RECOMB 1997 Proceedings

Santa Fe, NM, United States, January 20 - 23, 1997

PC Chair: Michael Waterman
Organization Committee: Sorin Istrail (chair), Bonnie Berger, Chris Fields, William Hart, Sylvia Spengler
Keynote Speakers: Rich Roberts, Eric Lander, Robert Lipshutz, David Botstein, Sam Karlin, Martin Karplus, Jonathan King, Temple Smith, Terry Speed
Website: https://recomb.org/recomb1997
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List of Publications

• Local rules for protein folding on a triangular lattice and generalized hydrophobicity in the HP model. Richa Agarwala, Serafim Batzoglou, Vlado Dančík, Scott E. Decatur, Martin Farach, Sridhar Hannenhalli, S. Muthukrishnan, Steven Skiena.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1997, pp 1–2. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/267521.267522
  • Journal: Local Rules for Protein Folding on a Triangular Lattice and Generalized Hydrophobicity in the HP Model. Richa Agarwala, Serafim Batzoglou, Vlado Dančík, Scott E. Decatur, Sridhar Hannenhalli, Martin Farach-Colton, S. Muthukrishnan, Steven Skiena. Journal of Computational Biology, 4(3): 275-296, 1997.
    • DOI: 10.1089/cmb.1997.4.275
• On the approximation of protein threading. Tatsuya Akutsu, Satoru Miyano.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1997, pp 3–8. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/267521.267523
  • Journal: On the approximation of protein threading. Tatsuya Akutsu, Satoru Miyano. Theoretical Computer Science, 210(2): 261-275, 1999.
    • DOI: 10.1016/s0304-3975(98)00089-9
• ReAligner: a program for refining DNA sequence multi-alignments. Eric L. Anson, Eugene W. Myers.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1997, pp 9–16. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/267521.267524
  • Journal: ReAligner: A Program for Refining DNA Sequence Multi-Alignments. Eric L. Anson, Eugene W. Myers. Journal of Computational Biology, 4(3): 369-383, 1997.
    • DOI: 10.1089/cmb.1997.4.369
• On constructing radiation hybrid maps. Amir Ben-Dor, Benny Chor.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1997, pp 17–26. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/267521.267525
  • Journal: On Constructing Radiation Hybrid Maps. Amir Ben‐Dor, Benny Chor. Journal of Computational Biology, 4(4): 517-533, 1997.
    • DOI: 10.1089/cmb.1997.4.517
• Sequence alignment with tandem duplication. Gary Benson.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1997, pp 27–36. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/267521.267526
  • Journal: Sequence Alignment with Tandem Duplication. Gary Benson. Journal of Computational Biology, 4(3): 351-367, 1997.
    • DOI: 10.1089/cmb.1997.4.351
• An iterative method for improved protein structural motif recognition. Bonnie Berger, Mona Singh.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1997, pp 37–46. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/267521.267527
  • Journal: An Iterative Method for Improved Protein Structural Motif Recognition. Bonnie Berger, Mona Singh. Journal of Computational Biology, 4(3): 261-273, 1997.
    • DOI: 10.1089/cmb.1997.4.261
• Chain growth algorithms for HP-type lattice proteins. Erich Bornberg-Bauer.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1997, pp 47–55. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/267521.267528
• Fabricating arrays of strings. J. Richard Bradley, Steven S. Skiena.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1997, pp 57–66. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/267521.267529
• The power of surface-based DNA computation. Weiping Cai, Anne E. Condon, Robert M. Corn, Elton Glaser, Zhengdong Fei, Tony Frutos, Zhen Guo, Max G. Lagally, Qinghua Liu, Lloyd M. Smith, Andrew Thiel.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1997, pp 67–74. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/267521.267530
• Sorting by reversals is difficult. Alberto Caprara.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1997, pp 75–83. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/267521.267531
• A branch-and-cut approach to physical mapping with end-probes. Thomas Christof, Michael Jünger, John Kececioglu, Petra Mutzel, Gerhard Reinelt.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1997, pp 84–92. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/267521.267532
  • Journal: A Branch-and-Cut Approach to Physical Mapping of Chromosomes by Unique End-Probes. Thomas Christof, Michael Jünger, John Kececioglu, Petra Mutzel, Gerhard Reinelt. Journal of Computational Biology, 4(4): 433-447, 1997.
