@inproceedings{Anson1999,
  author = {Eric Anson, Gene Myers},
  title = {Algorithms for whole genome shotgun sequencing},
  booktitle = {Research in Computational Molecular Biology. RECOMB 1999, pp 1–9. Association for Computing Machinery, New York, NY, USA.},
  pages = {1--9},
  year = {1999},
  doi = {10.1145/299432.299442},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 1999, pp 1–9. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {1--9},
  proceedings_doi = {10.1145/299432.299442}
}

@inproceedings{Bailey1999,
  author = {Timothy L. Bailey, William Noble Grundy},
  title = {Classifying proteins by family using the product of correlated p-values},
  booktitle = {Research in Computational Molecular Biology. RECOMB 1999, pp 10–14. Association for Computing Machinery, New York, NY, USA.},
  pages = {10--14},
  year = {1999},
  doi = {10.1145/299432.299444},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 1999, pp 10–14. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {10--14},
  proceedings_doi = {10.1145/299432.299444}
}

@inproceedings{Bejerano1999,
  author = {Gill Bejerano, Golan Yona},
  title = {Modeling protein families using probabilistic suffix trees},
  booktitle = {Research in Computational Molecular Biology. RECOMB 1999, pp 15–24. Association for Computing Machinery, New York, NY, USA.},
  pages = {15--24},
  year = {1999},
  doi = {10.1145/299432.299445},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 1999, pp 15–24. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {15--24},
  proceedings_doi = {10.1145/299432.299445}
}

@inproceedings{Bieńkowska1999,
  author = {Jadwiga R. Bieńkowska, Robert G. Rogers, Temple F. Smith},
  title = {A method for optimal design of a threading scoring function},
  booktitle = {Research in Computational Molecular Biology. RECOMB 1999, pp 25–32. Association for Computing Machinery, New York, NY, USA.},
  pages = {25--32},
  year = {1999},
  doi = {10.1145/299432.299446},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 1999, pp 25–32. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {25--32},
  proceedings_doi = {10.1145/299432.299446}
}

@article{Ben‐Dor1999,
  author = {Amir Ben‐Dor, Ron Shamir, Zohar Yakhini},
  title = {Clustering Gene Expression Patterns},
  journal = {Journal of Computational Biology},
  volume = {6},
  number = {3-4},
  pages = {281--297},
  year = {1999},
  doi = {10.1089/106652799318274},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 1999, pp 33–42. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {33--42},
  proceedings_doi = {10.1145/299432.299448}
}

@inproceedings{Bize1999,
  author = {Laurent Bize, Florence Muri, Franck Samson, François Rodolphe, S. Dusko Ehrlich, Bernard Prum, Philippe Bessières},
  title = {Searching gene transfers on Bacillus subtilis using hidden Markov models},
  booktitle = {Research in Computational Molecular Biology. RECOMB 1999, pp 43–49. Association for Computing Machinery, New York, NY, USA.},
  pages = {43--49},
  year = {1999},
  doi = {10.1145/299432.299449},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 1999, pp 43–49. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {43--49},
  proceedings_doi = {10.1145/299432.299449}
}

@article{Berman2000,
  author = {Piotr Berman, Zheng Zhang, Yuri I. Wolf, Eugene V. Koonin, Webb Miller},
  title = {Winnowing Sequences from a Database Search},
  journal = {Journal of Computational Biology},
  volume = {7},
  number = {1-2},
  pages = {293--302},
  year = {2000},
  doi = {10.1089/10665270050081531},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 1999, pp 50–58. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {50--58},
  proceedings_doi = {10.1145/299432.299451}
}

@inproceedings{Berry1999,
  author = {Vincent Berry, David Bryant},
  title = {Faster reliable phylogenetic analysis},
  booktitle = {Research in Computational Molecular Biology. RECOMB 1999, pp 59–68. Association for Computing Machinery, New York, NY, USA.},
  pages = {59--68},
  year = {1999},
  doi = {10.1145/299432.299457},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 1999, pp 59–68. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {59--68},
  proceedings_doi = {10.1145/299432.299457}
}

@article{Bundschuh2000,
  author = {Ralf Bundschuh, Terence Hwa},
  title = {An analytic study of the phase transition line in local sequence alignment with gaps},
  journal = {Discrete Applied Mathematics},
  volume = {104},
  number = {1-3},
  pages = {113--142},
  year = {2000},
  doi = {10.1016/s0166-218x(00)00188-8},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 1999, pp 70–76. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {70--76},
  proceedings_doi = {10.1145/299432.349874}
}

