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ORCIDChristian N. S. Pedersen
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- affiliation: Aarhus University, Bioinformatics Research Center
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Journal Articles
- 2018
[j29]Maria Luisa Matey-Hernandez
, Lasse Maretty, Jacob Malte Jensen, Bent Petersen, Jonas Andreas Sibbesen, Siyang Liu, Palle Villesen, Laurits Skov, Kirstine Belling, Christian Theil Have, José M. G. Izarzugaza, Marie Grosjean, Jette Bork-Jensen, Jakob Grove, Thomas D. Als, Shujia Huang, Yuqi Chang, Ruiqi Xu, Weijian Ye, Junhua Rao, Xiaosen Guo, Jihua Sun, Hongzhi Cao, Chen Ye, John van Beusekom, Thomas Espeseth, Esben N. Flindt, Rune M. Friborg, Anders E. Halager, Stephanie Le Hellard, Christina M. Hultman, Francesco Lescai, Shengting Li, Ole Lund, Peter Løngreen, Thomas Mailund, Ole Mors, Christian N. S. Pedersen, Thomas Sicheritz-Pontén, Patrick F. Sullivan, Ali Syed, David Westergaard, Rachita Yadav, Ning Li, Xun Xu, Torben Hansen, Anders Krogh, Lars Bolund, Thorkild I. A. Sørensen, Oluf Pedersen, Ramneek Gupta, Simon Rasmussen, Søren Besenbacher, Anders D. Børglum, Jun Wang, Hans Eiberg, Karsten Kristiansen, Mikkel Heide Schierup, Søren Brunak:
Benchmarking the HLA typing performance of Polysolver and Optitype in 50 Danish parental trios. BMC Bioinform. 19(1): 239:1-239:12 (2018)- 2017
- [j28]Dan Søndergaard, Svend V. Nielsen, Christian N. S. Pedersen, Søren Besenbacher:
Prediction of Primary Tumors in Cancers of Unknown Primary. J. Integr. Bioinform. 14(2) (2017) - [j27]Lasse Maretty, Jacob Malte Jensen, Bent Petersen, Jonas Andreas Sibbesen, Siyang Liu, Palle Villesen, Laurits Skov, Kirstine Belling, Christian Theil Have, José M. G. Izarzugaza, Marie Grosjean, Jette Bork-Jensen, Jakob Grove, Thomas D. Als, Shujia Huang, Yuqi Chang, Ruiqi Xu, Weijian Ye, Junhua Rao, Xiaosen Guo, Jihua Sun, Hongzhi Cao, Chen Ye, John van Beusekom, Thomas Espeseth, Esben N. Flindt, Rune M. Friborg, Anders E. Halager, Stephanie Le Hellard, Christina M. Hultman, Francesco Lescai, Shengting Li, Ole Lund, Peter Løngreen, Thomas Mailund, Maria Luisa Matey-Hernandez, Ole Mors, Christian N. S. Pedersen, Thomas Sicheritz-Pontén, Patrick F. Sullivan, Ali Syed, David Westergaard, Rachita Yadav, Ning Li, Xun Xu, Torben Hansen, Anders Krogh, Lars Bolund, Thorkild I. A. Sørensen, Oluf Pedersen, Ramneek Gupta, Simon Rasmussen, Søren Besenbacher, Anders D. Børglum, Jun Wang, Hans Eiberg, Karsten Kristiansen, Søren Brunak, Mikkel Heide Schierup:
Sequencing and de novo assembly of 150 genomes from Denmark as a population reference. Nat. 548(7665): 87-91 (2017) - 2016
- [j26]Michael Knudsen, Dan Søndergaard, Claus Tofting-Olesen, Frederik T. Hansen, Ditlev Egeskov Brodersen, Christian N. S. Pedersen:
Computational discovery of specificity-conferring sites in non-ribosomal peptide synthetases. Bioinform. 32(3): 325-329 (2016) - 2014
- [j25]Andreas Sand, Morten Kragelund Holt, Jens Johansen, Gerth Stølting Brodal, Thomas Mailund, Christian N. S. Pedersen:
tqDist: a library for computing the quartet and triplet distances between binary or general trees. Bioinform. 30(14): 2079-2080 (2014) - 2013
