Papers - Christian Nørgaard Storm Pedersen

Journals

A sub-cubic time algorithm for computing the quartet distance between two general trees. Jesper Nielsen, Anders K. Kristensen, Thomas Mailung, Christian N. S. Pedersen. Algorithms in Molecular Biology, volume 6:15, 2011. [PDF] [WWW]
Molecular Docking with Ligand Attached Water Molecules. Mette Lie, Rene Thomsen, Christian N. S. Pedersen, Birgit Schiøtt, Mikael H. Christensen. Journal of Chemical Information and Modeling, volume 41:4, pages 909-917, 2011. [PDF] [WWW]
Inference of Large Phylogenies using Neighbour-Joining. Martin Simonsen, Thomas Mailund, Christian N. S. Pedersen. Communications in Computer and Information Science (Biomedical Engineering Systems and Technologies: 3rd International Joint Conference, BIOSTEC 2010, Revised Selected Papers), volume 127, pages 334-344, Springer Verlag, 2011. [PDF] [WWW]
Using Inverted Indices for Accelerating LINGO Calculations. Thomas Greve Kristensen, Jesper Nielsen, Christian N. S. Pedersen. Journal of Chemical Information and Modeling, volume 51:3, pages 597-600, 2011. [PDF] [WWW]
A Tree Based Method for the Rapid Screening of Chemical Fingerprints. Thomas Greve Kristensen, Jesper Nielsen, Christian N. S. Pedersen. Algorithms in Molecular Biology, volume 5:9, 2010. [PDF] [WWW]
A fast algorithm for genome wide haplotype pattern mining. Søren Besenbacher, Christian N. S. Pedersen, Thomas Mailund. BMC Bioinformatics, volume 10, 2009. [PDF] [WWW]
Computing the All-Pairs Quartet Distance in a Set of Evolutionary Trees. Martin Stissing, Thomas Mailund, Christian N.S. Pedersen, Gerth Stølting Brodal, Rolf Fagerberg. Journal of Bioinformatics and Computational Biology, volume 6:1, pages 37-50, 2008. [PDF]
Experiences with GeneRecon on MiG. Thomas Mailund, Christian N. S. Pedersen, Jonas Bardino, Brian Vinter, Hans Henrik Karlsen. Future Generation Computer Systems, volume 23, pages 580-586, 2007. [PDF]
Fast Calculation of the Quartet Distance Between Trees of Arbitrary Degrees. Chris Christiansen, Thomas Mailund, Christian N. S. Pedersen, Martin Randers, Martin Stissing. Algorithms for Molecular Biology, volume 1:16, 2006. [PDF] [WWW]
GeneRecon - a coalescent based tool for fine-scale association mapping. Thomas Mailund, Mikkel H. Schierup, Christian N. S. Pedersen, Jesper N. Madsen, Jotun Hein, Leif Schauser. Bioinformatics volume 22:18, pages 2317-2318, 2006. [PDF] [WWW]
Recrafting the Neighbor-Joining Method. Thomas Mailund, Gerth Stølting Brodal, Rolf Fagerberg, Christian N. S. Pedersen, Derek Philips. BMC Bioinformatics, volume 7:29, 2006. [PDF] [WWW]
CoaSim: A flexible environment for simulating genetic data under coalescent models. Thomas Mailund, Mikkel H. Schierup, Christian N. S. Pedersen, Peter J. M. Mechlenborg, Jesper N. Madsen, Leif Schauser. BMC Bioinformatics, volume 6:252, 2005. [PDF] [WWW]
RBT - A tool for building refined Buneman trees. Søren Besenbacher, Thomas Mailund, Lasse Westh-Nielsen, and Christian N. S. Pedersen. Bioinformatics, volume 21, pages 1711 - 1712, Oxford University Press, 2005. [PDF] [WWW]
QuickJoin - Fast Neighbour-Joining Tree Reconstruction. Thomas Mailund and Christian N. S. Pedersen. Bioinformatics, volume 20, pages 3261 - 3262, Oxford University Press, 2004. [PDF] [WWW]
QDist - Quartet Distance between Evolutionary Trees. Thomas Mailund and Christian N. S. Pedersen. Bioinformatics, volume 20, pages 1636--1637, Oxford University Press, 2004. [PDF] [WWW]
Recursions for Statistical Multiple Alignment. Jotun Hein, Jens Ledet Jensen, Christian N. S. Pedersen. Proceedings of the National Academy of Science, U.S.A. (PNAS), volume 100, pages 14960-14965, 2003. [PDF] [WWW]
Computing the Quartet Distance Between Evolutionary Trees in Time O(n log n). Gerth Stølting Brodal, Rolf Fagerberg and Christian N. S. Pedersen. Algorithmica, volume 38, pages 377-395, Springer Verlag, 2003. [PDF]
The Consensus String Problem and the Complexity of Comparing Hidden Markov Models. Rune B. Lyngsø and Christian N. S. Pedersen. Journal of Computing and System Science, volume 65, pages 545-569, Academic Press, 2002. [PDF] [WWW]
Pseudoknot Prediction in Energy Based Models. Rune B. Lyngsø and Christian N. S. Pedersen. Journal of Computational Biology, volume 7(3), pages 409-427, Mary Ann Liebert Publishers, 2000. [PDF] [WWW]
Finding Maximal Pairs with Bounded Gap. Gerth Stølting Brodal, Rune B. Lyngsø, Christian N. S. Pedersen and Jens Stoye. Journal of Discrete Algorithms, volume 1(1), pages 77-104, Hermes Science Publishing, 2000. [PDF]
Fast Evaluation of Internal Loops in RNA Secondary Structure Prediction. Rune B. Lyngsø, Michael Zuker and Christian N. S. Pedersen. Bioinformatics, volume 15(6), pages 440-445, Oxford University Press, 1999. [PDF] [WWW]

