Dr. Tobias Doerks

EMBL private
EMBL - European Molecular Biology Laboratory                   
Meyerhofstra?e 1
69117 Heidelberg, Germany
(+49) 6221-387-456
(+49) 6221-705569

Background (complete curriculum vitae (german))
1992-1998: Undergraduate studies in Biology at J.W.-Goethe-Universitaet Frankfurt a.M.
since August 1997 member of humangenetics workgroup (Prof.Dr. Anna Starzinski-Powitz)
and visitor at EMBL
diploma thesis : "Methodenentwicklung und Anwendungsbeispiele
fuer Protein- und Nukleotidsequenzanalysen"
functional characterization of unknown protein families (UPFs)
web-tool developement : prediction of Intrinsic Features


1998-2001 PhD student at EMBL ``Annotation and classification of nuclear domains'',
member of Bork Group (Biocomputing) Download of thesis and presentation (german)

Dec 2001-Jun 2003 employee at Anadays Pharmaceuticals Europe GmbH
setup of a bioinformatics department

since July 2003 postdoctoral research at EMBL Bork Group (Biocomputing)

since July 2005 junior groupleader equivalent position at EMBL Bork Group (Biocomputing)
granted by the NGFN - Nationales Genomforschungsnetz / NGFN plus

February 2008 founding of Life Science company biobyte solutions GmbH

Scientific interests
functional prediction of proteins, comparative sequence analysis, domain hunting
genomic context analysis, meta genomics, phylogenetic analysis

T. Doerks, A. Bairoch, P. Bork
``Protein annotation: detective work for function prediction``
Trends in Genetics 1998 Jun; 14(6): 248-250

M. A. Huynen, T. Doerks, F. Eisenhaber, C. Orengo, S. Sunyaev, Y. Yuan and P. Bork.
``Homology based fold predictions for Mycoplasma genitalium proteins''
J Mol Biol. 1998 Jul 17; 280(3): 323-326

P. Bork, T. Doerks, TA. Springer, B. Snel.
``Domains in plexins: links to integrins and transcription factors''
Trends Biochem Sci. 1999 Jul;24(7):261-263

J. Schultz, R. R. Copley, T. Doerks, C. P. Ponting, P. Bork
``SMART: a web-based tool for the study of genetically mobile domains.''
Nucleic Acids Res 2000 Jan 1;28(1):231-234

Stutz F, Bachi A, Doerks T, Braun IC, Seraphin B, Wilm M, Bork P, Izaurralde E.
``REF, an evolutionary conserved family of hnRNP-like proteins,
interacts with TAP/Mex67p and participates in mRNA nuclear export.''
RNA 2000 Apr;6(4):638-50

Schultz J, Doerks T, Ponting CP, Copley RR, Bork P.
``More than 1,000 putative new human signalling proteins revealed by EST data mining''
Nat Genet 2000 Jun;25(2):201-204

Doerks T, Bork P, Kamberov E, Makarova O, Muecke S, Margolis B
``L27, a novel heterodimerization domain in receptor targeting proteins Lin-2 and Lin-7''
Trends Biochem Sci 2000 Jul;25(7):317-318

Suyama M, Doerks T, Braun IC, Sattler M, Izauralde E, Bork P
``Prediction of structural domains of TAP reveals details of its interaction with p15 and nucleoporins''
EMBO Reports 2000 Jul; vol.1 no.1 : 53-58

Dandekar T, Huynen M, Regula JT, Ueberle B, Zimmermann CU, Andrade MA, Doerks T, Sanchez-Pulido L, Snel B, Suyama M, Yuan YP, Herrmann R, Bork P.
``Re-annotating the Mycoplasma pneumoniae genome sequence: adding value, function and reading frames.''
Nucleic Acids Res 2000 Sep 1;28(17):3278-3288

Doerks T, Strauss M, Brendel M, Bork P
``GRAM, a novel domain in glucosyltransferases, myotubularins and other putative membrane-associated proteins''
Trends Biochem Sci 2000 Oct;25(10):483-5

Doerks T, Copley RR, Bork P
``DDT, a novel domain in differrent transcription and chromosome remodeling factors''
Trends Biochem Sci 2001 Mar 1;26(3):145-146

International Human Genome Sequencing Consortium
``Initial sequencing and analysis of the human genome''
Nature 2001 Feb 15;409(6822):860-921

Francesca D. Ciccarelli, Richard R. Copley, Tobias Doerks, Robert B. Russell and Peer Bork
``CASH - a beta-helix domain widespread among carbohydrate-binding proteins''
Trends Biochem Sci 2002 Feb;27(2):59-62

Tobias Doerks*, Richard Copley*, Joerg Schultz, Chris Ponting and Peer Bork
``Systematic identification of novel protein domain families associated with nuclear functions''
Genome Res 2002 Jan;12(1):47-56

