Researcher Profile

Researcher Profile

Benjamin Franklin Pugh, PhD

Benjamin Franklin Pugh, PhD

Evan Pugh University Professor, Willaman Chair in Molecular Biology and Professor, Biochemistry & Molecular Biology
Scientific Program:Mechanisms of Carcinogenesis
bfp2@psu.edu

Research Interests

  • Genome
  • Genes
  • Nucleosomes
  • DNA
  • TATA-Box Binding Protein
  • Transcription Factor TFIID
  • Chromatin
  • Proteins
  • Yeasts
  • Saccharomyces cerevisiae
  • Gene Expression
  • Transcription Factors

Recent Publications

2019

Yamada, N, Lai, W, Farrell, N, Pugh, BF & Mahony, SA 2019, 'Characterizing protein-DNA binding event subtypes in ChIP-exo data' Bioinformatics, vol. 35, no. 6, pp. 903-913. https://doi.org/10.1093/bioinformatics/bty703

2018

Yamada, N, Lai, W, Farrell, N, Pugh, BF & Mahony, SA 2018, Characterizing protein-DNA binding event subtypes in CHIP-exo data. in Research in Computational Molecular Biology - 22nd Annual International Conference, RECOMB 2018, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 10812 LNBI, Springer Verlag, pp. 291-292, 22nd International Conference on Research in Computational Molecular Biology, RECOMB 2018, Paris, France, 4/21/18.
Rossi, M, Lai, W & Pugh, BF 2018, 'Genome-wide determinants of sequence-specific DNA binding of general regulatory factors', Genome research, vol. 28, no. 4, pp. 497-508. https://doi.org/10.1101/gr.229518.117
Miller, JE, Zhang, L, Jiang, H, Li, Y, Pugh, BF & Reese, JC 2018, 'Genome-wide mapping of decay factor-mRNA interactions in yeast identifies nutrient-responsive transcripts as targets of the deadenylase Ccr4', G3: Genes, Genomes, Genetics, vol. 8, no. 1, pp. 315-330. https://doi.org/10.1534/g3.117.300415
Niu, B, Coslo, DM, Bataille, AR, Albert, I, Pugh, BF & Omiecinski, CJ 2018, 'In vivo genome-wide binding interactions of mouse and human constitutive androstane receptors reveal novel gene targets', Nucleic acids research, vol. 46, no. 16, pp. 8385-8403. https://doi.org/10.1093/nar/gky692
Rossi, M, Lai, W & Pugh, BF 2018, 'Simplified ChIP-exo assays' Nature communications, vol. 9, no. 1, 2842. https://doi.org/10.1038/s41467-018-05265-7
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 2018, 'The SAGA/TREX-2 subunit Sus1 binds widely to transcribed genes and affects mRNA turnover globally', Epigenetics and Chromatin, vol. 11, no. 1, 13. https://doi.org/10.1186/s13072-018-0184-2
Vinayachandran, V, Reja, R, Rossi, M, Park, B, Rieber, L, Mittal, C, Mahony, SA & Pugh, BF 2018, 'Widespread and precise reprogramming of yeast protein-genome interactions in response to heat shock', Genome research, vol. 28, no. 3, pp. 357-366. https://doi.org/10.1101/gr.226761.117

2017

Rossi, M, Lai, W & Pugh, BF 2017, 'Correspondence: DNA shape is insufficient to explain binding', Nature Communications, vol. 8, 15643. https://doi.org/10.1038/ncomms15643
Lai, W & Pugh, BF 2017, 'Genome-wide uniformity of human 'open' pre-initiation complexes', Genome research, vol. 27, no. 1, pp. 15-26. https://doi.org/10.1101/gr.210955.116
Lai, W & Pugh, BF 2017, 'Understanding nucleosome dynamics and their links to gene expression and DNA replication', Nature Reviews Molecular Cell Biology, vol. 18, no. 9, pp. 548-562. https://doi.org/10.1038/nrm.2017.47

