Research in Computational Molecular Biology

1. Considering Unknown Unknowns - Reconstruction of Non-confoundable Causal Relations in Biological Networks

   • Mohammad Javad Sadeh, Giusi Moffa, Rainer Spang

   Pages 234-248

2. Inference of Tumor Phylogenies with Improved Somatic Mutation Discovery

   • Raheleh Salari, Syed Shayon Saleh, Dorna Kashef-Haghighi, David Khavari, Daniel E. Newburger, Robert B. West et al.

   Pages 249-263

3. Abstract: Using the Fast Fourier Transform to Accelerate the Computational Search for RNA Conformational Switches

   • Evan Senter, Saad Sheikh, Ivan Dotu, Yann Ponty, Peter Clote

   Pages 264-265

4. MethylCRF, an Algorithm for Estimating Absolute Methylation Levels at Single CpG Resolution from Methylation Enrichment and Restriction Enzyme Sequencing Methods

   • Michael Stevens, Jeffrey B. Cheng, Mingchao Xie, Joseph F. Costello, Ting Wang

   Pages 266-268

5. Counting Motifs in the Entire Biological Network from Noisy and Incomplete Data

   • Ngoc Hieu Tran, Kwok Pui Choi, Louxin Zhang

   Pages 269-270

6. Extracting Structural Information from Residual Chemical Shift Anisotropy: Analytic Solutions for Peptide Plane Orientations and Applications to Determine Protein Structure

   • Chittaranjan Tripathy, Anthony K. Yan, Pei Zhou, Bruce Randall Donald

   Pages 271-284

7. Genome-Wide Survival Analysis of Somatic Mutations in Cancer

   • Fabio Vandin, Alexandra Papoutsaki, Benjamin J. Raphael, Eli Upfal

   Pages 285-286

8. Spectral Library Generating Function for Assessing Spectrum-Spectrum Match Significance

   • Mingxun Wang, Nuno Bandeira

   Pages 287-288

9. SPARSE: Quadratic Time Simultaneous Alignment and Folding of RNAs without Sequence-Based Heuristics

   • Sebastian Will, Christina Schmiedl, Milad Miladi, Mathias Möhl, Rolf Backofen

   Pages 289-290

10. An Algorithm for Constructing Parsimonious Hybridization Networks with Multiple Phylogenetic Trees

    • Yufeng Wu

    Pages 291-303

11. Fast and Accurate Calculation of Protein Depth by Euclidean Distance Transform

    • Dong Xu, Hua Li, Yang Zhang

    Pages 304-316

12. Inference of Spatial Organizations of Chromosomes Using Semi-definite Embedding Approach and Hi-C Data

    • ZhiZhuo Zhang, Guoliang Li, Kim-Chuan Toh, Wing-Kin Sung

    Pages 317-332

13. Boosting Prediction Performance of Protein-Protein Interaction Hot Spots by Using Structural Neighborhood Properties

    • Lei Deng, Jihong Guan, Xiaoming Wei, Yuan Yi, Shuigeng Zhou

    Pages 333-344

14. Back Matter

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This book constitutes the refereed proceedings of the 17th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2013, held in Beijing, China, in April 2013. The 32 revised full papers were carefully reviewed and selected from 167 submissions. The papers cover a wide range of topics including molecular sequence analysis; genes and regulatory elements; molecular evolution; gene expression; biological networks; sequencing and genotyping technologies; genomics; epigenomics; metagenomics; population, statistical genetics; systems biology; computational proteomics; computational structural biology; imaging; large-scale data management.

• DNA sequencing
• RNA
• machine learning
• pattern matching
• unphased genotypes
• algorithm analysis and problem complexity

• School of Mathematics, Peking University, Beijing, P.R. China

  Minghua Deng

• Bioinformatics Division, TNLIST/Department of Automation, Tsinghua University, Beijing, P.R. China

  Rui Jiang

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

  Fengzhu Sun

• Department of Automation, Tsinghua University, Beijing, China

  Xuegong Zhang

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