Paul G Giresi

Paul G Giresi

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Paul G Giresi

Paul G Giresi

Publications by authors named "Paul G Giresi"

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Chromatin Accessibility Landscape of Cutaneous T Cell Lymphoma and Dynamic Response to HDAC Inhibitors.

Cancer Cell 2017 07 15;32(1):27-41.e4. Epub 2017 Jun 15.

Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University School of Medicine, CCSR 2155c, 269 Campus Drive, Stanford, CA 94305-5168, USA; Department of Dermatology, Stanford University School of Medicine, Stanford, CA 94305, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ccell.2017.05.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5559384PMC
July 2017

A novel ATAC-seq approach reveals lineage-specific reinforcement of the open chromatin landscape via cooperation between BAF and p63.

Genome Biol 2015 Dec 18;16:284. Epub 2015 Dec 18.

Program in Epithelial Biology, Stanford University, 269 Campus Drive, Stanford, CA, 94305, USA.

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http://dx.doi.org/10.1186/s13059-015-0840-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4699366PMC
December 2015

Individuality and variation of personal regulomes in primary human T cells.

Cell Syst 2015 Jul;1(1):51-61

Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305.

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http://dx.doi.org/10.1016/j.cels.2015.06.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4522940PMC
July 2015

STAT3 acts through pre-existing nucleosome-depleted regions bound by FOS during an epigenetic switch linking inflammation to cancer.

Epigenetics Chromatin 2015 14;8. Epub 2015 Feb 14.

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115 USA.

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http://dx.doi.org/10.1186/1756-8935-8-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4362815PMC
March 2015

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position.

Nat Methods 2013 Dec 6;10(12):1213-8. Epub 2013 Oct 6.

1] Department of Genetics, Stanford University School of Medicine, Stanford, California, USA. [2] Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, USA. [3] Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA.

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http://greenleaf.stanford.edu/assets/pdf/buenrostro_2013_nat
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http://dx.doi.org/10.1038/nmeth.2688DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3959825PMC
December 2013

Hierarchical mechanisms for direct reprogramming of fibroblasts to neurons.

Cell 2013 Oct 24;155(3):621-35. Epub 2013 Oct 24.

Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University, Stanford, CA 94305, USA; Program in Cancer Biology, Stanford University, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1016/j.cell.2013.09.028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3871197PMC
October 2013

A detailed protocol for formaldehyde-assisted isolation of regulatory elements (FAIRE).

Curr Protoc Mol Biol 2013 ;Chapter 21:Unit21.26

Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.

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http://dx.doi.org/10.1002/0471142727.mb2126s102DOI Listing
June 2013

Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA.

Nat Protoc 2012 Jan 19;7(2):256-67. Epub 2012 Jan 19.

Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.

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http://dx.doi.org/10.1038/nprot.2011.444DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3784247PMC
January 2012

ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions.

Genome Biol 2011 Jul 25;12(7):R67. Epub 2011 Jul 25.

Department of Biostatistics, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.

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http://dx.doi.org/10.1186/gb-2011-12-7-r67DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3218829PMC
July 2011

Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements).

Methods 2009 Jul 18;48(3):233-9. Epub 2009 Mar 18.

Department of Biology and Carolina Center for the Genome Sciences, University of North Carolina at Chapel Hill, CB #3280, 408 Fordham Hall, Chapel Hill, NC 27599-3280, USA.

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http://linkinghub.elsevier.com/retrieve/pii/S104620230900050
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http://dx.doi.org/10.1016/j.ymeth.2009.03.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2710428PMC
July 2009

FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin.

Genome Res 2007 Jun 19;17(6):877-85. Epub 2006 Dec 19.

Department of Biology and the Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3280, USA.

