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 online

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 Proc LSS Comput Syst Bioinform Conf. August, 2007. Vol. 6, p. 133-143. online

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, Jagalur 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

Lee, Audrey, Ileana Streinu, and Oliver Brock. A Methodology for Efficiently Sampling the Conformation Space of Molecular Structures. Physical Biology 2:S108-S115, November 2005. html pdf

Brock, Oliver and TJ Brunette. Predicting Protein Structure with Guided Conformation Space Search. Technical Report 05-63. Computer Science Department, University of Massachusetts Amherst, November 2005. pdf

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

Lee, Audrey, Oliver Brock, and Ileana Streinu. A Methodology for Efficiently Sampling the Conformation Space of Molecular Structures. Technical Report 05-40. Computer Science Department, University of Massachusetts Amherst, July 2005. pdf

Brunette, TJ and Oliver Brock. Improving Protein Structure Prediction with Model-Based Search. Bioinformatics 21(Suppl. 1):66-74, June 2005. Special Issue for the Internaitonal Conference on Intelligent Systems for Molecular Biology (ISMB), Detoit, USA pdf

Brunette, TJ and Oliver Brock. Model-Based Search to Determine Minima in Molecular Energy Landscapes. Technical Report 04-48. Computer Science Department, University of Massachusetts Amherst, September 2004. 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

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

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