Publications by authors named "Jan Gorodkin"

91Publications

Good guide, bad guide: spacer sequence-dependent cleavage efficiency of Cas12a.

Nucleic Acids Res 2020 04;48(6):3228-3243

Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands.

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http://dx.doi.org/10.1093/nar/gkz1240DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7102956PMC
April 2020

A splice-site variant in the lncRNA gene cosegregates in the large Volkmann cataract family.

Mol Vis 2019 20;25:1-11. Epub 2019 Jan 20.

Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Panum Institute, University of Copenhagen, Copenhagen N, Denmark.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6377377PMC
June 2019

Special Issue: Computational Analysis of RNA Structure and Function.

Authors:
Jan Gorodkin

Genes (Basel) 2019 01 16;10(1). Epub 2019 Jan 16.

Center for Non-Coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg C, Denmark.

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http://dx.doi.org/10.3390/genes10010055DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6357010PMC
January 2019

Identification and characterization of novel conserved RNA structures in Drosophila.

BMC Genomics 2018 Dec 11;19(1):899. Epub 2018 Dec 11.

Center for non-coding RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, Frederiksberg C, DK-1870, Denmark.

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http://dx.doi.org/10.1186/s12864-018-5234-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6288889PMC
December 2018

Multiple Sequence Alignments Enhance Boundary Definition of RNA Structures.

Genes (Basel) 2018 Dec 4;9(12). Epub 2018 Dec 4.

Center for Non-Coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg C, Denmark.

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http://www.mdpi.com/2073-4425/9/12/604
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http://dx.doi.org/10.3390/genes9120604DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6315940PMC
December 2018

Cytoscape StringApp: Network Analysis and Visualization of Proteomics Data.

J Proteome Res 2019 02 5;18(2):623-632. Epub 2018 Dec 5.

Novo Nordisk Foundation Center for Protein Research , University of Copenhagen , 2200 Copenhagen N, Denmark.

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http://dx.doi.org/10.1021/acs.jproteome.8b00702DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6800166PMC
February 2019

WebCircRNA: Classifying the Circular RNA Potential of Coding and Noncoding RNA.

Genes (Basel) 2018 Nov 6;9(11). Epub 2018 Nov 6.

Center for Non-Coding RNA in Technology and Health, University of Copenhagen, 1870 Frederiksberg C, Denmark.

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http://www.mdpi.com/2073-4425/9/11/536
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http://dx.doi.org/10.3390/genes9110536DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6266491PMC
November 2018

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

Genome Biol 2018 10 26;19(1):177. Epub 2018 Oct 26.

Center for Non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg, Denmark.

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https://genomebiology.biomedcentral.com/articles/10.1186/s13
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http://dx.doi.org/10.1186/s13059-018-1534-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6203265PMC
October 2018

Inferring disease-associated long non-coding RNAs using genome-wide tissue expression profiles.

Bioinformatics 2019 05;35(9):1494-1502

Department of Veterinary and Animal Sciences, Center for Non-coding RNA in Technology and Health, University of Copenhagen, Frederiksberg C, Denmark.

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https://academic.oup.com/bioinformatics/advance-article/doi/
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http://dx.doi.org/10.1093/bioinformatics/bty859DOI Listing
May 2019

Warburg Effect Metabolism Drives Neoplasia in a Drosophila Genetic Model of Epithelial Cancer.

Curr Biol 2018 10 4;28(20):3220-3228.e6. Epub 2018 Oct 4.

Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3, Copenhagen 2200 N, Denmark. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S09609822183111
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http://dx.doi.org/10.1016/j.cub.2018.08.035DOI Listing
October 2018

Genome-wide identification of clusters of predicted microRNA binding sites as microRNA sponge candidates.

PLoS One 2018 24;13(8):e0202369. Epub 2018 Aug 24.

Center for non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0202369PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6108476PMC
February 2019

IFN-λ and microRNAs are important modulators of the pulmonary innate immune response against influenza A (H1N2) infection in pigs.

PLoS One 2018 20;13(4):e0194765. Epub 2018 Apr 20.

Section for Protein Science and Signaling Biology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0194765PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5909910PMC
July 2018

TISSUES 2.0: an integrative web resource on mammalian tissue expression.

