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Research Output 1987 2019

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Article
2019
1 Citation (Scopus)

Characterizing protein-DNA binding event subtypes in ChIP-exo data

Yamada, N., Lai, W. K. M., Farrell, N., Pugh, B. F. & Mahony, S., Mar 15 2019, In : Bioinformatics. 35, 6, p. 903-913 11 p.

Research output: Contribution to journalArticle

DNA-binding Protein
Chromatin Immunoprecipitation
Chromatin
DNA-Binding Proteins
DNA
2018
5 Citations (Scopus)

Genome-wide determinants of sequence-specific DNA binding of general regulatory factors

Rossi, M. J., Lai, W. K. M. & Pugh, B. F., Apr 2018, In : Genome research. 28, 4, p. 497-508 12 p.

Research output: Contribution to journalArticle

Chromatin
Genome
Genetic Promoter Regions
Consensus Sequence
Chromosome Mapping
5 Citations (Scopus)

Genome-wide mapping of decay factor-mRNA interactions in yeast identifies nutrient-responsive transcripts as targets of the deadenylase Ccr4

Miller, J. E., Zhang, L., Jiang, H., Li, Y., Pugh, B. F. & Reese, J. C., Jan 1 2018, In : G3: Genes, Genomes, Genetics. 8, 1, p. 315-330 16 p.

Research output: Contribution to journalArticle

Catabolite Repression
Chromosome Mapping
RNA Stability
Yeasts
Food
3 Citations (Scopus)

In vivo genome-wide binding interactions of mouse and human constitutive androstane receptors reveal novel gene targets

Niu, B., Coslo, D. M., Bataille, A. R., Albert, I., Franklin Pugh, B. & Omiecinski, C. J., Jan 1 2018, In : Nucleic acids research. 46, 16, p. 8385-8403 19 p.

Research output: Contribution to journalArticle

Genome
Genes
Liver
Biological Phenomena
Systems Biology
4 Citations (Scopus)

Simplified ChIP-exo assays

Rossi, M. J., Lai, W. K. M. & Pugh, B. F., Dec 1 2018, In : Nature communications. 9, 1, 2842.

Research output: Contribution to journalArticle

Libraries
Noise
Assays
genome
Genome
3 Citations (Scopus)

The SAGA/TREX-2 subunit Sus1 binds widely to transcribed genes and affects mRNA turnover globally

García-Molinero, V., García-Martínez, J., Reja, R., Furió-Tarí, P., Antúnez, O., Vinayachandran, V., Conesa, A., Pugh, B. F., Pérez-Ortín, J. E. & Rodríguez-Navarro, S., Mar 29 2018, In : Epigenetics and Chromatin. 11, 1, 13.

Research output: Contribution to journalArticle

Acetyltransferases
Transcription Factor TFIID
Messenger RNA
Yeasts
Genes
10 Citations (Scopus)

Widespread and precise reprogramming of yeast protein-genome interactions in response to heat shock

Vinayachandran, V., Reja, R., Rossi, M. J., Park, B., Rieber, L., Mittal, C., Mahony, S. & Pugh, B. F., Mar 2018, In : Genome research. 28, 3, p. 357-366 10 p.

Research output: Contribution to journalArticle

Heat-Shock Response
Fungal Proteins
Genome
Shock
Nucleosomes
2017
8 Citations (Scopus)

Genome-wide uniformity of human 'open' pre-initiation complexes

Lai, W. K. M. & Pugh, B. F., Jan 2017, In : Genome research. 27, 1, p. 15-26 12 p.

Research output: Contribution to journalArticle

Genome
Peptide Initiation Factors
Nucleosomes
Chromatin Immunoprecipitation
DNA
2016
78 Citations (Scopus)

Genome-wide nucleosome specificity and function of chromatin remodellers in ES cells

De Dieuleveult, M., Yen, K., Hmitou, I., Depaux, A., Boussouar, F., Dargham, D. B., Jounier, S., Humbertclaude, H., Ribierre, F., Baulard, C., Farrell, N. P., Park, B., Keime, C., Carrière, L., Berlivet, S., Gut, M., Gut, I., Werner, M., Deleuze, J. F., Olaso, R. & 4 others, Aude, J. C., Chantalat, S., Pugh, B. F. & Gérard, M., Feb 4 2016, In : Nature. 530, 7588, p. 113-116 4 p.

