Thomas R Gingeras

Thomas R Gingeras

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Thomas R Gingeras

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Genome-wide analysis of polymerase III-transcribed elements suggests cell-type-specific enhancer function.

Genome Res 2019 09 14;29(9):1402-1414. Epub 2019 Aug 14.

Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.

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http://dx.doi.org/10.1101/gr.249789.119DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6724667PMC
September 2019

The fractured landscape of RNA-seq alignment: the default in our STARs.

Nucleic Acids Res 2018 06;46(10):5125-5138

Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Woodbury, NY 11797, USA.

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http://dx.doi.org/10.1093/nar/gky325DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6007662PMC
June 2018

Optimizing RNA-Seq Mapping with STAR.

Methods Mol Biol 2016 ;1415:245-62

Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY, 11746, USA.

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http://dx.doi.org/10.1007/978-1-4939-3572-7_13DOI Listing
December 2017

High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing.

Nat Genet 2017 Dec 6;49(12):1731-1740. Epub 2017 Nov 6.

Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.

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http://dx.doi.org/10.1038/ng.3988DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5709232PMC
December 2017

Conserved noncoding transcription and core promoter regulatory code in early development.

Elife 2017 12 20;6. Epub 2017 Dec 20.

Watson School of Biological Sciences, Cold Spring Harbor Laboratory, New York, United States.

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http://dx.doi.org/10.7554/eLife.29005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5754203PMC
December 2017

Comparative transcriptomics in human and mouse.

Nat Rev Genet 2017 07 8;18(7):425-440. Epub 2017 May 8.

Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain.

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http://dx.doi.org/10.1038/nrg.2017.19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6413734PMC
July 2017

Gene-specific patterns of expression variation across organs and species.

Genome Biol 2016 07 8;17(1):151. Epub 2016 Jul 8.

Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.

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http://dx.doi.org/10.1186/s13059-016-1008-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4937605PMC
July 2016

Extracellular vesicle-mediated transfer of processed and functional RNY5 RNA.

RNA 2015 Nov 21;21(11):1966-79. Epub 2015 Sep 21.

Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.

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http://dx.doi.org/10.1261/rna.053629.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4604435PMC
November 2015

Multiplicity of 5' cap structures present on short RNAs.

PLoS One 2014 31;9(7):e102895. Epub 2014 Jul 31.

RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Japan; RIKEN Omics Science Center, Yokohama, Kanagawa, Japan.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0102895PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4117478PMC
October 2015

Mapping RNA-seq Reads with STAR.

Curr Protoc Bioinformatics 2015 Sep 3;51:11.14.1-11.14.19. Epub 2015 Sep 3.

Cold Spring Harbor Laboratory, Cold Spring Harbor, New York.

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http://dx.doi.org/10.1002/0471250953.bi1114s51DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4631051PMC
September 2015

A comparative encyclopedia of DNA elements in the mouse genome.