- [j24]Andreas Sand, Martin Kristiansen, Christian N. S. Pedersen, Thomas Mailund:
zipHMMlib: a highly optimised HMM library exploiting repetitions in the input to speed up the forward algorithm. BMC Bioinform. 14: 339 (2013) - [j23]Andreas Sand, Gerth Stølting Brodal, Rolf Fagerberg, Christian N. S. Pedersen, Thomas Mailund:
A practical O(n log2 n) time algorithm for computing the triplet distance on binary trees. BMC Bioinform. 14(S-2): S18 (2013) - [j22]Zsuzsanna Sükösd, Bjarne Knudsen, James W. J. Anderson, Ádám Novák, Jørgen Kjems, Christian N. S. Pedersen:
Characterising RNA secondary structure space using information entropy. BMC Bioinform. 14(S-2): S22 (2013) - 2012
- [j21]Rolf Hilker, Corinna Sickinger, Christian N. S. Pedersen, Jens Stoye:
UniMoG - a unifying framework for genomic distance calculation and sorting based on DCJ. Bioinform. 28(19): 2509-2511 (2012) - [j20]Zsuzsanna Sükösd, Bjarne Knudsen, Jørgen Kjems, Christian N. S. Pedersen:
PPfold 3.0: fast RNA secondary structure prediction using phylogeny and auxiliary data. Bioinform. 28(20): 2691-2692 (2012) - [j19]Vikas Gupta, Katharina Markmann, Christian N. S. Pedersen, Jens Stougaard, Stig U. Andersen:
shortran: a pipeline for small RNA-seq data analysis. Bioinform. 28(20): 2698-2700 (2012) - 2011
- [j18]Jesper Buus Nielsen, Anders K. Kristensen, Thomas Mailund, Christian N. S. Pedersen:
A sub-cubic time algorithm for computing the quartet distance between two general trees. Algorithms Mol. Biol. 6: 15 (2011) - [j17]Thomas Greve Kristensen, Jesper Buus Nielsen, Christian N. S. Pedersen:
Using Inverted Indices for Accelerating LINGO Calculations. J. Chem. Inf. Model. 51(3): 597-600 (2011) - [j16]Mette Alstrup Lie, René Thomsen, Christian N. S. Pedersen, Birgit Schiøtt, Mikael H. Christensen:
Molecular Docking with Ligand Attached Water Molecules. J. Chem. Inf. Model. 51(4): 909-917 (2011) - 2010
- [j15]Thomas Greve Kristensen, Jesper Buus Nielsen, Christian N. S. Pedersen:
A tree-based method for the rapid screening of chemical fingerprints. Algorithms Mol. Biol. 5: 9 (2010) - 2009
- [j14]Søren Besenbacher, Christian N. S. Pedersen, Thomas Mailund:
A fast algorithm for genome-wide haplotype pattern mining. BMC Bioinform. 10(S-1) (2009) - 2008
- [j13]Martin Stig Stissing, Thomas Mailund, Christian N. S. Pedersen, Gerth Stølting Brodal, Rolf Fagerberg:
Computing the All-Pairs Quartet Distance on a Set of Evolutionary Trees. J. Bioinform. Comput. Biol. 6(1): 37-50 (2008) - 2007
- [j12]Thomas Mailund, Christian N. S. Pedersen, Jonas Bardino, Brian Vinter, Henrik Hoey Karlsen:
Experiences with GeneRecon on MiG. Future Gener. Comput. Syst. 23(4): 580-586 (2007) - 2006
- [j11]Chris Christiansen, Thomas Mailund, Christian N. S. Pedersen, Martin Randers, Martin Stig Stissing:
Fast calculation of the quartet distance between trees of arbitrary degrees. Algorithms Mol. Biol. 1 (2006) - [j10]Thomas Mailund, Mikkel H. Schierup, Christian N. S. Pedersen, Jesper N. Madsen, Jotun Hein, Leif Schauser:
GeneRecon - a coalescent based tool for fine-scale association mapping. Bioinform. 22(18): 2317-2318 (2006) - [j9]Thomas Mailund, Gerth Stølting Brodal, Rolf Fagerberg, Christian N. S. Pedersen, Derek Phillips:
