RECOMB 2006 Proceedings

Venice, Italy, April 2-5, 2006

PC Chair: Alberto Apostolico
Organization Committee: Concettina Guerra (chair), Matteo Comin, Eleazar Eskin, Raffaele Giancarlo, Giuseppe Lancia, Cinzia Pizzi, Angela Visco, Nicola Vitacolonna
Keynote Speakers: Anne-Claude Gavin, David Haussler, Ajay Royyuru, David Sankoff, Michael Waterman, Carl Zimmer, Roman Zubarev

List of Publications

  • Integrated Protein Interaction Networks for 11 Microbes. Balaji S. Srinivasan, Antal F. Novak, Jason A. Flannick, Serafim Batzoglou, Harley H. McAdams.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2006. Lecture Notes in Computer Science, vol 3909, pp 1-14, Springer, Cham.
  • Hypergraph Model of Multi-residue Interactions in Proteins: Sequentially-Constrained Partitioning Algorithms for Optimization of Site-Directed Protein Recombination. Xiaoduan Ye, Alan M. Friedman, Chris Bailey-Kellogg.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2006. Lecture Notes in Computer Science, vol 3909, pp 15-29, Springer, Cham.
  • Biological Networks: Comparison, Conservation, and Evolutionary Trees. Benny Chor, Tamir Tuller.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2006. Lecture Notes in Computer Science, vol 3909, pp 30-44, Springer, Cham.
  • Assessing Significance of Connectivity and Conservation in Protein Interaction Networks. Mehmet Koyutürk, Ananth Grama, Wojciech Szpankowski.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2006. Lecture Notes in Computer Science, vol 3909, pp 45-59, Springer, Cham.
  • Clustering Short Gene Expression Profiles. Ling Wang, Marco Ramoni, Paola Sebastiani.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2006. Lecture Notes in Computer Science, vol 3909, pp 60-68, Springer, Cham.
  • A Patient-Gene Model for Temporal Expression Profiles in Clinical Studies. Naftali Kaminski, Ziv Bar-Joseph.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2006. Lecture Notes in Computer Science, vol 3909, pp 69-82, Springer, Cham.
  • An Improved Statistic for Detecting Over-Represented Gene Ontology Annotations in Gene Sets. Steffen Grossmann, Sebastian Bauer, Peter N. Robinson, Martin Vingron.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2006. Lecture Notes in Computer Science, vol 3909, pp 85-98, Springer, Cham.
  • Protein Function Annotation Based on Ortholog Clusters Extracted from Incomplete Genomes Using Combinatorial Optimization. Akshay Vashist, Casimir Kulikowski, Ilya Muchnik.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2006. Lecture Notes in Computer Science, vol 3909, pp 99-113, Springer, Cham.
  • Detecting MicroRNA Targets by Linking Sequence, MicroRNA and Gene Expression Data. Jim C. Huang, Quaid D. Morris, Brendan J. Frey.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2006. Lecture Notes in Computer Science, vol 3909, pp 114-129, Springer, Cham.
  • RNA Secondary Structure Prediction Via Energy Density Minimization. Can Alkan, Emre Karakoc, S. Cenk Sahinalp, Peter Unrau, H. Alexander Ebhardt, Kaizhong Zhang, Jeremy Buhler.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2006. Lecture Notes in Computer Science, vol 3909, pp 130-142, Springer, Cham.
  • Structural Alignment of Pseudoknotted RNA. Banu Dost, Buhm Han, Shaojie Zhang, Vineet Bafna.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2006. Lecture Notes in Computer Science, vol 3909, pp 143-158, Springer, Cham.
  • CONTRAlign: Discriminative Training for Protein Sequence Alignment. Chuong B. Do, Samuel S. Gross, Serafim Batzoglou.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2006. Lecture Notes in Computer Science, vol 3909, pp 160-174, Springer, Cham.
  • Clustering Near-Identical Sequences for Fast Homology Search. Michael Cameron, Yaniv Bernstein, Hugh E. Williams.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2006. Lecture Notes in Computer Science, vol 3909, pp 175-189, Springer, Cham.
  • New Methods for Detecting Lineage-Specific Selection. Adam Siepel, Katherine S. Pollard, David Haussler.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2006. Lecture Notes in Computer Science, vol 3909, pp 190-205, Springer, Cham.
  • A Probabilistic Model for Gene Content Evolution with Duplication, Loss, and Horizontal Transfer. Miklós Csűrös, István Miklós.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2006. Lecture Notes in Computer Science, vol 3909, pp 206-220, Springer, Cham.
  • A Sublinear-Time Randomized Approximation Scheme for the Robinson-Foulds Metric. Nicholas D. Pattengale, Bernard M.E. Moret.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2006. Lecture Notes in Computer Science, vol 3909, pp 221-230, Springer, Cham.
  • Algorithms to Distinguish the Role of Gene-Conversion from Single-Crossover Recombination in the Derivation of SNP Sequences in Populations. Yun S. Song, Zhihong Ding, Dan Gusfield, Charles H. Langley, Yufeng Wu.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2006. Lecture Notes in Computer Science, vol 3909, pp 231-245, Springer, Cham.
  • Efficient Enumeration of Phylogenetically Informative Substrings. Stanislav Angelov, Boulos Harb, Sampath Kannan, Sanjeev Khanna, Junhyong Kim.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2006. Lecture Notes in Computer Science, vol 3909, pp 248-264, Springer, Cham.
  • Phylogenetic Profiling of Insertions and Deletions in Vertebrate Genomes. Sagi Snir, Lior Pachter.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2006. Lecture Notes in Computer Science, vol 3909, pp 265-280, Springer, Cham.
