Research in Computational Molecular Biology

1. Front Matter

   PDF

2. Bacterial Community Reconstruction Using Compressed Sensing

   • Amnon Amir, Or Zuk

   Pages 1-15

3. Constrained De Novo Sequencing of Peptides with Application to Conotoxins

   • Swapnil Bhatia, Yong J. Kil, Beatrix Ueberheide, Brian Chait, Lemmuel L. Tayo, Lourdes J. Cruz et al.

   Pages 16-30

4. Metabolic Network Analysis Demystified

   • Leonid Chindelevitch, Aviv Regev, Bonnie Berger

   Pages 31-33

5. Causal Reasoning on Biological Networks: Interpreting Transcriptional Changes

   • Leonid Chindelevitch, Daniel Ziemek, Ahmed Enayetallah, Ranjit Randhawa, Ben Sidders, Christoph Brockel et al.

   Pages 34-37

6. Hapsembler: An Assembler for Highly Polymorphic Genomes

   • Nilgun Donmez, Michael Brudno

   Pages 38-52

7. Discovery and Characterization of Chromatin States for Systematic Annotation of the Human Genome

   • Jason Ernst, Manolis Kellis

   Pages 53-53

8. Disease Gene Prioritization Based on Topological Similarity in Protein-Protein Interaction Networks

   • Sinan Erten, Gurkan Bebek, Mehmet Koyutürk

   Pages 54-68

9. Understanding Gene Sequence Variation in the Context of Transcription Regulation in Yeast

   • Irit Gat-Viks, Renana Meller, Martin Kupiec, Ron Shamir

   Pages 69-69

10. Identifying Branched Metabolic Pathways by Merging Linear Metabolic Pathways

    • Allison P. Heath, George N. Bennett, Lydia E. Kavraki

    Pages 70-84

11. A Probabilistic Model for Sequence Alignment with Context-Sensitive Indels

    • Glenn Hickey, Mathieu Blanchette

    Pages 85-103

12. Simultaneous Structural Variation Discovery in Multiple Paired-End Sequenced Genomes

    • Fereydoun Hormozdiari, Iman Hajirasouliha, Andrew McPherson, Evan E. Eichler, S. Cenk Sahinalp

    Pages 104-105

13. Variable Selection through Correlation Sifting

    • Jim C. Huang, Nebojsa Jojic

    Pages 106-123

14. Weighted Genomic Distance Can Hardly Impose a Bound on the Proportion of Transpositions

    • Shuai Jiang, Max A. Alekseyev

    Pages 124-133

15. PSAR: Measuring Multiple Sequence Alignment Reliability by Probabilistic Sampling

    • Jaebum Kim, Jian Ma

    Pages 134-135

16. Pedigree Reconstruction Using Identity by Descent

    • Bonnie Kirkpatrick, Shuai Cheng Li, Richard M. Karp, Eran Halperin

    Pages 136-152

17. A Quantitative Model of Glucose Signaling in Yeast Reveals an Incoherent Feed Forward Loop Leading to a Specific, Transient Pulse of Transcription

    • Sooraj KuttyKrishnan, Jeffrey Sabina, Laura Langton, Mark Johnston, Michael R. Brent

    Pages 153-153

18. Inferring Mechanisms of Compensation from E-MAP and SGA Data Using Local Search Algorithms for Max Cut

    • Mark D. M. Leiserson, Diana Tatar, Lenore J. Cowen, Benjamin J. Hescott

    Pages 154-167

19. IsoLasso: A LASSO Regression Approach to RNA-Seq Based Transcriptome Assembly

    • Wei Li, Jianxing Feng, Tao Jiang

    Pages 168-188

20. Haplotype Reconstruction in Large Pedigrees with Many Untyped Individuals

    • Xin Li, Jing Li

    Pages 189-203

This book constitutes the refereed proceedings of the 15th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2011, held in Vancouver, Canada, in March 2011. The 43 revised full papers were carefully reviewed and selected from 153 submissions. The papers cover a wide range of topics including molecular sequence analysis; recognition of genes and regulatory elements; molecular evolution; gene expression; biological networks; sequencing and genotyping technologies; genomics; population, statistical genetics; systems biology; imaging; computational proteomics; molecular structural biology.

• bioinformatics
• computational biology
• computational life science
• human genome project and systems modeling
• mathematical biology
• pattern matching
• proteonomics
• synthetic biology
• algorithm analysis and problem complexity

• EBU3b, University of California San Diego, La Jolla, USA

  Vineet Bafna

• School of Computing Science, Simon Fraser University, Burnaby, Canada

  S. Cenk Sahinalp

Policies and ethics