Comparison of Coding DNA. - Christian N. S. Pedersen; Rune B. Lyngsø; Jotun Hein (CPM, 1998)

Finding Maximal Pairs with Bounded Gap. - Gerth Stølting Brodal; Rune B. Lyngsø; Christian N. S. Pedersen; Jens Stoye (CPM, 1999)

Metrics and Similarity Measures for Hidden Markov Models. - Rune B. Lyngsø; Christian N. S. Pedersen; Henrik Nielsen (ISMB, 1999)

Internal loops in RNA secondary structure prediction. - Rune B. Lyngsø; Michael Zuker; Christian N. S. Pedersen (RECOMB, 1999)

Fast evaluation of internal loops in RNA secondary structure prediction. - Rune B. Lyngsø; Michael Zuker; Christian N. S. Pedersen (Bioinform., 1999)

Finding Maximal Quasiperiodicities in Strings. - Gerth Stølting Brodal; Christian N. S. Pedersen (CPM, 2000)

Pseudoknots in RNA secondary structures. - Rune B. Lyngsø; Christian N. S. Pedersen (RECOMB, 2000)

RNA Pseudoknot Prediction in Energy-Based Models. - Rune B. Lyngsø; Christian N. S. Pedersen (J. Comput. Biol., 2000)

The Complexity of Constructing Evolutionary Trees Using Experiments. - Gerth Stølting Brodal; Rolf Fagerberg; Christian N. S. Pedersen; Anna Östlin (ICALP, 2001)

Computing the Quartet Distance between Evolutionary Trees in Time O(n log2 n). - Gerth Stølting Brodal; Rolf Fagerberg; Christian N. S. Pedersen (ISAAC, 2001)

Complexity of Comparing Hidden Markov Models. - Rune B. Lyngsø; Christian N. S. Pedersen (ISAAC, 2001)

Comparing a Hidden Markov Model and a Stochastic Context-Free Grammar. - Arun K. Jagota; Rune B. Lyngsø; Christian N. S. Pedersen (WABI, 2001)

Solving the String Statistics Problem in Time O(n log n). - Gerth Stølting Brodal; Rune B. Lyngsø; Anna Östlin; Christian N. S. Pedersen (ICALP, 2002)

Comparative Methods for Gene Structure Prediction in Homologous Sequences. - Christian N. S. Pedersen; Tejs Scharling (WABI, 2002)

The consensus string problem and the complexity of comparing hidden Markov models. - Rune B. Lyngsø; Christian N. S. Pedersen (J. Comput. Syst. Sci., 2002)

Computing Refined Buneman Trees in Cubic Time. - Gerth Stølting Brodal; Rolf Fagerberg; Anna Östlin; Christian N. S. Pedersen; S. Srinivasa Rao 001 (WABI, 2003)

Computing the Quartet Distance between Evolutionary Trees in Time O(n log n). - Gerth Stølting Brodal; Rolf Fagerberg; Christian N. S. Pedersen (Algorithmica, 2004)

QDist-quartet distance between evolutionary trees. - Thomas Mailund; Christian N. S. Pedersen (Bioinform., 2004)

QuickJoin - fast neighbour-joining tree reconstruction. - Thomas Mailund; Christian N. S. Pedersen (Bioinform., 2004)

Initial Experiences with GeneRecon on MiG. - Thomas Mailund; Christian N. S. Pedersen; Jonas Bardino; Brian Vinter; Henrik Hoey Karlsen (GCA, 2005)

Computing the Quartet Distance Between Trees of Arbitrary Degree. - Chris Christiansen; Thomas Mailund; Christian N. S. Pedersen; Martin Randers (WABI, 2005)

RBT - a tool for building refined Buneman trees. - Søren Besenbacher; Thomas Mailund; Lasse Westh-Nielsen; Christian N. S. Pedersen (Bioinform., 2005)

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 Bioinform., 2005)

Fast calculation of the quartet distance between trees of arbitrary degrees. - Chris Christiansen; Thomas Mailund; Christian N. S. Pedersen; Martin Randers; Martin Stig Stissing (Algorithms Mol. Biol., 2006)

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 (Bioinform., 2006)

Recrafting the neighbor-joining method. - Thomas Mailund; Gerth Stølting Brodal; Rolf Fagerberg; Christian N. S. Pedersen; Derek Phillips (BMC Bioinform., 2006)

Computing the Quartet Distance Between Evolutionary Trees of Bounded Degree. - Martin Stig Stissing; Christian N. S. Pedersen; Thomas Mailund; Gerth Stølting Brodal; Rolf Fagerberg (APBC, 2007)

Experiences with GeneRecon on MiG. - Thomas Mailund; Christian N. S. Pedersen; Jonas Bardino; Brian Vinter; Henrik Hoey Karlsen (Future Gener. Comput. Syst., 2007)

Rapid Neighbour-Joining. - Martin Simonsen; Thomas Mailund; Christian N. S. Pedersen (WABI, 2008)

Computing the All-Pairs Quartet Distance on a Set of Evolutionary Trees. - Martin Stig Stissing; Thomas Mailund; Christian N. S. Pedersen; Gerth Stølting Brodal; Rolf Fagerberg (J. Bioinform. Comput. Biol., 2008)

Optimal Overlay of Ligands with Flexible Bonds Using Differential Evolution. - Thomas Greve Kristensen; Christian N. S. Pedersen (IJCBS, 2009)

A Quadratic Time Algorithm for Computing the Quartet Distance between Two General Trees. - Thomas Mailund; Jesper Buus Nielsen; Christian N. S. Pedersen (IJCBS, 2009)