Research output: Contribution to journalArticle

Nucleosomes
Embryonic Stem Cells
Chromatin
Genome
Genetic Promoter Regions
8 Citations (Scopus)

Genome-wide organization of GATA1 and TAL1 determined at high resolution

Han, G. C., Vinayachandran, V., Bataille, A. R., Park, B., Chan-Salis, K. Y., Keller, C. A., Long, M., Mahony, S., Hardison, R. C. & Pugh, B. F., Jan 1 2016, In : Molecular and cellular biology. 36, 1, p. 157-172 16 p.

Research output: Contribution to journalArticle

High-Throughput Nucleotide Sequencing
Chromatin Immunoprecipitation
DNA Sequence Analysis
GATA1 Transcription Factor
Genome
62 Citations (Scopus)

Genomic Nucleosome Organization Reconstituted with Pure Proteins

Krietenstein, N., Wal, M., Watanabe, S., Park, B., Peterson, C. L., Pugh, B. F. & Korber, P., Oct 20 2016, In : Cell. 167, 3, p. 709-721.e12

Research output: Contribution to journalArticle

Nucleosomes
Redundancy
Proteins
Chromatin
Genes
22 Citations (Scopus)

Genomic organization of human transcription initiation complexes

Pugh, B. F. & Venters, B. J., Feb 2016, In : PloS one. 11, 2, e0149339.

Research output: Contribution to journalArticle

Transcription
transcription (genetics)
Genes
Transcription Factor TFIIB
genomics
71 Citations (Scopus)

RNA Polymerase II Regulates Topoisomerase 1 Activity to Favor Efficient Transcription

Baranello, L., Wojtowicz, D., Cui, K., Devaiah, B. N., Chung, H. J., Chan-Salis, K. Y., Guha, R., Wilson, K., Zhang, X., Zhang, H., Piotrowski, J., Thomas, C. J., Singer, D. S., Pugh, B. F., Pommier, Y., Przytycka, T. M., Kouzine, F., Lewis, B. A., Zhao, K. & Levens, D., Apr 7 2016, In : Cell. 165, 2, p. 357-371 15 p.

Research output: Contribution to journalArticle

RNA Polymerase II
Transcription
Chromatin Immunoprecipitation
DNA
Topology
25 Citations (Scopus)

Structural evidence for Nap1-dependent H2A–H2B deposition and nucleosome assembly

Aguilar-Gurrieri, C., Larabi, A., Vinayachandran, V., Patel, N. A., Yen, K., Reja, R., Ebong, I. O., Schoehn, G., Robinson, C. V., Pugh, B. F. & Panne, D., Jul 1 2016, In : EMBO Journal. 35, 13, p. 1465-1482 18 p.

Research output: Contribution to journalArticle

Nucleosomes
Oligomerization
Histone Chaperones
Burial
Exonucleases
37 Citations (Scopus)

Tail and Kinase Modules Differently Regulate Core Mediator Recruitment and Function In Vivo

Jeronimo, C., Langelier, M. F., Bataille, A. R., Pascal, J. M., Pugh, B. F. & Robert, F., Nov 3 2016, In : Molecular cell. 64, 3, p. 455-466 12 p.

Research output: Contribution to journalArticle

Phosphotransferases
Head
RNA Polymerase II
Yeasts
Genome
23 Citations (Scopus)

The Histone Modification Domain of Paf1 Complex Subunit Rtf1 Directly Stimulates H2B Ubiquitylation through an Interaction with Rad6

Van Oss, S. B., Shirra, M. K., Bataille, A. R., Wier, A. D., Yen, K., Vinayachandran, V., Byeon, I. J. L., Cucinotta, C. E., Héroux, A., Jeon, J., Kim, J., VanDemark, A. P., Pugh, B. F. & Arndt, K. M., Nov 17 2016, In : Molecular cell. 64, 4, p. 815-825 11 p.

