All of the RECOMB Proceedings papers are available at http://link.springer.com/book/10.1007/978-3-319-31957-5.
Hormozdiari, Farhad, Fereydoun Hormozdiari, Carl Kingsford, Paul Medvedev, and Fabio Vandin.
The Second Decade of the International Conference on Research in Computational Molecular Biology http://link.springer.com/chapter/10.1007/978-3-319-31957-5_1
Data for the 20th anniversary article is available here:
https://docs.google.com/spreadsheets/d/19_X2RWwXfJXkrvTCAHCgZHSKxB_OgZ_dTs7T_MVotBM/edit
Antipov, Dmitry, Nolan Hartwick, Max Shen, Michael Rayko, Alla Lapidus and Pavel Pevzner.
plasmidSPAdes: Assembling Plasmids from Whole Genome Sequencing Data
http://biorxiv.org/content/early/2016/04/15/048942
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 http://link.springer.com/chapter/10.1007/978-3-319-31957-5_12
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 http://dx.doi.org/10.1038/nmeth.3688
Cristea, Simona, Jack Kuipers and Niko Beerenwinkel.
pathTiMEx: Joint Inference of Mutually Exclusive Cancer Pathways and their Dependencies in Tumor Progression http://link.springer.com/chapter/10.1007%2F978-3-319-31957-5_5
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
http://biorxiv.org/content/early/2016/04/05/047357
Donmez, Nilgun, Salem Malikic, Alexander Wyatt, Colin Collins, Martin Gleave and Cenk Sahinalp.
Clonality inference from single tumor samples using low coverage sequence data http://link.springer.com/chapter/10.1007/978-3-319-31957-5_6
El-Kebir, Mohammed, Gryte Satas, Layla Oesper and Ben Raphael.
Multi-State Perfect Phylogeny Mixture Deconvolution and Applications to Cancer Sequencing http://arxiv.org/abs/1604.02605
Ezpeleta, Joaquín, Flavia J. Krsticevic, Pilar Bulacio and Elizabeth Tapia.
Designing robust watermark barcodes for multiplex long-read sequencing
http://arxiv.org/abs/1604.01344
Fusi, Nicolo and Jennifer Listgarten.
Flexible Modelling of Genetic Effects on Function-Valued Traits
http://link.springer.com/chapter/10.1007/978-3-319-31957-5_7
Gupta, Nitish, Komal Sanjeev, Tim Wall, Carl Kingsford and Rob Patro.
Efficient Index Maintenance Under Dynamic Genome Modification
http://arxiv.org/abs/1604.03132
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
http://link.springer.com/chapter/10.1007/978-3-319-31957-5_9
Hansen, Tommy and Fabio Vandin.
Finding Mutated Subnetworks Associated with Survival Time in Cancer
http://arxiv.org/abs/1604.02467
Hashemifar, Somaye, Qixing Huang and Jinbo Xu.
Joint alignment of multiple protein-protein interaction networks via convex optimization http://arxiv.org/abs/1604.03482
Jahn, Katharina, Jack Kuipers and Niko Beerenwinkel.
Tree inference for single-cell data
http://biorxiv.org/content/early/2016/04/09/047795
Kolmogorov, Mikhail, Eamonn Kennedy, Zhuxin Dong, Gregory Timp and Pavel Pezvner.
Single-Molecule Protein Identification by Sub-Nanopore Sensors
http://arxiv.org/abs/1604.02270
Kowada, Luis Antonio B., Daniel Doerr, Simone Dantas and Jens Stoye.
New Genome Similarity Measures based on Conserved Gene Adjacencies http://link.springer.com/chapter/10.1007/978-3-319-31957-5_15
Kshirsagar, Meghana, Jaime Carbonell, Judith Klein-Seetharaman and Keerthiram Murugesan.
Multitask matrix completion for learning protein interactions across diseases http://link.springer.com/chapter/10.1007/978-3-319-31957-5_4
Kwon, Sunyoung, Gyuwan Kim, Byunghan Lee, Sungroh Yoon and Young-Han Kim.
NASCUP: Nucleic Acid Sequence Classification by Universal Probability
http://arxiv.org/abs/1511.04944
Li, Yang, Shiguo Zhou, David Schwartz and Jian Ma.
Allele-Specific Quantification of Structural Variations in Cancer Genomes
http://dx.doi.org/10.1101/048207
Lin, Yu, Max W. Shen, Jeffrey Yuan and Pavel Pevzner.
Assembly of Long Error-Prone Reads Using de Bruijn Graphs
http://dx.doi.org/10.1101/048413
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
http://arxiv.org/abs/1604.02512
Luo, Yunan, Jianyang Zeng, Bonnie Berger and Jian Peng.
Low-density locality-sensitive hashing boosts metagenomic binning
http://arxiv.org/abs/1604.02699
Ma, Xiuli, Guangyu Zhou, Jingjing Wang, Jian Peng and Jiawei Han.