Proceedings

GPU-Accelerated High-Accuracy Molecular Docking using Guided Differential Evolution. Martin Simonsen, Rene Thomsen, Mikael H. Christensen, Christian N. S. Pedersen. To appear in Proceedings of the Genetic and Evolutuonary Computation Conference (GECCO 2011), real world application track, July 2011. [WWW]
Rapid Computation of Distance Estimators from Nucletide and Amino Acid Alignments. Martin Simonsen, Christian N. S. Pedersen. In Proceedings of 26th Annual ACM Symposium on Applied Computing (SAC 2011), bioinformatics track, pages 83-88, ACM Press, March 2011. [PDF] [WWW]
HMMlib: A C++ Library fro General Hidden Markov Models Exploiting Modern CPUs. Andreas Sand, Asbjørn T. Brask, Christian N. S. Pedersen, Thomas Mailund. In Proceedings of the 2nd International Workshop on High Performance Computational Systems Biology (HiBi 2010), September 2010. [PDF] [WWW]
Data Structures for Accelerating Tanimoto Queries. Thomas Greve Kristensen, Christian N. S. Pedersen. In Proceedings of the 10th Workshop in Algorithms in Bioinformatics (WABI 2010), volume 6293 of Lecture Notes in Computer Science, pages 28 - 39, Springer Verlag, September 2010. [PDF] [WWW]
Building Very Large Neighbour-Joining Trees. Martin Simonsen, Thomas Mailund, Christian N. S. Pedersen. In Proceedings of the 1st Conference on Bioinformatics, part of the 3rd International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2010), January 2010. [PDF]
A Tree Based Method for the Rapid Screening of Chemical Fingerprints. Thomas Greve Kristensen, Jesper Nielsen, Christian N. S. Pedersen. In Proceedings of the 9th Workshop in Algorithms in Bioinformatics (WABI 2009), volume 5724 of Lecture Notes in Computer Science, pages 194- 205, Springer Verlag, September 2009.
Optimal Overlay of Ligands with Flexible Bonds using Differential Evolution. Thomas Greve Kristensen, Christian N. S. Pedersen. In Proccedings of IJCBS 2009 (Workshop on Bioinformatics Algorithms), August 2009.
A sub-cubic time algorithm for computing the quartet distance between two general trees. Thomas Mailund, Jesper Nielsen, Christian N. S. Pedersen. In Proceedings of IJCBS 2009 (Workshop on Bioinformatics Algorithms), August 2009.
A fast algorithm for genome wide haplotype pattern mining. Søren Besenbacher, Christian N. S. Pedersen, Thomas Mailund. In Proceedings of the 7th Asia-Pacific Bioinformatics Conference (APBC 2009), pages 772 - 780, January 2009.
Rapid neighbour-joining. Martin Simonsen, Thomas Mailund, Christian N. S. Pedersen. In Proceedings of the 8th Workshop in Algorithms in Bioinformatics (WABI 2008), volume 5251 of Lecture Notes in Computer Science, Springer Verlag, October 2008. [PDF]
Computing the Quartet Distance between Evolutionary Trees of Bounded Degree. Martin Stissing, Christian N. S. Pedersen, Thomas Mailund, Gerth Stølting Brodal, Rolf Fagerberg. In Proceedings of the 5th Asia-Pacific Bioinformatics Conference (APBC 2007), pages 101 - 110, January 2007.
Computing the All-Pairs Quartet Distance on a Set of Evolutionary Trees. Martin Stissing, Thomas Mailund, Christian N. S. Pedersen, Gerth Stølting Brodal, Rolf Fagerberg. In Proceedings of the 5th Asia-Pacific Bioinformatics Conference (APBC 2007), pages 91-100, January 2007.
Computing the quartet distance between trees of arbitrary degree. Chris Christensen, Thomas Mailund, Christian N. S. Pedersen and Martin Randers. In Proceedings of the 5th Workshop in Algorithms in Bioinformatics (WABI 2005), volume 3692 of Lecture Notes in Computer Science, pages 77-88, Springer Verlag, October 2005. [PDF] [WWW]
Quartet Distance between General Trees. Chris Christensen, Thomas Mailund, Christian N. S. Pedersen and Martin Randers. In Proceedings of the International Conference on Numerical Analysis and Applied Mathematics (ICNAAM 2005), pages 796-799, Wiley-VCH Verlag, September 2005.
Initial experiences with GeneRecon on MiG. Jonas Bardino, Thomas Mailund, Christian N. S. Pedersen and Brian Vinter. In Proceedings of the 2005 International Conference on Grid Computing and Applications (GCA 2005), CSREA Press, June 2005.
