| Year |
Citation |
Score |
| 2023 |
van Breugel ME, van Kruijsbergen I, Mittal C, Lieftink C, Brouwer I, van den Brand T, Kluin RJC, Hoekman L, Menezes RX, van Welsem T, Del Cortona A, Malik M, Beijersbergen RL, Lenstra TL, Verstrepen KJ, ... Pugh BF, et al. Locus-specific proteome decoding reveals Fpt1 as a chromatin-associated negative regulator of RNA polymerase III assembly. Molecular Cell. PMID 37995691 DOI: 10.1016/j.molcel.2023.10.037 |
0.474 |
|
| 2023 |
Arora S, Yang J, Akiyama T, James DQ, Morrissey A, Blanda T, Badjatia N, Lai WKM, Ko MSH, Pugh BF, Mahony S. Joint sequence & chromatin neural networks characterize the differential abilities of Forkhead transcription factors to engage inaccessible chromatin. Biorxiv : the Preprint Server For Biology. PMID 37873361 DOI: 10.1101/2023.10.06.561228 |
0.405 |
|
| 2022 |
Mittal C, Lang O, Lai WKM, Pugh BF. An integrated SAGA and TFIID PIC assembly pathway selective for poised and induced promoters. Genes & Development. 36: 985-1001. PMID 36302553 DOI: 10.1101/gad.350026.122 |
0.42 |
|
| 2022 |
John J, Jabbar J, Badjatia N, Rossi MJ, Lai WKM, Pugh BF. Genome-wide promoter assembly in measured at single-base resolution. Genome Research. 32: 878-892. PMID 35483960 DOI: 10.1101/gr.276544.121 |
0.489 |
|
| 2021 |
Zhao T, Vvedenskaya IO, Lai WK, Basu S, Pugh BF, Nickels BE, Kaplan CD. Ssl2/TFIIH function in transcription start site scanning by RNA Polymerase II in . Elife. 10. PMID 34652274 DOI: 10.7554/eLife.71013 |
0.375 |
|
| 2021 |
Lai WKM, Mariani L, Rothschild G, Smith ER, Venters BJ, Blanda TR, Kuntala PK, Bocklund K, Mairose J, Dweikat SN, Mistretta K, Rossi MJ, James D, Anderson JT, Phanor SK, ... ... Pugh BF, et al. A ChIP-exo screen of 887 Protein Capture Reagents Program transcription factor antibodies in human cells. Genome Research. PMID 34426512 DOI: 10.1101/gr.275472.121 |
0.684 |
|
| 2021 |
Rossi MJ, Kuntala PK, Lai WKM, Yamada N, Badjatia N, Mittal C, Kuzu G, Bocklund K, Farrell NP, Blanda TR, Mairose JD, Basting AV, Mistretta KS, Rocco DJ, Perkinson ES, ... ... Pugh BF, et al. A high-resolution protein architecture of the budding yeast genome. Nature. PMID 33692541 DOI: 10.1038/s41586-021-03314-8 |
0.577 |
|
| 2021 |
Badjatia N, Rossi MJ, Bataille AR, Mittal C, Lai WKM, Pugh BF. Acute stress drives global repression through two independent RNA polymerase II stalling events in Saccharomyces. Cell Reports. 34: 108640. PMID 33472084 DOI: 10.1016/j.celrep.2020.108640 |
0.449 |
|
| 2020 |
Kumar A, Zhong Y, Albrecht A, Sang PB, Maples A, Liu Z, Vinayachandran V, Reja R, Lee CF, Kumar A, Chen J, Xiao J, Park B, Shen J, Liu B, ... ... Pugh BF, et al. Actin R256 Mono-methylation Is a Conserved Post-translational Modification Involved in Transcription. Cell Reports. 32: 108172. PMID 32997990 DOI: 10.1016/j.celrep.2020.108172 |
0.311 |
|
| 2020 |
Yamada N, Rossi MJ, Farrell N, Pugh BF, Mahony S. Alignment and quantification of ChIP-exo crosslinking patterns reveal the spatial organization of protein-DNA complexes. Nucleic Acids Research. PMID 32747934 DOI: 10.1093/Nar/Gkaa618 |
0.442 |
|
| 2020 |
Qiu C, Jin H, Vvedenskaya I, Llenas JA, Zhao T, Malik I, Visbisky AM, Schwartz SL, Cui P, Čabart P, Han KH, Lai WKM, Metz RP, Johnson CD, Sze SH, ... Pugh BF, et al. Universal promoter scanning by Pol II during transcription initiation in Saccharomyces cerevisiae. Genome Biology. 21: 132. PMID 32487207 DOI: 10.1186/S13059-020-02040-0 |
