Jakob Hull Havgaard
Associate Professor
Preclinical Disease Biology
Ridebanevej 9, 1870 Frederiksberg C
- Published
CRISPR-Cas9 off-targeting assessment with nucleic acid duplex energy parameters
Alkan, F., Wenzel, Anne, Anthon, Christian, Havgaard, Jakob Hull & Gorodkin, Jan, 2018, In: Genome Biology. 19, 13 p., 177.Research output: Contribution to journal › Journal article › Research › peer-review
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Semiautomated improvement of RNA alignments
Andersen, E. S., Lind-Thomsen, A., Knudsen, B., Kristensen, S. E., Havgaard, Jakob Hull, Torarinsson, E., Larsen, N., Zwieb, C., Sestoft, P., Kjems, J. & Gorodkin, Jan, 2007, In: RNA: A publication of the RNA Society. 13, 11, p. 1850-1859 10 p.Research output: Contribution to journal › Journal article › Research › peer-review
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Structured RNAs and synteny regions in the pig genome
Anthon, Christian, Tafer, H., Havgaard, Jakob Hull, Thomsen, B., Hedegaard, J., Seemann, Ernst Stefan, Pundhir, Sachin, Kehr, S., Bartschat, S., Nielsen, M., Nielsen, R. O., Fredholm, Merete, Stadler, P. F. & Gorodkin, Jan, 2014, In: BMC Genomics. 15, 27 p., 459.Research output: Contribution to journal › Journal article › Research › peer-review
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The Bacillaceae-1 RNA motif comprises two distinct classes
González-Tortuero, E., Anthon, Christian, Havgaard, Jakob Hull, Geissler, Adrian Sven, Breüner, A., Hjort, C., Gorodkin, Jan & Seemann, Ernst Stefan, 2022, In: Gene. 841, 146756.Research output: Contribution to journal › Journal article › Research › peer-review
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Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 expressed sequence tags
Gorodkin, J., Cirera, S., Hedegaard, J., Gilchrist, M. J., Panitz, F., Jørgensen, C., Scheibye-Knudsen, K., Arvin, T., Lumholdt, S., Sawera, M., Green, T., Nielsen, B., Havgaard, J. H., Rosenkilde, C., Wang, J., Li, H., Li, R., Liu, B., Hu, S., Dong, W. & 16 others, , 2007, In: Genome Biology. 8, R45, p. R45 16 p.Research output: Contribution to journal › Journal article › Research › peer-review
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De novo prediction of structured RNAs from genomic sequences
Gorodkin, Jan, Hofacker, I. L., Þórarinsson, E., Yao, Z., Havgaard, Jakob Hull & Ruzzo, W. L., 2010, In: Trends in Biotechnology. 28, 1, p. 9-19 11 p.Research output: Contribution to journal › Journal article › Research › peer-review
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MicroRNA sequence motifs reveal asymmetry between the stem arms
Gorodkin, Jan, Havgaard, Jakob Hull, Ensterö, M., Sawera, M., Jensen, P., Öhman, M. & Fredholm, Merete, 2006, In: Computational Biology and Chemistry. 30, 4, p. 249-254 6 p.Research output: Contribution to journal › Journal article › Research › peer-review
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Fast pairwise structural RNA alignments by pruning of the dynamical programming matrix
Havgaard, Jakob Hull, Torarinsson, E. & Gorodkin, Jan, 2007, In: PLoS Computational Biology. 3, 10, p. 1896-1908 13 p.Research output: Contribution to journal › Journal article › Research › peer-review
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Comparative ncRNA gene and structure prediction using Foldalign and FoldalignM
Havgaard, Jakob Hull, Kaur, S. & Gorodkin, Jan, 2012, In: Current Protocols in Bioinformatics. 39, p. 12.11.1-12.11.15 5 p.Research output: Contribution to journal › Journal article › Research › peer-review
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RNA Structural Alignments, Part I: Sankoff-Based Approaches for Structural Alignments
Havgaard, Jakob Hull & Gorodkin, Jan, 2014, RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods. Gorodkin, J. & Ruzzo, W. L. (eds.). p. 275-90 16 p. (Methods in molecular biology (Clifton, N.J.)).Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review
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Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%
Havgaard, Jakob Hull, Lyngsø, R. B., Stormo, G. D. & Gorodkin, Jan, 2005, In: Bioinformatics. 21, 9, p. 1815-1824 10 p.Research output: Contribution to journal › Journal article › Research › peer-review
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The FOLDALIGN web server for pairwise structural RNA alignment and mutual motif search
Havgaard, Jakob Hull, Lyngsø, R. B. & Gorodkin, Jan, 2005, In: Nucleic Acids Research. 33, p. W650-W653 4 p.Research output: Contribution to journal › Journal article › Research › peer-review
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Structural alignment of RNA with FOLDALIGN
Havgaard, Jakob Hull, 2007, Frederiksberg: Center for Skov, Landskab og Planlægning/Københavns Universitet. 128 p.Research output: Book/Report › Ph.D. thesis › Research
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Optimizing RNA structures by sequence extensions using RNAcop
Hecker, N., Christensen-Dalsgaard, M., Seemann, Ernst Stefan, Havgaard, Jakob Hull, Stadler, P. F., Hofacker, I. L., Nielsen, Henrik & Gorodkin, Jan, 2015, In: Nucleic Acids Research. 43, 17, p. 8135-8145 11 p.Research output: Contribution to journal › Journal article › Research › peer-review
