Thomas Sicheritz-Ponten

Thomas Sicheritz-Ponten

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Thomas Sicheritz-Ponten

Thomas Sicheritz-Ponten

Publications by authors named "Thomas Sicheritz-Ponten"

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81Publications

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The microbial composition of dried fish prepared according to Greenlandic Inuit traditions and industrial counterparts.

Food Microbiol 2020 Feb 13;85:103305. Epub 2019 Aug 13.

Department of Food Science, Faculty of Science, The University of Copenhagen, Rolighedsvej 26, 1958, Frederiksberg C, Denmark. Electronic address:

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http://dx.doi.org/10.1016/j.fm.2019.103305DOI Listing
February 2020

Protective role of the vulture facial skin and gut microbiomes aid adaptation to scavenging.

Acta Vet Scand 2018 Oct 11;60(1):61. Epub 2018 Oct 11.

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

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https://actavetscand.biomedcentral.com/articles/10.1186/s130
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http://dx.doi.org/10.1186/s13028-018-0415-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6182802PMC
October 2018

Comparative genomics sheds light on niche differentiation and the evolutionary history of comammox Nitrospira.

ISME J 2018 06 7;12(7):1779-1793. Epub 2018 Mar 7.

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

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http://dx.doi.org/10.1038/s41396-018-0083-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6018701PMC
June 2018

Norgal: extraction and de novo assembly of mitochondrial DNA from whole-genome sequencing data.

BMC Bioinformatics 2017 Nov 21;18(1):510. Epub 2017 Nov 21.

Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet, Building 208, Kgs Lyngby, 2800, Denmark.

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http://dx.doi.org/10.1186/s12859-017-1927-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5699183PMC
November 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

Upstream Freshwater and Terrestrial Sources Are Differentially Reflected in the Bacterial Community Structure along a Small Arctic River and Its Estuary.

Front Microbiol 2016 21;7:1474. Epub 2016 Sep 21.

Center for Permafrost, University of CopenhagenCopenhagen, Denmark; Department of Environmental Science, Aarhus UniversityRoskilde, Denmark.

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http://dx.doi.org/10.3389/fmicb.2016.01474DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5030300PMC
September 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

Whole-genome analyses resolve early branches in the tree of life of modern birds.

Authors:
Erich D Jarvis Siavash Mirarab Andre J Aberer Bo Li Peter Houde Cai Li Simon Y W Ho Brant C Faircloth Benoit Nabholz Jason T Howard Alexander Suh Claudia C Weber Rute R da Fonseca Jianwen Li Fang Zhang Hui Li Long Zhou Nitish Narula Liang Liu Ganesh Ganapathy Bastien Boussau Md Shamsuzzoha Bayzid Volodymyr Zavidovych Sankar Subramanian Toni Gabaldón Salvador Capella-Gutiérrez Jaime Huerta-Cepas Bhanu Rekepalli Kasper Munch Mikkel Schierup Bent Lindow Wesley C Warren David Ray Richard E Green Michael W Bruford Xiangjiang Zhan Andrew Dixon Shengbin Li Ning Li Yinhua Huang Elizabeth P Derryberry Mads Frost Bertelsen Frederick H Sheldon Robb T Brumfield Claudio V Mello Peter V Lovell Morgan Wirthlin Maria Paula Cruz Schneider Francisco Prosdocimi José Alfredo Samaniego Amhed Missael Vargas Velazquez Alonzo Alfaro-Núñez Paula F Campos Bent Petersen Thomas Sicheritz-Ponten An Pas Tom Bailey Paul Scofield Michael Bunce David M Lambert Qi Zhou Polina Perelman Amy C Driskell Beth Shapiro Zijun Xiong Yongli Zeng Shiping Liu Zhenyu Li Binghang Liu Kui Wu Jin Xiao Xiong Yinqi Qiuemei Zheng Yong Zhang Huanming Yang Jian Wang Linnea Smeds Frank E Rheindt Michael Braun Jon Fjeldsa Ludovic Orlando F Keith Barker Knud Andreas Jønsson Warren Johnson Klaus-Peter Koepfli Stephen O'Brien David Haussler Oliver A Ryder Carsten Rahbek Eske Willerslev Gary R Graves Travis C Glenn John McCormack Dave Burt Hans Ellegren Per Alström Scott V Edwards Alexandros Stamatakis David P Mindell Joel Cracraft Edward L Braun Tandy Warnow Wang Jun M Thomas P Gilbert Guojie Zhang

Science 2014 Dec;346(6215):1320-31

China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China. Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100 Copenhagen, Denmark.

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http://dx.doi.org/10.1126/science.1253451DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4405904PMC
December 2014

Bacterial diversity in snow on North Pole ice floes.