Database (Oxford) 2018 01;2018

Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.

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http://dx.doi.org/10.1093/database/bay003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5808782PMC
January 2018

Comparative RNA Genomics.

Methods Mol Biol 2018 ;1704:363-400

Center for non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, University of Copenhagen, Grønnegårdsvej 3, DK-1870 Frederiksberg C, Denmark.

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http://link.springer.com/10.1007/978-1-4939-7463-4_14
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http://dx.doi.org/10.1007/978-1-4939-7463-4_14DOI Listing
December 2018

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

BMC Genomics 2017 Dec 2;18(1):935. Epub 2017 Dec 2.

Center for non-coding RNA in Technology and Health (RTH), University of Copenhagen, Groennegaardsvej 3, Frederiksberg, 1870, Denmark.

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http://dx.doi.org/10.1186/s12864-017-4309-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5712110PMC
December 2017

Translational co-regulation of a ligand and inhibitor by a conserved RNA element.

Nucleic Acids Res 2018 01;46(1):104-119

Cell & Developmental Biology Unit, Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK.

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http://dx.doi.org/10.1093/nar/gkx938DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5758872PMC
January 2018

Associating transcription factors and conserved RNA structures with gene regulation in the human brain.

Sci Rep 2017 07 18;7(1):5776. Epub 2017 Jul 18.

Center for non-coding RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, 1870, Frederiksberg C, Denmark.

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http://dx.doi.org/10.1038/s41598-017-06200-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5516038PMC
July 2017

RNAscClust: clustering RNA sequences using structure conservation and graph based motifs.

Bioinformatics 2017 Jul;33(14):2089-2096

Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg im Breisgau, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btx114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5870858PMC
July 2017

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

Gene 2017 Jun 16;615:35-40. Epub 2017 Mar 16.

The Granulocyte Research Laboratory, Department of Hematology, National University Hospital, University of Copenhagen, Copenhagen, Denmark; Section of Haematology-Oncology, Department of Clinical Genetics, National University Hospital, University of Copenhagen, Copenhagen, Denmark. Electronic address:

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http://dx.doi.org/10.1016/j.gene.2017.03.015DOI Listing
June 2017

RIsearch2: suffix array-based large-scale prediction of RNA-RNA interactions and siRNA off-targets.

Nucleic Acids Res 2017 05;45(8):e60

Center for non-coding RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg C, Denmark.

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http://dx.doi.org/10.1093/nar/gkw1325DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5416843PMC
May 2017

RAIN: RNA-protein Association and Interaction Networks.

Database (Oxford) 2017 10;2017. Epub 2017 Jan 10.

Center for Non-coding RNA in Technology and Health, University of Copenhagen, Copenhagen,, Groennegaardsvej 3, DK-1870 Frederiksberg C, Denmark.

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http://dx.doi.org/10.1093/database/baw167DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5225963PMC
November 2017

Joint Profiling of miRNAs and mRNAs Reveals miRNA Mediated Gene Regulation in the Göttingen Minipig Obesity Model.

PLoS One 2016 30;11(11):e0167285. Epub 2016 Nov 30.

Animal Genetics, Department of Veterinary Clinical and Animal Science, Faculty of Health Sciences, University of Copenhagen, Frederiksberg, Denmark.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0167285PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5130236PMC
July 2017

Foldalign 2.5: multithreaded implementation for pairwise structural RNA alignment.

Bioinformatics 2016 04 24;32(8):1238-40. Epub 2015 Dec 24.

Center for Non-Coding RNA in Technology and Health, IKVH, University of Copenhagen, Frederiksberg, Denmark and.

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http://dx.doi.org/10.1093/bioinformatics/btv748DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4824132PMC
April 2016

RNA 3D Modules in Genome-Wide Predictions of RNA 2D Structure.

PLoS One 2015 28;10(10):e0139900. Epub 2015 Oct 28.

Center for non-coding RNA in Technology and Health, University of Copenhagen, Frederiksberg, Denmark; Department of Veterinary Clinical and Animal Science, Faculty of Health and Medical Science, University of Copenhagen, Frederiksberg, Denmark.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0139900PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4624896PMC
June 2016

Full-length RNA structure prediction of the HIV-1 genome reveals a conserved core domain.

