and Brahma complexes and constitutes part of Origin Recognition Complex-binding sites in the Drosophila genome. PMID:23609538
Balancing selection on a regulatory region exhibiting ancient variation that predates human-neandertal divergence. PMID:23593015
The evolutionarily conserved protein CG9186 is associated with lipid droplets, required for their positioning and for fat storage. PMID:23525007
A conserved upstream motif orchestrates autonomous, germline-enriched expression of Caenorhabditis elegans piRNAs. PMID:23516384
GEI-8, a homologue of vertebrate nuclear receptor corepressor NCoR/SMRT, regulates gonad development and neuronal functions in Caenorhabditis elegans. PMID:23484030
DNA methylation: Bidding the CpG island goodbye. PMID:23467495
Patterning and regulatory associations of DNA methylation are mirrored by histone modifications in insects. PMID:23458712
The genetic architecture of degenerin/epithelial sodium channels in Drosophila. PMID:23449991
Sex-biased networks and nodes of sexually antagonistic conflict in Drosophila. PMID:23431497
Two new and distinct roles for Drosophila Argonaute-2 in the nucleus: alternative pre-mRNA splicing and transcriptional repression. PMID:23392611
Genome-wide localization of exosome components to active promoters and chromatin insulators in Drosophila. PMID:23358822
BRAF mutation-specific promoter methylation of FOX genes in colorectal cancer. PMID:23324568
In vivo regulation of E2F1 by Polycomb group genes in Drosophila. PMID:23275887
HERV-H RNA is abundant in human embryonic stem cells and a precise marker for pluripotency. PMID:23253934
Predicting spatial and temporal gene expression using an integrative model of transcription factor occupancy and chromatin state. PMID:23236268
Gene set control analysis predicts hematopoietic control mechanisms from genome-wide transcription factor binding data. PMID:23220237
Tissue-specific regulation of chromatin insulator function. PMID:23209434
Multiple cis-elements and trans-acting factors regulate dynamic spatio-temporal transcription of let-7 in Caenorhabditis elegans. PMID:23201578
Fife, a Drosophila Piccolo-RIM homolog, promotes active zone organization and neurotransmitter release. PMID:23197698
NCBI Epigenomics: what's new for 2013. PMID:23193265
Identification of genetic suppressors of the Sin3A knockdown wing phenotype. PMID:23166712
HP1a recruitment to promoters is independent of H3K9 methylation in Drosophila melanogaster. PMID:23166515
Polycomb group proteins bind an engrailed PRE in both the "ON" and "OFF" transcriptional states of engrailed. PMID:23139817
Histone H3 lysine 4 methylation revisited. PMID:23117820
Transcriptional pausing controls a rapid antiviral innate immune response in Drosophila. PMID:23084920
Drosophila Ninjurin A induces nonapoptotic cell death. PMID:23028562
InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data. PMID:23023984
Integration of ChIP-seq and machine learning reveals enhancers and a predictive regulatory sequence vocabulary in melanocytes. PMID:23019145
Transcription termination between polo and snap, two closely spaced tandem genes of D. melanogaster. PMID:22992452
Identification of E2F target genes that are rate limiting for dE2F1-dependent cell proliferation. PMID:22972499
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. PMID:22955991
Itga2b regulation at the onset of definitive hematopoiesis and commitment to differentiation. PMID:22952660
RPN-6 determines C. elegans longevity under proteotoxic stress conditions. PMID:22922647
Nuclear organization and genome function. PMID:22905954
A genome-scale resource for in vivo tag-based protein function exploration in C. elegans. PMID:22901814
fussel (fuss)--A negative regulator of BMP signaling in Drosophila melanogaster. PMID:22879948
Why is DNA methylation of Igf2 CpG island shore affected during ageing? PMID:22879347
Mechanism of generation of therapy related leukemia in response to anti-topoisomerase II agents. PMID:22829791
Ecdysone induced gene expression is associated with acetylation of histone H3 lysine 23 in Drosophila melanogaster. PMID:22808194
Drosophila CTCF tandemly aligns with other insulator proteins at the borders of H3K27me3 domains. PMID:22722341
Transvection is common throughout the Drosophila genome. PMID:22649078
SAYP and Brahma are important for 'repressive' and 'transient' Pol II pausing. PMID:22638575
