List of accepted papers for WABI 2016 (May 31, 2016) ==================================================== Qiang Kou, Si Wu, Nikola Tolic, Ljiljana Pasa-Tolic and Xiaowen Liu: Mass graphs and their applications in top-down proteomics Lianrong Pu, Daming Zhu and Haitao Jiang: A new approximation algorithm for unsigned translocation sorting Leena Salmela and Alexandru I. Tomescu: Safely filling gaps with partial solutions common to all solutions Sorina Maciuca, Carlos Del Ojo Elias, Gil McVean and Zamin Iqbal: A natural encoding of genetic variation in a Burrows-Wheeler Transform to enable mapping and genome inference Adam Novak, Erik Garrison and Benedict Paten: A Graph Extension of the Positional Burrows-Wheeler Transform and its Applications Yun Deng and David Fernández-Baca: Fast Compatibility Testing for Phylogenies with Nested Taxa Yannis Almirantis, Panagiotis Charalampopoulos, Jia Gao, Costas Iliopoulos, Manal Mohamed, Solon Pissis and Dimitris Polychronopoulos: Optimal Computation of Avoided Words Diego P. Rubert, Pedro Feijao, Marilia Braga, Jens Stoye and Fábio V. Martinez: A Linear Time Approximation Algorithm for the DCJ Distance for Genomes with Bounded Number of Duplicates Broňa Brejová, Askar Gafurov, Dana Pardubska, Michal Sabo and Tomas Vinar: Isometric Gene Tree Reconciliation Revisited Daniel Doerr, Pedro Feijao, Metin Balaban and Cedric Chauve: The gene family-free median of three Guillaume Fertin, Geraldine Jean and Eric Tannier: Genome Rearrangements on both Gene Order and Intergenic Regions Riccardo Dondi, Nadia El-Mabrouk and Manuel Lafond: Correction of Weighted Orthology and Paralogy Relations - Complexity and Algorithmic Results Emilie Renard, Samuel Branders and Pierre-Antoine Absil: Independent Component Analysis to Remove Batch Eects from Merged Microarray Datasets Sven Jager, Benjamin Schiller, Thorsten Strufe and Kay Hamacher: StreAM-Tg: Algorithms for Analyzing Coarse Grained RNA Dynamics based on Markov Models of Connectivity-Graphs Marius Erbert, Steffen Rechner and Matthias Müller-Hannemann: Gerbil: A fast and memory-efficient k-mer counter with GPU-support Dan Deblasio and John Kececioglu: Predicting core columns of protein multiple sequence alignments for improved parameter advising Yaron Orenstein, David Pellow, Guillaume Marcais, Ron Shamir and Carl Kingsford: Compact universal k-mer hitting sets Mohammed El-Kebir, Ben Raphael, Ron Shamir, Roded Sharan, Simone Zaccaria, Meirav Zehavi and Ron Zeira: Copy-Number Evolution Problems: Complexity and Algorithms Arnon Benshahar, Michal Ziv-Ukelson, Danny Hermelin and Vered Caspi: A Biclique Approach to Reference Anchored Gene Blocks and its Applications to Pathogenicity Islands Anna Bomersbach, Marco Chiarandini and Fabio Vandin: An Efficient Branch and Cut Algorithm to Find Frequently Mutated Subnetworks in Cancer Jay Ghurye and Mihai Pop: Better Identification of Repeats In Metagenomic Scaffolding Alexander Loboda, Maxim Artyomov and Alexey Sergushichev: Solving generalized maximum-weight connected subgraph problem for network enrichment analysis Brian Brubach: Further Improvement in Approximating the Maximum Duo-Preservation String Mapping Problem Matthieu David, Guillaume Fertin and Dominique Tessier: SpecTrees: an efficient without a priori data structure for MS/MS spectra identification Ludovic Gillet, Simon Rösch, Thomas Tschager and Peter Widmayer: A Better Scoring Model for De Novo Peptide Sequencing: The Symmetric Difference between Explained and Measured Masses Christopher Schröder and Sven Rahmann: A hybrid parameter estimation algorithm for beta mixtures and applications to methylation state classification Svend V Nielsen, Simon Simonsen and Asger Hobolth: Inferring Population Genetic Parameters: Particle filtering, HMM, Ripley's $K$-function or Runs of Homozygosity?