Publications by authors named "Simon Rasmussen"

98Publications

: Use of whole genome sequences to validate methods used for identification.

J Clin Microbiol 2020 Nov 18. Epub 2020 Nov 18.

The Regional Department of Clinical Microbiology, Region Zealand, Slagelse, Denmark.

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http://dx.doi.org/10.1128/JCM.02503-20DOI Listing
November 2020

A systemic review and metaanalysis of postoperative outcomes in urgent and elective bowel resection in patients with Crohn's disease.

Int J Colorectal Dis 2020 Oct 13. Epub 2020 Oct 13.

Department of surgery, Aalborg University Hospital, Hobrovej 22, 9000, Aalborg, Denmark.

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http://dx.doi.org/10.1007/s00384-020-03786-6DOI Listing
October 2020

Population genomics of the Viking world.

Nature 2020 09 16;585(7825):390-396. Epub 2020 Sep 16.

Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.

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http://dx.doi.org/10.1038/s41586-020-2688-8DOI Listing
September 2020

A G(enomic)P(ositioning)S(ystem) for Plant RNAPII Transcription.

Trends Plant Sci 2020 08 11;25(8):744-764. Epub 2020 Apr 11.

Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Bülowsvej 34, 1870 Frederiksberg C, Denmark. Electronic address:

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http://dx.doi.org/10.1016/j.tplants.2020.03.005DOI Listing
August 2020

Genetic factors underlying the bidirectional relationship between autoimmune and mental disorders - Findings from a Danish population-based study.

Brain Behav Immun 2020 Jun 11. Epub 2020 Jun 11.

CORE-Copenhagen Research Centre for Mental Health, Mental Health Centre Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark; Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. Electronic address:

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http://dx.doi.org/10.1016/j.bbi.2020.06.014DOI Listing
June 2020

Gut microbial changes of patients with psychotic and affective disorders: A systematic review.

Schizophr Res 2020 Jan 14. Epub 2020 Jan 14.

Copenhagen Research Centre for Mental Health - CORE, Mental Health Centre Copenhagen, Copenhagen University Hospital, Gentofte Hospitalsvej 15, 4. sal, 2900 Hellerup, Denmark. Electronic address:

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http://dx.doi.org/10.1016/j.schres.2019.12.014DOI Listing
January 2020

GIGYF1/2-Driven Cooperation between ZNF598 and TTP in Posttranscriptional Regulation of Inflammatory Signaling.

Cell Rep 2019 03;26(13):3511-3521.e4

Department of Cellular and Molecular Medicine, Center for Healthy Aging, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2019.03.006DOI Listing
March 2019

Emergence and Spread of Basal Lineages of Yersinia pestis during the Neolithic Decline.

Cell 2019 01 6;176(1-2):295-305.e10. Epub 2018 Dec 6.

Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet 208, 2800 Kongens Lyngby, Denmark. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2018.11.005DOI Listing
January 2019

Author Correction: 137 ancient human genomes from across the Eurasian steppes.

Nature 2018 11;563(7729):E16

Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.

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http://dx.doi.org/10.1038/s41586-018-0488-1DOI Listing
November 2018

137 ancient human genomes from across the Eurasian steppes.

Nature 2018 05 9;557(7705):369-374. Epub 2018 May 9.

Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.

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http://www.nature.com/articles/s41586-018-0094-2
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http://dx.doi.org/10.1038/s41586-018-0094-2DOI Listing
May 2018

Physiological and Genetic Adaptations to Diving in Sea Nomads.

Cell 2018 04;173(3):569-580.e15

Centre for GeoGenetics, University of Copenhagen, Copenhagen 1350, Denmark; Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK; Wellcome Trust, Sanger Institute, Hinxton CB10 1SA, UK. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2018.03.054DOI Listing
April 2018

Biosynthesis of bioactive diterpenoids in the medicinal plant Vitex agnus-castus.

Plant J 2018 03 14;93(5):943-958. Epub 2018 Feb 14.

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

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http://dx.doi.org/10.1111/tpj.13822DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5838521PMC
March 2018

[Enlarged vestibular aqueduct in a ten-year-old girl].

Ugeskr Laeger 2017 Oct;179(44)

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October 2017

Hepatic artery aneurysm causing gastrointestinal haemorrhage - Case report and literature review.

Int J Surg Case Rep 2017 4;41:12-16. Epub 2017 Oct 4.

Department of Gastrointestinal Surgery, Aalborg University Hospital, Denmark; Department of Clinical Medicine, Aalborg University, Denmark. Electronic address:

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http://dx.doi.org/10.1016/j.ijscr.2017.08.067DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5742007PMC
October 2017

Genomic characterization, phylogenetic analysis, and identification of virulence factors in Aerococcus sanguinicola and Aerococcus urinae strains isolated from infection episodes.

