Manolis Kellis

Manolis Kellis

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Manolis Kellis

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Integrative construction of regulatory region networks in 127 human reference epigenomes by matrix factorization.

Nucleic Acids Res 2019 Aug;47(14):7235-7246

MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1093/nar/gkz538DOI Listing
August 2019

Joint profiling of DNA methylation and chromatin architecture in single cells.

Nat Methods 2019 Aug 5. Epub 2019 Aug 5.

Ludwig Institute for Cancer Research, La Jolla, CA, USA.

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http://dx.doi.org/10.1038/s41592-019-0502-zDOI Listing
August 2019

Single-cell transcriptomic analysis of Alzheimer's disease.

Nature 2019 Jun 1;570(7761):332-337. Epub 2019 May 1.

Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA.

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http://dx.doi.org/10.1038/s41586-019-1195-2DOI Listing
June 2019

Rate of brain aging and are synergistic risk factors for Alzheimer's disease.

Life Sci Alliance 2019 06 27;2(3). Epub 2019 May 27.

Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA

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http://dx.doi.org/10.26508/lsa.201900303DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6537750PMC
June 2019

Elucidation of Codon Usage Signatures across the Domains of Life.

Mol Biol Evol 2019 May 20. Epub 2019 May 20.

Computer Science and Artificial Intelligence Lab, MIT, Cambridge, MA, USA.

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http://dx.doi.org/10.1093/molbev/msz124DOI Listing
May 2019

A gene expression atlas of embryonic neurogenesis in reveals complex spatiotemporal regulation of lncRNAs.

Development 2019 Mar 28;146(6). Epub 2019 Mar 28.

Laboratory for Systems Biology of Neural Tissue Differentiation, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrueck Centre for Molecular Medicine (MDC) in the Helmholtz Association, Robert-Roessle-Strasse 12, 13125 Berlin, Germany

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http://dev.biologists.org/lookup/doi/10.1242/dev.175265
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http://dx.doi.org/10.1242/dev.175265DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6451322PMC
March 2019

Association studies of up to 1.2 million individuals yield new insights into the genetic etiology of tobacco and alcohol use.

Authors:
Mengzhen Liu Yu Jiang Robbee Wedow Yue Li David M Brazel Fang Chen Gargi Datta Jose Davila-Velderrain Daniel McGuire Chao Tian Xiaowei Zhan Hélène Choquet Anna R Docherty Jessica D Faul Johanna R Foerster Lars G Fritsche Maiken Elvestad Gabrielsen Scott D Gordon Jeffrey Haessler Jouke-Jan Hottenga Hongyan Huang Seon-Kyeong Jang Philip R Jansen Yueh Ling Reedik Mägi Nana Matoba George McMahon Antonella Mulas Valeria Orrù Teemu Palviainen Anita Pandit Gunnar W Reginsson Anne Heidi Skogholt Jennifer A Smith Amy E Taylor Constance Turman Gonneke Willemsen Hannah Young Kendra A Young Gregory J M Zajac Wei Zhao Wei Zhou Gyda Bjornsdottir Jason D Boardman Michael Boehnke Dorret I Boomsma Chu Chen Francesco Cucca Gareth E Davies Charles B Eaton Marissa A Ehringer Tõnu Esko Edoardo Fiorillo Nathan A Gillespie Daniel F Gudbjartsson Toomas Haller Kathleen Mullan Harris Andrew C Heath John K Hewitt Ian B Hickie John E Hokanson Christian J Hopfer David J Hunter William G Iacono Eric O Johnson Yoichiro Kamatani Sharon L R Kardia Matthew C Keller Manolis Kellis Charles Kooperberg Peter Kraft Kenneth S Krauter Markku Laakso Penelope A Lind Anu Loukola Sharon M Lutz Pamela A F Madden Nicholas G Martin Matt McGue Matthew B McQueen Sarah E Medland Andres Metspalu Karen L Mohlke Jonas B Nielsen Yukinori Okada Ulrike Peters Tinca J C Polderman Danielle Posthuma Alexander P Reiner John P Rice Eric Rimm Richard J Rose Valgerdur Runarsdottir Michael C Stallings Alena Stančáková Hreinn Stefansson Khanh K Thai Hilary A Tindle Thorarinn Tyrfingsson Tamara L Wall David R Weir Constance Weisner John B Whitfield Bendik Slagsvold Winsvold Jie Yin Luisa Zuccolo Laura J Bierut Kristian Hveem James J Lee Marcus R Munafò Nancy L Saccone Cristen J Willer Marilyn C Cornelis Sean P David David A Hinds Eric Jorgenson Jaakko Kaprio Jerry A Stitzel Kari Stefansson Thorgeir E Thorgeirsson Gonçalo Abecasis Dajiang J Liu Scott Vrieze

Nat Genet 2019 02 14;51(2):237-244. Epub 2019 Jan 14.

