@article{Arslan2001,
  author = {Abdullah N. Arslan, Ömer Eğeci̇oğlu, Pavel A. Pevzner},
  title = {A new approach to sequence comparison: normalized sequence alignment},
  journal = {Bioinformatics},
  volume = {17},
  number = {4},
  pages = {327--337},
  year = {2001},
  doi = {10.1093/bioinformatics/17.4.327},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2001, pp 2–11. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {2--11},
  proceedings_doi = {10.1145/369133.369146}
}

@article{Barash2002,
  author = {Yoseph Barash, Nir Friedman},
  title = {Context-Specific Bayesian Clustering for Gene Expression Data},
  journal = {Journal of Computational Biology},
  volume = {9},
  number = {2},
  pages = {169--191},
  year = {2002},
  doi = {10.1089/10665270252935403},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2001, pp 12–21. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {12--21},
  proceedings_doi = {10.1145/369133.369150}
}

@inproceedings{Beigel2001,
  author = {Richard Beigel, Noga Alon, Simon Kasif, Mehmet Serkan Apaydin, Lance Fortnow},
  title = {An optimal procedure for gap closing in whole genome shotgun sequencing},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2001, pp 22–30. Association for Computing Machinery, New York, NY, USA.},
  pages = {22--30},
  year = {2001},
  doi = {10.1145/369133.369152},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2001, pp 22–30. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {22--30},
  proceedings_doi = {10.1145/369133.369152}
}

@article{Ben‐Dor2001,
  author = {Amir Ben‐Dor, Nir Friedman, Zohar Yakhini},
  title = {Statistical benchmarking and class discovery in gene expression data},
  journal = {Nature Genetics},
  volume = {27},
  number = {S4},
  pages = {96},
  year = {2001},
  doi = {10.1038/87368},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2001, pp 31–38. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {31--38},
  proceedings_doi = {10.1145/369133.369167}
}

@inproceedings{Bilu2001,
  author = {Yonatan Bilu, Michal Linial},
  title = {On the predictive power of sequence similarity in yeast},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2001, pp 39–48. Association for Computing Machinery, New York, NY, USA.},
  pages = {39--48},
  year = {2001},
  doi = {10.1145/369133.369168},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2001, pp 39–48. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {39--48},
  proceedings_doi = {10.1145/369133.369168}
}

@article{Blanchette2002,
  author = {Mathieu Blanchette, Benno Schwikowski, Martin Tompa},
  title = {Algorithms for Phylogenetic Footprinting},
  journal = {Journal of Computational Biology},
  volume = {9},
  number = {2},
  pages = {211--223},
  year = {2002},
  doi = {10.1089/10665270252935421},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2001, pp 49–58. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {49--58},
  proceedings_doi = {10.1145/369133.369170}
}

@article{Cowen2002,
  author = {Lenore Cowen, Phil Bradley, Matthew Menke, Jonathan King, Bonnie Berger},
  title = {Predicting the Beta-Helix Fold from Protein Sequence Data},
  journal = {Journal of Computational Biology},
  volume = {9},
  number = {2},
  pages = {261--276},
  year = {2002},
  doi = {10.1089/10665270252935458},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2001, pp 59–67. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {59--67},
  proceedings_doi = {10.1145/369133.369171}
}

@article{Buhler2002,
  author = {Jeremy Buhler, Martin Tompa},
  title = {Finding Motifs Using Random Projections},
  journal = {Journal of Computational Biology},
  volume = {9},
  number = {2},
  pages = {225--242},
  year = {2002},
  doi = {10.1089/10665270252935430},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2001, pp 69–76. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {69--76},
  proceedings_doi = {10.1145/369133.369172}
}

@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 2001, pp 77–85. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {77--85},
  proceedings_doi = {10.1145/369133.369173}
}

