Center Faculty Publications

2011

• B. Halldorsson, D. Aguiar, S. Istrail, Haplotype Phasing by Multi-Assembly of Shared Haplotypes: Phase-Dependent Interactions Between Rare Variants, presented at the Pacific Symposium on Biocomputing, Big Island, Hawaii, January 3-7, 2011.
  

• S. Istrail, R. Tarpine, K. Schutter, and D. Aguiar, Practical Computational Methods for Regulatory Genomics: A cis-Lexicon and cis-Browser for Gene Regulatory Networks, In I. Ladunga (ed.) Computational Biology of Transcription Factor Binding,Methods in Molecular Biology 674, DOI 10.1007/978-1-60761-854-6_22, Springer Science+Business Media, LLC, Humana Press, 2010
• B. Halldorsson, D. Aguiar, R. Tarpine, S. Istrail, The Clark Phase-able Sample Size Problem: Long-range Phasing and Loss of Heterozygosity in GWAS, Journal of Computation Biology, March 2011, 18(3): 323-33
• J. Nam, P. Dong, R. Tarpine, S. Istrail and E. Davidson, Functional cis-regulatory genomics for systems biology, Proceedings of the National Academy of Sciences, vol. 107, no. 8, pp. 3930-3935, 2010
• F. Lam, R. Tarpine and S. Istrail, The Imperfect Ancestral Recombination Graph Reconstruction Problem: A Hierarchy of Upper Bounds, Journal of Computational Biology, vol. 17, no. 6, pp. 767-781, 2010
• S. Istrail, P. Pevzner, R. Shamir, F. Sun (Editors), Special Issue Dedicated to Michael Waterman on the Occasion of his 67th Birthday: Parts III-IV, Communications in Information and Systems, China, vol. 10, nos. 3-4, pp. 1-115, 2010
  

• S. Istrail, P. Pevzner, R. Shamir, F. Sun (Editors), Special Issue Dedicated to Michael Waterman on the Occasion of his 67th Birthday: Parts I-II, Communications in Information and Systems, China, vol. 9, nos. 1-2, pp. 235-347, 2009
• Tarpine, R., Istrail, S. On the Concept of Cis-Regulatory Information: From Sequence Motifs to Logic Functions. Algorithmic Bioprocesses, Springer-Verlag, Berlin Heidelberg, pp. 731-742, 2009
• S. Istrail, F. Lam, Combinatorial Algorithms for Protein Folding in Lattice Models: A Survey of Mathematical Results, Communications in Information and Systems, vol. 9, no. 4, pp. 303-346, 2009

• E. Corona, B. Raphael, E. Eskin, Identifying Deletion Polymorphisms from Haplotypes, Proceedings of the 11Th Annual International Conference on Research in Computational Biology, RECOMB (2007)
• S. Istrail, P. Pevzner, R. Shamir (Editors), Computational Molecular Biology Series, Issue V. Discrete Applied Mathematics, Volume 155, Issues 6-7, Pages 673-888, 1 April (2007)
• S. Yooseph, G. Sutton, D.B. Rusch, A.L. Halpern, S.J. Williamson, K.Remington, J.A. Eisen, K..B. Heidelberg, G. Manning, W. Li, L. Jaroszewski, P. Cieplak, C.S. Miller, H. Li, S. T. Mashiyama, M. P. Joachimiak, C. van Belle, J. Chandonia, D. A. Soergel, Y. Zhai, K. Natarajan, S. Lee, B. Raphael, V. Bafna, R. Friedman, S. E. Brenner, A. Godzik, D. Eisenberg, J.E. Dixon, S. S. Taylor, R.L. Strausberg, M. Frazier, J.C. Venter. The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families., PLOS Biology. 5(3):e16 (2007)
• Poelwijk FJ, Kiviet DJ, Weinreich DM, Tans SJ, Empirical fitness landscapes reveal accessible evolutionary paths. Nature, January, 25 445(7126):383-6 (2007)

