Ernest Fraenkel

Ernest Fraenkel

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Ernest Fraenkel

Publications by authors named "Ernest Fraenkel"

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Bioenergetic deficits in Huntington's disease iPSC-derived neural cells and rescue with glycolytic metabolites.

Hum Mol Genet 2019 Feb 15. Epub 2019 Feb 15.

Division of Neurobiology, Departments of Psychiatry, Neurology, Pharmacology, and Neuroscience, Johns Hopkins University School of Medicine, 600 North Wolfe Street, CMSC 8-121, Baltimore, Maryland 21287 USA.

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http://dx.doi.org/10.1093/hmg/ddy430DOI Listing
February 2019

Shallow Sparsely-Connected Autoencoders for Gene Set Projection.

Pac Symp Biocomput 2019 ;24:374-385

Department of Biological Engineering, Massachusetts Institute of Technology, 21 Ames St. Cambridge, MA, 02139, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6417803PMC
January 2019

Discovering Altered Regulation and Signaling Through Network-based Integration of Transcriptomic, Epigenomic, and Proteomic Tumor Data.

Methods Mol Biol 2018 ;1711:13-26

Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.

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http://dx.doi.org/10.1007/978-1-4939-7493-1_2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6309679PMC
October 2018

Turning omics data into therapeutic insights.

Curr Opin Pharmacol 2018 10 24;42:95-101. Epub 2018 Aug 24.

Computational & Systems Biology Program and the Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S14714892173020
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http://dx.doi.org/10.1016/j.coph.2018.08.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6204089PMC
October 2018

Synthesizing Signaling Pathways from Temporal Phosphoproteomic Data.

Cell Rep 2018 09;24(13):3607-3618

Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, USA; Morgridge Institute for Research, Madison, WI, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S22111247183138
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http://dx.doi.org/10.1016/j.celrep.2018.08.085DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6295338PMC
September 2018

Tissue and cellular rigidity and mechanosensitive signaling activation in Alexander disease.

Nat Commun 2018 05 15;9(1):1899. Epub 2018 May 15.

Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.

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http://dx.doi.org/10.1038/s41467-018-04269-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5954157PMC
May 2018

Genome-wide Analyses Identify KIF5A as a Novel ALS Gene.