Nucleic Acids Res 2015 Dec 17;43(21):10168-79. Epub 2015 Oct 17.

iNANO, Interdisciplinary Nanoscience Center, Aarhus University, DK-8000 Aarhus C, Denmark

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http://dx.doi.org/10.1093/nar/gkv1039DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4666355PMC
December 2015

Optimizing RNA structures by sequence extensions using RNAcop.

Nucleic Acids Res 2015 Sep 17;43(17):8135-45. Epub 2015 Aug 17.

Center for non-coding RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg C, Denmark Department of Veterinary Clinical and Animal Science, University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg C, Denmark

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http://dx.doi.org/10.1093/nar/gkv813DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4787817PMC
September 2015

Gender and Obesity Specific MicroRNA Expression in Adipose Tissue from Lean and Obese Pigs.

PLoS One 2015 29;10(7):e0131650. Epub 2015 Jul 29.

Animal Genetics, Department of Veterinary Clinical and Animal Science, Faculty of Health Sciences, University of Copenhagen, Frederiksberg, Denmark; Center for non-coding RNA in Technology and Health, Computational Biology and Bioinformatics, Department of Veterinary Clinical and Animal Science, Faculty of Health Sciences, University of Copenhagen, Frederiksberg, Denmark.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0131650PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4519260PMC
April 2016

Differential and coherent processing patterns from small RNAs.

Sci Rep 2015 Jul 13;5:12062. Epub 2015 Jul 13.

Center for non-coding RNA in Technology and Health, IKVH, University of Copenhagen, Grønnegårdsvej 3, 1870, Frederiksberg C, Denmark.

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http://dx.doi.org/10.1038/srep12062DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4499813PMC
July 2015

Simultaneous DNA and RNA Mapping of Somatic Mitochondrial Mutations across Diverse Human Cancers.

PLoS Genet 2015 Jun 30;11(6):e1005333. Epub 2015 Jun 30.

Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.

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http://dx.doi.org/10.1371/journal.pgen.1005333DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4488357PMC
June 2015

Emerging applications of read profiles towards the functional annotation of the genome.

Front Genet 2015 19;6:188. Epub 2015 May 19.

Center for non-coding RNA in Technology and Health, Department of Veterinary Clinical and Animal Sciences (IKVH), University of Copenhagen Frederiksberg C, Denmark.

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http://dx.doi.org/10.3389/fgene.2015.00188DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4437211PMC
June 2015

Transcriptomic landscape of lncRNAs in inflammatory bowel disease.

Genome Med 2015 13;7(1):39. Epub 2015 May 13.

Center for non-coding RNA in Technology and Health, University of Copenhagen, Frederiksberg, 1870 Denmark ; Department of Pediatrics E, Copenhagen Diabetes Research Center (CPH-DIRECT), Herlev University Hospital, Herlev, 2730 Denmark ; Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200 Denmark.

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http://dx.doi.org/10.1186/s13073-015-0162-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4437449PMC
May 2015

Quality Assessment of Domesticated Animal Genome Assemblies.

Bioinform Biol Insights 2015 6;9(Suppl 4):49-58. Epub 2016 Jun 6.

Center for non-coding RNA in Technology and Health, Department of Veterinary Clinical and Animal Sciences, University of Copenhagen, København, Denmark.

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http://dx.doi.org/10.4137/BBI.S29333DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4898645PMC
June 2016

Profiling of ribose methylations in RNA by high-throughput sequencing.

Angew Chem Int Ed Engl 2015 Jan 21;54(2):451-5. Epub 2014 Nov 21.

Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N (Denmark).

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http://doi.wiley.com/10.1002/anie.201408362
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http://dx.doi.org/10.1002/anie.201408362DOI Listing
January 2015

Spatially conserved regulatory elements identified within human and mouse Cd247 gene using high-throughput sequencing data from the ENCODE project.

Gene 2014 Jul 3;545(1):80-7. Epub 2014 May 3.

Center for Non-coding RNA in Technology and Health, University of Copenhagen, Grønnegå̊rdsvej 3, 1870 Frederiksberg C, Denmark; IKVH, University of Copenhagen, Grønnegå̊rdsvej 3, 1870 Frederiksberg C, Denmark.

