Accepted Papers

All of the RECOMB Proceedings papers are available at


Hormozdiari, Farhad, Fereydoun Hormozdiari, Carl Kingsford, Paul Medvedev, and Fabio Vandin.
The Second Decade of the International Conference on Research in Computational Molecular Biology  
Data for the 20th anniversary article is available here:


Antipov, Dmitry, Nolan Hartwick, Max Shen, Michael Rayko, Alla Lapidus and Pavel Pevzner.
plasmidSPAdes: Assembling Plasmids from Whole Genome Sequencing Data

Artyomenko, Alexander, Nicholas Wu, Serghei Mangul, Eleazar Eskin, Ren Sun and Alex Zelikovsky.
Long single-molecule reads can resolve the complexity of the Influenza virus composed of rare, closely related mutant variants 

Calviello, Lorenzo, Neelanjan Mukherjee, Emanuel Wyler, Henrik Zauber, Antje Hirsekorn, Matthias Selbach, Markus Landthaler, Benedikt Obermayer and Uwe Ohler.
Detecting actively translated open reading frames in ribosome profiling data  

Cristea, Simona, Jack Kuipers and Niko Beerenwinkel.
pathTiMEx: Joint Inference of Mutually Exclusive Cancer Pathways and their Dependencies in Tumor Progression  

Dao, Phuong, Jan Hoinka, Yijie Wang, Mayumi Takahashi, Jiehua Zhou, Fabrizio Costa, John Rossi, John Burnett, Rolf Backofen and Teresa Przytycka.
AptaTRACE: Elucidating Sequence-Structure Binding Motifs by Uncovering Selection Trends in HT-SELEX Experiments

Donmez, Nilgun, Salem Malikic, Alexander Wyatt, Colin Collins, Martin Gleave and Cenk Sahinalp.
Clonality inference from single tumor samples using low coverage sequence data  

El-Kebir, Mohammed, Gryte Satas, Layla Oesper and Ben Raphael.
Multi-State Perfect Phylogeny Mixture Deconvolution and Applications to Cancer Sequencing              

Ezpeleta, Joaquín, Flavia J. Krsticevic, Pilar Bulacio and Elizabeth Tapia.
Designing robust watermark barcodes for multiplex long-read sequencing

Fusi, Nicolo and Jennifer Listgarten.
Flexible Modelling of Genetic Effects on Function-Valued Traits

Gupta, Nitish, Komal Sanjeev, Tim Wall, Carl Kingsford and Rob Patro.
Efficient Index Maintenance Under Dynamic Genome Modification

Hallen, Mark, Jonathan Jou and Bruce Donald.
LUTE (Local Unpruned Tuple Expansion): Accurate continuously flexible protein design with general energy functions and rigid-rotamer-like efficiency

Hansen, Tommy and Fabio Vandin.
Finding Mutated Subnetworks Associated with Survival Time in Cancer

Hashemifar, Somaye, Qixing Huang and Jinbo Xu.
Joint alignment of multiple protein-protein interaction networks via convex optimization  

Jahn, Katharina, Jack Kuipers and Niko Beerenwinkel.
Tree inference for single-cell data

Kolmogorov, Mikhail, Eamonn Kennedy, Zhuxin Dong, Gregory Timp and Pavel Pezvner.
Single-Molecule Protein Identification by Sub-Nanopore Sensors

Kowada, Luis Antonio B., Daniel Doerr, Simone Dantas and Jens Stoye.
New Genome Similarity Measures based on Conserved Gene Adjacencies  

Kshirsagar, Meghana, Jaime Carbonell, Judith Klein-Seetharaman and Keerthiram Murugesan.
Multitask matrix completion for learning protein interactions across diseases  

Kwon, Sunyoung, Gyuwan Kim, Byunghan Lee, Sungroh Yoon and Young-Han Kim.
NASCUP: Nucleic Acid Sequence Classification by Universal Probability  

Li, Yang, Shiguo Zhou, David Schwartz and Jian Ma.
Allele-Specific Quantification of Structural Variations in Cancer Genomes

Lin, Yu, Max W. Shen, Jeffrey Yuan and Pavel Pevzner.
Assembly of Long Error-Prone Reads Using de Bruijn Graphs

Lu, Yang, Ting Chen, Jed Fuhrman and Fengzhu Sun.
COCACOLA: binning metagenomic contigs using sequence COmposition, read CoverAge, CO-alignment, and paired-end read LinkAge