Authors:
Aude Nicolas Kevin P Kenna Alan E Renton Nicola Ticozzi Faraz Faghri Ruth Chia Janice A Dominov Brendan J Kenna Mike A Nalls Pamela Keagle Alberto M Rivera Wouter van Rheenen Natalie A Murphy Joke J F A van Vugt Joshua T Geiger Rick A Van der Spek Hannah A Pliner Shankaracharya Bradley N Smith Giuseppe Marangi Simon D Topp Yevgeniya Abramzon Athina Soragia Gkazi John D Eicher Aoife Kenna Gabriele Mora Andrea Calvo Letizia Mazzini Nilo Riva Jessica Mandrioli Claudia Caponnetto Stefania Battistini Paolo Volanti Vincenzo La Bella Francesca L Conforti Giuseppe Borghero Sonia Messina Isabella L Simone Francesca Trojsi Fabrizio Salvi Francesco O Logullo Sandra D'Alfonso Lucia Corrado Margherita Capasso Luigi Ferrucci Cristiane de Araujo Martins Moreno Sitharthan Kamalakaran David B Goldstein Aaron D Gitler Tim Harris Richard M Myers Hemali Phatnani Rajeeva Lochan Musunuri Uday Shankar Evani Avinash Abhyankar Michael C Zody Julia Kaye Steven Finkbeiner Stacia K Wyman Alex LeNail Leandro Lima Ernest Fraenkel Clive N Svendsen Leslie M Thompson Jennifer E Van Eyk James D Berry Timothy M Miller Stephen J Kolb Merit Cudkowicz Emily Baxi Michael Benatar J Paul Taylor Evadnie Rampersaud Gang Wu Joanne Wuu Giuseppe Lauria Federico Verde Isabella Fogh Cinzia Tiloca Giacomo P Comi Gianni Sorarù Cristina Cereda Philippe Corcia Hannu Laaksovirta Liisa Myllykangas Lilja Jansson Miko Valori John Ealing Hisham Hamdalla Sara Rollinson Stuart Pickering-Brown Richard W Orrell Katie C Sidle Andrea Malaspina John Hardy Andrew B Singleton Janel O Johnson Sampath Arepalli Peter C Sapp Diane McKenna-Yasek Meraida Polak Seneshaw Asress Safa Al-Sarraj Andrew King Claire Troakes Caroline Vance Jacqueline de Belleroche Frank Baas Anneloor L M A Ten Asbroek José Luis Muñoz-Blanco Dena G Hernandez Jinhui Ding J Raphael Gibbs Sonja W Scholz Mary Kay Floeter Roy H Campbell Francesco Landi Robert Bowser Stefan M Pulst John M Ravits Daniel J L MacGowan Janine Kirby Erik P Pioro Roger Pamphlett James Broach Glenn Gerhard Travis L Dunckley Christopher B Brady Neil W Kowall Juan C Troncoso Isabelle Le Ber Kevin Mouzat Serge Lumbroso Terry D Heiman-Patterson Freya Kamel Ludo Van Den Bosch Robert H Baloh Tim M Strom Thomas Meitinger Aleksey Shatunov Kristel R Van Eijk Mamede de Carvalho Maarten Kooyman Bas Middelkoop Matthieu Moisse Russell L McLaughlin Michael A Van Es Markus Weber Kevin B Boylan Marka Van Blitterswijk Rosa Rademakers Karen E Morrison A Nazli Basak Jesús S Mora Vivian E Drory Pamela J Shaw Martin R Turner Kevin Talbot Orla Hardiman Kelly L Williams Jennifer A Fifita Garth A Nicholson Ian P Blair Guy A Rouleau Jesús Esteban-Pérez Alberto García-Redondo Ammar Al-Chalabi Ekaterina Rogaeva Lorne Zinman Lyle W Ostrow Nicholas J Maragakis Jeffrey D Rothstein Zachary Simmons Johnathan Cooper-Knock Alexis Brice Stephen A Goutman Eva L Feldman Summer B Gibson Franco Taroni Antonia Ratti Cinzia Gellera Philip Van Damme Wim Robberecht Pietro Fratta Mario Sabatelli Christian Lunetta Albert C Ludolph Peter M Andersen Jochen H Weishaupt William Camu John Q Trojanowski Vivianna M Van Deerlin Robert H Brown Leonard H van den Berg Jan H Veldink Matthew B Harms Jonathan D Glass David J Stone Pentti Tienari Vincenzo Silani Adriano Chiò Christopher E Shaw Bryan J Traynor John E Landers

Neuron 2018 03;97(6):1268-1283.e6

Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA. Electronic address:

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http://dx.doi.org/10.1016/j.neuron.2018.02.027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5867896PMC
March 2018

The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations.

Authors:
Alexandra B Keenan Sherry L Jenkins Kathleen M Jagodnik Simon Koplev Edward He Denis Torre Zichen Wang Anders B Dohlman Moshe C Silverstein Alexander Lachmann Maxim V Kuleshov Avi Ma'ayan Vasileios Stathias Raymond Terryn Daniel Cooper Michele Forlin Amar Koleti Dusica Vidovic Caty Chung Stephan C Schürer Jouzas Vasiliauskas Marcin Pilarczyk Behrouz Shamsaei Mehdi Fazel Yan Ren Wen Niu Nicholas A Clark Shana White Naim Mahi Lixia Zhang Michal Kouril John F Reichard Siva Sivaganesan Mario Medvedovic Jaroslaw Meller Rick J Koch Marc R Birtwistle Ravi Iyengar Eric A Sobie Evren U Azeloglu Julia Kaye Jeannette Osterloh Kelly Haston Jaslin Kalra Steve Finkbiener Jonathan Li Pamela Milani Miriam Adam Renan Escalante-Chong Karen Sachs Alex Lenail Divya Ramamoorthy Ernest Fraenkel Gavin Daigle Uzma Hussain Alyssa Coye Jeffrey Rothstein Dhruv Sareen Loren Ornelas Maria Banuelos Berhan Mandefro Ritchie Ho Clive N Svendsen Ryan G Lim Jennifer Stocksdale Malcolm S Casale Terri G Thompson Jie Wu Leslie M Thompson Victoria Dardov Vidya Venkatraman Andrea Matlock Jennifer E Van Eyk Jacob D Jaffe Malvina Papanastasiou Aravind Subramanian Todd R Golub Sean D Erickson Mohammad Fallahi-Sichani Marc Hafner Nathanael S Gray Jia-Ren Lin Caitlin E Mills Jeremy L Muhlich Mario Niepel Caroline E Shamu Elizabeth H Williams David Wrobel Peter K Sorger Laura M Heiser Joe W Gray James E Korkola Gordon B Mills Mark LaBarge Heidi S Feiler Mark A Dane Elmar Bucher Michel Nederlof Damir Sudar Sean Gross David F Kilburn Rebecca Smith Kaylyn Devlin Ron Margolis Leslie Derr Albert Lee Ajay Pillai