Microb Pathog 2017 Nov 21;112:327-340. Epub 2017 Sep 21.

Department of Clinical Microbiology, Slagelse Hospital, Slagelse, Denmark; Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark. Electronic address:

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http://dx.doi.org/10.1016/j.micpath.2017.09.042DOI Listing
November 2017

Highly accessible AU-rich regions in 3' untranslated regions are hotspots for binding of regulatory factors.

PLoS Comput Biol 2017 04 14;13(4):e1005460. Epub 2017 Apr 14.

Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen, Denmark.

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http://dx.doi.org/10.1371/journal.pcbi.1005460DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5409497PMC
April 2017

Genome Sequence of , Which Produces Red Colorants for the Food Industry.

Genome Announc 2017 Mar 2;5(9). Epub 2017 Mar 2.

Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark.

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http://genomea.asm.org/lookup/doi/10.1128/genomeA.01736-16
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http://dx.doi.org/10.1128/genomeA.01736-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5334594PMC
March 2017

Metagenomic analysis of rapid gravity sand filter microbial communities suggests novel physiology of Nitrospira spp.

ISME J 2016 11 29;10(11):2569-2581. Epub 2016 Apr 29.

Department of Environmental Engineering, Technical University of Denmark, Kongens Lyngby, Denmark.

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http://dx.doi.org/10.1038/ismej.2016.63DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5113852PMC
November 2016

A genomic history of Aboriginal Australia.

Nature 2016 Oct 21;538(7624):207-214. Epub 2016 Sep 21.

Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.

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http://dx.doi.org/10.1038/nature18299DOI Listing
October 2016

Reads2Type: a web application for rapid microbial taxonomy identification.

BMC Bioinformatics 2015 Nov 25;16:398. Epub 2015 Nov 25.

Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, Kgs. Lyngby, DK-2800, Denmark.

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http://dx.doi.org/10.1186/s12859-015-0829-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4659212PMC
November 2015

POPULATION GENETICS. Genomic evidence for the Pleistocene and recent population history of Native Americans.

Authors:
Maanasa Raghavan Matthias Steinrücken Kelley Harris Stephan Schiffels Simon Rasmussen Michael DeGiorgio Anders Albrechtsen Cristina Valdiosera María C Ávila-Arcos Anna-Sapfo Malaspinas Anders Eriksson Ida Moltke Mait Metspalu Julian R Homburger Jeff Wall Omar E Cornejo J Víctor Moreno-Mayar Thorfinn S Korneliussen Tracey Pierre Morten Rasmussen Paula F Campos Peter de Barros Damgaard Morten E Allentoft John Lindo Ene Metspalu Ricardo Rodríguez-Varela Josefina Mansilla Celeste Henrickson Andaine Seguin-Orlando Helena Malmström Thomas Stafford Suyash S Shringarpure Andrés Moreno-Estrada Monika Karmin Kristiina Tambets Anders Bergström Yali Xue Vera Warmuth Andrew D Friend Joy Singarayer Paul Valdes Francois Balloux Ilán Leboreiro Jose Luis Vera Hector Rangel-Villalobos Davide Pettener Donata Luiselli Loren G Davis Evelyne Heyer Christoph P E Zollikofer Marcia S Ponce de León Colin I Smith Vaughan Grimes Kelly-Anne Pike Michael Deal Benjamin T Fuller Bernardo Arriaza Vivien Standen Maria F Luz Francois Ricaut Niede Guidon Ludmila Osipova Mikhail I Voevoda Olga L Posukh Oleg Balanovsky Maria Lavryashina Yuri Bogunov Elza Khusnutdinova Marina Gubina Elena Balanovska Sardana Fedorova Sergey Litvinov Boris Malyarchuk Miroslava Derenko M J Mosher David Archer Jerome Cybulski Barbara Petzelt Joycelynn Mitchell Rosita Worl Paul J Norman Peter Parham Brian M Kemp Toomas Kivisild Chris Tyler-Smith Manjinder S Sandhu Michael Crawford Richard Villems David Glenn Smith Michael R Waters Ted Goebel John R Johnson Ripan S Malhi Mattias Jakobsson David J Meltzer Andrea Manica Richard Durbin Carlos D Bustamante Yun S Song Rasmus Nielsen Eske Willerslev

Science 2015 Aug 21;349(6250):aab3884. Epub 2015 Jul 21.

Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.