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http://dx.doi.org/10.1016/j.gene.2014.05.004DOI Listing
July 2014

De novo discovery of structured ncRNA motifs in genomic sequences.

Methods Mol Biol 2014 ;1097:303-18

Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA.

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http://dx.doi.org/10.1007/978-1-62703-709-9_15DOI Listing
November 2014

RNA structural alignments, part I: Sankoff-based approaches for structural alignments.

Methods Mol Biol 2014 ;1097:275-90

Center for non-coding RNA in Technology and Health, IKVH, University of Copenhagen, Frederiksberg C, Denmark.

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http://dx.doi.org/10.1007/978-1-62703-709-9_13DOI Listing
November 2014

Concepts and introduction to RNA bioinformatics.

Methods Mol Biol 2014 ;1097:1-31

Center for non-coding RNA in Technology and Health, IKVH, University of Copenhagen, Frederiksberg C, Denmark.

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http://dx.doi.org/10.1007/978-1-62703-709-9_1DOI Listing
November 2014

Transcriptome-wide analysis of UTRs in non-small cell lung cancer reveals cancer-related genes with SNV-induced changes on RNA secondary structure and miRNA target sites.

PLoS One 2014 8;9(1):e82699. Epub 2014 Jan 8.

Center for non-coding RNA in Technology and Health, Section for Animal Genetics, Bioinformatics and Breeding, IKVH, University of Copenhagen, Frederiksberg, Denmark.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0082699PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3885406PMC
September 2014

Protein-driven inference of miRNA-disease associations.

Bioinformatics 2014 Feb 21;30(3):392-7. Epub 2013 Nov 21.

Center for non-coding RNA in Technology and Health, Department of Veterinary Clinical and Animal Sciences, Department of Disease Systems Biology, Novo Nordisk Foundation Center for Protein Research and The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Denmark.

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http://dx.doi.org/10.1093/bioinformatics/btt677DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3904518PMC
February 2014

Automated identification of RNA 3D modules with discriminative power in RNA structural alignments.

Nucleic Acids Res 2013 Dec 4;41(22):9999-10009. Epub 2013 Sep 4.

Center for non-coding RNA in Technology and Health, Department of Veterinary Clinical and Animal Science, University of Copenhagen, Grønnegårdsvej 3, DK-1870 Frederiksberg, Denmark, Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Vienna, Austria and Research Group Bioinformatics and Computational Biology, University of Vienna, Währingerstraße 17, A-1090 Vienna, Austria.

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http://dx.doi.org/10.1093/nar/gkt795DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3905863PMC
December 2013

MicroRNA discovery by similarity search to a database of RNA-seq profiles.

Front Genet 2013 11;4:133. Epub 2013 Jul 11.

Center for non-coding RNA in Technology and Health, Department of Veterinary Clinical and Animal Sciences (IKVH), University of Copenhagen Frederiksberg C, Denmark.

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http://dx.doi.org/10.3389/fgene.2013.00133DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3708161PMC
July 2013

The RNAsnp web server: predicting SNP effects on local RNA secondary structure.

Nucleic Acids Res 2013 Jul 29;41(Web Server issue):W475-9. Epub 2013 Apr 29.

Center for non-coding RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg C, Denmark.

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http://dx.doi.org/10.1093/nar/gkt291DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3977658PMC
July 2013

RNAsnp: efficient detection of local RNA secondary structure changes induced by SNPs.

Hum Mutat 2013 Apr;34(4):546-56

Center for non-coding RNA in Technology and Health, University of Copenhagen, Frederiksberg, Denmark.

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http://dx.doi.org/10.1002/humu.22273DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3708107PMC
April 2013

Analyses of pig genomes provide insight into porcine demography and evolution.