Tobias Doerks, Saskia Huber, Erich Buchner and Peer Bork
``BSD, a novel domain in transcription factors and other chromatin-associated proteins''
Nucleic Acids Res 2002 Jan 1;30:1-3

Richard R. Copley, Tobias Doerks, Ivica Letunic and Peer Bork
``Protein Domain Analysis in the Era of Complete Genoms''
FEBS Lett 2002 Feb 20;513(1):129-34

Pierre Nicodeme, Tobias Doerks and Martin Vingron
``Motif Statistics Applied to Proteome Analysis''
Bioinformatics 2002 Oct;18 Suppl 2:S161-71

Eugen Kerkhoff, Jeremy C. Simpson, Cornelia B. Leberfinger, Ines M. Otto, Tobias Doerks, Peer Bork, Ulf R. Rapp, Thomas Raabe and Rainer Pepperkok
``The Spir actin organizers are involved in vesicle transport processes''
Curr Biol 2001 Dec 11;11(24):1963-8

Francesca D. Ciccarelli, Tobias Doerks and Peer Bork
``AMOP, a protein module alternatively spliced in cancer cells.''
Trends Biochem Sci 2002 Mar;27(3):113-5

Tobias Doerks, Miguel A. Andrade, Warren Lathe 3rd, Christian von Mering and Peer Bork
``Global analysis of bacterial transcription factors to predict cellular target processes''
Trends Genet. 2004 Mar;20(3):126-31

Letunic I, Copley RR, Schmidt S, Ciccarelli FD, Doerks T, Schultz J, Ponting CP, Bork P.
``SMART 4.0: towards genomic data integration.''
Nucleic Acids Res 2004 Jan 1;32(1):D142-4

Tobias Doerks, Christian von Mering and Peer Bork
``Functional clues for hypothetical proteins based on genomic context analysis in prokaryotes''
Nucleic Acids Res. 2004 Dec 01;32(21):6321-6

Jan O. Korbel*, Tobias Doerks*, Lars J. Jensen, Carolina Perez-Iratxeta, Szymon Kaczanowski, Sean D. Hooper, Miguel A. Andrade & Peer Bork
``Systematic association of genes to phenotypes by genome and literature mining''
PLoS Biol. 2005 May;3(5):e134. Epub 2005 Apr 5

Raimund Tenhaken*, Tobias Doerks* & Peer Bork
``DCD - a novel plant specific domain in proteins involved in development and programmed cell death''
BMC Bioinformatics 2005, 6:169 (11Jul2005)

Ciccarelli FD*, Doerks T*, von Mering C, Creevey CJ, Snel B & Bork P.
``Toward automatic reconstruction of a highly resolved tree of life''
Science. 2006 Mar 3;311(5765):1283-7. related press release and interview with Deutschland Funk

Behm-Ansmant I, Rehwinkel J, Doerks T, Stark A, Bork P, Izaurralde E.
``mRNA degradation by miRNAs and GW182 requires both CCR4:NOT deadenylase and DCP1:DCP2 decapping complexes''
Genes Dev. 2006 Jul 15;20(14):1885-98. Epub 2006 Jun 30

Campillos M, Doerks T, Shah PK, Bork P.
``Computational characterization of multiple Gag-like human proteins.''
Trends Genet. 2006 Nov;22(11):585-9. Epub 2006 Sep 18.

von Mering C, J Jensen L, Kuhn M, Chaffron S, Doerks T, Kruger B, Snel B, Bork P.
``STRING 7--recent developments in the integration and prediction of protein interactions.''
Nucleic Acids Res. 2007 Jan;35

von Mering C, Hugenholtz P, Raes J, Tringe SG, Doerks T, Jensen LJ, Ward N, Bork P.
``Quantitative phylogenetic assessment of microbial communities in diverse environments.''
Science. 2007 Feb 23;315(5815):1126-30. Epub 2007 Feb 1.

Harrington ED, Singh AH, Doerks T, Letunic I, von Mering C, Jensen LJ, Raes J, Bork P.
``Quantitative assessment of protein function prediction from metagenomics shotgun sequences.''
Proc Natl Acad Sci U S A. 2007 Aug 23

Eulalio A, Rehwinkel J, Stricker M, Huntzinger E, Yang SF, Doerks T, Dorner S, Bork P, Boutros M, Izaurralde E.
``Target-specific requirements for enhancers of decapping in miRNA-mediated gene silencing.''
Genes Dev. 2007 Oct 15;21(20):2558-70. Epub 2007 Sep 27

Jensen LJ, Julien P, Kuhn M, von Mering C, Muller J, Doerks T, Bork P.
``eggNOG: automated construction and annotation of orthologous groups of genes.''
Nucleic Acids Res. 2008 Jan;36

Singh AH, Doerks T, Letunic I, Raes J, Bork P.
``Discovering functional novelty in metagenomes: examples from light-mediated processes.''
J Bacteriol. 2008 Oct 10.