Recrafting the neighbor-joining method. BMC Bioinform. 7: 29 (2006) - 2005
- [j8]Søren Besenbacher, Thomas Mailund, Lasse Westh-Nielsen, Christian N. S. Pedersen:
RBT - a tool for building refined Buneman trees. Bioinform. 21(8): 1711-1712 (2005) - [j7]Thomas Mailund, Mikkel H. Schierup, Christian N. S. Pedersen, Peter J. M. Mechlenborg, Jesper N. Madsen, Leif Schauser:
CoaSim: A flexible environment for simulating genetic data under coalescent models. BMC Bioinform. 6: 252 (2005) - 2004
- [j6]Gerth Stølting Brodal, Rolf Fagerberg, Christian N. S. Pedersen:
Computing the Quartet Distance between Evolutionary Trees in Time O(n log n). Algorithmica 38(2): 377-395 (2004) - [j5]Thomas Mailund, Christian N. S. Pedersen:
QDist-quartet distance between evolutionary trees. Bioinform. 20(10): 1636-1637 (2004) - [j4]Thomas Mailund, Christian N. S. Pedersen:
QuickJoin - fast neighbour-joining tree reconstruction. Bioinform. 20(17): 3261-3262 (2004) - 2002
- [j3]Rune B. Lyngsø, Christian N. S. Pedersen:
The consensus string problem and the complexity of comparing hidden Markov models. J. Comput. Syst. Sci. 65(3): 545-569 (2002) - 2000
- [j2]Rune B. Lyngsø, Christian N. S. Pedersen:
RNA Pseudoknot Prediction in Energy-Based Models. J. Comput. Biol. 7(3-4): 409-427 (2000) - 1999
- [j1]Rune B. Lyngsø, Michael Zuker, Christian N. S. Pedersen:
Fast evaluation of internal loops in RNA secondary structure prediction. Bioinform. 15(6): 440-445 (1999)
Conference and Workshop Papers
- 2013
- [c27]Gerth Stølting Brodal, Rolf Fagerberg, Thomas Mailund, Christian N. S. Pedersen, Andreas Sand:
Efficient algorithms for computing the triplet and quartet distance between trees of arbitrary degree. SODA 2013: 1814-1832 - 2011
- [c26]Martin Simonsen, Christian N. S. Pedersen, Mikael H. Christensen, René Thomsen:
GPU-accelerated high-accuracy molecular docking using guided differential evolution: real world applications. GECCO 2011: 1803-1810 - [c25]Martin Simonsen, Christian N. S. Pedersen:
Rapid computation of distance estimators from nucleotide and amino acid alignments. SAC 2011: 89-93 - 2010
- [c24]Martin Simonsen, Thomas Mailund, Christian N. S. Pedersen:
Building Very Large Neighbour-joining Trees. BIOINFORMATICS 2010: 26-32 - [c23]Martin Simonsen, Thomas Mailund, Christian N. S. Pedersen:
Inference of Large Phylogenies Using Neighbour-Joining. BIOSTEC (Selected Papers) 2010: 334-344 - [c22]Thomas Greve Kristensen, Christian N. S. Pedersen:
Data Structures for Accelerating Tanimoto Queries on Real Valued Vectors. WABI 2010: 28-39 - 2009
- [c21]Thomas Greve Kristensen, Christian N. S. Pedersen:
Optimal Overlay of Ligands with Flexible Bonds Using Differential Evolution. IJCBS 2009: 331-334 - [c20]Thomas Mailund, Jesper Buus Nielsen, Christian N. S. Pedersen:
A Quadratic Time Algorithm for Computing the Quartet Distance between Two General Trees. IJCBS 2009: 565-568 - [c19]Thomas Greve Kristensen, Jesper Buus Nielsen, Christian N. S. Pedersen:
A Tree Based Method for the Rapid Screening of Chemical Fingerprints. WABI 2009: 194-205 - 2008
- [c18]Martin Simonsen, Thomas Mailund, Christian N. S. Pedersen:
Rapid Neighbour-Joining. WABI 2008: 113-122 - 2007