Department of Psychology, University of Minnesota Twin Cities, Minneapolis, MN, USA.

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http://www.nature.com/articles/s41588-018-0307-5
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http://dx.doi.org/10.1038/s41588-018-0307-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6358542PMC
February 2019

ncdDetect2: improved models of the site-specific mutation rate in cancer and driver detection with robust significance evaluation.

Bioinformatics 2019 Jan;35(2):189-199

Department of Molecular Medicine, Aarhus University, Palle Juul-Jensens Boulevard 99, DK-8200 Aarhus N, Denmark.

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http://dx.doi.org/10.1093/bioinformatics/bty511DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6330011PMC
January 2019

Target site specificity and in vivo complexity of the mammalian arginylome.

Sci Rep 2018 Nov 1;8(1):16177. Epub 2018 Nov 1.

Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.

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http://dx.doi.org/10.1038/s41598-018-34639-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6212499PMC
November 2018

RANGER-DTL 2.0: rigorous reconstruction of gene-family evolution by duplication, transfer and loss.

Bioinformatics 2018 09;34(18):3214-3216

Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, USA.

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http://dx.doi.org/10.1093/bioinformatics/bty314DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6137995PMC
September 2018

Publisher Correction: N-methyladenosine RNA modification regulates embryonic neural stem cell self-renewal through histone modifications.

Nat Neurosci 2018 Aug;21(8):1139

Tumor Initiation and Maintenance Program, NCI-designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.

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http://dx.doi.org/10.1038/s41593-018-0169-2DOI Listing
August 2018

Analyses of mRNA structure dynamics identify embryonic gene regulatory programs.

Nat Struct Mol Biol 2018 08 30;25(8):677-686. Epub 2018 Jul 30.

Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.

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http://dx.doi.org/10.1038/s41594-018-0091-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6690192PMC
August 2018

Chromatin Accessibility Impacts Transcriptional Reprogramming in Oocytes.

Cell Rep 2018 Jul;24(2):304-311

Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2018.06.030DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6057489PMC
July 2018

N-methyladenosine RNA modification regulates embryonic neural stem cell self-renewal through histone modifications.

Nat Neurosci 2018 02 15;21(2):195-206. Epub 2018 Jan 15.

Tumor Initiation and Maintenance Program, NCI-designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.

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http://dx.doi.org/10.1038/s41593-017-0057-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6317335PMC
February 2018

Chromatin-state discovery and genome annotation with ChromHMM.

Nat Protoc 2017 Dec 9;12(12):2478-2492. Epub 2017 Nov 9.

Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.

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http://dx.doi.org/10.1038/nprot.2017.124DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5945550PMC
December 2017

Evidence of reduced recombination rate in human regulatory domains.

Genome Biol 2017 10 20;18(1):193. Epub 2017 Oct 20.

Computer Science and Artificial Intelligence Lab (CSAIL), Massachusetts Institute of Technology, Massachusetts, USA.

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http://dx.doi.org/10.1186/s13059-017-1308-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5651596PMC
October 2017

Genomic analyses identify hundreds of variants associated with age at menarche and support a role for puberty timing in cancer risk.

