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Staff at EMBL

Tobias Doerks

Genome Annotator
Bork Group

EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany

E-mail: send a mail

Publications

Experimental characterization of the human non-sequence-specific nucleic acid interactome. Durnberger, G., Burckstummer, T., Huber, K., Giambruno, R., Doerks, T., Karayel, E., Burkard, T.R., Kaupe, I., Muller, A.C., Schonegger, A., Ecker, G.F., Lohninger, H., Bork, P., Bennett, K.L., Superti-Furga, G. & Colinge, J. Genome Biol. 2013 Jul 31;14(7):R81. Europe PMC

Annotation of the M. tuberculosis hypothetical orfeome: adding functional information to more than half of the uncharacterized proteins. Doerks, T., van Noort, V., Minguez, P. & Bork, P. PLoS One. 2012;7(4):e34302. doi: 10.1371/journal.pone.0034302. Epub 2012 Apr 2. Europe PMC

A 15q24 microdeletion in transient myeloproliferative disease (TMD) and acute megakaryoblastic leukaemia (AMKL) implicates PML and SUMO3 in the leukaemogenesis of TMD/AMKL. Haemmerling, S., Behnisch, W., Doerks, T., Korbel, J.O., Bork, P., Moog, U., Hentze, S., Grasshoff, U., Bonin, M., Riess, O., Janssen, J.W., Jauch, A., Bartram, C.R., Reinhardt, D., Koch, K.A., Bandapalli, O.R. & Kulozik, A.E. Br J Haematol. 2012 Apr;157(2):180-7. doi: 10.1111/j.1365-2141.2012.09028.x. Epub2012 Feb 1. Europe PMC

SMART 7: recent updates to the protein domain annotation resource. Letunic, I., Doerks, T. & Bork, P. Nucleic Acids Res. 2012 Jan;40(Database issue):D302-5. doi: 10.1093/nar/gkr931.Epub 2011 Nov 3. Europe PMC

eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. Powell, S., Szklarczyk, D., Trachana, K., Roth, A., Kuhn, M., Muller, J., Arnold, R., Rattei, T., Letunic, I., Doerks, T., Jensen, L.J., von Mering, C. & Bork, P. Nucleic Acids Res. 2012 Jan;40(Database issue):D284-9. Epub 2011 Nov 16. Europe PMC

Orthology prediction methods: a quality assessment using curated protein families. Trachana, K., Larsson, T.A., Powell, S., Chen, W.H., Doerks, T., Muller, J. & Bork, P. Bioessays. 2011 Oct;33(10):769-80. doi: 10.1002/bies.201100062. Epub 2011Aug 19. Europe PMC

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Szklarczyk, D., Franceschini, A., Kuhn, M., Simonovic, M., Roth, A., Minguez, P., Doerks, T., Stark, M., Muller, J., Bork, P., Jensen, L.J. & von Mering, C. Nucleic Acids Res. 2011 Jan;39(Database issue):D561-8. Epub 2010 Nov 2. Europe PMC

Transcriptome complexity in a genome-reduced bacterium. Guell, M., van Noort, V., Yus, E., Chen, W.H., Leigh-Bell, J., Michalodimitrakis, K., Yamada, T., Arumugam, M., Doerks, T., Kuhner, S., Rode, M., Suyama, M., Schmidt, S., Gavin, A.C., Bork, P. & Serrano, L. Science. 2009 Nov 27;326(5957):1268-71. Europe PMC

SMART 6: recent updates and new developments. Letunic, I., Doerks, T. & Bork, P. Nucleic Acids Res. 2009 Jan;37(Database issue):D229-32. Epub 2008 Oct 31. Europe PMC

eggNOG: automated construction and annotation of orthologous groups of genes. Jensen, L.J., Julien, P., Kuhn, M., von Mering, C., Muller, J., Doerks, T. & Bork, P. Nucleic Acids Res. 2008 Jan;36(Database issue):D250-4. Epub 2007 Oct 16. Europe PMC

