ALGO 2012
September 9-14, Ljubljana, Slovenia

 Accepted papers

  • Natalie Castellana, Andrey Lushnikov, Piotr Rotkiewicz, Natasha Sefcovic, Pavel Pevzner, Adam Godzik and Kira Vyatkina  MORPH-PRO: A Novel Algorithm and Web Server for Protein Morphing                                        
  • Leo van Iersel, Steven Kelk, Nela Lekic and Celine Scornavacca  A practical approximation algorithm for solving massive instances of hybridization number                                       
  • Matthias Bernt, Kun-Mao Chao, Jyun-Wei Kao, Martin Middendorf and Eric Tannier  Preserving Inversion Phylogeny Reconstruction                                   
  • Hosein Mohimani, Sangtae Kim and Pavel Pevzner  MS-DPR: An algorithm for computing statistical significance of spectral identifications of non-linear peptides                                  
  • Yasuo Tabei     Succinct Multibit Tree: Compact Representation of Multibit Trees by Using Succinct Data Structures in Chemical Fingerprint Searches                                     
  • Alexander Bowe, Taku Onodera, Kunihiko Sadakane and Tetsuo Shibuya      Succinct de Bruijn Graphs                                       
  • Niko Välimäki and Simon J. Puglisi      Distributed String Mining for High-Throughput Sequencing Data                                   
  • Rayan Chikhi and Guillaume Rizk Space-efficient and exact de Bruijn graph representation based on a Bloom filter                                        
  • Markus J. Bauer, Anthony J. Cox, Giovanna Rosone and Marinella Sciortino        Lightweight LCP Construction for Next-Generation Sequencing Datasets                                    
  • Constantinos Tsirogiannis, Brody Sandel and Dimitris Cheliotis  Efficient Computation of Popular Phylogenetic Tree Measures                                     
  • Akshay Deepak, David Fernández-Baca and Michelle McMahon        Extracting Conflict-free Information from Multi-labeled Trees                                   
  • Antoine Thomas, Aida Ouangraoua and Jean-Stéphane Varré Tandem halving problems by DCJ                                 
  • Shay Houri and Roded Sharan     Sign assignment problems on protein networks                                    
  • Daniel Brown and Daniel Dexter  SibJoin: A Fast Heuristic for Half-Sibling Reconstruction                                        
  • Bjarni Halldorsson, Dima Blokh and Roded Sharan Estimating population size via line graph reconstruction                                        
  • Poly H. Da Silva, Marilia Braga, Raphael Machado and Simone Dantas      DCJ-indel distance with distinct operation costs                                        
  • Yun Zhu and Luay Nakhleh        Reconstructing the Evolution of Molecular Interaction Networks under the DMC and Link Dynamics Models                                   
  • Brad Shutters, Sudheer Vakati and David Fernández-Baca  Improved Lower Bounds on the Compatibility of Multi-State Characters                                    
  • Xuefeng Cui, Shuai Cheng Li, Dongbo Bu, Babak Alipanahi Ramandi and Ming Li     How accurately can we model protein structures with dihedral angles?                                    
  • Yen Yi Lin, Phuong Dao, Faraz Hach, Marzieh Bakhshi, Fan Mo, Anna Lapuk, Colin Collins and S. Cenk Sahinalp     CLIIQ: Accurate Comparative Detection and Quantification of Expressed Isoforms in a Population                                  
  • Robert Gysel, Kristian Stevens and Dan Gusfield Reducing Problems in Unrooted Tree Compatibility to Restricted Triangulations of Intersection Graphs                                    
  • Nimrod Milo, Shay Zakov, Erez Katzenelson, Eitan Bachmat, Yefim Dinitz and Michal Ziv-Ukelson   RNA Tree Comparisons Via Unrooted Unordered Alignments                                  
  • Daniel Brown and Jakub Truszkowski      Fast phylogenetic tree reconstruction using locality-sensitive hashing                                  
  • Thi Hau Nguyen, Jean-Philippe Doyon, Stephanie Pointet, Anne-Muriel Arigon Chifolleau, Vincent Ranwez and Vincent Berry Accounting for gene tree uncertainty improves gene tree accuracy as well as duplications, transfers and losses  predictions                                     
  • Song Gao, Denis Bertrand and Niranjan Nagarajan FinIS: Improved in silico finishing using an exact quadratic programming formulation                                    
  • Birte Kehr, Knut Reinert and Aaron Darling      Hidden Breakpoints in Genome Alignments                                 
  • Anthony Cox, Tobias Jakobi, Giovanna Rosone and Ole Schulz-Trieglaff    Comparing DNA sequence collections by direct comparison of compressed text indexes                                      
  • Philippe Rinaudo, Yann Ponty, Dominique Barth and Alain Denise  Tree decomposition and parameterized algorithms for RNA structure-sequence alignment including tertiary interactions and pseudoknots (extended abstract)                                        
  • Anirban Bhar, Martin Haubrock, Anirban Mukhopadhyay, Ujjwal Maulik, Sanghamitra Bandyopadhyay and Edgar Wingender       δ-TRIMAX: Extracting Triclusters and Analysing Coregulation in Time Series Gene Expression Data                                
  • Nikolay Vyahhi, Son Pham and Pavel Pevnzer      From de Bruijn Graphs to Rectangle Graphs for Genome Assembly                                   
  • Yi Shi, Xiaoping Liao, Xinhua Zhang, Guohui Lin and Dale Schuurmans     Sparse Learning based Linear Coherent Bi-clustering                                     
  • Manuel Lafond, Krister M. Swenson and Nadia El-Mabrouk  An optimal reconciliation algorithm for gene trees with polytomies                                      
  • Phillip E. C. Compeau and Pavel A. Pevzner      A Simplified View of DCJ-Indel Distance                                 
  • Geet Duggal, Rob Patro, Emre Sefer, Hao Wang, Darya Filippova, Samir Khuller and Carl Kingsford Resolving Spatial Inconsistencies in Chromosome Conformation Data                                       
  • Olga Tanaseichuk, James Borneman and Tao Jiang  A Probabilistic Approach to Accurate Abundance-Based Binning of Metagenomic Reads