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PUBLICATIONS

Unbiased, Genome-wide in vivo Mapping of Transcriptional Regulatory Elements Reveals Sex Differences in Chromatin Structure Associated with Sex-specific Liver Gene Expression
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
PLoS Comput Biol. 6(4): e1000773 (2010)
GEO

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

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.
Online supplemental material
Nature Genetics Published online: 22 February 2009

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)