Yutao Fu

Yutao Fu

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Yutao Fu

Yutao Fu

Publications by authors named "Yutao Fu"

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27Publications

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ACT: aggregation and correlation toolbox for analyses of genome tracks.

Bioinformatics 2011 Apr 23;27(8):1152-4. Epub 2011 Feb 23.

Program in Computational Biology and Bioinformatics, Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA.

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http://dx.doi.org/10.1093/bioinformatics/btr092DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072554PMC
April 2011

The insulator binding protein CTCF positions 20 nucleosomes around its binding sites across the human genome.

PLoS Genet 2008 Jul 25;4(7):e1000138. Epub 2008 Jul 25.

Bioinformatics Program, Boston University, Boston, Massachusetts, USA.

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http://dx.doi.org/10.1371/journal.pgen.1000138DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2453330PMC
July 2008

Nucleosome positioning signals in genomic DNA.

Genome Res 2007 Aug 9;17(8):1170-7. Epub 2007 Jul 9.

Bioinformatics Program, Boston University, Boston, MA 02215, USA.

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http://www.genome.org/cgi/doi/10.1101/gr.6101007
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http://dx.doi.org/10.1101/gr.6101007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933512PMC
August 2007

Analysis of overrepresented motifs in human core promoters reveals dual regulatory roles of YY1.

Genome Res 2007 Jun;17(6):798-806

Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA.

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http://dx.doi.org/10.1101/gr.5754707DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1891339PMC
June 2007

Transcription factor binding and modified histones in human bidirectional promoters.

Genome Res 2007 Jun;17(6):818-27

Department of Biomedical Engineering, Boston University, Boston, Massachusetts, 02215, USA.

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http://dx.doi.org/10.1101/gr.5623407DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1891341PMC
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

Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome.

Nat Genet 2007 Mar 4;39(3):311-8. Epub 2007 Feb 4.

Ludwig Institute for Cancer Research, University of California San Diego (UCSD) School of Medicine, 9500 Gilman Drive, La Jolla, California 92093-0653 USA.

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http://dx.doi.org/10.1038/ng1966DOI Listing
March 2007

Global mapping of c-Myc binding sites and target gene networks in human B cells.

Proc Natl Acad Sci U S A 2006 Nov 8;103(47):17834-9. Epub 2006 Nov 8.

Department of Medicine and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.

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http://www.pnas.org/cgi/doi/10.1073/pnas.0604129103
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http://dx.doi.org/10.1073/pnas.0604129103DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1635161PMC
November 2006

Improvement of TRANSFAC matrices using multiple local alignment of transcription factor binding site sequences.

Genome Inform 2005 ;16(1):68-72

Bioinformatics Program, Boston University, Boston, MA 02215, USA.

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January 2006

Gene expression module discovery using gibbs sampling.

Genome Inform 2004 ;15(1):239-48

Boston University Bioinformatics Program, Boston, MA 02215, USA.

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May 2005

SeqVISTA: a new module of integrated computational tools for studying transcriptional regulation.

Nucleic Acids Res 2004 Jul;32(Web Server issue):W235-41

Bioinformatics Program, Boston University, 44 Cummington Street, Boston, MA 02215, USA.

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http://dx.doi.org/10.1093/nar/gkh483DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC441621PMC
July 2004

MotifViz: an analysis and visualization tool for motif discovery.

Nucleic Acids Res 2004 Jul;32(Web Server issue):W420-3

Bioinformatics Program, Boston University, Boston, MA 02215, USA.

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http://dx.doi.org/10.1093/nar/gkh426DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC441564PMC
July 2004

Detection of functional DNA motifs via statistical over-representation.

Nucleic Acids Res 2004 26;32(4):1372-81. Epub 2004 Feb 26.

Bioinformatics Program, Boston University, 44 Cummington Street, Boston, MA 02215, USA.

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http://dx.doi.org/10.1093/nar/gkh299DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC390287PMC
June 2004

Protistan grazing analysis by flow cytometry using prey labeled by in vivo expression of fluorescent proteins.

Appl Environ Microbiol 2003 Nov;69(11):6848-55

Bigelow Laboratory for Ocean Sciences, West Boothbay Harbor, Maine 04575, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC262319PMC
http://dx.doi.org/10.1128/aem.69.11.6848-6855.2003DOI Listing
November 2003