@inproceedings{Burkhardt1999,
  author = {Stefan Burkhardt, Andreas Crauser, Paolo Ferragina, Hans-Peter Lenhof, Eric Rivals, Martin Vingron},
  title = {q-gram based database searching using a suffix array (QUASAR)},
  booktitle = {Research in Computational Molecular Biology. RECOMB 1999, pp 77–83. Association for Computing Machinery, New York, NY, USA.},
  pages = {77--83},
  year = {1999},
  doi = {10.1145/299432.299460},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 1999, pp 77–83. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {77--83},
  proceedings_doi = {10.1145/299432.299460}
}

@inproceedings{Caprara1999,
  author = {Alberto Caprara},
  title = {Formulations and hardness of multiple sorting by reversals},
  booktitle = {Research in Computational Molecular Biology. RECOMB 1999, pp 84–93. Association for Computing Machinery, New York, NY, USA.},
  pages = {84--93},
  year = {1999},
  doi = {10.1145/299432.299461},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 1999, pp 84–93. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {84--93},
  proceedings_doi = {10.1145/299432.299461}
}

@article{Chen2001,
  author = {Ting Chen, Vladimir Filkov, Steven Skiena},
  title = {Identifying gene regulatory networks from experimental data},
  journal = {Parallel Computing},
  volume = {27},
  number = {1-2},
  pages = {141--162},
  year = {2001},
  doi = {10.1016/s0167-8191(00)00092-2},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 1999, pp 94–103. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {94--103},
  proceedings_doi = {10.1145/299432.299462}
}

@article{Chew1999,
  author = {L. Paul Chew, D.P. Huttenlocher, Klara Kedem, Jon Kleinberg},
  title = {Fast Detection of Common Geometric Substructure in Proteins},
  journal = {Journal of Computational Biology},
  volume = {6},
  number = {3-4},
  pages = {313--325},
  year = {1999},
  doi = {10.1089/106652799318292},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 1999, pp 104–113. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {104--113},
  proceedings_doi = {10.1145/299432.299464}
}

@inproceedings{Christof1999,
  author = {Thomas Christof, John Kececioglu},
  title = {Computing physical maps of chromosomes with nonoverlapping probes by branch-and-cut},
  booktitle = {Research in Computational Molecular Biology. RECOMB 1999, pp 115–123. Association for Computing Machinery, New York, NY, USA.},
  pages = {115--123},
  year = {1999},
  doi = {10.1145/299432.299465},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 1999, pp 115–123. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {115--123},
  proceedings_doi = {10.1145/299432.299465}
}

@inproceedings{Cohen1999,
  author = {Barry Cohen, Steven Skiena},
  title = {Optimizing combinatorial library construction via split synthesis},
  booktitle = {Research in Computational Molecular Biology. RECOMB 1999, pp 124–133. Association for Computing Machinery, New York, NY, USA.},
  pages = {124--133},
  year = {1999},
  doi = {10.1145/299432.299467},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 1999, pp 124–133. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {124--133},
  proceedings_doi = {10.1145/299432.299467}
}

@inproceedings{Dančík1999,
  author = {Vlado Dančík, Theresa A. Addona, Karl R. Clauser, James E. Vath},
  title = {De Novo peptide sequencing via tandem mass spectrometry: a graph-theoretical approach},
  booktitle = {Research in Computational Molecular Biology. RECOMB 1999, pp 135–144. Association for Computing Machinery, New York, NY, USA.},
  pages = {135--144},
  year = {1999},
  doi = {10.1145/299432.299471},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 1999, pp 135–144. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {135--144},
  proceedings_doi = {10.1145/299432.299471}
}

@inproceedings{Dombkowski1999,
  author = {Alan A. Dombkowski, Gordon M. Crippen},
  title = {A solvation potential with improved contact definitions and optimized by extensive threading},
  booktitle = {Research in Computational Molecular Biology. RECOMB 1999, pp 145–153. Association for Computing Machinery, New York, NY, USA.},
  pages = {145--153},
  year = {1999},
  doi = {10.1145/299432.299474},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 1999, pp 145–153. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {145--153},
  proceedings_doi = {10.1145/299432.299474}
}

@inproceedings{El-Mabrouk1999,
  author = {Nadia El-Mabrouk, David Bryant, David Sankoff},
  title = {Reconstructing the pre-doubling genome},
  booktitle = {Research in Computational Molecular Biology. RECOMB 1999, pp 154–163. Association for Computing Machinery, New York, NY, USA.},
  pages = {154--163},
  year = {1999},
  doi = {10.1145/299432.299475},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 1999, pp 154–163. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {154--163},
  proceedings_doi = {10.1145/299432.299475}
}

