Stefan E Seemann

Stefan E Seemann

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Stefan E Seemann

Stefan E Seemann

Publications by authors named "Stefan E Seemann"

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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

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

DotAligner: identification and clustering of RNA structure motifs.

Genome Biol 2017 12 28;18(1):244. Epub 2017 Dec 28.

RNA Biology and Plasticity Group, Garvan Institute of Medical Research, 384 Victoria Street, Sydney, NSW 2010, Australia.

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https://genomebiology.biomedcentral.com/articles/10.1186/s13
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http://dx.doi.org/10.1186/s13059-017-1371-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5747123PMC
December 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

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

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

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

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

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

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

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

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

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

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

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