| 2007 | |
| [84] | Sorin Istrail, Smadar Ben-Tabou De-Leon, Eric H. Davidson, "The regulatory genome and the computer", In Developmental Biology, vol. 310, no. 2, pp. 187-195, 2007. [bib] [pdf] [doi] |
| 2006 | |
| [83] | Roded Sharan, Bjarni V Halldorsson, Sorin Istrail, "Islands of Tractability for Parsimony Haplotyping", In IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 3, no. 3, pp. 303-311, 2006. [bib] [pdf] |
| [82] | Manoj P. Samanta, Waraporn Tongprasit, Sorin Istrail, R. Andrew Cameron, Qiang Tu, Eric H. Davidson, Viktor Stolc, "The Transcriptome of the Sea Urchin Embryo", In Science, vol. 314, no. 5801, pp. 960-962, 2006. [bib] [pdf] [doi] |
| [81] | Bjarni V Halldorsson, Roded Sharan, Sorin Istrail, "Islands of Tractability for Parsimony Haplotyping", In Stanford Computational Systems Biology, 2006. [bib] [pdf] |
| [80] | Sea Urchin Genome Sequencing Consortium, Erica Sodergren, George M. Weinstock, Eric H Davidson, R. Andrew Cameron, Richard A. Gibbs, Robert C. Angerer, Lynne M. Angerer, Maria Ina Arnone, David R. Burgess, Robert D. Burke, James A. Coffman, Michael Dean, Maurice R. Elphick, Charles A. Ettensohn, Kathy R. Foltz, Amro Hamdoun, Richard O. Hynes, William H. Klein, William Marzluff, David R. McClay, Robert L. Morris, Arcady Mushegian, Jonathan P. Rast, L. Courtney Smith, Michael C. Thorndyke, Victor D. Vacquier, Gary M. Wessel, Greg Wray, Lan Zhang, Christine G. Elsik, Olga Ermolaeva, Wratko Hlavina, Gretchen Hofmann, Paul Kitts, Melissa J. Landrum, Aaron J. Mackey, Donna Maglott, Georgia Panopoulou, Albert J. Poustka, Kim Pruitt, Victor Sapojnikov, Xingzhi Song, Alexandre Souvorov, Victor Solovyev, Zheng Wei, Charles A. Whittaker, Kim Worley, K. James Durbin, Yufeng Shen, Olivier Fedrigo, David Garfield, Ralph Haygood, Alexander Primus, Rahul Satija, Tonya Severson, Manuel L. Gonzalez-Garay, Andrew R. Jackson, Aleksandar Milosavljevic, Mark Tong, Christopher E. Killian, Brian T. Livingston, Fred H. Wilt, Nikki Adams, Robert Bell??, Seth Carbonneau, Rocky Cheung, Patrick Cormier, Bertrand Cosson, Jenifer Croce, Antonio Fernandez-Guerra, Anne-Marie Genevi??re, Manisha Goel, Hemant Kelkar, Julia Morales, Odile Mulner-Lorillon, Anthony J. Robertson, Jared V. Goldstone, Bryan Cole, David Epel, Bert Gold, Mark E. Hahn, Meredith Howard-Ashby, Mark Scally, John J. Stegeman, Erin L. Allgood, Jonah Cool, Kyle M. Judkins, Shawn S. McCafferty, Ashlan M. Musante, Robert A. Obar, Amanda P. Rawson, Blair J. Rossetti, Ian R. Gibbons, Matthew P. Hoffman, Andrew Leone, Sorin Istrail, Stefan C. Materna, Manoj P. Samanta, Viktor et al. Stolc, "The Genome of the Sea Urchin Strongylocentrotus purpuratus", In Science, vol. 314, no. 5801, pp. 941-952, 2006. [bib] [pdf] [doi] |
| 2005 | |
| [79] | Sorin Istrail, Eric Davidson, "Logic functions of the genomic cis-regulatory code", In Proceedings of the National Academy of Sciences, vol. 102, no. 14, pp. 4954-4959, 2005. [bib] [pdf] |
| [78] | Liliana Florea, Valentina Di Francesco, Jason Miller, Russell Turner, Alison Yao, Michael Harris, Brian Walenz, Clark Mobarry, Gennady V. Merkulov, Rosane Charlab, Ian Dew, Zuoming Deng, Sorin Istrail, Peter Li, Granger Sutton, "Gene and alternative splicing annotation with AIR", In Genome Research, vol. 15, no. 1, pp. 54-66, 2005. [bib] [pdf] |
