Kenzie

Kenzie MacIsaac

Ph.D. Candidate
MIT Department of Electrical Engineering and Computer Science
68-318, 31 Ames Street
Cambridge, MA 02139

Email: my last name in lower case (at) mit (dot) edu

Research interests

Computational Biology
Machine Learning
Transcriptional Regulation


Publications

  • Odom DT, Dowell RD, Jacobsen ES, Gordon W, Danford TW, MacIsaac KD, Rolfe PA, Conboy CM, Gifford DK, Fraenkel E. "Tissue-specific transcriptional regulation has diverged significantly between human and mouse." Nat Genet. 2007 Jun;39(6):730-2.
  • Marson A, Kretschmer K, Frampton GM, Jacobsen ES, Polansky JK, MacIsaac KD, Levine SS, Fraenkel E, von Boehmer H, Young RA. "Foxp3 occupancy and regulation of key target genes during T-cell stimulation." Nature 2007, Feb 22;445(7130):931-5.
  • *Qi Y, *Rolfe A, *MacIsaac KD, Gerber GK, Pokholok D, Zeitlinger J, Danford T, Dowell RD, Fraenkel E, Jaakkola TS, Young RA, Gifford DK. "High-resolution computational models of genome binding events." Nature Biotechnology 2006, Aug;24(8):963-70 manuscript
  • MacIsaac KD and E Fraenkel "Practical strategies for discovering regulatory DNA sequence motifs." PLoS Computational Biology 2006, 2(4): e36 manuscript
  • *MacIsaac KD, *Wang T, Gordon DB, Gifford DK, Stormo GD, Fraenkel E "An improved map of conserved regulatory sites for Saccharomyces cerevisiae." BMC Bioinformatics 2006, 7:113 manuscript
  • MacIsaac KD, Gordon DB, Nekludova L, Odom DT, Schreiber J, Gifford DK, Young RA, Fraenkel E "A hypothesis-based approach for identifying the binding specificity of regulatory proteins from chromatin immunoprecipitation data." Bioinformatics. 2006 Feb. 15; 22(4):423-9 manuscript
  • 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 "Transcriptional regulatory code of a eukaryotic genome." Nature. 2004 Sep. 2; 431(7004):99-104. manuscript
  • Buist PH, Behrouzian B, MacIsaac KD, Cassel S, Rollin P, Imberty A, Gautier C, Perez S, Genix P "Stereochemical analysis of D-glucopyranosyl-sulfoxides via a combined NMR, molecular modeling and x-ray crystallographic approach." Tetrahedron Assym.1999; 10:2881-2889.

    • Talks

  • "Practical strategies for motif discovery" (with Ernest Fraenkel, MIT) A tutorial at the International Conference on Systems Biology, October 2005, Boston, MA.
  • "Design and construction of a genetic set-reset latch" (with Stephen W. Davies, University of Toronto) at Cold Spring Harbor meeting "Systems Biology: genomic approaches to transcriptional regulation", March 2003, Cold Spring Harbor, NY

    • Teaching

  • Fall 2005, MIT, Teaching assistant for 6.867 "Machine Learning".
  • Winter 2003, University of Toronto, Teaching assistant for BME205 "Engineering Biology".

    • Links

    Fraenkel Lab (Biological Engineering)
    David Gifford's Computational Genomics group (CSAIL)
    Personal links