Authors:
Feng Yue Yong Cheng Alessandra Breschi Jeff Vierstra Weisheng Wu Tyrone Ryba Richard Sandstrom Zhihai Ma Carrie Davis Benjamin D Pope Yin Shen Dmitri D Pervouchine Sarah Djebali Robert E Thurman Rajinder Kaul Eric Rynes Anthony Kirilusha Georgi K Marinov Brian A Williams Diane Trout Henry Amrhein Katherine Fisher-Aylor Igor Antoshechkin Gilberto DeSalvo Lei-Hoon See Meagan Fastuca Jorg Drenkow Chris Zaleski Alex Dobin Pablo Prieto Julien Lagarde Giovanni Bussotti Andrea Tanzer Olgert Denas Kanwei Li M A Bender Miaohua Zhang Rachel Byron Mark T Groudine David McCleary Long Pham Zhen Ye Samantha Kuan Lee Edsall Yi-Chieh Wu Matthew D Rasmussen Mukul S Bansal Manolis Kellis Cheryl A Keller Christapher S Morrissey Tejaswini Mishra Deepti Jain Nergiz Dogan Robert S Harris Philip Cayting Trupti Kawli Alan P Boyle Ghia Euskirchen Anshul Kundaje Shin Lin Yiing Lin Camden Jansen Venkat S Malladi Melissa S Cline Drew T Erickson Vanessa M Kirkup Katrina Learned Cricket A Sloan Kate R Rosenbloom Beatriz Lacerda de Sousa Kathryn Beal Miguel Pignatelli Paul Flicek Jin Lian Tamer Kahveci Dongwon Lee W James Kent Miguel Ramalho Santos Javier Herrero Cedric Notredame Audra Johnson Shinny Vong Kristen Lee Daniel Bates Fidencio Neri Morgan Diegel Theresa Canfield Peter J Sabo Matthew S Wilken Thomas A Reh Erika Giste Anthony Shafer Tanya Kutyavin Eric Haugen Douglas Dunn Alex P Reynolds Shane Neph Richard Humbert R Scott Hansen Marella De Bruijn Licia Selleri Alexander Rudensky Steven Josefowicz Robert Samstein Evan E Eichler Stuart H Orkin Dana Levasseur Thalia Papayannopoulou Kai-Hsin Chang Arthur Skoultchi Srikanta Gosh Christine Disteche Piper Treuting Yanli Wang Mitchell J Weiss Gerd A Blobel Xiaoyi Cao Sheng Zhong Ting Wang Peter J Good Rebecca F Lowdon Leslie B Adams Xiao-Qiao Zhou Michael J Pazin Elise A Feingold Barbara Wold James Taylor Ali Mortazavi Sherman M Weissman John A Stamatoyannopoulos Michael P Snyder Roderic Guigo Thomas R Gingeras David M Gilbert Ross C Hardison Michael A Beer Bing Ren

Nature 2014 Nov;515(7527):355-64

Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA.

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http://dx.doi.org/10.1038/nature13992DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4266106PMC
November 2014

Considerations when investigating lncRNA function in vivo.

Elife 2014 Aug 14;3:e03058. Epub 2014 Aug 14.

Chris P Ponting is in the MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom; Wellcome Trust Sanger Institute, Cambridge, United Kingdom

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4132285PMC
http://dx.doi.org/10.7554/eLife.03058DOI Listing
August 2014

Comparative analysis of the transcriptome across distant species.

Nature 2014 Aug;512(7515):445-8

1] Department of Genome Sciences and University of Washington School of Medicine, William H. Foege Building S350D, 1705 Northeast Pacific Street, Box 355065 Seattle, Washington 98195-5065, USA [2].

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http://dx.doi.org/10.1038/nature13424DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4155737PMC
August 2014

RAMPAGE: promoter activity profiling by paired-end sequencing of 5'-complete cDNAs.

Curr Protoc Mol Biol 2013 Nov 11;104:Unit 25B.11. Epub 2013 Nov 11.

Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York.

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http://dx.doi.org/10.1002/0471142727.mb25b11s104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4372803PMC
November 2013

De novo DNA demethylation and noncoding transcription define active intergenic regulatory elements.

Genome Res 2013 Oct 28;23(10):1601-14. Epub 2013 Jun 28.

Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA;

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http://dx.doi.org/10.1101/gr.157271.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3787258PMC
October 2013

High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression.

Genome Res 2013 Jan 30;23(1):169-80. Epub 2012 Aug 30.

Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.

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http://genome.cshlp.org/cgi/doi/10.1101/gr.139618.112
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http://dx.doi.org/10.1101/gr.139618.112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530677PMC
January 2013

STAR: ultrafast universal RNA-seq aligner.

Bioinformatics 2013 Jan 25;29(1):15-21. Epub 2012 Oct 25.

Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.

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http://dx.doi.org/10.1093/bioinformatics/bts635DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530905PMC
January 2013

Landscape of transcription in human cells.

Nature 2012 Sep;489(7414):101-8

Centre for Genomic Regulation and UPF, Doctor Aiguader 88, Barcelona 08003, Catalonia, Spain.

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http://dx.doi.org/10.1038/nature11233DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3684276PMC
September 2012

An effort to make sense of antisense transcription in bacteria.