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http://dx.doi.org/10.1101/gr.5533506DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1891346PMC
June 2007

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

Authors:
Ewan Birney John A Stamatoyannopoulos Anindya Dutta Roderic Guigó Thomas R Gingeras Elliott H Margulies Zhiping Weng Michael Snyder Emmanouil T Dermitzakis Robert E Thurman Michael S Kuehn Christopher M Taylor Shane Neph Christoph M Koch Saurabh Asthana Ankit Malhotra Ivan Adzhubei Jason A Greenbaum Robert M Andrews Paul Flicek Patrick J Boyle Hua Cao Nigel P Carter Gayle K Clelland Sean Davis Nathan Day Pawandeep Dhami Shane C Dillon Michael O Dorschner Heike Fiegler Paul G Giresi Jeff Goldy Michael Hawrylycz Andrew Haydock Richard Humbert Keith D James Brett E Johnson Ericka M Johnson Tristan T Frum Elizabeth R Rosenzweig Neerja Karnani Kirsten Lee Gregory C Lefebvre Patrick A Navas Fidencio Neri Stephen C J Parker Peter J Sabo Richard Sandstrom Anthony Shafer David Vetrie Molly Weaver Sarah Wilcox Man Yu Francis S Collins Job Dekker Jason D Lieb Thomas D Tullius Gregory E Crawford Shamil Sunyaev William S Noble Ian Dunham France Denoeud Alexandre Reymond Philipp Kapranov Joel Rozowsky Deyou Zheng Robert Castelo Adam Frankish Jennifer Harrow Srinka Ghosh Albin Sandelin Ivo L Hofacker Robert Baertsch Damian Keefe Sujit Dike Jill Cheng Heather A Hirsch Edward A Sekinger Julien Lagarde Josep F Abril Atif Shahab Christoph Flamm Claudia Fried Jörg Hackermüller Jana Hertel Manja Lindemeyer Kristin Missal Andrea Tanzer Stefan Washietl Jan Korbel Olof Emanuelsson Jakob S Pedersen Nancy Holroyd Ruth Taylor David Swarbreck Nicholas Matthews Mark C Dickson Daryl J Thomas Matthew T Weirauch James Gilbert Jorg Drenkow Ian Bell XiaoDong Zhao K G Srinivasan Wing-Kin Sung Hong Sain Ooi Kuo Ping Chiu Sylvain Foissac Tyler Alioto Michael Brent Lior Pachter Michael L Tress Alfonso Valencia Siew Woh Choo Chiou Yu Choo Catherine Ucla Caroline Manzano Carine Wyss Evelyn Cheung Taane G Clark James B Brown Madhavan Ganesh Sandeep Patel Hari Tammana Jacqueline Chrast Charlotte N Henrichsen Chikatoshi Kai Jun Kawai Ugrappa Nagalakshmi Jiaqian Wu Zheng Lian Jin Lian Peter Newburger Xueqing Zhang Peter Bickel John S Mattick Piero Carninci Yoshihide Hayashizaki Sherman Weissman Tim Hubbard Richard M Myers Jane Rogers Peter F Stadler Todd M Lowe Chia-Lin Wei Yijun Ruan Kevin Struhl Mark Gerstein Stylianos E Antonarakis Yutao Fu Eric D Green Ulaş Karaöz Adam Siepel James Taylor Laura A Liefer Kris A Wetterstrand Peter J Good Elise A Feingold Mark S Guyer Gregory M Cooper George Asimenos Colin N Dewey Minmei Hou Sergey Nikolaev Juan I Montoya-Burgos Ari Löytynoja Simon Whelan Fabio Pardi Tim Massingham Haiyan Huang Nancy R Zhang Ian Holmes James C Mullikin Abel Ureta-Vidal Benedict Paten Michael Seringhaus Deanna Church Kate Rosenbloom W James Kent Eric A Stone Serafim Batzoglou Nick Goldman Ross C Hardison David Haussler Webb Miller Arend Sidow Nathan D Trinklein Zhengdong D Zhang Leah Barrera Rhona Stuart David C King Adam Ameur Stefan Enroth Mark C Bieda Jonghwan Kim Akshay A Bhinge Nan Jiang Jun Liu Fei Yao Vinsensius B Vega Charlie W H Lee Patrick Ng Atif Shahab Annie Yang Zarmik Moqtaderi Zhou Zhu Xiaoqin Xu Sharon Squazzo Matthew J Oberley David Inman Michael A Singer Todd A Richmond Kyle J Munn Alvaro Rada-Iglesias Ola Wallerman Jan Komorowski Joanna C Fowler Phillippe Couttet Alexander W Bruce Oliver M Dovey Peter D Ellis Cordelia F Langford David A Nix Ghia Euskirchen Stephen Hartman Alexander E Urban Peter Kraus Sara Van Calcar Nate Heintzman Tae Hoon Kim Kun Wang Chunxu Qu Gary Hon Rosa Luna Christopher K Glass M Geoff Rosenfeld Shelley Force Aldred Sara J Cooper Anason Halees Jane M Lin Hennady P Shulha Xiaoling Zhang Mousheng Xu Jaafar N S Haidar Yong Yu Yijun Ruan Vishwanath R Iyer Roland D Green Claes Wadelius Peggy J Farnham Bing Ren Rachel A Harte Angie S Hinrichs Heather Trumbower Hiram Clawson Jennifer Hillman-Jackson Ann S Zweig Kayla Smith Archana Thakkapallayil Galt Barber Robert M Kuhn Donna Karolchik Lluis Armengol Christine P Bird Paul I W de Bakker Andrew D Kern Nuria Lopez-Bigas Joel D Martin Barbara E Stranger Abigail Woodroffe Eugene Davydov Antigone Dimas Eduardo Eyras Ingileif B Hallgrímsdóttir Julian Huppert Michael C Zody Gonçalo R Abecasis Xavier Estivill Gerard G Bouffard Xiaobin Guan Nancy F Hansen Jacquelyn R Idol Valerie V B Maduro Baishali Maskeri Jennifer C McDowell Morgan Park Pamela J Thomas Alice C Young Robert W Blakesley Donna M Muzny Erica Sodergren David A Wheeler Kim C Worley Huaiyang Jiang George M Weinstock Richard A Gibbs Tina Graves Robert Fulton Elaine R Mardis Richard K Wilson Michele Clamp James Cuff Sante Gnerre David B Jaffe Jean L Chang Kerstin Lindblad-Toh Eric S Lander Maxim Koriabine Mikhail Nefedov Kazutoyo Osoegawa Yuko Yoshinaga Baoli Zhu Pieter J de Jong
June 2007