Research output: Contribution to journalArticle

Histone Code
Ubiquitination
gamma-Glutamyl Hydrolase
Ubiquitin
Histones
99 Citations (Scopus)

The Pioneer Transcription Factor FoxA Maintains an Accessible Nucleosome Configuration at Enhancers for Tissue-Specific Gene Activation

Iwafuchi-Doi, M., Donahue, G., Kakumanu, A., Watts, J. A., Mahony, S., Pugh, B. F., Lee, D., Kaestner, K. H. & Zaret, K. S., Apr 7 2016, In : Molecular cell. 62, 1, p. 79-91 13 p.

Research output: Contribution to journalArticle

Nucleosomes
Transcriptional Activation
Transcription Factors
Histones
Chromatin
2015
17 Citations (Scopus)

ATF4 gene network mediates cellular response to the anticancer PAD inhibitor YW3-56 in triple-negative breast cancer cells

Wang, S., Chen, X. A., Hu, J., Jiang, J. K., Li, Y., Chan-Salis, K. Y., Gu, Y., Chen, G., Thomas, C., Pugh, B. F. & Wang, Y., Jan 1 2015, In : Molecular cancer therapeutics. 14, 4, p. 877-888 12 p.

Research output: Contribution to journalArticle

Triple Negative Breast Neoplasms
Gene Regulatory Networks
Endoplasmic Reticulum Stress
YW3-56
p53 Genes
37 Citations (Scopus)

Molecular mechanisms of ribosomal protein gene coregulation

Reja, R., Vinayachandran, V., Ghosh, S. & Pugh, B. F., Sep 15 2015, In : Genes and Development. 29, 18, p. 1942-1954 13 p.

Research output: Contribution to journalArticle

Ribosomal Proteins
Nucleosomes
Transcription Factor TFIID
Base Pairing
Genes
51 Citations (Scopus)

The Nuclear Pore-Associated TREX-2 Complex Employs Mediator to Regulate Gene Expression

Schneider, M., Hellerschmied, D., Schubert, T., Amlacher, S., Vinayachandran, V., Reja, R., Pugh, B. F., Clausen, T. & Köhler, A., Aug 27 2015, In : Cell. 162, 5, p. 1016-1028 13 p.

Research output: Contribution to journalArticle

Mediator Complex
Nuclear Pore
Transcription
Gene expression
Gene Expression
2014
42 Citations (Scopus)

A Comprehensive and High-Resolution Genome-wide Response of p53 to Stress

Chang, G. S., Chen, X. A., Park, B., Rhee, H. S., Li, P., Han, K. H., Mishra, T., Chan-Salis, K. Y., Li, Y., Hardison, R. C., Wang, Y. & Pugh, B. F., Jul 24 2014, In : Cell Reports. 8, 2, p. 514-527 14 p.

Research output: Contribution to journalArticle

Genes
Transcription Factor TFIIB
Genome
Transcription
Antisense RNA
91 Citations (Scopus)

Subnucleosomal structures and nucleosome asymmetry across a genome

Rhee, H. S., Bataille, A. R., Zhang, L. & Pugh, B. F., Dec 4 2014, In : Cell. 159, 6, p. 1377-1388 12 p.

Research output: Contribution to journalArticle

Nucleosomes
Histones
Genes
Genome
Transcription
2013
133 Citations (Scopus)

A Genome-wide Map of CTCF Multivalency Redefines the CTCF Code

Nakahashi, H., Kwon, K. R. K., Resch, W., Vian, L., Dose, M., Stavreva, D., Hakim, O., Pruett, N., Nelson, S., Yamane, A., Qian, J., Dubois, W., Welsh, S., Phair, R. D., Pugh, B. F., Lobanenkov, V., Hager, G. L. & Casellas, R., May 30 2013, In : Cell Reports. 3, 5, p. 1678-1689 12 p.

