Computational Genomics

Massachusetts Institute of Technology
Computer Science and Artificial Intelligence Laboratory



Computational Biology

  • A multi-parametric flow cytometric assay to analyze DNA-protein interactionsM. Arbab, S. Mahony, H. Cho, J. M. Chick, P. A. Rolfe, J. P. van Hoff, V. W. Morris, S. P. Gygi, R. L. Maas, D. K. Gifford, R. I. Sherwood. Nucleic Acids Res. 2013 Jan. 41(2), . [pdf]

  • Global gene deletion analysis exploring yeast filamentous growth. O. Ryan, R. S. Shaprio, C. F. Kurat, D. Mayhew, A. Baryshnikova, B. Chin, Z. Y. Lin, M. J. Cox, F. Vizeacoumar, D. Cheung, S. Bahr, K. Tsui, F. Tebbji, A. Sellam, F. Istel, T. Schwarzmuller T, T. B. Reynolds, K. Kuchler, D. K. Gifford, M. Whiteway, G. Giaever, C. Nislow, M. Costanzo, A. C. Gingras, R. D. Mitra, B. Andrews, G. R. Fink, L. E. Cowen, C Boone. Science. 2012 Sep 14'337(6100):1353-6. [pdf]

  • High resolution genome wide binding event finding and motif discovery reveals transcription factor spatial binding constraints. Y. Guo, S. Mahony, D. K. Gifford. PLoS Comput Biol. 2012 Aug;8(8):e1002638. [pdf]

  • Ruler arrays reveal haploid genomic structural variation. P. A. Rolfe, D. A. Bernstein, P. Grisafi, D. K. Gifford. PLoS One. 2012;7(8):e43210. [pdf]

  • Lineage-based identification of cellular states and expression programs. T. Hashimoto, T. Jaakkola, R. Sherwood, E.O. Mazzoni, H. Wichterle, D. Gifford. Bioinformatics. 2012 Jun 15;28(12):i250-7. [pdf]

  • High Resolution genetic mapping with pooled sequencing. M. D. Edwards, D. K. Gifford. BMC Bioinformations 2012 Aor 19l13 Suppl 6:S8. [pdf]

  • Embryonic stem cell-based mapping of developmental transcriptional programs. E. O. Mazzoni, S. Mahony, M. Iacovino, C. A. Morrison, G. Mountoufaris, M. Closser, W. A. Whyte, R. A. Young, M. Kyba, D. K. Gifford, H. Wichterle H. Nat Methods. 2011 Nov 13;8(12):1056-8. doi: 10.1038/nmeth.1775. [pdf]

  • ReadDB provides efficient storage for mapped short reads.P. A. Rolfe, D. K. Gifford. BMC Bioinformatics. 2011 Jul 7;12:278. [pdf]

  • Discovering regulatory overlapping RNA transcripts. T. Danford, R. Dowell, S Agarwala, P. Grisafi, G. Fink, D. Gifford. J Comput Biol. 2011 Mar;18(3):295-303. [pdf]

  • Ligand-dependent dynamics of retinoic acid receptor binding during early neurogenesis. S. Mahony, E. O. Mazzoni, S. McCuine, R. A. Young, H. Wichterle, D. K.Gifford. Genome Biol. 2011;12(1):R2. Epub 2011 Jan 13. [pdf]

  • Rapid haplotype inference for nuclear families. A. L. Williams, D. E. Housman, M. C. Rinard, D. K. Gifford. Genome Biol. 2010;11(10):R108. Epub 2010 Oct 29. [pdf]

  • Discovering homotypic binding events at high spatial resolution.Y. Guo, G. Papachristoudis, R. C. Altshuler, G. K. Gerber, T. S. Jaakkola, D. K. Giffo, S. Mahony. Bioinformatics. 2010 Dec 15;26(24):3028-34. Epub 2010 Oct 21. [pdf]

  • Global control of motor neuron topography mediated by the repressive actions of a single hox gene. H. Jung, J. Lacombe, E.O. Mazzoni, K. F. Liem Jr, J. Grinstein, S. Mahony, D. Mukhopadhyay, D. K. Gifford, R. A. Young, K. V. Anderson, H. Wichterle, J. S. Dasen. Neuron. 2010 Sep 9;67(5):781-96. [pdf]