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Adipocyte gene expression and DNA methylation patterns differ significantly between lean and obese pigs
Jacobsen, M. J., Havgaard, Jakob Hull, Mentzel, Caroline M. Junker, Sørensen, P. M., Pundhir, Sachin, Anthon, Christian, Karlskov-Mortensen, Peter, Bruun, Camilla Vibeke Sichlau, Cirera, Susanna, Gorodkin, Jan, Jørgensen, Claus Bøttcher, Barrès, Romain & Fredholm, Merete, 9 Nov 2016, In: Journal of Animal Science. 94, Supplement 4, p. 46-47 2 p., P2019.Research output: Contribution to journal › Conference abstract in journal › Research › peer-review
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Epigenetic and Transcriptomic Characterization of Pure Adipocyte Fractions From Obese Pigs Identifies Candidate Pathways Controlling Metabolism
Jacobsen, M. J., Havgaard, Jakob Hull, Anthon, Christian, Mentzel, Caroline M. Junker, Cirera, Susanna, Krogh, P. M., Pundhir, Sachin, Karlskov-Mortensen, Peter, Bruun, C. S., Lesnik, P., Guerin, M., Gorodkin, Jan, Jørgensen, Claus Bøttcher, Fredholm, Merete & Barrès, Romain, 2019, In: Frontiers in Genetics. 10, 13 p., 1268.Research output: Contribution to journal › Journal article › Research › peer-review
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Assessing the miRNA sponge potential of RUNX1T1 in t(8;21) acute myeloid leukemia
Junge, A., Zandi, R., Havgaard, Jakob Hull, Gorodkin, Jan & Cowland, J. B., 2017, In: Gene. 615, p. 35-40 6 p.Research output: Contribution to journal › Journal article › Research › peer-review
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Structural profiles of human miRNA families from pairwise clustering
Kaczkowski, B., Þórarinsson, E., Reiche, K., Havgaard, Jakob Hull, Stadler, P. F. & Gorodkin, Jan, 2009, In: Bioinformatics. 25, 3, p. 291-294 4 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Alignment-free comparative genomic screen for structured RNAs using coarse-grained secondary structure dot plots
Kato, Y., Gorodkin, Jan & Havgaard, Jakob Hull, Dec 2017, In: BMC Genomics. 18, 1, 935.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
RNAscClust: Clustering RNA sequences using structure conservation and graph based motifs
Miladi, M., Junge, A., Costa, F., Seemann, Ernst Stefan, Havgaard, Jakob Hull, Gorodkin, Jan & Backofen, R., 2017, In: Bioinformatics. 33, 14, p. 2089-2096 8 p.Research output: Contribution to journal › Journal article › Research › peer-review
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SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation
Panitz, F., Stengaard, H., Hornshøj, H., Gorodkin, J., Hedegaard, J., Cirera, S., Thomsen, B. S., Madsen, L. B., Høj, A., Vingborg, R., Zahn, B., Wang, X., Wang, X., Wernersson, R., Jørgensen, C. B., Scheibye-Knudsen, K., Arvin, T., Lumholdt, S., Sawera, M., Green, T. & 5 others, , 2007, In: Bioinformatics. 23, 13, p. i387-91 5 p.Research output: Contribution to journal › Journal article › Research › peer-review
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Using GPU to accelerate the pairwise structural RNA alignment with base pair probabilities
Sundfeld, D., Teodoro, G., Havgaard, Jakob Hull, Gorodkin, Jan & Melo, A. C. M. A., 2020, In: Concurrency Computation. 32, 10, e5468.Research output: Contribution to journal › Journal article › Research › peer-review
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CUDA-Sankoff: Using GPU to Accelerate the Pairwise Structural RNA Alignment
Sundfeld, D., Havgaard, Jakob Hull, Gorodkin, Jan & De Melo, A. C. M. A., 2017, Proceedings: 2017 25th Euromicro International Conference on Parallel, Distributed and Network-Based Processing, PDP 2017. IEEE, p. 295-302 8 p. 7912663Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review
- Published
Foldalign 2.5: multithreaded implementation for pairwise structural RNA alignment
Sundfeld, D., Havgaard, Jakob Hull, de Melo, A. C. M. A. & Gorodkin, Jan, 2016, In: Bioinformatics. 32, 8, p. 1238-1240 3 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Thousands of corresponding human and mouse genomic regions unalignable in primary sequence contain common RNA structure
Torarinsson, E., Sawera, M., Havgaard, Jakob Hull, Fredholm, Merete & Gorodkin, Jan, 2006, In: Genome Research. 16, 7, p. 885-889 5 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Multiple structural alignment and clustering of RNA sequences: sequence analysis
Torarinsson, E., Havgaard, Jakob Hull & Gorodkin, Jan, 2007, In: Bioinformatics. 23, 8, p. 926-32 7 p.Research output: Contribution to journal › Journal article › Research › peer-review
ID: 4240647
Most downloads
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2867
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Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 expressed sequence tags
Research output: Contribution to journal › Journal article › Research › peer-review
Published -
1257
downloads
Fast pairwise structural RNA alignments by pruning of the dynamical programming matrix
Research output: Contribution to journal › Journal article › Research › peer-review
Published -
879
downloads
Structured RNAs and synteny regions in the pig genome
Research output: Contribution to journal › Journal article › Research › peer-review
Published