Pugh, B.

selected publications

Histone acetylation readers Bdf1 and Yaf9 direct SWR1 remodeler to +1 nucleosome. Science advances. 2025 Academic Article GET IT
High-Resolution Genome-Wide Maps Reveal Widespread Presence of Torsional Insulation. 2025 GET IT
Molecular basis of global promoter sensing and nucleosome capture by the SWR1 chromatin remodeler. Cell. 2024 Academic Article GET IT
Locus-specific proteome decoding reveals Fpt1 as a chromatin-associated negative regulator of RNA polymerase III assembly. Molecular cell. 2023 Academic Article GET IT
GenoPipe: identifying the genotype of origin within (epi)genomic datasets. Nucleic acids research. 2023 Academic Article GET IT
Joint sequence & chromatin neural networks characterize the differential abilities of Forkhead transcription factors to engage inaccessible chromatin. 2023 GET IT
GenoPipe: identifying the genotype of origin within (epi)genomic datasets. 2023 GET IT
An integrated SAGA and TFIID PIC assembly pathway selective for poised and induced promoters. Genes & development. 2022 Academic Article GET IT
Times cited: 9
Genome-wide promoter assembly in E. coli measured at single-base resolution. Genome research. 2022 Academic Article GET IT
Times cited: 5
PEGR: a flexible management platform for reproducible epigenomic and genomic research. Genome biology. 2022 Academic Article GET IT
STENCIL: A web templating engine for visualizing and sharing life science datasets. PLoS computational biology. 2022 Academic Article GET IT
Ssl2/TFIIH function in transcription start site scanning by RNA polymerase II in Saccharomyces cerevisiae. eLife. 2021 Academic Article GET IT
Times cited: 6
A ChIP-exo screen of 887 Protein Capture Reagents Program transcription factor antibodies in human cells. Genome research. 2021 Academic Article GET IT
Times cited: 13
Protein architecture of the yeast genome. Nature. 2021 Article GET IT
Times cited: 585
A high-resolution protein architecture of the budding yeast genome. Nature. 2021 Academic Article GET IT
Times cited: 128
What do Transcription Factors Interact With?. Journal of molecular biology. 2021 Review GET IT
Times cited: 41
Acute stress drives global repression through two independent RNA polymerase II stalling events in Saccharomyces. Cell reports. 2021 Academic Article GET IT
Times cited: 12
Alignment and quantification of ChIP-exo crosslinking patterns reveal the spatial organization of protein-DNA complexes. Nucleic acids research. 2020 Academic Article GET IT
Times cited: 3
Actin R256 Mono-methylation Is a Conserved Post-translational Modification Involved in Transcription. Cell reports. 2020 Academic Article GET IT
Times cited: 9
PEGR: a management platform for ChIP-based next generation sequencing pipelines. PEARC20 : Practice and Experience in Advanced Research Computing 2020 : Catch the wave : July 27-31, 2020, Portland, Or Virtual Conference. Practice and Experience in Advanced Research Computing (Conference) (2020 : Online). 2020 Academic Article GET IT
Times cited: 2
Universal promoter scanning by Pol II during transcription initiation in Saccharomyces cerevisiae. Genome biology. 2020 Academic Article GET IT
Times cited: 32
Phase separation directs ubiquitination of gene-body nucleosomes. Nature. 2020 Academic Article GET IT
Times cited: 104
ChExMix: A Method for Identifying and Classifying Protein-DNA Interaction Subtypes. Journal of computational biology : a journal of computational molecular cell biology. 2020 Academic Article GET IT
Times cited: 4
Characterizing protein-DNA binding event subtypes in ChIP-exo data. Bioinformatics (Oxford, England). 2019 Academic Article GET IT
Times cited: 20
In vivo genome-wide binding interactions of mouse and human constitutive androstane receptors reveal novel gene targets. Nucleic acids research. 2018 Academic Article GET IT
Times cited: 29
Simplified ChIP-exo assays. Nature communications. 2018 Academic Article GET IT