  • Control of transcription by cell size. C. Y. Wu, P. A. Rolfe, D. K. Gifford. PLoS Biol. 2010 Nov 2;8(11):e1000523. pdf

  • "Genotype to Phenotype: A Complex Problem." R. D. Dowell, O. Ryan, A. Jansen, D. Cheung, S. Agarwala, T. Danford, D. A. Bernstein, P. A. Rolfe, L. E. Heisler, B. Chin, C. Nislow, G. Giaever, P. C. Phillips, G. R. Fink, D. K. Gifford, and C. Boone. Science 23, April, 2010, p. 469. pdf

  • "Feed-forward Regulation of a Cell Fate Determinant by an RNA-binding Protein Generates Asymmetry in Yeast." J. J. Wolff, R. D. Dowell, S. Mahony, M. Rabani, D. K. Gifford, and G. R. Fink. Genetics 2010

  • "Toggle involving cis-interfering noncoding RNAs controls variegated gene expression in yeast". S. L. Bumgarner, R. D. Dowell, P. Grisafi, D. K. Gifford, and G. R. Fink. PNAS 106(43), October, 2009, pp18321-18326. pdf

  • "Analysis of the mouse embryonic stem cell regulatory networks obtained by ChIP-chip and ChIP-PET." D. Mathur, T. W. Danford, L. A. Boyer, R. A. Young, D. K. Gifford, and R. Jaenisch. Genome Biol. 2008;9(8). pdf

  • "Tissue-specific transcriptional regulation has diverged significantly between human and mouse." D. T. Odom, R. D. Dowell, E. S. Jacobsen, W. Gordon, T. W. Danford, K. D. MacIsaac, P. A. Rolfe, C. M. Conboy, D. K. Gifford, and E. Fraenkel. Nature Genetics 39:6, 730-732, June, 2007. pdf

  • "Automated Discovery of Functional Generality of Human Gene Expression Programs". G. K. Gerber, R. D. Dowell, T. S. Jaakkola, and D. K. Gifford PLOS Computational Biology, 3:8, August 2007. pdf

  • Semi-supervised analysis of gene expression profiles for lineage-specific development in the Caenorhabditis elegans embryo." Y. Qi, P. E. Missiuro, A. Kapoor, C. P. Hunter, T. S. Jaakkola D. K. Gifford,and H. Ge. Bioinformatics 15;22(14), July 2006, pp. 417-423. pdf

  • "Control of developmental regulators by Polycomb in human enbryonic stem cells." T. I. Lee, R. G. Jenner, L. A. Boyer, M. G. Guenther, S. S. Levine, R. M Kumar, B. Chevalier, S. E. Johnstone, M. F. Cole, K. Isono, H. Koseki, T. Fuchikami, K. Abe, H. L. Murray, J. P. Zucker, B. Yuan, G. W. Bell, E. Herbolsheimer, N. M. Hannett, K. Sun, D. T. Odom, A. P. Otte, T. L. Volkert, D. P. Bartel, D. A. Melton, D. K. Gifford, R. Jaenisch, and R. A. Young. Cell 125(2), April, 2006, pp 301-313. pdf
  • "An improved map of conserved regulatory sties for Saccharomyces cerevisiae." K. D. MacIsaac, T. Wang, D. B. Gordon, D. K. Gifford, G. D. Stormo, and E. Fraenkel. BMC Bioinformatics. March, 2006. pdf

  • "A hypothesis-based approach for identifying the binding specificity of regulatory proteins from chromatin immunoprecipitation data." K. D. MacIsaac, D. B. Gordon, L. Nekludova, D. T. Odom, J. Schreiber, D. K. Gifford, R. A. Young, and E. Fraenkel. Bioinformatics. Feb., 2006. pdf

  • "Polycomb complexes repress developmental regulators in murine embryonic stem cells. L. A. Boyer, K. Plath, J. Zeitlinger, T. Brambrink, L. A. Medeiros, T. I Lee., S. S. Levine, M. Wernig, A. Tajonar, M. K. Ray, G. W. Bell, A. P. Otte, M. Vidal, D. K. Gifford, R. A. Young, and R. Jaenisch. Nature 441:349-353, May 2006. pdf

  • "Coordinated binding of NF-kB family members in the response of human cells to lipopolysaccharide." J. Schreiber, R. G. Jenner, H. L. Murray, G. K. Gerber, D. K. Gifford and R. A. Young. Proceedings of the National Academy of Sciences (PNAS), 103(10):5899-5904, 2006. pdf

