Staff at EMBL
Tobias Doerks
Genome Annotator
Bork Group
EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
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Publications
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. PubMed
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. PubMed
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. PubMed
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. PubMed
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. PubMed
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. PubMed
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. PubMed
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. PubMed
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. PubMed
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. PubMed
Computational characterization of multiple Gag-like human proteins. Campillos, M., Doerks, T., Shah, P.K. & Bork, P. Trends Genet. 2006 Sep 15;. PubMed
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 Jun 30;. PubMed
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. PubMed
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. PubMed
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. PubMed
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. PubMed
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. PubMed
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. PubMed
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. PubMed
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. PubMed
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. PubMed
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. PubMed
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. PubMed
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. PubMed
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. PubMed
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. PubMed
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. PubMed
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. PubMed
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. PubMed
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. PubMed
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 PubMed
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. PubMed
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. PubMed
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 PubMed
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. PubMed
Protein annotation: detective work for function prediction. Doerks, T., Bairoch, A. & Bork, P. Trends Genet 1998 Jun 14(6) 248-250 PubMed