Stefan Canzar: Publications

Articles in Journals

• S. ANDREOTTI, K. REINERT, S. Canzar
  The Duplication-Loss Small Phylogeny Problem: From Cherries to Trees
  Journal of Computational Biology, accepted 2013.
• T. MAGOC, S. PABINGER, S. Canzar , X. LIU, Q. SU D. PUIU, L. J. TALLON, S. L. SALZBERG
  GAGE-B: An Evaluation of Genome Assemblers for Bacterial Organisms
  Bioinformatics, accepted 2013.
• S. Canzar , K. ELBASSIONI, J. MESTRE
  A Polynomial Delay Algorithm for Enumerating Approximate Solutions to the Interval Constrained Coloring Problem
  ACM Journal on Experimental Algorithmics, accepted 2013.
• S. Canzar , K. ELBASSIONI, G. W. KLAU, J. MESTRE
  On Tree-Constrained Matchings and Generalizations
  Algorithmica, accepted 2013.
• S. Canzar , M. El-KEBIR, R. POOL, K. ELBASSIONI, A. K. MALDE, A. E. MARK, D. P. GEERKE, L. STOUGIE, G. W. KLAU
  Charge Group Partitioning in Biomolecular Simulation
  Journal of Computational Biology, 2013, volume 20(3), pages 167-187.
• T. MARSCHALL, I. COSTA, S. Canzar , M. BAUER, G. W. KLAU , A. SCHLIEP, A. SCHÖNHUTH
  CLEVER: Clique-Enumerating Variant Finder
  Bioinformatics, 2012, volume 28(22), pages 2875-2882.
• S. Canzar , N. C. TOUSSAINT , G. W. KLAU
  An Exact Algorithm for Side-Chain Placement in Protein Design
  Optimization Letters, special issue on 10th International Symposium on Experimental Algorithms (SEA), 2011, volume 5(3), pages 393-406.
• E. ALTHAUS, S. Canzar , K. ELBASSIONI , A. KARRENBAUER , J. MESTRE
  Approximation Algorithms for the Interval Constrained Coloring Problem
  Algorithmica, 2010.
• E. ALTHAUS , S. Canzar , C. EHRLER, M. R. EMMETT , A. KARRENBAUE R , A. G. MARSHALL , A. MEYER-BAESE , J. TIPTON, H. ZHANG
  Computing H/D-Exchange rates of single residues from data of proteolytic fragments
  BMC Bioinformatics, 2010, 11:424.
• E. ALTHAUS, S. Canzar
  A Lagrangian relaxation approach for the multiple sequence alignment problem
  Journal of Combinatorial Optimization, 2008, volume 16(2), pages 127-154.

Articles in Refereed Conference Proceedings

• S. BÖCKER, S. Canzar , G. W. KLAU
  The generalized Robinson-Foulds metric
  In Proceedings of the 13th Workshop on Algorithms in Bioinformatics (WABI),
  accepted 2013.
• T. MARSCHALL, I. COSTA, S. Canzar, M. BAUER, G. KLAU, A. SCHLIEP, A. SCHOENHUTH
  CLEVER: Clique-Enumerating Variant Finder
  RECOMB-seq and ISMB-HitSeq, to appear.
• S. Canzar , M. El-KEBIR, R. POOL, K. ELBASSIONI, A. K. MALDE, A. E. MARK, D. P. GEERKE, L. STOUGIE, G. W. KLAU
  Charge Group Partitioning in Biomolecular Simulation
  In Proceedings of the 16th Annual International Conference on Research in Computational Molecular Biology (RECOMB),
  Lecture Notes in Computer Science, Springer, 2012.
• S. Canzar , T. MARSCHALL, S. RAHMANN, C. SCHWIEGELSHOHN
  Solving the Minimum String Cover Problem
  In Proceedings of the 14th Meeting on Algorithm Engineering and Experiments (ALENEX), 2012.
• S. Canzar , M. EL-KEBIR
  A Mathematical Programming Approach to Marker-Assisted Gene Pyramiding
  In Proceedings of the 11th Workshop on Algorithms in Bioinformatics (WABI),
  Lecture Notes in Bioinformatics, Springer, 2011.
• S. Canzar , K. ELBASSIONI , G. W. KLAU , J. MESTRE
  On Tree-Constrained Matchings and Generalizations
  In Proceedings of the 38th International Colloquium on Automata, Languages and Programming (ICALP),
  Lecture Notes in Computer Science, Springer, 2011.
• S. Canzar , K. ELBASSIONI , A. ELMASRY , R. RAMAN
  On the Approximability of the Maximum Interval Coloring Problem
  In Proceedings of the 21st International Symposium on Algorithms and Computation (ISAAC),
  Lecture Notes in Computer Science, Springer, 2010.
• S. Canzar , K. ELBASSIONI , J. MESTRE
  A Polynomial Delay Algorithm for Enumerating Approximate Solutions to the Interval Constrained Coloring Problem
  In Proceedings of the Twelfth Workshop on Algorithm Engineering and Experiments (ALENEX), 2010.
• E. ALTHAUS , S. Canzar , C. EHRLER, M. R. EMMETT , A. KARRENBAUE R , A. G. MARSHALL , A. MEYER-BAESE , J. TIPTON, H. ZHANG
  Discrete Fitting of Hydrogen-Deuterium-Exchange-data of Overlapping Fragments
  In Proceedings of the International Conference on Bioinformatics & Computational Biology (BIOCOMP), 2009.
• E. ALTHAUS , S. Canzar , M. R. EMMETT , A. KARRENBAUE R , A. G. MARSHALL , A. MEYER-BAESE , H. ZHANG
  Computing H/D-Exchange Speeds of Single Residues from Data of Peptic Fragments.
  In Proceedings of the 23rd Annual ACM Symposium on Applied Computing (SAC), 2008.
• E. ALTHAUS, S. Canzar
  LASA: A tool for non-heuristic alignment of multiple sequences.
  In Proceedings of the Second International Conference on Bioinformatics Research and Development (BIRD),
  Communications in Computer and Information Science, Springer, 2008, pages 489-498.
• E. ALTHAUS, S. Canzar , K. ELBASSIONI , A. KARRENBAUER , J. MESTRE
  Approximating the Interval Constrained Coloring Problem.
  In Proceedings of the 11th Scandinavian Workshop on Algorithm Theory (SWAT),
  Lecture Notes in Computer Science, Springer, 2008, pages 210-221.
• E. ALTHAUS, S. Canzar
  A Lagrangian Relaxation Approach for the Multiple Sequence Alignment Problem.
  In Proceedings of the First International Conference on Combinatorial Optimization and Applications (COCOA),
  Lecture Notes in Computer Science, Springer, 2007, pages 267-278.
• S. Canzar , J. REMY
  Shape Distributions and Protein Similarity
  In Proceedings of the German Conference on Bioinformatics (GCB),
  Lecture Notes in Informatics, 2006, pages 1-10.