Anshul Kundaje

Anshul Kundaje

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Anshul Kundaje

Anshul Kundaje

Publications by authors named "Anshul Kundaje"

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The ENCODE Blacklist: Identification of Problematic Regions of the Genome.

Sci Rep 2019 Jun 27;9(1):9354. Epub 2019 Jun 27.

Graduate Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI, USA.

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http://dx.doi.org/10.1038/s41598-019-45839-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6597582PMC
June 2019

Brief Report: Cell Cycle Dynamics of Human Pluripotent Stem Cells Primed for Differentiation.

Stem Cells 2019 May 28. Epub 2019 May 28.

Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, California, USA.

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http://doi.wiley.com/10.1002/stem.3041
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http://dx.doi.org/10.1002/stem.3041DOI Listing
May 2019

mtDNA Chromatin-like Organization Is Gradually Established during Mammalian Embryogenesis.

iScience 2019 Feb 8;12:141-151. Epub 2019 Jan 8.

Department of Life Sciences, Faculty of Natural Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel. Electronic address:

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http://dx.doi.org/10.1016/j.isci.2018.12.032DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6352746PMC
February 2019

Discovery of common and rare genetic risk variants for colorectal cancer.

Authors:
Jeroen R Huyghe Stephanie A Bien Tabitha A Harrison Hyun Min Kang Sai Chen Stephanie L Schmit David V Conti Conghui Qu Jihyoun Jeon Christopher K Edlund Peyton Greenside Michael Wainberg Fredrick R Schumacher Joshua D Smith David M Levine Sarah C Nelson Nasa A Sinnott-Armstrong Demetrius Albanes M Henar Alonso Kristin Anderson Coral Arnau-Collell Volker Arndt Christina Bamia Barbara L Banbury John A Baron Sonja I Berndt Stéphane Bézieau D Timothy Bishop Juergen Boehm Heiner Boeing Hermann Brenner Stefanie Brezina Stephan Buch Daniel D Buchanan Andrea Burnett-Hartman Katja Butterbach Bette J Caan Peter T Campbell Christopher S Carlson Sergi Castellví-Bel Andrew T Chan Jenny Chang-Claude Stephen J Chanock Maria-Dolores Chirlaque Sang Hee Cho Charles M Connolly Amanda J Cross Katarina Cuk Keith R Curtis Albert de la Chapelle Kimberly F Doheny David Duggan Douglas F Easton Sjoerd G Elias Faye Elliott Dallas R English Edith J M Feskens Jane C Figueiredo Rocky Fischer Liesel M FitzGerald David Forman Manish Gala Steven Gallinger W James Gauderman Graham G Giles Elizabeth Gillanders Jian Gong Phyllis J Goodman William M Grady John S Grove Andrea Gsur Marc J Gunter Robert W Haile Jochen Hampe Heather Hampel Sophia Harlid Richard B Hayes Philipp Hofer Michael Hoffmeister John L Hopper Wan-Ling Hsu Wen-Yi Huang Thomas J Hudson David J Hunter Gemma Ibañez-Sanz Gregory E Idos Roxann Ingersoll Rebecca D Jackson Eric J Jacobs Mark A Jenkins Amit D Joshi Corinne E Joshu Temitope O Keku Timothy J Key Hyeong Rok Kim Emiko Kobayashi Laurence N Kolonel Charles Kooperberg Tilman Kühn Sébastien Küry Sun-Seog Kweon Susanna C Larsson Cecelia A Laurie Loic Le Marchand Suzanne M Leal Soo Chin Lee Flavio Lejbkowicz Mathieu Lemire Christopher I Li Li Li Wolfgang Lieb Yi Lin Annika Lindblom Noralane M Lindor Hua Ling Tin L Louie Satu Männistö Sanford D Markowitz Vicente Martín Giovanna Masala Caroline E McNeil Marilena Melas Roger L Milne Lorena Moreno Neil Murphy Robin Myte Alessio Naccarati Polly A Newcomb Kenneth Offit Shuji Ogino N Charlotte Onland-Moret Barbara Pardini Patrick S Parfrey Rachel Pearlman Vittorio Perduca Paul D P Pharoah Mila Pinchev Elizabeth A Platz Ross L Prentice Elizabeth Pugh Leon Raskin Gad Rennert Hedy S Rennert Elio Riboli Miguel Rodríguez-Barranco Jane Romm Lori C Sakoda Clemens Schafmayer Robert E Schoen Daniela Seminara Mitul Shah Tameka Shelford Min-Ho Shin Katerina Shulman Sabina Sieri Martha L Slattery Melissa C Southey Zsofia K Stadler Christa Stegmaier Yu-Ru Su Catherine M Tangen Stephen N Thibodeau Duncan C Thomas Sushma S Thomas Amanda E Toland Antonia Trichopoulou Cornelia M Ulrich David J Van Den Berg Franzel J B van Duijnhoven Bethany Van Guelpen Henk van Kranen Joseph Vijai Kala Visvanathan Pavel Vodicka Ludmila Vodickova Veronika Vymetalkova Korbinian Weigl Stephanie J Weinstein Emily White Aung Ko Win C Roland Wolf Alicja Wolk Michael O Woods Anna H Wu Syed H Zaidi Brent W Zanke Qing Zhang Wei Zheng Peter C Scacheri John D Potter Michael C Bassik Anshul Kundaje Graham Casey Victor Moreno Goncalo R Abecasis Deborah A Nickerson Stephen B Gruber Li Hsu Ulrike Peters

