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

by Shelley, Brandon C., Mandefro, Berhan, Sareen, Dhruv, Svendsen, Clive N., Milani, Pamela, Escalante, Renan A., Patel-Murray, Natasha Leanna, Xin, Xiaofeng, Adam, Miriam, Fraenkel, Ernest
Published 2017

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

by Tuncbag, Nurcan, Braunstein, Alfredo, Pagnani, Andrea, Huang, Shao-Shan Carol, Chayes, Jennifer, Borgs, Christian, Zecchina, Riccardo, Fraenkel, Ernest, Tuncbag, Nurcan, Huang, Shao-Shan Carol, Fraenkel, Ernest
Published 2013

Integrated network analyses for functional genomic studies in cancer

by Fraenkel, Ernest, Wilson, Jennifer Lynn, Hemann, Michael, Lauffenburger, Douglas A
Published 2014

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

by Shelley, Brandon C., Mandefro, Berhan, Sareen, Dhruv, Svendsen, Clive N., Milani, Pamela, Escalante, Renan A., Patel-Murray, Natasha Leanna, Xin, Xiaofeng, Adam, Miriam, Fraenkel, Ernest
Published 2017

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

by Mendillo, Marc L., Santagata, Sandro, Bell, George W., Hu, Rong, Tamimi, Rulla M, Fraenkel, Ernest, Ince, Tan A., Whitesell, Luke, Lindquist, Susan, Koeva, Martina I
Published 2014

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

by Yildirim, Ferah, Ng, Christopher, Kappes, Vincent, Ehrenberger, Tobias, Rigby, Siobhan K., Stivanello, Victoria, Gipson, Theresa A., Soltis, Anthony R., Vanhoutte, Peter, Caboche, Jocelyne, Housman, David E., Fraenkel, Ernest
Published 2020

Network Modeling Identifies Patient-specific Pathways in Glioblastoma

by Pokorny, Jenny L., Sio, Terence T., Iyekegbe, Dennis O., Sarkaria, Jann N., Tuncbag, Nurcan, Milani, Pamela, Johnson, Hannah, Dalin, Simona, Fraenkel, Ernest, White, Forest M.
Published 2017

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

by Ng, Christopher W., Yildirim, Ferah, Yap, Soon Ming Micha, Matthews, Bryan, Velez, Patricio J., Labadorf, Adam, Fraenkel, Ernest, Dalin, Simona, Housman, David E
Published 2013

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

by Lan, Alex, Smoly, Ilan Y., Rapaport, Guy, Lindquist, Susan, Fraenkel, Ernest, Yeger-Lotem, Esti
Published 2011

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

by Lan, Alex, Smoly, Ilan Y., Rapaport, Guy, Fraenkel, Ernest, Lindquist, Susan, Yeger-Lotem, Esti
Published 2012

Direct Recruitment of Polycomb Repressive Complex 1 to Chromatin by Core Binding Transcription Factors

by Yu, Ming, Mazor, Tali, Huang, Hui, Huang, Hsuan-Ting, Kathrein, Katie L, Woo, Andrew J, Chouinard, Candace R., Labadorf, Adam, Akie, Thomas E, Moran, Tyler B., Xie, Huafeng, Zacharek, Sima, Taniuchi, Ichiro, Roeder, Robert G, Kim, Carla F., Zon, Leonard I, Fraenkel, Ernest, Cantor, Alan B.
Published 2014

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

by Beeharry, Neil, Fink, Lauren, Bhattacharjee, Vikram, Huang, Shao-shan Carol, Zhou, Yan, Yen, Tim, Ursu, Oana, Gosline, Sara Calafell, Fraenkel, Ernest
Published 2018

Targeting H3K4 trimethylation in Huntington disease

by Ng, Christopher W., Yildirim, Ferah, Labadorf, Adam, Fraenkel, Ernest, Vashishtha, Malini, Kratter, Ian H., Bodai, Laszlo, Song, Wan, Lau, Alice L., Vogel-Ciernia, Annie, Troncosco, Juan, Ross, Christopher A., Bates, Gillian P., Krainc, Dimitri, Sadri-Vakili, Ghazaleh, Finkbeiner, Steven, Marsh, J. Lawrence, Thompson, Leslie M., Wasylenko, Theresa Anne, Housman, David E
Published 2014

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

by Zhen, Aileen W., Nguyen, Nancy H., Gibert, Yann, Motola, Shmulik, Buckett, Peter, Wessling-Resnick, Marianne, Fraenkel, Ernest, Fraenkel, Paula G.
Published 2014

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

by Tuncbag, Nurcan, Gosline, Sara Calafell, Kedaigle, Amanda Joy, Soltis, Anthony Robert, Gitter, Anthony, Fraenkel, Ernest
Published 2017

Immortalized striatal precursor neurons from Huntington's disease patient-derived iPS cells as a platform for target identification and screening for experimental therapeutics

by Akimov, Sergey S, Jiang, Mali, Kedaigle, Amanda Joy, Arbez, Nicolas, Marque, Leonard O, Eddings, Chelsy R, Ranum, Paul T, Whelan, Emma, Tang, Anthony, Wang, Ronald, DeVine, Lauren R, Talbot, Conover C, Cole, Robert N, Ratovitski, Tamara, Davidson, Beverly L, Fraenkel, Ernest, Ross, Christopher A
Published 2021

Turning omics data into therapeutic insights

by Kedaigle, Amanda Joy, Fraenkel, Ernest
Published 2018

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

by Khurana, Vikram, Chung, Chee Yeun, Auluck, Pavan K., Fanning, Saranna, Tardiff, Daniel F., Bartels, Theresa, Eichhorn, Stephen W., Benyamini, Hadar, Lou, Yali, Nutter-Upham, Andy, Baru, Valeriya, Freyzon, Yelena, Costanzo, Michael, San Luis, Bryan-Joseph, Schöndorf, David C., Barrasa, M. Inmaculada, Ehsani, Sepehr, Sanjana, Neville, Zhong, Quan, Gasser, Thomas, Bartel, David P., Vidal, Marc, Deleidi, Michela, Boone, Charles, Berger, Bonnie, Lindquist, Susan, Peng, Jian, Koeva, Martina I, Tuncbag, Nurcan, Fraenkel, Ernest
Published 2018

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

by Lo, Kinyui Alice, Bauchmann, Mary K., Baumann, Amy P., Donahue, Christopher J., Thiede, Mark A., Hayes, Lisa S., Des Etages, Shelley Ann G., Fraenkel, Ernest
Published 2011

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

by Gurtan, Allan M, JnBaptiste, Courtney K, Bosson, Andrew, Milani, Pamela, Matthews, Bryan J, Yap, Yoon S, Sharp, Phillip A., Fraenkel, Ernest, Gosline, Sara Jane Calafell, Gurtan, Allan M., Sharp, Phillip A., Dalin, Simona, JnBaptiste, Courtney Kenneil, Matthews, Bryan, Yap, Yoon Sing
Published 2016