• M. Chaisson, B. Raphael, P. Pevzner, Micro-inversions in Mammalian Evolution, Proceedings of the National Academy of Sciences, USA. 103(52):19824-9 (2006)
• Ding Y, Chan CY, and Lawrence CE, Clustering of RNA Secondary Structures with Application to Messenger RNAs, J Mol Biol, 359(3):554-71 (2006)
• N.C. Jones, D. Zhi, B. Raphael, AliWABA: Alignment on the Web through an A-Bruijn Approach, Nucleic Acids Research. July 1;34:W613-6 (2006)
• Polz, Martin, Dana E. Hunt, Sarah P. Preheim and Daniel M. Weinreich, Patterns and mechanisms of genetic and phenotypic differentiation in marine microbes. Phil. Trans. Roy. Soc. B 361: doi 10.1098/rstb.2006.1928 (2006)
• Manoj P. Samanta, Waraporn Tongprasit, Sorin Istrail, R. Andrew Cameron, Qiang Tu, Eric H. Davidson, Viktor Stolc, The Transcriptome of the Sea Urchin Embryo, Science, vol. 314, pp. 960-962 November (2006)
• Sharan, R., Halldorsson, B. V., Istrail, S., Islands of Tractability for Parsimony Haplotyping, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 3, No. 3, pp. 303-311 (2006)
• E. Sodergren, G. Weinstock, E. Davidson, ...S. Istrail,... The Genome of the Sea Urchin Strongylocentrotus purpuratus, Science, vol 314., pp. 941-952, November (2006)
• S. Volik, B. Raphael, et al., Decoding the Fine-scale Structure of a Breast Cancer Genome and Transcriptome. Genome Research, 16(3):394-404 (2006)
• Watson, Richard A., Daniel M. Weinreich, and John Wakeley, Effects of Intra-gene Epistasis on the Benefit of Sexual Recombination. Biochemical Society Transactions 34:560-561 (2006)
• Weinreich, Daniel M., Nigel Delaney, Mark A. DePristo and Daniel L. Hartl, Darwinian evolution can follow only very few mutational paths to fitter proteins. Science 312:111-114 (2006)
• D. Zhi, B. Raphael, A.Price, H. Tang, P. Pevzner, Identifying Repeat Domains in Large Genomes. Genome Biology, 7(1):R7 (2006)

