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Franklin Pugh

Research Profile

Genes & Molecular Sequences

Genome, Fungal

Living Beings

Saccharomyces cerevisiae

Chemicals & Drugs

Physiology

Procedures

Chromatin Immunoprecipitation

Co-author Network

Publications

TOP 3
B Franklin Pugh
Molecular biology: The ends justify the means.
Ho Sung Rhee; B Franklin Pugh
ChIP-exo method for identifying genomic location of DNA-binding proteins with near-single-nucleotide accuracy.
Jessica M Bryant; Greg Donahue; Jérôme Govin; B Franklin Pugh; Liye Zhang; Shelley L Berger
The linker histone plays a dual role during gametogenesis in Saccharomyces cerevisiae.

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All Publications

2013: B Franklin Pugh
Molecular biology: The ends justify the means.
Nature 2013;497(7447):48-9.
2012: Ho Sung Rhee; B Franklin Pugh
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.] 2012;Chapter 21():Unit 21.24.
2012: Jessica M Bryant; Greg Donahue; Jérôme Govin; B Franklin Pugh; Liye Zhang; Shelley L Berger
The linker histone plays a dual role during gametogenesis in Saccharomyces cerevisiae.
Molecular and cellular biology 2012;32(14):2771-83.
2012: Kuangyu Yen; Vinesh Vinayachandran; Kiran Batta; R Thomas Koerber; B Franklin Pugh
Genome-wide nucleosome specificity and directionality of chromatin remodelers.
Cell 2012;149(7):1461-73.
2012: Gue Su Chang; Ludwig Eichinger; Marius Felder; Gernot Glöckner; Cizhong Jiang; Travis N Mavrich; Rolf Müller; Angelika A Noegel; Stephan C Schuster; Lynn P Tomsho; Elissa Ward; B Franklin Pugh
Unusual combinatorial involvement of poly-A/T tracts in organizing genes and chromatin in Dictyostelium.
Genome research 2012;22(6):1098-106.
2012: Jung-Shin Lee; B Franklin Pugh; Christopher Seidel; Alexander S Garrett; Deqing Hu; Jessica Jackson; Yoh-hei Takahashi; Kuangyu Yen; Ali Shilatifard
Codependency of H2B monoubiquitination and nucleosome reassembly on Chd1.
Genes & development 2012;26(9):914-9.
2012: Ho Sung Rhee; B Franklin Pugh
Genome-wide structure and organization of eukaryotic pre-initiation complexes.
Nature 2012;483(7389):295-301.
2012: Megha Wal; B Franklin Pugh
Genome-wide mapping of nucleosome positions in yeast using high-resolution MNase ChIP-Seq.
Methods in enzymology 2012;513():233-50.
2011: Kiran Batta; David B Goffman; Kuangyu Yen; Zhenhai Zhang; B Franklin Pugh
Genome-wide function of H2B ubiquitylation in promoter and genic regions.
Genes & development 2011;25(21):2254-65.
2011: Payel Sen; Sujana Ghosh; B Franklin Pugh; Blaine Bartholomew
A new, highly conserved domain in Swi2/Snf2 is required for SWI/SNF remodeling.
Nucleic acids research 2011;39(21):9155-66.
2011: Ilya Ioshikhes; Sergey Hosid; B Franklin Pugh
Variety of genomic DNA patterns for nucleosome positioning.
Genome research 2011;21(11):1863-71.
2011: Liye Zhang; Hong Ma; B Franklin Pugh
Stable and dynamic nucleosome states during a meiotic developmental process.
Genome research 2011;21(6):875-84.
2011: Bryan J Venters; Jordan D Irvin; Paul Gramlich; B Franklin Pugh
Genome-wide transcriptional dependence on conserved regions of Mot1.
Molecular and cellular biology 2011;31(11):2253-61.
2011: Zhenhai Zhang; Christian J Wippo; Megha Wal; Elissa Ward; Philipp Korber; B Franklin Pugh
A packing mechanism for nucleosome organization reconstituted across a eukaryotic genome.
Science (New York, N.Y.) 2011;332(6032):977-80.
2011: Bryan J Venters; Shinichiro Wachi; Travis N Mavrich; Barbara E Andersen; Peony Jena; Andrew J Sinnamon; Priyanka Jain; Noah S Rolleri; Cizhong Jiang; Christine Hemeryck-Walsh; B Franklin Pugh
A comprehensive genomic binding map of gene and chromatin regulatory proteins in Saccharomyces.
Molecular cell 2011;41(4):480-92.
2011: Zhenhai Zhang; B Franklin Pugh
High-resolution genome-wide mapping of the primary structure of chromatin.
Cell 2011;144(2):175-86.
2011: Zhenhai Zhang; B Franklin Pugh
Genomic organization of H2Av containing nucleosomes in Drosophila heterochromatin.
PloS one 2011;6(6):e20511.
2011: Sujana Ghosh; B Franklin Pugh
Sequential recruitment of SAGA and TFIID in a genomic response to DNA damage in Saccharomyces cerevisiae.
