13th Workshop on Algorithms in Bioinformatics
WABI 2013
September 02-04
Sophia Antipolis, France


Workshop on Algorithms in Bioinformatics 2013 - Accepted papers

Nicolas Wieseke, Matthias Bernt and Martin Middendorf. Unifying Parsimonious Tree Reconciliation
Michał Modzelewski and Norbert Dojer. MSARC: Multiple Sequence Alignment by Residue Clustering
Arnon Mazza, Irit Gat-Viks, Hesso Farhan and Roded Sharan. A Minimum-Labeling Approach for Reconstructing Protein Networks across Multiple Conditions
Rolf Backofen, Markus Fricke, Manja Marz, Jing Qin and Peter F. Stadler. Graph-Distance within RNA Secondary Structure Ensembles
Sudheer Vakati and David Fernández-Baca. Characterizing Compatibility and Agreement of Unrooted Trees via Cuts in Graphs
Denisa Duma, Mary Wootters, Anna Gilbert, Hung Q. Ngo, Atri Rudra, Matthew Alpert, Timothy J. Close, Gianfranco Ciardo and Stefano Lonardi. Accurate Decoding of Pooled Sequenced Data Using Compressed Sensing
João Paulo Pereira Zanetti, Priscila Biller and João Meidanis. On the matrix median problem
Jesper Jansson, Chuanqi Shen and Wing-Kin Sung. Algorithms for the Majority Rule (+) Consensus Tree and the Frequency Difference Consensus Tree
Taku Onodera, Kunihiko Sadakane and Tetsuo Shibuya. Detecting Superbubbles in Assembly Graphs
Laurent Bulteau, Guillaume Fertin, Christian Komusiewicz and Irena Rusu. Fixed-Parameter Algorithm for Minimum Common String Partition with Few Duplications
Kamil Salikhov, Gustavo Sacomoto and Gregory Kucherov. Using cascading Bloom filters to improve the memory usage for de Brujin graphs
Gustavo Sacomoto, Marie-France Sagot and Vincent Lacroix. A polynomial delay algorithm for the enumeration of bubbles with length constraints in directed graphs and its application to the detection of alternative splicing in RNA-seq data
Limor Leibovich and Zohar Yakhini. Mutual Enrichment in Ranked Lists and the Statistical Assessment of Position Weight Matrix Motifs
Evgeny Kapun and Fedor Tsarev. On NP-Hardness of the Paired de Bruijn Sound Cycle Problem
Nishanth Nair, Yu Lin, Philipp Bucher and Bernard Moret. Differentiation trees for cell developmental history from histone modifications
Constantinos Tsirogiannis and Brody Sandel. Computing the Skewness of the Phylogenetic Mean Pairwise Distance in Linear Time
Sebastian Böcker, Stefan Canzar and Gunnar W. Klau. The generalized Robinson-Foulds metric
Son Pham, Ilya Minkin, Nikolay Vyahhi, Anand Patel and Mikhail Kolmogorov. Sibelia: A scalable and comprehensive synteny block generation tool for closely related microbial genomes
Michal Nánási, Tomas Vinar and Broňa Brejová. Probabilistic Approaches to Alignment with Tandem Repeats
Alexandru I. Tomescu, Anna Kuosmanen, Romeo Rizzi and Veli Mäkinen. A Novel Combinatorial Method for Estimating Transcript Expression with RNA-Seq: Bounding the Number of Paths
Ramanuja Simha and Hagit Shatkay. Protein (Multi-)Location Prediction: Using Location Inter-Dependencies in a Probabilistic Framework
Charalampos Tsourakakis. Modeling Intratumor Gene Copy Number Heterogeneity using Fluorescence in Situ Hybridization data
Viraj Deshpande and Eric Fung. A hybrid assembly using high throughput short and long reads
Darya Filippova, Robert Patro, Geet Duggal and Carl Kingsford. Multiscale Identification of Topological Domains in Chromatin
Xuefeng Cui, Shuai Cheng Li, Dongbo Bu and Ming Li. Towards Reliable Automatic Protein Structure Alignment
Balaji Venkatachalam, Dan Gusfield and Yelena Frid. Faster Algorithms for RNA-folding using the Four-Russians method


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