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, Gut, M, Gut, I, Werner, M, Deleuze, JF, Olaso, R, Aude, JC, Chantalat, S, Pugh, BF & Gérard, M 2016, 'Genome-wide nucleosome specificity and function of chromatin remodellers in ES cells', Nature, vol. 530, no. 7588, pp. 113-116. https://doi.org/10.1038/nature16505
Han, GC, Vinayachandran, V, Bataille, AR, Park, B, Chan-Salis, KY, Keller Capone, CA, Long, M, Mahony, SA, Hardison, RC & Pugh, BF 2016, 'Genome-wide organization of GATA1 and TAL1 determined at high resolution', Molecular and cellular biology, vol. 36, no. 1, pp. 157-172. https://doi.org/10.1128/MCB.00806-15
Krietenstein, N, Wal, M, Watanabe, S, Park, B, Peterson, CL, Pugh, BF & Korber, P 2016, 'Genomic Nucleosome Organization Reconstituted with Pure Proteins', Cell, vol. 167, no. 3, pp. 709-721.e12. https://doi.org/10.1016/j.cell.2016.09.045
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 2016, 'RNA Polymerase II Regulates Topoisomerase 1 Activity to Favor Efficient Transcription', Cell, vol. 165, no. 2, pp. 357-371. https://doi.org/10.1016/j.cell.2016.02.036
Aguilar-Gurrieri, C, Larabi, A, Vinayachandran, V, Patel, NA, Yen, K, Reja, R, Ebong, IO, Schoehn, G, Robinson, CV, Pugh, BF & Panne, D 2016, 'Structural evidence for Nap1-dependent H2A–H2B deposition and nucleosome assembly', EMBO Journal, vol. 35, no. 13, pp. 1465-1482. https://doi.org/10.15252/embj.201694105
Jeronimo, C, Langelier, MF, Bataille, AR, Pascal, JM, Pugh, BF & Robert, F 2016, 'Tail and Kinase Modules Differently Regulate Core Mediator Recruitment and Function In Vivo', Molecular cell, vol. 64, no. 3, pp. 455-466. https://doi.org/10.1016/j.molcel.2016.09.002
Van Oss, SB, Shirra, MK, Bataille, AR, Wier, AD, Yen, K, Vinayachandran, V, Byeon, IJL, Cucinotta, CE, Héroux, A, Jeon, J, Kim, J, VanDemark, AP, Pugh, BF & Arndt, KM 2016, 'The Histone Modification Domain of Paf1 Complex Subunit Rtf1 Directly Stimulates H2B Ubiquitylation through an Interaction with Rad6', Molecular cell, vol. 64, no. 4, pp. 815-825. https://doi.org/10.1016/j.molcel.2016.10.008
Iwafuchi-Doi, M, Donahue, G, Kakumanu, A, Watts, JA, Mahony, SA, Pugh, BF, Lee, D, Kaestner, KH & Zaret, KS 2016, 'The Pioneer Transcription Factor FoxA Maintains an Accessible Nucleosome Configuration at Enhancers for Tissue-Specific Gene Activation', Molecular cell, vol. 62, no. 1, pp. 79-91. https://doi.org/10.1016/j.molcel.2016.03.001

2015

Wang, S, Chen, XA, Hu, J, Jiang, JK, Li, Y, Chan-Salis, KY, Gu, Y, Chen, G, Thomas, C, Pugh, BF & Wang, Y 2015, 'ATF4 gene network mediates cellular response to the anticancer PAD inhibitor YW3-56 in triple-negative breast cancer cells' Molecular cancer therapeutics, vol. 14, no. 4, pp. 877-888. https://doi.org/10.1158/1535-7163.MCT-14-1093-T
Reja, R, Vinayachandran, V, Ghosh, S & Pugh, BF 2015, 'Molecular mechanisms of ribosomal protein gene coregulation', Genes and Development, vol. 29, no. 18, pp. 1942-1954. https://doi.org/10.1101/gad.268896.115
Mahony, SA & Pugh, BF 2015, 'Protein-DNA binding in high-resolution', Critical Reviews in Biochemistry and Molecular Biology, vol. 50, no. 4, pp. 269-283. https://doi.org/10.3109/10409238.2015.1051505
Schneider, M, Hellerschmied, D, Schubert, T, Amlacher, S, Vinayachandran, V, Reja, R, Pugh, BF, Clausen, T & Köhler, A 2015, 'The Nuclear Pore-Associated TREX-2 Complex Employs Mediator to Regulate Gene Expression', Cell, vol. 162, no. 5, pp. 1016-1028. https://doi.org/10.1016/j.cell.2015.07.059

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