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http://dx.doi.org/10.1126/science.aab3884DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4733658PMC
August 2015

Drosophila Imp iCLIP identifies an RNA assemblage coordinating F-actin formation.

Genome Biol 2015 Jun 9;16:123. Epub 2015 Jun 9.

Department of Biology, Center for Computational and Applied Transcriptomics, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen, Denmark.

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http://dx.doi.org/10.1186/s13059-015-0687-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4477473PMC
June 2015

Rectal Hodgkin lymphoma in a patient with ulcerative colitis: a case study.

Diagn Pathol 2015 Apr 16;10:25. Epub 2015 Apr 16.

Institute of Pathology, Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark.

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http://dx.doi.org/10.1186/s13000-015-0271-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4427961PMC
April 2015

Benchmarking of methods for genomic taxonomy.

J Clin Microbiol 2014 May 26;52(5):1529-39. Epub 2014 Feb 26.

Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark.

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http://dx.doi.org/10.1128/JCM.02981-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3993634PMC
May 2014

Genome-scale cold stress response regulatory networks in ten Arabidopsis thaliana ecotypes.

BMC Genomics 2013 Oct 22;14:722. Epub 2013 Oct 22.

Department of Biology, Norwegian University of Science and Technology, Trondheim N-7491, Norway.

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http://dx.doi.org/10.1186/1471-2164-14-722DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3829657PMC
October 2013

On the accuracy of short read mapping.

Methods Mol Biol 2013 ;1038:39-59

Department of Biology, The Bioinformatics Centre, University of Copenhagen, Copenhagen, Denmark.

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http://dx.doi.org/10.1007/978-1-62703-514-9_3DOI Listing
February 2014

cWords - systematic microRNA regulatory motif discovery from mRNA expression data.

Silence 2013 May 20;4(1). Epub 2013 May 20.

Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen N, 2200, Denmark.

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http://dx.doi.org/10.1186/1758-907X-4-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3682869PMC
May 2013

Transcriptome responses to combinations of stresses in Arabidopsis.

Plant Physiol 2013 Apr 27;161(4):1783-94. Epub 2013 Feb 27.

Center for Biological Sequence Analysis , Technical University of Denmark, Lyngby, Denmark.

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http://dx.doi.org/10.1104/pp.112.210773DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3613455PMC
April 2013

Targeted metabolic engineering guided by computational analysis of single-nucleotide polymorphisms (SNPs).

Methods Mol Biol 2013 ;985:409-28

Department of Chemical and Biological Engineering, Industrial Biotechnology, Chalmers University of Technology, Gothenburg, Sweden.

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http://dx.doi.org/10.1007/978-1-62703-299-5_20DOI Listing
July 2013

snpTree--a web-server to identify and construct SNP trees from whole genome sequence data.

BMC Genomics 2012 13;13 Suppl 7:S6. Epub 2012 Dec 13.

National Food Institute, Technical University of Denmark, 2800 Kgs Lyngby, Denmark.

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http://dx.doi.org/10.1186/1471-2164-13-S7-S6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3521233PMC
June 2013

Identification of acquired antimicrobial resistance genes.

J Antimicrob Chemother 2012 Nov 10;67(11):2640-4. Epub 2012 Jul 10.

National Food Institute, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark.

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http://dx.doi.org/10.1093/jac/dks261DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3468078PMC
November 2012

Multilocus sequence typing of total-genome-sequenced bacteria.

J Clin Microbiol 2012 Apr 11;50(4):1355-61. Epub 2012 Jan 11.

Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark.

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http://dx.doi.org/10.1128/JCM.06094-11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3318499PMC
April 2012

Microbial community structure of Arctic multiyear sea ice and surface seawater by 454 sequencing of the 16S RNA gene.

ISME J 2012 Jan 30;6(1):11-20. Epub 2011 Jun 30.

University of Washington, School of Oceanography and Astrobiology Program, Seattle, WA, USA.

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http://dx.doi.org/10.1038/ismej.2011.76DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3246233PMC
January 2012

The transcriptionally active regions in the genome of Bacillus subtilis.

Mol Microbiol 2009 Sep 4;73(6):1043-57. Epub 2009 Aug 4.

Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark.

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http://doi.wiley.com/10.1111/j.1365-2958.2009.06830.x
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http://dx.doi.org/10.1111/j.1365-2958.2009.06830.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2784878PMC
September 2009

Innate recognition of intracellular pathogens: detection and activation of the first line of defense.

APMIS 2009 May;117(5-6):323-37

Institute of Medical Microbiology and Immunology, University of Aarhus, Aarhus, Denmark.

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http://dx.doi.org/10.1111/j.1600-0463.2009.02456.xDOI Listing
May 2009