Helsinki · Finland

20–24 August 2018

ALGO2018

WABI 2018: Program

18th Workshop on Algorithms in Bioinformatics

Keynote speaker

Mihai Pop

Mihai Pop · University of Maryland

Dr. Pop is a Professor in the Department of Computer Science and the Center for Bioinformatics and Computational Biology at the University of Maryland, College Park (UMCP) and currently serves as the Interim Director of the University of Maryland Institute for Advanced Computer Studies, and as the Director of the Center for Health-related Informatics and Bioimaging. Dr. Pop received his Ph.D. in Computer Science at Johns Hopkins University where he focused on algorithms for computer graphics and Geographic Information Systems (GIS) applications. Dr. Pop's current research interests include metagenomic assembly and analysis algorithms, software testing in bioinformatics, and dynamic models of microbial communities. His lab has developed a number of widely used open-source software tools, such as the assembly suite AMOS, the NGS aligner Bowtie, and the metagenomic assembly package MetAMOS. He also co-led the data analysis working group for the Human Microbiome Project and led the sub-group responsible for the assembly of the data generated in this project. Dr. Pop is actively involved in teaching at the undergraduate and graduate levels and is strongly interested in the development of educational resources for introductory computer science and bioinformatics.

Accepted papers

Mai Alzamel, Lorraine Ayad, Giulia Bernardini, Roberto Grossi, Costas S. Iliopoulos, Nadia Pisanti, Solon P. Pissis and Giovanna Rosone. Degenerate String Comparison and Applications
Tamal Dey and Sayan Mandal. Protein Classification with Improved Topological Data Analysis
Kai Dührkop, Marie Anne Lataretu, Walton Timothy James White and Sebastian Böcker. Heuristic algorithms for the Maximum Colorful Subtree problem
Nicola Prezza, Nadia Pisanti, Marinella Sciortino and Giovanna Rosone. Detecting Mutations by eBWT
Jouni Sirén, Erik Garrison, Adam M. Novak, Benedict Paten and Richard Durbin. Haplotype-aware graph indexes
Barak Sternberg and Roded Sharan. A dynamic algorithm for network propagation
Till Hartmann and Sven Rahmann. Spalter: A meta machine learning approach to distinguish true DNA variants from sequencing artefacts
Riku Walve, Pasi Rastas and Leena Salmela. Kermit: Guided Long Read Assembly using Coloured Overlap Graphs
Saugata Basu, Filippo Utro and Laxmi Parida. Essential Simplices in Persistent Homology and Subtle Admixture Detection
Tuukka Norri, Bastien Cazaux, Dmitry Kosolobov and Veli Mäkinen. Minimum Segmentation for Pan-genomic Founder Reconstruction in Optimal Time
Martin S. Engler, Bertrand Caron, Lourens Veen, Daan P. Geerke, Alan E. Mark and Gunnar W. Klau. Multiple-choice knapsack for assigning partial atomic charges in drug-like molecules
Stéphane Chrétien, Christophe Guyeux and Serge Moulin. l1-penalised ordinal polytomous regression estimators
Qiuyi Yang, Satish Rao and Tandy Warnow. New absolute fast converging phylogeny estimation methods with improved scalability and accuracy
Riccardo Dondi, Manuel Lafond and Celine Scornavacca. Reconciling Multiple Genes Trees via Segmental Duplications and Losses
Martin Muggli, Simon Puglisi and Christina Boucher. A Succinct Solution to RMap Alignment
Mohammed El-Kebir. Parsimonious Migration History Problem: Complexity and Algorithms
Morteza Chalabi Hajkarim, Eli Upfal and Fabio Vandin. Differentially Mutated Subnetworks Discovery
Christina Boucher, Travis Gagie, Alan Kuhnle and Giovanni Manzini. Prefix-Free Parsing for Building Big BWTs
Ryan Elworth, Chabrielle Allen, Travis Benedict, Peter Dulworth and Luay Nakhleh. DGEN: A Test Statistic for Detection of General Introgression Scenarios
Mehrdad Mansouri, Julian Booth, Margaryta Vityaz, Cedric Chauve and Leonid Chindelevitch. PRINCE: Accurate Approximation of the Copy Number of Tandem Repeats
Nikolai Karpov, Salem Malikic, M. Khaledur Rahman and S. Cenk Sahinalp. A Multi-label Tree Edit Distance for Comparing "Clonal Trees" of Tumor Progression
Yohei Rosen and Benedict Paten. An average-case sublinear exact Li and Stephens forward algorithm
Hooman Zabeti, Tamon Stephen, Bonnie Berger and Leonid Chindelevitch. A duality-based method for identifying elemental balance violations in metabolic network models
Lavinia Egidi, Felipe A. Louza, Giovanni Manzini and Guilherme P. Telles. External memory BWT and LCP computation for sequence collections with applications
Szymon Majewski, Michał Ciach, Michał Startek, Wanda Niemyska, Błażej Miasojedow and Anna Gambin. The Wasserstein distance as a dissimilarity measure for mass spectra with application to spectral deconvolution

Poster session

The poster session will be in the afternoon of Monday, 20 August 2018.

ALGO program

Please see the ALGO 2018 web pages for more information on ALGO keynote speakers and social program.