Publications

2020

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

Charlene Smith-Geater, Sarah J Hernandez, Ryan G Lim, Miriam Adam, Jie Wu, Jennifer T Stocksdale, Brook T Wassie, Maxwell Philip Gold, Keona Q Wang, Ricardo Miramontes, Lexi Kopan, Iliana Orellana, Shona Joy, Paul J Kemp, Nicholas D Allen, Ernest Fraenkel, Leslie M Thompson

APOE4 is Associated with Differential Regional Vulnerability to Bioenergetic Deficits in Aged APOE Mice

Estela Area-Gomez, Delfina Larrea, Marta Pera, Rishi R Agrawal, David N Guilfoyle, Leila Pirhaji, Kathleen Shannon, Hirra A Arain, Archana Ashok, Qiuying Chen, Allissa A Dillman, Helen Y Figueroa, Mark R Cookson, Steven S Gross, Ernest Fraenkel, Karen E Duff, Tal Nuriel

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

Natasha L. Patel-Murray, Miriam Adam, Nhan Huynh, Brook T. Wassie, Pamela Milani, Ernest Fraenkel

Treatment with JQ1, a BET bromodomain inhibitor, is selectively detrimental to R6/2 Huntington’s disease mice.

Amanda J Kedaigle, Jack C Reidling, Ryan G Lim, Miriam Adam, Jie Wu, Brook Wassie, Jennifer T Stocksdale, Malcolm S Casale, Ernest Fraenkel, Leslie M Thompson

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

The HD iPSC Consortium

2019

Early epigenomic and transcriptional changes reveal Elk-1 transcription factor as a therapeutic target in Huntington’s disease.

Ferah Yildirim, Christopher W. Ng, Vincent Kappes, Tobias Ehrenberger, Siobhan K. Rigby, Victoria Stivanello, Theresa A. Gipson, Anthony R. Soltis, Peter Vanhoutte, Jocelyne Caboche, David E. Housman, Ernest Fraenkel

Zfp281 (ZBP-99) plays a functionally redundant role with Zfp148 (ZBP-89) during erythroid development.

Andrew J. Woo, Chelsea-Ann A. Patry, Alireza Ghamari, Gabriela Pregernig, Daniel Yuan, Kangni Zheng, Taylor Piers, Moira Hibbs, Ji Li, Miguel Fidalgo, Jenny Y. Wang, Joo-Hyeon Lee, Peter J. Leedman, Jianlong Wang, Ernest Fraenkel, Alan B. Cantor

Postmortem Cortex Samples Identify Distinct Molecular Subtypes of ALS: Retrotransposon Activation, Oxidative Stress, and Activated Glia

Oliver H. Tam, Nikolay V. Rozhkov, Regina Shaw, Duyang Kim, Isabel Hubbard, Samantha Fennessey, Nadia Propp, The NYGC ALS Consortium, Delphine Fagegaltier, Brent T. Harris, Lyle W. Ostrow, Hemali Phatnani, John Ravits, Josh Dubnau, Molly Gale Hammell

Characteristics of myeloproliferative neoplasms in patients exposed to ionizing radiation following the Chernobyl nuclear accident.

Larysa Poluben, Maneka Puligandla, Donna Neuberg, Christine R. Bryke, Yahsuan Hsu, Oleksandr Shumeiko, Xin Yuan, Olga Voznesensky, German Pihan, Miriam Adam, Ernest Fraenkel, Roni Rasnic, Michal Linial, Sergiy Klymenko, Steven P. Balk, Paula G. Fraenkel

Shallow Sparsely-Connected Autoencoders for Gene Set Projection.