@inproceedings{Floratos1999,
  author = {Aris Floratos, Isidore Rigoutsos, Laxmi Parida, Gustova Stolovitzky, Yuan Gao},
  title = {Sequence homology detection through large scale pattern discovery},
  booktitle = {Research in Computational Molecular Biology. RECOMB 1999, pp 164–173. Association for Computing Machinery, New York, NY, USA.},
  pages = {164--173},
  year = {1999},
  doi = {10.1145/299432.299477},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 1999, pp 164–173. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {164--173},
  proceedings_doi = {10.1145/299432.299477}
}

@article{Forst1999,
  author = {Christian V. Forst, Klaus Schulten},
  title = {Evolution of Metabolisms: A New Method for the Comparison of Metabolic Pathways Using Genomics Information},
  journal = {Journal of Computational Biology},
  volume = {6},
  number = {3-4},
  pages = {343--360},
  year = {1999},
  doi = {10.1089/106652799318319},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 1999, pp 174–181. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {174--181},
  proceedings_doi = {10.1145/299432.299481}
}

@inproceedings{Grant1999,
  author = {G. R. Grant, R. S. Spielman, E. Manduchi, V. G. Cheung, W. J. Ewens},
  title = {Significance testing for genomic mismatch scanning},
  booktitle = {Research in Computational Molecular Biology. RECOMB 1999, pp 182–187. Association for Computing Machinery, New York, NY, USA.},
  pages = {182--187},
  year = {1999},
  doi = {10.1145/299432.299482},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 1999, pp 182–187. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {182--187},
  proceedings_doi = {10.1145/299432.299482}
}

@inproceedings{Hartuv1999,
  author = {Erez Hartuv, Armin Schmitt, Jörg Lange, Sebastian Meier-Ewert, Hans Lehrach, Ron Shamir},
  title = {An algorithm for clustering cDNAs for gene expression analysis},
  booktitle = {Research in Computational Molecular Biology. RECOMB 1999, pp 188–197. Association for Computing Machinery, New York, NY, USA.},
  pages = {188--197},
  year = {1999},
  doi = {10.1145/299432.299483},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 1999, pp 188–197. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {188--197},
  proceedings_doi = {10.1145/299432.299483}
}

@inproceedings{Huson1999,
  author = {Daniel H. Huson, Scott Nettles, Tandy J. Warnow},
  title = {Obtaining highly accurate topology estimates of evolutionary trees from very short sequences},
  booktitle = {Research in Computational Molecular Biology. RECOMB 1999, pp 198–207. Association for Computing Machinery, New York, NY, USA.},
  pages = {198--207},
  year = {1999},
  doi = {10.1145/299432.299484},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 1999, pp 198–207. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {198--207},
  proceedings_doi = {10.1145/299432.299484}
}

@inproceedings{Karp1999,
  author = {Richard M. Karp, Roland Stoughton, Ka Yee Yeung},
  title = {Algorithms for choosing differential gene expression experiments},
  booktitle = {Research in Computational Molecular Biology. RECOMB 1999, pp 208–217. Association for Computing Machinery, New York, NY, USA.},
  pages = {208--217},
  year = {1999},
  doi = {10.1145/299432.299485},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 1999, pp 208–217. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {208--217},
  proceedings_doi = {10.1145/299432.299485}
}

@inproceedings{Kelley1999,
  author = {Lawrence A. Kelley, Robert M. MacCallum, Michael J. E. Sternberg},
  title = {Recognition of remote protein homologies using three-dimensional information to generate a position specific scoring matrix in the program 3D-PSSM},
  booktitle = {Research in Computational Molecular Biology. RECOMB 1999, pp 218–225. Association for Computing Machinery, New York, NY, USA.},
  pages = {218--225},
  year = {1999},
  doi = {10.1145/299432.299486},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 1999, pp 218–225. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {218--225},
  proceedings_doi = {10.1145/299432.299486}
}

@article{Kleinberg1999,
  author = {Jon Kleinberg},
  title = {Efficient Algorithms for Protein Sequence Design and the Analysis of Certain Evolutionary Fitness Landscapes},
  journal = {Journal of Computational Biology},
  volume = {6},
  number = {3-4},
  pages = {387--404},
  year = {1999},
  doi = {10.1089/106652799318346},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 1999, pp 226–237. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {226--237},
  proceedings_doi = {10.1145/299432.299487}
}

@inproceedings{Lathrop1999,
  author = {Richard H. Lathrop},
  title = {An anytime algorithm for gapped block protein threading with pair interactions},
  booktitle = {Research in Computational Molecular Biology. RECOMB 1999, pp 238–249. Association for Computing Machinery, New York, NY, USA.},
  pages = {238--249},
  year = {1999},
  doi = {10.1145/299432.299488},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 1999, pp 238–249. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {238--249},
  proceedings_doi = {10.1145/299432.299488}
}