Research output: Contribution to journalArticle

Zinc Fingers
Zinc
Genes
Genome
Cluster Analysis
45 Citations (Scopus)

Genomic organization of human transcription initiation complexes

Venters, B. J. & Pugh, B. F., Sep 24 2013, In : Nature. 502, 7469, p. 53-58 6 p.

Research output: Contribution to journalArticle

Transcription Factor TFIIB
TATA-Box Binding Protein
Human Genome
Genome
Peptide Initiation Factors
62 Citations (Scopus)

Kinetic competition between elongation rate and binding of NELF controls promoter-proximal pausing

Li, J., Liu, Y., Rhee, H. S., Ghosh, S. K. B., Bai, L., Pugh, B. F. & Gilmour, D. S., Jun 6 2013, In : Molecular cell. 50, 5, p. 711-722 12 p.

Research output: Contribution to journalArticle

Transcription Initiation Site
Genes
Small Nuclear RNA
RNA Polymerase II
Drosophila
103 Citations (Scopus)

XSWR-C and INO80 chromatin remodelers recognize nucleosome-free regions near +1 nucleosomes

Yen, K., Vinayachandran, V. & Pugh, B. F., Sep 12 2013, In : Cell. 154, 6, 1 p.

Research output: Contribution to journalArticle

Nucleosomes
Chromatin
Genes
Chromatin Assembly and Disassembly
Histones
2012
80 Citations (Scopus)
DNA-Binding Proteins
Chromatin Immunoprecipitation
Nucleotides
DNA
Exonucleases
44 Citations (Scopus)

Codependency of H2B monoubiquitination and nucleosome reassembly on Chdl

Lee, J. S., Garrett, A. S., Yen, K., Takahashi, Y. H., Hu, D., Jackson, J., Seidel, C., Franklin Pugh, B. & Shilatifard, A., May 1 2012, In : Genes and Development. 26, 9, p. 914-919 6 p.

Research output: Contribution to journalArticle

Histone Code
Nucleosomes
Histones
Yeasts
Genome
1 Citation (Scopus)

Erratum: Genome-wide structure and organization of eukaryotic pre-initiation complexes

Sung Rhee, H. & Franklin Pugh, B., Jul 2012, In : Nature. 487, 7405, 1 p.

Research output: Contribution to journalArticle

Genome
169 Citations (Scopus)

Genome-wide nucleosome specificity and directionality of chromatin remodelers

Yen, K., Vinayachandran, V., Batta, K., Koerber, R. T. & Pugh, B. F., Jun 22 2012, In : Cell. 149, 7, p. 1461-1473 13 p.

Research output: Contribution to journalArticle

Nucleosomes
Chromatin
Genes
Genome
Saccharomyces
266 Citations (Scopus)

Genome-wide structure and organization of eukaryotic pre-initiation complexes

Rhee, H. S. & Pugh, B. F., Mar 15 2012, In : Nature. 483, 7389, p. 295-301 7 p.

Research output: Contribution to journalArticle

Transcription Factor TFIID
Nucleosomes
Exonucleases
Genome
Transcription Factor TFIIA
14 Citations (Scopus)

The linker histone plays a dual role during gametogenesis in saccharomyces cerevisiae

Bryant, J. M., Govin, J., Zhang, L., Donahue, G., Pugh, B. F. & Berger, S. L., Jul 1 2012, In : Molecular and cellular biology. 32, 14, p. 2771-2783 13 p.

Research output: Contribution to journalArticle

Gametogenesis
Spores
Histones
Saccharomyces cerevisiae
Meiosis
24 Citations (Scopus)

Unusual combinatorial involvement of poly-A/T tracts in organizing genes and chromatin in Dictyostelium

Chang, G. S., Noegel, A. A., Mavrich, T. N., Müller, R., Tomsho, L., Ward, E., Felder, M., Jiang, C., Eichinger, L., Glöckner, G., Schuster, S. C. & Pugh, B. F., Jun 1 2012, In : Genome research. 22, 6, p. 1098-1106 9 p.

