Research in Computational Molecular Biology

Front Matter ....Pages I-XIV
 Long Reads Enable Accurate Estimates of Complexity of Metagenomes  (Anton Bankevich, Pavel Pevzner)....Pages 1-20
 Chromatyping: Reconstructing Nucleosome Profiles from NOMe Sequencing Data  (Shounak Chakraborty, Stefan Canzar, Tobias Marschall, Marcel H. Schulz)....Pages 21-36
 GTED: Graph Traversal Edit Distance  (Ali Ebrahimpour Boroojeny, Akash Shrestha, Ali Sharifi-Zarchi, Suzanne Renick Gallagher, S. Cenk Sahinalp, Hamidreza Chitsaz)....Pages 37-53
 Statistical Inference of Peroxisome Dynamics  (Cyril Galitzine, Pierre M. Jean Beltran, Ileana M. Cristea, Olga Vitek)....Pages 54-74
 Loss-Function Learning for Digital Tissue Deconvolution  (Franziska Görtler, Stefan Solbrig, Tilo Wettig, Peter J. Oefner, Rainer Spang, Michael Altenbuchinger)....Pages 75-89
 Inference of Population Structure from Ancient DNA  (Tyler A. Joseph, Itsik Pe’er)....Pages 90-104
 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
 Modeling Dependence in Evolutionary Inference for Proteins  (Gary Larson, Jeffrey L. Thorne, Scott Schmidler)....Pages 122-137
 Constrained De Novo Sequencing of neo-Epitope Peptides Using Tandem Mass Spectrometry  (Sujun Li, Alex DeCourcy, Haixu Tang)....Pages 138-153
 Reverse de Bruijn: Utilizing Reverse Peptide Synthesis to Cover All Amino Acid k-mers  (Yaron Orenstein)....Pages 154-166
 Circular Networks from Distorted Metrics  (Sebastien Roch, Kun-Chieh Wang)....Pages 167-176
 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
 Context-Specific Nested Effects Models  (Yuriy Sverchkov, Yi-Hsuan Ho, Audrey Gasch, Mark Craven)....Pages 194-210
 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
 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
Back Matter ....Pages 241-298