Times cited: 67
The SAGA/TREX-2 subunit Sus1 binds widely to transcribed genes and affects mRNA turnover globally. Epigenetics & chromatin. 2018 Academic Article GET IT
Times cited: 19
Genome-wide determinants of sequence-specific DNA binding of general regulatory factors. Genome research. 2018 Academic Article GET IT
Times cited: 31
Widespread and precise reprogramming of yeast protein-genome interactions in response to heat shock. Genome research. 2018 Academic Article GET IT
Times cited: 53
Genome-Wide Mapping of Decay Factor-mRNA Interactions in Yeast Identifies Nutrient-Responsive Transcripts as Targets of the Deadenylase Ccr4. G3 (Bethesda, Md.). 2018 Academic Article GET IT
Times cited: 22
Correspondence: DNA shape is insufficient to explain binding. Nature communications. 2017 Academic Article GET IT
Times cited: 7
Understanding nucleosome dynamics and their links to gene expression and DNA replication. Nature reviews. Molecular cell biology. 2017 Review GET IT
Times cited: 363
Genome-wide uniformity of human 'open' pre-initiation complexes. Genome research. 2016 Academic Article GET IT
Times cited: 17
The Histone Modification Domain of Paf1 Complex Subunit Rtf1 Directly Stimulates H2B Ubiquitylation through an Interaction with Rad6. Molecular cell. 2016 Academic Article GET IT
Times cited: 73
Genomic Nucleosome Organization Reconstituted with Pure Proteins. Cell. 2016 Academic Article GET IT
Times cited: 186
Tail and Kinase Modules Differently Regulate Core Mediator Recruitment and Function In Vivo. Molecular cell. 2016 Academic Article GET IT
Times cited: 102
Structural evidence for Nap1-dependent H2A-H2B deposition and nucleosome assembly. The EMBO journal. 2016 Academic Article GET IT
Times cited: 56
RNA Polymerase II Regulates Topoisomerase 1 Activity to Favor Efficient Transcription. Cell. 2016 Academic Article GET IT
Times cited: 204
The Pioneer Transcription Factor FoxA Maintains an Accessible Nucleosome Configuration at Enhancers for Tissue-Specific Gene Activation. Molecular cell. 2016 Academic Article GET IT
Times cited: 287
Genomic Organization of Human Transcription Initiation Complexes. PloS one. 2016 Academic Article GET IT
Times cited: 37
Genome-wide nucleosome specificity and function of chromatin remodellers in ES cells. Nature. 2016 Academic Article GET IT
Times cited: 157
Genome-Wide Organization of GATA1 and TAL1 Determined at High Resolution. Molecular and cellular biology. 2015 Academic Article GET IT
Times cited: 35
Molecular mechanisms of ribosomal protein gene coregulation. Genes & development. 2015 Academic Article GET IT
Times cited: 77
The Nuclear Pore-Associated TREX-2 Complex Employs Mediator to Regulate Gene Expression. Cell. 2015 Academic Article GET IT
Times cited: 101
Protein-DNA binding in high-resolution. Critical reviews in biochemistry and molecular biology. 2015 Review GET IT
Times cited: 36
ATF4 Gene Network Mediates Cellular Response to the Anticancer PAD Inhibitor YW3-56 in Triple-Negative Breast Cancer Cells. Molecular cancer therapeutics. 2015 Academic Article GET IT
Times cited: 58
Subnucleosomal structures and nucleosome asymmetry across a genome. Cell. 2014 Academic Article GET IT
Times cited: 179
Retraction: Genomic organization of human transcription initiation complexes. Nature. 2014 Article GET IT
Times cited: 1
A comprehensive and high-resolution genome-wide response of p53 to stress. Cell reports. 2014 Academic Article GET IT
Times cited: 58
Genomic organization of human transcription initiation complexes. Nature. 2013 Academic Article GET IT
Times cited: 50
SWR-C and INO80 chromatin remodelers recognize nucleosome-free regions near +1 nucleosomes. Cell. 2013 Academic Article GET IT
Times cited: 161
Kinetic competition between elongation rate and binding of NELF controls promoter-proximal pausing. Molecular cell. 2013 Academic Article GET IT
Times cited: 93
