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Tobias Doerks - Publications

Affiliations: 
Structural and Computational Biology European Molecular Biology Laboratory (EMBL), Heidelberg, Baden-Württemberg, Germany 
Website:
http://doerks.de/
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55 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2018 Kayser K, Degenhardt F, Holzapfel S, Horpaopan S, Peters S, Spier I, Morak M, Vangala D, Rahner N, von Knebel-Doeberitz M, Schackert HK, Engel C, Büttner R, Wijnen J, Doerks T, et al. Copy number variation analysis and targeted NGS in 77 families with suspected Lynch syndrome reveals novel potential causative genes. International Journal of Cancer. PMID 29987844 DOI: 10.1002/Ijc.31725  0.611
2015 Djuika CF, Huerta-Cepas J, Przyborski JM, Deil S, Sanchez CP, Doerks T, Bork P, Lanzer M, Deponte M. Prokaryotic ancestry and gene fusion of a dual localized peroxiredoxin in malaria parasites. Microbial Cell (Graz, Austria). 2: 5-13. PMID 28357258 DOI: 10.15698/Mic2015.01.182  0.561
2015 Vonkova I, Saliba AE, Deghou S, Anand K, Ceschia S, Doerks T, Galih A, Kugler KG, Maeda K, Rybin V, van Noort V, Ellenberg J, Bork P, Gavin AC. Lipid Cooperativity as a General Membrane-Recruitment Principle for PH Domains. Cell Reports. 12: 1519-30. PMID 26299969 DOI: 10.1016/J.Celrep.2015.07.054  0.707
2015 Letunic I, Doerks T, Bork P. SMART: recent updates, new developments and status in 2015. Nucleic Acids Research. 43: D257-60. PMID 25300481 DOI: 10.1093/Nar/Gku949  0.795
2014 Bock T, Chen WH, Ori A, Malik N, Silva-Martin N, Huerta-Cepas J, Powell ST, Kastritis PL, Smyshlyaev G, Vonkova I, Kirkpatrick J, Doerks T, Nesme L, Baßler J, Kos M, et al. An integrated approach for genome annotation of the eukaryotic thermophile Chaetomium thermophilum. Nucleic Acids Research. 42: 13525-33. PMID 25398899 DOI: 10.1093/Nar/Gku1147  0.797
2014 Trachana K, Forslund K, Larsson T, Powell S, Doerks T, von Mering C, Bork P. A phylogeny-based benchmarking test for orthology inference reveals the limitations of function-based validation. Plos One. 9: e111122. PMID 25369365 DOI: 10.1371/Journal.Pone.0111122  0.803
2013 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, et al. Experimental characterization of the human non-sequence-specific nucleic acid interactome. Genome Biology. 14: R81. PMID 23902751 DOI: 10.1186/Gb-2013-14-7-R81  0.592
2012 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. 7: e34302. PMID 22485162 DOI: 10.1371/Journal.Pone.0034302  0.787
2012 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, et al. A 15q24 microdeletion in transient myeloproliferative disease (TMD) and acute megakaryoblastic leukaemia (AMKL) implicates PML and SUMO3 in the leukaemogenesis of TMD/AMKL. British Journal of Haematology. 157: 180-7. PMID 22296450 DOI: 10.1111/J.1365-2141.2012.09028.X  0.661
2012 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 Research. 40: D284-9. PMID 22096231 DOI: 10.1093/Nar/Gkr1060  0.79
2012 Letunic I, Doerks T, Bork P. SMART 7: recent updates to the protein domain annotation resource. Nucleic Acids Research. 40: D302-5. PMID 22053084 DOI: 10.1093/Nar/Gkr931  0.786
2011 Creevey CJ, Muller J, Doerks T, Thompson JD, Arendt D, Bork P. Identifying single copy orthologs in Metazoa. Plos Computational Biology. 7: e1002269. PMID 22144877 DOI: 10.1371/Journal.Pcbi.1002269  0.806
2011 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 : News and Reviews in Molecular, Cellular and Developmental Biology. 33: 769-80. PMID 21853451 DOI: 10.1002/Bies.201100062  0.799
2011 Creevey CJ, Doerks T, Fitzpatrick DA, Raes J, Bork P. Universally distributed single-copy genes indicate a constant rate of horizontal transfer. Plos One. 6: e22099. PMID 21850220 DOI: 10.1371/Journal.Pone.0022099  0.773
2011 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 Research. 39: D561-8. PMID 21045058 DOI: 10.1093/Nar/Gkq973  0.815
2010 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 Research. 38: D190-5. PMID 19900971 DOI: 10.1093/Nar/Gkp951  0.835
