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Research in Computational Molecular Biology

20th Annual Conference, RECOMB 2016, Santa Monica, CA, USA, April 17-21, 2016, Proceedings

  • Conference proceedings
  • © 2016

Overview

Editors:
  1. Mona Singh

    1. Princeton University, Princeton, USA

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Part of the book series: Lecture Notes in Computer Science (LNCS, volume 9649)

Part of the book sub series: Lecture Notes in Bioinformatics (LNBI)

Included in the following conference series:

Conference proceedings info: RECOMB 2016.

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Table of contents (16 papers)

  1. Front Matter

    Pages I-XXXIV
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  2. RECOMB Retrospective

    1. Front Matter

      Pages 1-1
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    2. The Second Decade of the International Conference on Research in Computational Molecular Biology (RECOMB)

      • Farhad Hormozdiari, Fereydoun Hormozdiari, Carl Kingsford, Paul Medvedev, Fabio Vandin
      Pages 3-16

  3. Extended Abstracts

    1. Front Matter

      Pages 17-17
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    2. A MAD-Bayes Algorithm for State-Space Inference and Clustering with Application to Querying Large Collections of ChIP-Seq Data Sets

      • Chandler Zuo, Kailei Chen, Sündüz KeleÅŸ
      Pages 19-36

    3. Accurate Recovery of Ribosome Positions Reveals Slow Translation of Wobble-Pairing Codons in Yeast

      • Hao Wang, Joel McManus, Carl Kingsford
      Pages 37-52

    4. Multitask Matrix Completion for Learning Protein Interactions Across Diseases

      • Meghana Kshirsagar, Jaime G. Carbonell, Judith Klein-Seetharaman, Keerthiram Murugesan
      Pages 53-64

    5. pathTiMEx: Joint Inference of Mutually Exclusive Cancer Pathways and Their Dependencies in Tumor Progression

      • Simona Cristea, Jack Kuipers, Niko Beerenwinkel
      Pages 65-82

    6. Clonality Inference from Single Tumor Samples Using Low Coverage Sequence Data

      • Nilgun Donmez, Salem Malikic, Alexander W. Wyatt, Martin E. Gleave, Colin C. Collins, S. Cenk Sahinalp
      Pages 83-94

    7. Flexible Modelling of Genetic Effects on Function-Valued Traits

      • Nicolo Fusi, Jennifer Listgarten
      Pages 95-110

    8. MetaFlow: Metagenomic Profiling Based on Whole-Genome Coverage Analysis with Min-Cost Flows

      • Ahmed Sobih, Alexandru I. Tomescu, Veli Mäkinen
      Pages 111-121

    9. LUTE (Local Unpruned Tuple Expansion): Accurate Continuously Flexible Protein Design with General Energy Functions and Rigid-rotamer-like Efficiency

      • Mark A. Hallen, Jonathan D. Jou, Bruce R. Donald
      Pages 122-136

    10. Improving Bloom Filter Performance on Sequence Data Using \(k\)-mer Bloom Filters

      • David Pellow, Darya Filippova, Carl Kingsford
      Pages 137-151

    11. Safe and Complete Contig Assembly Via Omnitigs

      • Alexandru I. Tomescu, Paul Medvedev
      Pages 152-163

    12. Long Single-Molecule Reads Can Resolve the Complexity of the Influenza Virus Composed of Rare, Closely Related Mutant Variants

      • Alexander Artyomenko, Nicholas C. Wu, Serghei Mangul, Eleazar Eskin, Ren Sun, Alex Zelikovsky
      Pages 164-175

    13. Structural Variation Detection with Read Pair Information—An Improved Null-Hypothesis Reduces Bias

      • Kristoffer Sahlin, Mattias FrÃ¥nberg, Lars Arvestad
      Pages 176-188

    14. On Computing Breakpoint Distances for Genomes with Duplicate Genes

      • Mingfu Shao, Bernard M. E. Moret
      Pages 189-203

    15. New Genome Similarity Measures Based on Conserved Gene Adjacencies

      • Luis Antonio B. Kowada, Daniel Doerr, Simone Dantas, Jens Stoye
      Pages 204-224

    16. Fast Phylogenetic Biodiversity Computations Under a Non-uniform Random Distribution

      • Constantinos Tsirogiannis, Brody Sandel
      Pages 225-236

  4. Back Matter

    Pages 237-274
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Other volumes

  1. Research in Computational Molecular Biology

Keywords

About this book

This book constitutes the proceedings of the 20th Annual Conference on Research in Computational Molecular Biology, RECOMB 2016, held in Santa Monica, CA, USA, in April 2016.

The 15 regular papers presented in this volume were carefully reviewed and selected from 172 submissions. 20 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.

Editors and Affiliations

  • Princeton University, Princeton, USA

    Mona Singh

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