Target-specific requirements for enhancers of decapping in miRNA-mediated gene silencing. Eulalio, A., Rehwinkel, J., Stricker, M., Huntzinger, E., Yang, S.F., Doerks, T., Dorner, S., Bork, P., Boutros, M. & Izaurralde, E. Genes Dev. 2007 Oct 15;21(20):2558-70. Epub 2007 Sep 27. Europe PMC

Quantitative assessment of protein function prediction from metagenomics shotgun sequences. Harrington, E.D., Singh, A.H., Doerks, T., Letunic, I., von Mering, C., Jensen, L.J., Raes, J. & Bork, P. Proc Natl Acad Sci U S A. 2007 Aug 28;104(35):13913-8. Epub 2007 Aug 23. Europe PMC

Quantitative phylogenetic assessment of microbial communities in diverse environments. von Mering, C., Hugenholtz, P., Raes, J., Tringe, S.G., Doerks, T., Jensen, L.J., Ward, N. & Bork, P. Science. 2007 Feb 23;315(5815):1126-30. Epub 2007 Feb 1. Europe PMC

STRING 7--recent developments in the integration and prediction of protein interactions. von Mering, C., Jensen, L.J., Kuhn, M., Chaffron, S., Doerks, T., Kruger, B., Snel, B. & Bork, P. Nucleic Acids Res. 2007 Jan;35(Database issue):D358-62. Epub 2006 Nov 10. Europe PMC

Computational characterization of multiple Gag-like human proteins. Campillos, M., Doerks, T., Shah, P.K. & Bork, P. Trends Genet. 2006 Nov;22(11):585-9. Epub 2006 Sep 18. Europe PMC

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

Toward automatic reconstruction of a highly resolved tree of life. Ciccarelli, F.D., Doerks, T., von Mering, C., Creevey, C.J., Snel, B. & Bork, P. Science. 2006 Mar 3;311(5765):1283-7. Europe PMC

DCD - a novel plant specific domain in proteins involved in development and programmed cell death. Tenhaken, R., Doerks, T. & Bork, P. BMC Bioinformatics 2005 Jul 11;6:169. Europe PMC

Systematic association of genes to phenotypes by genome and literature mining. Korbel, J.O., Doerks, T., Jensen, L.J., Perez-Iratxeta, C., Kaczanowski, S., Hooper, S.D., Andrade, M.A. & Bork, P. PLoS Biol 2005 Apr 5;3(5):e134. Europe PMC

Global analysis of bacterial transcription factors to predict cellular target processes. Doerks, T., Andrade, M.A., Lathe W, 3rd, von Mering, C. & Bork, P. Trends Genet 2004 Mar;20(3):126-31. Europe PMC

SMART 4.0: towards genomic data integration. Letunic, I., Copley, R.R., Schmidt, S., Ciccarelli, F.D., Doerks, T., Schultz, J., Ponting, C.P. & Bork, P. Nucleic Acids Res 2004 Jan 1;32(1):D142-4. Europe PMC

Functional clues for hypothetical proteins based on genomic context analysis in prokaryotes. Doerks, T., von Mering, C. & Bork, P. Nucleic Acids Res ;32(21):6321-6. Print 2004. Europe PMC

BSD: a novel domain in transcription factors and synapse-associated proteins. Doerks, T., Huber, S., Buchner, E. & Bork, P. Trends Biochem Sci 2002 Apr;27(4):168-70. Europe PMC

AMOP, a protein module alternatively spliced in cancer cells. Ciccarelli, F.D., Doerks, T. & Bork, P. Trends Biochem Sci 2002 Mar;27(3):113-5. Europe PMC

Protein domain analysis in the era of complete genomes. Copley, R.R., Doerks, T., Letunic, I. & Bork, P. FEBS Lett 2002 Feb 20;513(1):129-34. Europe PMC

CASH – a beta-helix domain widespread among carbohydrate-binding proteins. Ciccarelli, F.D., Copley, R.R., Doerks, T., Russell, R.B. & Bork, P. Trends Biochem Sci 2002 Feb;27(2):59-62. Europe PMC