2009 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, et al. Transcriptome complexity in a genome-reduced bacterium. Science (New York, N.Y.). 326: 1268-71. PMID 19965477 DOI: 10.1126/Science.1176951  0.788
2009 Letunic I, Doerks T, Bork P. SMART 6: recent updates and new developments. Nucleic Acids Research. 37: D229-32. PMID 18978020 DOI: 10.1093/Nar/Gkn808  0.781
2009 Jensen LJ, Kuhn M, Stark M, Chaffron S, Creevey C, Muller J, Doerks T, Julien P, Roth A, Simonovic M, Bork P, von Mering C. STRING 8--a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Research. 37: D412-6. PMID 18940858 DOI: 10.1093/Nar/Gkn760  0.815
2009 Singh AH, Doerks T, Letunic I, Raes J, Bork P. Discovering functional novelty in metagenomes: examples from light-mediated processes. Journal of Bacteriology. 191: 32-41. PMID 18849420 DOI: 10.1128/Jb.01084-08  0.807
2008 Foerstner KU, Doerks T, Muller J, Raes J, Bork P. A nitrile hydratase in the eukaryote Monosiga brevicollis. Plos One. 3: e3976. PMID 19096720 DOI: 10.1371/Journal.Pone.0003976  0.788
2008 Foerstner KU, Doerks T, Creevey CJ, Doerks A, Bork P. A computational screen for type I polyketide synthases in metagenomics shotgun data. Plos One. 3: e3515. PMID 18953415 DOI: 10.1371/Journal.Pone.0003515  0.787
2008 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 Research. 36: D250-4. PMID 17942413 DOI: 10.1093/Nar/Gkm796  0.832
2007 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 & Development. 21: 2558-70. PMID 17901217 DOI: 10.1101/Gad.443107  0.483
2007 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. Proceedings of the National Academy of Sciences of the United States of America. 104: 13913-8. PMID 17717083 DOI: 10.1073/Pnas.0702636104  0.825
2007 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 (New York, N.Y.). 315: 1126-30. PMID 17272687 DOI: 10.1126/Science.1133420  0.778
2007 von Mering C, Jensen LJ, Kuhn M, Chaffron S, Doerks T, Krüger B, Snel B, Bork P. STRING 7--recent developments in the integration and prediction of protein interactions. Nucleic Acids Research. 35: D358-62. PMID 17098935 DOI: 10.1093/Nar/Gkl825  0.83
2006 Campillos M, Doerks T, Shah PK, Bork P. Computational characterization of multiple Gag-like human proteins. Trends in Genetics : Tig. 22: 585-9. PMID 16979784 DOI: 10.1016/J.Tig.2006.09.006  0.825
2006 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 & Development. 20: 1885-98. PMID 16815998 DOI: 10.1101/Gad.1424106  0.498
2006 Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P. Toward automatic reconstruction of a highly resolved tree of life. Science (New York, N.Y.). 311: 1283-7. PMID 16513982 DOI: 10.1126/Science.1123061  0.795
2005 Tenhaken R, Doerks T, Bork P. DCD - a novel plant specific domain in proteins involved in development and programmed cell death. Bmc Bioinformatics. 6: 169. PMID 16008837 DOI: 10.1186/1471-2105-6-169  0.578
2005 Korbel JO, Doerks T, Jensen LJ, Perez-Iratxeta C, Kaczanowski S, Hooper SD, Andrade MA, Bork P. Systematic association of genes to phenotypes by genome and literature mining. Plos Biology. 3: e134. PMID 15799710 DOI: 10.1371/Journal.Pbio.0030134  0.803
2004 Doerks T, von Mering C, Bork P. Functional clues for hypothetical proteins based on genomic context analysis in prokaryotes. Nucleic Acids Research. 32: 6321-6. PMID 15576358 DOI: 10.1093/Nar/Gkh973  0.766
2004 Doerks T, Andrade MA, Lathe W, von Mering C, Bork P. Global analysis of bacterial transcription factors to predict cellular target processes. Trends in Genetics : Tig. 20: 126-31. PMID 15049306 DOI: 10.1016/J.Tig.2004.01.006  0.811
2004 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 Research. 32: D142-4. PMID 14681379 DOI: 10.1093/Nar/Gkh088  0.845
2002 Nicodème P, Doerks T, Vingron M. Proteome analysis based on motif statistics. Bioinformatics (Oxford, England). 18: S161-71. PMID 12385999 DOI: 10.1093/BIOINFORMATICS/18.SUPPL_2.S161  0.404
2002 Doerks T, Huber S, Buchner E, Bork P. BSD: a novel domain in transcription factors and synapse-associated proteins. Trends in Biochemical Sciences. 27: 168-70. PMID 11943536 DOI: 10.1016/S0968-0004(01)02042-4  0.605