Cell Syst 2018 01 29;6(1):13-24. Epub 2017 Nov 29.

NIH, Bethesda, MD 20892, USA.

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http://dx.doi.org/10.1016/j.cels.2017.11.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5799026PMC
January 2018

Hepatic Dysfunction Caused by Consumption of a High-Fat Diet.

Cell Rep 2017 Dec;21(11):3317-3328

Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2017.11.059DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5734865PMC
December 2017

Network modeling of kinase inhibitor polypharmacology reveals pathways targeted in chemical screens.

PLoS One 2017 12;12(10):e0185650. Epub 2017 Oct 12.

Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0185650PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5638242PMC
October 2017

Identifying therapeutic targets by combining transcriptional data with ordinal clinical measurements.

Nat Commun 2017 09 20;8(1):623. Epub 2017 Sep 20.

Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts, 02139, USA.

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http://dx.doi.org/10.1038/s41467-017-00353-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5606996PMC
September 2017

The whole-genome landscape of medulloblastoma subtypes.

Nature 2017 07;547(7663):311-317

Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany.

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http://dx.doi.org/10.1038/nature22973DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5905700PMC
July 2017

PCSF: An R-package for network-based interpretation of high-throughput data.

PLoS Comput Biol 2017 Jul 31;13(7):e1005694. Epub 2017 Jul 31.

Dalle Molle Institute for Artificial Intelligence Research (USI/SUPSI), Manno, Switzerland.

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http://dx.doi.org/10.1371/journal.pcbi.1005694DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5552342PMC
July 2017

Huntington's Disease iPSC-Derived Brain Microvascular Endothelial Cells Reveal WNT-Mediated Angiogenic and Blood-Brain Barrier Deficits.

Cell Rep 2017 05;19(7):1365-1377

Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA; UCI MIND, University of California, Irvine, Irvine, CA 92697, USA; Neurobiology and Behavior, University of California, Irvine, Irvine, CA 92697, USA; Psychiatry and Human Behavior, University of California, Irvine, Irvine, CA 92697, USA; Sue and Bill Gross Stem Cell Center, University of California, Irvine, Irvine, CA 92697, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2017.04.021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5646270PMC
May 2017

Revealing disease-associated pathways by network integration of untargeted metabolomics.

Nat Methods 2016 09 1;13(9):770-6. Epub 2016 Aug 1.

Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.

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http://dx.doi.org/10.1038/nmeth.3940DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5209295PMC
September 2016

Pathway-based network modeling finds hidden genes in shRNA screen for regulators of acute lymphoblastic leukemia.

Integr Biol (Camb) 2016 07 17;8(7):761-74. Epub 2016 Jun 17.

Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, 16-343, Cambridge MA 02139, USA.

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http://dx.doi.org/10.1039/c6ib00040aDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5224708PMC
July 2016

Network Modeling Identifies Patient-specific Pathways in Glioblastoma.

Sci Rep 2016 06 29;6:28668. Epub 2016 Jun 29.

Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, USA.

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http://dx.doi.org/10.1038/srep28668DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4926112PMC
June 2016

Poly-glutamine expanded huntingtin dramatically alters the genome wide binding of HSF1.

J Huntingtons Dis 2012 ;1(1):33-45

Department of Biological Engineering, Massachusetts Institute of Technology, 77 Mass Ave., Cambridge, MA, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3537492PMC
May 2016

Cell freezing protocol suitable for ATAC-Seq on motor neurons derived from human induced pluripotent stem cells.

Sci Rep 2016 05 5;6:25474. Epub 2016 May 5.

Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, United States of America.