    • DOI: 10.1089/cmb.1997.4.433
• Monte Carlo sequence alignment. Gary A. Churchill.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1997, pp 93–97. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/267521.267534
• Numerical taxonomy on data: experimental results. Jaime Cohen, Martin Farach.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1997, pp 98. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/267521.267535
  • Journal: Numerical Taxonomy on Data: Experimental Results. Jaime Cohen, Martı́n Farach-Colton. Journal of Computational Biology, 4(4): 547-558, 1997.
    • DOI: 10.1089/cmb.1997.4.547
• On the complexity and approximation of syntenic distance. B. DasGupta, T. Jiang, S. Kannan, M. Li, Z. Sweedyk.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1997, pp 99–108. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/267521.267536
  • Journal: On the complexity and approximation of syntenic distance. Bhaskar Dasgupta, Tao Jiang, Sampath Kannan, Ming Li, Elizabeth Sweedyk. Discrete Applied Mathematics, 88(1-3): 59-82, 1998.
    • DOI: 10.1016/s0166-218x(98)00066-3
• Protein structure prediction and potential energy landscape analysis using continuous global minimization. Ken A. Dill, Andrew T. Phillips, J. Ben Rosen.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1997, pp 109–117. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/267521.267537
  • Journal: Protein Structure and Energy Landscape Dependence on Sequence Using a Continuous Energy Function. Ken A. Dill, Andrew T. Phillips, J. Ben Rosen. Journal of Computational Biology, 4(3): 227-239, 1997.
    • DOI: 10.1089/cmb.1997.4.227
• An algorithmic approach to multiple complete digest mapping. Daniel P. Fasulo, Tao Jiang, Richard M. Karp, Reuben Settergren, Edward C. Thayer.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1997, pp 118–127. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/267521.267538
  • Journal: An Algorithmic Approach to Multiple Complete Digest Mapping. Daniel Fasulo, Tao Jiang, Richard M. Karp, Reuben Settergren, Edward C. Thayer. Journal of Computational Biology, 6(2): 187-207, 1999.
    • DOI: 10.1089/cmb.1999.6.187
• On the computational complexity of sequence design problems. William E. Hart.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1997, pp 128–136. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/267521.267539
• Lattice and off-lattice side chain models of protein folding: linear time structure prediction better than 86% of optimal. William E. Hart, Sorin Istrail.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1997, pp 137–146. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/267521.267540
  • Journal: Lattice and Off-Lattice Side Chain Models of Protein Folding: Linear Time Structure Prediction Better than 86% of Optimal. William E. Hart, Sorin Istrail. Journal of Computational Biology, 4(3): 241-259, 1997.
    • DOI: 10.1089/cmb.1997.4.241
• The application of Markov chain Monte Carlo methods to radiation hybrid mapping. Simon C. Heath.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1997, pp 147–150. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/267521.267541
  • Journal: Markov Chain Monte Carlo Methods for Radiation Hybrid Mapping. Simon C. Heath. Journal of Computational Biology, 4(4): 505-515, 1997.
    • DOI: 10.1089/cmb.1997.4.505
• Algorithms for computing and integrating physical maps using unique probes. Mudita Jain, Eugene W. Myers.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1997, pp 151–161. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/267521.267542
  • Journal: Algorithms for Computing and Integrating Physical Maps Using Unique Probes. Mudita Jain, Eugene W. Myers. Journal of Computational Biology, 4(4): 449-466, 1997.
    • DOI: 10.1089/cmb.1997.4.449
• Mapping clones with a given ordering or interleaving. Tao Jiang, Richard M. Karp.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1997, pp 162. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/267521.267543
  • Journal: Mapping Clones with a Given Ordering or Interleaving. Tao Jiang, Richard M. Karp. Algorithmica, 21(3): 262-284, 1998.
