Research in Computational Molecular Biology

1. Front Matter

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2. Protein Structure by Semidefinite Facial Reduction

   • Babak Alipanahi, Nathan Krislock, Ali Ghodsi, Henry Wolkowicz, Logan Donaldson, Ming Li

   Pages 1-11

3. Ancestry Inference in Complex Admixtures via Variable-Length Markov Chain Linkage Models

   • Sivan Bercovici, Jesse M. Rodriguez, Megan Elmore, Serafim Batzoglou

   Pages 12-28

4. Charge Group Partitioning in Biomolecular Simulation

   • Stefan Canzar, Mohammed El-Kebir, René Pool, Khaled Elbassioni, Alpesh K. Malde, Alan E. Mark et al.

   Pages 29-43

5. Increased Methylation Variation in Epigenetic Domains across Cancer Types

   • Hector Corrada Bravo

   Pages 44-44

6. Estimating the Accuracy of Multiple Alignments and its Use in Parameter Advising

   • Dan F. DeBlasio, Travis J. Wheeler, John D. Kececioglu

   Pages 45-59

7. Quantifying the Dynamics of Coupled Networks of Switches and Oscillators

   • Matthew R. Francis, Elana J. Fertig

   Pages 60-61

8. lobSTR: A Short Tandem Repeat Profiler for Personal Genomes

   • Melissa Gymrek, David Golan, Saharon Rosset, Yaniv Erlich

   Pages 62-63

9. Hap-seq: An Optimal Algorithm for Haplotype Phasing with Imputation Using Sequencing Data

   • Dan He, Buhm Han, Eleazar Eskin

   Pages 64-78

10. Ballast: A Ball-Based Algorithm for Structural Motifs

    • Lu He, Fabio Vandin, Gopal Pandurangan, Chris Bailey-Kellogg

    Pages 79-93

11. Evolution of Genome Organization by Duplication and Loss: An Alignment Approach

    • Patrick Holloway, Krister Swenson, David Ardell, Nadia El-Mabrouk

    Pages 94-112

12. LoopWeaver – Loop Modeling by the Weighted Scaling of Verified Proteins

    • Daniel Holtby, Shuai Cheng Li, Ming Li

    Pages 113-126

13. A Robust Method for Transcript Quantification with RNA-seq Data

    • Yan Huang, Yin Hu, Corbin D. Jones, James N. MacLeod, Derek Y. Chiang, Yufeng Liu et al.

    Pages 127-147

14. Modeling the Breakage-Fusion-Bridge Mechanism: Combinatorics and Cancer Genomics

    • Marcus Kinsella, Vineet Bafna

    Pages 148-162

15. TrueSight: Self-training Algorithm for Splice Junction Detection Using RNA-seq

    • Yang Li, Hong-Mei Li, Paul Burns, Mark Borodovsky, Gene E. Robinson, Jian Ma

    Pages 163-164

16. Synthetic Sequence Design for Signal Location Search

    • Yaw-Ling Lin, Charles Ward, Steven Skiena

    Pages 165-179

17. The Three-Dimensional Architecture of a Bacterial Genome and Its Alteration by Genetic Perturbation

    • Marc A. Marti-Renom

    Pages 180-180

18. Discovery of Complex Genomic Rearrangements in Cancer Using High-Throughput Sequencing

    • Andrew McPherson, Chunxiao Wu, Alexander Wyatt, Sohrab Shah, Colin Collins, S. Cenk Sahinalp

    Pages 181-182

19. Network-Based Prediction and Analysis of HIV Dependency Factors

    • T. M. Murali, Matthew D. Dyer, David Badger, Brett M. Tyler, Michael G. Katze

    Pages 183-183

20. Structure-Guided Deimmunization of Therapeutic Proteins

    • Andrew S. Parker, Karl E. Griswold, Chris Bailey-Kellogg

    Pages 184-198

This book constitutes the refereed proceedings of the 16th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2012, held in Barcelona, Spain, in April 2012. The 31 revised full papers presented together with 5 keynote lectures were carefully reviewed and selected from 200 submissions. The papers feature current research in all areas of computational molecular biology, including: molecular sequence analysis; recognition of genes and regulatory elements; molecular evolution; protein structure; structural genomics; analysis of gene expression; biological networks; sequencing and genotyping technologies; drug design; probabilistic and combinatorial algorithms; systems biology; computational proteomics; structural and functional genomics; information systems for computational biology and imaging.

• combinatorial pattern matching
• database search
• multi-objective optimization
• nuclear magnetic resonance
• synthetic biology
• algorithm analysis and problem complexity
• data structures

• Computer Science Department, Tel-Aviv University, Tel-Aviv, Israel

  Benny Chor

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