0.432 |
|
| 2020 |
Gallego LD, Schneider M, Mittal C, Romanauska A, Gudino Carrillo RM, Schubert T, Pugh BF, Köhler A. Phase separation directs ubiquitination of gene-body nucleosomes. Nature. 579: 592-597. PMID 32214243 DOI: 10.1038/S41586-020-2097-Z |
0.456 |
|
| 2020 |
Yamada N, Kuntala PK, Pugh BF, Mahony S. ChExMix: A Method for Identifying and Classifying Protein-DNA Interaction Subtypes. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 32023130 DOI: 10.1089/Cmb.2019.0466 |
0.444 |
|
| 2018 |
Yamada N, Lai WKM, Farrell N, Pugh BF, Mahony S. Characterizing protein-DNA binding event subtypes in ChIP-exo data. Bioinformatics (Oxford, England). PMID 30165373 DOI: 10.1093/Bioinformatics/Bty703 |
0.443 |
|
| 2018 |
Niu B, Coslo DM, Bataille AR, Albert I, Pugh BF, Omiecinski CJ. In vivo genome-wide binding interactions of mouse and human constitutive androstane receptors reveal novel gene targets. Nucleic Acids Research. PMID 30102401 DOI: 10.1093/Nar/Gky692 |
0.459 |
|
| 2018 |
Rossi MJ, Lai WKM, Pugh BF. Simplified ChIP-exo assays. Nature Communications. 9: 2842. PMID 30030442 DOI: 10.1038/S41467-018-05265-7 |
0.418 |
|
| 2018 |
García-Molinero V, García-Martínez J, Reja R, Furió-Tarí P, Antúnez O, Vinayachandran V, Conesa A, Pugh BF, Pérez-Ortín JE, Rodríguez-Navarro S. The SAGA/TREX-2 subunit Sus1 binds widely to transcribed genes and affects mRNA turnover globally. Epigenetics & Chromatin. 11: 13. PMID 29598828 DOI: 10.1186/S13072-018-0184-2 |
0.567 |
|
| 2018 |
Rossi MJ, Lai WKM, Pugh BF. Genome-wide determinants of sequence-specific DNA binding of general regulatory factors. Genome Research. PMID 29563167 DOI: 10.1101/Gr.229518.117 |
0.512 |
|
| 2018 |
Vinayachandran V, Reja R, Rossi MJ, Park B, Rieber L, Mittal C, Mahony S, Pugh BF. Widespread and precise reprogramming of yeast protein-genome interactions in response to heat shock. Genome Research. PMID 29444801 DOI: 10.1101/Gr.226761.117 |
0.535 |
|
| 2017 |
Miller JE, Zhang L, Jiang H, Li Y, Pugh BF, Reese JC. Genome-Wide Mapping of Decay Factor-mRNA Interactions in Yeast Identifies Nutrient Responsive Transcripts as Targets of the Deadenylase Ccr4. G3 (Bethesda, Md.). PMID 29158339 DOI: 10.1534/G3.117.300415 |
0.438 |
|
| 2017 |
Rossi MJ, Lai WKM, Pugh BF. Correspondence: DNA shape is insufficient to explain binding. Nature Communications. 8: 15643. PMID 28580956 DOI: 10.1038/Ncomms15643 |
0.366 |
|
| 2017 |
Lai WKM, Pugh BF. Understanding nucleosome dynamics and their links to gene expression and DNA replication. Nature Reviews. Molecular Cell Biology. PMID 28537572 DOI: 10.1038/Nrm.2017.47 |
0.548 |
|
| 2016 |
Lai WK, Pugh BF. Genome-wide uniformity of human 'open' pre-initiation complexes. Genome Research. PMID 27927716 DOI: 10.1101/Gr.210955.116 |
0.551 |
|
| 2016 |
Van Oss SB, Shirra MK, Bataille AR, Wier AD, Yen K, Vinayachandran V, Byeon IL, Cucinotta CE, Héroux A, Jeon J, Kim J, VanDemark AP, Pugh BF, Arndt KM. The Histone Modification Domain of Paf1 Complex Subunit Rtf1 Directly Stimulates H2B Ubiquitylation through an Interaction with Rad6. Molecular Cell. PMID 27840029 DOI: 10.1016/J.Molcel.2016.10.008 |
0.529 |
|
| 2016 |
Jeronimo C, Langelier MF, Bataille AR, Pascal JM, Pugh BF, Robert F. Tail and Kinase Modules Differently Regulate Core Mediator Recruitment and Function In Vivo. Molecular Cell. PMID 27773677 DOI: 10.1016/J.Molcel.2016.09.002 |
0.487 |
|
| 2016 |