Linking the epigenome to the genome: correlation of different features to DNA methylation of CpG islands. PMID:22558141
Conserved Motifs and Prediction of Regulatory Modules in Caenorhabditis elegans. PMID:22540038
Engrailed cooperates directly with Extradenticle and Homothorax on a distinct class of homeodomain binding sites to repress sloppy paired. PMID:22537495
Systematic evaluation of factors influencing ChIP-seq fidelity. PMID:22522655
Multidimensional regulation of gene expression in the C. elegans embryo. PMID:22508763
Transcriptome responses of insect fat body cells to tissue culture environment. PMID:22493724
Protein landscape at Drosophila melanogaster telomere-associated sequence repeats. PMID:22493064
Analysis of C. elegans intestinal gene expression and polyadenylation by fluorescence-activated nuclei sorting and 3'-end-seq. PMID:22467213
Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks. PMID:22456606
Epigenetic features are significantly associated with alternative splicing. PMID:22455468
Considerations for creating and annotating the budding yeast Genome Map at SGD: a progress report. PMID:22434826
MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets. PMID:22424423
Unveiling combinatorial regulation through the combination of ChIP information and in silico cis-regulatory module detection. PMID:22422841
Gene expression of the tumour suppressor LKB1 is mediated by Sp1, NF-Y and FOXO transcription factors. PMID:22412893
Repression of germline RNAi pathways in somatic cells by retinoblastoma pathway chromatin complexes. PMID:22412383
Coupling polymerase pausing and chromatin landscapes for precise regulation of transcription. PMID:22406341
Akirin links twist-regulated transcription with the Brahma chromatin remodeling complex during embryogenesis. PMID:22396663
Partitioning transcript variation in Drosophila: abundance, isoforms, and alleles. PMID:22384353
Roles of major facilitator superfamily transporters in phosphate response in Drosophila. PMID:22359624
CCDC-55 is required for larval development and distal tip cell migration in Caenorhabditis elegans. PMID:22285439
P-element homing is facilitated by engrailed polycomb-group response elements in Drosophila melanogaster. PMID:22276200
LCGbase: A Comprehensive Database for Lineage-Based Co-regulated Genes. PMID:22267903
IQSeq: integrated isoform quantification analysis based on next-generation sequencing. PMID:22238592
The influence of assortativity on the robustness of signal-integration logic in gene regulatory networks. PMID:22155134
The epigenome in early vertebrate development. PMID:22139962
Sparse linear modeling of next-generation mRNA sequencing (RNA-Seq) data for isoform discovery and abundance estimation. PMID:22135461
Genome-wide analysis of retrogene polymorphisms in Drosophila melanogaster. PMID:22135405
Construction and analysis of an integrated regulatory network derived from high-throughput sequencing data. PMID:22125477
Saccharomyces Genome Database: the genomics resource of budding yeast. PMID:22110037
A remarkably stable TipE gene cluster: evolution of insect Para sodium channel auxiliary subunits. PMID:22098672
Protein composition of interband regions in polytene and cell line chromosomes of Drosophila melanogaster. PMID:22093916
modMine: flexible access to modENCODE data. PMID:22080565
Introduction to bioinformatics: sequencing technology. PMID:22053303
Developmental regulation of N-terminal H2B methylation in Drosophila melanogaster. PMID:22053083
The MOF-containing NSL complex associates globally with housekeeping genes, but activates only a defined subset. PMID:22039099
Proteomic and functional genomic landscape of receptor tyrosine kinase and ras to extracellular signal-regulated kinase signaling. PMID:22028469
Distinct epigenomic features in end-stage failing human hearts. PMID:22025602
Intronic L1 retrotransposons and nested genes cause transcriptional interference by inducing intron retention, exonization and cryptic polyadenylation. PMID:22022525
Identical functional organization of nonpolytene and polytene chromosomes in Drosophila melanogaster. PMID:22022482
Analysis of primary structure of chromatin with next-generation sequencing. PMID:22022339
MicroRNA expression and regulation in human, chimpanzee, and macaque brains. PMID:22022286
CpG deamination creates transcription factor-binding sites with high efficiency. PMID:22016335
