Practical strategies for discovering regulatory DNA sequence motifs.

by Kenzie D MacIsaac, Ernest Fraenkel
Published 2006-04-01

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

by Murodzhon Akhmedov, Amanda Kedaigle, Renan Escalante Chong, Roberto Montemanni, Francesco Bertoni, Ernest Fraenkel, Ivo Kwee
Published 2017-07-01

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

by Kenzie D MacIsaac, Kinyui A Lo, William Gordon, Shmulik Motola, Tali Mazor, Ernest Fraenkel
Published 2010-04-01

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

by Nurcan Tuncbag, Sara J C Gosline, Amanda Kedaigle, Anthony R Soltis, Anthony Gitter, Ernest Fraenkel
Published 2016-04-01

Comparative proteomic analysis highlights metabolic dysfunction in α-synucleinopathy

by Souvarish Sarkar, Michael A. Murphy, Eric B. Dammer, Abby L. Olsen, Srikant Rangaraju, Ernest Fraenkel, Mel B. Feany
Published 2020-12-01

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

by Oana Ursu, Sara J C Gosline, Neil Beeharry, Lauren Fink, Vikram Bhattacharjee, Shao-Shan Carol Huang, Yan Zhou, Tim Yen, Ernest Fraenkel
Published 2017-01-01

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

by Michael A Lodato, Christopher W Ng, Joseph A Wamstad, Albert W Cheng, Kevin K Thai, Ernest Fraenkel, Rudolf Jaenisch, Laurie A Boyer
Published 2013-01-01

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

by Anthony R. Soltis, Shmulik Motola, Santiago Vernia, Christopher W. Ng, Norman J. Kennedy, Simona Dalin, Bryan J. Matthews, Roger J. Davis, Ernest Fraenkel
Published 2017-03-01

Linking proteomic and transcriptional data through the interactome and epigenome reveals a map of oncogene-induced signaling.

by Shao-shan Carol Huang, David C Clarke, Sara J C Gosline, Adam Labadorf, Candace R Chouinard, William Gordon, Douglas A Lauffenburger, Ernest Fraenkel
Published 2013-01-01

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

by 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
Published 2011-01-01

Tissue and cellular rigidity and mechanosensitive signaling activation in Alexander disease

by 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
Published 2018-05-01

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

by 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
Published 2016-01-01

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

by 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
Published 2013-10-01

Identifying therapeutic targets by combining transcriptional data with ordinal clinical measurements

by 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
Published 2017-09-01

Synthesizing Signaling Pathways from Temporal Phosphoproteomic Data

by Ali Sinan Köksal, Kirsten Beck, Dylan R. Cronin, Aaron McKenna, Nathan D. Camp, Saurabh Srivastava, Matthew E. MacGilvray, Rastislav Bodík, Alejandro Wolf-Yadlin, Ernest Fraenkel, Jasmin Fisher, Anthony Gitter
Published 2018-09-01

Hepatic Dysfunction Caused by Consumption of a High-Fat Diet

by 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
Published 2017-12-01

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

by 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
Published 2017-05-01

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

by 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
Published 2020-03-01

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

by Oliver H. Tam, Nikolay V. Rozhkov, Regina Shaw, Duyang Kim, Isabel Hubbard, Samantha Fennessey, Nadia Propp, Delphine Fagegaltier, Brent T. Harris, Lyle W. Ostrow, Hemali Phatnani, John Ravits, Josh Dubnau, Molly Gale Hammell, Hemali Phatnani, Justin Kwan, Dhruv Sareen, James R. Broach, Zachary Simmons, Ximena Arcila-Londono, Edward B. Lee, Vivianna M. Van Deerlin, Neil A. Shneider, Ernest Fraenkel, Lyle W. Ostrow, Frank Baas, Noah Zaitlen, James D. Berry, Andrea Malaspina, Pietro Fratta, Gregory A. Cox, Leslie M. Thompson, Steve Finkbeiner, Efthimios Dardiotis, Timothy M. Miller, Siddharthan Chandran, Suvankar Pal, Eran Hornstein, Daniel J. MacGowan, Terry Heiman-Patterson, Molly G. Hammell, Nikolaos.A. Patsopoulos, Oleg Butovsky, Joshua Dubnau, Avindra Nath, Robert Bowser, Matt Harms, Eleonora Aronica, Mary Poss, Jennifer Phillips-Cremins, John Crary, Nazem Atassi, Dale J. Lange, Darius J. Adams, Leonidas Stefanis, Marc Gotkine, Robert Baloh, Suma Babu, Towfique Raj, Sabrina Paganoni, Ophir Shalem, Colin Smith, Bin Zhang, Brent T. Harris
Published 2019-10-01

Cancer systems biology : functional insights and therapeutic strategies for medulloblastoma from omic data integration

by Ehrenberger, Tobias.
Published 2019