Maxwell Gold, Alexander Lenail, and Ernest Fraenkel

2018

Synthesizing Signaling Pathways from Temporal Phosphoproteomic Data

Ali Sinan Koksal, Kirsten Beck, Dylan R. Cronin, Aaron McKenna, Nathan D. Camp, Saurabh Srivastava, Matthew E. MacGilvray, Rastislav Bodik, Alejandro Wolf-Yadlin, Ernest Fraenkel, Jasmin Fisher, Anthony Gitter

Turning omics data into therapeutic insights

Amanda Kedaigle, Ernest Fraenkel

Unexpected similarities between C9ORF72 and sporadic forms of ALS/FTD suggest a common disease mechanism

Erin G Conlon, Delphine Fagegaltier, Phaedra Agius, Julia Davis-Porada, James Gregory, Isabel Hubbard, Kristy Kang, Duyang Kim, The New York Genome Center ALS Consortium, Hemali Phatnani, Neil A Shneider, James L Manley

Proteomics, Post-translational Modifications, and Integrative Analyses Reveal Molecular Heterogeneity within Medulloblastoma Subgroups

Tenley C. Archer, Tobias Ehrenberger, Filip Mundt, Maxwell P. Gold, Karsten Krug, Clarence K. Mah, Elizabeth L. Mahoney, Colin J. Daniel, Alexander LeNail, Divya Ramamoorthy, Philipp Mertins, D. R. Mani, Hailei Zhang, Michael A. Gillette, Karl Clauser, Michael Noble, Lauren C. Tang, Jessica Pierre-François, Jacob Silterra, James Jensen, Pablo Tamayo, Andrey Korshunov, Stefan M. Pfister, Marcel Kool, Paul A. Northcott, Rosalie C. Sears, Jonathan O. Lipton, Steven A. Carr, Jill P. Mesirov, Scott L. Pomeroy, Ernest Fraenkel

Tissue and cellular rigidity and mechanosensitive signaling activation in Alexander disease

Liqun Wang, Jing Xia, Jonathan Li, Tracy L. Hagemann, Jeffrey R. Jones, Ernest Fraenkel, David A. Weitz, Su-Chun Zhang, Albee Messing & Mel B. Feany

Genome-wide Analyses Identify KIF5A as a Novel ALS Gene

Genomic Translation for ALS Care (GTAC) Consortium, NYGC ALS Consortium, Answer ALS Foundation, ALS Sequencing Consortium, Clinical Research in ALS and Related Disorders for Therapeutic Development (CReATe) Consortium, SLAGEN Consortium, French ALS Consortium, ITALSGEN Consortium, Project MinE ALS Sequencing Consortium.

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

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’Correspondence information about the author Avi Ma’ayanEmail the author 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

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

Amanda J. Kedaigle and Ernest Fraenkel

Functional Genomics Approach Identifies Novel Signaling Regulators of TGFa Ectodomain Shedding

Jennifer L. Wilson, Eirini Kefaloyianni, Lauren Stopfer, Christina Harrison, Venkata S. Sabbisetti, Ernest Fraenkel, Douglas A. Lauffenburger and Andreas Herrlich

2017

Hepatic Dysfunction Caused by Consumption of a High-Fat Diet

Anthony R. Soltis, Norman J. Kennedy, Xiaofeng Xin, Feng Zhou, Scott B. Ficarro, Yoon Sing Yap, Bryan J. Matthews, Douglas A. Lauffenburger, Forest M. White, Jarrod A. Marto, Roger J. Davis, Ernest Fraenkel

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

Oana Ursu, Sara J. C. Gosline, Neil Beeharry, Lauren Fink, Vikram Bhattacharjee, Shao-shan Carol Huang, Yan Zhou, Tim Yen, Ernest Fraenkel

Identifying therapeutic targets by combining transcriptional data with ordinal clinical measurements

Leila Pirhaji, Pamela Milani, Simona Dalin, Brook T. Wassie, Denise E. Dunn, Robert J. Fenster, Julian Avila-Pacheco, Paul Greengard, Clary B. Clish, Myriam Heiman, Donald C. Lo & Ernest Fraenkel

