Jakob Hull Havgaard

Research output

Research output per year 2005 2007 2017 2022

• 1048 Citations
• 22 Journal article
• 1 Ph.D. thesis
• 1 Book chapter
• 1 Article in proceedings
• 1 More
  • 1 Conference abstract in journal

Research output per year

Research output per year

Search results

• 2022

  The Bacillaceae-1 RNA motif comprises two distinct classes

  González-Tortuero, E., Anthon, C., Havgaard, J. H., Geissler, A. S., Breüner, A., Hjort, C., Gorodkin, J. & Seemann, S. E., 2022, In: Gene. 841, 146756.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  File
  1 Citation (Scopus)

  33 Downloads (Pure)
• 2020

  Using GPU to accelerate the pairwise structural RNA alignment with base pair probabilities

  Sundfeld, D., Teodoro, G., Havgaard, J. H., Gorodkin, J. & Melo, A. C. M. A., 2020, In: Concurrency Computation. 32, 10, e5468.

  Research output: Contribution to journal › Journal article › Research › peer-review
  4 Citations (Scopus)
• 2019

  Epigenetic and Transcriptomic Characterization of Pure Adipocyte Fractions From Obese Pigs Identifies Candidate Pathways Controlling Metabolism

  Jacobsen, M. J., Havgaard, J. H., Anthon, C., Mentzel, C. M. J., Cirera, S., Krogh, P. M., Pundhir, S., Karlskov-Mortensen, P., Bruun, C. S., Lesnik, P., Guerin, M., Gorodkin, J., Jørgensen, C. B., Fredholm, M. & Barrès, R., 2019, In: Frontiers in Genetics. 10, 13 p., 1268.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  File
  8 Citations (Scopus)

  121 Downloads (Pure)
• 2018

  CRISPR-Cas9 off-targeting assessment with nucleic acid duplex energy parameters

  Alkan, F., Wenzel, A., Anthon, C., Havgaard, J. H. & Gorodkin, J., 2018, In: Genome Biology. 19, 13 p., 177.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  File
  109 Citations (Scopus)

  197 Downloads (Pure)
• 2017

  Alignment-free comparative genomic screen for structured RNAs using coarse-grained secondary structure dot plots

  Kato, Y., Gorodkin, J. & Havgaard, J. H., Dec 2017, In: BMC Genomics. 18, 1, 935.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  File
  1 Citation (Scopus)

  181 Downloads (Pure)

• Assessing the miRNA sponge potential of RUNX1T1 in t(8;21) acute myeloid leukemia

  Junge, A., Zandi, R., Havgaard, J. H., Gorodkin, J. & Cowland, J. B., 2017, In: Gene. 615, p. 35-40 6 p.

  Research output: Contribution to journal › Journal article › Research › peer-review
  12 Citations (Scopus)

• CUDA-Sankoff: Using GPU to Accelerate the Pairwise Structural RNA Alignment

  Sundfeld, D., Havgaard, J. H., Gorodkin, J. & 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. 7912663

  Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review
  5 Citations (Scopus)

• RNAscClust: Clustering RNA sequences using structure conservation and graph based motifs

  Miladi, M., Junge, A., Costa, F., Seemann, S. E., Havgaard, J. H., Gorodkin, J. & Backofen, R., 2017, In: Bioinformatics. 33, 14, p. 2089-2096 8 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  File
  26 Citations (Scopus)

  123 Downloads (Pure)
• 2016

  Adipocyte gene expression and DNA methylation patterns differ significantly between lean and obese pigs

  Jacobsen, M. J., Havgaard, J. H., Mentzel, C. M. J., Sørensen, P. M., Pundhir, S., Anthon, C., Karlskov-Mortensen, P., Bruun, C. V. S., Cirera Salicio, S., Gorodkin, J., Jorgensen, C. B., Barrès, R. & Fredholm, M., 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

  Open Access

• Foldalign 2.5: multithreaded implementation for pairwise structural RNA alignment

  Sundfeld, D., Havgaard, J. H., de Melo, A. C. M. A. & Gorodkin, J., 2016, In: Bioinformatics. 32, 8, p. 1238-1240 3 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  File
  29 Citations (Scopus)

  167 Downloads (Pure)
• 2015

  Optimizing RNA structures by sequence extensions using RNAcop

  Hecker, N., Christensen-Dalsgaard, M., Seemann, E. S., Havgaard, J. H., Stadler, P. F., Hofacker, I. L., Nielsen, H. & Gorodkin, J., 2015, In: Nucleic Acids Research. 43, 17, p. 8135-8145 11 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  File
  4 Citations (Scopus)

  399 Downloads (Pure)
• 2014

  RNA Structural Alignments, Part I: Sankoff-Based Approaches for Structural Alignments

  Havgaard, J. H. & Gorodkin, J., 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

