@inproceedings{Akutsu2000,
  author = {Tatsuya Akutsu, Hiroki Arimura, Shinichi Shimozono},
  title = {On approximation algorithms for local multiple alignment},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2000, pp 1–7. Association for Computing Machinery, New York, NY, USA.},
  pages = {1--7},
  year = {2000},
  doi = {10.1145/332306.332311},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2000, pp 1–7. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {1--7},
  proceedings_doi = {10.1145/332306.332311}
}

@article{Akutsu2000,
  author = {Tatsuya Akutsu, Satoru Miyano, Satoru Kuhara},
  title = {Algorithms for Identifying Boolean Networks and Related Biological Networks Based on Matrix Multiplication and Fingerprint Function},
  journal = {Journal of Computational Biology},
  volume = {7},
  number = {3-4},
  pages = {331--343},
  year = {2000},
  doi = {10.1089/106652700750050817},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2000, pp 8–14. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {8--14},
  proceedings_doi = {10.1145/332306.332317}
}

@article{Althaus2000,
  author = {Ernst Althaus, Oliver Kohlbacher, Hans‐Peter Lenhof, Peter Müller},
  title = {A Combinatorial Approach to Protein Docking with Flexible Side Chains},
  journal = {Journal of Computational Biology},
  volume = {535},
  number = {4},
  pages = {15--24},
  year = {2000},
  doi = {10.1089/106652702760277336},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2000, pp 15–24. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {15--24},
  proceedings_doi = {10.1145/332306.332319}
}

@article{Apostolico2000,
  author = {Alberto Apostolico, Gill Bejerano},
  title = {Optimal Amnesic Probabilistic Automata or How to Learn and Classify Proteins in Linear Time and Space},
  journal = {Journal of Computational Biology},
  volume = {7},
  number = {3-4},
  pages = {381--393},
  year = {2000},
  doi = {10.1089/106652700750050844},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2000, pp 25–32. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {25--32},
  proceedings_doi = {10.1145/332306.332321}
}

@article{Bailey‐Kellogg2000,
  author = {Chris Bailey‐Kellogg, Alik S. Widge, John J. Kelley, Marcelo J. Berardi, John H. Bushweller, Bruce R. Donald},
  title = {The NOESY Jigsaw: Automated Protein Secondary Structure and Main-Chain Assignment from Sparse, Unassigned NMR Data},
  journal = {Journal of Computational Biology},
  volume = {7},
  number = {3-4},
  pages = {537--558},
  year = {2000},
  doi = {10.1089/106652700750050934},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2000, pp 33–44. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {33--44},
  proceedings_doi = {10.1145/332306.332323}
}

@article{Batzoglou1999,
  author = {Serafim Batzoglou, Bonnie Berger, Jill P. Mesirov, Eric S. Lander},
  title = {Sequencing a Genome by Walking with Clone-End Sequences: A Mathematical Analysis},
  journal = {Genome Research},
  volume = {9},
  number = {12},
  pages = {1163--1174},
  year = {1999},
  doi = {10.1101/gr.9.12.1163},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2000, pp 45. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {45},
  proceedings_doi = {10.1145/332306.332325}
}

@article{Batzoglou2000,
  author = {Serafim Batzoglou, Lior Pachter, Jill P. Mesirov, Bonnie Berger, Eric S. Lander},
  title = {Human and Mouse Gene Structure: Comparative Analysis and Application to Exon Prediction},
  journal = {Genome Research},
  volume = {10},
  number = {7},
  pages = {950--958},
  year = {2000},
  doi = {10.1101/gr.10.7.950},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2000, pp 46–53. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {46--53},
  proceedings_doi = {10.1145/332306.332326}
}

@article{Ben‐Dor2000,
  author = {Amir Ben‐Dor, Laurakay Bruhn, Nir Friedman, Iftach Nachman, Michèl Schummer, Zohar Yakhini},
  title = {Tissue Classification with Gene Expression Profiles},
  journal = {Journal of Computational Biology},
  volume = {7},
  number = {3-4},
  pages = {559--583},
  year = {2000},
  doi = {10.1089/106652700750050943},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2000, pp 54–64. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {54--64},
  proceedings_doi = {10.1145/332306.332328}
}

@article{Ben‐Dor2000,
  author = {Amir Ben‐Dor, Richard M. Karp, Benno Schwikowski, Zohar Yakhini},
  title = {Universal DNA Tag Systems: A Combinatorial Design Scheme},
  journal = {Journal of Computational Biology},
  volume = {7},
  number = {3-4},
  pages = {503--519},
  year = {2000},
  doi = {10.1089/106652700750050916},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2000, pp 65–75. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {65--75},
  proceedings_doi = {10.1145/332306.332346}
}