Extremophiles 2014 Nov 21;18(6):945-51. Epub 2014 Jun 21.

Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark.

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http://dx.doi.org/10.1007/s00792-014-0660-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4196135PMC
November 2014

The microbiome of New World vultures.

Nat Commun 2014 Nov 25;5:5498. Epub 2014 Nov 25.

Department of Environmental Science, Aarhus University, 4000 Roskilde, Denmark.

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http://dx.doi.org/10.1038/ncomms6498DOI Listing
November 2014

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

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

The chemical interactome space between the human host and the genetically defined gut metabotypes.

ISME J 2013 Apr 22;7(4):730-42. Epub 2012 Nov 22.

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

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http://dx.doi.org/10.1038/ismej.2012.141DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3603391PMC
April 2013

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

Enterotypes of the human gut microbiome.

Nature 2011 May 20;473(7346):174-80. Epub 2011 Apr 20.

European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.

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http://www-huber.embl.de/pub/pdf/Arumugam_Nature_2011.pdf
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http://www.nature.com/doifinder/10.1038/nature09944
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http://dx.doi.org/10.1038/nature09944DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3728647PMC
May 2011

InterMap3D: predicting and visualizing co-evolving protein residues.

Bioinformatics 2009 Aug 15;25(15):1963-5. Epub 2009 Jun 15.

Center for Biological Sequence Analysis, Technical University of Denmark, DK-2800 Lyngby, Denmark.

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http://dx.doi.org/10.1093/bioinformatics/btp335DOI Listing
August 2009

Horizontal gene transfer in eukaryotic parasites: a case study of Entamoeba histolytica and Trichomonas vaginalis.

Methods Mol Biol 2009 ;532:489-500

Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK.

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http://link.springer.com/10.1007/978-1-60327-853-9_28
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http://dx.doi.org/10.1007/978-1-60327-853-9_28DOI Listing
May 2009

Global features of the Alcanivorax borkumensis SK2 genome.

Environ Microbiol 2008 Mar 12;10(3):614-25. Epub 2007 Dec 12.

Klinische Forschergruppe, OE6711, Medizinische Hochschule Hannover, Carl-Neuberg-Strasse 1, D-30625 Hannover, Germany.

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http://dx.doi.org/10.1111/j.1462-2920.2007.01483.xDOI Listing
March 2008

Genome update: distribution of two-component transduction systems in 250 bacterial genomes.

Microbiology 2005 Nov;151(Pt 11):3447-52

Center for Biological Sequence Analysis, BioCentrum-DTU, Building 208, The Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark.

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http://dx.doi.org/10.1099/mic.0.28423-0DOI Listing
November 2005

Genome update: sigma factors in 240 bacterial genomes.

Microbiology 2005 Oct;151(Pt 10):3147-50

Center for Biological Sequence Analysis, BioCentrum-DTU, Building 208, The Technical University of Denmark, DK-2800 Kgs Lyngby, Denmark.

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http://dx.doi.org/10.1099/mic.0.28339-0DOI Listing
October 2005

Genome update: prediction of secreted proteins in 225 bacterial proteomes.

Microbiology 2005 Jun;151(Pt 6):1725-7

Center for Biological Sequence Analysis, BioCentrum-DTU, The Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark.

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http://dx.doi.org/10.1099/mic.0.28029-0DOI Listing
June 2005

Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence.

Proteomics 2004 Jun;4(6):1633-49

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

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http://doi.wiley.com/10.1002/pmic.200300771
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http://dx.doi.org/10.1002/pmic.200300771DOI Listing
June 2004

A first glimpse into the pattern and scale of gene transfer in Apicomplexa.

Int J Parasitol 2004 Mar;34(3):265-74

Center for Tropical and Emerging Global Diseases, University of Georgia, 623 Biological Sciences, Athens, GA 30602-2606, USA.

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http://linkinghub.elsevier.com/retrieve/pii/S002075190300360
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http://dx.doi.org/10.1016/j.ijpara.2003.11.025DOI Listing
March 2004

GenePublisher: Automated analysis of DNA microarray data.

Nucleic Acids Res 2003 Jul;31(13):3471-6

Center for Biological Sequence Analysis, BioCentrum-DTU, 2800 Lyngby, Denmark.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC169191PMC
http://dx.doi.org/10.1093/nar/gkg629DOI Listing
July 2003

Analysis of two large functionally uncharacterized regions in the Methanopyrus kandleri AV19 genome.

BMC Genomics 2003 Apr 2;4(1):12. Epub 2003 Apr 2.

Center for Biological Sequence Analysis, BioCentrum-DTU, Building 208, The Technical University of Denmark, DK-2800 Lyngby, Denmark.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC156604PMC
http://dx.doi.org/10.1186/1471-2164-4-12DOI Listing
April 2003