Authors:
Felix R Day Deborah J Thompson Hannes Helgason Daniel I Chasman Hilary Finucane Patrick Sulem Katherine S Ruth Sean Whalen Abhishek K Sarkar Eva Albrecht Elisabeth Altmaier Marzyeh Amini Caterina M Barbieri Thibaud Boutin Archie Campbell Ellen Demerath Ayush Giri Chunyan He Jouke J Hottenga Robert Karlsson Ivana Kolcic Po-Ru Loh Kathryn L Lunetta Massimo Mangino Brumat Marco George McMahon Sarah E Medland Ilja M Nolte Raymond Noordam Teresa Nutile Lavinia Paternoster Natalia Perjakova Eleonora Porcu Lynda M Rose Katharina E Schraut Ayellet V Segrè Albert V Smith Lisette Stolk Alexander Teumer Irene L Andrulis Stefania Bandinelli Matthias W Beckmann Javier Benitez Sven Bergmann Murielle Bochud Eric Boerwinkle Stig E Bojesen Manjeet K Bolla Judith S Brand Hiltrud Brauch Hermann Brenner Linda Broer Thomas Brüning Julie E Buring Harry Campbell Eulalia Catamo Stephen Chanock Georgia Chenevix-Trench Tanguy Corre Fergus J Couch Diana L Cousminer Angela Cox Laura Crisponi Kamila Czene George Davey Smith Eco J C N de Geus Renée de Mutsert Immaculata De Vivo Joe Dennis Peter Devilee Isabel Dos-Santos-Silva Alison M Dunning Johan G Eriksson Peter A Fasching Lindsay Fernández-Rhodes Luigi Ferrucci Dieter Flesch-Janys Lude Franke Marike Gabrielson Ilaria Gandin Graham G Giles Harald Grallert Daniel F Gudbjartsson Pascal Guénel Per Hall Emily Hallberg Ute Hamann Tamara B Harris Catharina A Hartman Gerardo Heiss Maartje J Hooning John L Hopper Frank Hu David J Hunter M Arfan Ikram Hae Kyung Im Marjo-Riitta Järvelin Peter K Joshi David Karasik Manolis Kellis Zoltan Kutalik Genevieve LaChance Diether Lambrechts Claudia Langenberg Lenore J Launer Joop S E Laven Stefania Lenarduzzi Jingmei Li Penelope A Lind Sara Lindstrom YongMei Liu Jian'an Luan Reedik Mägi Arto Mannermaa Hamdi Mbarek Mark I McCarthy Christa Meisinger Thomas Meitinger Cristina Menni Andres Metspalu Kyriaki Michailidou Lili Milani Roger L Milne Grant W Montgomery Anna M Mulligan Mike A Nalls Pau Navarro Heli Nevanlinna Dale R Nyholt Albertine J Oldehinkel Tracy A O'Mara Sandosh Padmanabhan Aarno Palotie Nancy Pedersen Annette Peters Julian Peto Paul D P Pharoah Anneli Pouta Paolo Radice Iffat Rahman Susan M Ring Antonietta Robino Frits R Rosendaal Igor Rudan Rico Rueedi Daniela Ruggiero Cinzia F Sala Marjanka K Schmidt Robert A Scott Mitul Shah Rossella Sorice Melissa C Southey Ulla Sovio Meir Stampfer Maristella Steri Konstantin Strauch Toshiko Tanaka Emmi Tikkanen Nicholas J Timpson Michela Traglia Thérèse Truong Jonathan P Tyrer André G Uitterlinden Digna R Velez Edwards Veronique Vitart Uwe Völker Peter Vollenweider Qin Wang Elisabeth Widen Ko Willems van Dijk Gonneke Willemsen Robert Winqvist Bruce H R Wolffenbuttel Jing Hua Zhao Magdalena Zoledziewska Marek Zygmunt Behrooz Z Alizadeh Dorret I Boomsma Marina Ciullo Francesco Cucca Tõnu Esko Nora Franceschini Christian Gieger Vilmundur Gudnason Caroline Hayward Peter Kraft Debbie A Lawlor Patrik K E Magnusson Nicholas G Martin Dennis O Mook-Kanamori Ellen A Nohr Ozren Polasek David Porteous Alkes L Price Paul M Ridker Harold Snieder Tim D Spector Doris Stöckl Daniela Toniolo Sheila Ulivi Jenny A Visser Henry Völzke Nicholas J Wareham James F Wilson Amanda B Spurdle Unnur Thorsteindottir Katherine S Pollard Douglas F Easton Joyce Y Tung Jenny Chang-Claude David Hinds Anna Murray Joanne M Murabito Kari Stefansson Ken K Ong John R B Perry

Nat Genet 2017 Jun 24;49(6):834-841. Epub 2017 Apr 24.

MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, UK.

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http://dx.doi.org/10.1038/ng.3841DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5841952PMC
June 2017

Multi-scale chromatin state annotation using a hierarchical hidden Markov model.

Nat Commun 2017 04 7;8:15011. Epub 2017 Apr 7.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02215, USA.

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http://dx.doi.org/10.1038/ncomms15011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5385569PMC
April 2017

Evolutionary Dynamics of Abundant Stop Codon Readthrough.

Mol Biol Evol 2016 12 7;33(12):3108-3132. Epub 2016 Sep 7.

MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA

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http://dx.doi.org/10.1093/molbev/msw189DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5100048PMC
December 2016

SwiSpot: modeling riboswitches by spotting out switching sequences.

Bioinformatics 2016 11 4;32(21):3252-3259. Epub 2016 Jul 4.

Department of Information Engineering, University of Pisa, Largo L. Lazzarino, Pisa, IT 56122, Italy.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btw401DOI Listing
November 2016

Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions.

Nat Biotechnol 2016 Nov 3;34(11):1180-1190. Epub 2016 Oct 3.

Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA.

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http://dx.doi.org/10.1038/nbt.3678DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5125825PMC
November 2016

Soft X-Ray Tomography Reveals Gradual Chromatin Compaction and Reorganization during Neurogenesis In Vivo.

Cell Rep 2016 11;17(8):2125-2136

Department of Anatomy, University of California San Francisco, San Francisco, CA 94158, USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; National Center for X-Ray Tomography, University of California San Francisco, San Francisco, CA 94158, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2016.10.060DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5135017PMC
November 2016

Joint Bayesian inference of risk variants and tissue-specific epigenomic enrichments across multiple complex human diseases.

Nucleic Acids Res 2016 Oct 12;44(18):e144. Epub 2016 Jul 12.