Krietenstein N, Wal M, Watanabe S, Park B, Peterson CL, Pugh BF, Korber P. Genomic Nucleosome Organization Reconstituted with Pure Proteins. Cell. 167: 709-721.e12. PMID 27768892 DOI: 10.1016/J.Cell.2016.09.045 |
0.571 |
|
| 2016 |
Aguilar-Gurrieri C, Larabi A, Vinayachandran V, Patel NA, Yen K, Reja R, Ebong IO, Schoehn G, Robinson CV, Pugh BF, Panne D. Structural evidence for Nap1-dependent H2A-H2B deposition and nucleosome assembly. The Embo Journal. PMID 27225933 DOI: 10.15252/Embj.201694105 |
0.403 |
|
| 2016 |
Iwafuchi-Doi M, Donahue G, Kakumanu A, Watts JA, Mahony S, Pugh BF, Lee D, Kaestner KH, Zaret KS. The Pioneer Transcription Factor FoxA Maintains an Accessible Nucleosome Configuration at Enhancers for Tissue-Specific Gene Activation. Molecular Cell. 62: 79-91. PMID 27058788 DOI: 10.1016/J.Molcel.2016.03.001 |
0.564 |
|
| 2016 |
Baranello L, Wojtowicz D, Cui K, Devaiah BN, Chung HJ, Chan-Salis KY, Guha R, Wilson K, Zhang X, Zhang H, Piotrowski J, Thomas CJ, Singer DS, Pugh BF, Pommier Y, et al. RNA Polymerase II Regulates Topoisomerase 1 Activity to Favor Efficient Transcription. Cell. 165: 357-371. PMID 27058666 DOI: 10.1016/J.Cell.2016.02.036 |
0.535 |
|
| 2016 |
Pugh BF, Venters BJ. Genomic Organization of Human Transcription Initiation Complexes. Plos One. 11: e0149339. PMID 26866362 DOI: 10.1371/Journal.Pone.0149339 |
0.793 |
|
| 2016 |
de Dieuleveult M, Yen K, Hmitou I, Depaux A, Boussouar F, Dargham DB, Jounier S, Humbertclaude H, Ribierre F, Baulard C, Farrell NP, Park B, Keime C, Carrière L, Berlivet S, ... ... Pugh BF, et al. Genome-wide nucleosome specificity and function of chromatin remodellers in ES cells. Nature. PMID 26814966 DOI: 10.1038/Nature16505 |
0.599 |
|
| 2016 |
Pugh BF. Abstract IA02: Genomic organization of yeast chromatin and gene regulatory complexes Cancer Research. 76. DOI: 10.1158/1538-7445.Chromepi15-Ia02 |
0.611 |
|
| 2015 |
Han GC, Vinayachandran V, Bataille AR, Park B, Chan-Salis KY, Keller CA, Long M, Mahony S, Hardison RC, Pugh BF. Genome-wide organization of GATA1 and TAL1 determined at high resolution. Molecular and Cellular Biology. PMID 26503782 DOI: 10.1128/Mcb.00806-15 |
0.568 |
|
| 2015 |
Reja R, Vinayachandran V, Ghosh S, Pugh BF. Molecular mechanisms of ribosomal protein gene coregulation. Genes & Development. 29: 1942-54. PMID 26385964 DOI: 10.1101/Gad.268896.115 |
0.763 |
|
| 2015 |
Schneider M, Hellerschmied D, Schubert T, Amlacher S, Vinayachandran V, Reja R, Pugh BF, Clausen T, Köhler A. The Nuclear Pore-Associated TREX-2 Complex Employs Mediator to Regulate Gene Expression. Cell. 162: 1016-28. PMID 26317468 DOI: 10.1016/J.Cell.2015.07.059 |
0.53 |
|
| 2015 |
Mahony S, Pugh BF. Protein-DNA binding in high-resolution. Critical Reviews in Biochemistry and Molecular Biology. 50: 269-83. PMID 26038153 DOI: 10.3109/10409238.2015.1051505 |
0.493 |
|
| 2015 |
Schneider M, Hellerschmied D, Schubert T, Amlacher S, Vinayachandran V, Reja R, Pugh BF, Clausen T, Köhler A. The Nuclear Pore-Associated TREX-2 Complex Employs Mediator to Regulate Gene Expression Cell. 162: 1016-1028. DOI: 10.1016/j.cell.2015.07.059 |
0.325 |
|
| 2014 |
Rhee HS, Bataille AR, Zhang L, Pugh BF. Subnucleosomal structures and nucleosome asymmetry across a genome. Cell. 159: 1377-88. PMID 25480300 DOI: 10.1016/J.Cell.2014.10.054 |
0.714 |
|
| 2014 |
Venters BJ, Pugh BF. Retraction: Genomic organization of human transcription initiation complexes. Nature. 513: 444. PMID 25079311 DOI: 10.1038/Nature13588 |
0.741 |
|
