B. Franklin Pugh

ScholarGPS® ID: 67365446197800

Affiliation
Cornell University, Ithaca, United States
Affiliation History

Field
Life Sciences
Discipline
Molecular and Cell Biology
Top Specialties
DNA | Binding Protein | Chromatin | Yeast | Genomics | Saccharomyces Cerevisiae | Histone | Drosophila | Gene Expression | Nucleic Acid | RNA | Transcription Factor | Computational Biology
Metrics Summary
Publication Count
125
Predicted Citations
20,125
Predicted h-index
72
Ranking

Publications and Citation History

Publications based on Top Specialties

Types of Publication

  • Publications
  • Books
  • Patents
  • NIH/NSF
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Locus-specific proteome decoding reveals Fpt1 as a chromatin-associated negative regulator of RNA polymerase III assembly (journal article)
van Breugel, Maria Elize | van Kruijsbergen, Ila | Mittal, Chitvan | Lieftink, Cor | Brouwer, Ineke | van den Brand, Teun | Kluin, Roelof J.C. | Hoekman, Liesbeth | Menezes, Renée X. | van Welsem, Tibor | ... | van Leeuwen, Fred
Molecular Cell, volume 83, issue 23, pages 4205-4221.e9 (2023).
10.1016/j.molcel.2023.10.037
Cited by (2) | Cite | Source
PEGR: a flexible management platform for reproducible epigenomic and genomic research (journal article)
Shao, Danying | Kellogg, Gretta D. | Nematbakhsh, Ali | Kuntala, Prashant K. | Mahony, Shaun | Pugh, B. Franklin | Lai, William K. M.
Genome Biology, volume 23, issue 1 (2022).
10.1186/s13059-022-02671-5
Cite | Source
An integrated SAGA and TFIID PIC assembly pathway selective for poised and induced promoters (journal article)
Mittal, Chitvan | Lang, Olivia | Lai, William K.M. | Pugh, B. Franklin
Genes & Development (2022).
10.1101/gad.350026.122
Cite | Source
ScriptManager: an interactive platform for reducing barriers to genomics analysis (conference)
Lang, Olivia | Pugh, B Franklin | Lai, William KM
PEARC '22: Practice and Experience in Advanced Research Computing (2022)
Boston MA USA
10.1145/3491418.3535161
Cited by (1) | Cite | Source
Genome-wide promoter assembly in E. coli measured at single-base resolution (journal article)
John, Jordan | Jabbar, Javaid | Badjatia, Nitika | Rossi, Matthew J. | Lai, William K.M. | Pugh, B. Franklin
Genome Research (2022).
10.1101/gr.276544.121
Cite | Source
STENCIL: A web templating engine for visualizing and sharing life science datasets (journal article)
Sun, Qi | Nematbakhsh, Ali | Kuntala, Prashant K. | Kellogg, Gretta | Pugh, B. Franklin | Lai, William K. M.
PLOS Computational Biology, volume 18, issue 2, pages e1009859- (2022).
10.1371/journal.pcbi.1009859
Cite | Source
A ChIP-exo screen of 887 Protein Capture Reagents Program transcription factor antibodies in human cells (journal article)
Lai, William K.M. | Mariani, Luca | Rothschild, Gerson | Smith, Edwin R. | Venters, Bryan J. | Blanda, Thomas R. | Kuntala, Prashant K. | Bocklund, Kylie | Mairose, Joshua | Dweikat, Sarah N. | ... | Pugh, B. Franklin
Genome Research, volume 31, issue 9, pages 1663-1679 (2021).
10.1101/gr.275472.121
Cited by (7) | Cite | Source
What do Transcription Factors Interact With? (journal article)
Chen, Haining | Pugh, B. Franklin
Journal of Molecular Biology, volume 433, issue 14, pages 166883- (2021).
10.1016/j.jmb.2021.166883
Cited by (29) | Cite | Source
Protein architecture of the yeast genome (journal article)
Pugh, B. Franklin
Nature (2021).
10.1038/d41586-021-01118-4
Cite | Source
A high-resolution protein architecture of the budding yeast genome (journal article)
