Research in Computational Molecular Biology

1. Front Matter

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2. Efficient Algorithms for Detecting Signaling Pathways in Protein Interaction Networks

   1. Efficient Algorithms for Detecting Signaling Pathways in Protein Interaction Networks

      • Jacob Scott, Trey Ideker, Richard M. Karp, Roded Sharan

      Pages 1-13

   2. Towards an Integrated Protein-Protein Interaction Network

      • Ariel Jaimovich, Gal Elidan, Hanah Margalit, Nir Friedman

      Pages 14-30

   3. The Factor Graph Network Model for Biological Systems

      • Irit Gat-Viks, Amos Tanay, Daniela Raijman, Ron Shamir

      Pages 31-47

   4. Pairwise Local Alignment of Protein Interaction Networks Guided by Models of Evolution

      • Mehmet Koyutürk, Ananth Grama, Wojciech Szpankowski

      Pages 48-65

   5. 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

      Pages 66-82

   6. Efficient Calculation of Interval Scores for DNA Copy Number Data Analysis

      • Doron Lipson, Yonatan Aumann, Amir Ben-Dor, Nathan Linial, Zohar Yakhini

      Pages 83-100

3. Keynote

   1. A Regulatory Network Controlling Drosophila Development

      • Dmitri Papatsenko, Mike Levine

      Pages 101-101

4. Keynote

   1. Yeast Cells as a Discovery Platform for Neurodegenerative Disease

      • Susan Lindquist, Ernest Fraenkel, Tiago Outeiro, Aaron Gitler, Julie Su, Anil Cashikar et al.

      Pages 102-102

   2. 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 et al.

      Pages 103-117

   3. Avoiding Local Optima in Single Particle Reconstruction

      • Marshall Bern, Jindong Chen, Hao Chi Wong

      Pages 118-132

   4. A High-Throughput Approach for Associating microRNAs with Their Activity Conditions

      • Chaya Ben-Zaken Zilberstein, Michal Ziv-Ukelson, Ron Y. Pinter, Zohar Yakhini

      Pages 133-151

   5. RNA-RNA Interaction Prediction and Antisense RNA Target Search

      • Can Alkan, Emre Karakoç, Joseph H. Nadeau, S. Cenk Şahinalp, Kaizhong Zhang

      Pages 152-171

   6. Consensus Folding of Unaligned RNA Sequences Revisited

      • Vineet Bafna, Haixu Tang, Shaojie Zhang

      Pages 172-187

5. Keynote

   1. Discovery and Annotation of Genetic Modules

      • Charles DeLisi

      Pages 188-188

   2. Efficient q-Gram Filters for Finding All ε-Matches over a Given Length

      • Kim R. Rasmussen, Jens Stoye, Eugene W. Myers

      Pages 189-203

   3. A Polynomial Time Solvable Formulation of Multiple Sequence Alignment

      • Sing-Hoi Sze, Yue Lu, Qingwu Yang

      Pages 204-216

   4. A Fundamental Decomposition Theory for Phylogenetic Networks and Incompatible Characters

      • Dan Gusfield, Vikas Bansal

      Pages 217-232

   5. Reconstruction of Reticulate Networks from Gene Trees

      • Daniel H. Huson, Tobias Klöpper, Pete J. Lockhart, Mike A. Steel

      Pages 233-249

   6. A Hybrid Micro-Macroevolutionary Approach to Gene Tree Reconstruction

      • Dannie Durand, Bjarni V. Halldórsson, Benjamin Vernot

      Pages 250-264

This volume contains the papers presented at the 9th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2005), which was held in Cambridge, Massachusetts, on May 14–18, 2005. The RECOMB conference series was started in 1997 by Sorin Istrail, Pavel Pevzner and Michael Waterman. The list of previous meetings is shown below in the s- tion “Previous RECOMB Meetings. ” RECOMB 2005 was hosted by the Broad Institute of MIT and Harvard, and Boston University’s Center for Advanced - nomic Technology, and was excellently organized by the Organizing Committee Co-chairs Jill Mesirov and Simon Kasif. This year, 217 papers were submitted, of which the Program Committee - lected 39 for presentation at the meeting and inclusion in this proceedings. Each submission was refereed by at least three members of the Program Committee. After the completion of the referees’ reports, an extensive Web-based discussion took place for making decisions. From RECOMB 2005, the Steering Committee decided to publish the proceedings as a volume of Lecture Notes in Bioinf- matics (LNBI) for which the founders of RECOMB are also the editors. The prominent volume number LNBI 3500 was assigned to this proceedings. The RECOMB conference series is closely associated with the Journal of Compu- tional Biology which traditionally publishes special issues devoted to presenting full versions of selected conference papers. The RECOMB Program Committee consistedof42members,aslistedonaseparatepage. Iwouldliketothank the RECOMB 2005 Program Committee members for their dedication and hard work.

• Annotation
• Microarray
• Resolution
• algorithms
• bioinformatics
• calculus
• cognition
• computational biology
• computational graph theory
• computational molecular biology
• genome
• haplotype data analysis
• pattern matching
• protein fold recognition
• protein interaction networks
• algorithm analysis and problem complexity
• data structures

• Human Genome Center, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo, Japan

  Satoru Miyano

• Broad Institute of MIT and Harvard, Cambridge, USA

  Jill Mesirov

• Computational Genomics Laboratory, Department of Bioengineering, Boston University, Boston, USA

  Simon Kasif

• Center for Molecular Biology and Computer Sciecne Department, Brown University, Providence, USA

  Sorin Istrail

• University of California, San Diego, USA

  Pavel A. Pevzner

• Department of Molecular and Computational Biology, University of Southern California, Los Angeles, USA

  Michael Waterman

Policies and ethics