RECOMB 1998 Proceedings

New York, NY, United States, March 22 - 25, 1998

PC Chair: Pavel Pevzner
Organization Committee: Gary Benson (chair), Craig Benham, Martin Farach, Eugene Kolker
Keynote Speakers: Ruben Abagyan, Charles Cantor, David Cox, Ron Davis, Klaus Gubernator, Joshua Lederberg, Michael Levitt, David Schwartz, John Yates
Website: https://recomb.org/recomb1998
Export: JSON | BibTeX

List of Publications

• Detecting non-adjoining correlations with signals in DNA. Pankaj Agarwal, Vineet Bafna.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1998, pp 2–8. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/279069.279076
• From four-taxon trees to phylogenies (preliminary report): the case of mammalian evolution. Amir Ben-Dor, Benny Chor, Dan Graur, Ron Ophir, Dan Pelleg.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1998, pp 9–19. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/279069.279078
  • Journal: Constructing Phylogenies from Quartets: Elucidation of Eutherian Superordinal Relationships. Amir Ben‐Dor, Benny Chor, Dan Graur, Ron Ophir, Dan Pelleg. Journal of Computational Biology, 5(3): 377-390, 1998.
    • DOI: 10.1089/cmb.1998.5.377
• An algorithm for finding tandem repeats of unspecified pattern size. Gary Benson.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1998, pp 20–29. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/279069.279079
• Protein folding in the hydrophobic-hydrophilic (HP) is NP-complete. Bonnie Berger, Tom Leighton.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1998, pp 30–39. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/279069.279080
  • Journal: Protein Folding in the Hydrophobic-Hydrophilic (HP) Model is NP-Complete. Bonnie Berger, Tom Leighton. Journal of Computational Biology, 5(1): 27-40, 1998.
    • DOI: 10.1089/cmb.1998.5.27
• Better methods for solving parsimony and compatibility. Maria Bonet, Mike Steel, Tandy Warnow, Shibu Yooseph.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1998, pp 40–49. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/279069.279081
  • Journal: Better Methods for Solving Parsimony and Compatibility. Maria Bonet, Mike Steel, Tandy Warnow, Shibu Yooseph. Journal of Computational Biology, 5(3): 391-407, 1998.
    • DOI: 10.1089/cmb.1998.5.391
• The hierarchical organization of molecular structure computations. Cheng Che Chen, Jaswinder Pal Singh, Russ B. Altman.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1998, pp 51–59. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/279069.279086
  • Journal: Hierarchical Organization of Molecular Structure Computations. Cheng Che Chen, Jaswinder Pal Singh, Russ B. Altman. Journal of Computational Biology, 5(3): 409-422, 1998.
    • DOI: 10.1089/cmb.1998.5.409
• On the complexity of protein folding. Pierluigi Crescenzi, Deborah Goldman, Christos Papadimitriou, Antonio Piccolboni, Mihalis Yannakakis.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1998, pp 61–62. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/279069.279089
  • Journal: On the Complexity of Protein Folding. Pierluigi Crescenzi, Deborah Goldman, Christos Papadimitriou, Antonio Piccolboni, Mihalis Yannakakis. Journal of Computational Biology, 5(3): 423-465, 1998.
    • DOI: 10.1089/cmb.1998.5.423
• Constructing maps using the span and inclusion relations. Dan Fasulo, Tao Jiang, Richard M. Karp, Nitin Sharma.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1998, pp 64–73. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/279069.279090
• How fast a protein chain can fold to its most stable structure?. Alexei V. Finkelstein, Azat Ya. Badretdinov.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1998, pp 74–78. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/279069.279091
• A formally exact method to numerically analyze local denaturation in superhelical DNA. Richard M. Fye, Craig J. Benhan.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1998, pp 79–84. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/279069.279093
  • Journal: Exact method for numerically analyzing a model of local denaturation in superhelically stressed DNA. Richard M. Fye, Craig J. Benhan. Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics, 59(3): 3408-3426, 1999.
