Publications by authors named "Ernest Fraenkel"

74Publications

Aberrant Development Corrected in Adult-Onset Huntington's Disease iPSC-Derived Neuronal Cultures via WNT Signaling Modulation.

Stem Cell Reports 2020 03 27;14(3):406-419. Epub 2020 Feb 27.

Department of Psychiatry and Human Behavior, University of California Irvine, Irvine, CA 92697, USA; Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA 96267, USA; Department of Memory Impairment and Neurological Disorders, University of California Irvine, Irvine, CA 92697, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Biological Chemistry, University of California Irvine, Irvine, CA 92617, USA. Electronic address:

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http://dx.doi.org/10.1016/j.stemcr.2020.01.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7066322PMC
March 2020

A Multi-Omics Interpretable Machine Learning Model Reveals Modes of Action of Small Molecules.

Sci Rep 2020 01 22;10(1):954. Epub 2020 Jan 22.

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

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http://dx.doi.org/10.1038/s41598-020-57691-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6976599PMC
January 2020

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 2020

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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