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http://dx.doi.org/10.1038/srep25474DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4857123PMC
May 2016

Network-Based Interpretation of Diverse High-Throughput Datasets through the Omics Integrator Software Package.

PLoS Comput Biol 2016 Apr 20;12(4):e1004879. Epub 2016 Apr 20.

Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1004879DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4838263PMC
April 2016

Multiplexed barcoded CRISPR-Cas9 screening enabled by CombiGEM.

Proc Natl Acad Sci U S A 2016 Mar 10;113(9):2544-9. Epub 2016 Feb 10.

Synthetic Biology Group, Massachusetts Institute of Technology (MIT) Synthetic Biology Center, MIT, Cambridge, MA 02139; Research Laboratory of Electronics, MIT, Cambridge, MA 02139; Department of Biological Engineering, MIT, Cambridge, MA 02139; Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA 02139;

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http://dx.doi.org/10.1073/pnas.1517883113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4780610PMC
March 2016

Elucidating MicroRNA Regulatory Networks Using Transcriptional, Post-transcriptional, and Histone Modification Measurements.

Cell Rep 2016 Jan 31;14(2):310-9. Epub 2015 Dec 31.

Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2015.12.031DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4831719PMC
January 2016

SAMNetWeb: identifying condition-specific networks linking signaling and transcription.

Bioinformatics 2015 Apr 19;31(7):1124-6. Epub 2014 Nov 19.

Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu748DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4382899PMC
April 2015

The small molecule, genistein, increases hepcidin expression in human hepatocytes.

Hepatology 2013 Oct 19;58(4):1315-25. Epub 2013 Aug 19.

Division of Hematology/Oncology, Beth Israel Deaconess Medical Center and Department of Medicine, Harvard Medical School, Boston, MA.

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http://dx.doi.org/10.1002/hep.26490DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3770762PMC
October 2013

Analysis of in vitro insulin-resistance models and their physiological relevance to in vivo diet-induced adipose insulin resistance.

Cell Rep 2013 Oct 3;5(1):259-70. Epub 2013 Oct 3.

Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA.

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http://dx.doi.org/10.1016/j.celrep.2013.08.039DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3874466PMC
October 2013

Integrated network analyses for functional genomic studies in cancer.

Semin Cancer Biol 2013 Aug 27;23(4):213-8. Epub 2013 Jun 27.

Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, USA.

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http://dx.doi.org/10.1016/j.semcancer.2013.06.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3844556PMC
August 2013

Targeting H3K4 trimethylation in Huntington disease.

Proc Natl Acad Sci U S A 2013 Aug 19;110(32):E3027-36. Epub 2013 Jul 19.

Department of Psychiatry and Human Behavior and UCI Institute of Memory Impairments and Neurological Disorders, University of California, Irvine, CA 92697, USA.

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http://dx.doi.org/10.1073/pnas.1311323110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3740882PMC
August 2013

SOX2 co-occupies distal enhancer elements with distinct POU factors in ESCs and NPCs to specify cell state.

PLoS Genet 2013 21;9(2):e1003288. Epub 2013 Feb 21.

Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1003288DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3578749PMC
June 2013

Extensive changes in DNA methylation are associated with expression of mutant huntingtin.

Proc Natl Acad Sci U S A 2013 Feb 22;110(6):2354-9. Epub 2013 Jan 22.

Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.

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http://dx.doi.org/10.1073/pnas.1221292110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3568325PMC
February 2013

SAMNet: a network-based approach to integrate multi-dimensional high throughput datasets.

Integr Biol (Camb) 2012 Nov;4(11):1415-27

Dept. of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1039/c2ib20072dDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3501250PMC
November 2012

Swimming upstream: identifying proteomic signals that drive transcriptional changes using the interactome and multiple "-omics" datasets.

Methods Cell Biol 2012 ;110:57-80

Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.

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http://dx.doi.org/10.1016/B978-0-12-388403-9.00003-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3870464PMC
July 2012

SteinerNet: a web server for integrating 'omic' data to discover hidden components of response pathways.

Nucleic Acids Res 2012 Jul 25;40(Web Server issue):W505-9. Epub 2012 May 25.

Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1093/nar/gks445DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3394335PMC
July 2012

Genome-wide profiling of H3K56 acetylation and transcription factor binding sites in human adipocytes.