    • DOI: 10.1103/physreve.59.3408
• Algorithmic determination of core positions in the VL and VH domains of immunoglobulin molecules. Israel Gelfand, Alexander Kister, Casimir Kulikowski, Ognyan Stoyanov.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1998, pp 85–93. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/279069.279095
  • Journal: Algorithmic Determination of Core Positions in the VL and VH Domains of Immunoglobulin Molecules. I. Gelfand, Alexander Kister, Casimir A. Kulikowski, Ognyan Stoyanov. Journal of Computational Biology, 5(3): 467-477, 1998.
    • DOI: 10.1089/cmb.1998.5.467
• Family-based homology detection via pairwise sequence comparison. William Noble Grundy.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1998, pp 94–100. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/279069.279098
  • Journal: Homology Detection via Family Pairwise Search. William Noble Grundy. Journal of Computational Biology, 5(3): 479-491, 1998.
    • DOI: 10.1089/cmb.1998.5.479
• Dynamic programming alignment accuracy. Ian Holmes, Richard Durbin.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1998, pp 102–108. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/279069.279102
  • Journal: Dynamic Programming Alignment Accuracy. Ian Holmes, Richard Durbin. Journal of Computational Biology, 5(3): 493-504, 1998.
    • DOI: 10.1089/cmb.1998.5.493
• Optimal detection of sequence similarity by local alignment. Terence Hwa, Michael Lässig.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1998, pp 109–116. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/279069.279103
  • Preprint: arXiv:cond-mat/9712081
• Algorithms for optical mapping. Richard M. Karp, Ron Shamir.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1998, pp 117–124. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/279069.279104
  • Journal: Algorithms for Optical Mapping. Richard M. Karp, Ron Shamir. Journal of Computational Biology, 7(1-2): 303-316, 2000.
    • DOI: 10.1089/10665270050081540
• The ordinal quartet method. Paul E. Kearney.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1998, pp 125–134. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/279069.279105
• Genome analysis using clusters of orthologous groups (COGs). Eugene V. Koonin, Roman L. Tatusov, Michael Y. Galperin, Michael N. Rosanov.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1998, pp 135–139. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/279069.279106
• Beyond mutation matrices: physical-chemistry based evolutionary models. Jeffrey M. Koshi, David P. Mindell, Richard A. Goldstein.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1998, pp 140–145. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/279069.279107
• Estimation for restriction sites observed by optical mapping using reversible-jump Markov chain Monte Carlo. Jae K. Lee, Vlado Dančík, Michael S. Waterman.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1998, pp 147–152. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/279069.279108
  • Journal: Estimation for Restriction Sites Observed by Optical Mapping Using Reversible-Jump Markov Chain Monte Carlo. Jae K Lee, Vlado Dančík, Michael S. Waterman. Journal of Computational Biology, 5(3): 505-515, 1998.
    • DOI: 10.1089/cmb.1998.5.505
• A polyhedral approach to RNA sequence structure alignment. Hans-Peter Lenhof, Knut Reinert, Martin Vingron.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1998, pp 153–162. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/279069.279109
  • Journal: A Polyhedral Approach to RNA Sequence Structure Alignment. Hans‐Peter Lenhof, Knut Reinert, Martin Vingron. Journal of Computational Biology, 5(3): 153-162, 1998.
    • DOI: 10.1089/cmb.1998.5.517
• Assessment of ab initio protein structure prediction. Arthur M. Lesk.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1998, pp 163–171. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/279069.279110
• A structure based similarity measure for nucleic acid sequence comparison. Rongxiang Liu, Tom W. Blackwell, David U. States.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1998, pp 173–181. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/279069.279112
• On reconstructing species trees from gene trees in term of duplications and losses. Bin Ma, Ming Li, Louxin Zhang.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1998, pp 182–191. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/279069.279113
• Partitioning K clones: hardness results and practical algorithms for the K-populations problem. Laxmi Parida, Bud Mishra.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1998, pp 192–201. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/279069.279114
  • Journal: Partitioning single-molecule maps into multiple populations: algorithms and probabilistic analysis. Laxmi Parida, Bud Mishra. Discrete Applied Mathematics, 104(1-3): 203-227, 2000.