Impact of the genome on the epigenome is manifested in DNA methylation patterns of imprinted regions in monozygotic and dizygotic twins. PMID:21991322
Phosphatidylcholine synthesis for lipid droplet expansion is mediated by localized activation of CTP:phosphocholine cytidylyltransferase. PMID:21982710
HIF-1 and SKN-1 coordinate the transcriptional response to hydrogen sulfide in Caenorhabditis elegans. PMID:21980473
JAK/Stat signaling regulates heart precursor diversification in Drosophila. PMID:21965617
Cohesin selectively binds and regulates genes with paused RNA polymerase. PMID:21962715
Using the Drosophila melanogaster D17-c3 cell culture system to study cell motility. PMID:21959242
Observing copepods through a genomic lens. PMID:21933388
Drosophila, genetic screens, and cardiac function. PMID:21921272
Integrated genome-wide analysis of transcription factor occupancy, RNA polymerase II binding and steady-state RNA levels identify differentially regulated functional gene classes. PMID:21914722
Regulated functional alternative splicing in Drosophila. PMID:21908400
CpG islands undermethylation in human genomic regions under selective pressure. PMID:21829712
Synthetic spike-in standards for RNA-seq experiments. PMID:21816910
Drosophila RNAi screening in a postgenomic world. PMID:21752787
Determinants of antigenicity and specificity in immune response for protein sequences. PMID:21693021
Heterochromatin boundaries are hotspots for de novo kinetochore formation. PMID:21685892
RNA-seq: technical variability and sampling. PMID:21645359
Microarrays, deep sequencing and the true measure of the transcriptome. PMID:21627854
Quadruplex formation is necessary for stable PNA invasion into duplex DNA of BCL2 promoter region. PMID:21593130
Genome Surveyor 2.0: cis-regulatory analysis in Drosophila. PMID:21593125
Coordinated expression of cell death genes regulates neuroblast apoptosis. PMID:21558369
PeakRanger: a cloud-enabled peak caller for ChIP-seq data. PMID:21554709
Methods and strategies for gene structure curation in WormBase. PMID:21543339
An epigenetic signature for monoallelic olfactory receptor expression. PMID:21529909
Transcription initiation from within P elements generates hypomorphic mutations in Drosophila melanogaster. PMID:21527778
Selectable genetic markers for nematode transgenesis. PMID:21431833
Molecular biology: A fly in the face of genomics. PMID:21430772
Evolution of a tissue-specific splicing network. PMID:21406555
A modENCODE snapshot. PMID:21390030
ChIP-chip versus ChIP-seq: lessons for experimental design and data analysis. PMID:21356108
ACT: aggregation and correlation toolbox for analyses of genome tracks. PMID:21349863
A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets. PMID:21324173
LIN-28 co-transcriptionally binds primary let-7 to regulate miRNA maturation in Caenorhabditis elegans. PMID:21297634
MM-ChIP enables integrative analysis of cross-platform and between-laboratory ChIP-chip or ChIP-seq data. PMID:21284836
Clcn4-2 genomic structure differs between the X locus in Mus spretus and the autosomal locus in Mus musculus: AT motif enrichment on the X. PMID:21282478
Quantitative analysis of DNA methylation at all human imprinted regions reveals preservation of epigenetic stability in adult somatic tissue. PMID:21281512
Polyglutamine Atrophin provokes neurodegeneration in Drosophila by repressing fat. PMID:21278706
Combinatorial chromatin modification patterns in the human genome revealed by subspace clustering. PMID:21266477
Transcription initiation patterns indicate divergent strategies for gene regulation at the chromatin level. PMID:21249180
Composite effects of polymorphisms near multiple regulatory elements create a major-effect QTL. PMID:21249179
Where gene discovery turns into systems biology: genome-scale RNAi screens in Drosophila. PMID:21197652
ArchAlign: coordinate-free chromatin alignment reveals novel architectures. PMID:21182771
The developmental transcriptome of Drosophila melanogaster. PMID:21179090
Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. PMID:21177976
Identification of functional elements and regulatory circuits by Drosophila modENCODE. PMID:21177974
Chromatin signatures of the Drosophila replication program. PMID:21177973
Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin. PMID:21177972
Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data. PMID:21177971
Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans. PMID:21177963
The transcriptional diversity of 25 Drosophila cell lines. PMID:21177962
Genome-wide analysis of promoter architecture in Drosophila melanogaster. PMID:21177961
Computational and experimental identification of mirtrons in Drosophila melanogaster and Caenorhabditis elegans. PMID:21177960
A global analysis of C. elegans trans-splicing. PMID:21177958
Assessing computational methods of cis-regulatory module prediction. PMID:21152003
An assessment of histone-modification antibody quality. PMID:21131980
Conserved catalytic and C-terminal regulatory domains of the C-terminal binding protein corepressor fine-tune the transcriptional response in development. PMID:21078873
NCBI Epigenomics: a new public resource for exploring epigenomic data sets. PMID:21075792
Genomic differentiation between temperate and tropical Australian populations of Drosophila melanogaster. PMID:21059887
Enrichment of mRNA-like noncoding RNAs in the divergence of Drosophila males. PMID:21041796
miRBase: integrating microRNA annotation and deep-sequencing data. PMID:21037258
ENCODE whole-genome data in the UCSC genome browser (2011 update). PMID:21037257
DroID 2011: a comprehensive, integrated resource for protein, transcription factor, RNA and gene interactions for Drosophila. PMID:21036869
REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila. PMID:20965965
FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data. PMID:20964841
Allele-specific and heritable chromatin signatures in humans. PMID:20846943
Chromatin landscape dictates HSF binding to target DNA elements. PMID:20844575
Preferential re-replication of Drosophila heterochromatin in the absence of geminin. PMID:20838463
Evolution of the Drosophila feminizing switch gene Sex-lethal. PMID:20837995
Meiosis: making a break for it. PMID:20829015
The Drosophila homolog of the mammalian imprint regulator, CTCF, maintains the maternal genomic imprint in Drosophila melanogaster. PMID:20673338
Discovery and characterization of chromatin states for systematic annotation of the human genome. PMID:20657582
Annotating non-coding regions of the genome. PMID:20628352
Specificity of Notch pathway activation: twist controls the transcriptional output in adult muscle progenitors. PMID:20610485
Estimating enrichment of repetitive elements from high-throughput sequence data. PMID:20584328
Lineage programming: navigating through transient regulatory states via binary decisions. PMID:20537527
Adaptive impact of the chimeric gene Quetzalcoatl in Drosophila melanogaster. PMID:20534482
Next-generation genomics: an integrative approach. PMID:20531367
High-resolution mapping studies of chromatin and gene regulatory elements. PMID:20514362
Most "dark matter" transcripts are associated with known genes. PMID:20502517
Re-programming of C. elegans male epidermal precursor fates by Wnt, Hox, and LIN-12/Notch activities. PMID:20478294
The case for cloud computing in genome informatics. PMID:20441614
Mapping the complexity of transcription control in higher eukaryotes. PMID:20441601
Nuclear hormone receptors in nematodes: evolution and function. PMID:20438802
Deciphering the genome's regulatory code: the many languages of DNA. PMID:20394065
The developmental expression dynamics of Drosophila melanogaster transcription factors. PMID:20384991
Genomic screening with RNAi: results and challenges. PMID:20367032
Drosophila RB proteins repress differentiation-specific genes via two different mechanisms. PMID:20176807
Expansion of the eukaryotic proteome by alternative splicing. PMID:20110989
Drosophila ORC localizes to open chromatin and marks sites of cohesin complex loading. PMID:19996087
Learning the transcriptional regulatory code. PMID:19920814
ENCODE whole-genome data in the UCSC Genome Browser. PMID:19920125
Why are we where we are? Understanding replication origins and initiation sites in eukaryotes using ChIP-approaches. PMID:19904620
Systems biology from a yeast omics perspective. PMID:19903479
FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database. PMID:19884132
Gene networks in Drosophila melanogaster: integrating experimental data to predict gene function. PMID:19758432
Implications of chimaeric non-co-linear transcripts. PMID:19741701
ChIP-seq: advantages and challenges of a maturing technology. PMID:19736561
modMine: flexible access to modENCODE data PubMed citations: 84.