| 2014 |
Chang GS, Chen XA, Park B, Rhee HS, Li P, Han KH, Mishra T, Chan-Salis KY, Li Y, Hardison RC, Wang Y, Pugh BF. A comprehensive and high-resolution genome-wide response of p53 to stress. Cell Reports. 8: 514-27. PMID 25043190 DOI: 10.1016/J.Celrep.2014.06.030 |
0.673 |
|
| 2013 |
Venters BJ, Pugh BF. Genomic organization of human transcription initiation complexes. Nature. 502: 53-8. PMID 24048476 DOI: 10.1038/Nature12535 |
0.785 |
|
| 2013 |
Yen K, Vinayachandran V, Pugh BF. SWR-C and INO80 chromatin remodelers recognize nucleosome-free regions near +1 nucleosomes. Cell. 154: 1246-56. PMID 24034248 DOI: 10.1016/J.Cell.2013.08.043 |
0.517 |
|
| 2013 |
Li J, Liu Y, Rhee HS, Ghosh SK, Bai L, Pugh BF, Gilmour DS. Kinetic competition between elongation rate and binding of NELF controls promoter-proximal pausing. Molecular Cell. 50: 711-22. PMID 23746353 DOI: 10.1016/J.Molcel.2013.05.016 |
0.73 |
|
| 2013 |
Nakahashi H, Kwon KR, Resch W, Vian L, Dose M, Stavreva D, Hakim O, Pruett N, Nelson S, Yamane A, Qian J, Dubois W, Welsh S, Phair RD, Pugh BF, et al. A genome-wide map of CTCF multivalency redefines the CTCF code. Cell Reports. 3: 1678-89. PMID 23707059 DOI: 10.1016/J.Celrep.2013.04.024 |
0.442 |
|
| 2013 |
Pugh BF. Molecular biology: The ends justify the means. Nature. 497: 48-9. PMID 23615607 DOI: 10.1038/Nature12098 |
0.561 |
|
| 2013 |
Pugh BF. Genome-wide interplay between chromatin and the transcription machinery Epigenetics & Chromatin. 6. DOI: 10.1186/1756-8935-6-S1-O19 |
0.614 |
|
| 2012 |
Rhee HS, Pugh BF. ChIP-exo method for identifying genomic location of DNA-binding proteins with near-single-nucleotide accuracy. Current Protocols in Molecular Biology / Edited by Frederick M. Ausubel ... [Et Al.]. Unit 21.24. PMID 23026909 DOI: 10.1002/0471142727.Mb2124S100 |
0.687 |
|
| 2012 |
Wal M, Pugh BF. Genome-wide mapping of nucleosome positions in yeast using high-resolution MNase ChIP-Seq. Methods in Enzymology. 513: 233-50. PMID 22929772 DOI: 10.1016/B978-0-12-391938-0.00010-0 |
0.464 |
|
| 2012 |
Yen K, Vinayachandran V, Batta K, Koerber RT, Pugh BF. Genome-wide nucleosome specificity and directionality of chromatin remodelers. Cell. 149: 1461-73. PMID 22726434 DOI: 10.1016/J.Cell.2012.04.036 |
0.807 |
|
| 2012 |
Bryant JM, Govin J, Zhang L, Donahue G, Pugh BF, Berger SL. The linker histone plays a dual role during gametogenesis in Saccharomyces cerevisiae. Molecular and Cellular Biology. 32: 2771-83. PMID 22586276 DOI: 10.1128/Mcb.00282-12 |
0.539 |
|
| 2012 |
Lee JS, Garrett AS, Yen K, Takahashi YH, Hu D, Jackson J, Seidel C, Pugh BF, Shilatifard A. Codependency of H2B monoubiquitination and nucleosome reassembly on Chd1. Genes & Development. 26: 914-9. PMID 22549955 DOI: 10.1101/Gad.186841.112 |
0.494 |
|
| 2012 |
Chang GS, Noegel AA, Mavrich TN, Müller R, Tomsho L, Ward E, Felder M, Jiang C, Eichinger L, Glöckner G, Schuster SC, Pugh BF. Unusual combinatorial involvement of poly-A/T tracts in organizing genes and chromatin in Dictyostelium. Genome Research. 22: 1098-106. PMID 22434426 DOI: 10.1101/Gr.131649.111 |
0.48 |
|
| 2012 |
Rhee HS, Pugh BF. Genome-wide structure and organization of eukaryotic pre-initiation complexes. Nature. 483: 295-301. PMID 22258509 DOI: 10.1038/Nature10799 |
0.754 |
|
| 2011 |
Rhee HS, Pugh BF. Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution. Cell. 147: 1408-19. PMID 22153082 DOI: 10.1016/J.Cell.2011.11.013 |
0.718 |
|
| 2011 |