• Vineet Bafna, Sorin Istrail, Guiseppe Lancia, and Romeo Rizzi, Polynomial and APX-hard cases of the individual haplotyping problem. Theoretical Computer Science, 109-125 (2005)
• Conlan S., Lawrence C, McCue LA, Rhodopseudomonas palustris Regulons Detected by Cross-Species Analysis of Alphaproteobacterial Genomes. Appl Environl Microbiol, 71 (11):7442-7452 (2005)
• Francisco M. De La Vega, Hadar Isaac, Andrew Collins, Charles R. Scafe, Bjarni V. Halldrsson, Xiaoping Su, Ross A. Lippert, Francis Kalush, Stephen J. O'Brian, Andrew Clark, Sorin Istrail, Michael W. Hunkapiller, Eugene G. Spier, and Dennis Gilbert, The linkage disequilibrium maps of three human chromosomes across four populations reflect their demographic history and a common underlying recombination pattern. Genome Research, March 21 (2005)
• DePristo, Mark A, Daniel M. Weinreich and Daniel L. Hartl, Missense meanderings through sequence space: a biophysical perspective on protein evolution. Nature Reviews Genetics 6(8):678-687 (2005)
• Ding Y., Chan CY., and Lawrence CE., RNA Secondary Structure Prediction by Centroids in a Boltzmann Weighted Ensemble, RNA, 11 (8):1157-1166 (2005)
• Florea, L., V. Di Francesco, J. Miller, R. Turner, C. Mobarry, A. Yao, M. Harris, B. Walenz, I. Dew, G. Merkulov, R. Charlab, Z. Deng, S. Istrail, P. Li, G. Sutton, Gene and alternative splicing annotation with AIR, Genome Research 15(1), 54-66 (2005)
• Bjarni Halldorsson, Roded Sharan, and Sorin Istrail, Islands of Tractability for Parsimony Haplotyping, Proceedings of the Stanford Computational Systems Biology 2005, pp. 65-72 (IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press) (2005)
• Sorin Istrail and Eric Davidson, Logic functions of the genomic cis-regulatory code, Proceedings of the National Academy of Sciences, vol. 102, No. 14, 4954-4959 (2005)
• G. Mesirov, S. Kasif, S. Istrail, P. Pevzner, M.Waterman (Editors), Proceedings of the 9th International Conference on Computational Molecular Biology (RECOMB 2004), Lecture Notes in Bioinformatics, Springer-Verlag, Boston (2005)
• Newberg LA, McCue LA, Lawrence CE, The Relative Inefficiency of Sequence Weights Approaches in Determining A Nucleotide Position Weight Matrix, Statist App Gen Mol Biol, 4:13 (2005)
• Weinreich, Daniel M., The Rank Ordering of Genotypic Fitness Values Predicts Genetic Constraint on Natural Selection on Landscapes Lacking Sign Epistasis. Genetics 171(3): 1397-1405 (2005)
• Weinreich, Daniel M. and Lin Chao, Rapid evolutionary escape by large populations from local peaks is likely in nature. Evolution: 59:1175-1182 (2005)
• Weinreich, Daniel M., Richard A. Watson and Lin Chao, Perspectives: Sign epistasis and constraint on evolutionary trajectories. (Cover article) Evolution 59:1165-1174 (2005)

• Auger I., Lawrence CE Discussions on a Bayesian Approach to DNA Sequence Segmentation. Biometrics 60(3):581 (2004)
• A. Caprara, R. Carr, S. Istrail, G. Lancia, and B. Walenz, 1001 Optimal PDB Structure Alignments: Integer Programming Methods for Finding the Maximum Contact Map Overlap, Journal of Computational Biology vol 11, No. 1, pp 27-52 (2004)
• D. Gusfield, P. Bourne, S. Istrail, P. Pevzner, M.Waterman (Editors), Proceedings of the 8th International Conference on Computational Molecular Biology (RECOMB 2004), ACM Press, San Diego (2004)
• Bjarni V. Halldorsson, Vineet Bafna, Ross Lippert, Russell S. Schwartz, Francisco M. De La Vega, Andrew G. Clark, Sorin Istrail, Optimal haplotype block free selection of tagging SNPs for genome-wide association studies, Genome Research (2004)
• Bjarni V. Halldorsson, Sorin Istrail, Francisco M. De La Vega, Optimal Selection of SNP Markers for Disease Association Studies, Human Heredity, vol. 58, p. 190-202 (2004)
• Sorin Istrail, Liliana Florea, Bjarni V. Halldorsson, Oliver Kohlbacher, Russell S. Schwartz, Von Bing Yap, Jonathan Yewdell, Stephen Hoffman,
  Comparative Immuno-Peptidomics 13 of Humans and their Pathogens, Proceedings of the National Academy of Sciences (2004)
• 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, Proceedings of the National Academy of Sciences, 101:1916-21 (2004)
• S. Istrail, M. Waterman, A. Clark (Editors), Proceedings of the 1st RECOMB Satellite Workshop Computational Methods for SNPs and Haplotype Inference, Piscataway, NJ November 21-22, Lecture Notes in Bioinformatics, (LNBI 2983) (2004)
• Lippert, R., X. Zhao, L. Florea, C. Mobarry, S. Istrail, Finding anchors for genomic sequence comparison, Proceedings of the 8th Annual International 10 Conference on Research in Computational Biology (RECOMB04), ACM Press (2004)
• B. Raphael, L. Liu, and G. Varghese, A Uniform Projection Method for Motif Discovery in DNA Sequences. IEEE Transactions on Computational Biology and Bioinformatics, 1(2): 91-94 (2004)
• B. Raphael, P. Pevzner, Reconstructing Tumor Amplisomes, Bioinformatics, 20 Suppl 1:I265-I273 (2004)
• B. Raphael, D. Zhi, H. Tang, P. Pevzner, A Novel Method for Multiple Alignment of Sequences with Repeated and Shuffled Domains. Genome Research, 14(11):2336-46 (2004)
• Thompson W, Palumbo MJ, Wasserman WW, Liu JS, Lawrence CE, Decoding Human Regulatory Circuits. Genome Res, 14: 1967-1974 (2004)