Luo, Yunan, Jianyang Zeng, Bonnie Berger and Jian Peng.
Low-density locality-sensitive hashing boosts metagenomic binning

Ma, Xiuli, Guangyu Zhou, Jingjing Wang, Jian Peng and Jiawei Han.
Complexes Detection in Biological Networks via Diversified Dense Subgraphs Mining

Maryanto Gunawan, Andreas Dwi, Bhaskar Dasgupta and Louxin Zhang.
Locating a Tree in a Reticulation-Visible Network in Cubic Time

Nurk, Sergey, Dmitry Meleshko and Pavel Pevzner.
metaSPAdes: a new versatile de novo metagenomics assembler

Pellow, David, Darya Filippova and Carl Kingsford.
Improving Bloom filter performance on sequence data using k-mer Bloom filters  

Popic, Victoria and Serafim Batzoglou.
Efficient Privacy-Preserving Read Mapping Using Locality Sensitive Hashing and Secure Kmer Voting  

Rajagopal, Nisha, Sharanya Srinivasan, Kameron Kooshesh, Yuchun Guo, Matthew Edwards, Budhaditya Banerjee, Tahin Syed, Bart Emons, David Gifford and Richard Sherwood.
High-throughput mapping of regulatory DNA

Rozov, Roye, Aya Brown Kav, David Bogumil, Itzhak Mizrahi, Eran Halperin and Ron Shamir.
Recycler: an algorithm for detecting plasmids from de novo assembly graphs  

Sahlin, Kristoffer, Mattias Frånberg and Lars Arvestad.
Structural variation detection with read pair information — An improved null-hypothesis reduces bias  

Salmela, Leena, Riku Walve, Eric Rivals and Esko Ukkonen.
Accurate selfcorrection of errors in long reads using de Bruijn graphs

Sefer, Emre and Ziv Bar-Joseph.
Shall we dense? Comparing design strategies for time series expression experiments  

Shao, Mingfu and Bernard Moret.
On Computing Pairwise Breakpoint Distances

Shlemov, Alexander, Sergey Bankevich, Andrey Bzikadze and Yana Safonova.
IgReC 2.0: New algorithmic challenges of adaptive immune repertoire construction  

Simmons, Sean, Cenk Sahinalp and Bonnie Berger.
Enabling Privacy-Preserving GWAS in Heterogenous Human Populations  

Singh, Shashank, Sabrina Rashid, Saket Navlakha and Ziv Bar-Joseph.
Distributed Gradient Descent in Bacterial Food Search

Sobih, Ahmed, Alexandru I. Tomescu and Veli Mäkinen.
MetaFlow: Metagenomic profiling based on whole-genome coverage analysis with min-cost flows              

Srivastava, Avi, Hirak Sarkar, Laraib Malik, and Robert Patro.
Accurate, Fast and Lightweight Clustering of de novo Transcriptomes using Fragment Equivalence Classes

Steuerman, Yael and Irit Gat-Viks.
Exploiting Gene-Expression Deconvolution to Probe the Genetics of the Immune System  

Tomescu, Alexandru I., and Paul Medvedev.
Safe and Complete Contig Assembly Via Omnitigs

Tsirogiannis, Constantinos, and Brody Sandel.
Fast Phylogenetic Biodiversity Computations Under a Non-Uniform Random Distribution  

Wang, Hao, Joel McManus and Carl Kingsford.
Accurate Recovery of Ribosome Positions Reveals Slow Translation of Wobble-Pairing Codons in Yeast  

Welch, Joshua, Ziqing Liu, Li Wang, Junjie Liu, Paul Lerou, Jeremy Purvis, Li Qian, Alexander Hartemink and Jan Prins.
SLICER: Inferring Branched, Nonlinear Cellular Trajectories from Single Cell RNA-seq Data              

Wiedenhoeft, John, Eric Brugel and Alexander Schliep.
Fast Bayesian Inference of Copy Number Variants using Hidden Markov Models with Wavelet Compression

Yang, Yuqing, Ning Chen and Ting Chen.
mLDM: a Statistical Model for Sparse Microbial Association Discovery

Zou, Chenchen, Yuping Zhang and Zhengqing Ouyang.
Multi-track modeling for genome-scale reconstruction of 3D chromatin structure from Hi-C data              

Zuo, Chandler, Kailei Chen and Sunduz Keles.
A MAD-Bayes Algorithm for State-space Inference and Clustering with Application to Querying Large Collections of ChIP-Seq Data Sets