Complete Publications and Downloads

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

  • PLoS Comput Biol 9(2): e1002887. doi:10.1371/journal.pcbi.1002887
    • 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
  • Journal of Computational Biology. February 2013, 20(2): 124-136. doi:10.1089/cmb.2012.0092.
    • 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
  • Proc Natl Acad Sci U S A. 2013 Feb 5;110(6):2354-9. doi:10.1073/pnas.1221292110
  • GEO
    • SAMNet: a network-based approach to integrate multi-dimensional high throughput datasets
    Sara J. C. Gosline , Sarah J. Spencer , Oana Ursu and Ernest Fraenkel
  • Integrative Biology (2012) doi:10.1039/C2IB20072D
    • 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
  • Cell (2012) doi: 10.1016/j.cell.2012.06.031
    • 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
  • Journal of Huntington's Disease (2012) doi: 10.3233/JHD-2012-120020.
    • SteinerNet: A Web Server for Integrating "Omic" data to Discover Hidden Components of Response Pathways
    Tuncbag, Nurcan; McCallum, Scott; Huang, Shao-shan; Fraenkel, Ernest
  • Nucl. Acids Res. (2012) doi: 10.1093/nar/gks445. PubMed PMID: 22638579
  • SteinerNet
    • 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
  • RECOMB 2012, LNBI 7262, pp. 127-147, 2012.
  • paper
    • Swimming Upstream: Identifying Proteomic Signals that Drive Transcriptional Changes using the Interactome and Multiple "-Omics" Datasets.
    Huang SS, Fraenkel E.
  • Methods Cell Biol. 2012;110:57-80. PubMed PMID: 22482945
    • 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.
  • Mol Cell. 2012 Feb 10;45(3):330-43.
    • 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
  • Sci. Signal. 4, rs11 (2011).
    • NCBI deposited data:
  • ChIP-SEQ of ETV3-HA in 293T cells transfected with ETV3-HA and treated with U0126
  • Negative control for ChIP-SEQ of ETV3-HA in 293T cells (cells not transfected with ETV3-HA)
  • ChIP-SEQ of ETV3-HA in 293T cells transfected with ETV3-HA and treated with PMA
    • Genome-Wide Profiling of H3K56 Acetylation and Transcription Factor Binding Sites in Human Adipocytes
    Lo KA, Bauchmann MK, Baumann AP, Donahue CJ, Thiede MA, et al.
  • PLoS ONE 6(6): e19778.doi:10.137/journal.pone.0019778
  • GEO
    • ResponseNet: revealing signaling and regulatory networks linking genetic and transcriptomic screening data
  • Nucl. Acids Res. (2011) first published online May 16, 2011 doi:10.1093/nar/gkr359
    • 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
  • Mol. Cell. Biol. 2010 Sep 27. [Epub ahead of print]
  • GEO
    • 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
  • PLoS Comput Biol. 6(4): e1000773 (2010)
  • GEO
    • 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
  • Molecular Cell 36: 682-695, 2009
  • GEO
    • Integrating proteomic, transcriptional, and interactome data reveals hidden components of signaling and regulatory networks
    Huang SS, Fraenkel E
  • Sci Signaling 2: ra40 (2009)
  • full text
  • Online supplemental material: protein protein interactions with weights and transcription factor to target weights
    • 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
  • Nature Genetics Published online: 22 February 2009
  • Online supplemental material
    • WebMOTIFS: automated discovery, filtering and scoring of DNA sequence motifs using multiple programs and Bayesian approaches
    Romer, K.A., Kayombya, G.R., Fraenkel E
  • Online Motif Discovery
  • Nucleic Acids Res. 2007 Web Server Issue
    • 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
  • Online supplemental material
  • Nature Genetics 39: 730 - 732 (2007)
    • 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
  • Nature 445(7130): 931-935 (2007)
    • 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
  • Nat Biotechnol. 24(8):963-970 (2006)
    • Practical strategies for discovering regulatory DNA sequence motifs
    MacIsaac KD, Fraenkel E
  • PLoS Comput Biol. 2(4):e36 (2006)
    • An improved map of conserved regulatory sites for Saccharomyces cerevisiae
    MacIsaac KD, Wang T, Gordon DB, Gifford DK, Stormo GD, Fraenkel E
  • Online supplemental material
  • BMC Bioinformatics 7:113 (2006)
    • 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
  • Online Motif Discovery Using THEME
  • Online supplemental material
  • Bioinformatics 22(4):423-9(2006)
    • 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
  • Mol Syst Biol. 2:2006.0017 (2006)
    • TAMO: a flexible, object-oriented framework for analyzing transcriptional regulation using DNA-sequence motifs
    Gordon DB, Nekludova L, McCallum S, Fraenkel E
  • Source code and documentation for TAMO
  • Bioinformatics 21(14):3164-5 (2005)
    • 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
  • Supporting data
  • Nature. 2004 Sep 2;431(7004):99-104.
    • 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
  • Science 303(5662):1378-1381 (2004)
    • 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
  • Nature Biotechnology 21(11):1337-1342 (2003)
    • 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
  • Science 298(5594):799-804 (2002)