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

Murodzhon Akhmedov, Amanda Kedaigle, Renan Escalante Chong, Roberto Montemanni, Francesco Bertoni, Ernest Fraenkel, Ivo Kwee

The whole-genome landscape of medulloblastoma subtypes

Paul A. Northcott, Ivo Buchhalter, A. Sorana Morrissy, Volker Hovestadt, Joachim Weischenfeldt, Tobias Ehrenberger, et. al., Ernest Fraenkel, Jan O. Korbel, Benedikt Brors, Matthias Schlesner, Roland Eils, Marco A. Marra, Stefan M. Pfister, Michael D. Taylor & Peter Lichter

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

Ryan G Lim, Chris Quan, Andrea M Reyes-Ortiz, Sarah E Lutz, Amanda J Kedaigle, Theresa A Gipson, Jie Wu, Gad D Vatine, Jennifer Stocksdale, Malcolm S Casale, Clive N Svendsen, Ernest Fraenkel, David E Housman, Dritan Agalliu, Leslie M Thompson

Developmental alterations in Huntington’s disease neural cells and pharmacological rescue in cells and mice.

HD iPSC Consortium, with MIT group: Amanda Kedaigle, Ferah Yildirim, Pamela Milani, Theresa Gipson, Christopher Ng, David Housman, & Ernest Fraenkel

Genome-Scale Networks Link Neurodegenerative Disease Genes to α-Synuclein through Specific Molecular Pathways

Vikram Khurana, Jian Peng, Chee Yeun Chung, Pavan K. Auluck, Saranna Fanning, Daniel F. Tardiff, Theresa Bartels, Martina Koeva, Stephen W. Eichhorn, Hadar Benyamini, Yali Lou, Andy Nutter-Upham, Valeriya Baru, Yelena Freyzon, Nurcan Tuncbag, Michael Costanzo, Bryan-Joseph San Luis, David C. Schöndorf, M. Inmaculada Barrasa, Sepehr Ehsani, Neville Sanjana, Quan Zhong, Thomas Gasser, David P. Bartel, Marc Vidal, Michela Deleidi, Charles Boone, Ernest Fraenkel, Bonnie Berger, Susan Lindquist

Hyper- and hypo- nutrition studies of the hepatic transcriptome and epigenome suggest that PPARα regulates anaerobic glycolysis

Anthony R. Soltis, Shmulik Motola, Santiago Vernia, Christopher W. Ng, Norman J. Kennedy, Simona Dalin, Bryan J. Matthews, Roger J. Davis, and Ernest Fraenkel

2016

Revealing disease-associated pathways by network integration of untargeted metabolomics

Leila Pirhaji, Pamela Milani, Mathias Leidl, Timothy Curran, Julian Avila-Pacheco, Clary B Clish, Forest M White, Alan Saghatelian, and Ernest Fraenkel

Network Modeling Identifies Patient-specific Pathways in Glioblastoma.

Nurcan Tuncbag, Pamela Milani, Jenny L. Pokorny, Hannah Johnson, Terence T. Sio, Simona Dalin, Dennis O. Iyekebe, Forest M. White, Jann N. Sarkaria, Ernest Fraenkel

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

Jennifer L. Wilson, Simona Dalin, Sara Gosline, Michael Hemann, Ernest Fraenkel, Douglas A. Lauffenburger

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

Pamela Milani, Renan Escalante-Chong, Brandon C. Shelley, Natasha L. Patel-Murray, Xiaofeng Xin, Miriam Adam, Berhan Mandefro, Dhruv Sareen, Clive N. Svendsen, Ernest Fraenkel

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

Nurcan Tuncbag, Sara J.C. Gosline, Amanda Kedaigle, Anthony R. Soltis, Anthony Gitter, Ernest Fraenkel

DiSCoVERing Innovative Therapies for Rare Tumors: Combining Genetically Accurate Disease Models with In Silico Analysis to Identify Novel Therapeutic Targets.

