Research in Computational Molecular Biology

1. Front Matter

   Pages I-XVII

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2. Efficient Alignment Free Sequence Comparison with Bounded Mismatches

   • Srinivas Aluru, Alberto Apostolico, Sharma V. Thankachan

   Pages 1-12

3. DockStar: A Novel ILP Based Integrative Method for Structural Modelling of Multimolecular Protein Complexes (Extended Abstract)

   • Naama Amir, Dan Cohen, Haim J. Wolfson

   Pages 13-15

4. CRISPR Detection from Short Reads Using Partial Overlap Graphs

   • Ilan Ben-Bassat, Benny Chor

   Pages 16-27

5. HapTree-X: An Integrative Bayesian Framework for Haplotype Reconstruction from Transcriptome and Genome Sequencing Data

   • Emily Berger, Deniz Yorukoglu, Bonnie Berger

   Pages 28-29

6. Read Clouds Uncover Variation in Complex Regions of the Human Genome

   • Alex Bishara, Yuling Liu, Dorna Kashef-Haghighi, Ziming Weng, Daniel E. Newburger, Robert West et al.

   Pages 30-31

7. Learning Microbial Interaction Networks from Metagenomic Count Data

   • Surojit Biswas, Meredith McDonald, Derek S. Lundberg, Jeffery L. Dangl, Vladimir Jojic

   Pages 32-43

8. Immunoglobulin Classification Using the Colored Antibody Graph

   • Stefano R. Bonissone, Pavel A. Pevzner

   Pages 44-59

9. CIDANE: Comprehensive Isoform Discovery and Abundance Estimation

   • Stefan Canzar, Sandro Andreotti, David Weese, Knut Reinert, Gunnar W. Klau

   Pages 60-61

10. Diffusion Component Analysis: Unraveling Functional Topology in Biological Networks

    • Hyunghoon Cho, Bonnie Berger, Jian Peng

    Pages 62-64

11. Fragmentation Trees Reloaded

    • Kai Dührkop, Sebastian Böcker

    Pages 65-79

12. KGSrna: Efficient 3D Kinematics-Based Sampling for Nucleic Acids

    • Rasmus Fonseca, Henry van den Bedem, Julie Bernauer

    Pages 80-95

13. Locating a Tree in a Phylogenetic Network in Quadratic Time

    • Philippe Gambette, Andreas D. M. Gunawan, Anthony Labarre, Stéphane Vialette, Louxin Zhang

    Pages 96-107

14. Constructing Structure Ensembles of Intrinsically Disordered Proteins from Chemical Shift Data

    • Huichao Gong, Sai Zhang, Jiangdian Wang, Haipeng Gong, Jianyang Zeng

    Pages 108-121

15. Comets (Constrained Optimization of Multistate Energies by Tree Search): A Provable and Efficient Algorithm to Optimize Binding Affinity and Specificity with Respect to Sequence

    • Mark A. Hallen, Bruce R. Donald

    Pages 122-135

16. Efficient and Accurate Multiple-Phenotypes Regression Method for High Dimensional Data Considering Population Structure

    • Jong Wha J. Joo, Eun Yong Kang, Elin Org, Nick Furlotte, Brian Parks, Aldons J. Lusis et al.

    Pages 136-153

17. BWM*: A Novel, Provable, Ensemble-Based Dynamic Programming Algorithm for Sparse Approximations of Computational Protein Design

    • Jonathan D. Jou, Swati Jain, Ivelin Georgiev, Bruce R. Donald

    Pages 154-166

18. An Efficient Nonlinear Regression Approach for Genome-Wide Detection of Marginal and Interacting Genetic Variations

    • Seunghak Lee, Aurélie Lozano, Prabhanjan Kambadur, Eric P. Xing

    Pages 167-187

19. Exploration of Designability of Proteins Using Graph Features of Contact Maps: Beyond Lattice Models

    • Sumudu P. Leelananda, Robert L. Jernigan, Andrzej Kloczkowski

    Pages 188-201

20. CoMEt: A Statistical Approach to Identify Combinations of Mutually Exclusive Alterations in Cancer

    • Mark D. M. Leiserson, Hsin-Ta Wu, Fabio Vandin, Benjamin J. Raphael

    Pages 202-204

This book constitutes the refereed proceedings of the 19th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2015, held in Warsaw, Poland, in April 2015. The 36 extended abstracts were carefully reviewed and selected from 170 submissions. They report on original research in all areas of computational molecular biology and bioinformatics.

• bioinformatics
• biological networks
• cancer
• chromatin structure
• computational biology
• computational proteomics
• data structure
• deep learning
• gene regulation
• genetics
• hierarchical model
• machine learning
• metagenomics
• molecular biology
• molecular evolution
• molecular sequence analysis
• protein folding
• ribonucleic acid
• simulation
• systems biology

• National Center of Biotechnology Information, Bethesda, USA

  Teresa M. Przytycka

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