84 articles citing: modMine: flexible access to modENCODE data

HumanMine: advanced data searching, analysis and cross-species comparison. PMID:35820040
R-loop Mapping and Characterization During Drosophila Embryogenesis Reveals Developmental Plasticity in R-loop Signatures. PMID:35609632
Caenorhabditis elegans transposable elements harbor diverse transcription factor DNA-binding sites. PMID:35088854
Heritable shifts in redox metabolites during mitochondrial quiescence reprogramme progeny metabolism. PMID:34545253
Filtering of Data-Driven Gene Regulatory Networks Using Drosophila melanogaster as a Case Study. PMID:34394179
Polycomb-group recruitment to a Drosophila target gene is the default state that is inhibited by a transcriptional activator. PMID:34272248
Automated generation of context-specific gene regulatory networks with a weighted approach in Drosophila melanogaster. PMID:34123358
Spatiotemporal recruitment of RhoGTPase protein GRAF inhibits actomyosin ring constriction in Drosophila cellularization. PMID:33835025
Evolution of Developmental GATA Factors in Nematodes. PMID:33207804
Methylmercury myotoxicity targets formation of the myotendinous junction. PMID:32800841
Insights into HP1a-Chromatin Interactions. PMID:32784937
Transcriptional repression of Myc underlies the tumour suppressor function of AGO1 in Drosophila. PMID:32527935
The Dm-Myb Oncoprotein Contributes to Insulator Function and Stabilizes Repressive H3K27me3 PcG Domains. PMID:32160531
WormQTL2: an interactive platform for systems genetics in Caenorhabditis elegans. PMID:31960906
Diversification of the Caenorhabditis heat shock response by Helitron transposable elements. PMID:31825311
Global chromatin conformation differences in the Drosophila dosage compensated chromosome X. PMID:31767860
Self-sperm induce resistance to the detrimental effects of sexual encounters with males in hermaphroditic nematodes. PMID:31282863
NF-κB Shapes Metabolic Adaptation by Attenuating Foxo-Mediated Lipolysis in Drosophila. PMID:31080057
The NSL complex-mediated nucleosome landscape is required to maintain transcription fidelity and suppression of transcription noise. PMID:30819819
Evolutionary rate covariation analysis of E-cadherin identifies Raskol as a regulator of cell adhesion and actin dynamics in Drosophila. PMID:30763317
Wingless promotes EGFR signaling in follicle stem cells to maintain self-renewal. PMID:30389852
Selective interactions between diverse STEs organize the ANT-C Hox cluster. PMID:30310129
The Systems Biology of Single-Cell Aging. PMID:30267677
Machine learning identifies interacting genetic variants contributing to breast cancer risk: A case study in Finnish cases and controls. PMID:30177847
Collaborative repressive action of the antagonistic ETS transcription factors Pointed and Yan fine-tunes gene expression to confer robustness in Drosophila. PMID:29848501
Using WormBase: A Genome Biology Resource for Caenorhabditis elegans and Related Nematodes. PMID:29761466
Degenerate Pax2 and Senseless binding motifs improve detection of low-affinity sites required for enhancer specificity. PMID:29617378
Variant cell cycles regulated by Notch signaling control cell size and ensure a functional blood-brain barrier. PMID:29440220
Single-cell absolute contact probability detection reveals chromosomes are organized by multiple low-frequency yet specific interactions. PMID:29170434
Convergence of topological domain boundaries, insulators, and polytene interbands revealed by high-resolution mapping of chromatin contacts in the early Drosophila melanogaster embryo. PMID:29148971
Chromatin accessibility dynamics reveal novel functional enhancers in C. elegans. PMID:29141961
Short poly(A) tails are a conserved feature of highly expressed genes. PMID:29106412
Recent Advances in the Systems Biology of Aging. PMID:29020802
The Effect of Common Inversion Polymorphisms In(2L)t and In(3R)Mo on Patterns of Transcriptional Variation in Drosophila melanogaster. PMID:28916647
Emerging Omics Approaches in Aging Research. PMID:28874057
Inwardly rectifying potassium channels influence Drosophila wing morphogenesis by regulating Dpp release. PMID:28684627
Sex and Genetic Background Influence Superoxide Dismutase (cSOD)-Related Phenotypic Variation in Drosophila melanogaster. PMID:28624774
Multifunctional glial support by Semper cells in the Drosophila retina. PMID:28562601
Application of a systems approach to study developmental gene regulation. PMID:28510076
ChARM: Discovery of combinatorial chromatin modification patterns in hepatitis B virus X-transformed mouse liver cancer using association rule mining. PMID:28105934
Drosophila poised enhancers are generated during tissue patterning with the help of repression. PMID:27979994