@inproceedings{LaValle1999,
  author = {Steven M. LaValle, Paul W. Finn, Lydia E. Kavraki, Jeal-Claude Latombe},
  title = {Efficient database screening for rational drug design using pharmacophore-constrained conformational search},
  booktitle = {Research in Computational Molecular Biology. RECOMB 1999, pp 250–260. Association for Computing Machinery, New York, NY, USA.},
  pages = {250--260},
  year = {1999},
  doi = {10.1145/299432.299489},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 1999, pp 250–260. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {250--260},
  proceedings_doi = {10.1145/299432.299489}
}

@article{Lyngsø1999,
  author = {R B Lyngsø, Michael Zuker, Clara Nautrup Pedersen},
  title = {Fast evaluation of internal loops in RNA secondary structure prediction.},
  journal = {Bioinformatics},
  volume = {15},
  number = {6},
  pages = {440--445},
  year = {1999},
  doi = {10.1093/bioinformatics/15.6.440},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 1999, pp 260–267. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {260--267},
  proceedings_doi = {10.1145/299432.299490}
}

@article{Mayraz1999,
  author = {Guy Mayraz, Ron Shamir},
  title = {Construction of Physical Maps from Oligonucleotide Fingerprints Data},
  journal = {Journal of Computational Biology},
  volume = {6},
  number = {2},
  pages = {237--252},
  year = {1999},
  doi = {10.1089/cmb.1999.6.237},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 1999, pp 268–277. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {268--277},
  proceedings_doi = {10.1145/299432.299497}
}

@inproceedings{Mitchell1999,
  author = {Julie C. Mitchell, J. Ben Rosen, Andrew T. Phillips, Lynn F. Ten Eyck},
  title = {Coupled optimization in protein docking},
  booktitle = {Research in Computational Molecular Biology. RECOMB 1999, pp 280–284. Association for Computing Machinery, New York, NY, USA.},
  pages = {280--284},
  year = {1999},
  doi = {10.1145/299432.299502},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 1999, pp 280–284. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {280--284},
  proceedings_doi = {10.1145/299432.299502}
}

@article{Pachter1999,
  author = {Lior Pachter, Serafim Batzoglou, Valentin I. Spitkovsky, Eric Banks, Eric S. Lander, Daniel J. Kleitman, Bonnie Berger},
  title = {A Dictionary-Based Approach for Gene Annotation},
  journal = {Journal of Computational Biology},
  volume = {6},
  number = {3-4},
  pages = {419--430},
  year = {1999},
  doi = {10.1089/106652799318364},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 1999, pp 285–294. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {285--294},
  proceedings_doi = {10.1145/299432.299504}
}

@inproceedings{Preparata1999,
  author = {Franco P. Preparata, Alan M. Frieze, Eli Upfal},
  title = {On the power of universal bases in sequencing by hybridization},
  booktitle = {Research in Computational Molecular Biology. RECOMB 1999, pp 295–301. Association for Computing Machinery, New York, NY, USA.},
  pages = {295--301},
  year = {1999},
  doi = {10.1145/299432.299505},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 1999, pp 295–301. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {295--301},
  proceedings_doi = {10.1145/299432.299505}
}

@inproceedings{Sankoff1999,
  author = {David Sankoff, Mathieu Blanchette},
  title = {Probability models for genome rearrangement and linear invariants for phylogenetic inference},
  booktitle = {Research in Computational Molecular Biology. RECOMB 1999, pp 302–309. Association for Computing Machinery, New York, NY, USA.},
  pages = {302--309},
  year = {1999},
  doi = {10.1145/299432.299506},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 1999, pp 302–309. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {302--309},
  proceedings_doi = {10.1145/299432.299506}
}

@inproceedings{Totrov1999,
  author = {Maxim Totrov, Ruben Abagyan},
  title = {Derivation of sensitive discrimination potential for virtual ligand screening},
  booktitle = {Research in Computational Molecular Biology. RECOMB 1999, pp 312–320. Association for Computing Machinery, New York, NY, USA.},
  pages = {312--320},
  year = {1999},
  doi = {10.1145/299432.299509},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 1999, pp 312–320. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {312--320},
  proceedings_doi = {10.1145/299432.299509}
}

@inproceedings{Bayley1999,
  author = {Martin J. Bayley, Valerie J. Gillet, Peter Willett, John Bradshaw, Darren V. S. Green},
  title = {Computational analysis of molecular diversity for drug discovery},
  booktitle = {Research in Computational Molecular Biology. RECOMB 1999, pp 321–330. Association for Computing Machinery, New York, NY, USA.},
  pages = {321--330},
  year = {1999},
  doi = {10.1145/299432.299510},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 1999, pp 321–330. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {321--330},
  proceedings_doi = {10.1145/299432.299510}
}