Batta K, Zhang Z, Yen K, Goffman DB, Pugh BF. Genome-wide function of H2B ubiquitylation in promoter and genic regions. Genes & Development. 25: 2254-65. PMID 22056671 DOI: 10.1101/gad.177238.111 |
0.82 |
|
| 2011 |
Sen P, Ghosh S, Pugh BF, Bartholomew B. A new, highly conserved domain in Swi2/Snf2 is required for SWI/SNF remodeling. Nucleic Acids Research. 39: 9155-66. PMID 21835776 DOI: 10.1093/Nar/Gkr622 |
0.639 |
|
| 2011 |
Ioshikhes I, Hosid S, Pugh BF. Variety of genomic DNA patterns for nucleosome positioning. Genome Research. 21: 1863-71. PMID 21750105 DOI: 10.1101/gr.116228.110 |
0.311 |
|
| 2011 |
Zhang Z, Pugh BF. Genomic organization of H2Av containing nucleosomes in Drosophila heterochromatin. Plos One. 6: e20511. PMID 21738578 DOI: 10.1371/Journal.Pone.0020511 |
0.646 |
|
| 2011 |
Zhang Z, Wippo CJ, Wal M, Ward E, Korber P, Pugh BF. A packing mechanism for nucleosome organization reconstituted across a eukaryotic genome. Science (New York, N.Y.). 332: 977-80. PMID 21596991 DOI: 10.1126/Science.1200508 |
0.701 |
|
| 2011 |
Zhang L, Ma H, Pugh BF. Stable and dynamic nucleosome states during a meiotic developmental process. Genome Research. 21: 875-84. PMID 21515815 DOI: 10.1101/Gr.117465.110 |
0.517 |
|
| 2011 |
Venters BJ, Irvin JD, Gramlich P, Pugh BF. Genome-wide transcriptional dependence on conserved regions of Mot1. Molecular and Cellular Biology. 31: 2253-61. PMID 21444714 DOI: 10.1128/Mcb.01464-10 |
0.835 |
|
| 2011 |
Venters BJ, Wachi S, Mavrich TN, Andersen BE, Jena P, Sinnamon AJ, Jain P, Rolleri NS, Jiang C, Hemeryck-Walsh C, Pugh BF. A comprehensive genomic binding map of gene and chromatin regulatory proteins in Saccharomyces. Molecular Cell. 41: 480-92. PMID 21329885 DOI: 10.1016/J.Molcel.2011.01.015 |
0.794 |
|
| 2011 |
Zhang Z, Pugh BF. High-resolution genome-wide mapping of the primary structure of chromatin. Cell. 144: 175-86. PMID 21241889 DOI: 10.1016/J.Cell.2011.01.003 |
0.628 |
|
| 2011 |
Ghosh S, Pugh BF. Sequential recruitment of SAGA and TFIID in a genomic response to DNA damage in Saccharomyces cerevisiae. Molecular and Cellular Biology. 31: 190-202. PMID 20956559 DOI: 10.1128/MCB.00317-10 |
0.693 |
|
| 2010 |
Pugh BF. A preoccupied position on nucleosomes. Nature Structural & Molecular Biology. 17: 923. PMID 20683475 DOI: 10.1038/Nsmb0810-923 |
0.332 |
|
| 2010 |
Samorodnitsky E, Pugh BF. Genome-wide modeling of transcription preinitiation complex disassembly mechanisms using ChIP-chip data. Plos Computational Biology. 6: e1000733. PMID 20369017 DOI: 10.1371/Journal.Pcbi.1000733 |
0.799 |
|
| 2010 |
Schuster SC, Miller W, Ratan A, Tomsho LP, Giardine B, Kasson LR, Harris RS, Petersen DC, Zhao F, Qi J, Alkan C, Kidd JM, Sun Y, Drautz DI, Bouffard P, ... ... Pugh BF, et al. Complete Khoisan and Bantu genomes from southern Africa. Nature. 463: 943-7. PMID 20164927 DOI: 10.1038/Nature08795 |
0.534 |
|
| 2009 |
Jiang C, Pugh BF. A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae genome. Genome Biology. 10: R109. PMID 19814794 DOI: 10.1186/Gb-2009-10-10-R109 |
0.439 |
|
| 2009 |
Koerber RT, Rhee HS, Jiang C, Pugh BF. Interaction of transcriptional regulators with specific nucleosomes across the Saccharomyces genome. Molecular Cell. 35: 889-902. PMID 19782036 DOI: 10.1016/J.Molcel.2009.09.011 |
0.791 |
|
| 2009 |
Venters BJ, Pugh BF. How eukaryotic genes are transcribed. Critical Reviews in Biochemistry and Molecular Biology. 44: 117-41. PMID 19514890 DOI: 10.1080/10409230902858785 |
