RECOMB 2005 Proceedings

Cambridge, MA, United States, May 14-18, 2005

PC Chair: Satoru Miyano
Organization Committee: Jill P. Mesirov (co-chair), Simon Kasif (co-chair)
Keynote Speakers: David Altshuler, Wolfgang Baumeister, James Collins, Charles DeLisi, Jonathan King, Eric Lander, Michael Levine, Susan Lindquist

List of Publications

  • Efficient Algorithms for Detecting Signaling Pathways in Protein Interaction Networks. Jacob Scott, Trey Ideker, Richard M. Karp, Roded Sharan.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 3500, pp 1-13, Springer, Cham.
  • Towards an Integrated Protein-Protein Interaction Network. Ariel Jaimovich, Gal Elidan, Hanah Margalit, Nir Friedman.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 3500, pp 14-30, Springer, Cham.
  • The Factor Graph Network Model for Biological Systems. Irit Gat-Viks, Amos Tanay, Daniela Raijman, Ron Shamir.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 3500, pp 31-47, Springer, Cham.
  • Pairwise Local Alignment of Protein Interaction Networks Guided by Models of Evolution. Mehmet Koyutürk, Ananth Grama, Wojciech Szpankowski.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 3500, pp 48-65, Springer, Cham.
  • Finding Novel Transcripts in High-Resolution Genome-Wide Microarray Data Using the GenRate Model. Brendan J. Frey, Quaid D. Morris, Mark Robinson, Timothy R. Hughes.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 3500, pp 66-82, Springer, Cham.
  • Efficient Calculation of Interval Scores for DNA Copy Number Data Analysis. Doron Lipson, Yonatan Aumann, Amir Ben-Dor, Nathan Linial, Zohar Yakhini.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 3500, pp 83-100, Springer, Cham.
  • RIBRA An Error-Tolerant Algorithm for the NMR Backbone Assignment Problem. Kuen-Pin Wu, Jia-Ming Chang, Jun-Bo Chen, Chi-Fon Chang, Wen-Jin Wu, Tai-Huang Huang, Ting-Yi Sung, Wen-Lian Hsu.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 3500, pp 103-117, Springer, Cham.
  • Avoiding Local Optima in Single Particle Reconstruction. Marshall Bern, Jindong Chen, Hao Chi Wong.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 3500, pp 118-132, Springer, Cham.
  • A High-Throughput Approach for Associating microRNAs with Their Activity Conditions. Chaya Ben-Zaken Zilberstein, Michal Ziv-Ukelson, Ron Y. Pinter, Zohar Yakhini.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 3500, pp 133-151, Springer, Cham.
  • RNA-RNA Interaction Prediction and Antisense RNA Target Search. Can Alkan, Emre Karakoç, Joseph H. Nadeau, S. Cenk Şahinalp, Kaizhong Zhang.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 3500, pp 152-171, Springer, Cham.
  • Consensus Folding of Unaligned RNA Sequences Revisited. Vineet Bafna, Haixu Tang, Shaojie Zhang.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 3500, pp 172-187, Springer, Cham.
  • Efficient q-Gram Filters for Finding All e-Matches over a Given Length. Kim R. Rasmussen, Jens Stoye, Eugene W. Myers.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 3500, pp 189-203, Springer, Cham.
  • A Polynomial Time Solvable Formulation of Multiple Sequence Alignment. Sing-Hoi Sze, Yue Lu, Qingwu Yang.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 3500, pp 204-216, Springer, Cham.
  • A Fundamental Decomposition Theory for Phylogenetic Networks and Incompatible Characters. Dan Gusfield, Vikas Bansal.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 3500, pp 217-232, Springer, Cham.
  • Reconstruction of Reticulate Networks from Gene Trees. Daniel H. Huson, Tobias Klöpper, Pete J. Lockhart, Mike A. Steel.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 3500, pp 233-249, Springer, Cham.
  • A Hybrid Micro-macroevolutionary Approach to Gene Tree Reconstruction. Dannie Durand, Bjarni V. Halldórsson, Benjamin Vernot.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 3500, pp 250-264, Springer, Cham.
  • Constructing a Smallest Refining Galled Phylogenetic Network. Trinh N.D. Huynh, Jesper Jansson, Nguyen Bao Nguyen, Wing-Kin Sung.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 3500, pp 265-280, Springer, Cham.
  • Information Theoretic Approaches to Whole Genome Phylogenies. David Burstein, Igor Ulitsky, Tamir Tuller, Benny Chor.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 3500, pp 283-295, Springer, Cham.