| [77] | Francisco M. De La Vega, Hadar Isaac, Andrew Collins, Charles R. Scafe, Bjarni V. Halldorsson, Xiaoping Su, Ross A. Lippert, Yu Wang, Marion Laig-Webster, Ryan T. Koehler, Janet S. Ziegle, Lewis T. Wogan, Junko F. Stevens, Kyle M. Leinen, Sheri J. Olson, Karl J. Guegler, Xiaoqing You, Lily H. Xu, Heinz G. Hemken, Francis Kalush, Mitsuo Itakura, Yi Zheng, Guy de Th??, Stephen J. O'Brien, Andrew G. Clark, Sorin Istrail, Michael W. Hunkapiller, Eugene G. Spier, Dennis A. Gilbert, "The linkage disequilibrium maps of three human chromosomes across four populations reflect their demographic history and a common underlying recombination pattern", In Genome Research, vol. 15, no. 4, pp. 454-462, 2005. [bib] [pdf] |
| 2004 | |
| [76] | Ross Lippert, Xiaoyue Zhao, Liliana Florea, Clark Mobarry, Sorin Istrail, "Finding anchors for genomic sequence comparison", In 8th Annual International Conference on Research in Computational Biology (RECOMB04), ACM Press, 2004. [bib] [pdf] |
| [75] | Sorin Istrail, Granger G. Sutton, Liliana Florea, Aaron L. Halpern, Clark M. Mobarry, Ross Lippert, Brian Walenz, Hagit Shatkay, Ian Dew, Jason R. Miller, Michael J. Flanigan, Nathan J. Edwards, Randall Bolanos, Daniel Fasulo, Bjarni V. Halldorsson, Sridhar Hannenhalli, Russell Turner, Shibu Yooseph, Fu Lu, Deborah R. Nusskern, Bixiong Chris Shue, Xiangqun Holly Zheng, Fei Zhong, Arthur L. Delcher, Daniel H. Huson, Saul A. Kravitz, Laurent Mouchard, Knut Reinert, Karin A. Remington, Andrew G. Clark, Michael S. Waterman, Evan E. Eichler, Mark D. Adams, Michael W. Hunkapiller, Eugene W. Myers, J. Craig Venter, "Whole Genome Shotgun Assembly and Comparison of Human Genome Assemblies", In Proceedings of the National Academy of Sciences, vol. 101, no. 7, pp. 1916-1921, 2004. [bib] [pdf] |
| [74] | Sorin Istrail, Liliana Florea, Bjarni V Halldorsson, Oliver Kohlbacher, Russell Schwartz, Von Bing Yap, Jonathan Yewdell, Stephen Hoffman, "Comparative Immuno-Peptidomics of Humans and their Pathogens", In Proceedings of the National Academy of Sciences, vol. 101, no. 36, pp. 13268-13272, 2004. [bib] [pdf] |
| [73] | Bjarni V Halldorsson, Vineet Bafna, Ross Lippert, Russell Schwartz, Francisco M. De La Vega, Andrew G. Clark, Sorin Istrail, "Optimal haplotype block free selection of tagging SNPs for genome-wide association studies", In Genome Research, vol. 14, no. 8, pp. 1633-1640, 2004. [bib] [pdf] |
| [72] | Alberto Caprara, Robert Carr, Sorin Istrail, Giuseppe Lancia, Brian Walenz, "1001 optimal PDB structure alignments: integer programming methods for finding the maximum contact map overlap", In Journal of Computational Biology, vol. 11, no. 1, pp. 27-52, 2004. [bib] [pdf] [doi] |
| 2003 | |
| [71] | Russell Schwartz, Bjarni V Halldorsson, Vineet Bafna, Andrew G. Clark, Sorin Istrail, "Robustness of Inference of Haplotype Block Structure", In Journal of Computational Biology, vol. 10, pp. 13-19, 2003. [bib] [pdf] |
| [70] | Russell Schwartz, Andrew G. Clark, Sorin Istrail, "Inferring Piecewise Ancestral History from Haploid Sequences", In First RECOMB Satellite on Computational Methods for SNPs and Haplotype Inference, (RECOMB SNP&HAP03), Springer, 2003. [bib] [pdf] |
| [69] | Bjarni V Halldorsson, Vineet Bafna, Nathan J. Edwards, Ross Lippert, Shibu Yooseph, Sorin Istrail, "A survey of computational methods for determining haplotypes", In First RECOMB Satellite on Computational Methods for SNPs and Haplotype Inference, (RECOMB SNP&HAP03), Springer, pp. 26-47, 2003. [bib] [pdf] |
| [68] | Bjarni V Halldorsson, Vineet Bafna, Nathan J. Edwards, Ross Lippert, Shibu Yooseph, Sorin Istrail, "Combinatorial problems arising in SNP and haplotype analysis", In Fourth International Conference on Discrete Mathematics and Theoretical Computer Science, (CDMTCS03), Springer, pp. 26-47, 2003. [bib] [pdf] |