  • Maximal Accurate Forests from Distance Matrices. Constantinos Daskalakis, Cameron Hill, Alexandar Jaffe, Radu Mihaescu, Elehanan Mossel, Satish Rao.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2006. Lecture Notes in Computer Science, vol 3909, pp 281-295, Springer, Cham.
  • Leveraging Information Across HLA Alleles/Supertypes Improves Epitope Prediction. David Heckerman, Carl Kadie, Jennifer Listgarten.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2006. Lecture Notes in Computer Science, vol 3909, pp 296-308, Springer, Cham.
  • Improving Prediction of Zinc Binding Sites by Modeling the Linkage Between Residues Close in Sequence. Sauro Menchetti, Andrea Passerini, Paolo Frasconi, Claudia Andreini, Antonio Rosato.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2006. Lecture Notes in Computer Science, vol 3909, pp 309-320, Springer, Cham.
  • An Important Connection Between Network Motifs and Parsimony Models. Teresa M. Przytycka.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2006. Lecture Notes in Computer Science, vol 3909, pp 321-335, Springer, Cham.
  • Permutation Filtering: A Novel Concept for Significance Analysis of Large-Scale Genomic Data. Stefanie Scheid, Rainer Spang.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2006. Lecture Notes in Computer Science, vol 3909, pp 338-347, Springer, Cham.
  • Genome-Wide Discovery of Modulators of Transcriptional Interactions in Human B Lymphocytes. Kai Wang, Ilya Nemenman, Nilanjana Banerjee, Adam A. Margolin, Andrea Califano.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2006. Lecture Notes in Computer Science, vol 3909, pp 348-362, Springer, Cham.
  • A New Approach to Protein Identification. Nuno Bandeira, Dekel Tsur, Ari Frank, Pavel Pevzner.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2006. Lecture Notes in Computer Science, vol 3909, pp 363-378, Springer, Cham.
  • Markov Methods for Hierarchical Coarse-Graining of Large Protein Dynamics. Chakra Chennubhotla, Ivet Bahar.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2006. Lecture Notes in Computer Science, vol 3909, pp 379-393, Springer, Cham.
  • Simulating Protein Motions with Rigidity Analysis. Shawna Thomas, Xinyu Tang, Lydia Tapia, Nancy M. Amato.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2006. Lecture Notes in Computer Science, vol 3909, pp 394-409, Springer, Cham.
  • Predicting Experimental Quantities in Protein Folding Kinetics Using Stochastic Roadmap Simulation. Tsung-Han Chiang, Mehmet Serkan Apaydin, Douglas L. Brutlag, David Hsu, Jean-Claude Latombe.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2006. Lecture Notes in Computer Science, vol 3909, pp 410-424, Springer, Cham.
  • Alignment Statistics for Long-Range Correlated Genomic Sequences. Philipp W. Messer, Ralf Bundschuh, Martin Vingron, Peter F. Arndt.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2006. Lecture Notes in Computer Science, vol 3909, pp 426-440, Springer, Cham.
  • Simple and Fast Inverse Alignment. John Kececioglu, Eagu Kim.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2006. Lecture Notes in Computer Science, vol 3909, pp 441-455, Springer, Cham.
  • Motif Yggdrasil: Sampling from a Tree Mixture Model. Samuel A. Andersson, Jens Lagergren.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2006. Lecture Notes in Computer Science, vol 3909, pp 458-472, Springer, Cham.
  • A Study of Accessible Motifs and RNA Folding Complexity. Ydo Wexler, Chaya Zilberstein, Michal Ziv-Ukelson.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2006. Lecture Notes in Computer Science, vol 3909, pp 473-487, Springer, Cham.
  • A Parameterized Algorithm for Protein Structure Alignment. Jinbo Xu, Feng Jiao, Bonnie Berger.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2006. Lecture Notes in Computer Science, vol 3909, pp 488-499, Springer, Cham.
  • Geometric Sieving: Automated Distributed Optimization of 3D Motifs for Protein Function Prediction. Brian Y. Chen, Viacheslav Y. Fofanov, Drew H. Bryant, Bradley D. Dodson, David M. Kristensen, Andreas M. Lisewski, Marek Kimmel, Olivier Lichtarge, Lydia E. Kavraki.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2006. Lecture Notes in Computer Science, vol 3909, pp 500-515, Springer, Cham.
  • A Branch-and-Reduce Algorithm for the Contact Map Overlap Problem. Wei Xie, Nikolaos V. Sahinidis.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2006. Lecture Notes in Computer Science, vol 3909, pp 516-529, Springer, Cham.
  • A Novel Minimized Dead-End Elimination Criterion and Its Application to Protein Redesign in a Hybrid Scoring and Search Algorithm for Computing Partition Functions over Molecular Ensembles. Ivelin Georgiev, Ryan H. Lilien, Bruce R. Donald.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2006. Lecture Notes in Computer Science, vol 3909, pp 530-545, Springer, Cham.
  • Sorting by Weighted Reversals, Transpositions, and Inverted Transpositions. Martin Bader, Enno Ohlebusch.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2006. Lecture Notes in Computer Science, vol 3909, pp 563-577, Springer, Cham.
  • A Parsimony Approach to Genome-Wide Ortholog Assignment. Zheng Fu, Xin Chen, Vladimir Vacic, Peng Nan, Yang Zhong, Tao Jiang.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2006. Lecture Notes in Computer Science, vol 3909, pp 578-594, Springer, Cham.
  • Detecting the Dependent Evolution of Biosequences. Jeremy Darot, Chen-Hsiang Yeang, David Haussler.
    • Proceedings: Research in Computational Molecular Biology. RECOMB 2006. Lecture Notes in Computer Science, vol 3909, pp 595-610, Springer, Cham.