  • Maximum Likelihood of Evolutionary Trees Is Hard. Benny Chor, Tamir Tuller.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 3500, pp 296-310, Springer, Cham.
  • Graph Theoretical Insights into Evolution of Multidomain Proteins. Teresa Przytycka, George Davis, Nan Song, Dannie Durand.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 3500, pp 311-325, Springer, Cham.
  • Peptide Sequence Tags for Fast Database Search in Mass-Spectrometry. Ari Frank, Stephen Tanner, Pavel Pevzner.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 3500, pp 326-341, Springer, Cham.
  • A Hidden Markov Model Based Scoring Function for Mass Spectrometry Database Search. Yunhu Wan, Ting Chen.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 3500, pp 342-356, Springer, Cham.
  • EigenMS: De Novo Analysis of Peptide Tandem Mass Spectra by Spectral Graph Partitioning. Marshall Bern, David Goldberg.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 3500, pp 357-372, Springer, Cham.
  • Using Multiple Alignments to Improve Gene Prediction. Samuel S. Gross, Michael R. Brent.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 3500, pp 374-388, Springer, Cham.
  • Learning Interpretable SVMs for Biological Sequence Classification. S. Sonnenburg, G. Rätsch, C. Schäfer.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 3500, pp 389-407, Springer, Cham.
  • Segmentation Conditional Random Fields (SCRFs): A New Approach for Protein Fold Recognition. Yan Liu, Jaime Carbonell, Peter Weigele, Vanathi Gopalakrishnan.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 3500, pp 408-422, Springer, Cham.
  • Rapid Protein Side-Chain Packing via Tree Decomposition. Jinbo Xu.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 3500, pp 423-439, Springer, Cham.
  • Recognition of Binding Patterns Common to a Set of Protein Structures. Maxim Shatsky, Alexandra Shulman-Peleg, Ruth Nussinov, Haim J. Wolfson.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 3500, pp 440-455, Springer, Cham.
  • Predicting Protein-Peptide Binding Affinity by Learning Peptide-Peptide Distance Functions. Chen Yanover, Tomer Hertz.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 3500, pp 456-471, Springer, Cham.
  • A Practical Approach to Significance Assessment in Alignment with Gaps. Nicholas Chia, Ralf Bundschuh.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 3500, pp 474-488, Springer, Cham.
  • Alignment of Optical Maps. Anton Valouev, Lei Li, Yu-Chi Liu, David C. Schwartz, Yi Yang, Yu Zhang, Michael S. Waterman.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 3500, pp 489-504, Springer, Cham.
  • Modeling the Combinatorial Functions of Multiple Transcription Factors. Chen-Hsiang Yeang, Tommi Jaakkola.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 3500, pp 506-521, Springer, Cham.
  • Predicting Transcription Factor Binding Sites Using Structural Knowledge. Tommy Kaplan, Nir Friedman, Hanah Margalit.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 3500, pp 522-537, Springer, Cham.
  • Motif Discovery Through Predictive Modeling of Gene Regulation. Manuel Middendorf, Anshul Kundaje, Mihir Shah, Yoav Freund, Chris H. Wiggins, Christina Leslie.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 3500, pp 538-552, Springer, Cham.
  • HAPLOFREQ Estimating Haplotype Frequencies Efficiently. Eran Halperin, Elad Hazan.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 3500, pp 553-568, Springer, Cham.
  • Improved Recombination Lower Bounds for Haplotype Data. Vineet Bafna, Vikas Bansal.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 3500, pp 569-584, Springer, Cham.
  • A Linear-Time Algorithm for the Perfect Phylogeny Haplotyping (PPH) Problem. Zhihong Ding, Vladimir Filkov, Dan Gusfield.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 3500, pp 585-600, Springer, Cham.
  • Stability of Rearrangement Measures in the Comparison of Genome Sequences. David Sankoff, Matthew Mazowita.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 3500, pp 603-614, Springer, Cham.
  • On Sorting by Translocations. Anne Bergeron, Julia Mixtacki, Jens Stoye.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 3500, pp 615-630, Springer, Cham.