Research in Computational Molecular Biology

1. Front Matter

   Pages I-XIV

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2. Long Reads Enable Accurate Estimates of Complexity of Metagenomes

   • Anton Bankevich, Pavel Pevzner

   Pages 1-20

3. Chromatyping: Reconstructing Nucleosome Profiles from NOMe Sequencing Data

   • Shounak Chakraborty, Stefan Canzar, Tobias Marschall, Marcel H. Schulz

   Pages 21-36

4. GTED: Graph Traversal Edit Distance

   • Ali Ebrahimpour Boroojeny, Akash Shrestha, Ali Sharifi-Zarchi, Suzanne Renick Gallagher, S. Cenk Sahinalp, Hamidreza Chitsaz

   Pages 37-53

5. Statistical Inference of Peroxisome Dynamics

   • Cyril Galitzine, Pierre M. Jean Beltran, Ileana M. Cristea, Olga Vitek

   Pages 54-74

6. Loss-Function Learning for Digital Tissue Deconvolution

   • Franziska Görtler, Stefan Solbrig, Tilo Wettig, Peter J. Oefner, Rainer Spang, Michael Altenbuchinger

   Pages 75-89

7. Inference of Population Structure from Ancient DNA

   • Tyler A. Joseph, Itsik Pe’er

   Pages 90-104

8. Using Minimum Path Cover to Boost Dynamic Programming on DAGs: Co-linear Chaining Extended

   • Anna Kuosmanen, Topi Paavilainen, Travis Gagie, Rayan Chikhi, Alexandru Tomescu, Veli Mäkinen

   Pages 105-121

9. Modeling Dependence in Evolutionary Inference for Proteins

   • Gary Larson, Jeffrey L. Thorne, Scott Schmidler

   Pages 122-137

10. Constrained De Novo Sequencing of neo-Epitope Peptides Using Tandem Mass Spectrometry

    • Sujun Li, Alex DeCourcy, Haixu Tang

    Pages 138-153

11. Reverse de Bruijn: Utilizing Reverse Peptide Synthesis to Cover All Amino Acid k-mers

    • Yaron Orenstein

    Pages 154-166

12. Circular Networks from Distorted Metrics

    • Sebastien Roch, Kun-Chieh Wang

    Pages 167-176

13. A Nested 2-Level Cross-Validation Ensemble Learning Pipeline Suggests a Negative Pressure Against Crosstalk snoRNA-mRNA Interactions in Saccharomyces Cerevisae

    • Antoine Soulé, Jean-Marc Steyaert, Jérôme Waldispühl

    Pages 177-193

14. Context-Specific Nested Effects Models

    • Yuriy Sverchkov, Yi-Hsuan Ho, Audrey Gasch, Mark Craven

    Pages 194-210

15. Algorithmic Framework for Approximate Matching Under Bounded Edits with Applications to Sequence Analysis

    • Sharma V. Thankachan, Chaitanya Aluru, Sriram P. Chockalingam, Srinivas Aluru

    Pages 211-224

16. Accurate Reconstruction of Microbial Strains from Metagenomic Sequencing Using Representative Reference Genomes

    • Zhemin Zhou, Nina Luhmann, Nabil-Fareed Alikhan, Christopher Quince, Mark Achtman

    Pages 225-240

17. Back Matter

    Pages 241-298

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This book constitutes the proceedings of the 22nd Annual Conference on Research in Computational Molecular Biology, RECOMB 2018, held in Paris, France, in April 2018.

The 16 extended and 22 short abstracts presented were carefully reviewed and selected from 193 submissions. The 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.

• accessibility
• artificial intelligence
• bioinformatics
• clustering
• cross-validation
• data mining
• image processing
• image reconstruction
• linear programming
• parameter estimation
• probabilistic models
• probability
• problem solving
• reconstruction
• random processes
• reconstruction
• signal processing
• social networks
• stochastic process

• Computer Science Department, Princeton University, Princeton, USA

  Benjamin J. Raphael

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