Molecular and cellular biology 2011;31(1):190-202.
2010: B Franklin Pugh
A preoccupied position on nucleosomes.
Nature structural & molecular biology 2010;17(8):923.
2010: Eric Samorodnitsky; B Franklin Pugh
Genome-wide modeling of transcription preinitiation complex disassembly mechanisms using ChIP-chip data.
PLoS computational biology 2010;6(4):e1000733.
2009: R Thomas Koerber; Ho Sung Rhee; Cizhong Jiang; B Franklin Pugh
Interaction of transcriptional regulators with specific nucleosomes across the Saccharomyces genome.
Molecular cell 2009;35(6):889-902.
2009: Bryan J Venters; B Franklin Pugh
How eukaryotic genes are transcribed.
Critical reviews in biochemistry and molecular biology 2009;44(2-3):117-41.
2009: Cizhong Jiang; B Franklin Pugh
Nucleosome positioning and gene regulation: advances through genomics.
Nature reviews. Genetics 2009;10(3):161-72.
2009: Bryan J Venters; B Franklin Pugh
A canonical promoter organization of the transcription machinery and its regulators in the Saccharomyces genome.
Genome research 2009;19(3):360-71.
2009: Cizhong Jiang; B Franklin Pugh
A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae genome.
Genome biology 2009;10(10):R109.
2008: Hongjie Yao; Pingxin Li; Bryan J Venters; Suting Zheng; Paul R Thompson; B Franklin Pugh; Yanming Wang
Histone Arg modifications and p53 regulate the expression of OKL38, a mediator of apoptosis.
The Journal of biological chemistry 2008;283(29):20060-8.
2008: Travis N Mavrich; Ilya P Ioshikhes; Bryan J Venters; Cizhong Jiang; Lynn P Tomsho; Ji Qi; Stephan C Schuster; Istvan Albert; B Franklin Pugh
A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome.
Genome research 2008;18(7):1073-83.
2008: Travis N Mavrich; Cizhong Jiang; Ilya P Ioshikhes; Xiaoyong Li; Bryan J Venters; Sara J Zanton; Lynn P Tomsho; Ji Qi; Robert L Glaser; Stephan C Schuster; David S Gilmour; Istvan Albert; B Franklin Pugh
Nucleosome organization in the Drosophila genome.
Nature 2008;453(7193):358-62.
2008: Istvan Albert; Shinichiro Wachi; Cizhong Jiang; B Franklin Pugh
GeneTrack--a genomic data processing and visualization framework.
Bioinformatics (Oxford, England) 2008;24(10):1305-6.
2008: Chanhyo Lee; Xiaoyong Li; Aaron Hechmer; Michael Eisen; Mark D Biggin; Bryan J Venters; Cizhong Jiang; Jian Li; B Franklin Pugh; David S Gilmour
NELF and GAGA factor are linked to promoter-proximal pausing at many genes in Drosophila.
Molecular and cellular biology 2008;28(10):3290-300.
2008: Yousry Y Azmy; Anshuman Gupta; B Franklin Pugh
Computational modelling of genome-wide [corrected] transcription assembly networks using a fluidics analogy.
PloS one 2008;3(8):e3095.
2007: Melissa Durant; B Franklin Pugh
NuA4-directed chromatin transactions throughout the Saccharomyces cerevisiae genome.
Molecular and cellular biology 2007;27(15):5327-35.
2007: Istvan Albert; Travis N Mavrich; Lynn P Tomsho; Ji Qi; Sara J Zanton; Stephan C Schuster; B Franklin Pugh
Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome.
Nature 2007;446(7135):572-6.
2007: Bryan J Venters; B Franklin Pugh
Chromatin meets RNA polymerase II.
Genome biology 2007;8(11):319.
2007: Kathryn L Huisinga; B Franklin Pugh
A TATA binding protein regulatory network that governs transcription complex assembly.
Genome biology 2007;8(4):R46.
2006: Ilya P Ioshikhes; Istvan Albert; Sara J Zanton; B Franklin Pugh
Nucleosome positions predicted through comparative genomics.
Nature genetics 2006;38(10):1210-5.
2006: B Franklin Pugh
HATs off to PIC assembly.
Molecular cell 2006;23(6):776-7.
2006: Sara J Zanton; B Franklin Pugh
Full and partial genome-wide assembly and disassembly of the yeast transcription machinery in response to heat shock.
Genes & development 2006;20(16):2250-65.
2006: Melissa Durant; B Franklin Pugh
Genome-wide relationships between TAF1 and histone acetyltransferases in Saccharomyces cerevisiae.
Molecular and cellular biology 2006;26(7):2791-802.
2006: Jordan D Irvin; B Franklin Pugh
Genome-wide transcriptional dependence on TAF1 functional domains.
The Journal of biological chemistry 2006;281(10):6404-12.
2004: Sara J Zanton; B Franklin Pugh
Changes in genomewide occupancy of core transcriptional regulators during heat stress.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(48):16843-8.