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

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http://dx.doi.org/10.1093/nar/gkw627DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5062982PMC
October 2016

52 Genetic Loci Influencing Myocardial Mass.

Authors:
Pim van der Harst Jessica van Setten Niek Verweij Georg Vogler Lude Franke Matthew T Maurano Xinchen Wang Irene Mateo Leach Mark Eijgelsheim Nona Sotoodehnia Caroline Hayward Rossella Sorice Osorio Meirelles Leo-Pekka Lyytikäinen Ozren Polašek Toshiko Tanaka Dan E Arking Sheila Ulivi Stella Trompet Martina Müller-Nurasyid Albert V Smith Marcus Dörr Kathleen F Kerr Jared W Magnani Fabiola Del Greco M Weihua Zhang Ilja M Nolte Claudia T Silva Sandosh Padmanabhan Vinicius Tragante Tõnu Esko Gonçalo R Abecasis Michiel E Adriaens Karl Andersen Phil Barnett Joshua C Bis Rolf Bodmer Brendan M Buckley Harry Campbell Megan V Cannon Aravinda Chakravarti Lin Y Chen Alessandro Delitala Richard B Devereux Pieter A Doevendans Anna F Dominiczak Luigi Ferrucci Ian Ford Christian Gieger Tamara B Harris Eric Haugen Matthias Heinig Dena G Hernandez Hans L Hillege Joel N Hirschhorn Albert Hofman Norbert Hubner Shih-Jen Hwang Annamaria Iorio Mika Kähönen Manolis Kellis Ivana Kolcic Ishminder K Kooner Jaspal S Kooner Jan A Kors Edward G Lakatta Kasper Lage Lenore J Launer Daniel Levy Alicia Lundby Peter W Macfarlane Dalit May Thomas Meitinger Andres Metspalu Stefania Nappo Silvia Naitza Shane Neph Alex S Nord Teresa Nutile Peter M Okin Jesper V Olsen Ben A Oostra Josef M Penninger Len A Pennacchio Tune H Pers Siegfried Perz Annette Peters Yigal M Pinto Arne Pfeufer Maria Grazia Pilia Peter P Pramstaller Bram P Prins Olli T Raitakari Soumya Raychaudhuri Ken M Rice Elizabeth J Rossin Jerome I Rotter Sebastian Schafer David Schlessinger Carsten O Schmidt Jobanpreet Sehmi Herman H W Silljé Gianfranco Sinagra Moritz F Sinner Kamil Slowikowski Elsayed Z Soliman Timothy D Spector Wilko Spiering John A Stamatoyannopoulos Ronald P Stolk Konstantin Strauch Sian-Tsung Tan Kirill V Tarasov Bosco Trinh Andre G Uitterlinden Malou van den Boogaard Cornelia M van Duijn Wiek H van Gilst Jorma S Viikari Peter M Visscher Veronique Vitart Uwe Völker Melanie Waldenberger Christian X Weichenberger Harm-Jan Westra Cisca Wijmenga Bruce H Wolffenbuttel Jian Yang Connie R Bezzina Patricia B Munroe Harold Snieder Alan F Wright Igor Rudan Laurie A Boyer Folkert W Asselbergs Dirk J van Veldhuisen Bruno H Stricker Bruce M Psaty Marina Ciullo Serena Sanna Terho Lehtimäki James F Wilson Stefania Bandinelli Alvaro Alonso Paolo Gasparini J Wouter Jukema Stefan Kääb Vilmundur Gudnason Stephan B Felix Susan R Heckbert Rudolf A de Boer Christopher Newton-Cheh Andrew A Hicks John C Chambers Yalda Jamshidi Axel Visel Vincent M Christoffels Aaron Isaacs Nilesh J Samani Paul I W de Bakker

J Am Coll Cardiol 2016 09;68(13):1435-1448

Department of Medical Genetics, University Medical Center Utrecht, Utrecht, the Netherlands; Department of Epidemiology, University Medical Center Utrecht, Utrecht, the Netherlands.

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http://dx.doi.org/10.1016/j.jacc.2016.07.729DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5478167PMC
September 2016

Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases.

Nat Methods 2016 Apr 7;13(4):366-70. Epub 2016 Mar 7.

Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.

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http://dx.doi.org/10.1038/nmeth.3799DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4967716PMC
April 2016

Improved Identification and Analysis of Small Open Reading Frame Encoded Polypeptides.

Anal Chem 2016 Apr 24;88(7):3967-75. Epub 2016 Mar 24.

Salk Institute for Biological Studies, Clayton Foundation Laboratories for Peptide Biology , 10010 North Torrey Pines Road, La Jolla, California 92037, United States.

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http://dx.doi.org/10.1021/acs.analchem.6b00191DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4939623PMC
April 2016

HaploReg v4: systematic mining of putative causal variants, cell types, regulators and target genes for human complex traits and disease.

Nucleic Acids Res 2016 Jan 10;44(D1):D877-81. Epub 2015 Dec 10.

Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA The Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA

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http://dx.doi.org/10.1093/nar/gkv1340DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702929PMC
January 2016

FTO Obesity Variant and Adipocyte Browning in Humans.

N Engl J Med 2016 01;374(2):192-3

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http://dx.doi.org/10.1056/NEJMc1513316DOI Listing
January 2016

FTO Obesity Variant Circuitry and Adipocyte Browning in Humans.

N Engl J Med 2015 Sep 19;373(10):895-907. Epub 2015 Aug 19.

From Beth Israel Deaconess Medical Center and Hebrew SeniorLife, Gerontology Division, Harvard Medical School, Boston (M.C., Y.-H.H.); Massachusetts Institute of Technology (MIT) Computer Science and Artificial Intelligence Laboratory (M.C., G.Q., W.M., N.A.A., M.K.), and Broad Institute of MIT and Harvard, Cambridge (M.C., G.Q., W.M., M.K.); Clinical Cooperation Group "Nutrigenomics and Type 2 Diabetes," Helmholtz Center Munich (M.C., H.H.), and Else Kröner-Fresenius Center for Nutritional Medicine, Klinikum rechts der Isar, ZIEL-Institute for Food and Health, Technische Universität München (M.C., V.G., I.S.S., H.H.), Munich, Germany; KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, and Hormone Laboratory, Haukeland University Hospital, Bergen, Norway (S.N.D., C.H., G.M.); Program in Developmental and Stem Cell Biology, Hospital for Sick Children, and Department of Molecular Genetics, University of Toronto (K.-H.K., V.P., J.L., C.-C.H.), and Department of Medicine, Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital (J.L.B., D.J.D.), Toronto; and the Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden (P.-A.S.).

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http://dx.doi.org/10.1056/NEJMoa1502214DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4959911PMC
September 2015

PRC2 Is Required to Maintain Expression of the Maternal Gtl2-Rian-Mirg Locus by Preventing De Novo DNA Methylation in Mouse Embryonic Stem Cells.

Cell Rep 2015 Sep 20;12(9):1456-70. Epub 2015 Aug 20.

Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute (DFCI), Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute (HHMI), Boston, MA 02115, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2015.07.053DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5384103PMC
September 2015

Deep learning for regulatory genomics.

Nat Biotechnol 2015 Aug;33(8):825-6

Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.

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http://dx.doi.org/10.1038/nbt.3313DOI Listing
August 2015

Systematic chromatin state comparison of epigenomes associated with diverse properties including sex and tissue type.

Nat Commun 2015 Aug 18;6:7973. Epub 2015 Aug 18.

1] Electrical Engineering and Computer Science Department, Computer Science and Artificial Intelligence Laboratory, MIT, 32 Vassar Street, 32D-524, Cambridge, Massachusetts 02139, USA [2] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.

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http://dx.doi.org/10.1038/ncomms8973DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4557131PMC
August 2015

Activity-Induced DNA Breaks Govern the Expression of Neuronal Early-Response Genes.

Cell 2015 Jun 4;161(7):1592-605. Epub 2015 Jun 4.

Picower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; The Broad Institute of Harvard and MIT, Cambridge, MA 02139, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2015.05.032DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4886855PMC
June 2015

Context influences on TALE-DNA binding revealed by quantitative profiling.

Nat Commun 2015 Jun 11;6:7440. Epub 2015 Jun 11.

1] Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA [2] Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, Massachusetts 02138, USA [3] Harvard-MIT Division of Health Sciences and Technology (HST), Harvard Medical School, Boston, Massachusetts 02115, USA [4] Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA.

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http://dx.doi.org/10.1038/ncomms8440DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4467457PMC
June 2015

Alzheimer's loci: epigenetic associations and interaction with genetic factors.

Ann Clin Transl Neurol 2015 Jun 24;2(6):636-47. Epub 2015 Apr 24.

Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Departments of Neurology and Psychiatry, Brigham and Women's Hospital Boston, Massachusetts, 02115 ; Department of Neurology, Harvard Medical School Boston, Massachusetts, 02115 ; Medical and Population Genetics, Broad Institute of MIT and Harvard Cambridge, Massachusetts, 02142.

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http://dx.doi.org/10.1002/acn3.201DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4479524PMC
June 2015

Sharing and Specificity of Co-expression Networks across 35 Human Tissues.

PLoS Comput Biol 2015 May 13;11(5):e1004220. Epub 2015 May 13.

Department of Computer Science, Stanford University, Stanford, California, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1004220DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4430528PMC
May 2015

Improved gene tree error correction in the presence of horizontal gene transfer.

Bioinformatics 2015 Apr 5;31(8):1211-8. Epub 2014 Dec 5.

Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA, Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, USA and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge and Broad Institute, Cambridge, MA, USA Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA, Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, USA and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge and Broad Institute, Cambridge, MA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu806DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4393519PMC
April 2015

Large-scale imputation of epigenomic datasets for systematic annotation of diverse human tissues.

