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John J, Jabbar J, Badjatia N, Rossi MJ, Lai WKM, Pugh BF. Genome-wide promoter assembly in E. coli measured at single-base resolution. Genome Res. 2022 May;32(5):878-892. doi: 10.1101/gr.276544.121. Epub 2022 Apr 28. PubMed PMID: 35483960; PubMed Central PMCID: PMC9104697.
Shao D, Kellogg GD, Nematbakhsh A, Kuntala PK, Mahony S, Pugh BF, Lai WKM. PEGR: a flexible management platform for reproducible epigenomic and genomic research. Genome Biol. 2022 Apr 19;23(1):99. doi: 10.1186/s13059-022-02671-5. PubMed PMID: 35440038; PubMed Central PMCID: PMC9016988.
Sun Q, Nematbakhsh A, Kuntala PK, Kellogg G, Pugh BF, Lai WKM. STENCIL: A web templating engine for visualizing and sharing life science datasets. PLoS Comput Biol. 2022 Feb;18(2):e1009859. doi: 10.1371/journal.pcbi.1009859. eCollection 2022 Feb. PubMed PMID: 35139076; PubMed Central PMCID: PMC8863220.
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 Saccharomyces cerevisiae. Elife. 2021 Oct 15;10. doi: 10.7554/eLife.71013. PubMed PMID: 34652274; PubMed Central PMCID: PMC8589449.
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, Zhang W, Zhao Z, Shah AP, Novitzky K, McAnarney E, Keogh MC, Shilatifard A, Basu U, Bulyk ML, Pugh BF. A ChIP-exo screen of 887 Protein Capture Reagents Program transcription factor antibodies in human cells. Genome Res. 2021 Sep;31(9):1663-1679. doi: 10.1101/gr.275472.121. Epub 2021 Aug 23. PubMed PMID: 34426512; PubMed Central PMCID: PMC8415381.
Chen H, Pugh BF. What do Transcription Factors Interact With?. J Mol Biol. 2021 Jul 9;433(14):166883. doi: 10.1016/j.jmb.2021.166883. Epub 2021 Feb 20. Review. PubMed PMID: 33621520; PubMed Central PMCID: PMC8184585.
Pugh BF. Protein architecture of the yeast genome. Nature. 2021 May 21;. doi: 10.1038/d41586-021-01118-4. [Epub ahead of print] PubMed PMID: 34021291.
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, Kellogg GD, Mahony S, Pugh BF. A high-resolution protein architecture of the budding yeast genome. Nature. 2021 Apr;592(7853):309-314. doi: 10.1038/s41586-021-03314-8. Epub 2021 Mar 10. PubMed PMID: 33692541; PubMed Central PMCID: PMC8035251.
Mittal C, Rossi MJ, Pugh B. High similarity among ChEC-seq datasets. bioRxiv. 2021 February. doi: https://doi.org/10.1101/2021.02.04.429774.
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 Rep. 2021 Jan 19;34(3):108640. doi: 10.1016/j.celrep.2020.108640. PubMed PMID: 33472084; PubMed Central PMCID: PMC7879390.
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 Res. 2020 Nov 18;48(20):11215-11226. doi: 10.1093/nar/gkaa618. PubMed PMID: 32747934; PubMed Central PMCID: PMC7672471.
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, Person MD, Trybus KM, Zhang KYJ, Pugh BF, Kamm KE, Milewicz DM, Shen X, Kapoor P. Actin R256 Mono-methylation Is a Conserved Post-translational Modification Involved in Transcription. Cell Rep. 2020 Sep 29;32(13):108172. doi: 10.1016/j.celrep.2020.108172. PubMed PMID: 32997990; PubMed Central PMCID: PMC8860185.
Shao D, Kellogg G, Mahony S, Lai W, Pugh B. PEGR: a management platform for ChIP-based next generation sequencing pipelines. Practice and Experience in Advanced Research Computing (PEARC ’20), July 26–30, 2020, Portland, OR, USA. 2020 July. doi: https://dl.acm.org/doi/10.1145/3311790.3396621.
Shao D, Kellogg G, Mahony S, Lai W, Pugh BF. PEGR: a management platform for ChIP-based next generation sequencing pipelines. PEARC20 (2020). 2020 Jul;2020:285-292. doi: 10.1145/3311790.3396621. Epub 2020 Jul 26. PubMed PMID: 35662897; PubMed Central PMCID: PMC9161112.
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, Nickels BE, Kaplan CD. Universal promoter scanning by Pol II during transcription initiation in Saccharomyces cerevisiae. Genome Biol. 2020 Jun 2;21(1):132. doi: 10.1186/s13059-020-02040-0. PubMed PMID: 32487207; PubMed Central PMCID: PMC7265651.
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. 2020 Mar;579(7800):592-597. doi: 10.1038/s41586-020-2097-z. Epub 2020 Mar 11. PubMed PMID: 32214243; PubMed Central PMCID: PMC7481934.
