Damian Szklarczyk

Damian Szklarczyk

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Damian Szklarczyk

Damian Szklarczyk

Publications by authors named "Damian Szklarczyk"

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28Publications

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Tree reconciliation combined with subsampling improves large scale inference of orthologous group hierarchies.

BMC Bioinformatics 2019 May 6;20(1):228. Epub 2019 May 6.

Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, Zurich, 8057, Switzerland.

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http://dx.doi.org/10.1186/s12859-019-2828-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6501302PMC
May 2019

Viruses.STRING: A Virus-Host Protein-Protein Interaction Database.

Viruses 2018 09 23;10(10). Epub 2018 Sep 23.

Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200 Copenhagen N, Danmark.

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http://www.mdpi.com/1999-4915/10/10/519
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http://dx.doi.org/10.3390/v10100519DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6213343PMC
September 2018

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper.

Mol Biol Evol 2017 08;34(8):2115-2122

Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.

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http://dx.doi.org/10.1093/molbev/msx148DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5850834PMC
August 2017

The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible.

Nucleic Acids Res 2017 01 18;45(D1):D362-D368. Epub 2016 Oct 18.

Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland

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http://dx.doi.org/10.1093/nar/gkw937DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5210637PMC
January 2017

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences.

Nucleic Acids Res 2016 Jan 17;44(D1):D286-93. Epub 2015 Nov 17.

Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany Germany Molecular Medicine Partnership Unit (MMPU), University Hospital Heidelberg and European Molecular Biology Laboratory, Heidelberg 69117, Germany Max Delbrück Centre for Molecular Medicine, Berlin 13125, Germany

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http://nar.oxfordjournals.org/content/early/2015/11/17/nar.g
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http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gkv1248
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http://dx.doi.org/10.1093/nar/gkv1248DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702882PMC
January 2016

WeGET: predicting new genes for molecular systems by weighted co-expression.

Nucleic Acids Res 2016 Jan 17;44(D1):D567-73. Epub 2015 Nov 17.

Centre for Molecular and Biomolecular Informatics (CMBI), Radboud University Medical Centre, Geert Grooteplein Zuid 26-28, 6525 GA Nijmegen, Nijmegen, The Netherlands Centre for Systems Biology and Bioenergetics (CSBB), Radboud University Medical Centre, Geert Grooteplein Zuid 10, 6500 HB Nijmegen, Nijmegen, The Netherlands

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http://dx.doi.org/10.1093/nar/gkv1228DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702868PMC
January 2016

STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data.

Nucleic Acids Res 2016 Jan 20;44(D1):D380-4. Epub 2015 Nov 20.

Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden

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http://dx.doi.org/10.1093/nar/gkv1277DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702904PMC
January 2016

Protein-protein interaction databases.

Methods Mol Biol 2015 ;1278:39-56

Faculty of Health Sciences, Novo Nordisk Foundation Centre for Protein Research, University of Copenhagen, Blegdamsvej 3B, 2200, København N, Denmark.

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http://dx.doi.org/10.1007/978-1-4939-2425-7_3DOI Listing
December 2015

Version 4.0 of PaxDb: Protein abundance data, integrated across model organisms, tissues, and cell-lines.

Proteomics 2015 Sep 12;15(18):3163-8. Epub 2015 Mar 12.

Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Switzerland.

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http://dx.doi.org/10.1002/pmic.201400441DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6680238PMC
September 2015

STRING v10: protein-protein interaction networks, integrated over the tree of life.

Nucleic Acids Res 2015 Jan 28;43(Database issue):D447-52. Epub 2014 Oct 28.

Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland

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http://dx.doi.org/10.1093/nar/gku1003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383874PMC
January 2015

STITCH 4: integration of protein-chemical interactions with user data.

Nucleic Acids Res 2014 Jan 28;42(Database issue):D401-7. Epub 2013 Nov 28.

Biotechnology Center, TU Dresden, 01062 Dresden, Germany, Institute of Molecular Life Sciences, University of Zurich and Swiss Institute of Bioinformatics, Winterthurerstrasse 190, 8057 Zurich, Switzerland, Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany and Max-Delbrück-Centre for Molecular Medicine, Robert-Rössle-Strasse 10, 13092 Berlin, Germany.

