Publications by authors named "Joel Rozowsky"

75Publications

Pollen-derived RNAs Are Found in the Human Circulation.

iScience 2019 Sep 24;19:916-926. Epub 2019 Aug 24.

Department of Medicine, Division of Cardiovascular Medicine, University of Massachusetts Medical School, 368 Plantation St., AS7-1051, Worcester, MA 01605, USA. Electronic address:

View Article

Download full-text PDF

Source
https://linkinghub.elsevier.com/retrieve/pii/S25890042193031
Publisher Site
http://dx.doi.org/10.1016/j.isci.2019.08.035DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6742912PMC
September 2019

exceRpt: A Comprehensive Analytic Platform for Extracellular RNA Profiling.

Cell Syst 2019 04 4;8(4):352-357.e3. Epub 2019 Apr 4.

Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA; Department of Computer Science, Yale University, New Haven, CT, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.cels.2019.03.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7079576PMC
April 2019

Isoform-Level Interpretation of High-Throughput Proteomics Data Enabled by Deep Integration with RNA-seq.

J Proteome Res 2018 10 6;17(10):3431-3444. Epub 2018 Sep 6.

Department of Psychiatry , Yale School of Medicine, Connecticut Mental Health Center , 34 Park Street , New Haven , Connecticut 06519 , United States.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.jproteome.8b00310DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6392456PMC
October 2018

Novel approaches for bioinformatic analysis of salivary RNA sequencing data for development.

Bioinformatics 2018 01;34(1):1-8

Center for Oral/Head & Neck Oncology Research, School of Dentistry, Division of Oral Biology & Medicine University of California at Los Angeles, Los Angeles, CA 90095, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btx504DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5859991PMC
January 2018

Structuring supplemental materials in support of reproducibility.

Genome Biol 2017 04 5;18(1):64. Epub 2017 Apr 5.

Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13059-017-1205-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5382465PMC
April 2017

Stroke and Circulating Extracellular RNAs.

Stroke 2017 04 13;48(4):828-834. Epub 2017 Mar 13.

From the Department of Quantitative Health Sciences (E.M.) and Department of Medicine (K.T., J.E.F.), University of Massachusetts Medical School, Worcester; Department of Cardiology, Massachusetts General Hospital, Boston (R.S.); Department of Cardiology, University of Michigan, Ann Arbor (V.M.); Yale University Medical School, Computational Biology, New Haven, CT (M.G., J.R., R.K.); The NHLBI's and Boston University's Framingham Heart Study, MA (M.G.L.); Biostatistics Department, Boston University School of Public Health, MA (M.G.L.); and The Framingham Heart Study, Population Sciences Branch, NHLBI, Bethesda, MD (D.L.).

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1161/STROKEAHA.116.015140DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5373984PMC
April 2017

Discordant Expression of Circulating microRNA from Cellular and Extracellular Sources.

PLoS One 2016 28;11(4):e0153691. Epub 2016 Apr 28.

University of Massachusetts Medical School, Department of Medicine, Division of Cardiovascular Medicine, Worcester, MA, 01605, United States of America.

View Article

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0153691PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4849639PMC
February 2017

A uniform survey of allele-specific binding and expression over 1000-Genomes-Project individuals.

Nat Commun 2016 Apr 18;7:11101. Epub 2016 Apr 18.

Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/ncomms11101DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4837449PMC
April 2016

The real cost of sequencing: scaling computation to keep pace with data generation.

Genome Biol 2016 Mar 23;17:53. Epub 2016 Mar 23.

Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13059-016-0917-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4806511PMC
March 2016

Temporal Dynamics of Collaborative Networks in Large Scientific Consortia.

Trends Genet 2016 05 20;32(5):251-253. Epub 2016 Mar 20.

Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA; Department of Computer Science, Yale University, New Haven, CT, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.tig.2016.02.006DOI Listing
May 2016

Loregic: a method to characterize the cooperative logic of regulatory factors.

PLoS Comput Biol 2015 Apr 17;11(4):e1004132. Epub 2015 Apr 17.

Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America; Department of Computer Science, Yale University, New Haven, Connecticut, United States of America.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1004132DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4401777PMC
April 2015

Decoding neuroproteomics: integrating the genome, translatome and functional anatomy.

Nat Neurosci 2014 Nov 28;17(11):1491-9. Epub 2014 Oct 28.