0.778 |
|
| 2009 |
Jiang C, Pugh BF. Nucleosome positioning and gene regulation: advances through genomics. Nature Reviews. Genetics. 10: 161-72. PMID 19204718 DOI: 10.1038/Nrg2522 |
0.598 |
|
| 2009 |
Venters BJ, Pugh BF. A canonical promoter organization of the transcription machinery and its regulators in the Saccharomyces genome. Genome Research. 19: 360-71. PMID 19124666 DOI: 10.1101/Gr.084970.108 |
0.812 |
|
| 2008 |
Azmy YY, Gupta A, Pugh BF. Computational modelling of genome-wide [corrected] transcription assembly networks using a fluidics analogy. Plos One. 3: e3095. PMID 18769485 DOI: 10.1371/Journal.Pone.0003095 |
0.478 |
|
| 2008 |
Mavrich TN, Ioshikhes IP, Venters BJ, Jiang C, Tomsho LP, Qi J, Schuster SC, Albert I, Pugh BF. A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome. Genome Research. 18: 1073-83. PMID 18550805 DOI: 10.1101/Gr.078261.108 |
0.786 |
|
| 2008 |
Yao H, Li P, Venters BJ, Zheng S, Thompson PR, Pugh BF, Wang Y. Histone Arg modifications and p53 regulate the expression of OKL38, a mediator of apoptosis. The Journal of Biological Chemistry. 283: 20060-8. PMID 18499678 DOI: 10.1074/Jbc.M802940200 |
0.743 |
|
| 2008 |
Mavrich TN, Jiang C, Ioshikhes IP, Li X, Venters BJ, Zanton SJ, Tomsho LP, Qi J, Glaser RL, Schuster SC, Gilmour DS, Albert I, Pugh BF. Nucleosome organization in the Drosophila genome. Nature. 453: 358-62. PMID 18408708 DOI: 10.1038/Nature06929 |
0.797 |
|
| 2008 |
Albert I, Wachi S, Jiang C, Pugh BF. GeneTrack--a genomic data processing and visualization framework. Bioinformatics (Oxford, England). 24: 1305-6. PMID 18388141 DOI: 10.1093/Bioinformatics/Btn119 |
0.304 |
|
| 2008 |
Lee C, Li X, Hechmer A, Eisen M, Biggin MD, Venters BJ, Jiang C, Li J, Pugh BF, Gilmour DS. NELF and GAGA factor are linked to promoter-proximal pausing at many genes in Drosophila. Molecular and Cellular Biology. 28: 3290-300. PMID 18332113 DOI: 10.1128/Mcb.02224-07 |
0.782 |
|
| 2008 |
Azmy YY, Gupta A, Pugh BF. Correction: Computational Modelling of Genome-Wide Transcription Assembly Networks Using a Fluidics Analogy Plos One. 3. DOI: 10.1371/Annotation/Aadfff4B-6947-475C-8121-225Ba113Adf8 |
0.393 |
|
| 2007 |
Venters BJ, Pugh BF. Chromatin meets RNA polymerase II. Genome Biology. 8: 319. PMID 18001505 DOI: 10.1186/Gb-2007-8-11-319 |
0.734 |
|
| 2007 |
Durant M, Pugh BF. NuA4-directed chromatin transactions throughout the Saccharomyces cerevisiae genome. Molecular and Cellular Biology. 27: 5327-35. PMID 17526728 DOI: 10.1128/Mcb.00468-07 |
0.722 |
|
| 2007 |
Huisinga KL, Pugh BF. A TATA binding protein regulatory network that governs transcription complex assembly. Genome Biology. 8: R46. PMID 17407552 DOI: 10.1186/Gb-2007-8-4-R46 |
0.592 |
|
| 2007 |
Albert I, Mavrich TN, Tomsho LP, Qi J, Zanton SJ, Schuster SC, Pugh BF. Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome. Nature. 446: 572-6. PMID 17392789 DOI: 10.1038/Nature05632 |
0.577 |
|
| 2006 |
Pugh BF. HATs off to PIC assembly. Molecular Cell. 23: 776-7. PMID 16973430 DOI: 10.1016/J.Molcel.2006.08.022 |
0.376 |
|
| 2006 |
Ioshikhes IP, Albert I, Zanton SJ, Pugh BF. Nucleosome positions predicted through comparative genomics. Nature Genetics. 38: 1210-5. PMID 16964265 DOI: 10.1038/Ng1878 |
0.545 |
|
| 2006 |
Zanton SJ, Pugh BF. Full and partial genome-wide assembly and disassembly of the yeast transcription machinery in response to heat shock. Genes & Development. 20: 2250-65. PMID 16912275 DOI: 10.1101/Gad.1437506 |
