Research in Computational Molecular Biology

1. Front Matter

   Pages I-XIV

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2. Boosting Alignment Accuracy by Adaptive Local Realignment

   • Dan DeBlasio, John Kececioglu

   Pages 1-17

3. A Concurrent Subtractive Assembly Approach for Identification of Disease Associated Sub-metagenomes

   • Wontack Han, Mingjie Wang, Yuzhen Ye

   Pages 18-33

4. A Flow Procedure for the Linearization of Genome Sequence Graphs

   • David Haussler, Maciej Smuga-Otto, Benedict Paten, Adam M. Novak, Sergei Nikitin, Maria Zueva et al.

   Pages 34-49

5. Dynamic Alignment-Free and Reference-Free Read Compression

   • Guillaume Holley, Roland Wittler, Jens Stoye, Faraz Hach

   Pages 50-65

6. A Fast Approximate Algorithm for Mapping Long Reads to Large Reference Databases

   • Chirag Jain, Alexander Dilthey, Sergey Koren, Srinivas Aluru, Adam M. Phillippy

   Pages 66-81

7. Determining the Consistency of Resolved Triplets and Fan Triplets

   • Jesper Jansson, Andrzej Lingas, Ramesh Rajaby, Wing-Kin Sung

   Pages 82-98

8. Progressive Calibration and Averaging for Tandem Mass Spectrometry Statistical Confidence Estimation: Why Settle for a Single Decoy?

   • Uri Keich, William Stafford Noble

   Pages 99-116

9. Resolving Multicopy Duplications de novo Using Polyploid Phasing

   • Mark J. Chaisson, Sudipto Mukherjee, Sreeram Kannan, Evan E. Eichler

   Pages 117-133

10. A Bayesian Active Learning Experimental Design for Inferring Signaling Networks

    • Robert Osazuwa Ness, Karen Sachs, Parag Mallick, Olga Vitek

    Pages 134-156

11. \(BBK^*\) (Branch and Bound over \(K^*\)): A Provable and Efficient Ensemble-Based Algorithm to Optimize Stability and Binding Affinity over Large Sequence Spaces

    • Adegoke A. Ojewole, Jonathan D. Jou, Vance G. Fowler, Bruce R. Donald

    Pages 157-172

12. Superbubbles, Ultrabubbles and Cacti

    • Benedict Paten, Adam M. Novak, Erik Garrison, Glenn Hickey

    Pages 173-189

13. EPR-Dictionaries: A Practical and Fast Data Structure for Constant Time Searches in Unidirectional and Bidirectional FM Indices

    • Christopher Pockrandt, Marcel Ehrhardt, Knut Reinert

    Pages 190-206

14. A Bayesian Framework for Estimating Cell Type Composition from DNA Methylation Without the Need for Methylation Reference

    • Elior Rahmani, Regev Schweiger, Liat Shenhav, Eleazar Eskin, Eran Halperin

    Pages 207-223

15. Towards Recovering Allele-Specific Cancer Genome Graphs

    • Ashok Rajaraman, Jian Ma

    Pages 224-240

16. Using Stochastic Approximation Techniques to Efficiently Construct Confidence Intervals for Heritability

    • Regev Schweiger, Eyal Fisher, Elior Rahmani, Liat Shenhav, Saharon Rosset, Eran Halperin

    Pages 241-256

17. Improved Search of Large Transcriptomic Sequencing Databases Using Split Sequence Bloom Trees

    • Brad Solomon, Carl Kingsford

    Pages 257-271

18. AllSome Sequence Bloom Trees

    • Chen Sun, Robert S. Harris, Rayan Chikhi, Paul Medvedev

    Pages 272-286

19. Longitudinal Genotype-Phenotype Association Study via Temporal Structure Auto-learning Predictive Model

    • Xiaoqian Wang, Jingwen Yan, Xiaohui Yao, Sungeun Kim, Kwangsik Nho, Shannon L. Risacher et al.

    Pages 287-302

20. Improving Imputation Accuracy by Inferring Causal Variants in Genetic Studies

    • Yue Wu, Farhad Hormozdiari, Jong Wha J. Joo, Eleazar Eskin

    Pages 303-317

This book constitutes the proceedings of the 21th Annual Conference on Research in Computational Molecular Biology, RECOMB 2017, held in Hong Kong, China, in May 2017.
The 22 regular papers presented in this volume were carefully reviewed and selected from 184 submissions. 16 short abstracts are included in the back matter of the volume. They report on original research in all areas of computational molecular biology and bioinformatics

• algorithms
• bioinformatics
• computational biology
• machine learning
• systems biology
• active learning
• Bayesian network
• biological networks
• computational complexity
• computational genomics
• computational proteomics
• data structures
• estimation
• genome
• metagenome
• molecular biology
• phylogenetic tree
• rank queries
• regression models
• spectrum identification

• Indiana University Bloomington, Bloomington, USA

  S. Cenk Sahinalp

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