Division of Molecular Psychiatry, Abraham Ribicoff Research Facilities, Connecticut Mental Health Center, Yale University School of Medicine, New Haven, Connecticut, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nn.3829DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4737617PMC
November 2014

MUSIC: identification of enriched regions in ChIP-Seq experiments using a mappability-corrected multiscale signal processing framework.

Genome Biol 2014 ;15(10):474

Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13059-014-0474-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4234855PMC
October 2015

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].

View Article

Download full-text PDF

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

Comparative analysis of pseudogenes across three phyla.

Proc Natl Acad Sci U S A 2014 Sep 25;111(37):13361-6. Epub 2014 Aug 25.

Program in Computational Biology and Bioinformatics and Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520; Department of Computer Science, Yale University, New Haven, CT 06511

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.1407293111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4169933PMC
September 2014

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.

View Article

Download full-text PDF

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

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.

View Article

Download full-text PDF

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

Tiling array data analysis: a multiscale approach using wavelets.

BMC Bioinformatics 2011 Feb 21;12:57. Epub 2011 Feb 21.

Diagnostic Radiology, Yale University, New Haven, CT, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/1471-2105-12-57DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3055839PMC
February 2011

A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets.

Genome Biol 2011 16;12(2):R15. Epub 2011 Feb 16.

Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, New Haven, CT 06520, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/gb-2011-12-2-r15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3188797PMC
February 2012

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project.

Authors:
Mark B Gerstein Zhi John Lu Eric L Van Nostrand Chao Cheng Bradley I Arshinoff Tao Liu Kevin Y Yip Rebecca Robilotto Andreas Rechtsteiner Kohta Ikegami Pedro Alves Aurelien Chateigner Marc Perry Mitzi Morris Raymond K Auerbach Xin Feng Jing Leng Anne Vielle Wei Niu Kahn Rhrissorrakrai Ashish Agarwal Roger P Alexander Galt Barber Cathleen M Brdlik Jennifer Brennan Jeremy Jean Brouillet Adrian Carr Ming-Sin Cheung Hiram Clawson Sergio Contrino Luke O Dannenberg Abby F Dernburg Arshad Desai Lindsay Dick Andréa C Dosé Jiang Du Thea Egelhofer Sevinc Ercan Ghia Euskirchen Brent Ewing Elise A Feingold Reto Gassmann Peter J Good Phil Green Francois Gullier Michelle Gutwein Mark S Guyer Lukas Habegger Ting Han Jorja G Henikoff Stefan R Henz Angie Hinrichs Heather Holster Tony Hyman A Leo Iniguez Judith Janette Morten Jensen Masaomi Kato W James Kent Ellen Kephart Vishal Khivansara Ekta Khurana John K Kim Paulina Kolasinska-Zwierz Eric C Lai Isabel Latorre Amber Leahey Suzanna Lewis Paul Lloyd Lucas Lochovsky Rebecca F Lowdon Yaniv Lubling Rachel Lyne Michael MacCoss Sebastian D Mackowiak Marco Mangone Sheldon McKay Desirea Mecenas Gennifer Merrihew David M Miller Andrew Muroyama John I Murray Siew-Loon Ooi Hoang Pham Taryn Phippen Elicia A Preston Nikolaus Rajewsky Gunnar Rätsch Heidi Rosenbaum Joel Rozowsky Kim Rutherford Peter Ruzanov Mihail Sarov Rajkumar Sasidharan Andrea Sboner Paul Scheid Eran Segal Hyunjin Shin Chong Shou Frank J Slack Cindie Slightam Richard Smith William C Spencer E O Stinson Scott Taing Teruaki Takasaki Dionne Vafeados Ksenia Voronina Guilin Wang Nicole L Washington Christina M Whittle Beijing Wu Koon-Kiu Yan Georg Zeller Zheng Zha Mei Zhong Xingliang Zhou Julie Ahringer Susan Strome Kristin C Gunsalus Gos Micklem X Shirley Liu Valerie Reinke Stuart K Kim LaDeana W Hillier Steven Henikoff Fabio Piano Michael Snyder Lincoln Stein Jason D Lieb Robert H Waterston

Science 2010 Dec 22;330(6012):1775-87. Epub 2010 Dec 22.

Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1126/science.1196914DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3142569PMC
December 2010

RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries.

Bioinformatics 2011 Jan 5;27(2):281-3. Epub 2010 Dec 5.

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btq643DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3018817PMC
January 2011

Annotating non-coding regions of the genome.