Recent improvements to the SMART domain-based sequence annotation resource. Letunic, I., Goodstadt, L., Dickens, N.J., Doerks, T., Schultz, J., Mott, R., Ciccarelli, F., Copley, R.R., Ponting, C.P. & Bork, P. Nucleic Acids Res 2002 Jan 1;30(1):242-4. Europe PMC

Systematic identification of novel protein domain families associated with nuclear functions. Doerks, T., Copley, R.R., Schultz, J., Ponting, C.P. & Bork, P. Genome Res 2002 Jan;12(1):47-56. Europe PMC

The Spir actin organizers are involved in vesicle transport processes. Kerkhoff, E., Simpson, J.C., Leberfinger, C.B., Otto, I.M., Doerks, T., Bork, P., Rapp, U.R., Raabe, T. & Pepperkok, R. Curr Biol 2001 Dec 11;11(24):1963-8. Europe PMC

DDT -- a novel domain in different transcription and chromosome remodeling factors. Doerks, T., Copley, R. & Bork, P. Trends Biochem Sci 2001 Mar;26(3):145-6. Europe PMC

GRAM, a novel domain in glucosyltransferases, myotubularins and other putative membrane-associated proteins. Doerks, T., Strauss, M., Brendel, M. & Bork, P. Trends Biochem Sci 2000 Oct;25(10):483-5. Europe PMC

Re-annotating the Mycoplasma pneumoniae genome sequence: adding value, function and reading frames. Dandekar, T., Huynen, M., Regula, J.T., Ueberle, B., Zimmermann, C.U., Andrade, M.A., Doerks, T., Sanchez-Pulido, L., Snel, B., Suyama, M., Yuan, Y.P., Herrmann, R. & Bork, P. Nucleic Acids Res 2000 Sep 1;28(17):3278-88. Europe PMC

Prediction of structural domains of TAP reveals details of its interaction with p15 and nucleoporins. Suyama, M., Doerks, T., Braun, I.C., Sattler, M., Izaurralde, E. & Bork, P. EMBO Rep. 2000 Jul;1(1):53-8. Europe PMC

L27, a novel heterodimerization domain in receptor targeting proteins Lin-2 and Lin-7. Doerks, T., Bork, P., Kamberov, E., Makarova, O., Muecke, S. & Margolis, B. Trends Biochem Sci 2000 Jul;25(7):317-8. Europe PMC

More than 1,000 putative new human signalling proteins revealed by EST data mining. Schultz, J., Doerks, T., Ponting, C.P., Copley, R.R. & Bork, P. Nat Genet 2000 Jun;25(2):201-4 Europe PMC

REF, an evolutionary conserved family of hnRNP-like proteins, interacts with TAP/Mex67p and participates in mRNA nuclear export. Stutz, F., Bachi, A., Doerks, T., Braun, I.C., Seraphin, B., Wilm, M., Bork, P. & Izaurralde, E. RNA 2000 Apr;6(4):638-50. Europe PMC

SMART: a web-based tool for the study of genetically mobile domains. Schultz, J., Copley, R.R., Doerks, T., Ponting, C.P. & Bork, P. Nucleic Acids Res 2000 Jan 1;28(1):231-4. Europe PMC

Domains in plexins: links to integrins and transcription factors. Bork, P., Doerks, T., Springer, T.A. & Snel, B. Trends Biochem Sci 1999 Jul;24(7):261-3 Europe PMC

Homology-based fold predictions for Mycoplasma genitalium proteins. Huynen, M., Doerks, T., Eisenhaber, F., Orengo, C., Sunyaev, S., Yuan, Y. & Bork, P. J Mol Biol 1998 Jul 17;280(3):323-6. Europe PMC

Protein annotation: detective work for function prediction. Doerks, T., Bairoch, A. & Bork, P. Trends Genet 1998 Jun 14(6) 248-250 Europe PMC