2002 Copley RR, Doerks T, Letunic I, Bork P. Protein domain analysis in the era of complete genomes. Febs Letters. 513: 129-34. PMID 11911892 DOI: 10.1016/S0014-5793(01)03289-6  0.84
2002 Ciccarelli FD, Doerks T, Bork P. AMOP, a protein module alternatively spliced in cancer cells. Trends in Biochemical Sciences. 27: 113-5. PMID 11893501 DOI: 10.1016/S0968-0004(01)02049-7  0.722
2002 Ciccarelli FD, Copley RR, Doerks T, Russell RB, Bork P. CASH--a beta-helix domain widespread among carbohydrate-binding proteins. Trends in Biochemical Sciences. 27: 59-62. PMID 11852237 DOI: 10.1016/S0968-0004(01)02046-1  0.794
2002 Doerks T, Copley RR, Schultz J, Ponting CP, Bork P. Systematic identification of novel protein domain families associated with nuclear functions. Genome Research. 12: 47-56. PMID 11779830 DOI: 10.1101/Gr.203201  0.751
2002 Letunic I, Goodstadt L, Dickens NJ, Doerks T, Schultz J, Mott R, Ciccarelli F, Copley RR, Ponting CP, Bork P. Recent improvements to the SMART domain-based sequence annotation resource. Nucleic Acids Research. 30: 242-4. PMID 11752305 DOI: 10.1093/Nar/30.1.242  0.814
2001 Kerkhoff E, Simpson JC, Leberfinger CB, Otto IM, Doerks T, Bork P, Rapp UR, Raabe T, Pepperkok R. The Spir actin organizers are involved in vesicle transport processes. Current Biology : Cb. 11: 1963-8. PMID 11747823 DOI: 10.1016/S0960-9822(01)00602-9  0.58
2001 Doerks T, Copley R, Bork P. DDT -- a novel domain in different transcription and chromosome remodeling factors. Trends in Biochemical Sciences. 26: 145-6. PMID 11246006 DOI: 10.1016/S0968-0004(00)01769-2  0.734
2001 Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, ... ... Doerks T, et al. Initial sequencing and analysis of the human genome. Nature. 409: 860-921. PMID 11237011 DOI: 10.1038/35057062  0.733
2000 Suyama M, Doerks T, Braun IC, Sattler M, Izaurralde E, Bork P. Prediction of structural domains of TAP reveals details of its interaction with p15 and nucleoporins. Embo Reports. 1: 53-8. PMID 11256625 DOI: 10.1093/Embo-Reports/Kvd009  0.687
2000 Doerks T, Strauss M, Brendel M, Bork P. GRAM, a novel domain in glucosyltransferases, myotubularins and other putative membrane-associated proteins. Trends in Biochemical Sciences. 25: 483-5. PMID 11050430 DOI: 10.1016/S0968-0004(00)01664-9  0.539
2000 Dandekar T, Huynen M, Regula JT, Ueberle B, Zimmermann CU, Andrade MA, Doerks T, Sánchez-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 Research. 28: 3278-88. PMID 10954595 DOI: 10.1093/Nar/28.17.3278  0.832
2000 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 in Biochemical Sciences. 25: 317-8. PMID 10871881 DOI: 10.1016/S0968-0004(00)01599-1  0.546
2000 Schultz J, Doerks T, Ponting CP, Copley RR, Bork P. More than 1,000 putative new human signalling proteins revealed by EST data mining. Nature Genetics. 25: 201-4. PMID 10835637 DOI: 10.1038/76069  0.776
2000 Stutz F, Bachi A, Doerks T, Braun IC, Séraphin 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 (New York, N.Y.). 6: 638-50. PMID 10786854 DOI: 10.1017/S1355838200000078  0.563
2000 Schultz J, Copley RR, Doerks T, Ponting CP, Bork P. SMART: a web-based tool for the study of genetically mobile domains. Nucleic Acids Research. 28: 231-4. PMID 10592234 DOI: 10.1093/Nar/28.1.231  0.754
1999 Bork P, Doerks T, Springer TA, Snel B. Domains in plexins: links to integrins and transcription factors. Trends in Biochemical Sciences. 24: 261-3. PMID 10390613 DOI: 10.1016/S0968-0004(99)01416-4  0.643
1998 Huynen M, Doerks T, Eisenhaber F, Orengo C, Sunyaev S, Yuan Y, Bork P. Homology-based fold predictions for Mycoplasma genitalium proteins. Journal of Molecular Biology. 280: 323-6. PMID 9665839 DOI: 10.1006/Jmbi.1998.1884  0.78
1998 Doerks T, Bairoch A, Bork P. Protein annotation: detective work for function prediction. Trends in Genetics : Tig. 14: 248-50. PMID 9635409 DOI: 10.1016/S0168-9525(98)01486-3  0.642
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