Authors:
Martien A M Groenen Alan L Archibald Hirohide Uenishi Christopher K Tuggle Yasuhiro Takeuchi Max F Rothschild Claire Rogel-Gaillard Chankyu Park Denis Milan Hendrik-Jan Megens Shengting Li Denis M Larkin Heebal Kim Laurent A F Frantz Mario Caccamo Hyeonju Ahn Bronwen L Aken Anna Anselmo Christian Anthon Loretta Auvil Bouabid Badaoui Craig W Beattie Christian Bendixen Daniel Berman Frank Blecha Jonas Blomberg Lars Bolund Mirte Bosse Sara Botti Zhan Bujie Megan Bystrom Boris Capitanu Denise Carvalho-Silva Patrick Chardon Celine Chen Ryan Cheng Sang-Haeng Choi William Chow Richard C Clark Christopher Clee Richard P M A Crooijmans Harry D Dawson Patrice Dehais Fioravante De Sapio Bert Dibbits Nizar Drou Zhi-Qiang Du Kellye Eversole João Fadista Susan Fairley Thomas Faraut Geoffrey J Faulkner Katie E Fowler Merete Fredholm Eric Fritz James G R Gilbert Elisabetta Giuffra Jan Gorodkin Darren K Griffin Jennifer L Harrow Alexander Hayward Kerstin Howe Zhi-Liang Hu Sean J Humphray Toby Hunt Henrik Hornshøj Jin-Tae Jeon Patric Jern Matthew Jones Jerzy Jurka Hiroyuki Kanamori Ronan Kapetanovic Jaebum Kim Jae-Hwan Kim Kyu-Won Kim Tae-Hun Kim Greger Larson Kyooyeol Lee Kyung-Tai Lee Richard Leggett Harris A Lewin Yingrui Li Wansheng Liu Jane E Loveland Yao Lu Joan K Lunney Jian Ma Ole Madsen Katherine Mann Lucy Matthews Stuart McLaren Takeya Morozumi Michael P Murtaugh Jitendra Narayan Dinh Truong Nguyen Peixiang Ni Song-Jung Oh Suneel Onteru Frank Panitz Eung-Woo Park Hong-Seog Park Geraldine Pascal Yogesh Paudel Miguel Perez-Enciso Ricardo Ramirez-Gonzalez James M Reecy Sandra Rodriguez-Zas Gary A Rohrer Lauretta Rund Yongming Sang Kyle Schachtschneider Joshua G Schraiber John Schwartz Linda Scobie Carol Scott Stephen Searle Bertrand Servin Bruce R Southey Goran Sperber Peter Stadler Jonathan V Sweedler Hakim Tafer Bo Thomsen Rashmi Wali Jian Wang Jun Wang Simon White Xun Xu Martine Yerle Guojie Zhang Jianguo Zhang Jie Zhang Shuhong Zhao Jane Rogers Carol Churcher Lawrence B Schook

Nature 2012 Nov;491(7424):393-8

Animal Breeding and Genomics Centre, Wageningen University, De Elst 1, 6708 WD, Wageningen, The Netherlands.

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http://www.umass.edu/vetimm/docs/Groenen_etal_2012.pdf
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http://www.nature.com/doifinder/10.1038/nature11622
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http://dx.doi.org/10.1038/nature11622DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3566564PMC
November 2012

Profiling microRNAs in lung tissue from pigs infected with Actinobacillus pleuropneumoniae.

BMC Genomics 2012 Sep 6;13:459. Epub 2012 Sep 6.

Department of Veterinary Clinical and Animal Sciences, Section of Anatomy, Cell Biology, Genetics and Bioinformatics, University of Copenhagen, Faculty of Health and Medical Sciences, Copenhagen, Denmark.

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http://dx.doi.org/10.1186/1471-2164-13-459DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3465251PMC
September 2012

Comparative ncRNA gene and structure prediction using Foldalign and FoldalignM.

Curr Protoc Bioinformatics 2012 Sep;Chapter 12:Unit12.11

Center for Non-Coding RNA in Technology and Health, Department of Veterinary Clinical and Animal Sciences, University of Copenhagen, Copenhagen, Denmark.

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http://dx.doi.org/10.1002/0471250953.bi1211s39DOI Listing
September 2012

RIsearch: fast RNA-RNA interaction search using a simplified nearest-neighbor energy model.

Bioinformatics 2012 Nov 24;28(21):2738-46. Epub 2012 Aug 24.

Center for non-coding RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, DK-1870 Frederiksberg, Denmark.