Research output: Contribution to journalArticle

Dictyostelium
Nucleosomes
Chromatin
Genes
Amoebozoa
2011
175 Citations (Scopus)

A Comprehensive Genomic Binding Map of Gene and Chromatin Regulatory Proteins in Saccharomyces

Venters, B. J., Wachi, S., Mavrich, T. N., Andersen, B. E., Jena, P., Sinnamon, A. J., Jain, P., Rolleri, N. S., Jiang, C., Hemeryck-Walsh, C. & Pugh, B. F., Feb 18 2011, In : Molecular cell. 41, 4, p. 480-492 13 p.

Research output: Contribution to journalArticle

Transcription Factor TFIID
Saccharomyces
Regulator Genes
Chromatin
Transfer RNA
21 Citations (Scopus)

A new, highly conserved domain in Swi2/Snf2 is required for SWI/SNF remodeling

Sen, P., Ghosh, S., Pugh, B. F. & Bartholomew, B., Nov 1 2011, In : Nucleic acids research. 39, 21, p. 9155-9166 12 p.

Research output: Contribution to journalArticle

Adenosine Triphosphate
Nucleosomes
Adenosine Triphosphatases
Catalytic Domain
DNA
199 Citations (Scopus)

A packing mechanism for nucleosome organization reconstituted across a eukaryotic genome

Zhang, Z., Wippo, C. J., Wal, M., Ward, E., Korber, P. & Pugh, B. F., May 20 2011, In : Science. 332, 6032, p. 977-980 4 p.

Research output: Contribution to journalArticle

Nucleosomes
Genome
Genes
Trans-Activators
DNA
407 Citations (Scopus)

Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution

Rhee, H. S. & Pugh, B. F., Dec 9 2011, In : Cell. 147, 6, p. 1408-1419 12 p.

Research output: Contribution to journalArticle

Nucleotides
Genes
Genome
DNA
DNA Contamination
106 Citations (Scopus)

Genome-wide function of H2B ubiquitylation in promoter and genic regions

Batta, K., Zhang, Z., Yen, K., Goffman, D. B. & Franklin Pugh, B., Nov 1 2011, In : Genes and Development. 25, 21, p. 2254-2265 12 p.

Research output: Contribution to journalArticle

Ubiquitination
Genetic Promoter Regions
Histone Code
Genome
Nucleosomes
4 Citations (Scopus)

Genome-wide transcriptional dependence on conserved regions of Mot1

Venters, B. J., Irvin, J. D., Gramlich, P. & Pugh, B. F., Jun 1 2011, In : Molecular and cellular biology. 31, 11, p. 2253-2261 9 p.

Research output: Contribution to journalArticle

TATA-Box Binding Protein
Genome
Genes
Adenosine Triphosphate
Saccharomyces cerevisiae Proteins
6 Citations (Scopus)

Genomic organization of H2Av containing nucleosomes in Drosophila heterochromatin

Zhang, Z. & Pugh, B. F., Jun 30 2011, In : PloS one. 6, 6, e20511.

Research output: Contribution to journalArticle

nucleosomes
Heterochromatin
Nucleosomes
heterochromatin
Euchromatin
23 Citations (Scopus)

Sequential recruitment of SAGA and TFIID in a genomic response to DNA damage in Saccharomyces cerevisiae

Ghosh, S. & Pugh, B. F., Jan 1 2011, In : Molecular and cellular biology. 31, 1, p. 190-202 13 p.

Research output: Contribution to journalArticle

Transcription Factor TFIID
DNA Damage
Saccharomyces cerevisiae
Methyl Methanesulfonate
Shock
61 Citations (Scopus)

Stable and dynamic nucleosome states during a meiotic developmental process

Zhang, L., Ma, H. & Pugh, B. F., Jun 1 2011, In : Genome research. 21, 6, p. 875-884 10 p.