A genome-wide map of CTCF multivalency redefines the CTCF code. Cell reports. 2013 Academic Article GET IT
Times cited: 237
Molecular biology: The ends justify the means. Nature. 2013 Comment GET IT
Times cited: 2
ChIP-exo method for identifying genomic location of DNA-binding proteins with near-single-nucleotide accuracy. Current protocols in molecular biology. 2012 Academic Article GET IT
Times cited: 142
Genome-wide nucleosome specificity and directionality of chromatin remodelers. Cell. 2012 Academic Article GET IT
Times cited: 246
The linker histone plays a dual role during gametogenesis in Saccharomyces cerevisiae. Molecular and cellular biology. 2012 Academic Article GET IT
Times cited: 27
Codependency of H2B monoubiquitination and nucleosome reassembly on Chd1. Genes & development. 2012 Academic Article GET IT
Times cited: 60
Unusual combinatorial involvement of poly-A/T tracts in organizing genes and chromatin in Dictyostelium. Genome research. 2012 Academic Article GET IT
Times cited: 28
Genome-wide structure and organization of eukaryotic pre-initiation complexes. Nature. 2012 Academic Article GET IT
Times cited: 396
Genome-wide mapping of nucleosome positions in yeast using high-resolution MNase ChIP-Seq. Methods in enzymology. 2012 Academic Article GET IT
Times cited: 48
Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution. Cell. 2011 Academic Article GET IT
Times cited: 622
Genome-wide function of H2B ubiquitylation in promoter and genic regions. Genes & development. 2011 Academic Article GET IT
Times cited: 155
A new, highly conserved domain in Swi2/Snf2 is required for SWI/SNF remodeling. Nucleic acids research. 2011 Academic Article GET IT
Times cited: 39
Variety of genomic DNA patterns for nucleosome positioning. Genome research. 2011 Academic Article GET IT
Times cited: 49
Genomic organization of H2Av containing nucleosomes in Drosophila heterochromatin. PloS one. 2011 Academic Article GET IT
Times cited: 7
A packing mechanism for nucleosome organization reconstituted across a eukaryotic genome. Science (New York, N.Y.). 2011 Academic Article GET IT
Times cited: 252
Stable and dynamic nucleosome states during a meiotic developmental process. Genome research. 2011 Academic Article GET IT
Times cited: 72
Genome-wide transcriptional dependence on conserved regions of Mot1. Molecular and cellular biology. 2011 Academic Article GET IT
Times cited: 5
A comprehensive genomic binding map of gene and chromatin regulatory proteins in Saccharomyces. Molecular cell. 2011 Academic Article GET IT
Times cited: 243
High-resolution genome-wide mapping of the primary structure of chromatin. Cell. 2011 Academic Article GET IT
Times cited: 135
Sequential recruitment of SAGA and TFIID in a genomic response to DNA damage in Saccharomyces cerevisiae. Molecular and cellular biology. 2010 Academic Article GET IT
Times cited: 29
A preoccupied position on nucleosomes. Nature structural & molecular biology. 2010 Letter GET IT
Times cited: 32
Genome-wide modeling of transcription preinitiation complex disassembly mechanisms using ChIP-chip data. PLoS computational biology. 2010 Academic Article GET IT
Times cited: 4
Complete Khoisan and Bantu genomes from southern Africa. Nature. 2010 Academic Article GET IT
Times cited: 316
A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae genome. Genome biology. 2009 Academic Article GET IT
Times cited: 193
Interaction of transcriptional regulators with specific nucleosomes across the Saccharomyces genome. Molecular cell. 2009 Academic Article GET IT
Times cited: 99
How eukaryotic genes are transcribed. Critical reviews in biochemistry and molecular biology. 2009 Review GET IT
Times cited: 134
Nucleosome positioning and gene regulation: advances through genomics. Nature reviews. Genetics. 2009 Review GET IT
Times cited: 846
A canonical promoter organization of the transcription machinery and its regulators in the Saccharomyces genome. Genome research. 2009 Academic Article GET IT