PLoS One 2011 2;6(6):e19778. Epub 2011 Jun 2.

Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0019778PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3107206PMC
October 2011

Large-scale discovery of ERK2 substrates identifies ERK-mediated transcriptional regulation by ETV3.

Sci Signal 2011 Oct 25;4(196):rs11. Epub 2011 Oct 25.

Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1126/scisignal.2002010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3779841PMC
October 2011

ResponseNet: revealing signaling and regulatory networks linking genetic and transcriptomic screening data.

Nucleic Acids Res 2011 Jul 16;39(Web Server issue):W424-9. Epub 2011 May 16.

Department of Computer Science, Ben-Gurion University of The Negev, Beer-Sheva 84105, Israel.

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http://dx.doi.org/10.1093/nar/gkr359DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125767PMC
July 2011

Sequence analysis of chromatin immunoprecipitation data for transcription factors.

Methods Mol Biol 2010 ;674:179-93

Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.

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http://dx.doi.org/10.1007/978-1-60761-854-6_11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3922641PMC
December 2010

Genomic characterization of Wilms' tumor suppressor 1 targets in nephron progenitor cells during kidney development.

Development 2010 Apr;137(7):1189-203

Department of Medicine, Children's Hospital Boston; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA.

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http://dx.doi.org/10.1242/dev.045732DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2835332PMC
April 2010

A quantitative model of transcriptional regulation reveals the influence of binding location on expression.

PLoS Comput Biol 2010 Apr 29;6(4):e1000773. Epub 2010 Apr 29.

Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1000773DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2861697PMC
April 2010

Integrating proteomic, transcriptional, and interactome data reveals hidden components of signaling and regulatory networks.

Sci Signal 2009 Jul 28;2(81):ra40. Epub 2009 Jul 28.

Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

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http://stke.sciencemag.org/cgi/doi/10.1126/scisignal.2000350
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http://dx.doi.org/10.1126/scisignal.2000350DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2889494PMC
July 2009

WebMOTIFS: automated discovery, filtering and scoring of DNA sequence motifs using multiple programs and Bayesian approaches.

Nucleic Acids Res 2007 Jul 21;35(Web Server issue):W217-20. Epub 2007 Jun 21.

Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1093/nar/gkm376DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933171PMC
July 2007

Foxp3 occupancy and regulation of key target genes during T-cell stimulation.

Nature 2007 Feb 21;445(7130):931-5. Epub 2007 Jan 21.

Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA.

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http://dx.doi.org/10.1038/nature05478DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3008159PMC
February 2007

High-resolution computational models of genome binding events.

Nat Biotechnol 2006 Aug;24(8):963-70

Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar Street, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1038/nbt1233DOI Listing
August 2006

Practical strategies for discovering regulatory DNA sequence motifs.

PLoS Comput Biol 2006 Apr;2(4):e36

Department of Electrical Engineering and Computer Science, Cambridge, Massachusetts, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.0020036DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1447654PMC
April 2006

An improved map of conserved regulatory sites for Saccharomyces cerevisiae.

BMC Bioinformatics 2006 Mar 7;7:113. Epub 2006 Mar 7.

Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA.

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http://dx.doi.org/10.1186/1471-2105-7-113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1435934PMC
March 2006

A hypothesis-based approach for identifying the binding specificity of regulatory proteins from chromatin immunoprecipitation data.

Bioinformatics 2006 Feb 6;22(4):423-9. Epub 2005 Dec 6.

MIT Computer Science and Artificial Intelligence, Laboratory 32, Vassar Street, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1093/bioinformatics/bti815DOI Listing
February 2006

TAMO: a flexible, object-oriented framework for analyzing transcriptional regulation using DNA-sequence motifs.

Bioinformatics 2005 Jul 19;21(14):3164-5. Epub 2005 May 19.

Whitehead Institute for Biomedical Research, Nine Cambridge Center Cambridge, MA 02142, USA.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/bti481DOI Listing
July 2005

Computational discovery of gene modules and regulatory networks.

Nat Biotechnol 2003 Nov 12;21(11):1337-42. Epub 2003 Oct 12.

MIT Computer Science and Artificial Intelligence Laboratory, 200 Technology Square, Cambridge, Massachusetts 02139, USA.

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http://dx.doi.org/10.1038/nbt890DOI Listing
November 2003