Genome Res
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Publication Venue For
- Local nucleosome dynamics and eviction following a double-strand break are reversible by NHEJ-mediated repair. 2021
- AP-1 subunits converge promiscuously at enhancers to potentiate transcription.. 31:538-550. 2021
- Correcting signal biases and detecting regulatory elements in STARR-seq data. 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
- 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