@article{Bussemaker2001,
  author = {Harmen J. Bussemaker, Hao Li, Eric D. Siggia},
  title = {Regulatory element detection using correlation with expression},
  journal = {Nature Genetics},
  volume = {27},
  number = {2},
  pages = {167--171},
  year = {2001},
  doi = {10.1038/84792},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2001, pp 86. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {86},
  proceedings_doi = {10.1145/369133.369174}
}

@inproceedings{Chen2001,
  author = {Ting Chen},
  title = {Gene-finding via tandem mass spectrometry},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2001, pp 87–94. Association for Computing Machinery, New York, NY, USA.},
  pages = {87--94},
  year = {2001},
  doi = {10.1145/369133.369176},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2001, pp 87–94. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {87--94},
  proceedings_doi = {10.1145/369133.369176}
}

@article{Chen2001,
  author = {Ting Chen, Jacob D. Jaffe, George M. Church},
  title = {Algorithms for Identifying Protein Cross-Links via Tandem Mass Spectrometry},
  journal = {Journal of Computational Biology},
  volume = {8},
  number = {6},
  pages = {571--583},
  year = {2001},
  doi = {10.1089/106652701753307494},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2001, pp 95–102. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {95--102},
  proceedings_doi = {10.1145/369133.369177}
}

@article{Csürös2002,
  author = {Miklós Csürös},
  title = {Fast Recovery of Evolutionary Trees with Thousands of Nodes},
  journal = {Journal of Computational Biology},
  volume = {9},
  number = {2},
  pages = {277--297},
  year = {2002},
  doi = {10.1089/10665270252935467},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2001, pp 104–113. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {104--113},
  proceedings_doi = {10.1145/369133.369178}
}

@article{Efrat2002,
  author = {Alon Efrat, Frank Hoffmann, Klaus Kriegel, Christof Schultz, Carola Wenk},
  title = {Geometric Algorithms for the Analysis of 2D-Electrophoresis Gels},
  journal = {Journal of Computational Biology},
  volume = {9},
  number = {2},
  pages = {299--315},
  year = {2002},
  doi = {10.1089/10665270252935476},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2001, pp 114–123. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {114--123},
  proceedings_doi = {10.1145/369133.369181}
}

@article{Filkov2002,
  author = {Vladimir Filkov, Steven Skiena, Jizu Zhi},
  title = {Analysis Techniques for Microarray Time-Series Data},
  journal = {Journal of Computational Biology},
  volume = {9},
  number = {2},
  pages = {317--330},
  year = {2002},
  doi = {10.1089/10665270252935485},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2001, pp 124–131. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {124--131},
  proceedings_doi = {10.1145/369133.369183}
}

@article{Friedman2002,
  author = {Nir Friedman, Matan Ninio, Itsik Pe’er, Tal Pupko},
  title = {A Structural EM Algorithm for Phylogenetic Inference},
  journal = {Journal of Computational Biology},
  volume = {9},
  number = {2},
  pages = {331--353},
  year = {2002},
  doi = {10.1089/10665270252935494},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2001, pp 132–140. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {132--140},
  proceedings_doi = {10.1145/369133.369182}
}

@article{Frieze2002,
  author = {Alan Frieze, Bjarni V. Halldórsson},
  title = {Optimal Sequencing by Hybridization in Rounds},
  journal = {Journal of Computational Biology},
  volume = {9},
  number = {2},
  pages = {355--369},
  year = {2002},
  doi = {10.1089/10665270252935502},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2001, pp 141–148. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {141--148},
  proceedings_doi = {10.1145/369133.369187}
}

@inproceedings{Hallett2001,
  author = {M. T. Hallett, J. Lagergren},
  title = {Efficient algorithms for lateral gene transfer problems},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2001, pp 149–156. Association for Computing Machinery, New York, NY, USA.},
  pages = {149--156},
  year = {2001},
  doi = {10.1145/369133.369188},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2001, pp 149–156. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {149--156},
  proceedings_doi = {10.1145/369133.369188}
}