0.554 |
|
| 2006 |
Durant M, Pugh BF. Genome-wide relationships between TAF1 and histone acetyltransferases in Saccharomyces cerevisiae. Molecular and Cellular Biology. 26: 2791-802. PMID 16537921 DOI: 10.1128/Mcb.26.7.2791-2802.2006 |
0.767 |
|
| 2006 |
Irvin JD, Pugh BF. Genome-wide transcriptional dependence on TAF1 functional domains. The Journal of Biological Chemistry. 281: 6404-12. PMID 16407318 DOI: 10.1074/Jbc.M513776200 |
0.763 |
|
| 2004 |
Zanton SJ, Pugh BF. Changes in genomewide occupancy of core transcriptional regulators during heat stress. Proceedings of the National Academy of Sciences of the United States of America. 101: 16843-8. PMID 15548603 DOI: 10.1073/Pnas.0404988101 |
0.445 |
|
| 2004 |
Alexander DE, Kaczorowski DJ, Jackson-Fisher AJ, Lowery DM, Zanton SJ, Pugh BF. Inhibition of TATA binding protein dimerization by RNA polymerase III transcription initiation factor Brf1. The Journal of Biological Chemistry. 279: 32401-6. PMID 15190063 DOI: 10.1074/Jbc.M405782200 |
0.487 |
|
| 2004 |
Pugh BF. Is acetylation the key to opening locked gates? Nature Structural & Molecular Biology. 11: 298-300. PMID 15048100 DOI: 10.1038/Nsmb0404-298 |
0.318 |
|
| 2004 |
Kou H, Pugh BF. Engineering dimer-stabilizing mutations in the TATA-binding protein. The Journal of Biological Chemistry. 279: 20966-73. PMID 15020592 DOI: 10.1074/Jbc.M401535200 |
0.378 |
|
| 2004 |
Basehoar AD, Zanton SJ, Pugh BF. Identification and distinct regulation of yeast TATA box-containing genes. Cell. 116: 699-709. PMID 15006352 DOI: 10.1016/S0092-8674(04)00205-3 |
0.531 |
|
| 2004 |
Huisinga KL, Pugh BF. A genome-wide housekeeping role for TFIID and a highly regulated stress-related role for SAGA in Saccharomyces cerevisiae. Molecular Cell. 13: 573-85. PMID 14992726 DOI: 10.1016/S1097-2765(04)00087-5 |
0.545 |
|
| 2003 |
Kou H, Irvin JD, Huisinga KL, Mitra M, Pugh BF. Structural and functional analysis of mutations along the crystallographic dimer interface of the yeast TATA binding protein. Molecular and Cellular Biology. 23: 3186-201. PMID 12697819 DOI: 10.1128/Mcb.23.9.3186-3201.2003 |
0.695 |
|
| 2002 |
Chitikila C, Huisinga KL, Irvin JD, Basehoar AD, Pugh BF. Interplay of TBP inhibitors in global transcriptional control. Molecular Cell. 10: 871-82. PMID 12419230 DOI: 10.1016/S1097-2765(02)00683-4 |
0.809 |
|
| 2000 |
Pugh BF. Control of gene expression through regulation of the TATA-binding protein. Gene. 255: 1-14. PMID 10974559 DOI: 10.1016/S0378-1119(00)00288-2 |
0.589 |
|
| 1999 |
Coleman RA, Taggart AK, Burma S, Chicca JJ, Pugh BF. TFIIA regulates TBP and TFIID dimers. Molecular Cell. 4: 451-7. PMID 10518227 DOI: 10.1016/S1097-2765(00)80453-0 |
0.501 |
|
| 1999 |
Jackson-Fisher AJ, Burma S, Portnoy M, Schneeweis LA, Coleman RA, Mitra M, Chitikila C, Pugh BF. Dimer dissociation and thermosensitivity kinetics of the Saccharomyces cerevisiae and human TATA binding proteins. Biochemistry. 38: 11340-8. PMID 10471284 DOI: 10.1021/Bi990911P |
0.77 |
|
| 1999 |
Jackson-Fisher AJ, Chitikila C, Mitra M, Pugh BF. A role for TBP dimerization in preventing unregulated gene expression. Molecular Cell. 3: 717-27. PMID 10394360 DOI: 10.1016/S1097-2765(01)80004-6 |
0.787 |
|
| 1998 |
Chicca JJ, Auble DT, Pugh BF. Cloning and biochemical characterization of TAF-172, a human homolog of yeast Mot1. Molecular and Cellular Biology. 18: 1701-10. PMID 9488487 DOI: 10.1128/Mcb.18.3.1701 |