Yamada N, Kuntala PK, Pugh BF, Mahony S. ChExMix: A Method for Identifying and Classifying Protein-DNA Interaction Subtypes. J Comput Biol. 2020 Mar;27(3):429-435. doi: 10.1089/cmb.2019.0466. Epub 2020 Feb 5. PubMed PMID: 32023130; PubMed Central PMCID: PMC7074916.
Aydin B, Kakumanu A, Rossillo M, Moreno-Estellés M, Garipler G, Ringstad N, Flames N, Mahony S, Mazzoni EO. Proneural factors Ascl1 and Neurog2 contribute to neuronal subtype identities by establishing distinct chromatin landscapes. Nat Neurosci. 2019 Jun;22(6):897-908. doi: 10.1038/s41593-019-0399-y. Epub 2019 May 13. PubMed PMID: 31086315; PubMed Central PMCID: PMC6556771.
Yamada N, Lai WKM, Farrell N, Pugh BF, Mahony S. Characterizing protein-DNA binding event subtypes in ChIP-exo data. Bioinformatics. 2019 Mar 15;35(6):903-913. doi: 10.1093/bioinformatics/bty703. PubMed PMID: 30165373; PubMed Central PMCID: PMC6419906.
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 Res. 2018 Sep 19;46(16):8385-8403. doi: 10.1093/nar/gky692. PubMed PMID: 30102401; PubMed Central PMCID: PMC6144799.
Rossi MJ, Lai WKM, Pugh BF. Simplified ChIP-exo assays. Nat Commun. 2018 Jul 20;9(1):2842. doi: 10.1038/s41467-018-05265-7. PubMed PMID: 30030442; PubMed Central PMCID: PMC6054642.
Rossi MJ, Lai WKM, Pugh BF. Genome-wide determinants of sequence-specific DNA binding of general regulatory factors. Genome Res. 2018 Apr;28(4):497-508. doi: 10.1101/gr.229518.117. Epub 2018 Mar 21. PubMed PMID: 29563167; PubMed Central PMCID: PMC5880240.
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. 2018 Mar 29;11(1):13. doi: 10.1186/s13072-018-0184-2. PubMed PMID: 29598828; PubMed Central PMCID: PMC5875001.
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 Res. 2018 Feb 14;. doi: 10.1101/gr.226761.117. [Epub ahead of print] PubMed PMID: 29444801; PubMed Central PMCID: PMC5848614.
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). 2018 Jan 4;8(1):315-330. doi: 10.1534/g3.117.300415. PubMed PMID: 29158339; PubMed Central PMCID: PMC5765359.
Lai WKM, Pugh BF. Understanding nucleosome dynamics and their links to gene expression and DNA replication. Nat Rev Mol Cell Biol. 2017 Sep;18(9):548-562. doi: 10.1038/nrm.2017.47. Epub 2017 May 24. Review. PubMed PMID: 28537572; PubMed Central PMCID: PMC5831138.
Rossi MJ, Lai WKM, Pugh BF. Correspondence: DNA shape is insufficient to explain binding. Nat Commun. 2017 Jun 5;8:15643. doi: 10.1038/ncomms15643. PubMed PMID: 28580956; PubMed Central PMCID: PMC5465349.
Lai WK, Pugh BF. Genome-wide uniformity of human 'open' pre-initiation complexes. Genome Res. 2017 Jan;27(1):15-26. doi: 10.1101/gr.210955.116. Epub 2016 Nov 10. PubMed PMID: 27927716; PubMed Central PMCID: PMC5204339.
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. Mol Cell. 2016 Nov 17;64(4):815-825. doi: 10.1016/j.molcel.2016.10.008. Epub 2016 Nov 10. PubMed PMID: 27840029; PubMed Central PMCID: PMC5131541.
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. Mol Cell. 2016 Nov 3;64(3):455-466. doi: 10.1016/j.molcel.2016.09.002. Epub 2016 Oct 20. PubMed PMID: 27773677; PubMed Central PMCID: PMC5824718.
Krietenstein N, Wal M, Watanabe S, Park B, Peterson CL, Pugh BF, Korber P. Genomic Nucleosome Organization Reconstituted with Pure Proteins. Cell. 2016 Oct 20;167(3):709-721.e12. doi: 10.1016/j.cell.2016.09.045. PubMed PMID: 27768892; PubMed Central PMCID: PMC5240917.
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. EMBO J. 2016 Jul 1;35(13):1465-82. doi: 10.15252/embj.201694105. Epub 2016 May 25. PubMed PMID: 27225933; PubMed Central PMCID: PMC4931181.
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. Mol Cell. 2016 Apr 7;62(1):79-91. doi: 10.1016/j.molcel.2016.03.001. PubMed PMID: 27058788; PubMed Central PMCID: PMC4826471.
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, Przytycka TM, Kouzine F, Lewis BA, Zhao K, Levens D. RNA Polymerase II Regulates Topoisomerase 1 Activity to Favor Efficient Transcription. Cell. 2016 Apr 7;165(2):357-71. doi: 10.1016/j.cell.2016.02.036. PubMed PMID: 27058666; PubMed Central PMCID: PMC4826470.