| [67] | Liliana Florea, Bjarni V Halldorsson, Oliver Kohlbacher, Russell Schwartz, Stephen Hoffman, Sorin Istrail, "Epitope prediction algorithms for peptide-based vaccine design", In Second Annual IEEE Computer Society Bioinformatics Conference (CSB03), IEEE Press, pp. 17-26, 2003. [bib] [pdf] |
| [66] | Liliana Florea, Bjarni V Halldorsson, Oliver Kohlbacher, Russell Schwartz, Stephen Hoffman, Sorin Istrail, "A Computational Pipeline for High-Throughput T-Cell Epitope Prediction", Celera Genomics, 2003. [bib] |
| [65] | Vineet Bafna, Bjarni V Halldorsson, Russell Schwartz, Andrew G. Clark, Sorin Istrail, "Haplotypes and Informative SNP Selection Algorithms: Don't Block Out Information", In 7th Annual International Conference on Computational Molecular Biology (RECOMB03), ACM Press, pp. 19-27, 2003. [bib] [pdf] |
| 2002 | |
| [64] | Russell Schwartz, Andrew G. Clark, Sorin Istrail, "Methods for inferring block-wise ancestral history from haploid sequences: The haplotype coloring problem", In 2nd Workshop on Algorithms in Bioinformatics, (WABI02), Springer, pp. 44-59, 2002. [bib] [pdf] |
| [63] | Romeo Rizzi, Vineet Bafna, Sorin Istrail, Giuseppe Lancia, "Practical Algorithms and Fixed-Parameter Tractability for the Single Individual SNP Haplotyping Problem", In 2nd Workshop on Algorithms in Bioinformatics, (WABI02), Springer, pp. 29-43, 2002. [bib] [pdf] |
| [62] | Ross Lippert, Russell Schwartz, Giuseppe Lancia, Sorin Istrail, "Algorithmic Strategies for the SNP Haplotype Assembly Problem", In Briefings in Bioinformatics, vol. 3, no. 1, pp. 1-9, 2002. [bib] [pdf] |
| [61] | Sorin Istrail, "The Haplotype Phasing Problem", Celera Genomics, 2002. [bib] |
| 2001 | |
| [60] | J. Craig Venter, Mark D. Adams, Eugene W. Myers, Peter W. Li, Richard J. Mural, Granger G. Sutton, Hamilton O. Smith, Mark Yandell, Cheryl A. Evans, Robert A. Holt, Jeannine D. Gocayne, Peter Amanatides, Richard M. Ballew, Daniel H. Huson, Jennifer Russo Wortman, Qing Zhang, Chinnappa D. Kodira, Xiangqun H. Zheng, Lin Chen, Marian Skupski, Gangadharan Subramanian, Paul D. Thomas, Jinghui Zhang, George L. Gabor Miklos, Catherine Nelson, Samuel Broder, Andrew G. Clark, Joe Nadeau, Victor A. McKusick, Norton Zinder, Arnold J. Levine, Richard J. Roberts, Mel Simon, Carolyn Slayman, Michael Hunkapiller, Randall Bolanos, Arthur Delcher, Ian Dew, Daniel Fasulo, Michael Flanigan, Liliana Florea, Aaron Halpern, Sridhar Hannenhalli, Saul Kravitz, Samuel Levy, Clark Mobarry, Knut Reinert, Karin Remington, Jane Abu-Threideh, Ellen Beasley, Kendra Biddick, Vivien Bonazzi, Rhonda Brandon, Michele Cargill, Ishwar Chandramouliswaran, Rosane Charlab, Kabir Chaturvedi, Zuoming Deng, Valentina Di Francesco, Patrick Dunn, Karen Eilbeck, Carlos Evangelista, Andrei E. Gabrielian, Weiniu Gan, Wangmao Ge, Fangcheng Gong, Zhiping Gu, Ping Guan, Thomas J. Heiman, Maureen E. Higgins, Rui-Ru Ji, Zhaoxi Ke, Karen A. Ketchum, Zhongwu Lai, Yiding Lei, Zhenya Li, Jiayin Li, Yong Liang, Xiaoying Lin, Fu Lu, Gennady V. Merkulov, Natalia Milshina, Helen M. Moore, Ashwinikumar K Naik, Vaibhav A. Narayan, Beena Neelam, Deborah Nusskern, Douglas B. Rusch, Steven Salzberg, Wei Shao, Bixiong Shue, Jingtao Sun, Zhen Yuan Wang, Aihui Wang, Xin Wang, Jian Wang, Ming-Hui Wei, Ron Wides, Chunlin Xiao, Chunhua et al. Yan, "The Sequence of the Human Genome", In Science, vol. 291, no. 5507, pp. 1304-1351, 2001. [bib] [pdf] |
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