| Thousands of corresponding human and mouse genomic regions unalignable in primary sequence contain common RNA structure E Torarinsson, M Sawera, JH Havgaard, M Fredholm, J Gorodkin Genome research 16 (7), 885-889, 2006 | 217 | 2006 |
| Multiple structural alignment and clustering of RNA sequences E Torarinsson, JH Havgaard, J Gorodkin Bioinformatics 23 (8), 926-932, 2007 | 204 | 2007 |
| Pairwise local structural alignment of RNA sequences with sequence similarity less than 40% JH Havgaard, RB Lyngsø, GD Stormo, J Gorodkin Bioinformatics 21 (9), 1815-1824, 2005 | 201 | 2005 |
| CRISPR-Cas9 off-targeting assessment with nucleic acid duplex energy parameters F Alkan, A Wenzel, C Anthon, JH Havgaard, J Gorodkin Genome biology 19, 1-13, 2018 | 162 | 2018 |
| Fast pairwise structural RNA alignments by pruning of the dynamical programming matrix JH Havgaard, E Torarinsson, J Gorodkin PLOS computational biology 3 (10), e193, 2007 | 156 | 2007 |
| The foldalign web server for pairwise structural RNA alignment and mutual motif search JH Havgaard, RB Lyngsø, J Gorodkin Nucleic acids research 33 (suppl_2), W650-W653, 2005 | 109 | 2005 |
| Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 expressed sequence tags J Gorodkin, S Cirera, J Hedegaard, MJ Gilchrist, F Panitz, C Jørgensen, ... Genome biology 8, 1-16, 2007 | 82 | 2007 |
| Structural profiles of human miRNA families from pairwise clustering B Kaczkowski, E Torarinsson, K Reiche, JH Havgaard, PF Stadler, ... Bioinformatics 25 (3), 291-294, 2009 | 79 | 2009 |
| De novo prediction of structured RNAs from genomic sequences J Gorodkin, IL Hofacker, E Torarinsson, Z Yao, JH Havgaard, WL Ruzzo Trends in biotechnology 28 (1), 9-19, 2010 | 76 | 2010 |
| Semiautomated improvement of RNA alignments ES Andersen, A Lind-Thomsen, B Knudsen, SE Kristensen, JH Havgaard, ... Rna 13 (11), 1850-1859, 2007 | 54 | 2007 |
| Foldalign 2.5: multithreaded implementation for pairwise structural RNA alignment D Sundfeld, JH Havgaard, ACMA de Melo, J Gorodkin Bioinformatics 32 (8), 1238-1240, 2016 | 47 | 2016 |
| SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation F Panitz, H Stengaard, H Hornshøj, J Gorodkin, J Hedegaard, S Cirera, ... Bioinformatics 23 (13), i387-i391, 2007 | 41 | 2007 |
| RNA structural alignments, part I: Sankoff-based approaches for structural alignments JH Havgaard, J Gorodkin RNA Sequence, Structure, and Function: Computational and Bioinformatic …, 2014 | 35 | 2014 |
| RNAscClust: clustering RNA sequences using structure conservation and graph based motifs M Miladi, A Junge, F Costa, SE Seemann, JH Havgaard, J Gorodkin, ... Bioinformatics 33 (14), 2089-2096, 2017 | 33 | 2017 |
| Structured RNAs and synteny regions in the pig genome C Anthon, H Tafer, JH Havgaard, B Thomsen, J Hedegaard, SE Seemann, ... BMC genomics 15, 1-27, 2014 | 27 | 2014 |
| MicroRNA sequence motifs reveal asymmetry between the stem arms J Gorodkin, JH Havgaard, M Ensterö, M Sawera, P Jensen, M Öhman, ... Computational Biology and Chemistry 30 (4), 249-254, 2006 | 19 | 2006 |
| Assessing the miRNA sponge potential of RUNX1T1 in t (8; 21) acute myeloid leukemia A Junge, R Zandi, JH Havgaard, J Gorodkin, JB Cowland Gene 615, 35-40, 2017 | 14 | 2017 |
| Epigenetic and transcriptomic characterization of pure adipocyte fractions from obese pigs identifies candidate pathways controlling metabolism MJ Jacobsen, JH Havgaard, C Anthon, CMJ Mentzel, S Cirera, PM Krogh, ... Frontiers in Genetics 10, 1268, 2019 | 13 | 2019 |
| CUDA-Sankoff: using GPU to accelerate the pairwise structural RNA alignment D Sundfeld, JH Havgaard, J Gorodkin, ACMA De Melo 2017 25th Euromicro International Conference on Parallel, Distributed and …, 2017 | 9 | 2017 |
| Using GPU to accelerate the pairwise structural RNA alignment with base pair probabilities D Sundfeld, G Teodoro, JH Havgaard, J Gorodkin, ACMA Melo Concurrency and Computation: Practice and Experience 32 (10), e5468, 2020 | 8 | 2020 |