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http://dx.doi.org/10.1093/bioinformatics/bts519DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3476332PMC
November 2012

RILogo: visualizing RNA-RNA interactions.

Bioinformatics 2012 Oct 23;28(19):2523-6. Epub 2012 Jul 23.

The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen DK-2200, Denmark.

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http://dx.doi.org/10.1093/bioinformatics/bts461DOI Listing
October 2012

Multiple independent analyses reveal only transcription factors as an enriched functional class associated with microRNAs.

BMC Syst Biol 2012 Jul 23;6:90. Epub 2012 Jul 23.

Center for Non-coding RNA in Technology and Health, Division of Genetics and Bioinformatics, IBHV, University of Copenhagen, Copenhagen, Denmark.

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http://dx.doi.org/10.1186/1752-0509-6-90DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3430561PMC
July 2012

Transcripts with in silico predicted RNA structure are enriched everywhere in the mouse brain.

BMC Genomics 2012 May 31;13:214. Epub 2012 May 31.

Center for non-coding RNA in Technology and Health, University of Copenhagen, Denmark.

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http://dx.doi.org/10.1186/1471-2164-13-214DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3464589PMC
May 2012

Sequence and expression analysis of gaps in human chromosome 20.

Nucleic Acids Res 2012 Aug 17;40(14):6660-72. Epub 2012 Apr 17.

Wilhelm Johannsen Centre for Functional Genome Research, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen N, Denmark.

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http://dx.doi.org/10.1093/nar/gks302DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3413113PMC
August 2012

deepBlockAlign: a tool for aligning RNA-seq profiles of read block patterns.

Bioinformatics 2012 Jan 3;28(1):17-24. Epub 2011 Nov 3.

Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, Universität Leipzig, Philipp-Rosenthal-Strasse 27, D-04107 Leipzig, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btr598DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3244762PMC
January 2012

From structure prediction to genomic screens for novel non-coding RNAs.

PLoS Comput Biol 2011 Aug 4;7(8):e1002100. Epub 2011 Aug 4.

Center for non-coding RNA in Technology and Health, IBHV University of Copenhagen, Frederiksberg, Denmark.

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http://dx.doi.org/10.1371/journal.pcbi.1002100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3150283PMC
August 2011

The PETfold and PETcofold web servers for intra- and intermolecular structures of multiple RNA sequences.

Nucleic Acids Res 2011 Jul 23;39(Web Server issue):W107-11. Epub 2011 May 23.

Center for Non-coding RNA in Technology and Health, Division of Genetics and Bioinformatics, IBHV, University of Copenhagen, Grønnegårdsvej 3, DK-1870 Frederiksberg, Denmark.

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http://dx.doi.org/10.1093/nar/gkr248DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125731PMC
July 2011

Fast local fragment chaining using sum-of-pair gap costs.

Algorithms Mol Biol 2011 Mar 18;6. Epub 2011 Mar 18.

Bioinformatics Group, Dept, of Computer Science, University of Leipzig, Germany.

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http://dx.doi.org/10.1186/1748-7188-6-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072320PMC
March 2011

Global microRNA analysis of the NCI-60 cancer cell panel.

Mol Cancer Ther 2011 Mar 20;10(3):375-84. Epub 2011 Jan 20.

Department of Biomarker Discovery, Exiqon A/S, Bygstubben 9, DK-2950 Vedbk, Denmark.

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http://dx.doi.org/10.1158/1535-7163.MCT-10-0605DOI Listing
March 2011

maxAlike: maximum likelihood-based sequence reconstruction with application to improved primer design for unknown sequences.

Bioinformatics 2011 Feb 1;27(3):317-25. Epub 2010 Dec 1.

Center for non-coding RNA in Technology and Health, IBHV, University of Copenhagen, Grønnegårdsvej 3, DK-1870 Frederiksberg, Denmark.

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http://dx.doi.org/10.1093/bioinformatics/btq651DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3031029PMC
February 2011

PETcofold: predicting conserved interactions and structures of two multiple alignments of RNA sequences.

Bioinformatics 2011 Jan 18;27(2):211-9. Epub 2010 Nov 18.

Center for non-coding RNA in Technology and Health, University of Copenhagen, Frederiksberg C, Denmark.