X chromosome repression by localization of the C. elegans dosage compensation machinery to sites of transcription initiation.

Nat Genet 2007 Mar 11;39(3):403-8. Epub 2007 Feb 11.

Department of Biology and Carolina Center for the Genome Sciences, 202 Fordham Hall, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3280, USA.

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http://www.nature.com/articles/ng1983
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http://dx.doi.org/10.1038/ng1983DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2753834PMC
March 2007

How to find an opening (or lots of them).

Nat Methods 2006 Jul;3(7):501-2

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http://dx.doi.org/10.1038/nmeth0706-501DOI Listing
July 2006

Regulation of nucleosome stability as a mediator of chromatin function.

Curr Opin Genet Dev 2006 Apr 28;16(2):171-6. Epub 2006 Feb 28.

Department of Biology and Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA.

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http://linkinghub.elsevier.com/retrieve/pii/S0959437X0600025
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http://dx.doi.org/10.1016/j.gde.2006.02.003DOI Listing
April 2006

Transcriptional profile of a myotube starvation model of atrophy.

J Appl Physiol (1985) 2005 Apr 17;98(4):1396-406. Epub 2004 Dec 17.

Dept. of Health Sciences, Boston Univ., 635 Commonwealth Ave., Boston, MA 02215, USA.

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http://dx.doi.org/10.1152/japplphysiol.01055.2004DOI Listing
April 2005

Identification of a molecular signature of sarcopenia.

Physiol Genomics 2005 Apr 1;21(2):253-63. Epub 2005 Feb 1.

Department of Health Sciences, Boston University, Boston, Massachusetts, USA.

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http://dx.doi.org/10.1152/physiolgenomics.00249.2004DOI Listing
April 2005

Global analysis of gene expression patterns during disuse atrophy in rat skeletal muscle.

J Physiol 2003 Aug 4;551(Pt 1):33-48. Epub 2003 Jul 4.

Department of Health Sciences, Boston University, 635 Commonwealth Avenue, Boston, MA 02215, USA.

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http://dx.doi.org/10.1113/jphysiol.2003.044701DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2343139PMC
August 2003