A fast algorithm for genome-wide haplotype pattern mining. - Søren Besenbacher; Christian N. S. Pedersen; Thomas Mailund (BMC Bioinform., 2009)

Building Very Large Neighbour-joining Trees. - Martin Simonsen; Thomas Mailund; Christian N. S. Pedersen (BIOINFORMATICS, 2010)

Inference of Large Phylogenies Using Neighbour-Joining. - Martin Simonsen; Thomas Mailund; Christian N. S. Pedersen (BIOSTEC (Selected Papers), 2010)

Data Structures for Accelerating Tanimoto Queries on Real Valued Vectors. - Thomas Greve Kristensen; Christian N. S. Pedersen (WABI, 2010)

A tree-based method for the rapid screening of chemical fingerprints. - Thomas Greve Kristensen; Jesper Buus Nielsen; Christian N. S. Pedersen (Algorithms Mol. Biol., 2010)

GPU-accelerated high-accuracy molecular docking using guided differential evolution: real world applications. - Martin Simonsen; Christian N. S. Pedersen; Mikael H. Christensen; René Thomsen (GECCO, 2011)

Rapid computation of distance estimators from nucleotide and amino acid alignments. - Martin Simonsen; Christian N. S. Pedersen (SAC, 2011)

A sub-cubic time algorithm for computing the quartet distance between two general trees. - Jesper Buus Nielsen; Anders K. Kristensen; Thomas Mailund; Christian N. S. Pedersen (Algorithms Mol. Biol., 2011)

Using Inverted Indices for Accelerating LINGO Calculations. - Thomas Greve Kristensen; Jesper Buus Nielsen; Christian N. S. Pedersen (J. Chem. Inf. Model., 2011)

Molecular Docking with Ligand Attached Water Molecules. - Mette Alstrup Lie; René Thomsen; Christian N. S. Pedersen; Birgit Schiøtt; Mikael H. Christensen (J. Chem. Inf. Model., 2011)

shortran: a pipeline for small RNA-seq data analysis. - Vikas Gupta; Katharina Markmann; Christian N. S. Pedersen; Jens Stougaard; Stig U. Andersen (Bioinform., 2012)

UniMoG - a unifying framework for genomic distance calculation and sorting based on DCJ. - Rolf Hilker; Corinna Sickinger; Christian N. S. Pedersen; Jens Stoye (Bioinform., 2012)

PPfold 3.0: fast RNA secondary structure prediction using phylogeny and auxiliary data. - Zsuzsanna Sükösd; Bjarne Knudsen; Jørgen Kjems; Christian N. S. Pedersen (Bioinform., 2012)

Efficient algorithms for computing the triplet and quartet distance between trees of arbitrary degree. - Gerth Stølting Brodal; Rolf Fagerberg; Thomas Mailund; Christian N. S. Pedersen; Andreas Sand (SODA, 2013)

A practical O(n log2 n) time algorithm for computing the triplet distance on binary trees. - Andreas Sand; Gerth Stølting Brodal; Rolf Fagerberg; Christian N. S. Pedersen; Thomas Mailund (BMC Bioinform., 2013)

zipHMMlib: a highly optimised HMM library exploiting repetitions in the input to speed up the forward algorithm. - Andreas Sand; Martin Kristiansen; Christian N. S. Pedersen; Thomas Mailund (BMC Bioinform., 2013)

Characterising RNA secondary structure space using information entropy. - Zsuzsanna Sükösd; Bjarne Knudsen; James W. J. Anderson; Ádám Novák; Jørgen Kjems; Christian N. S. Pedersen (BMC Bioinform., 2013)

GPU-Accelerated High-Accuracy Molecular Docking Using Guided Differential Evolution. - Martin Simonsen; Mikael H. Christensen; René Thomsen; Christian N. S. Pedersen (Massively Parallel Evolutionary Computation on GPGPUs, 2013)

tqDist: a library for computing the quartet and triplet distances between binary or general trees. - Andreas Sand; Morten Kragelund Holt; Jens Johansen; Gerth Stølting Brodal; Thomas Mailund; Christian N. S. Pedersen (Bioinform., 2014)

Computational discovery of specificity-conferring sites in non-ribosomal peptide synthetases. - Michael Knudsen; Dan Søndergaard; Claus Tofting-Olesen; Frederik T. Hansen; Ditlev Egeskov Brodersen; Christian N. S. Pedersen (Bioinform., 2016)

Prediction of Primary Tumors in Cancers of Unknown Primary. - Dan Søndergaard; Svend V. Nielsen; Christian N. S. Pedersen; Søren Besenbacher (J. Integr. Bioinform., 2017)

Sequencing and de novo assembly of 150 genomes from Denmark as a population reference. - Lasse Maretty; Jacob Malte Jensen; Bent Petersen; Jonas Andreas Sibbesen; Siyang Liu 007; Palle Villesen; Laurits Skov; Kirstine Belling; Christian Theil Have; José M. G. Izarzugaza; Marie Grosjean; Jette Bork-Jensen; et al. (Nat., 2017)

Benchmarking the HLA typing performance of Polysolver and Optitype in 50 Danish parental trios. - Maria Luisa Matey-Hernandez; Lasse Maretty; Jacob Malte Jensen; Bent Petersen; Jonas Andreas Sibbesen; Siyang Liu 007; Palle Villesen; Laurits Skov; Kirstine Belling; Christian Theil Have; José M. G. Izarzugaza; Marie Grosjean; et al. (BMC Bioinform., 2018)