Complexes Detection in Biological Networks via Diversified Dense Subgraphs Mining
http://publish.illinois.edu/guangyuzhou/files/2015/11/recomb.pdf
Maryanto Gunawan, Andreas Dwi, Bhaskar Dasgupta and Louxin Zhang.
Locating a Tree in a Reticulation-Visible Network in Cubic Time
http://arxiv.org/abs/1507.02119
Nurk, Sergey, Dmitry Meleshko and Pavel Pevzner.
metaSPAdes: a new versatile de novo metagenomics assembler
http://arxiv.org/abs/1604.03071
Pellow, David, Darya Filippova and Carl Kingsford.
Improving Bloom filter performance on sequence data using k-mer Bloom filters http://link.springer.com/chapter/10.1007/978-3-319-31957-5_10
Popic, Victoria and Serafim Batzoglou.
Efficient Privacy-Preserving Read Mapping Using Locality Sensitive Hashing and Secure Kmer Voting http://dx.doi.org/10.1101/046920
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
http://www.nature.com/nbt/journal/v34/n2/abs/nbt.3468.html
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 http://biorxiv.org/content/early/2016/04/05/029926
Sahlin, Kristoffer, Mattias Frånberg and Lars Arvestad.
Structural variation detection with read pair information — An improved null-hypothesis reduces bias http://link.springer.com/chapter/10.1007/978-3-319-31957-5_13
Salmela, Leena, Riku Walve, Eric Rivals and Esko Ukkonen.
Accurate selfcorrection of errors in long reads using de Bruijn graphs
http://arxiv.org/abs/1604.02233
Sefer, Emre and Ziv Bar-Joseph.
Shall we dense? Comparing design strategies for time series expression experiments http://www.cs.cmu.edu/~esefer/papers/gene_recomb.pdf
Shao, Mingfu and Bernard Moret.
On Computing Pairwise Breakpoint Distances
http://link.springer.com/chapter/10.1007/978-3-319-31957-5_14
Shlemov, Alexander, Sergey Bankevich, Andrey Bzikadze and Yana Safonova.
IgReC 2.0: New algorithmic challenges of adaptive immune repertoire construction http://arxiv.org/pdf/1604.02193.pdf
Simmons, Sean, Cenk Sahinalp and Bonnie Berger.
Enabling Privacy-Preserving GWAS in Heterogenous Human Populations http://groups.csail.mit.edu/cb/PrivGWAS/PrivStrat.pdf
Singh, Shashank, Sabrina Rashid, Saket Navlakha and Ziv Bar-Joseph.
Distributed Gradient Descent in Bacterial Food Search
http://arxiv.org/abs/1604.03052
Sobih, Ahmed, Alexandru I. Tomescu and Veli Mäkinen.
MetaFlow: Metagenomic profiling based on whole-genome coverage analysis with min-cost flows http://link.springer.com/chapter/10.1007/978-3-319-31957-5_8
Srivastava, Avi, Hirak Sarkar, Laraib Malik, and Robert Patro.
Accurate, Fast and Lightweight Clustering of de novo Transcriptomes using Fragment Equivalence Classes
http://arxiv.org/abs/1604.03250
Steuerman, Yael and Irit Gat-Viks.
Exploiting Gene-Expression Deconvolution to Probe the Genetics of the Immune System http://dx.doi.org/10.1371/journal.pcbi.1004856
Tomescu, Alexandru I., and Paul Medvedev.
Safe and Complete Contig Assembly Via Omnitigs
http://link.springer.com/chapter/10.1007/978-3-319-31957-5_11
Tsirogiannis, Constantinos, and Brody Sandel.
Fast Phylogenetic Biodiversity Computations Under a Non-Uniform Random Distribution http://link.springer.com/chapter/10.1007/978-3-319-31957-5_16
Wang, Hao, Joel McManus and Carl Kingsford.
Accurate Recovery of Ribosome Positions Reveals Slow Translation of Wobble-Pairing Codons in Yeast http://link.springer.com/chapter/10.1007/978-3-319-31957-5_3
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 http://dx.doi.org/10.1101/047845
Wiedenhoeft, John, Eric Brugel and Alexander Schliep.
Fast Bayesian Inference of Copy Number Variants using Hidden Markov Models with Wavelet Compression
http://biorxiv.org/content/early/2015/07/31/023705
Yang, Yuqing, Ning Chen and Ting Chen.
mLDM: a Statistical Model for Sparse Microbial Association Discovery
http://dx.doi.org/10.1101/042630
Zou, Chenchen, Yuping Zhang and Zhengqing Ouyang.
Multi-track modeling for genome-scale reconstruction of 3D chromatin structure from Hi-C data https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0896-1
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
http://link.springer.com/chapter/10.1007/978-3-319-31957-5_2