| RNA pseudoknot prediction in energy-based models RB Lyngsø, CNS Pedersen Journal of computational biology 7 (3-4), 409-427, 2000 | 418 | 2000 |
| HydDB: a web tool for hydrogenase classification and analysis D Søndergaard, CNS Pedersen, C Greening Scientific reports 6 (1), 1-8, 2016 | 329 | 2016 |
| Fast evaluation of internal loops in RNA secondary structure prediction. RB Lyngs√∏, M Zuker, CN Pedersen Bioinformatics (Oxford, England) 15 (6), 440-445, 1999 | 193 | 1999 |
| Novel variation and de novo mutation rates in population-wide de novo assembled Danish trios S Besenbacher, S Liu, JMG Izarzugaza, J Grove, K Belling, J Bork-Jensen, ... Nature communications 6 (1), 5969, 2015 | 174 | 2015 |
| Rapid neighbour-joining M Simonsen, T Mailund, CNS Pedersen Algorithms in Bioinformatics: 8th International Workshop, WABI 2008 …, 2008 | 170 | 2008 |
| Sequencing and de novo assembly of 150 genomes from Denmark as a population reference L Maretty, JM Jensen, B Petersen, JA Sibbesen, S Liu, P Villesen, L Skov, ... Nature 548 (7665), 87-91, 2017 | 146 | 2017 |
| Pseudoknots in RNA secondary structures RB Lyngsø, CNS Pedersen Proceedings of the fourth annual international conference on Computational …, 2000 | 126 | 2000 |
| Evolution of plant P-type ATPases CNS Pedersen, KB Axelsen, JF Harper, MG Palmgren Frontiers in plant science 3, 31, 2012 | 109 | 2012 |
| Metrics and similarity measures for hidden Markov models RB Lyngso, CN Pedersen, H Nielsen Proceedings of ISMB 99, 178-186, 1999 | 105 | 1999 |
| Molecular docking with ligand attached water molecules MA Lie, R Thomsen, CNS Pedersen, B Schiøtt, MH Christensen Journal of chemical information and modeling 51 (4), 909-917, 2011 | 93 | 2011 |
| Finding maximal pairs with bounded gap GS Brodal, RB Lyngsø, CNS Pedersen, J Stoye Combinatorial Pattern Matching: 10th Annual Symposium, CPM 99 Warwick …, 1999 | 91 | 1999 |
| CoaSim: a flexible environment for simulating genetic data under coalescent models T Mailund, MH Schierup, CNS Pedersen, PJM Mechlenborg, JN Madsen, ... BMC bioinformatics 6, 1-6, 2005 | 82 | 2005 |
| Computing the Quartet Distance between Evolutionary Trees in Time O(n log n) GS Brodal, R Fagerberg, CNS Pedersen Algorithmica 38, 377-395, 2004 | 81 | 2004 |
| The consensus string problem and the complexity of comparing hidden Markov models RB Lyngsø, CNS Pedersen Journal of Computer and System Sciences 65 (3), 545-569, 2002 | 69 | 2002 |
| Internal loops in RNA secondary structure prediction RB Lyngsø, M Zuker, CNS Pedersen Proceedings of the third annual international conference on Computational …, 1999 | 65 | 1999 |
| tqDist: a library for computing the quartet and triplet distances between binary or general trees A Sand, MK Holt, J Johansen, GS Brodal, T Mailund, CNS Pedersen Bioinformatics 30 (14), 2079-2080, 2014 | 62 | 2014 |
| Recrafting the neighbor-joining method T Mailund, GS Brodal, R Fagerberg, CNS Pedersen, D Phillips BMC bioinformatics 7, 1-8, 2006 | 59 | 2006 |
| A tree-based method for the rapid screening of chemical fingerprints TG Kristensen, J Nielsen, CNS Pedersen Algorithms for Molecular Biology 5 (1), 1-10, 2010 | 57 | 2010 |
| Recursions for statistical multiple alignment J Hein, JL Jensen, CNS Pedersen Proceedings of the National Academy of Sciences 100 (25), 14960-14965, 2003 | 55 | 2003 |
| PPfold 3.0: fast RNA secondary structure prediction using phylogeny and auxiliary data Z Sükösd, B Knudsen, J Kjems, CNS Pedersen Bioinformatics 28 (20), 2691-2692, 2012 | 54 | 2012 |