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http://dx.doi.org/10.1093/bioinformatics/btq634DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3018821PMC
January 2011

Hierarchical folding of multiple sequence alignments for the prediction of structures and RNA-RNA interactions.

Algorithms Mol Biol 2010 May 21;5:22. Epub 2010 May 21.

Bioinformatics Group, University of Freiburg, Georges-Köhler-Allee 106, Freiburg, 79110, Germany.

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http://dx.doi.org/10.1186/1748-7188-5-22DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2903599PMC
May 2010

A study of alternative splicing in the pig.

BMC Res Notes 2010 May 5;3:123. Epub 2010 May 5.

University of Copenhagen, Faculty of Life Sciences, Department of Basic Animal and Veterinary Sciences, Division of Genetics and Bioinformatics, Groennegaardsvej 3, 1870 Frederiksberg C, Denmark.

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http://bmcresnotes.biomedcentral.com/articles/10.1186/1756-0
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http://dx.doi.org/10.1186/1756-0500-3-123DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2882375PMC
May 2010

454 pyrosequencing based transcriptome analysis of Zygaena filipendulae with focus on genes involved in biosynthesis of cyanogenic glucosides.

BMC Genomics 2009 Dec 2;10:574. Epub 2009 Dec 2.

Plant Biochemistry Laboratory, Department of Plant Biology and Biotechnology, University of Copenhagen, 40 Thorvaldsensvej, DK-1871 Frederiksberg C, Copenhagen, Denmark.

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http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2
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http://dx.doi.org/10.1186/1471-2164-10-574DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2791780PMC
December 2009

De novo prediction of structured RNAs from genomic sequences.

Trends Biotechnol 2010 Jan 26;28(1):9-19. Epub 2009 Nov 26.

Section for Genetics and Bioinformatics, IBHV and Center for Applied Bioinformatics, University of Copenhagen, Grønnegårdsvej 3, DK-1870 Frederiksberg C, Denmark.

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http://dx.doi.org/10.1016/j.tibtech.2009.09.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4712260PMC
January 2010

The tedious task of finding homologous noncoding RNA genes.

RNA 2009 Dec 27;15(12):2075-82. Epub 2009 Oct 27.

Section for Genetics and Bioinformatics, IBHV, and Center for Applied Bioinformatics, University of Copenhagen, DK-1870 Frederiksberg, Denmark.

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http://dx.doi.org/10.1261/rna.1556009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779685PMC
December 2009

Structural profiles of human miRNA families from pairwise clustering.

Bioinformatics 2009 Feb 4;25(3):291-4. Epub 2008 Dec 4.

Division of Genetics and Bioinformatics, IBHV, University of Copenhagen, Frederiksberg C, Denmark.

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http://dx.doi.org/10.1093/bioinformatics/btn628DOI Listing
February 2009

Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments.

Nucleic Acids Res 2008 Nov 4;36(20):6355-62. Epub 2008 Oct 4.

Division of Genetics and Bioinformatics, IBHV and Center for Applied Bioinformatics, University of Copenhagen, Groennegårdsvej 3, DK-1870 Frederiksberg C, Denmark.

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http://dx.doi.org/10.1093/nar/gkn544DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2582601PMC
November 2008

Comparative genomics beyond sequence-based alignments: RNA structures in the ENCODE regions.

Genome Res 2008 Feb 20;18(2):242-51. Epub 2007 Dec 20.

Section for Genetics and Bioinformatics, IBVH, Faculty of Life Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark.

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http://dx.doi.org/10.1101/gr.6887408DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2203622PMC
February 2008

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

PLoS Comput Biol 2007 Oct 20;3(10):1896-908. Epub 2007 Aug 20.

Division of Genetics and Bioinformatics, University of Copenhagen, Frederiksberg, Denmark.

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http://dx.doi.org/10.1371/journal.pcbi.0030193DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2014794PMC
October 2007

EST analysis on pig mitochondria reveal novel expression differences between developmental and adult tissues.

BMC Genomics 2007 Oct 11;8:367. Epub 2007 Oct 11.

Division of Genetics and Bioinformatics, IBHV, University of Copenhagen, Grønnegårdsvej 3, DK-1870 Frederiksberg, Denmark.

