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David Kulp

Assistant Professor, Department of Computer Science University of Massachusetts Amherst Computer Science Building 140 Governors Drive Amherst, MA 01003-9264 Tel: (413) 545-2032 Fax: (413) 545-1249 email: dkulp «æ» cs·umass·edu

Research Interests

My current research interests are primarily resequencing by microarray hybridization and inferring regulatory networks using quantitative trait loci (QTL). More specifically, my research is composed of both technology development and the analysis of gene regulation. On the technology side, I am investigating alternative microarray design strategies for improved discrimination of single nucleotide polymorphisms. I am applying this microarray technology to identify allelic differences within strains of various organisms from mice to the Dengue virus. On the gene regulation side, I am developing new graphical models for the inference of regulatory relationships among genes and genetic markers and I am assessing the nature of genetic variation on the expression of alternatively spliced isoforms. I also work with colleagues on genome annotation projects, most notably the genomes of the microbes "Geobacter".

Bioinformatics Publications

Jagalur M, Pal C, Learned-Miller E, Zoeller RT, Kulp D (2007), "Analyzing in situ Gene Expression in the Mouse Brain with Image Registration, Feature Extraction and Block Clustering" (2007) BMC Bioinformatics (in press) pdf

Vishvanath Nene, et al. (2007) "Genome Sequence of Aedes aegypti, a Major Arbovirus Vector." Science 316(5832), 1718 - 1723. online

Jagalur, M., Kulp, D. (2007) "An Information Theoretic Method For Reconstructing Local Regulatory Network Modules from Polymorphic Samples" in Computation Systems Bioinformatics, Proceedings of the Conference CSB 2007.

Jagalur, M., Pal, C., Learned-Miller, E., Zoeller, R. T., Kulp, D. (2006). "The Processing and Analysis of in situ Gene Expression Images of the Mouse Brain". Advances in Neural Information Processing Systems (NIPS) Workshop on New Problems and Methods in Computational Biology. website pdf

Kulp D, Jagular M (2006). "Causal inference of regulator-target pairs by gene mapping of expression phenotypes." BMC Genomics 7:125 online

Sugnet CW, Srinivasan K, Clark TA, O'Brien G, Cline MS, Wang H, Williams A, Kulp D, Blume J, Haussler D, Ares M (2006). "Unusual Intron Conservation near Tissue-Regulated Exons Found by Splicing Microarrays." PLoS Comput Biol 2(1): e4 online

Zhan Y and Kulp D. (2005). "Model-P: basecalling for resequencing microarrays of diploid samples." Bioinformatics, 21 (Suppl 2), ii182-ii189. pdf

Smucker M, Kulp D, and Allan J. "Dirichlet Mixtures for Query Estimation in Information Retrieval," University of Massachusetts, Amherst, CIIR Technical Report 445, April 2005. pdf

Culotta A, Kulp D, and McCallum A. "Gene prediction with conditional random fields." Technical Report UM-CS-2005-028, University of Massachusetts, Amherst, April 2005. pdf

Di X, Matsuzaki H, Webster TA, Hubbell E, Liu G, Dong S, Bartell D, Huang J, Chiles R, Yang G, Shen MM, Kulp D, Kennedy GC, Mei R, Jones KW, Cawley S. (2005) "Dynamic model based algorithms for screening and genotyping over 100K SNPs on oligonucleotide microarrays." Bioinformatics, 21(9), 1958-63. pdf

Cheng, J., Sun, S., Tracy, A., Hubbell, E., Morris, J., Valmeekam, V., Kimbrough, A., Cline, M. S., Liu, G., Shigeta, R., Kulp, D., and Siani-Rose, M. A. (2004). "NetAffx Gene Ontology Mining Tool: a visual approach for microarray data analysis" Bioinformatics, 20, 1462-1463. pdf

Cheng, J., Cline, M., Martin, J., Finkelstein, D., Awad, T., Kulp, D., and Siani-Rose, M. A. (2004). "A knowledge-based clustering algorithm driven by Gene Ontology." J Biopharm Stat, 14(3), 687-700. pdf Δ

Cline, M., Shigeta, R., Wheeler, R., Siani-Rose, M. A., Kulp, D., and Loraine, A. E. (2004). "The effects of alternative splicing on transmembrane proteins in the mouse genome." Pacific Symposium on Biocomputing pdf

Wang, H., Hubbell, E., Hu, J. S., Mei, G., Cline, M., Lu, G., Clark, T., Siani-Rose, M. A., Ares, M., Kulp, D. C., and Haussler, D. (2003). "Gene structure-based splice variant deconvolution using a microarry platform." Bioinformatics, 19 Suppl 1, I315-I322. pdf

Mei, R., Hubbell, E., Bekiranov, S., Mittmann, M., Christians, F. C., Shen, M. M., Lu, G., Fang, J., Liu, W. M., Ryder, T., Kaplan, P., Kulp, D., and Webster, T. A. (2003). "Probe selection for high-density oligonucleotide arrays." Proc Natl Acad Sci, 100(20), 11237-42. pdf

Liu, W. M., Di, X., Yang, G., Matsuzaki, H., Huang, J., Mei, R., Ryder, T. B., Webster, T. A., Dong, S., Liu, G., Jones, K. W., Kennedy, G. C., and Kulp, D. (2003). "Algorithms for large-scale genotyping microarrays." Bioinformatics, 19(18), 2397-403. pdf

Li, J., Lin, S., Jia, H., Wu, H., Roe, B. A., Kulp, D., Stormo, G. D., and Dutcher, S. K. (2003). "Analysis of Chlamydomonas reinhardtii genome structure using large-scale sequencing of regions on linkage groups III and VI." J Eukaryot Microbiol, 50(3).

Kulp, D. (2003). "Protein-coding gene structure prediction using generalized hidden Markov models," PhD, University of California, Santa Cruz. pdf

Waterston, R. H., et al. (2002). "Initial sequencing and comparative analysis of the mouse genome." Nature, 420(6915), 520-62. pdf

Cline, M., Liu, G., Loraine, A. E., Shigeta, R., Cheng, J., Mei, G., Kulp, D., and Siani-Rose, M. A. (2002). "Structure-based comparison of four eukaryotic genomes." Pac Symp Biocomput, 127-38. pdf

Lander, E. S., et al. (2001). "Initial sequencing and analysis of the human genome." Nature, 409(6822), 860-921. pdf

Reese, M. G., Kulp, D., Tammana, H., and Haussler, D. (2000). "Genie--gene finding in Drosophila melanogaster." Genome Res, 10(4), 529-38. pdf

Adams, M. D., et al. (2000). "The genome sequence of Drosophila melanogaster." Science, 287(5461), 2185-95. pdf

Reese, M. G., Eeckman, F. H., Kulp, D., and Haussler, D. (1997). "Improved splice site detection in Genie." J Comput Biol, 4(3), 311-23. pdf

Kulp, D., Haussler, D., Reese, M. G., and Eeckman, F. H. (1997). "Integrating database homology in a probabilistic gene structure model." Pac Symp Biocomput, 232-44. pdf

Kulp, D., Haussler, D., Reese, M. G., and Eeckman, F. H. (1996). "A generalized hidden Markov model for the recognition of human genes in DNA." Proc Int Conf Intell Syst Mol Biol, 4, 134-42. pdf