Nat Rev Genet 2010 Aug 13;11(8):559-71. Epub 2010 Jul 13.

Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nrg2814DOI Listing
August 2010

Mapping accessible chromatin regions using Sono-Seq.

Proc Natl Acad Sci U S A 2009 Sep 18;106(35):14926-31. Epub 2009 Aug 18.

Program in Computational Biology, Yale University, New Haven, CT 06520, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.0905443106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2736440PMC
September 2009

An approach to comparing tiling array and high throughput sequencing technologies for genomic transcript mapping.

BMC Res Notes 2009 Jul 24;2:150. Epub 2009 Jul 24.

Molecular Biophysics and Biochemistry Department, Yale University, New Haven, CT 06520, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/1756-0500-2-150DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2764720PMC
July 2009

Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing.

BMC Genomics 2009 Jan 21;10:37. Epub 2009 Jan 21.

Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/1471-2164-10-37DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2656530PMC
January 2009

PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls.

Nat Biotechnol 2009 Jan 4;27(1):66-75. Epub 2009 Jan 4.

Molecular Biophysics & Biochemistry Dept., Yale University, PO Box 208114, New Haven, Connecticut 06520-8114, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nbt.1518DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2924752PMC
January 2009

Mismatch oligonucleotides in human and yeast: guidelines for probe design on tiling microarrays.

BMC Genomics 2008 Dec 31;9:635. Epub 2008 Dec 31.

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/1471-2164-9-635DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2642824PMC
December 2008

Modeling ChIP sequencing in silico with applications.

PLoS Comput Biol 2008 Aug 22;4(8):e1000158. Epub 2008 Aug 22.

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1000158DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2507756PMC
August 2008

Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome.

Genome Biol 2008 Jan 3;9(1):R3. Epub 2008 Jan 3.

Molecular, Cellular and Developmental Biology Department, KBT918, Yale University, New Haven, Connecticut 06511, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/gb-2008-9-1-r3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2395237PMC
January 2008

Divergence of transcription factor binding sites across related yeast species.

Science 2007 Aug;317(5839):815-9

Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1126/science.1140748DOI Listing
August 2007

Toward a universal microarray: prediction of gene expression through nearest-neighbor probe sequence identification.

Nucleic Acids Res 2007 7;35(15):e99. Epub 2007 Aug 7.

Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkm549DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1976448PMC
October 2007

Transcription factor binding site identification in yeast: a comparison of high-density oligonucleotide and PCR-based microarray platforms.

Funct Integr Genomics 2007 Oct 19;7(4):335-45. Epub 2007 Jul 19.

Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s10142-007-0054-7DOI Listing
October 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

What is a gene, post-ENCODE? History and updated definition.

Genome Res 2007 Jun;17(6):669-81

Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06511, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.6339607DOI Listing
June 2007

Tilescope: online analysis pipeline for high-density tiling microarray data.

Genome Biol 2007 ;8(5):R81

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.

View Article

Download full-text PDF

Source
http://genomebiology.biomedcentral.com/articles/10.1186/gb-2
Publisher Site
http://dx.doi.org/10.1186/gb-2007-8-5-r81DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1929149PMC
September 2007

Assessing the need for sequence-based normalization in tiling microarray experiments.

Bioinformatics 2007 Apr 25;23(8):988-97. Epub 2007 Mar 25.

Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btm052DOI Listing
April 2007

Extrapolating traditional DNA microarray statistics to tiling and protein microarray technologies.

Methods Enzymol 2006 ;411:282-311

Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/S0076-6879(06)11015-0DOI Listing
December 2006

Design optimization methods for genomic DNA tiling arrays.

Genome Res 2006 Feb 19;16(2):271-81. Epub 2005 Dec 19.

Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CN 06520, USA. P50 HG02357

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.4452906DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1361723PMC
February 2006

Global identification of human transcribed sequences with genome tiling arrays.

Science 2004 Dec 11;306(5705):2242-6. Epub 2004 Nov 11.

Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520-8103, USA.

View Article

Download full-text PDF

Source
http://www.sciencemag.org/cgi/doi/10.1126/science.1103388
Publisher Site
http://dx.doi.org/10.1126/science.1103388DOI Listing
December 2004

Major molecular differences between mammalian sexes are involved in drug metabolism and renal function.

Dev Cell 2004 Jun;6(6):791-800

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.devcel.2004.05.005DOI Listing
June 2004