Research in Computational Molecular Biology

1. Front Matter

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2. Tractatus: An Exact and Subquadratic Algorithm for Inferring Identical-by-Descent Multi-shared Haplotype Tracts

   • Derek Aguiar, Eric Morrow, Sorin Istrail

   Pages 1-17

3. HapTree: A Novel Bayesian Framework for Single Individual Polyplotyping Using NGS Data

   • Emily Berger, Deniz Yorukoglu, Jian Peng, Bonnie Berger

   Pages 18-19

4. Changepoint Analysis for Efficient Variant Calling

   • Adam Bloniarz, Ameet Talwalkar, Jonathan Terhorst, Michael I. Jordan, David Patterson, Bin Yu et al.

   Pages 20-34

5. On the Representation of de Bruijn Graphs

   • Rayan Chikhi, Antoine Limasset, Shaun Jackman, Jared T. Simpson, Paul Medvedev

   Pages 35-55

6. Exact Learning of RNA Energy Parameters from Structure

   • Hamidreza Chitsaz, Mohammad Aminisharifabad

   Pages 56-68

7. An Alignment-Free Regression Approach for Estimating Allele-Specific Expression Using RNA-Seq Data

   • Chen-Ping Fu, Vladimir Jojic, Leonard McMillan

   Pages 69-84

8. The Generating Function Approach for Peptide Identification in Spectral Networks

   • Adrian Guthals, Christina Boucher, Nuno Bandeira

   Pages 85-99

9. Decoding Coalescent Hidden Markov Models in Linear Time

   • Kelley Harris, Sara Sheehan, John A. Kamm, Yun S. Song

   Pages 100-114

10. AptaCluster – A Method to Cluster HT-SELEX Aptamer Pools and Lessons from Its Application

    • Jan Hoinka, Alexey Berezhnoy, Zuben E. Sauna, Eli Gilboa, Teresa M. Przytycka

    Pages 115-128

11. Learning Sequence Determinants of Protein: Protein Interaction Specificity with Sparse Graphical Models

    • Hetunandan Kamisetty, Bornika Ghosh, Christopher James Langmead, Chris Bailey-Kellogg

    Pages 129-143

12. On Sufficient Statistics of Least-Squares Superposition of Vector Sets

    • Arun S. Konagurthu, Parthan Kasarapu, Lloyd Allison, James H. Collier, Arthur M. Lesk

    Pages 144-159

13. IDBA-MTP: A Hybrid MetaTranscriptomic Assembler Based on Protein Information

    • Henry C. M. Leung, S. M. Yiu, Francis Y. L. Chin

    Pages 160-172

14. MRFalign: Protein Homology Detection through Alignment of Markov Random Fields

    • Jianzhu Ma, Sheng Wang, Zhiyong Wang, Jinbo Xu

    Pages 173-174

15. An Integrated Model of Multiple-Condition ChIP-Seq Data Reveals Predeterminants of Cdx2 Binding

    • Shaun Mahony, Matthew D. Edwards, Esteban O. Mazzoni, Richard I. Sherwood, Akshay Kakumanu, Carolyn A. Morrison et al.

    Pages 175-176

16. PASTA: Ultra-Large Multiple Sequence Alignment

    • Siavash Mirarab, Nam Nguyen, Tandy Warnow

    Pages 177-191

17. Fast Flux Module Detection Using Matroid Theory

    • Arne C. Müller, Frank J. Bruggeman, Brett G. Olivier, Leen Stougie

    Pages 192-206

18. Building a Pangenome Reference for a Population

    • Ngan Nguyen, Glenn Hickey, Daniel R. Zerbino, Brian Raney, Dent Earl, Joel Armstrong et al.

    Pages 207-221

19. CSAX: Characterizing Systematic Anomalies in eXpression Data

    • Keith Noto, Carla Brodley, Saeed Majidi, Diana W. Bianchi, Donna K. Slonim

    Pages 222-236

20. WhatsHap: Haplotype Assembly for Future-Generation Sequencing Reads

    • Murray Patterson, Tobias Marschall, Nadia Pisanti, Leo van Iersel, Leen Stougie, Gunnar W. Klau et al.

    Pages 237-249

This book constitutes the refereed proceedings of the 18th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2014, held in Pittsburgh, PA, USA, in April 2014. The 35 extended abstracts were carefully reviewed and selected from 154 submissions. They report on original research in all areas of computational molecular biology and bioinformatics.

• RNA
• bioinformatics
• clustering algorithms
• computational biology
• computational proteomics
• genetics
• machine learning
• molecular biology
• molecular evolution
• molecular sequence analysis
• ribonucleic acid
• systems biology
• algorithm analysis and problem complexity

• School of Computer Science, Tel Aviv University, Tel Aviv, Israel

  Roded Sharan

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