@inproceedings{Bieńkowska2000,
  author = {Jadwiga R. Bieńkowska, Lihua Yu, Sophia Zarakhovich, Robert G. Rogers, Temple F. Smith},
  title = {Comprehensive statistical method for protein fold recognition},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2000, pp 76–85. Association for Computing Machinery, New York, NY, USA.},
  pages = {76--85},
  year = {2000},
  doi = {10.1145/332306.332347},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2000, pp 76–85. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {76--85},
  proceedings_doi = {10.1145/332306.332347}
}

@article{Bundschuh2002,
  author = {Ralf Bundschuh},
  title = {Rapid Significance Estimation in Local Sequence Alignment with Gaps},
  journal = {Journal of Computational Biology},
  volume = {9},
  number = {2},
  pages = {243--260},
  year = {2002},
  doi = {10.1089/10665270252935449},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2000, pp 86–95. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {86--95},
  proceedings_doi = {10.1145/332306.332350}
}

@article{Chen2000,
  author = {Kevin Chen, Dannie Durand, Martı́n Farach-Colton},
  title = {NOTUNG: A Program for Dating Gene Duplications and Optimizing Gene Family Trees},
  journal = {Journal of Computational Biology},
  volume = {7},
  number = {3-4},
  pages = {429--447},
  year = {2000},
  doi = {10.1089/106652700750050871},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2000, pp 96–106. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {96--106},
  proceedings_doi = {10.1145/332306.332351}
}

@inproceedings{Chen2000,
  author = {Xin Chen, Sam Kwong, Ming Li},
  title = {A compression algorithm for DNA sequences and its applications in genome comparison},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2000, pp 107. Association for Computing Machinery, New York, NY, USA.},
  pages = {107},
  year = {2000},
  doi = {10.1145/332306.332352},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2000, pp 107. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {107},
  proceedings_doi = {10.1145/332306.332352}
}

@article{Chor2000,
  author = {Benny Chor, Michael D. Hendy, Barbara R. Holland, David Penny},
  title = {Multiple Maxima of Likelihood in Phylogenetic Trees: An Analytic Approach},
  journal = {Molecular Biology and Evolution},
  volume = {17},
  number = {10},
  pages = {1529--1541},
  year = {2000},
  doi = {10.1093/oxfordjournals.molbev.a026252},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2000, pp 108–117. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {108--117},
  proceedings_doi = {10.1145/332306.332353}
}

@inproceedings{Desper2000,
  author = {Richard Desper, Martin Vingron},
  title = {Tree fitting: an algebraic approach using profile distances},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2000, pp 119–126. Association for Computing Machinery, New York, NY, USA.},
  pages = {119--126},
  year = {2000},
  doi = {10.1145/332306.332354},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2000, pp 119–126. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {119--126},
  proceedings_doi = {10.1145/332306.332354}
}

@article{Friedman2000,
  author = {Nir Friedman, Michal Linial, Iftach Nachman, Dana Pe’er},
  title = {Using Bayesian Networks to Analyze Expression Data},
  journal = {Journal of Computational Biology},
  volume = {7},
  number = {3-4},
  pages = {601--620},
  year = {2000},
  doi = {10.1089/106652700750050961},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2000, pp 127–135. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {127--135},
  proceedings_doi = {10.1145/332306.332355}
}

@article{Hallett1999,
  author = {Michael Hallett, Jens Lagergren},
  title = {New algorithms for the duplication-loss model},
  journal = {Repository for Publications and Research Data (ETH Zurich)},
  volume = {330},
  year = {1999},
  doi = {10.3929/ethz-a-006653457},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2000, pp 138–146. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {138--146},
  proceedings_doi = {10.1145/332306.332359}
}

@article{Hart2000,
  author = {Reece K. Hart, Ajay K. Royyuru, Gustavo Stolovitzky, Andrea Califano},
  title = {Systematic and Fully Automated Identification of Protein Sequence Patterns},
  journal = {Journal of Computational Biology},
  volume = {7},
  number = {3-4},
  pages = {585--600},
  year = {2000},
  doi = {10.1089/106652700750050952},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2000, pp 147–154. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {147--154},
  proceedings_doi = {10.1145/332306.332360}
}

@article{Heber2000,
  author = {Steffen Heber, Jens Stoye, Marcus Frohme, Jörg D. Hoheisel, Martin Vingron},
  title = {Contig Selection in Physical Mapping},
  journal = {Journal of Computational Biology},
  volume = {7},
  number = {3-4},
  pages = {395--408},
  year = {2000},
  doi = {10.1089/106652700750050853},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2000, pp 155–164. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {155--164},
  proceedings_doi = {10.1145/332306.332361}
}

