Hi, my name is Tim.
I'm a PhD student in Computer Science at MIT. My advisor is David Gifford.
I can be reached via email at

Research

I'm a member of the Computational Genomics Group. We use computational methods (smart algorithms and the clever organization of data) to study the transcriptional regulation of genes.
Our research focuses on the analysis of ChIP-chip (Chromatin-Immunoprecipitation on a microarray chip), ChIP-Seq (Chromatin immunoprecipitation followed by sequencing), gene expression and genomic sequence data, and their use in uncovering the binding sites of transcription factors or genomic regions that are bound by particular proteins. This data, along with gene expression, transcription factor motif, gene-functional, and sequence data, can be used to decipher gene regulatory programs.
I'm also interested in methods of machine learning, specifically graphical models. I'm exploring how algorithms for constrained learning of Bayesian Networks can be used to build biologically-relevant models of regulatory networks and developmental programs.
I am also deeply involved in building and maintaining the software and database system which supports our group's analysis projects. This system goes by the name GSE, which stands for "Genomic Spatial Events" Database.

Teaching

I've been a Teaching Assistant for two graduate-level courses here at MIT:

Publications

My name has appeared in the author lists of a few publications.
Discovering Regulatory Overlapping RNA Transcripts. T. Danford, R. Dowell, S. Agarwala, P. Grisafi, G. Fink, D. Gifford. Proceedings of the 14th Annual International Conference on Research in Computational Molecular Biology pp. 110-122, (2010).
[link] Analysis of the mouse embryonic stem cell regulatory networks obtained by ChIP-chip and ChIP-PET. D. Mathur, T. Danford, L. Boyer, R. Young, D. Gifford, and R. Jaenisch. Genome Biology 9:R126 (2008)
[link] GSE: A Comprehensive Database System for the Representation, Retrieval, and Analysis of Microarray Data. T. Danford, P.A. Rolfe, D.K. Gifford. Pacific Symposium on Biocomputing 13:539-550(2008)
[link] Tissue-specific transcriptional regulation has diverged significantly between human and mouse. Odom DT, Dowell RD, Jacobsen ES, Gordon W, Danford TW, MacIsaac KD, Rolfe PA, Conboy CM, Gifford DK, & Fraenkel E Nature Genetics 39, 730 - 732 (2007).
[link] High-resolution computational models of genome binding events. A. Qi, P.A. Rolfe, K. MacIsaac, G.K. Gerber, D. Pokholok, J. Zeitlinger, T. Danford, R.D. Dowell, E. Fraenkel, T.S. Jaakkola, R.A. Young, and D.K. Gifford. Nature Biotechnology. 24:963-960 (2006)
[link] Zebrafish promoter microarrays identify actively transcribed embryonic genes. Wardle FC, Odom DT, Bell GW, Yuan B, Danford TW, Wiellette EL, Herbolsheimer E, Sive HL, Young RA, Smith JC. Genome Biology. 7(8). (2006)
[link] Core Transcriptional Regulatory Circuitry in Human Hepatocytes. D.T. Odom, R.D. Dowell, E.S. Jacobsen, L. Nekludova, P.A. Rolfe, T.W. Danford, D.K. Gifford, E. Fraenkel, G.I. Bell, and R.A. Young. Molecular Systems Biology 2:2006.0017 (May 2006).
[link] Transcriptional regulatory code of a eukaryotic genome. C. Harbison, D. B. Gordon, T. I Lee, N. J. Rinaldi, K. D. MacIsaac, T. W. Danford, N. M. Hannett, J.B. Tagne, D. B. Reynolds, J. Yoo, E. G. Jennings, J. Zeitlinger, D. K. Pokholok, M. Kellis, P. A. Rolfe, K. T. Takusagawa, E. S. Lander, D. K. Gifford, E. Fraenkel, and R. A. Young. Nature, 431:99-104 (September 2004).