Pugh BF, Venters BJ. Genomic Organization of Human Transcription Initiation Complexes. PLoS One. 2016;11(2):e0149339. doi: 10.1371/journal.pone.0149339. eCollection 2016. PubMed PMID: 26866362; PubMed Central PMCID: PMC4750860.
de Dieuleveult M, Yen K, Hmitou I, Depaux A, Boussouar F, Bou Dargham D, Jounier S, Humbertclaude H, Ribierre F, Baulard C, Farrell NP, Park B, Keime C, Carrière L, Berlivet S, Gut M, Gut I, Werner M, Deleuze JF, Olaso R, Aude JC, Chantalat S, Pugh BF, Gérard M. Genome-wide nucleosome specificity and function of chromatin remodellers in ES cells. Nature. 2016 Feb 4;530(7588):113-6. doi: 10.1038/nature16505. Epub 2016 Jan 27. PubMed PMID: 26814966; PubMed Central PMCID: PMC4871117.
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. Mol Cell Biol. 2016 Jan 1;36(1):157-72. doi: 10.1128/MCB.00806-15. Print 2016 Jan 1. PubMed PMID: 26503782; PubMed Central PMCID: PMC4702602.
Reja R, Vinayachandran V, Ghosh S, Pugh BF. Molecular mechanisms of ribosomal protein gene coregulation. Genes Dev. 2015 Sep 15;29(18):1942-54. doi: 10.1101/gad.268896.115. PubMed PMID: 26385964; PubMed Central PMCID: PMC4579351.
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. 2015 Aug 27;162(5):1016-28. doi: 10.1016/j.cell.2015.07.059. PubMed PMID: 26317468; PubMed Central PMCID: PMC4644235.
Mahony S, Pugh BF. Protein-DNA binding in high-resolution. Crit Rev Biochem Mol Biol. 2015;50(4):269-83. doi: 10.3109/10409238.2015.1051505. Epub 2015 Jun 3. Review. PubMed PMID: 26038153; PubMed Central PMCID: PMC4580520.
Wang S, Chen XA, Hu J, Jiang JK, Li Y, Chan-Salis KY, Gu Y, Chen G, Thomas C, Pugh BF, Wang Y. ATF4 Gene Network Mediates Cellular Response to the Anticancer PAD Inhibitor YW3-56 in Triple-Negative Breast Cancer Cells. Mol Cancer Ther. 2015 Apr;14(4):877-88. doi: 10.1158/1535-7163.MCT-14-1093-T. Epub 2015 Jan 22. PubMed PMID: 25612620; PubMed Central PMCID: PMC4394025.
Rhee HS, Bataille AR, Zhang L, Pugh BF. Subnucleosomal structures and nucleosome asymmetry across a genome. Cell. 2014 Dec 4;159(6):1377-88. doi: 10.1016/j.cell.2014.10.054. PubMed PMID: 25480300; PubMed Central PMCID: PMC4258235.
Venters BJ, Pugh BF. Retraction: Genomic organization of human transcription initiation complexes. Nature. 2014 Sep 18;513(7518):444. doi: 10.1038/nature13588. Epub 2014 Jul 23. PubMed PMID: 25079311; PubMed Central PMCID: PMC4384692.
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 Rep. 2014 Jul 24;8(2):514-27. doi: 10.1016/j.celrep.2014.06.030. Epub 2014 Jul 17. PubMed PMID: 25043190; PubMed Central PMCID: PMC4113076.
Venters BJ, Pugh BF. Genomic organization of human transcription initiation complexes. Nature. 2013 Oct 3;502(7469):53-8. doi: 10.1038/nature12535. Epub 2013 Sep 18. PubMed PMID: 24048476; PubMed Central PMCID: PMC4018585.
Yen K, Vinayachandran V, Pugh BF. SWR-C and INO80 chromatin remodelers recognize nucleosome-free regions near +1 nucleosomes. Cell. 2013 Sep 12;154(6):1246-56. doi: 10.1016/j.cell.2013.08.043. PubMed PMID: 24034248; PubMed Central PMCID: PMC4090706.
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. Mol Cell. 2013 Jun 6;50(5):711-22. doi: 10.1016/j.molcel.2013.05.016. PubMed PMID: 23746353; PubMed Central PMCID: PMC3695833.
Nakahashi H, Kieffer 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, Lobanenkov V, Hager GL, Casellas R. A genome-wide map of CTCF multivalency redefines the CTCF code. Cell Rep. 2013 May 30;3(5):1678-1689. doi: 10.1016/j.celrep.2013.04.024. Epub 2013 May 23. PubMed PMID: 23707059; PubMed Central PMCID: PMC3770538.
Pugh BF. Molecular biology: The ends justify the means. Nature. 2013 May 2;497(7447):48-9. doi: 10.1038/nature12098. Epub 2013 Apr 24. PubMed PMID: 23615607.
Rhee HS, Pugh BF. ChIP-exo method for identifying genomic location of DNA-binding proteins with near-single-nucleotide accuracy. Curr Protoc Mol Biol. 2012 Oct;Chapter 21:Unit 21.24. doi: 10.1002/0471142727.mb2124s100. PubMed PMID: 23026909; PubMed Central PMCID: PMC3813302.
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