Allison R. Hanaford, Tenley C. Archer, Antoinette Price, Ulf D. Kahlert, Jarek Maciaczyk, Guido Nikkhah, Jong Wook Kim, Tobias Ehrenberger, Paul A. Clemons, Vlado Dan.í Brinton Seashore-Ludlow, Vasanthi Viswanathan, Michelle L. Stewart, Matthew G. Rees, Alykhan Shamji, Stuart Schreiber, Ernest Fraenkel, Scott L. Pomeroy, Jill P. Mesirov, Pablo Tamayo, Charles G. Eberhart, Eric H. Raabe

Multiplexed barcoded CRISPR-Cas9 screening enabled by CombiGEM

Alan S.L. Wong, Gigi C.G. Choi, Cheryl H. Cui, Gabriela Pregernig, Pamela Milani, Miriam Adam, Samuel D. Perli, Samuel W. Kazer, Aleth Gaillard, Mario Harmann, Alex K. Shalek, Ernest Fraenkel, Timothy K. Lu

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

Sara J.C. Gosline, Allan M. Gurtan, Courtney K JnBaptiste, Andrew Bosson, Pamela Milani, Simona Dalin, Bryan J. Matthews, Yoon S. Yap, Phillip A. Sharp, Ernest Fraenkel

Chromatin Landscape and Epigenetic Signatures in Neurological Disorders: Emerging Perspectives for Biological and Clinical Research

Pamela Milani and Ernest Fraenkel

Network Modeling of Heterogeneous Diseases

Ernest Fraenkel and Martina Koeva

2015

Bmi1 promotes erythroid development through regulating ribosome biogenesis

Rui Gao, Sisi Chen, Michihiro Kobayashi, Hao Yu, Yingchi Zhang, Yang Wan, Sara K. Young, Anthony Soltis, Ming Yu, Sasidhar Vemula, Ernest Fraenkel, Alan Cantor, Yevgeniy Antipin, Yang Xu, Mervin C. Yoder, Ronald C. Wek, Steven R. Ellis, Reuben Kapur, Xiaofan Zhu, and Yan Liu

2014

Sharing Information to Reconstruct Patient-Specific Pathways in Heterogeneous Diseases

Anthony Gitter, Alfredo Braunstein, Andrea Pagnani, Carlo Baldassi, Christian Borgs, Jennifer Chayes, Riccardo Zecchina, Ernest Fraenkel

SAMNetWeb: Identifying condition-specific networks linking signaling and transcription

Sara JC Gosline, Coyin Oh, Ernest Fraenkel

2013

Analysis of In Vitro Insulin-Resistance Models and Their Physiological Relevance to In Vivo Diet-Induced Adipose Insulin Resistance

Kinyui Alice Lo, Adam Labadorf, Norman J. Kennedy, Myoung Sook Han, Yoon Sing Yap, Bryan Matthews, Xiaofeng Xin, Lei Sun, Roger J. Davis, Harvey F. Lodish, Ernest Fraenkel

Targeting H3K4 trimethylation in Huntington disease.

Vashishtha M, Ng CW, Yildirim F, Gipson TA, Kratter IH, Bodai L, Song W, Lau A, Labadorf A, Vogel-Ciernia A, Troncosco J, Ross CA, Bates GP, Krainc D, Sadri-Vakili G, Finkbeiner S, Marsh JL, Housman DE, Fraenkel E, Thompson LM.

Integrated network analyses for functional genomic studies in cancer.

Wilson JL, Hemann MT, Fraenkel E, Lauffenburger DA.

The Small Molecule Genistein Increases Hepcidin Expression in Human Hepatocytes.

Zhen AW, Nguyen NH, Gibert Y, Motola S, Buckett P, Wessling-Resnick M, Fraenkel E, Fraenkel PG

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

Lodato MA, Ng CW, Wamstad JA, Cheng AW, Thai KK, Fraenkel E, Jaenisch R, Boyer LA.