- [c17]Martin Stig Stissing, Thomas Mailund, Christian N. S. Pedersen, Gerth Stølting Brodal, Rolf Fagerberg:
Computing the All-Pairs Quartet Distance on a Set of Evolutionary Trees. APBC 2007: 91-100 - [c16]Martin Stig Stissing, Christian N. S. Pedersen, Thomas Mailund, Gerth Stølting Brodal, Rolf Fagerberg:
Computing the Quartet Distance Between Evolutionary Trees of Bounded Degree. APBC 2007: 101-110 - 2005
- [c15]Thomas Mailund, Christian N. S. Pedersen, Jonas Bardino, Brian Vinter, Henrik Hoey Karlsen:
Initial Experiences with GeneRecon on MiG. GCA 2005: 141-146 - [c14]Chris Christiansen, Thomas Mailund, Christian N. S. Pedersen, Martin Randers:
Computing the Quartet Distance Between Trees of Arbitrary Degree. WABI 2005: 77-88 - 2003
- [c13]Gerth Stølting Brodal, Rolf Fagerberg, Anna Östlin, Christian N. S. Pedersen, S. Srinivasa Rao:
Computing Refined Buneman Trees in Cubic Time. WABI 2003: 259-270 - 2002
- [c12]Gerth Stølting Brodal, Rune B. Lyngsø, Anna Östlin, Christian N. S. Pedersen:
Solving the String Statistics Problem in Time O(n log n). ICALP 2002: 728-739 - [c11]Christian N. S. Pedersen, Tejs Scharling:
Comparative Methods for Gene Structure Prediction in Homologous Sequences. WABI 2002: 220-234 - 2001
- [c10]Gerth Stølting Brodal, Rolf Fagerberg, Christian N. S. Pedersen, Anna Östlin:
The Complexity of Constructing Evolutionary Trees Using Experiments. ICALP 2001: 140-151 - [c9]Rune B. Lyngsø, Christian N. S. Pedersen:
Complexity of Comparing Hidden Markov Models. ISAAC 2001: 416-428 - [c8]Gerth Stølting Brodal, Rolf Fagerberg, Christian N. S. Pedersen:
Computing the Quartet Distance between Evolutionary Trees in Time O(n log2 n). ISAAC 2001: 731-742 - [c7]Arun K. Jagota, Rune B. Lyngsø, Christian N. S. Pedersen:
Comparing a Hidden Markov Model and a Stochastic Context-Free Grammar. WABI 2001: 69-94 - 2000
- [c6]Gerth Stølting Brodal, Christian N. S. Pedersen:
Finding Maximal Quasiperiodicities in Strings. CPM 2000: 397-411 - [c5]Rune B. Lyngsø, Christian N. S. Pedersen:
Pseudoknots in RNA secondary structures. RECOMB 2000: 201-209 - 1999
- [c4]Gerth Stølting Brodal, Rune B. Lyngsø, Christian N. S. Pedersen, Jens Stoye:
Finding Maximal Pairs with Bounded Gap. CPM 1999: 134-149 - [c3]Rune B. Lyngsø, Christian N. S. Pedersen, Henrik Nielsen:
Metrics and Similarity Measures for Hidden Markov Models. ISMB 1999: 178-186 - [c2]Rune B. Lyngsø, Michael Zuker, Christian N. S. Pedersen:
Internal loops in RNA secondary structure prediction. RECOMB 1999: 260-267 - 1998
- [c1]Christian N. S. Pedersen, Rune B. Lyngsø, Jotun Hein:
Comparison of Coding DNA. CPM 1998: 153-173
Parts in Books or Collections
- 2013
- [p1]Martin Simonsen, Mikael H. Christensen, René Thomsen, Christian N. S. Pedersen:
GPU-Accelerated High-Accuracy Molecular Docking Using Guided Differential Evolution. Massively Parallel Evolutionary Computation on GPGPUs 2013: 349-367
Editorship
- 2016
- [e1]Martin C. Frith, Christian Nørgaard Storm Pedersen:
Algorithms in Bioinformatics - 16th International Workshop, WABI 2016, Aarhus, Denmark, August 22-24, 2016. Proceedings. Lecture Notes in Computer Science 9838, Springer 2016, ISBN 978-3-319-43680-7 [contents]
Coauthor Index
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