    • DOI: 10.1007/pl00009215
• Faster and simpler algorithm for sorting signed permutations by reversals. Haim Kaplan, Ron Shamir, Robert E. Tarjan.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1997, pp 163. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/267521.267544
  • Journal: A Faster and Simpler Algorithm for Sorting Signed Permutations by Reversals. Haim Kaplan, Ron Shamir, Robert E. Tarjan. SIAM Journal on Computing, 29(3): 880-892, 2000.
    • DOI: 10.1137/s0097539798334207
• Chimeric alignment by dynamic programming: algorithm and biological uses. George A. Komatsoulis, Michael S. Waterman.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1997, pp 174–180. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/267521.267546
  • Journal: A new computational method for detection of chimeric 16S rRNA artifacts generated by PCR amplification from mixed bacterial populations. George A. Komatsoulis, Michael S. Waterman. Applied and Environmental Microbiology, 63(6): 2338-2346, 1997.
    • DOI: 10.1128/aem.63.6.2338-2346.1997
• New contact measures for the protein docking problem. Hans-Peter Lenhof.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1997, pp 182–191. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/267521.267547
• An algorithm for haplotype analysis. Shili Lin, Terence P. Speed.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1997, pp 192–200. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/267521.267548
  • Journal: An Algorithm for Haplotype Analysis. Shili Lin, Terence P. Speed. Journal of Computational Biology, 4(4): 535-546, 1997.
    • DOI: 10.1089/cmb.1997.4.535
• Supervised learning of hidden Markov models for sequence discrimination. Hiroshi Mamitsuka.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1997, pp 202–208. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/267521.267551
  • Journal: A Learning Method of Hidden Markov Models for Sequence Discrimination. Hiroshi Mamitsuka. Journal of Computational Biology, 3(3): 361-373, 1996.
    • DOI: 10.1089/cmb.1996.3.361
• Towards constructing physical maps by optical mapping: an effective, simple, combinatorial approach. S. Muthukrishnan, Laxmi Parida.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1997, pp 209–219. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/267521.267552
• Progressive multiple alignment with constraints. Gene Myers, Sanford Selznick, Zheng Zhang, Webb Miller.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1997, pp 220–225. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/267521.267758
  • Journal: Progressive Multiple Alignment with Constraints. Gene Myers, Sanford Selznick, Zheng Zhang, Webb Miller. Journal of Computational Biology, 3(4): 563-572, 1996.
    • DOI: 10.1089/cmb.1996.3.563
• Simulating Boolean circuits on a DNA computer. Mitsunori Ogihara, Animesh Ray.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1997, pp 226–231. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/267521.267759
  • Journal: Simulating Boolean Circuits on a DNA Computer. Mitsunori Ogihara, Animesh Ray. Algorithmica, 25(2-3): 239-250, 1999.
    • DOI: 10.1007/pl00008276
• Improved splice site detection in Genie. Martin G. Reese, Frank H. Eeckman, David Kulp, David Haussler.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1997, pp 232–240. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/267521.267766
  • Journal: Improved Splice Site Detection in Genie. Martin G. Reese, Frank H. Eeckman, David Kulp, David Haussler. Journal of Computational Biology, 4(3): 311-323, 1997.
    • DOI: 10.1089/cmb.1997.4.311
• A branch-and-cut algorithm for multiple sequence alignment. K. Reinert, H.-P. Lenhof, P. Mutzel, K. Mehlhorn, J. D. Kececioglu.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1997, pp 241–250. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/267521.267845
• Beyond islands: runs in clone-probe matrices. David B. Wilson, David S. Greenberg, Cynthia A. Phillips.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1997, pp 320–329. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/267521.267891
• Reference-based gene model prediction on DNA contigs. Ying Xu, Edward C. Uberbacher.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1997, pp 330–336. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/267521.267892
• Aligning a DNA sequence with a protein sequence. Zheng Zhang, William R. Pearson, Webb Miller.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1997, pp 337–343. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/267521.267893
  • Journal: Aligning a DNA Sequence with a Protein Sequence. Zheng Zhang, William R. Pearson, Webb Miller. Journal of Computational Biology, 4(3): 339-349, 1997.
    • DOI: 10.1089/cmb.1997.4.339
• Fast and numerically stable parametric alignment of biosequences. Ralf Zimmer, Thomas Lengauer.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1997, pp 344–353. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/267521.267894