Thomas D Tullius

Thomas D Tullius

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Thomas D Tullius

Thomas D Tullius

Publications by authors named "Thomas D Tullius"

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GBshape: a genome browser database for DNA shape annotations.

Nucleic Acids Res 2015 Jan 17;43(Database issue):D103-9. Epub 2014 Oct 17.

Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA Departments of Chemistry, Physics, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA

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http://dx.doi.org/10.1093/nar/gku977DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4384032PMC
January 2015

Chemical probing of RNA with the hydroxyl radical at single-atom resolution.

Nucleic Acids Res 2014 Nov 13;42(20):12758-67. Epub 2014 Oct 13.

Department of Chemistry, Boston University, Boston, MA 02215, USA Program in Bioinformatics, Boston University, Boston, MA 02215, USA

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http://dx.doi.org/10.1093/nar/gku934DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4227780PMC
November 2014

Comparative analysis of metazoan chromatin organization.

Nature 2014 Aug;512(7515):449-52

1] Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA [2] Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA [3] Informatics Program, Children's Hospital, Boston, Massachusetts 02215, USA.

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http://dx.doi.org/10.1038/nature13415DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4227084PMC
August 2014

A computational method to search for DNA structural motifs in functional genomic elements.

Methods Mol Biol 2011 ;759:367-79

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

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http://dx.doi.org/10.1007/978-1-61779-173-4_21DOI Listing
December 2011

DNA shape, genetic codes, and evolution.

Curr Opin Struct Biol 2011 Jun 23;21(3):342-7. Epub 2011 Mar 23.

Genome Informatics Section, Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.

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http://dx.doi.org/10.1016/j.sbi.2011.03.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3112471PMC
June 2011

The relationship between fine scale DNA structure, GC content, and functional elements in 1% of the human genome.

Genome Inform 2008 ;20:199-211

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

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July 2009

Local DNA topography correlates with functional noncoding regions of the human genome.

Science 2009 Apr 12;324(5925):389-92. Epub 2009 Mar 12.

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

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http://dx.doi.org/10.1126/science.1169050DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2749491PMC
April 2009

Footprinting protein-DNA complexes using the hydroxyl radical.

Nat Protoc 2008 ;3(6):1092-1100

Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, USA.

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http://dx.doi.org/10.1038/nprot.2008.72DOI Listing
September 2008

Effects of discontinuities in the DNA template on abortive initiation and promoter escape by Escherichia coli RNA polymerase.

J Biol Chem 2007 Sep 24;282(37):26917-27. Epub 2007 Jul 24.

Department of Chemistry, Boston University, Boston, MA 02215, USA.

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http://dx.doi.org/10.1074/jbc.M702473200DOI Listing
September 2007

Detection of DNA structural motifs in functional genomic elements.

Genome Res 2007 Jun;17(6):940-6

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

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http://www.genome.org/cgi/doi/10.1101/gr.5602807
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http://dx.doi.org/10.1101/gr.5602807DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1891352PMC
June 2007

Construction of a genome-scale structural map at single-nucleotide resolution.

Genome Res 2007 Jun;17(6):947-53

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

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http://dx.doi.org/10.1101/gr.6073107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1891353PMC
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

Platinum anticancer drug damage enforces a particular rotational setting of DNA in nucleosomes.

Proc Natl Acad Sci U S A 2005 Aug 22;102(35):12311-6. Epub 2005 Aug 22.

Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1073/pnas.0506025102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1194956PMC
August 2005

Mapping nucleic acid structure by hydroxyl radical cleavage.

Curr Opin Chem Biol 2005 Apr;9(2):127-34

Department of Chemistry, Boston University, Boston MA 02215, USA.

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http://dx.doi.org/10.1016/j.cbpa.2005.02.009DOI Listing
April 2005

Gapped DNA is anisotropically bent.

Proc Natl Acad Sci U S A 2003 Apr 18;100(7):3743-7. Epub 2003 Mar 18.

Protometrix, Inc., 66 High Street, Guilford, CT 06437, USA.

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http://dx.doi.org/10.1073/pnas.0737062100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC152992PMC
April 2003

A general synthesis of specifically deuterated nucleotides for studies of DNA and RNA.

Bioorg Med Chem Lett 2002 Nov;12(21):3093-6

Department of Chemistry, Boston University, Boston, MA 02215, USA.

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http://dx.doi.org/10.1016/s0960-894x(02)00650-9DOI Listing
November 2002

Interchange of DNA-binding modes in the deformed and ultrabithorax homeodomains: a structural role for the N-terminal arm.

J Mol Biol 2002 Nov;323(4):665-83

Department of Chemistry, University of Michigan-Flint, Flint, MI 48502, USA.

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http://dx.doi.org/10.1016/s0022-2836(02)00996-8DOI Listing
November 2002

Probing DNA structure with hydroxyl radicals.

Authors:
Thomas D Tullius

Curr Protoc Nucleic Acid Chem 2002 Feb;Chapter 6:Unit 6.7

Boston University, Boston, Massachussetts, USA.

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http://dx.doi.org/10.1002/0471142700.nc0607s07DOI Listing
February 2002

Oxidative Strand Scission of Nucleic Acids: Routes Initiated by Hydrogen Abstraction from the Sugar Moiety.

Chem Rev 1998 May;98(3):1089-1108

Department of Chemistry, State University of New York at Geneseo, Geneseo, New York 14454, and Department of Chemistry, Boston University, Boston, Massachusetts 02215.

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http://dx.doi.org/10.1021/cr960437iDOI Listing
May 1998