Transcriptome Analysis of Drosophila melanogaster Third Instar Larval Ring Glands Points to Novel Functions and Uncovers a Cytochrome p450 Required for Development. PMID:27974438
MicroRNA mir-34 provides robustness to environmental stress response via the DAF-16 network in C. elegans. PMID:27905558
TFBSbank: a platform to dissect the big data of protein-DNA interaction in human and model species. PMID:27899608
Combgap Promotes Ovarian Niche Development and Chromatin Association of EcR-Binding Regions in BR-C. PMID:27846223
Cross-species Conservation of context-specific networks. PMID:27531214
Stuxnet Facilitates the Degradation of Polycomb Protein during Development. PMID:27326929
The Genetic Architecture of Natural Variation in Recombination Rate in Drosophila melanogaster. PMID:27035832
A Systems Approach to Reverse Engineer Lifespan Extension by Dietary Restriction. PMID:26959186
Slowed aging during reproductive dormancy is reflected in genome-wide transcriptome changes in Drosophila melanogaster. PMID:26758761
Hymenoptera Genome Database: integrating genome annotations in HymenopteraMine. PMID:26578564
Genetics on the Fly: A Primer on the Drosophila Model System. PMID:26564900
The Spalt Transcription Factors Generate the Transcriptional Landscape of the Drosophila melanogaster Wing Pouch Central Region. PMID:26241320
toxoMine: an integrated omics data warehouse for Toxoplasma gondii systems biology research. PMID:26130662
Heterochromatin, histone modifications, and nuclear architecture in disease vectors. PMID:26097808
Cross-organism analysis using InterMine. PMID:26097192
The GATA factor elt-1 regulates C. elegans developmental timing by promoting expression of the let-7 family microRNAs. PMID:25816370
Drosophila muller f elements maintain a distinct set of genomic properties over 40 million years of evolution. PMID:25740935
FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations. PMID:25398896
VAS: a convenient web portal for efficient integration of genomic features with millions of genetic variants. PMID:25306238
esyN: network building, sharing and publishing. PMID:25181461
Short stories on zebrafish long noncoding RNAs. PMID:25110965
Bioinformatics on the cloud computing platform Azure. PMID:25050811
High-throughput capturing and characterization of mutations in essential genes of Caenorhabditis elegans. PMID:24884423
Control of metazoan heme homeostasis by a conserved multidrug resistance protein. PMID:24836561
InterMine: extensive web services for modern biology. PMID:24753429
Interactive visualization and analysis of large-scale sequencing datasets using ZENBU. PMID:24727769
Endogenously imprinted genes in Drosophila melanogaster. PMID:24658702
Resources for functional genomics studies in Drosophila melanogaster. PMID:24653003
Navigating and mining modENCODE data. PMID:24636835
Astrogenomics: big data, old problems, old solutions? PMID:23953643
Cloud-based uniform ChIP-Seq processing tools for modENCODE and ENCODE. PMID:23875683
Highly parallel assays of tissue-specific enhancers in whole Drosophila embryos. PMID:23852450
A negative-feedback loop between the detoxification/antioxidant response factor SKN-1 and its repressor WDR-23 matches organism needs with environmental conditions. PMID:23836880
RSR-2, the Caenorhabditis elegans ortholog of human spliceosomal component SRm300/SRRM2, regulates development by influencing the transcriptional machinery. PMID:23754964
InterMOD: integrated data and tools for the unification of model organism research. PMID:23652793
Natural variation of the Y chromosome suppresses sex ratio distortion and modulates testis-specific gene expression in Drosophila simulans. PMID:23591516
The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies. PMID:23398680
Structure-based whole-genome realignment reveals many novel noncoding RNAs. PMID:23296921
Identifying targets of the Sox domain protein Dichaete in the Drosophila CNS via targeted expression of dominant negative proteins. PMID:23289785
CBS: an open platform that integrates predictive methods and epigenetics information to characterize conserved regulatory features in multiple Drosophila genomes. PMID:23228284
InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data. PMID:23023984
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. PMID:22955991
Cscan: finding common regulators of a set of genes by using a collection of genome-wide ChIP-seq datasets. PMID:22669907
http://dx.doi.org/10.1093/nar/GKR921

http://dx.doi.org/10.1093/bioinformatics/bts577

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More detailed information about this field from each metasource.