Research output: Contribution to journalArticle

Nucleosomes
Chromatin
Histone Code
Chromosomes
Genome
32 Citations (Scopus)

Variety of genomic DNA patterns for nucleosome positioning

Ioshikhes, I., Hosid, S. & Pugh, B. F., Nov 1 2011, In : Genome research. 21, 11, p. 1863-1871 9 p.

Research output: Contribution to journalArticle

Nucleosomes
DNA
Histones
Regulator Genes
2010
257 Citations (Scopus)

Complete Khoisan and Bantu genomes from southern Africa

Schuster, S. C., Miller, W., Ratan, A., Tomsho, L. P., Giardine, B., Kasson, L. R., Harris, R. S., Petersen, D. C., Zhao, F., Qi, J., Alkan, C., Kidd, J. M., Sun, Y., Drautz, D. I., Bouffard, P., Muzny, D. M., Reid, J. G., Nazareth, L. V., Wang, Q., Burhans, R. & 28 others, Riemer, C., Wittekindt, N. E., Moorjani, P., Tindall, E. A., Danko, C. G., Teo, W. S., Buboltz, A. M., Zhang, Z., Ma, Q., Oosthuysen, A., Steenkamp, A. W., Oostuisen, H., Venter, P., Gajewski, J., Zhang, Y., Pugh, B. F., Makova, K. D., Nekrutenko, A., Mardis, E. R., Patterson, N., Pringle, T. H., Chiaromonte, F., Mullikin, J. C., Eichler, E. E., Hardison, R. C., Gibbs, R. A., Harkins, T. T. & Hayes, V. M., Feb 18 2010, In : Nature. 463, 7283, p. 943-947 5 p.

Research output: Contribution to journalArticle

Southern Africa
Genome
Botswana
Medical History Taking
Exome
4 Citations (Scopus)

Genome-wide modeling of transcription preinitiation complex disassembly mechanisms using ChIP-chip data

Samorodnitsky, E. & Pugh, B. F., Apr 1 2010, In : PLoS computational biology. 6, 4

Research output: Contribution to journalArticle

Disassembly
Transcription
Genome
Chip
genome
2009
134 Citations (Scopus)

A canonical promoter organization of the transcription machinery and its regulators in the Saccharomyces genome

Venters, B. J. & Pugh, B. F., Mar 1 2009, In : Genome research. 19, 3, p. 360-371 12 p.

Research output: Contribution to journalArticle

Saccharomyces
Nucleosomes
Genetic Promoter Regions
Genome
Regulator Genes
157 Citations (Scopus)

A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae genome

Jiang, C. & Pugh, B. F., Oct 8 2009, In : Genome biology. 10, 10, R109.

Research output: Contribution to journalArticle

nucleosomes
Nucleosomes
Saccharomyces cerevisiae
genome
Genome
77 Citations (Scopus)

Interaction of Transcriptional Regulators with Specific Nucleosomes across the Saccharomyces Genome

Koerber, R. T., Rhee, H. S., Jiang, C. & Pugh, B. F., Sep 24 2009, In : Molecular cell. 35, 6, p. 889-902 14 p.

Research output: Contribution to journalArticle

Saccharomyces
Nucleosomes
Genome
Proteins
RNA Polymerase II
2008
473 Citations (Scopus)

A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome

Mavrich, T. N., Ioshikhes, I. P., Venters, B. J., Jiang, C., Tomsho, L. P., Qi, J., Schuster, S. C., Albert, I. & Pugh, B. F., Jul 1 2008, In : Genome research. 18, 7, p. 1073-1083 11 p.

Research output: Contribution to journalArticle

Nucleosomes
Statistical Models
Yeasts
Genome
Genetic Promoter Regions

Computational modelling of genome-side transcription assembly networks using a fluidics analogy

Azmy, Y. Y., Gupta, A. & Pugh, B. F., Aug 28 2008, In : PloS one. 3, 8, e3095.

Research output: Contribution to journalArticle

Fluidics
Transcription
transcription (genetics)
Genes
Genome