Computing Refined Buneman Trees in Cubic Time. Gerth Stølting Brodal, Rolf Fagerberg, Anna Östlin, Christian N. S. Pedersen and S. S. Rao. In Proceedings of the 3rd Workshop in Algorithms in Bioinformatics (WABI 2003), volume 2812 of Lecture Notes in Computer Science, pages 259-270, Springer Verlag, September 2003.
Comparative Methods for Gene Structure Prediction in Homologous Sequences. Christian N. S. Pedersen and Tejs Scharling. In Proceedings of the 2nd Workshop on Algorithms in Bioinformatics (WABI 2002), volume 2452 of Lecture Notes in Compter Science, pages 220-234, Springer Verlag, September 2002.
Solving the String Statistics Problem in Time O(n log n). Gerth Stølting Brodal, Rune Bang Lyngsø, Christian N. S. Pedersen and Anna Östlin. In Proceedings of the 29th International Colloquium on Automata, Languages, and Programming (ICALP 2001), volume 2380 of Lecture Notes in Computer Science, pages 728-739, Springer Verlag, July 2002.
Complexity of Comparing Hidden Markov Models. Rune B. Lyngsø and Christian N. S. Pedersen. In Proceedings of the 12th International Symposium on Algorithms and Computation (ISAAC 2001), volume 2223 of Lecture Notes in Computer Science, pages 416-428, Springer Verlag, December 2001.
Computing the Quartet Distance Between Evolutionary Trees in Time O(n log² n). Gerth Stølting Brodal, Rolf Fagerberg and Christian N. S. Pedersen. In Proceedings of the 12th International Symposium on Algorithms and Computation (ISAAC 2001), volume 2223 of Lecture Notes in Computer Science, pages 731-742, Springer Verlag, December 2001.
Comparing an HMM and an SCFG. Arun Jagota, Rune B. Lyngsø, Christian N. S. Pedersen. In Proceedings of the 1st Workshop on Algorithms in Bioinformatics (WABI 2001), volume 2149 of Lecture Notes in Computer Science, pages 69-84, Springer Verlag, August 2001.
The Complexity of Constructing Evolutionary Trees Using Experiments. Gerth Stølting Brodal, Rolf Fagerberg, Christian N. S. Pedersen and Anna "Ostlin. In Proceedings of the 28th International Colloquium on Automata, Languages, and Programming (ICALP 2001), volume 2076 of Lecture Notes in Computer Science, pages 140-151, Springer Verlag, July 2001.
Finding Maximal Quasiperiodicities in Strings. Gerth Stølting Brodal and Christian N. S. Pedersen. In Proceedings of the 11th Annual Symposium on Combinatorial Pattern Matching (CPM 2000), volume 1848 of Lecture Notes in Computer Science, pages 397-411, Springer Verlag, June 2000.
Protein Folding in the 2D HP Model. Rune B. Lyngsø and Christian N. S. Pedersen. In Proceedings of the 1st Journ'ees Ouvertes: Biologie, Informatique et Math'ematiques (JOBIM 2000), Montpellier, France, May 2000.
Pseudoknots in RNA Secondary Structures. Rune B. Lyngsø and Christian N. S. Pedersen. In Proceedings of the 4th Annual International Conference on Computational Molecular Biology (RECOMB 2000), pages 201-209, ACM Press, April 2000.
Metrics and Similarity Measures for Hidden Markov Models. Rune B. Lyngsø, Christian N. S. Pedersen and Henrik Nielsen. In Proceedings of the 7th International Conference on Intelligent Systems for Molecular Biology (ISBM 1999), pages 178-186, AAAI Press, August 1999.
Finding Maximal Pairs with Bounded Gap. Gerth Stølting Brodal, Rune B. Lyngsø, Christian N. S. Pedersen and Jens Stoye. In Proceedings of the 10th Annual Symposium on Combinatorial Pattern Matching (CPM 1999), volume 1645 of Lecture Notes in Computer Science, pages 134-149, Springer Verlag, July 1999.
Internal Loops in RNA Secondary Structure Prediction. Rune B. Lyngsø, Christian N. S. Pedersen and Michael Zuker. In Proceedings of the 3rd Annual International Conference on Computational Molecular Biology (RECOMB 1999), pages 260-267, ACM Press, April 1999.
Comparison of Coding DNA. Christian N. S. Pedersen, Rune B. Lyngsø and Jotun Hein. In Proceedings of the 9th Annual Symposium of Combinatorial Pattern Matching (CPM 1998), volume 1448 of Lecture Notes in Computer Science, pages 153-173, Springer Verlag, July 1998.

Thesis

Algorithms in Computational Biology. Christian N. S. Pedersen. PhD Thesis, Department of Computer Science, University of Aarhus, August 1999. BRICS DS-00-4, March 2000.