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http://dx.doi.org/10.1093/nar/gkt1207DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3964996PMC
January 2014

eggNOG v4.0: nested orthology inference across 3686 organisms.

Nucleic Acids Res 2014 Jan 1;42(Database issue):D231-9. Epub 2013 Dec 1.

European Molecular Biology Laboratory, Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany, University of Zurich and Swiss Institute of Bioinformatics, Institute of Molecular Life Sciences, Winterthurerstrasse 190, 8057 Zurich, Switzerland, Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109-5234, USA, Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), C/Dr. Aiguader 88, 08003 Barcelona, Spain, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain, CUBE-Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Althanstraße 14, 1090 Vienna, Austria, Institute of Biological, Environmental & Rural Sciences, Aberystwyth University, Penglais, Aberystwyth, Ceredigion, SY23 3FG, UK, Biotechnology Center, TU Dresden, 01062 Dresden, Germany, Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, 2200, Copenhagen N, Denmark and Max-Delbrück-Centre for Molecular Medicine, Robert-Rössle-Strasse 10, 13092 Berlin, Germany.

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http://dx.doi.org/10.1093/nar/gkt1253DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3964997PMC
January 2014

"Orphan" retrogenes in the human genome.

Mol Biol Evol 2013 Feb 12;30(2):384-96. Epub 2012 Oct 12.

Laboratory of Bionformatics, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland.

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http://dx.doi.org/10.1093/molbev/mss235DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3548309PMC
February 2013

STRING v9.1: protein-protein interaction networks, with increased coverage and integration.

Nucleic Acids Res 2013 Jan 29;41(Database issue):D808-15. Epub 2012 Nov 29.

Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Switzerland.

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http://dx.doi.org/10.1093/nar/gks1094DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531103PMC
January 2013

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

Proteomic analysis of a pleistocene mammoth femur reveals more than one hundred ancient bone proteins.

J Proteome Res 2012 Feb 14;11(2):917-26. Epub 2011 Dec 14.

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/10.1021/pr200721uDOI Listing
February 2012

STITCH 3: zooming in on protein-chemical interactions.

Nucleic Acids Res 2012 Jan 9;40(Database issue):D876-80. Epub 2011 Nov 9.

Biotechnology Center, TU Dresden, 01062 Dresden, Germany.

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http://dx.doi.org/10.1093/nar/gkr1011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245073PMC
January 2012

Pre-Clovis mastodon hunting 13,800 years ago at the Manis site, Washington.

Science 2011 Oct;334(6054):351-3

Center for the Study of the First Americans, Department of Anthropology, Texas A&M University, 4352 TAMU, College Station, TX 77843-4352, USA.

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http://dx.doi.org/10.1126/science.1207663DOI Listing
October 2011

Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level.

Mol Cell Proteomics 2011 Mar 7;10(3):M110.003590. Epub 2010 Dec 7.

Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health Sciences, DK-2200 Copenhagen.

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http://dx.doi.org/10.1074/mcp.M110.003590DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3047152PMC
March 2011

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored.

Nucleic Acids Res 2011 Jan 2;39(Database issue):D561-8. Epub 2010 Nov 2.

Faculty of Health Sciences, Novo Nordisk Foundation Centre for Protein Research, University of Copenhagen, Denmark.

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http://dx.doi.org/10.1093/nar/gkq973DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013807PMC
January 2011

Specific CLK inhibitors from a novel chemotype for regulation of alternative splicing.

Chem Biol 2011 Jan;18(1):67-76

University of Oxford, Nuffield Department of Clinical Medicine, Structural Genomics Consortium, Old Road Campus Research Building, Oxford OX37DQ, UK.

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http://dx.doi.org/10.1016/j.chembiol.2010.11.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3145970PMC
January 2011

STITCH 2: an interaction network database for small molecules and proteins.

Nucleic Acids Res 2010 Jan 6;38(Database issue):D552-6. Epub 2009 Nov 6.

Biotechnology Center, TU Dresden, 01062 Dresden, Germany.

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http://dx.doi.org/10.1093/nar/gkp937DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808890PMC
January 2010