Linking Proteomic and Transcriptional Data through the Interactome and Epigenome Reveals a Map of Oncogene-induced Signaling

Shao-shan Carol Huang, David C. Clarke, Sara J. C. Gosline, Adam Labadorf, Candace R. Chouinard, William Gordon, Douglas A. Lauffenburger and Ernest Fraenkel

Simultaneous Reconstruction of Multiple Signaling Pathways via the Prize-Collecting Steiner Forest Problem

Nurcan Tuncbag, Alfredo Braunstein, Andrea Pagnani, Shao-Shan Carol Huang, Jennifer Chayes, Christian Borgs, Riccardo Zecchina and Ernest Fraenkel

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

Christopher W. Ng, Ferah Yildirim, Yoon Sing Yap, Simona Dalin, Bryan J. Matthews, Patricio J. Velez, Adam Labadorf, David E. Housman and Ernest Fraenkel

2012

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

Sara J. C. Gosline , Sarah J. Spencer , Oana Ursu and Ernest Fraenkel

HSF1 Drives a Transcriptional Program Distinct from Heat Shock to Support Highly Malignant Human Cancers

Marc L. Medillo, Sandro Santagata, Martina Koeva, George W. Bell, Rong Hu, Rulia M. Tamimi, Ernest Fraenkel, Tan A. Ince, Luke Whitesell and Susan Lindquist

Polyglutamine Expanded Huntingtin Dramatically Alters the Genome-Wide Binding of HSF1

Laura Riva, Martina Koeva, Ferah Yildirim, Leila Pirhaji, Deepika Dinesh, Tali Mazor, Martin L. Duennwald and Ernest Fraenkel

SteinerNet: A Web Server for Integrating ‘Omic’ data to Discover Hidden Components of Response Pathways

Tuncbag, Nurcan; McCallum, Scott; Huang, Shao-shan; Fraenkel, Ernest

Simultaneous reconstruction of multiple signaling pathways via the prize-collecting Steiner forest problem

Nurcan Tuncbag, Alfredo Braunstein, Andrea Pagnani, Shao-Shan Carol Huang, Jennifer Chayes, Christian Borgs, Riccardo Zecchina, Ernest Fraenkel

Swimming Upstream: Identifying Proteomic Signals that Drive Transcriptional Changes using the Interactome and Multiple Omics Datasets.

Huang SS, Fraenkel E.

Direct recruitment of polycomb repressive complex 1 to chromatin by core binding transcription factors.

Yu M, Mazor T, Huang H, Huang HT, Kathrein KL, Woo AJ, Chouinard CR, Labadorf A, Akie TE, Moran TB, Xie H, Zacharek S, Taniuchi I, Roeder RG, Kim CF, Zon LI, Fraenkel E, Cantor AB.

2011

Large-Scale Discovery of ERK2 Substrates Identifies ERK-Mediated Transcrioptional Regulation by ETV3

Scott M. Carlson, Candace R. Chouinard, Adam Labadorf, Carol J. Lam, Katrin Schmelzle, Ernest Fraenkel, Forest M. White

Genome-Wide Profiling of H3K56 Acetylation and Transcription Factor Binding Sites in Human Adipocytes

Kinyui Alice Lo, Mary K. Bauchmann, Amy P. Baumann, Christopher J. Donahue, Mark A. Thiede, Lisa S. Hayes, Shelley Ann G. des Etages, Ernest Fraenkel

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

Alex Lan, Ilan Y. Smoly, Guy Rapaport, Susan Lindquist, Ernest Fraenkel and Esti Yeger-Lotem

2010

Unbiased, Genome-wide in vivo Mapping of Transcriptional Regulatory Elements Reveals Sex Differences in Chromatin Structure Associated with Sex-specific Liver Gene Expression