  File

• Structured RNAs and synteny regions in the pig genome

  Anthon, C., Tafer, H., Havgaard, J. H., Thomsen, B., Hedegaard, J., Seemann, E. S., Pundhir, S., Kehr, S., Bartschat, S., Nielsen, M., Nielsen, R. O., Fredholm, M., Stadler, P. F. & Gorodkin, J., 2014, In: BMC Genomics. 15, 27 p., 459.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  File
  19 Citations (Scopus)

  1051 Downloads (Pure)
• 2012

  Comparative ncRNA gene and structure prediction using Foldalign and FoldalignM

  Havgaard, J. H., Kaur, S. & Gorodkin, J., 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
  5 Citations (Scopus)
• 2010

  De novo prediction of structured RNAs from genomic sequences

  Gorodkin, J., Hofacker, I. L., Þórarinsson, E., Yao, Z., Havgaard, J. H. & 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
  56 Citations (Scopus)
• 2009

  Structural profiles of human miRNA families from pairwise clustering

  Kaczkowski, B., Þórarinsson, E., Reiche, K., Havgaard, J. H., Stadler, P. F. & Gorodkin, J., 2009, In: Bioinformatics. 25, 3, p. 291-294 4 p.

  Research output: Contribution to journal › Journal article › Research › peer-review
  56 Citations (Scopus)
• 2007

  Fast pairwise structural RNA alignments by pruning of the dynamical programming matrix

  Havgaard, J. H., Torarinsson, E. & Gorodkin, J., 2007, In: PLoS Computational Biology. 3, 10, p. 1896-1908 13 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  File
  98 Citations (Scopus)

  1303 Downloads (Pure)

• Multiple structural alignment and clustering of RNA sequences: sequence analysis

  Torarinsson, E., Havgaard, J. H. & Gorodkin, J., 2007, In: Bioinformatics. 23, 8, p. 926-32 7 p.

  Research output: Contribution to journal › Journal article › Research › peer-review
  132 Citations (Scopus)

• 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, Li, W., Yu, J., Wang, J., Staefeldt, H-H., Wernersson, R., Madsen, L. B., Thomsen, B. S., Hornshøj, H., Bujie, Z., Wang, X., Wang, X., Bolund, L., Brunak, S., Yang, H., Bendixen, C. & Fredholm, M., 2007, In: Genome Biology. 8, R45, p. R45 16 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  File
  65 Citations (Scopus)

  2955 Downloads (Pure)

• Semiautomated improvement of RNA alignments

  Andersen, E. S., Lind-Thomsen, A., Knudsen, B., Kristensen, S. E., Havgaard, J. H., Torarinsson, E., Larsen, N., Zwieb, C., Sestoft, P., Kjems, J. & Gorodkin, J., 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
  36 Citations (Scopus)

• 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, Nielsen, B., Havgaard, J. H., Brunak, S., Fredholm, M. & Bendixen, C., 2007, In: Bioinformatics. 23, 13, p. i387-91 5 p.

  Research output: Contribution to journal › Journal article › Research › peer-review
  27 Citations (Scopus)

• Structural alignment of RNA with FOLDALIGN

  Havgaard, J. H., 2007, Frederiksberg: Center for Skov, Landskab og Planlægning/Københavns Universitet. 128 p.

  Research output: Book/Report › Ph.D. thesis › Research

  Open Access

  File
  423 Downloads (Pure)
• 2006

  MicroRNA sequence motifs reveal asymmetry between the stem arms

  Gorodkin, J., Havgaard, J. H., Ensterö, M., Sawera, M., Jensen, P., Öhman, M. & Fredholm, M., 2006, In: Computational Biology and Chemistry. 30, 4, p. 249-254 6 p.

  Research output: Contribution to journal › Journal article › Research › peer-review
  20 Citations (Scopus)

• Thousands of corresponding human and mouse genomic regions unalignable in primary sequence contain common RNA structure

  Torarinsson, E., Sawera, M., Havgaard, J. H., Fredholm, M. & Gorodkin, J., 2006, In: Genome Research. 16, 7, p. 885-889 5 p.

  Research output: Contribution to journal › Journal article › Research › peer-review
  140 Citations (Scopus)
• 2005

  Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%

  Havgaard, J. H., Lyngsø, R. B., Stormo, G. D. & Gorodkin, J., 2005, In: Bioinformatics. 21, 9, p. 1815-1824 10 p.

  Research output: Contribution to journal › Journal article › Research › peer-review
  131 Citations (Scopus)

• The FOLDALIGN web server for pairwise structural RNA alignment and mutual motif search

  Havgaard, J. H., Lyngsø, R. B. & Gorodkin, J., 2005, In: Nucleic Acids Research. 33, p. W650-W653 4 p.

  Research output: Contribution to journal › Journal article › Research › peer-review
  64 Citations (Scopus)