  • "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) [pdf]     Supplemental material      Download the software

  • "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. Nature/EMBO Molecular Systems Biology, msb4100059, 2 May 2006. [pdf] 

  • "Genome-wide map of nucleosome acetylation and methylation in yeast." D. K. Pokholok, C. T. Harbison, S. Levine, M. Cole, N. M. Hannett, T. I. Lee, G. W. Bell, K. Walker, P. A. Rolfe, E. Herbolsheimer, J. Zeitlinger, F. Lewitter, D. K. Gifford, and R. A. Young. Cell 122(4), August, 2005. pp. 517-527. pdf

  • "Core Transcriptional Regulatory Circuitry in Human Embryonic Stem Cells." L. A. Boyer, T. I. Lee, M. F. Cole, S. E. Johnstone, S. S. Levine, J. P. Zucker, M. G. Guenther, R. M. Kuman, H. L. Murray, R. G. Jenner, D. K. Gifford, D. A. Melton , R. Jaenisch, and R. A. Young. Cell Vol. 122, 1-20, September, 2005. pdf

  • "Global postition and recruitment of HATS and HDACS in the yeast genome." F. Robert, D.K. Pokholok, N. M Hannett, N. J. Rinaldi, M. Chandy, A. Rolfe, J. L. Workman, D. K. Gifford, and R. A. Young. Mol. Cell 16(2), October, 2004, pp. 199-209 pdf

  • "Deconvolving cell cyle expression data with complementary information. Z. Bar-Joseph, S. Farkash, D. K. Gifford, I. Simon, R. Rosenfeld. Bioinformatics Vol. 20 Suppl. 1, 2004. pp i23-i30.pdf

  • "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. [pdf] 

  • "Control of Pancreas and Liver Gene Expression by HNF Transcription Factors." Odom, D. T., Zizlsperger, N., Gordon, D. B., Bell, G. W., Rinaldi, N. J., Murray, H. L., Volkert, T. L., Schreiber, J., Rolfe, P. A., Gifford, D. K., Fraenkel, E., Bell, G. I., Young, R. A. Science, 303:1378-1381, February, 2004. [pdf]

  • "Comparing the Continuous Representation of Time Series Gene Expression Profiles to Identify Differentially Expressed Genes." Z. Bar-Joseph, G.K. Gerber, I. Simon, D.K. Gifford, and T.S. Jaakkola. Proceedings of the National Academy of Sciences 2003 Sept. 2; 100(18):10146-10151. pdf

  • "Negative Information for Motif Discovery." Takusagawa, K. T., Gifford, D. K., Pacific Symposium on Biocomputing, 9:360-371, 2004. [pdf]

  • "Computational discovery of gene modules and regulatory networks." Bar-Joseph, Z., Gerber, G. K., Lee, T. I., Rinaldi, N. J., Yoo, J. Y., Robert, F., Gordon, D. B., Fraenkel, E., Jaakkola, T. S., Young, R. A., Gfford D. K. Nature Biotechnology, 21, pp. 1337-1342 November, 2003. [pdf]

  • "Continuous Representations of Time Series Gene Expression Data." Bar-Joseph, G. Gerber, D. Gifford, T. Jaakkola and I. Simon.  Journal of Computational Biology, 10(3-4) pp. 241-156. 

  • "K-ary Clustering with Optimal Leaf Ordering for Gene Expression Data."  Ziv Bar-Joseph, Erik D. Demaine, David K. Gifford, Angèle M. Hamel, Tommy S. Jaakkola and Nathan Srebro. Bioinformatics, Vol. 19, No. 9, 2003. [pdf]   [ps]

  • "Transcriptional Regulatory Networks In Saccharomyces cerevisiae."  T.I. Lee, N. J. Rinaldi, F. Robert, D. T. Odom, Z. Bar-Joseph, G. K. Gerber, ... D. K Gifford and R. A. Young.    Science, 298:799-804 (2002) [pdf]

  • "K-ary Clustering with Optimal Leaf Ordering for Gene Expression Data."  Ziv Bar-Joseph, Erik D. Demaine, David K. Gifford, Angèle M. Hamel, Tommi S. Jaakkola and Nathan Srebro. To appear in Proceedings of the 2nd Workshop on Algorithms in Bioinformatics (WABI 2002), Rome, Italy, September 17-11. [pdf]   [ps]