2004: Diane E Alexander; David J Kaczorowski; Amy J Jackson-Fisher; Drew M Lowery; Sara J Zanton; B Franklin Pugh
Inhibition of TATA binding protein dimerization by RNA polymerase III transcription initiation factor Brf1.
The Journal of biological chemistry 2004;279(31):32401-6.
2004: Haiping Kou; B Franklin Pugh
Engineering dimer-stabilizing mutations in the TATA-binding protein.
The Journal of biological chemistry 2004;279(20):20966-73.
2004: B Franklin Pugh
Is acetylation the key to opening locked gates?
Nature structural & molecular biology 2004;11(4):298-300.
2004: Andrew D Basehoar; Sara J Zanton; B Franklin Pugh
Identification and distinct regulation of yeast TATA box-containing genes.
Cell 2004;116(5):699-709.
2004: Kathryn L Huisinga; B Franklin Pugh
A genome-wide housekeeping role for TFIID and a highly regulated stress-related role for SAGA in Saccharomyces cerevisiae.
Molecular cell 2004;13(4):573-85.
2003: Haiping Kou; Jordan D Irvin; Kathryn L Huisinga; Madhusmita Mitra; B Franklin Pugh
Structural and functional analysis of mutations along the crystallographic dimer interface of the yeast TATA binding protein.
Molecular and cellular biology 2003;23(9):3186-201.
2002: Carmelata Chitikila; Kathryn L Huisinga; Jordan D Irvin; Andrew D Basehoar; B Franklin Pugh
Interplay of TBP inhibitors in global transcriptional control.
Molecular cell 2002;10(4):871-82.
2001: B Franklin Pugh; D S Gilmour
Genome-wide analysis of protein-DNA interactions in living cells.
Genome biology 2001;2(4):REVIEWS1013.
2000: B Franklin Pugh
Control of gene expression through regulation of the TATA-binding protein.
Gene 2000;255(1):1-14.
1999: Robert A. Coleman; A K Taggart; S Burma; J J Chicca; B Franklin Pugh
TFIIA regulates TBP and TFIID dimers.
Molecular cell 1999;4(3):451-7.
1999: Amy J Jackson-Fisher; S Burma; M Portnoy; Lumelle Schneeweis; Robert A. Coleman; Madhusmita Mitra; Carmelata Chitikila; B Franklin Pugh
Dimer dissociation and thermosensitivity kinetics of the Saccharomyces cerevisiae and human TATA binding proteins.
Biochemistry 1999;38(35):11340-8.
1999: Amy J Jackson-Fisher; Carmelata Chitikila; Madhusmita Mitra; B Franklin Pugh
A role for TBP dimerization in preventing unregulated gene expression.
Molecular cell 1999;3(6):717-27.
1998: J J Chicca; D T Auble; B Franklin Pugh
Cloning and biochemical characterization of TAF-172, a human homolog of yeast Mot1.
Molecular and cellular biology 1998;18(3):1701-10.
1997: C A Weideman; R C Netter; Lawrence R Benjamin; J J McAllister; Lumelle Schneeweis; Robert A. Coleman; B Franklin Pugh
Dynamic interplay of TFIIA, TBP and TATA DNA.
Journal of molecular biology 1997;271(1):61-75.
1997: Robert A. Coleman; B Franklin Pugh
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 1997;94(14):7221-6.
1997: B L Booth; B Franklin Pugh
Identification and characterization of a nuclease specific for the 3' end of the U6 small nuclear RNA.
The Journal of biological chemistry 1997;272(2):984-91.
1996: B Franklin Pugh
Mechanisms of transcription complex assembly.
Current opinion in cell biology 1996;8(3):303-11.
1996: A K Taggart; B Franklin Pugh
Dimerization of TFIID when not bound to DNA.
Science (New York, N.Y.) 1996;272(5266):1331-3.
1995: Robert A. Coleman; B Franklin Pugh
Evidence for functional binding and stable sliding of the TATA binding protein on nonspecific DNA.
The Journal of biological chemistry 1995;270(23):13850-9.
1995: Robert A. Coleman; A K Taggart; L R Benjamin; B Franklin Pugh
Dimerization of the TATA binding protein.
The Journal of biological chemistry 1995;270(23):13842-9.
1995: A J Jackson; M Ittmann; B Franklin Pugh
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 1995;15(1):94-101.
1995: B Franklin Pugh
Purification of the human TATA-binding protein, TBP.
Methods in molecular biology (Clifton, N.J.) 1995;37():359-67.
1995: B Franklin Pugh
Preparation of HeLa nuclear extracts.
Methods in molecular biology (Clifton, N.J.) 1995;37():349-57.
1992: A K Taggart; T S Fisher; B Franklin Pugh
The TATA-binding protein and associated factors are components of pol III transcription factor TFIIIB.
Cell 1992;71(6):1015-28.