Rossi, Matthew J. | Kuntala, Prashant K. | Lai, William K. M. | Yamada, Naomi | Badjatia, Nitika | Mittal, Chitvan | Kuzu, Guray | Bocklund, Kylie | Farrell, Nina P. | Blanda, Thomas R. | ... | Pugh, B. Franklin
Nature, volume 592, issue 7853, pages 309-314 (2021).
10.1038/s41586-021-03314-8
Cited by (99) | Cite | Source
Universal promoter scanning by Pol II during transcription initiation in Saccharomyces cerevisiae (journal article)
Qiu, Chenxi | Jin, Huiyan | Vvedenskaya, Irina | Llenas, Jordi Abante | Zhao, Tingting | Malik, Indranil | Visbisky, Alex M. | Schwartz, Scott L. | Cui, Ping | Čabart, Pavel | ... | Kaplan, Craig D.
Genome Biology, volume 21, issue 1 (2020).
10.1186/s13059-020-02040-0
Cited by (28) | Cite | Source
Alignment and quantification of ChIP-exo crosslinking patterns reveal the spatial organization of protein–DNA complexes (journal article)
Yamada, Naomi | Rossi, Matthew J | Farrell, Nina | Pugh, B Franklin | Mahony, Shaun
Nucleic Acids Research, volume 48, issue 20, pages 11215-11226 (2020).
10.1093/nar/gkaa618
Cited by (1) | Cite | Source
PEGR: a management platform for ChIP-based next generation sequencing pipelines (conference)
Shao, Danying | Kellogg, Gretta | Mahony, Shaun | Lai, William | Pugh, B. Franklin
PEARC '20: Practice and Experience in Advanced Research Computing (2020)
Portland OR USA
10.1145/3311790.3396621
Cited by (1) | Cite | Source
Phase separation directs ubiquitination of gene-body nucleosomes (journal article)
Gallego, Laura D. | Schneider, Maren | Mittal, Chitvan | Romanauska, Anete | Gudino Carrillo, Ricardo M. | Schubert, Tobias | Pugh, B. Franklin | Köhler, Alwin
Nature, volume 579, issue 7800, pages 592-597 (2020).
10.1038/s41586-020-2097-z
Cited by (89) | Cite | Source
ChExMix: A Method for Identifying and Classifying Protein–DNA Interaction Subtypes (journal article)
Yamada, Naomi | Kuntala, Prashant Kumar | Pugh, B. Franklin | Mahony, Shaun
Journal of Computational Biology, volume 27, issue 3, pages 429-435 (2020).
10.1089/cmb.2019.0466
Cited by (2) | Cite | Source
Characterizing protein–DNA binding event subtypes in ChIP-exo data (journal article)
Yamada, Naomi | Lai, William K M | Farrell, Nina | Pugh, B Franklin | Mahony, Shaun
Bioinformatics, volume 35, issue 6, pages 903-913 (2019).
10.1093/bioinformatics/bty703
Cited by (17) | Cite | Source | Open Access
The SAGA/TREX-2 subunit Sus1 binds widely to transcribed genes and affects mRNA turnover globally (journal article)
García-Molinero, Varinia | García-Martínez, José | Reja, Rohit | Furió-Tarí, Pedro | Antúnez, Oreto | Vinayachandran, Vinesh | Conesa, Ana | Pugh, B. Franklin | Pérez-Ortín, José E. | Rodríguez-Navarro, Susana
Epigenetics & Chromatin, volume 11, issue 1 (2018).
10.1186/s13072-018-0184-2
Cited by (17) | Cite | Source | Open Access
In vivo genome-wide binding interactions of mouse and human constitutive androstane receptors reveal novel gene targets (journal article)
Niu, Ben | Coslo, Denise M | Bataille, Alain R | Albert, Istvan | Pugh, B Franklin | Omiecinski, Curtis J
Nucleic Acids Research, volume 46, issue 16, pages 8385-8403 (2018).
10.1093/nar/gky692
Cited by (24) | Cite | Source | Open Access
Simplified ChIP-exo assays (journal article)
Rossi, Matthew J. | Lai, William K. M. | Pugh, B. Franklin
Nature Communications, volume 9, issue 1 (2018).
10.1038/s41467-018-05265-7
Cited by (53) | Cite | Source | Open Access
Characterizing protein-DNA binding event subtypes in ChIP-exo data (conference)
Yamada, Naomi | Lai, William K.M. | Farrell, Nina | Pugh, B. Franklin | Mahony, Shaun
Research in Computational Molecular Biology (2018)
Paris, France
10.1101/266536
Cited by (3) | Cite | Source | Open Access