Times cited: 149
Computational modelling of genome-wide [corrected] transcription assembly networks using a fluidics analogy. PloS one. 2008 Academic Article GET IT
A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome. Genome research. 2008 Academic Article GET IT
Times cited: 554
Histone Arg modifications and p53 regulate the expression of OKL38, a mediator of apoptosis. The Journal of biological chemistry. 2008 Academic Article GET IT
Times cited: 142
Nucleosome organization in the Drosophila genome. Nature. 2008 Academic Article GET IT
Times cited: 598
GeneTrack--a genomic data processing and visualization framework. Bioinformatics (Oxford, England). 2008 Academic Article GET IT
Times cited: 82
NELF and GAGA factor are linked to promoter-proximal pausing at many genes in Drosophila. Molecular and cellular biology. 2008 Academic Article GET IT
Times cited: 174
NuA4-directed chromatin transactions throughout the Saccharomyces cerevisiae genome. Molecular and cellular biology. 2007 Academic Article GET IT
Times cited: 64
Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome. Nature. 2007 Academic Article GET IT
Times cited: 543
A TATA binding protein regulatory network that governs transcription complex assembly. Genome biology. 2007 Academic Article GET IT
Times cited: 30
Chromatin meets RNA polymerase II. Genome biology. 2007 Conference Paper GET IT
Times cited: 4
HATs off to PIC assembly. Molecular cell. 2006 Comment GET IT
Times cited: 7
Nucleosome positions predicted through comparative genomics. Nature genetics. 2006 Academic Article GET IT
Times cited: 262
Full and partial genome-wide assembly and disassembly of the yeast transcription machinery in response to heat shock. Genes & development. 2006 Academic Article GET IT
Times cited: 87
Genome-wide relationships between TAF1 and histone acetyltransferases in Saccharomyces cerevisiae. Molecular and cellular biology. 2006 Academic Article GET IT
Times cited: 54
Genome-wide transcriptional dependence on TAF1 functional domains. The Journal of biological chemistry. 2006 Academic Article GET IT
Times cited: 13
Changes in genomewide occupancy of core transcriptional regulators during heat stress. Proceedings of the National Academy of Sciences of the United States of America. 2004 Academic Article GET IT
Times cited: 66
Inhibition of TATA binding protein dimerization by RNA polymerase III transcription initiation factor Brf1. The Journal of biological chemistry. 2004 Academic Article GET IT
Times cited: 4
Is acetylation the key to opening locked gates?. Nature structural & molecular biology. 2004 Comment GET IT
Times cited: 2
Engineering dimer-stabilizing mutations in the TATA-binding protein. The Journal of biological chemistry. 2004 Academic Article GET IT
Times cited: 10
Identification and distinct regulation of yeast TATA box-containing genes. Cell. 2004 Academic Article GET IT
Times cited: 508
A genome-wide housekeeping role for TFIID and a highly regulated stress-related role for SAGA in Saccharomyces cerevisiae. Molecular cell. 2004 Academic Article GET IT
Times cited: 437
Structural and functional analysis of mutations along the crystallographic dimer interface of the yeast TATA binding protein. Molecular and cellular biology. 2003 Academic Article GET IT
Times cited: 14
Interplay of TBP inhibitors in global transcriptional control. Molecular cell. 2002 Academic Article GET IT
Times cited: 52
Genome-wide analysis of protein-DNA interactions in living cells. Genome biology. 2001 Review GET IT
Times cited: 11
Control of gene expression through regulation of the TATA-binding protein. Gene. 2000 Review GET IT
Times cited: 156
TFIIA regulates TBP and TFIID dimers. Molecular cell. 1999 Academic Article GET IT
Times cited: 35
Dimer dissociation and thermosensitivity kinetics of the Saccharomyces cerevisiae and human TATA binding proteins. Biochemistry. 1999 Academic Article GET IT
