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

Research Interests

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

Recent Publications


Yamada, N, Kuntala, PK, Pugh, BF & Mahony, S 2020, 'ChExMix: A Method for Identifying and Classifying Protein-DNA Interaction Subtypes', Journal of Computational Biology, vol. 27, no. 3, pp. 429-435.
Gallego, LD, Schneider, M, Mittal, C, Romanauska, A, Gudino Carrillo, RM, Schubert, T, Pugh, BF & Köhler, A 2020, 'Phase separation directs ubiquitination of gene-body nucleosomes', Nature, vol. 579, no. 7800, pp. 592-597.
Qiu, C, Qiu, C, Jin, H, Vvedenskaya, I, Vvedenskaya, I, Llenas, JA, Llenas, JA, Zhao, T, Malik, I, Malik, I, Visbisky, AM, Schwartz, SL, Cui, P, Čabart, P, Čabart, P, Han, KH, Lai, W, Lai, WKM, Metz, RP, Johnson, CD, Sze, SH, Sze, SH, Pugh, BF, Pugh, BF, Nickels, BE, Nickels, BE & Kaplan, CD 2020, 'Universal promoter scanning by Pol II during transcription initiation in Saccharomyces cerevisiae', Genome biology, vol. 21, no. 1, 132.


Yamada, N, Lai, WKM, Farrell, N, Pugh, BF & Mahony, S 2019, 'Characterizing protein-DNA binding event subtypes in ChIP-exo data', Bioinformatics, vol. 35, no. 6, pp. 903-913.


Yamada, N, Lai, WKM, Farrell, N, Pugh, BF & Mahony, S 2018, Characterizing protein-DNA binding event subtypes in CHIP-exo data. in BJ Raphael (ed.), 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, MJ, Lai, WKM & Pugh, BF 2018, 'Genome-wide determinants of sequence-specific DNA binding of general regulatory factors', Genome research, vol. 28, no. 4, pp. 497-508.
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.
Niu, B, Coslo, DM, Bataille, AR, Albert, I, Franklin Pugh, B & 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.
Rossi, MJ, Lai, WKM & Pugh, BF 2018, 'Simplified ChIP-exo assays', Nature communications, vol. 9, no. 1, 2842.
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.
Vinayachandran, V, Reja, R, Rossi, MJ, Park, B, Rieber, L, Mittal, C, Mahony, S & 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.


Rossi, MJ, Lai, WKM & Pugh, BF 2017, 'Correspondence: DNA shape is insufficient to explain binding', Nature communications, vol. 8, 15643.
Lai, WKM & Pugh, BF 2017, 'Genome-wide uniformity of human 'open' pre-initiation complexes', Genome research, vol. 27, no. 1, pp. 15-26.
Lai, WKM & 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.


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.
Han, GC, Vinayachandran, V, Bataille, AR, Park, B, Chan-Salis, KY, Keller, CA, Long, M, Mahony, S, 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.
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.
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.
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.
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.
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.
Iwafuchi-Doi, M, Donahue, G, Kakumanu, A, Watts, JA, Mahony, S, 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.

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