Jensen LJ, Kuhn M, Stark M, Chaffron S, Creevey C, Muller J, Doerks T, Julien P, Roth A, Simonovic M, Bork P, Mering CV.
``STRING 8--a global view on proteins and their functional interactions in 630 organisms.''
Nucleic Acids Res. 2008 Oct 21.

Foerstner KU, Doerks T, Creevey CJ, Doerks A, Bork P.
``A computational screen for type I polyketide synthases in metagenomics shotgun data.''
PLoS ONE. 2008;3(10):e3515. Epub 2008 Oct 27.

Letunic I, Doerks T, Bork P.
``SMART 6: recent updates and new developments.''
Nucleic Acids Res. 2009 Jan;37(Database issue):D229-32. Epub 2008 Oct 31.

Jerzy Jankun, Tobias Doerks, Ansari M. Aleem, Wies awa ysiak-Szyd owska and Ewa Skrzypczak-Jankun
``Do Human Lipoxygenases have a PDZ Regulatory Domain?''
Current Molecular Medicine. 2008, 8: 768-773

Foerstner KU, Doerks T, Muller J, Raes J, Bork P.
``A nitrile hydratase in the eukaryote Monosiga brevicollis.''
PLoS ONE. 2008;3(12):e3976. Epub 2008 Dec 19.

Güell M, van Noort V, Yus E, Chen WH, Leigh-Bell J, Michalodimitrakis K, Yamada T, Arumugam M, Doerks T, Kühner S, Rode M, Suyama M, Schmidt S, Gavin AC, Bork P, Serrano L.
``Transcriptome complexity in a genome-reduced bacterium.''
Science. 2009 Nov 27;326(5957):1268-71

Muller J, Szklarczyk D, Julien P, Letunic I, Roth A, Kuhn M, Powell S, von Mering C, Doerks T, Jensen LJ, Bork P.
``eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations.''
Nucleic Acids Res. 2010 Jan;38(Database issue):D190-5.

Szklarczyk D, Franceschini A, Kuhn M, Simonovic M, Roth A, Minguez P, Doerks T, Stark M, Muller J, Bork P, Jensen LJ, von Mering C.
``The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored.''
Nucleic Acids Res. 2011 Jan;39(Database issue):D561-8

Creevey CJ, Doerks T, Fitzpatrick DA, Raes J, Bork P.
``Universally distributed single-copy genes indicate a constant rate of horizontal transfer.''
PLoS One. 2011;6(8):e22099

Trachana K, Larsson TA, Powell S, Chen WH, Doerks T, Muller J, Bork P.
``Orthology prediction methods: a quality assessment using curated protein families.''
Bioessays. 2011 Oct;33(10):769-80

Creevey CJ, Muller J, Doerks T, Thompson JD, Arendt D, Bork P.
``Identifying single copy orthologs in Metazoa.''
PLoS Comput Biol. 2011 Dec;7(12)

Letunic I, Doerks T, Bork P.
``SMART 7: recent updates to the protein domain annotation resource.''
Nucleic Acids Res. 2012 Jan;40(Database issue):D302-5

Powell S, Szklarczyk D, Trachana K, Roth A, Kuhn M, Muller J, Arnold R, Rattei T, Letunic I, Doerks T, Jensen LJ, von Mering C, Bork P.
``eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges.''
Nucleic Acids Res. 2012 Jan;40(Database issue):D284-9

Haemmerling S, Behnisch W, Doerks T, Korbel JO, Bork P, Moog U, Hentze S, Grasshoff U, Bonin M, Rieß O, Janssen JW, Jauch A, Bartram CR, Reinhardt D, Koch KA, Bandapalli OR, Kulozik AE.
``A 15q24 microdeletion in transient myeloproliferative disease (TMD) and acute megakaryoblastic leukaemia (AMKL) implicates PML and SUMO3 in the leukaemogenesis of TMD/AMKL.''
Br J Haematol. 2012 Apr;157(2):180-7

Doerks T, van Noort V, Minguez P, Bork P.
``Annotation of the M. tuberculosis hypothetical orfeome: adding functional information to more than half of the uncharacterized proteins.''
PLoS One. 2012;7(4):

Dürnberger G, Bürckstümmer T, Huber K, Giambruno R, Doerks T, Karayel E, Burkard TR, Kaupe I, Müller AC, Schönegger A, Ecker GF, Lohninger H, Bork P, Bennett KL, Superti-Furga G, Colinge J.
``Experimental characterization of the human non-sequence-specific nucleic acid interactome.''
Genome Biol. 2013 Jul 31;14(7)

(*These authors equally contributed to the work)

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