0.536 |
|
| 1997 |
Weideman CA, Netter RC, Benjamin LR, McAllister JJ, Schmiedekamp LA, Coleman RA, Pugh BF. Dynamic interplay of TFIIA, TBP and TATA DNA. Journal of Molecular Biology. 271: 61-75. PMID 9300055 DOI: 10.1006/jmbi.1997.1152 |
0.361 |
|
| 1997 |
Coleman RA, Pugh BF. 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. 94: 7221-6. PMID 9207072 DOI: 10.1073/Pnas.94.14.7221 |
0.419 |
|
| 1997 |
Booth BL, Pugh BF. Identification and characterization of a nuclease specific for the 3' end of the U6 small nuclear RNA. The Journal of Biological Chemistry. 272: 984-91. PMID 8995392 DOI: 10.1074/Jbc.272.2.984 |
0.323 |
|
| 1996 |
Pugh BF. Mechanisms of transcription complex assembly. Current Opinion in Cell Biology. 8: 303-11. PMID 8743879 DOI: 10.1016/S0955-0674(96)80002-0 |
0.511 |
|
| 1995 |
Jackson AJ, Ittmann M, Pugh BF. 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. 15: 94-101. PMID 7799973 |
0.369 |
|
| 1995 |
Pugh BF. Purification of the human TATA-binding protein, TBP. Methods in Molecular Biology (Clifton, N.J.). 37: 359-67. PMID 7780516 DOI: 10.1385/0-89603-288-4:359 |
0.322 |
|
| 1995 |
Coleman RA, Pugh BF. Evidence for functional binding and stable sliding of the TATA binding protein on nonspecific DNA. The Journal of Biological Chemistry. 270: 13850-9. PMID 7775443 |
0.355 |
|
| 1995 |
Coleman RA, Taggart AK, Benjamin LR, Pugh BF. Dimerization of the TATA binding protein. The Journal of Biological Chemistry. 270: 13842-9. PMID 7775442 DOI: 10.1074/jbc.270.23.13842 |
0.35 |
|
| 1992 |
Pugh BF, Tjian R. Diverse transcriptional functions of the multisubunit eukaryotic TFIID complex Journal of Biological Chemistry. 267: 679-682. PMID 1730659 |
0.318 |
|
| 1992 |
Taggart AK, Fisher TS, Pugh BF. The TATA-binding protein and associated factors are components of pol III transcription factor TFIIIB. Cell. 71: 1015-28. PMID 1458533 DOI: 10.1016/0092-8674(92)90396-T |
0.499 |
|
| 1991 |
Tanese N, Pugh BF, Tjian R. Coactivators for a proline-rich activator purified from the multisubunit human TFIID complex. Genes & Development. 5: 2212-24. PMID 1748279 DOI: 10.1101/Gad.5.12A.2212 |
0.372 |
|
| 1991 |
Pugh BF, Tjian R. Transcription from a TATA-less promoter requires a multisubunit TFIID complex Genes and Development. 5: 1935-1945. PMID 1657708 |
0.421 |
|
| 1990 |
Peterson MG, Tanese N, Pugh BF, Tjian R. Functional domains and upstream activation properties of cloned human TATA binding protein. Science (New York, N.Y.). 248: 1625-30. PMID 2363050 DOI: 10.1126/Science.2363050 |
0.359 |
|
| 1990 |
Pugh BF, Tjian R. Mechanism of transcriptional activation by Sp1: Evidence for coactivators Cell. 61: 1187-1197. PMID 2194667 DOI: 10.1016/0092-8674(90)90683-6 |
0.46 |
|
| 1990 |
Hoey T, Dynlacht BD, Peterson MG, Pugh BF, Tjian R. Isolation and characterization of the Drosophila gene encoding the TATA box binding protein, TFIID. Cell. 61: 1179-86. PMID 2194666 DOI: 10.1016/0092-8674(90)90682-5 |
0.514 |
|
| 1989 |
Pugh BF, Schutte BC, Cox MM. Extent of duplex DNA underwinding induced by RecA protein binding in the presence of ATP. Journal of Molecular Biology. 205: 487-92. PMID 2538631 DOI: 10.1016/0022-2836(89)90219-2 |
0.37 |
|
| 1988 |
Pugh BF, Cox MM. General mechanism for RecA protein binding to duplex DNA. Journal of Molecular Biology. 203: 479-93. PMID 3058986 DOI: 10.1016/0022-2836(88)90014-9 |
0.402 |
|
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