binding site
metasource: Fairsharing.org
version: FAIRsharing.org: modMine; modMine; DOI: https://doi.org/10.25504/FAIRsharing.ekzmjp; Last edited: June 22, 2021, 11:56 a.m.; Last accessed: Jan 03 2022 7:07 p.m.

chromatin immunoprecipitation - dna microarray
metasource: Fairsharing.org
version: FAIRsharing.org: modMine; modMine; DOI: https://doi.org/10.25504/FAIRsharing.ekzmjp; Last edited: June 22, 2021, 11:56 a.m.; Last accessed: Jan 03 2022 7:07 p.m.

chromatin immunoprecipitation - dna sequencing
metasource: Fairsharing.org
version: FAIRsharing.org: modMine; modMine; DOI: https://doi.org/10.25504/FAIRsharing.ekzmjp; Last edited: June 22, 2021, 11:56 a.m.; Last accessed: Jan 03 2022 7:07 p.m.

citation
metasource: Fairsharing.org
version: FAIRsharing.org: modMine; modMine; DOI: https://doi.org/10.25504/FAIRsharing.ekzmjp; Last edited: June 22, 2021, 11:56 a.m.; Last accessed: Jan 03 2022 7:07 p.m.

computational predictions
metasource: Fairsharing.org
version: FAIRsharing.org: modMine; modMine; DOI: https://doi.org/10.25504/FAIRsharing.ekzmjp; Last edited: June 22, 2021, 11:56 a.m.; Last accessed: Jan 03 2022 7:07 p.m.

dna sequence data
metasource: Fairsharing.org
version: FAIRsharing.org: modMine; modMine; DOI: https://doi.org/10.25504/FAIRsharing.ekzmjp; Last edited: June 22, 2021, 11:56 a.m.; Last accessed: Jan 03 2022 7:07 p.m.

gene ontology enrichment
metasource: Fairsharing.org
version: FAIRsharing.org: modMine; modMine; DOI: https://doi.org/10.25504/FAIRsharing.ekzmjp; Last edited: June 22, 2021, 11:56 a.m.; Last accessed: Jan 03 2022 7:07 p.m.

gene model annotation
metasource: Fairsharing.org
version: FAIRsharing.org: modMine; modMine; DOI: https://doi.org/10.25504/FAIRsharing.ekzmjp; Last edited: June 22, 2021, 11:56 a.m.; Last accessed: Jan 03 2022 7:07 p.m.

orthologous
metasource: Fairsharing.org
version: FAIRsharing.org: modMine; modMine; DOI: https://doi.org/10.25504/FAIRsharing.ekzmjp; Last edited: June 22, 2021, 11:56 a.m.; Last accessed: Jan 03 2022 7:07 p.m.

phenotype
metasource: Fairsharing.org
version: FAIRsharing.org: modMine; modMine; DOI: https://doi.org/10.25504/FAIRsharing.ekzmjp; Last edited: June 22, 2021, 11:56 a.m.; Last accessed: Jan 03 2022 7:07 p.m.

protein
metasource: Fairsharing.org
version: FAIRsharing.org: modMine; modMine; DOI: https://doi.org/10.25504/FAIRsharing.ekzmjp; Last edited: June 22, 2021, 11:56 a.m.; Last accessed: Jan 03 2022 7:07 p.m.

protein domain
metasource: Fairsharing.org
version: FAIRsharing.org: modMine; modMine; DOI: https://doi.org/10.25504/FAIRsharing.ekzmjp; Last edited: June 22, 2021, 11:56 a.m.; Last accessed: Jan 03 2022 7:07 p.m.

microarray data and other gene expression databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

data management
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:22.228175

genomics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:22.228175

proteomics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:22.228175

binding site chromatin immunoprecipitation - dna microarray chromatin immunoprecipitation - dna sequencing citation computational predictions dna sequences gene ontology enrichment gene model annotation orthology phenotype protein protein domain microarray data and other gene expression data management genomics proteomics

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