RNA Biol 2012 Aug 1;9(8):1039-44. Epub 2012 Aug 1.

Laboratory of Microbial Biofilms, Idab-CSIC-Universidad Pública de Navarra-Gobierno de Navarra, Pamplona, Spain.

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http://dx.doi.org/10.4161/rna.21167DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3551857PMC
August 2012

Modeling gene expression using chromatin features in various cellular contexts.

Genome Biol 2012 Jun 13;13(9):R53. Epub 2012 Jun 13.

Program in Bioinformatics and Integrative Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA.

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http://dx.doi.org/10.1186/gb-2012-13-9-r53DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3491397PMC
June 2012

Molecular biology: RNA discrimination.

Nature 2012 Feb 15;482(7385):310-1. Epub 2012 Feb 15.

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http://dx.doi.org/10.1038/482310aDOI Listing
February 2012

Genome-wide antisense transcription drives mRNA processing in bacteria.

Proc Natl Acad Sci U S A 2011 Dec 28;108(50):20172-7. Epub 2011 Nov 28.

Laboratory of Microbial Biofilms, Instituto de Agrobiotecnología, Consejo Superior de Investigaciones Científicas-Universidad Pública de Navarra-Gobierno de Navarra, 31006 Pamplona, Spain.

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http://dx.doi.org/10.1073/pnas.1113521108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3250193PMC
December 2011

Synthetic spike-in standards for RNA-seq experiments.

Genome Res 2011 Sep 4;21(9):1543-51. Epub 2011 Aug 4.

Section of Developmental Genomics, Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.

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http://dx.doi.org/10.1101/gr.121095.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3166838PMC
September 2011

Identification of functional elements and regulatory circuits by Drosophila modENCODE.

Science 2010 Dec 22;330(6012):1787-97. Epub 2010 Dec 22.

Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.

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http://compbio.mit.edu/publications/46_modENCODE_Science_10.
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http://www.sciencemag.org/cgi/doi/10.1126/science.1198374
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http://dx.doi.org/10.1126/science.1198374DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3192495PMC
December 2010

Genome-wide mapping indicates that p73 and p63 co-occupy target sites and have similar dna-binding profiles in vivo.

PLoS One 2010 Jul 14;5(7):e11572. Epub 2010 Jul 14.

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

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0011572PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2904373PMC
July 2010

High resolution transcriptome maps for wild-type and nonsense-mediated decay-defective Caenorhabditis elegans.

Genome Biol 2009 24;10(9):R101. Epub 2009 Sep 24.

Donnelly CCBR, College Street, University of Toronto, Toronto, M5S 3E1, Canada.

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http://dx.doi.org/10.1186/gb-2009-10-9-r101DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2768976PMC
February 2010

Implications of chimaeric non-co-linear transcripts.

Nature 2009 Sep;461(7261):206-11

Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA.

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http://www.nature.com/doifinder/10.1038/nature08452
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http://dx.doi.org/10.1038/nature08452DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4020519PMC
September 2009

Mapping the strand-specific transcriptome of fission yeast.

Nat Genet 2008 Aug;40(8):935-6

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http://www.nature.com/articles/ng0808-935
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http://dx.doi.org/10.1038/ng0808-935DOI Listing
August 2008

Differential analysis for high density tiling microarray data.

BMC Bioinformatics 2007 Sep 24;8:359. Epub 2007 Sep 24.

Affymetrix Inc,, Santa Clara, CA 95051, USA.

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http://dx.doi.org/10.1186/1471-2105-8-359DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2231405PMC
September 2007

Genome-wide transcription and the implications for genomic organization.

Nat Rev Genet 2007 Jun 8;8(6):413-23. Epub 2007 May 8.

Affymetrix, Inc., 3420 Central Expressway, Santa Clara, California 95051, USA.

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http://dx.doi.org/10.1038/nrg2083DOI Listing
June 2007

Origin of phenotypes: genes and transcripts.

Genome Res 2007 Jun;17(6):682-90

Affymetrix, Inc., Santa Clara, California 95051, USA.