Times cited: 19
A role for TBP dimerization in preventing unregulated gene expression. Molecular cell. 1999 Academic Article GET IT
Times cited: 63
Cloning and biochemical characterization of TAF-172, a human homolog of yeast Mot1. Molecular and cellular biology. 1998 Academic Article GET IT
Times cited: 59
Dynamic interplay of TFIIA, TBP and TATA DNA. Journal of molecular biology. 1997 Academic Article GET IT
Times cited: 48
Slow dimer dissociation of the TATA binding protein dictates the kinetics of DNA binding. Proceedings of the National Academy of Sciences of the United States of America. 1997 Academic Article GET IT
Times cited: 61
Identification and characterization of a nuclease specific for the 3' end of the U6 small nuclear RNA. The Journal of biological chemistry. 1997 Academic Article GET IT
Times cited: 21
Mechanisms of transcription complex assembly. Current opinion in cell biology. 1996 Review GET IT
Times cited: 84
Dimerization of TFIID when not bound to DNA. Science (New York, N.Y.). 1996 Academic Article GET IT
Times cited: 59
Dimerization of the TATA binding protein. The Journal of biological chemistry. 1995 Academic Article GET IT
Times cited: 89
Evidence for functional binding and stable sliding of the TATA binding protein on nonspecific DNA. The Journal of biological chemistry. 1995 Academic Article GET IT
Times cited: 117
Preparation of HeLa nuclear extracts. Methods in molecular biology (Clifton, N.J.). 1995 Academic Article GET IT
Times cited: 15
Purification of the human TATA-binding protein, TBP. Methods in molecular biology (Clifton, N.J.). 1995 Academic Article GET IT
Times cited: 23
The BN51 protein is a polymerase (Pol)-specific subunit of RNA Pol III which reveals a link between Pol III transcription and pre-rRNA processing. Molecular and cellular biology. 1995 Academic Article GET IT
Times cited: 9
The TATA-binding protein and associated factors are components of pol III transcription factor TFIIIB. Cell. 1992 Academic Article GET IT
Times cited: 113
Diverse transcriptional functions of the multisubunit eukaryotic TFIID complex. The Journal of biological chemistry. 1992 Review GET IT
Times cited: 161
Coactivators for a proline-rich activator purified from the multisubunit human TFIID complex. Genes & development. 1991 Academic Article GET IT
Times cited: 244
Transcription from a TATA-less promoter requires a multisubunit TFIID complex. Genes & development. 1991 Academic Article GET IT
Times cited: 481
Functional domains and upstream activation properties of cloned human TATA binding protein. Science (New York, N.Y.). 1990 Academic Article GET IT
Times cited: 320
Isolation and characterization of the Drosophila gene encoding the TATA box binding protein, TFIID. Cell. 1990 Academic Article GET IT
Times cited: 161
Mechanism of transcriptional activation by Sp1: evidence for coactivators. Cell. 1990 Academic Article GET IT
Times cited: 737
Extent of duplex DNA underwinding induced by RecA protein binding in the presence of ATP. Journal of molecular biology. 1989 Academic Article GET IT
Times cited: 41
General mechanism for RecA protein binding to duplex DNA. Journal of molecular biology. 1988 Academic Article GET IT
Times cited: 92
High salt activation of recA protein ATPase in the absence of DNA. The Journal of biological chemistry. 1988 Academic Article GET IT
Times cited: 79
Stable binding of recA protein to duplex DNA. Unraveling a paradox. The Journal of biological chemistry. 1987 Academic Article GET IT
Times cited: 119
recA protein binding to the heteroduplex product of DNA strand exchange. The Journal of biological chemistry. 1987 Academic Article GET IT
Times cited: 61

VIVO Weill Cornell Medical College

B. Pugh Professor of Systems and Computational Biomedicine

Publications

selected publications

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