Nat Genet 2019 01 3;51(1):76-87. Epub 2018 Dec 3.

Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.

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http://www.nature.com/articles/s41588-018-0286-6
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http://dx.doi.org/10.1038/s41588-018-0286-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6358437PMC
January 2019

Differential analysis of chromatin accessibility and histone modifications for predicting mouse developmental enhancers.

Nucleic Acids Res 2018 11;46(21):11184-11201

Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.

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http://dx.doi.org/10.1093/nar/gky753DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6265487PMC
November 2018

Umap and Bismap: quantifying genome and methylome mappability.

Nucleic Acids Res 2018 11;46(20):e120

Princess Margaret Cancer Centre, M5G 1L7, Toronto, ON, Canada.

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http://dx.doi.org/10.1093/nar/gky677DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6237805PMC
November 2018

Prediction of protein-ligand interactions from paired protein sequence motifs and ligand substructures.

Pac Symp Biocomput 2018 ;23:20-31

Program in Biomedical Informatics, Stanford University Stanford, CA 94305, USA,

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6211855PMC
August 2018

A common pattern of DNase I footprinting throughout the human mtDNA unveils clues for a chromatin-like organization.

Genome Res 2018 08 12;28(8):1158-1168. Epub 2018 Jul 12.

Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105 Israel.

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http://dx.doi.org/10.1101/gr.230409.117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6071632PMC
August 2018

Chromatin accessibility dynamics reveal novel functional enhancers in .

Genome Res 2017 12 15;27(12):2096-2107. Epub 2017 Nov 15.

Department of Genetics, Stanford University, Stanford, California 94305, USA.

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http://dx.doi.org/10.1101/gr.226233.117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5741055PMC
December 2017

Vicus: Exploiting local structures to improve network-based analysis of biological data.

PLoS Comput Biol 2017 Oct 12;13(10):e1005621. Epub 2017 Oct 12.

SickKids Research Institute, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1371/journal.pcbi.1005621DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5638230PMC
October 2017

High-Throughput Characterization of Cascade type I-E CRISPR Guide Efficacy Reveals Unexpected PAM Diversity and Target Sequence Preferences.

Genetics 2017 08 20;206(4):1727-1738. Epub 2017 Jun 20.

Department of Genetics, Stanford University School of Medicine, California 94305

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http://dx.doi.org/10.1534/genetics.117.202580DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5560783PMC
August 2017

Denoising genome-wide histone ChIP-seq with convolutional neural networks.

Bioinformatics 2017 Jul;33(14):i225-i233

Department of Computer Science, Stanford University, Stanford, CA, USA.

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https://academic.oup.com/bioinformatics/article/33/14/i225/3
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http://dx.doi.org/10.1093/bioinformatics/btx243DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5870713PMC
July 2017

Initiation of mtDNA transcription is followed by pausing, and diverges across human cell types and during evolution.

Genome Res 2017 03 3;27(3):362-373. Epub 2017 Jan 3.

Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, 84105 Israel.

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http://dx.doi.org/10.1101/gr.209924.116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5340964PMC
March 2017

An atlas of transcriptional, chromatin accessibility, and surface marker changes in human mesoderm development.

Sci Data 2016 12 20;3:160109. Epub 2016 Dec 20.

Department of Developmental Biology, Institute for Stem Cell Biology and Regenerative Medicine, Ludwig Center for Cancer Stem Cell Biology and Medicine, Stanford University School of Medicine, Stanford, California 94305, USA.

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http://dx.doi.org/10.1038/sdata.2016.109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5170597PMC
December 2016

Characterization of the direct targets of FOXO transcription factors throughout evolution.

Aging Cell 2016 08 8;15(4):673-85. Epub 2016 Apr 8.

Department of Genetics, Stanford University, 300 Pasteur Drive, Stanford, CA, 94305, USA.

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http://dx.doi.org/10.1111/acel.12479DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4933671PMC
August 2016

Impact of the X Chromosome and sex on regulatory variation.

Genome Res 2016 06 21;26(6):768-77. Epub 2016 Apr 21.

Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA; Department of Computer Science, Stanford University, Stanford, California 94305, USA;

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http://dx.doi.org/10.1101/gr.197897.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4889977PMC
June 2016

An Arntl2-Driven Secretome Enables Lung Adenocarcinoma Metastatic Self-Sufficiency.

Cancer Cell 2016 05 14;29(5):697-710. Epub 2016 Apr 14.

Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Cancer Biology Program, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ccell.2016.03.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4864124PMC
May 2016

Characterization of TCF21 Downstream Target Regions Identifies a Transcriptional Network Linking Multiple Independent Coronary Artery Disease Loci.

PLoS Genet 2015 May 28;11(5):e1005202. Epub 2015 May 28.

Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, California, United States of America; Cardiovascular Institute, Stanford University School of Medicine, Stanford, California, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1005202DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4447360PMC
May 2015

Integrative analysis of 111 reference human epigenomes.

Nature 2015 Feb;518(7539):317-30

1] Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, Massachusetts 02139, USA. [2] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA.

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http://dx.doi.org/10.1038/nature14248DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4530010PMC
February 2015

Conserved epigenomic signals in mice and humans reveal immune basis of Alzheimer's disease.

Nature 2015 Feb;518(7539):365-9

1] Broad Institute of Harvard University and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA [2] Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.

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http://dx.doi.org/10.1038/nature14252DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4530583PMC
February 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

Transcription factors bind negatively selected sites within human mtDNA genes.

Genome Biol Evol 2014 Sep 22;6(10):2634-46. Epub 2014 Sep 22.

Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel

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http://dx.doi.org/10.1093/gbe/evu210DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4224337PMC
September 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

H3K4me3 breadth is linked to cell identity and transcriptional consistency.

Cell 2014 Jul;158(3):673-88

Department of Genetics, Stanford University, Stanford CA 94305, USA; Paul F. Glenn Laboratories for the Biology of Aging, Stanford University, Stanford CA 94305, USA; Cancer Biology Program, Stanford University, Stanford CA 94305, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2014.06.027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4137894PMC
July 2014

Large-scale quality analysis of published ChIP-seq data.

G3 (Bethesda) 2014 Feb 19;4(2):209-23. Epub 2014 Feb 19.

Division of Biology, California Institute of Technology, Pasadena, California 91125.

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http://dx.doi.org/10.1534/g3.113.008680DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3931556PMC
February 2014

STAT3 targets suggest mechanisms of aggressive tumorigenesis in diffuse large B-cell lymphoma.

G3 (Bethesda) 2013 Dec 9;3(12):2173-85. Epub 2013 Dec 9.

Department of Genetics, Stanford University School of Medicine, Stanford, California 94305.

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http://dx.doi.org/10.1534/g3.113.007674DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3852380PMC
December 2013

Linking disease associations with regulatory information in the human genome.

Genome Res 2012 Sep;22(9):1748-59

Department of Computer Science, Stanford University, Stanford, California 94305, USA.

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http://genome.cshlp.org/cgi/doi/10.1101/gr.136127.111
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http://dx.doi.org/10.1101/gr.136127.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431491PMC
September 2012

Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors.

Genome Res 2012 Sep;22(9):1798-812

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

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http://dx.doi.org/10.1101/gr.139105.112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431495PMC
September 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

A predictive model of the oxygen and heme regulatory network in yeast.

PLoS Comput Biol 2008 Nov 14;4(11):e1000224. Epub 2008 Nov 14.

Department of Computer Science, Columbia University, New York, New York, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1000224DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2573020PMC
November 2008

Learning regulatory programs that accurately predict differential expression with MEDUSA.

Ann N Y Acad Sci 2007 Dec 12;1115:178-202. Epub 2007 Oct 12.

Department of Computer Science, Center for Computational Learning Systems, Columbia University, New York, NY 10065, USA.

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http://dx.doi.org/10.1196/annals.1407.020DOI Listing
December 2007

Combining sequence and time series expression data to learn transcriptional modules.

IEEE/ACM Trans Comput Biol Bioinform 2005 Jul-Sep;2(3):194-202

Department of Computer Science, Columbia University, New York 10027, USA.

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http://dx.doi.org/10.1109/TCBB.2005.34DOI Listing
November 2006

A classification-based framework for predicting and analyzing gene regulatory response.

BMC Bioinformatics 2006 Mar 20;7 Suppl 1:S5. Epub 2006 Mar 20.

Department of Computer Science, Columbia University, New York, NY 10027, USA.

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http://dx.doi.org/10.1186/1471-2105-7-S1-S5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1810316PMC
March 2006

Predicting genetic regulatory response using classification.

Bioinformatics 2004 Aug;20 Suppl 1:i232-40

Department of Physics, Columbia University, NY, NY 10027, USA.

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http://dx.doi.org/10.1093/bioinformatics/bth923DOI Listing
August 2004