Genome Res

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  Publication Venue For

  • Linking the dynamics of chromatin occupancy and transcription with predictive models..  31:1035-1046. 2021
  • Competition for DNA binding between paralogous transcription factors determines their genomic occupancy and regulatory functions. 2021
  • Correcting signal biases and detecting regulatory elements in STARR-seq data..  31:877-889. 2021
  • Local nucleosome dynamics and eviction following a double-strand break are reversible by NHEJ-mediated repair in the absence of DNA replication..  31:775-788. 2021
  • AP-1 subunits converge promiscuously at enhancers to potentiate transcription..  31:538-550. 2021
  • A new emu genome illuminates the evolution of genome configuration and nuclear architecture of avian chromosomes..  31:497-511. 2021
  • The Nubeam reference-free approach to analyze metagenomic sequencing reads..  30:1364-1375. 2020
  • Characterization of colibactin-associated mutational signature in an Asian oral squamous cell carcinoma and in other mucosal tumor types..  30:803-813. 2020
  • Nascent chromatin occupancy profiling reveals locus- and factor-specific chromatin maturation dynamics behind the DNA replication fork..  29:1123-1133. 2019
  • A new approach for rare variation collapsing on functional protein domains implicates specific genic regions in ALS..  29:809-818. 2019
  • Experimental and pan-cancer genome analyses reveal widespread contribution of acrylamide exposure to carcinogenesis in humans..  29:521-531. 2019
  • Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells..  29:449-463. 2019
  • Chromatin conformation and transcriptional activity are permissive regulators of DNA replication initiation in Drosophila..  28:1688-1700. 2018
  • Human cardiac cis-regulatory elements, their cognate transcription factors, and regulatory DNA sequence variants..  28:1577-1588. 2018
  • Glucocorticoid receptor recruits to enhancers and drives activation by motif-directed binding..  28:1272-1284. 2018
  • Corrigendum: Detecting differential copy number variation between groups of samples..  28:766.1. 2018
  • In-depth characterization of the cisplatin mutational signature in human cell lines and in esophageal and liver tumors..  28:654-665. 2018
  • Detecting differential copy number variation between groups of samples..  28:256-265. 2018
  • Nanopore sequencing of complex genomic rearrangements in yeast reveals mechanisms of repeat-mediated double-strand break repair..  27:2072-2082. 2017
  • Genome-scale mutational signatures of aflatoxin in cells, mice, and human tumors..  27:1475-1486. 2017
  • Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha..  27:1195-1206. 2017
  • Population genomics and the evolution of virulence in the fungal pathogen Cryptococcus neoformans..  27:1207-1219. 2017
  • Genomic variation within alpha satellite DNA influences centromere location on human chromosomes with metastable epialleles..  26:1301-1311. 2016
  • A new class of temporarily phenotypic enhancers identified by CRISPR/Cas9-mediated genetic screening..  26:397-405. 2016
  • Mapping nucleosome positions using DNase-seq..  26:351-364. 2016
  • Genomic approaches for understanding the genetics of complex disease..  25:1432-1441. 2015
  • Genome-wide specificity of DNA binding, gene regulation, and chromatin remodeling by TALE- and CRISPR/Cas9-based transcriptional activators..  25:1158-1169. 2015
  • Massively parallel quantification of the regulatory effects of noncoding genetic variation in a human cohort..  25:1206-1214. 2015
  • The 100-genomes strains, an S. cerevisiae resource that illuminates its natural phenotypic and genotypic variation and emergence as an opportunistic pathogen..  25:762-774. 2015
  • Whole-epigenome analysis in multiple myeloma reveals DNA hypermethylation of B cell-specific enhancers..  25:478-487. 2015
  • Genome accessibility is widely preserved and locally modulated during mitosis..  25:213-225. 2015
  • Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal..  25:41-56. 2015
  • Heterogeneous polymerase fidelity and mismatch repair bias genome variation and composition..  24:1751-1764. 2014
  • Microbiota modulate transcription in the intestinal epithelium without remodeling the accessible chromatin landscape..  24:1504-1516. 2014
  • A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples..  24:1180-1192. 2014
  • DNA replication and transcription programs respond to the same chromatin cues..  24:1102-1114. 2014
  • Inferring gene expression from ribosomal promoter sequences, a crowdsourcing approach..  23:1928-1937. 2013
  • Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data..  23:1730-1739. 2013
  • DNase-seq predicts regions of rotational nucleosome stability across diverse human cell types..  23:1118-1129. 2013
  • A dynamic H3K27ac signature identifies VEGFA-stimulated endothelial enhancers and requires EP300 activity..  23:917-927. 2013
  • Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions..  23:777-788. 2013
  • Dynamic DNA methylation across diverse human cell lines and tissues..  23:555-567. 2013
  • A heterozygous IDH1R132H/WT mutation induces genome-wide alterations in DNA methylation..  22:2339-2355. 2012
  • Genistein and bisphenol A exposure cause estrogen receptor 1 to bind thousands of sites in a cell type-specific manner..  22:2153-2162. 2012
  • Observation of dually decoded regions of the human genome using ribosome profiling data..  22:2219-2229. 2012
  • Spreading of X chromosome inactivation via a hierarchy of defined Polycomb stations..  22:1864-1876. 2012
  • ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia..  22:1813-1831. 2012
  • Predicting cell-type-specific gene expression from regions of open chromatin..  22:1711-1722. 2012
  • Effects of sequence variation on differential allelic transcription factor occupancy and gene expression..  22:860-869. 2012
  • Integrating genetic and gene expression evidence into genome-wide association analysis of gene sets..  22:386-397. 2012
  • Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells..  22:9-24. 2012
  • Developmental control of gene copy number by repression of replication initiation and fork progression..  22:64-75. 2012
  • High-resolution experimental and computational profiling of tissue-specific known and novel miRNAs in Arabidopsis..  22:163-176. 2012
  • High-resolution mapping of open chromatin in the rice genome..  22:151-162. 2012
  • Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration..  21:1659-1671. 2011
  • Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity..  21:1757-1767. 2011
  • High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells..  21:456-464. 2011
  • Chromatin signatures of the Drosophila replication program..  21:164-174. 2011
  • Developmental control of the DNA replication and transcription programs..  21:175-181. 2011
  • Epigenetic suppression of the TGF-beta pathway revealed by transcriptome profiling in ovarian cancer..  21:74-82. 2011
  • Ethical challenges in genotype-driven research recruitment..  20:705-709. 2010
  • Drosophila ORC localizes to open chromatin and marks sites of cohesin complex loading..  20:201-211. 2010
  • Genome structure of a Saccharomyces cerevisiae strain widely used in bioethanol production..  19:2258-2270. 2009
  • Genomic determination of the glucocorticoid response reveals unexpected mechanisms of gene regulation..  19:2163-2171. 2009
  • Distinguishing direct versus indirect transcription factor-DNA interactions..  19:2090-2100. 2009