  • "Combining Location and Expression Data for Principled Discovery of Genetic Regulatory Network Models." Alexander J. Hartemink, David K. Gifford, Tommi S. Jaakkola, and Richard A. Young.  Pacific Symposium on Biocomputing 2002, Kauai, January 2002. [pdf]   [ps]

  • "Bayesian Methods for Elucidating Genetic Regulatory Networks." Hartemink, A. J., Gifford, D. K., Jaakkola, T. S., Young, R. A“” IEEE Intelligent Systems in Biology, Vol. 17, No. 2, March, 2002, pp. 37-43. [pdf]   [ps]

  • Serial Regulation of Transcriptional Regulators in the Yeast Cell Cycle." Simon, I., Barnett, J., Hannett, N., Harbison, C. T., Rinaldi, N. J., Volkert, T. L. Wyrick, J. J., Zeitlinger, J., Gifford., D. K., Jaakkola, T. S., Young, R. A.,  Cell, 106, Sept., 2001, p. 667-708. [pdf]   [ps]

  • "A new approach to analyzing gene expression time series data."  Z. Bar-Joseph, G. Gerber, D. Gifford, T. Jaakkola and I. Simon.  In Proceedings of The Sixth Annual International Conference on Research in Computational Molecular Biology (RECOMB), 2002, pp 39-48.  [pdf]   [ps]

  • "Blazing pathways through genetic mountains."  Gifford, D. K.   Science 2001 Sep 14;293(5537):2049-51. [pdf]    [ps]

  • "Fast optimal leaf ordering for hierarchical clustering." Z. Bar-Joseph, D. Gifford, and T. Jaakkola.   Bioinformatics (Proceedings of ISMB 2001),, 17(S1), 2001, pp 22-19 . [pdf] [ps]

  • "Using Graphical Models and Genomic Expression Data to Statistically Validate Models of Genetic Regulatory Networks."  Alexander J. Hartemink, David K. Gifford, Tommi S. Jaakkola, and Richard A. Young Pacific Symposium on Biocomputing 2001, Hawaii, January 2001. [pdf]   [ps]

  • "Maximum Likelihood Estimation of Optimal Scaling Factors for Expression Array Normalization."  Alexander J. Hartemink, David K. Gifford, Tommi S. Jaakkola, and Richard A. Young SPIE BiOS 2001, San Jose, California, January 2001.  [pdf]   [ps]

Biological Computation

  • "Experimental Efficiency of Programmed Mutagenesis."  Julia Khodor and David K. Gifford. New Generation Computing 20:3, pp 307-315, 2002. [pdf]

  • "Programmed Mutagenesis is Universal." Julia Khodor, and David K. Gifford. Theory of Computing Systems 255, pp 483-499, 2002. [pdf]

  • "Simulating Biological Reactions: A Modular Approach."  Alexander J. Hartemink, Tarjei S. Mikkelsen, and David K. Gifford 5th Annual DIMACS Workshop on DNA-Based Computers, Boston, Massachusetts, June 1999. [pdf]  [ps]

  • "Automated Constraint-Based Nucleotide Sequence Selection for DNA Computation."  Alexander J. Hartemink, David K. Gifford, and Julia Khodor 4th Annual DIMACS Workshop on DNA-Based Computers, Philadelphia, Pennsylvania, June 1998. [pdf]  [ps]

  • "Design & Implementation of Computational Systems Based on Programmed Mutagenesis." Khodor, J. and Gifford, D. K. DIMACS Workshop on Nucleic Acid Selection and Computing, Princeton University, March, 1998.

  • "Thermodynamic Simulation of Deoxyoligonucleotide Hybridization for DNA Computation."  Alexander J. Hartemink and David K. Gifford 3rd Annual DIMACS Workshop on DNA-Based Computers, Philadelphia, Pennsylvania, June 1997.  [pdf] [ps]

  • "The Efficiency of Sequence-Specific Separation of DNA Mixtures for Biological Computing." Julia Khodor and David K. Gifford 3rd Annual DIMACS Workshop on DNA-Based Computers, Philadelphia, Pennsylvania, June 1997.  [pdf]  [ps]

Other Publications: 

  • These are group publications related to work in research areas previously investigated by the group.