    • DOI: 10.1016/s0166-218x(00)00191-8
• Estimation of allele frequencies from color-multiplexed electropherograms. David G. Politte, David R. Maffitt, David J. States.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1998, pp 202–206. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/279069.279115
• A unified approach to word statistics. Mireille Régnier.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1998, pp 207–213. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/279069.279116
  • Journal: A unified approach to word occurrence probabilities. Mireille Régnier. Discrete Applied Mathematics, 104(1-3): 259-280, 2000.
    • DOI: 10.1016/s0166-218x(00)00195-5
• A self-consistent field optimization approach to build energetically and geometrically correct lattice models of proteins. Boris A. Reva, Alexei V. Finkelstein, Jeffrey Skolnick.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1998, pp 214–220. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/279069.279117
• Motif discovery without alignment or enumeration. Isidore Rigoutsos, Aris Floratos.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1998, pp 221–227. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/279069.279118
• An algorithm for finding novel gapped motifs in DNA sequences. Emily Rocke, Martin Tompa.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1998, pp 228–233. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/279069.279119
• Identifying satellites in nucleic acid sequences. Marie-France Sagot, Eugene W. Myers.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1998, pp 234–242. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/279069.279120
  • Journal: Identifying Satellites and Periodic Repetitions in Biological Sequences. Marie‐France Sagot, Eugene W. Myers. Journal of Computational Biology, 5(3): 539-553, 1998.
    • DOI: 10.1089/cmb.1998.5.539
• Multiple genome rearrangements. David Sankoff, Mathieu Blanchette.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1998, pp 243–247. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/279069.279122
• Modeling DNA shuffling. Fengzhu Sun.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1998, pp 251–257. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/279069.279126
  • Journal: Modeling DNA Shuffling. Fengzhu Sun. Journal of Computational Biology, 6(1): 77-90, 1999.
    • DOI: 10.1089/cmb.1999.6.77
• Analysis of the position dependent amino acid probabilities and its application to the search for remote homologues. Shamil R. Sunyaev, Igor V. Rodchnkov, Frank Eisenhaber, Eugene N. Kuznetsov.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1998, pp 258–265. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/279069.279127
• Maxwell demon and topology simplification by type II topoisomerases. Alexander Vologodskii.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1998, pp 266–269. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/279069.279129
• The theoretical limits of DNA sequence discrimination of polyamides. Wynn L. Walker, David S. Goodsell, Elliot M. Landaw.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1998, pp 270–275. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/279069.279130
  • Journal: The theoretical limits of DNA sequence discrimination by linked polyamides. Wynn L. Walker, Elliot M. Landaw, Richard E. Dickerson, David S. Goodsell. Proceedings of the National Academy of Sciences, 95(8): 4315-4320, 1998.
    • DOI: 10.1073/pnas.95.8.4315
• Regression analysis of multiple protein structures. Thomas D. Wu, Trevor Hastie, Scott C. Schmidler, Douglas L. Brutlag.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1998, pp 276–284. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/279069.279132
  • Journal: Regression Analysis of Multiple Protein Structures. Thomas D. Wu, Scott C. Schmidler, Trevor Hastie, Douglas L. Brutlag. Journal of Computational Biology, 5(3): 585-595, 1998.
    • DOI: 10.1089/cmb.1998.5.585
• A new method for modeling and solving the protein fold recognition problem. Ying Xu, Dong Xu, Edward C. Uberbacher.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1998, pp 285–292. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/279069.279134