Guoyu Ling, Aarathi Sugathan, Tali Mazor, Ernest Fraenkel and David J. Waxman

A Quantitative Model of Transcriptional Regulation Reveals the Influence of Binding Location on Expression

Kenzie D. MacIsaac, Kinyui A. Lo, William Gordon, Shmulik Motola, Tali Mazor,Ernest Fraenkel

2009

Insights into GATA-1-Mediated Gene Activation versus Repression via Genome-wide Chromatin Occupancy Analysis

Ming Yu, Laura Riva, Huafeng Xie, Yocheved Schindler, Tyler B. Moran, Yong Cheng,Duonan Yu, Ross Hardison, Mitchell J. Weiss, Stuart H. Orkin, Bradley E. Bernstein,Ernest Fraenkel and Alan B. Cantor

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

Huang SS, Fraenkel E

Bridging high-throughput genetic and transcriptional data reveals cellular responses to alpha-synuclein toxicity

Yeger-Lotem E, Riva L, Su LJ, Gitler AD, Cashikar AG, King OD, Auluck PK,Geddie ML, Valastyan JS, Karger DR, Lindquist S, Fraenkel E

2007

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

Romer, K.A., Kayombya, G.R., Fraenkel E

Tissue-specific transcriptional regulation has diverged significantly between human and mouse

Odom, D.T., Dowell, R.D., Jacobsen, E.S., Gordon, W., Danford, T.D., MacIsaac,K., Rolfe, A., Conboy, C.M., Gifford, D.K., Fraenkel, E

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

Marson A, Kretschmer K, Frampton GM, Jacobsen ES, Polansky JK, MacIsaac KD,Levine SS, Fraenkel E, von Boehmer H, Young RA

2006

High-resolution computational models of genome binding events

Qi Y, Rolfe A, MacIsaac KD, Gerber GK, Pokholok D, Zeitlinger J, Danford T,Dowell RD, Fraenkel E, Jaakkola TS, Young RA, Gifford DK

Practical strategies for discovering regulatory DNA sequence motifs

MacIsaac KD, Fraenkel E

An improved map of conserved regulatory sites for Saccharomyces cerevisiae

MacIsaac KD, Wang T, Gordon DB, Gifford DK, Stormo GD, Fraenkel E

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

MacIsaac KD, Gordon DB, Nekludova L, Odom DT, Schreiber J, Gifford DK, Young RA,Fraenkel E

Core transcriptional regulatory circuitry in human hepatocytes

Odom DT, Dowell RD, Jacobsen ES, Nekludova L, Rolfe PA, Danford TW, Gifford DK,Fraenkel E, Bell GI, Young RA

2005

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

Gordon DB, Nekludova L, McCallum S, Fraenkel E

2004

Transcriptional regulatory code of a eukaryotic genome

Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, MacIsaac KD, Danford TW, Hannett NM,Tagne JB, Reynolds DB, Yoo J, Jennings EG, Zeitlinger J, Pokholok DK, Kellis M,Rolfe PA, Takusagawa KT, Lander ES, Gifford DK, Fraenkel E, Young RA

Control of pancreas and liver gene expression by HNF transcription factors

Odom DT, Zizlsperger N, Gordon DB, Bell GW, Rinaldi NJ, Murray HL, Volkert TL,Schreiber J, Rolfe PA, Gifford DK, Fraenkel E, Bell GI, Young RA

2003

Computational discovery of gene modules and regulatory networks

Bar-Joseph Z, Gerber GK, Lee TI, Rinaldi NJ, Yoo JY, Robert F, Gordon DB, Fraenkel E, Jaakkola TS, Young RA, Gifford DK

2002

Transcriptional regulatory networks in Saccharomyces cerevisiae

Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, Gerber GK, Hannett NM,Harbison CT, Thompson CM, Simon I, Zeitlinger J, Jennings EG, Murray HL,Gordon DB, Ren B, Wyrick JJ, Tagne JB, Volkert TL, Fraenkel E, Gifford DK,Young RA