Nat Biotechnol 2015 Apr 18;33(4):364-76. Epub 2015 Feb 18.

1] MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, Massachusetts, USA. [2] Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.

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http://dx.doi.org/10.1038/nbt.3157DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4512306PMC
April 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

BRCA1 recruitment to transcriptional pause sites is required for R-loop-driven DNA damage repair.

Mol Cell 2015 Feb;57(4):636-647

Department of Genetics, Harvard Medical School, Boston, MA 02215, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2015.01.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4351672PMC
February 2015

Mosquito genomics. Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes.

Authors:
Daniel E Neafsey Robert M Waterhouse Mohammad R Abai Sergey S Aganezov Max A Alekseyev James E Allen James Amon Bruno Arcà Peter Arensburger Gleb Artemov Lauren A Assour Hamidreza Basseri Aaron Berlin Bruce W Birren Stephanie A Blandin Andrew I Brockman Thomas R Burkot Austin Burt Clara S Chan Cedric Chauve Joanna C Chiu Mikkel Christensen Carlo Costantini Victoria L M Davidson Elena Deligianni Tania Dottorini Vicky Dritsou Stacey B Gabriel Wamdaogo M Guelbeogo Andrew B Hall Mira V Han Thaung Hlaing Daniel S T Hughes Adam M Jenkins Xiaofang Jiang Irwin Jungreis Evdoxia G Kakani Maryam Kamali Petri Kemppainen Ryan C Kennedy Ioannis K Kirmitzoglou Lizette L Koekemoer Njoroge Laban Nicholas Langridge Mara K N Lawniczak Manolis Lirakis Neil F Lobo Ernesto Lowy Robert M MacCallum Chunhong Mao Gareth Maslen Charles Mbogo Jenny McCarthy Kristin Michel Sara N Mitchell Wendy Moore Katherine A Murphy Anastasia N Naumenko Tony Nolan Eva M Novoa Samantha O'Loughlin Chioma Oringanje Mohammad A Oshaghi Nazzy Pakpour Philippos A Papathanos Ashley N Peery Michael Povelones Anil Prakash David P Price Ashok Rajaraman Lisa J Reimer David C Rinker Antonis Rokas Tanya L Russell N'Fale Sagnon Maria V Sharakhova Terrance Shea Felipe A Simão Frederic Simard Michel A Slotman Pradya Somboon Vladimir Stegniy Claudio J Struchiner Gregg W C Thomas Marta Tojo Pantelis Topalis José M C Tubio Maria F Unger John Vontas Catherine Walton Craig S Wilding Judith H Willis Yi-Chieh Wu Guiyun Yan Evgeny M Zdobnov Xiaofan Zhou Flaminia Catteruccia George K Christophides Frank H Collins Robert S Cornman Andrea Crisanti Martin J Donnelly Scott J Emrich Michael C Fontaine William Gelbart Matthew W Hahn Immo A Hansen Paul I Howell Fotis C Kafatos Manolis Kellis Daniel Lawson Christos Louis Shirley Luckhart Marc A T Muskavitch José M Ribeiro Michael A Riehle Igor V Sharakhov Zhijian Tu Laurence J Zwiebel Nora J Besansky

Science 2015 Jan 27;347(6217):1258522. Epub 2014 Nov 27.

Eck Institute for Global Health and Department of Biological Sciences, University of Notre Dame, 317 Galvin Life Sciences Building, Notre Dame, IN 46556, USA.

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http://dx.doi.org/10.1126/science.1258522DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4380271PMC
January 2015

Energy-based RNA consensus secondary structure prediction in multiple sequence alignments.

Methods Mol Biol 2014 ;1097:125-41

Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, Cambridge, MA, USA.

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http://dx.doi.org/10.1007/978-1-62703-709-9_7DOI Listing
November 2014

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

CHD8 regulates neurodevelopmental pathways associated with autism spectrum disorder in neural progenitors.

Proc Natl Acad Sci U S A 2014 Oct 7;111(42):E4468-77. Epub 2014 Oct 7.

Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114; Departments of Neurology and Broad Institute of M.I.T. and Harvard, Cambridge, MA 02142

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http://dx.doi.org/10.1073/pnas.1405266111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4210312PMC
October 2014

The NF-κB genomic landscape in lymphoblastoid B cells.

Cell Rep 2014 Sep 21;8(5):1595-606. Epub 2014 Aug 21.

Division of Infectious Disease, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2014.07.037DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4163118PMC
September 2014

Genetic association study of QT interval highlights role for calcium signaling pathways in myocardial repolarization.