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http://dx.doi.org/10.1101/gr.6525007DOI Listing
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

Characteristics of oligonucleotide tiling arrays measured by hybridizing full-length cDNA clones: causes of signal variation and false positive signals.

Genomics 2007 Apr 9;89(4):541-51. Epub 2007 Feb 9.

Genome Exploration Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Japan.

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http://dx.doi.org/10.1016/j.ygeno.2006.12.013DOI Listing
April 2007

Genome-wide analysis of estrogen receptor binding sites.

Nat Genet 2006 Nov 1;38(11):1289-97. Epub 2006 Oct 1.

Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 44 Binney St., Boston, Massachusetts 02115, USA.

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http://dx.doi.org/10.1038/ng1901DOI Listing
November 2006

Relationships between p63 binding, DNA sequence, transcription activity, and biological function in human cells.

Mol Cell 2006 Nov;24(4):593-602

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

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http://dx.doi.org/10.1016/j.molcel.2006.10.018DOI Listing
November 2006

HIV regulation of the IL-7R: a viral mechanism for enhancing HIV-1 replication in human macrophages in vitro.

J Leukoc Biol 2006 Jun 13;79(6):1328-38. Epub 2006 Apr 13.

Division of Emerging and Transfusion Transmitted Diseases, Office of Blood Research & Review, Center for Biologics Evaluation & Research, FDA, 1401 Rockville Pike, Rockville, MD 20852-1448, USA.

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http://dx.doi.org/10.1189/jlb.0704424DOI Listing
June 2006

The multitasking genome.

Nat Genet 2006 Jun;38(6):608-9

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http://dx.doi.org/10.1038/ng0606-608DOI Listing
June 2006

TUF love for "junk" DNA.

Cell 2006 Jun;125(7):1215-20

Affymetrix, Inc., Santa Clara, CA 95051, USA.

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http://dx.doi.org/10.1016/j.cell.2006.06.009DOI Listing
June 2006

Temporal profile of replication of human chromosomes.

Proc Natl Acad Sci U S A 2005 May 21;102(18):6419-24. Epub 2005 Apr 21.

Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA.

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http://dx.doi.org/10.1073/pnas.0405088102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1088349PMC
May 2005

Fifty years of molecular (DNA/RNA) diagnostics.

Clin Chem 2005 Mar 13;51(3):661-71. Epub 2005 Jan 13.

Affymetrix, Inc., Santa Clara, CA, USA.

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http://dx.doi.org/10.1373/clinchem.2004.045336DOI Listing
March 2005

Genomic maps and comparative analysis of histone modifications in human and mouse.

Cell 2005 Jan;120(2):169-81

Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA.

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http://dx.doi.org/10.1016/j.cell.2005.01.001DOI Listing
January 2005

MyD88 primes macrophages for full-scale activation by interferon-gamma yet mediates few responses to Mycobacterium tuberculosis.

J Exp Med 2003 Oct 29;198(7):987-97. Epub 2003 Sep 29.

Graduate Program in Immunology, Graduate School of Medical Sciences, Weill Medical College of Cornell University, Box 62, 1300 York Avenue, New York, NY 10021, USA.

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http://dx.doi.org/10.1084/jem.20030603DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2194223PMC
October 2003

Beyond expression profiling: next generation uses of high density oligonucleotide arrays.

Brief Funct Genomic Proteomic 2003 Apr;2(1):47-56

Affymetrix, Inc., Santa Clara, CA 95051, USA.

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http://dx.doi.org/10.1093/bfgp/2.1.47DOI Listing
April 2003

Microarrays and genetic epidemiology: a multipurpose tool for a multifaceted field.

Genet Epidemiol 2002 Jun;23(1):4-20

Affymetrix, Inc, Santa Clara, California 95051, USA.

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http://dx.doi.org/10.1002/gepi.216DOI Listing
June 2002

Large-scale transcriptional activity in chromosomes 21 and 22.

Science 2002 May;296(5569):916-9

Affymetrix, Santa Clara, CA 95051, USA., National Cancer Institute, Bethesda, MD 20892, USA.

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http://dx.doi.org/10.1126/science.1068597DOI Listing
May 2002