@article{Huson2002,
  author = {Daniel H. Huson, Knut Reinert, Eugene W. Myers},
  title = {The greedy path-merging algorithm for contig scaffolding},
  journal = {Journal of the ACM},
  volume = {49},
  number = {5},
  pages = {603--615},
  year = {2002},
  doi = {10.1145/585265.585267},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2001, pp 157–163. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {157--163},
  proceedings_doi = {10.1145/369133.369190}
}

@inproceedings{Langmead2001,
  author = {Christopher James Langmead, Bruce Randall Donald},
  title = {Extracting structural information using time-frequency analysis of protein NMR data},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2001, pp 164–175. Association for Computing Machinery, New York, NY, USA.},
  pages = {164--175},
  year = {2001},
  doi = {10.1145/369133.369191},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2001, pp 164–175. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {164--175},
  proceedings_doi = {10.1145/369133.369191}
}

@inproceedings{Kececioglu2001,
  author = {John Kececioglu, Jun Ju},
  title = {Separating repeats in DNA sequence assembly},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2001, pp 176–183. Association for Computing Machinery, New York, NY, USA.},
  pages = {176--183},
  year = {2001},
  doi = {10.1145/369133.369192},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2001, pp 176–183. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {176--183},
  proceedings_doi = {10.1145/369133.369192}
}

@inproceedings{Kohlbacher2001,
  author = {O. Kohlbacher, A. Burchardt, A. Moll, A. Hildebrandt, P. Bayer, H.-P Lenhof},
  title = {A NMR-spectra-based scoring function for protein docking},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2001, pp 184–192. Association for Computing Machinery, New York, NY, USA.},
  pages = {184--192},
  year = {2001},
  doi = {10.1145/369133.369194},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2001, pp 184–192. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {184--192},
  proceedings_doi = {10.1145/369133.369194}
}

@inproceedings{Lancia2001,
  author = {Giuseppe Lancia, Robert Carr, Brian Walenz, Sorin Istrail},
  title = {101 optimal PDB structure alignments: a branch-and-cut algorithm for the maximum contact map overlap problem},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2001, pp 193–202. Association for Computing Machinery, New York, NY, USA.},
  pages = {193--202},
  year = {2001},
  doi = {10.1145/369133.369199},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2001, pp 193–202. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {193--202},
  proceedings_doi = {10.1145/369133.369199}
}

@inproceedings{Li2001,
  author = {Wentian Li},
  title = {DNA segmentation as a model selection process},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2001, pp 204–210. Association for Computing Machinery, New York, NY, USA.},
  pages = {204--210},
  year = {2001},
  doi = {10.1145/369133.369202},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2001, pp 204–210. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {204--210},
  proceedings_doi = {10.1145/369133.369202},
  preprint_id = {arXiv:physics/0104027},
  preprint_doi = {10.48550/arXiv.physics/0104027}
}

@article{Jiang2002,
  author = {Tao Jiang, Guohui Lin, Bin Ma, Kaizhong Zhang},
  title = {A General Edit Distance between RNA Structures},
  journal = {Journal of Computational Biology},
  volume = {9},
  number = {2},
  pages = {371--388},
  year = {2002},
  doi = {10.1089/10665270252935511},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2001, pp 211–220. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {211--220},
  proceedings_doi = {10.1145/369133.369214}
}

@inproceedings{Myers2001,
  author = {Gene Myers},
  title = {Comparing sequence scaffolds},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2001, pp 224–230. Association for Computing Machinery, New York, NY, USA.},
  pages = {224--230},
  year = {2001},
  doi = {10.1145/369133.369218},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2001, pp 224–230. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {224--230},
  proceedings_doi = {10.1145/369133.369218}
}

@article{Navarro2003,
  author = {Gonzalo Navarro, Mathieu Raffinot},
  title = {Fast and Simple Character Classes and Bounded Gaps Pattern Matching, with Applications to Protein Searching},
  journal = {Journal of Computational Biology},
  volume = {10},
  number = {6},
  pages = {903--923},
  year = {2003},
  doi = {10.1089/106652703322756140},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2001, pp 231–240. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {231--240},
  proceedings_doi = {10.1145/369133.369220}
}