Authors:
Dan E Arking Sara L Pulit Lia Crotti Pim van der Harst Patricia B Munroe Tamara T Koopmann Nona Sotoodehnia Elizabeth J Rossin Michael Morley Xinchen Wang Andrew D Johnson Alicia Lundby Daníel F Gudbjartsson Peter A Noseworthy Mark Eijgelsheim Yuki Bradford Kirill V Tarasov Marcus Dörr Martina Müller-Nurasyid Annukka M Lahtinen Ilja M Nolte Albert Vernon Smith Joshua C Bis Aaron Isaacs Stephen J Newhouse Daniel S Evans Wendy S Post Daryl Waggott Leo-Pekka Lyytikäinen Andrew A Hicks Lewin Eisele David Ellinghaus Caroline Hayward Pau Navarro Sheila Ulivi Toshiko Tanaka David J Tester Stéphanie Chatel Stefan Gustafsson Meena Kumari Richard W Morris Åsa T Naluai Sandosh Padmanabhan Alexander Kluttig Bernhard Strohmer Andrie G Panayiotou Maria Torres Michael Knoflach Jaroslav A Hubacek Kamil Slowikowski Soumya Raychaudhuri Runjun D Kumar Tamara B Harris Lenore J Launer Alan R Shuldiner Alvaro Alonso Joel S Bader Georg Ehret Hailiang Huang W H Linda Kao James B Strait Peter W Macfarlane Morris Brown Mark J Caulfield Nilesh J Samani Florian Kronenberg Johann Willeit J Gustav Smith Karin H Greiser Henriette Meyer Zu Schwabedissen Karl Werdan Massimo Carella Leopoldo Zelante Susan R Heckbert Bruce M Psaty Jerome I Rotter Ivana Kolcic Ozren Polašek Alan F Wright Maura Griffin Mark J Daly David O Arnar Hilma Hólm Unnur Thorsteinsdottir Joshua C Denny Dan M Roden Rebecca L Zuvich Valur Emilsson Andrew S Plump Martin G Larson Christopher J O'Donnell Xiaoyan Yin Marco Bobbo Adamo P D'Adamo Annamaria Iorio Gianfranco Sinagra Angel Carracedo Steven R Cummings Michael A Nalls Antti Jula Kimmo K Kontula Annukka Marjamaa Lasse Oikarinen Markus Perola Kimmo Porthan Raimund Erbel Per Hoffmann Karl-Heinz Jöckel Hagen Kälsch Markus M Nöthen Marcel den Hoed Ruth J F Loos Dag S Thelle Christian Gieger Thomas Meitinger Siegfried Perz Annette Peters Hanna Prucha Moritz F Sinner Melanie Waldenberger Rudolf A de Boer Lude Franke Pieter A van der Vleuten Britt Maria Beckmann Eimo Martens Abdennasser Bardai Nynke Hofman Arthur A M Wilde Elijah R Behr Chrysoula Dalageorgou John R Giudicessi Argelia Medeiros-Domingo Julien Barc Florence Kyndt Vincent Probst Alice Ghidoni Roberto Insolia Robert M Hamilton Stephen W Scherer Jeffrey Brandimarto Kenneth Margulies Christine E Moravec Fabiola del Greco M Christian Fuchsberger Jeffrey R O'Connell Wai K Lee Graham C M Watt Harry Campbell Sarah H Wild Nour E El Mokhtari Norbert Frey Folkert W Asselbergs Irene Mateo Leach Gerjan Navis Maarten P van den Berg Dirk J van Veldhuisen Manolis Kellis Bouwe P Krijthe Oscar H Franco Albert Hofman Jan A Kors André G Uitterlinden Jacqueline C M Witteman Lyudmyla Kedenko Claudia Lamina Ben A Oostra Gonçalo R Abecasis Edward G Lakatta Antonella Mulas Marco Orrú David Schlessinger Manuela Uda Marcello R P Markus Uwe Völker Harold Snieder Timothy D Spector Johan Ärnlöv Lars Lind Johan Sundström Ann-Christine Syvänen Mika Kivimaki Mika Kähönen Nina Mononen Olli T Raitakari Jorma S Viikari Vera Adamkova Stefan Kiechl Maria Brion Andrew N Nicolaides Bernhard Paulweber Johannes Haerting Anna F Dominiczak Fredrik Nyberg Peter H Whincup Aroon D Hingorani Jean-Jacques Schott Connie R Bezzina Erik Ingelsson Luigi Ferrucci Paolo Gasparini James F Wilson Igor Rudan Andre Franke Thomas W Mühleisen Peter P Pramstaller Terho J Lehtimäki Andrew D Paterson Afshin Parsa Yongmei Liu Cornelia M van Duijn David S Siscovick Vilmundur Gudnason Yalda Jamshidi Veikko Salomaa Stephan B Felix Serena Sanna Marylyn D Ritchie Bruno H Stricker Kari Stefansson Laurie A Boyer Thomas P Cappola Jesper V Olsen Kasper Lage Peter J Schwartz Stefan Kääb Aravinda Chakravarti Michael J Ackerman Arne Pfeufer Paul I W de Bakker Christopher Newton-Cheh

Nat Genet 2014 Aug 22;46(8):826-36. Epub 2014 Jun 22.

1] Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, USA. [2] Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA. [3] Harvard Medical School, Boston, Massachusetts, USA. [4] Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts, USA. [5].

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http://dx.doi.org/10.1038/ng.3014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4124521PMC
August 2014

Evidence of efficient stop codon readthrough in four mammalian genes.

Nucleic Acids Res 2014 Aug 10;42(14):8928-38. Epub 2014 Jul 10.

School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland Department of Human Genetics, University of Utah, Salt Lake City, UT 84112-5330, USA

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http://dx.doi.org/10.1093/nar/gku608DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4132726PMC
August 2014

Distinct and predictive histone lysine acetylation patterns at promoters, enhancers, and gene bodies.

G3 (Bethesda) 2014 Aug 12;4(11):2051-63. Epub 2014 Aug 12.

Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093-0653 Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, and Moores Cancer Center, University of California, San Diego School of Medicine, La Jolla, California 92093

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http://dx.doi.org/10.1534/g3.114.013565DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4232531PMC
August 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

Pareto-optimal phylogenetic tree reconciliation.

Bioinformatics 2014 Jun;30(12):i87-95

Department of Computer Science, Harvey Mudd College, Claremont, CA 91711, Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA 02139, Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269 and Broad Institute, Cambridge, MA 02142, USADepartment of Computer Science, Harvey Mudd College, Claremont, CA 91711, Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA 02139, Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269 and Broad Institute, Cambridge, MA 02142, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu289DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4058917PMC
June 2014

RECOMB/ISCB systems biology, regulatory genomics, and DREAM 2013 special issue.

J Comput Biol 2014 May;21(5):371-2

1 Departments of Systems Biology, Biochemistry & Molecular Biophysics, Biomedical Informatics, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center , New York, New York.

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http://dx.doi.org/10.1089/cmb.2014.009pDOI Listing
May 2014

Evolutionary dynamics and tissue specificity of human long noncoding RNAs in six mammals.

Genome Res 2014 Apr 15;24(4):616-28. Epub 2014 Jan 15.

Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02140, USA;

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http://dx.doi.org/10.1101/gr.165035.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3975061PMC
April 2014

Most parsimonious reconciliation in the presence of gene duplication, loss, and deep coalescence using labeled coalescent trees.

Genome Res 2014 Mar 5;24(3):475-86. Epub 2013 Dec 5.

Department of Electrical Engineering and Computer Science, Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;

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http://genome.cshlp.org/cgi/doi/10.1101/gr.161968.113
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http://dx.doi.org/10.1101/gr.161968.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3941112PMC
March 2014

Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments.

Nucleic Acids Res 2014 Mar 13;42(5):2976-87. Epub 2013 Dec 13.

Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, MA 02139, USA and Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1093/nar/gkt1249DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3950668PMC
March 2014

Discovery of human sORF-encoded polypeptides (SEPs) in cell lines and tissue.

J Proteome Res 2014 Mar 14;13(3):1757-65. Epub 2014 Feb 14.

Department of Chemistry and Chemical Biology, Harvard University , 12 Oxford Street, Cambridge, Massachusetts 02138, United States.

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http://dx.doi.org/10.1021/pr401280wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3993966PMC
March 2014

Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo.

Nature 2014 Jan 15;505(7485):701-5. Epub 2013 Dec 15.

Department of Cellular and Molecular Pharmacology, California Institute of Quantitative Biology, Center for RNA Systems Biology, Howard Hughes Medical Institute, University of California, San Francisco, California 94158, USA.

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http://dx.doi.org/10.1038/nature12894DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3966492PMC
January 2014

Integrating and mining the chromatin landscape of cell-type specificity using self-organizing maps.

Genome Res 2013 Dec 29;23(12):2136-48. Epub 2013 Oct 29.

Department of Developmental and Cell Biology, University of California, Irvine, California 92697, USA;

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http://dx.doi.org/10.1101/gr.158261.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3847782PMC
December 2013

Reconciliation revisited: handling multiple optima when reconciling with duplication, transfer, and loss.

J Comput Biol 2013 Oct 14;20(10):738-54. Epub 2013 Sep 14.

1 Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology , Cambridge, Massachusetts.

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http://dx.doi.org/10.1089/cmb.2013.0073DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3791060PMC
October 2013

Network deconvolution as a general method to distinguish direct dependencies in networks.

Nat Biotechnol 2013 Aug 14;31(8):726-33. Epub 2013 Jul 14.

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

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http://dx.doi.org/10.1038/nbt.2635DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3773370PMC
August 2013

Response to comment on "Evidence of abundant purifying selection in humans for recently acquired regulatory functions".

Science 2013 May;340(6133):682

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

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http://dx.doi.org/10.1126/science.1233366DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4131756PMC
May 2013