• Vineet Bafna, Bjarni V. Halldorsson, Russell S. Schwartz, Andrew G. Clark, Sorin Istrail, Haplotypes and Informative SNP Selection Algorithms: Don't Block Out Information, Proceedings of the 7th Annual International Conference on Computational Molecular Biology (RECOMB03), ACM Press, pp. 19-27 (2003)
• Ding Y, Lawrence CE, A Statistical Sampling Algorithm for RNA Secondary Structure Prediction Nucleic Acids Res, 31(24): 7280-7301 (2003)
• Liliana Florea, Bjarni V. Halldorsson, Oliver Kohlbacher, Russell S. Schwartz, Stephen Hoffman, Sorin Istrail, Epitope prediction algorithms for peptide-based vaccine design, Proceedings of the Second Annual IEEE Computer Society Bioinformatics Conference (CSB03), IEEE Press, pp. 17-26 (2003)
• C. Guerra, S. Istrail (Editors), Mathematical Methods for Protein Structure Analysis and Design, Advanced Lectures, CIME Summer School on Mathematical Methods for Protein Structure and Design, Marina Franca, Italy, July 9-15, Lecture Notes in Bioinformatics, (LNBI 2666) (2003)
• Bjarni V. Halldorsson, Vineet Bafna, Nathan Edwards, Ross Lippert, Shibu Yooseph, Sorin Istrail, A survey of computational methods for determining haplotypes, Proceedings of the First RECOMB Satellite on Computational Methods for SNPs and Haplotype Inference, (RECOMB SNP&HAP03), Springer Lecture Notes in Bioinformatics, LNBI 2983, pp. 26-47 (2003)
• Bjarni V. Halldorsson, Vineet Bafna, Nathan Edwards, Ross Lippert, Shibu Yooseph, Sorin Istrail, Combinatorial problems arising in SNP and haplotype analysis, Proceedings of the Fourth International Conference on Discrete Mathematics and Theoretical Computer Science, (CDMTCS03), Springer Lecture Notes in Computer Science, pp. 26-47 (2003)
• W. Miller, M. Vingron, S. Istrail, P. Pevzner, M.Waterman (Editors), Proceedings of the 7th International Conference on Computational Molecular Biology (RECOMB 2003), ACM Press, Washington, DC (2003)
• B. Raphael, S. Volik, C. Collins, P. Pevzner, Reconstructing Tumor Genome Architectures, Bioinformatics, Suppl 2:ii162-171 (2003)
• R. Schwartz, A. Clark, S. Istrail, Inferring piecewise ancestral sequences from haploid sequences, Proceedings of the First RECOMB Satellite on Computational Methods for SNPs and Haplotype Inference, (RECOMB SNP&HAP03), Springer Lecture Notes in Bioinformatics, LNBI 2983 (2003)
• Russell S. Schwartz, Bjarni V. Halldorsson, Vineet Bafna, Andrew G. Clark, Sorin Istrail Robustness of Inference of Haplotype Block Structure. Journal of Computational Biology, 10:13-19 (2003)
• Sheldahl, Lea, Daniel M. Weinreich and David M. Rand, Recombination, dominance and selection on amino acid polymorphism in the Drosophila genome: Contrasting patterns on the X and fourth chromosomes, Genetics 165: 1195-1208 (2003)