@inproceedings{Kann2000,
  author = {Maricel Kann, Richard A. Goldstein},
  title = {Optimizing for success: a new score function for distantly related protein sequence comparison},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2000, pp 177–182. Association for Computing Machinery, New York, NY, USA.},
  pages = {177--182},
  year = {2000},
  doi = {10.1145/332306.332536},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2000, pp 177–182. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {177--182},
  proceedings_doi = {10.1145/332306.332536}
}

@inproceedings{Krececioglu2000,
  author = {John Krececioglu, Sanjay Shete, Jonathan Arnold},
  title = {Reconstructing distances in physical maps of chromosomes with nonoverlapping probes},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2000, pp 183–192. Association for Computing Machinery, New York, NY, USA.},
  pages = {183--192},
  year = {2000},
  doi = {10.1145/332306.332540},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2000, pp 183–192. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {183--192},
  proceedings_doi = {10.1145/332306.332540}
}

@inproceedings{Liwo2000,
  author = {Adam Liwo, Jaroslaw Pillardy, Cezary Czaplewski, Jooyoung Lee, Daniel R. Ripoll, Malgorzata Groth, Sylwia Rodziewicz-Motowidlo, Rajmund Kamierkiewicz, Ryszard J. Wawak, Stanislaw Oldziej, Harold A. Scheraga},
  title = {UNRES: a united-residue force field for energy-based prediction of protein structure—orgin and significance of multibody terms},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2000, pp 193–200. Association for Computing Machinery, New York, NY, USA.},
  pages = {193--200},
  year = {2000},
  doi = {10.1145/332306.332544},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2000, pp 193–200. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {193--200},
  proceedings_doi = {10.1145/332306.332544}
}

@article{Lyngsø2000,
  author = {Rune B. Lyngsø, Christian N. S. Pedersen},
  title = {Pseudoknots in RNA Secondary Structures},
  journal = {BRICS Report Series},
  volume = {7(1)},
  year = {2000},
  doi = {10.7146/brics.v7i1.20129},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2000, pp 201–209. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {201--209},
  proceedings_doi = {10.1145/332306.332551}
}

@article{Marsan2000,
  author = {Laurent Marsan, Marie-France Sagot},
  title = {Algorithms for Extracting Structured Motifs Using a Suffix Tree with an Application to Promoter and Regulatory Site Consensus Identification},
  journal = {Journal of Computational Biology},
  volume = {7},
  number = {3-4},
  pages = {345--362},
  year = {2000},
  doi = {10.1089/106652700750050826},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2000, pp 210–219. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {210--219},
  proceedings_doi = {10.1145/332306.332553}
}

@article{Tomita2000,
  author = {Masaru Tomita, Kenta Hashimoto, Koichi Takahashi, Yuri Matsuzaki, Ryo Matsushima, Kanako Saito, Katsuyuki Yugi, Fumihiko Miyoshi, Hisako Nakano, Sakura Tanida, Yûsuke Saito, Akiko Kawase, Naoko Watanabe, Thomas S. Simizu, Yoichi Nakayama},
  title = {The E-CELL project: Towards integrative simulation of cellular processes},
  journal = {New Generation Computing},
  volume = {18},
  number = {1},
  pages = {1--12},
  year = {2000},
  doi = {10.1007/bf03037563},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2000, pp 290–298. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {290--298},
  proceedings_doi = {10.1145/332306.332567}
}

@inproceedings{Xu2000,
  author = {Ying Xu, Dong Xu, Oakley H. Crawford, J. Ralph Einstein, Engin Serpersu},
  title = {Protein structure determination using protein threading and sparse NMR data},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2000, pp 299–307. Association for Computing Machinery, New York, NY, USA.},
  pages = {299--307},
  year = {2000},
  doi = {10.1145/332306.332568},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2000, pp 299–307. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {299--307},
  proceedings_doi = {10.1145/332306.332568}
}

@inproceedings{Yona2000,
  author = {Golan Yona, Michael Levitt},
  title = {A unified sequence-structure classification of protein sequences: combining sequence and structure in a map of the protein space},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2000, pp 308–317. Association for Computing Machinery, New York, NY, USA.},
  pages = {308--317},
  year = {2000},
  doi = {10.1145/332306.332569},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2000, pp 308–317. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {308--317},
  proceedings_doi = {10.1145/332306.332569}
}

@article{Zien2000,
  author = {Alexander Zien, Ralf Zimmer, Thomas Lengauer},
  title = {A Simple Iterative Approach to Parameter Optimization},
  journal = {Journal of Computational Biology},
  volume = {7},
  number = {3-4},
  pages = {483--501},
  year = {2000},
  doi = {10.1089/106652700750050907},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2000, pp 318–327. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {318--327},
  proceedings_doi = {10.1145/332306.332570}
}