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http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2
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http://dx.doi.org/10.1186/1471-2164-8-367DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2194790PMC
October 2007

Detection of RNA structures in porcine EST data and related mammals.

BMC Genomics 2007 Sep 10;8:316. Epub 2007 Sep 10.

Division of Genetics and Bioinformatics, IBHV, University of Copenhagen, Grønnegårdsvej 3, DK-1870 Frederiksberg, Denmark.

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http://dx.doi.org/10.1186/1471-2164-8-316DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2072958PMC
September 2007

Principles and limitations of computational microRNA gene and target finding.

DNA Cell Biol 2007 May;26(5):339-51

Bioinformatics Centre, University of Copenhagen, Copenhagen N, Denmark.

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http://dx.doi.org/10.1089/dna.2006.0551DOI Listing
May 2007

Multiple structural alignment and clustering of RNA sequences.

Bioinformatics 2007 Apr 25;23(8):926-32. Epub 2007 Feb 25.

Division of Genetics and Bioinformatics, IBHV and Center for Bioinformatics, University of Copenhagen, Frederiksberg C, Denmark.

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http://dx.doi.org/10.1093/bioinformatics/btm049DOI Listing
April 2007

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

Genome Res 2006 Jul 2;16(7):885-9. Epub 2006 Jun 2.

Division of Genetics and Bioinformatics, IBHV, The Royal Veterinary and Agricultural University, 1870 Frederiksberg C, Denmark.

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http://dx.doi.org/10.1101/gr.5226606DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1484455PMC
July 2006

The tmRDB and SRPDB resources.

Nucleic Acids Res 2006 Jan;34(Database issue):D163-8

Department of Molecular Biology, University of Aarhus, C.F. Moellers Allé, Building 139, 8000 Aarhus, Denmark.

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http://dx.doi.org/10.1093/nar/gkj142DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1347504PMC
January 2006

Mapping and expression studies of the mir17-92 cluster on pig chromosome 11.

Mamm Genome 2005 Aug 14;16(8):594-8. Epub 2005 Sep 14.

Division of Animal Genetics, Department of Animal and Veterinary Basic Sciences, The Royal Veterinary and Agricultural University, Groennegaardsvej 3, Frederiksberg C, Denmark.

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http://link.springer.com/10.1007/s00335-005-0013-3
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http://dx.doi.org/10.1007/s00335-005-0013-3DOI Listing
August 2005

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

Nucleic Acids Res 2005 Jul;33(Web Server issue):W650-3

Center for Bioinformatics and Division of Genetics, IBHV, The Royal Veterinary and Agricultural University Grønnegårdsvej 3, DK-1870 Frederiksberg C, Denmark.

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http://dx.doi.org/10.1093/nar/gki473DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1160234PMC
July 2005

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

Bioinformatics 2005 May 18;21(9):1815-24. Epub 2005 Jan 18.

Center for Bioinformatics and Division of Genetics, IBHV, The Royal Veterinary and Agricultural University, Frederiksberg, Denmark.

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http://dx.doi.org/10.1093/bioinformatics/bti279DOI Listing
May 2005

RNA interactions in the 5' region of the HIV-1 genome.

J Mol Biol 2004 Feb;336(2):369-79

Department of Molecular Biology, University of Aarhus, C.F. Møllers Allé, Building 130, DK-8000 C, Arhus, Denmark.

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http://dx.doi.org/10.1016/j.jmb.2003.12.010DOI Listing
February 2004

tmRDB (tmRNA database).

Nucleic Acids Res 2003 Jan;31(1):446-7

Department of Molecular Biology, The University of Texas Health Science Center at Tyler, 11937 US Highway 271, Tyler, TX 75708-3154, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC165466PMC
http://dx.doi.org/10.1093/nar/gkg019DOI Listing
January 2003

SRPDB: Signal Recognition Particle Database.

Nucleic Acids Res 2003 Jan;31(1):363-4

Department of Medical Biochemistry, University of Göteborg, Box 440, SE-405 30 Göteborg, Sweden.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC165554PMC
http://dx.doi.org/10.1093/nar/gkg107DOI Listing
January 2003