@article{Pachter2002,
  author = {Lior Pachter, Marina Alexandersson, Simon Cawley},
  title = {Applications of Generalized Pair Hidden Markov Models to Alignment and Gene Finding Problems},
  journal = {Journal of Computational Biology},
  volume = {9},
  number = {2},
  pages = {389--399},
  year = {2002},
  doi = {10.1089/10665270252935520},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2001, pp 241–248. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {241--248},
  proceedings_doi = {10.1145/369133.369227}
}

@article{Pavlidis2002,
  author = {Paul Pavlidis, Jason Weston, Jinsong Cai, William Stafford Noble},
  title = {Learning Gene Functional Classifications from Multiple Data Types},
  journal = {Journal of Computational Biology},
  volume = {9},
  number = {2},
  pages = {401--411},
  year = {2002},
  doi = {10.1089/10665270252935539},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2001, pp 249–255. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {249--255},
  proceedings_doi = {10.1145/369133.369228}
}

@inproceedings{Pevzner2001,
  author = {Pavel A. Pevzner, Haixu Tang, Michael S. Waterman},
  title = {A new approach to fragment assembly in DNA sequencing},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2001, pp 256–267. Association for Computing Machinery, New York, NY, USA.},
  pages = {256--267},
  year = {2001},
  doi = {10.1145/369133.369230},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2001, pp 256–267. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {256--267},
  proceedings_doi = {10.1145/369133.369230}
}

@article{Shamir2002,
  author = {Ron Shamir, Dekel Tsur},
  title = {Large Scale Sequencing by Hybridization},
  journal = {Journal of Computational Biology},
  volume = {9},
  number = {2},
  pages = {413--428},
  year = {2002},
  doi = {10.1089/10665270252935548},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2001, pp 269–277. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {269--277},
  proceedings_doi = {10.1145/369133.369233}
}

@inproceedings{Singh2001,
  author = {Mona Singh, Peter S. Kim},
  title = {Towards predicting coiled-coil protein interactions},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2001, pp 279–286. Association for Computing Machinery, New York, NY, USA.},
  pages = {279--286},
  year = {2001},
  doi = {10.1145/369133.369238},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2001, pp 279–286. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {279--286},
  proceedings_doi = {10.1145/369133.369238}
}

@article{Amato2002,
  author = {Nancy M. Amato, Guang Song},
  title = {Using Motion Planning to Study Protein Folding Pathways},
  journal = {Journal of Computational Biology},
  volume = {9},
  number = {2},
  pages = {149--168},
  year = {2002},
  doi = {10.1089/10665270252935395},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2001, pp 287–296. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {287--296},
  proceedings_doi = {10.1145/369133.369239}
}

@article{Tang2002,
  author = {Mengxiang Tang, Michael S. Waterman, Shibu Yooseph},
  title = {Zinc Finger Gene Clusters and Tandem Gene Duplication},
  journal = {Journal of Computational Biology},
  volume = {9},
  number = {2},
  pages = {429--446},
  year = {2002},
  doi = {10.1089/10665270252935557},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2001, pp 297–304. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {297--304},
  proceedings_doi = {10.1145/369133.369241}
}

@article{Thijs2002,
  author = {Gert Thijs, Kathleen Marchal, Magali Lescot, Stéphane Rombauts, Bart De Moor, Pierre Rouzé, Yves Moreau},
  title = {A Gibbs Sampling Method to Detect Overrepresented Motifs in the Upstream Regions of Coexpressed Genes},
  journal = {Journal of Computational Biology},
  volume = {9},
  number = {2},
  pages = {447--464},
  year = {2002},
  doi = {10.1089/10665270252935566},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2001, pp 305–312. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {305--312},
  proceedings_doi = {10.1145/369133.369253}
}