Jakob Hull Havgaard
Jakob Hull Havgaard
University of Copenhagen
Verified email at rth.dk - Homepage
Cited by
Cited by
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
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
Multiple structural alignment and clustering of RNA sequences
E Torarinsson, JH Havgaard, J Gorodkin
Bioinformatics 23 (8), 926-932, 2007
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
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
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 (4), 1-16, 2007
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
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
Semiautomated improvement of RNA alignments
ES Andersen, A Lind-Thomsen, B Knudsen, SE Kristensen, JH Havgaard, ...
Rna 13 (11), 1850-1859, 2007
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), 1-13, 2018
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
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
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
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), 1-27, 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
RNA structural alignments, part I: Sankoff-based approaches for structural alignments
JH Havgaard, J Gorodkin
RNA Sequence, Structure, and Function: Computational and Bioinformatic …, 2014
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
Comparative ncRNA gene and structure prediction using Foldalign and FoldalignM
J Havgaard, S Kaur, J Gorodkin
Current protocols in bioinformatics 39 (1), 12.11. 1-12.11. 15, 2012
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
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
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