Publications of T. Doerks

Publications of T. Doerks

Publications of T. Doerks

The individual publication lists here have to be considered only in the context of the Bork Group.
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2018 1 publication(s).

54.

Copy number variation analysis and targeted NGS in 77 families with suspected Lynch syndrome reveals novel potential causative genes.

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, Bork P, Moebus S, Herms S, Fischer S, Hoffmann P, Aretz S, Steinke-Lange V

2018 Dec 1; 143(11): 2800-2813. PubMed: 29987844.

2015 3 publication(s).

53.

Prokaryotic ancestry and gene fusion of a dual localized peroxiredoxin in malaria parasites.

Djuika CF, Huerta-Cepas J, Przyborski JM, Deil S, Sanchez CP, Doerks T, Bork P, Lanzer M, Deponte M

2015 Jan 5; 2(1): 5-13. PubMed: 28357258.

52.

SMART: recent updates, new developments and status in 2015.

Letunic I, Doerks T, Bork P

Nucleic Acids Res.

2015 Jan 28; 43: D257-60. Epub 2014 Oct 9; PubMed: 25300481.

51.

Lipid Cooperativity as a General Membrane-Recruitment Principle for PH Domains.

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

2015 Sep 1; 12(9): 1519-30. Epub 2015 Aug 20; PubMed: 26299969.

2014 2 publication(s).

50.

An integrated approach for genome annotation of the eukaryotic thermophile Chaetomium thermophilum.

Bock T, Chen WH, Ori A, Malik N, Silva-Martin N, Huerta-Cepas J, Powell S, Kastritis PL, Smyshlyaev G, Vonkova I, Kirkpatrick J, Doerks T, Nesme L, Baßler J, Kos M, Hurt E, Carlomagno T, Gavin AC, Barabas O, Müller CW, van Noort V, Beck M, Bork P

Nucleic Acids Res.

2014 Dec 16; 42(22): 13525-33. Epub 2014 Nov 14; PubMed: 25398899.

49.

A Phylogeny-Based Benchmarking Test for Orthology Inference Reveals the Limitations of Function-Based Validation.

Trachana K, Forslund K, Larsson TA, Powell S, Doerks T, von Mering C, Bork P

2014; 9(11): e111122. PubMed: 25369365.

2013 1 publication(s).

48.

Experimental characterization of the human non-sequence-specific nucleic acid interactome.

Duernberger G, Burckstummer T, Huber K, Giambruno R, Doerks T, Karayel E, Burkard TR, Kaupe I, Muller AC, Schonegger A, Ecker GF, Lohninger H, Bork P, Bennett KL, Superti-Furga G, Colinge J

2013 Jul 31; 14(7): R81. Epub 2013 Jul 31; PubMed: 23902751.

2012 4 publication(s).

47.

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

2012; 7(4): e34302. PubMed: 22485162.

46.

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 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

2012 Apr 1; 157(2): 180-7. Epub 2012 Feb 1; PubMed: 22296450.

45.

SMART 7: recent updates to the protein domain annotation resource.

Letunic I, Doerks T, Bork P

Nucleic Acids Res.

2012 Jan 3; 40(Database issue): D302-5. Epub 2011 Nov 3; PubMed: 22053084.

44.

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 LJ, von Mering C, Bork P

Nucleic Acids Res.

2012 Jan 1; 40: D284-9. Epub 2011 Nov 16; PubMed: 22096231.

2011 4 publication(s).

43.

Universally distributed single-copy genes indicate a constant rate of horizontal transfer.

Creevey CJ, Doerks T, Fitzpatrick DA, Raes J, Bork P

2011; 6(8): e22099. PubMed: 21850220.

42.

Identifying single copy orthologs in metazoa.

Creevey CJ, Muller J, Doerks T, Thompson JD, Arendt D, Bork P

PLoS Comput Biol.

2011 Dec; 7(12): e1002269. PubMed: 22144877.

41.

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 LJ, von Mering C

Nucleic Acids Res.

2011 Jan 2; 39: D561-8. Epub 2010 Nov 2; PubMed: 21045058.

40.

Orthology prediction methods: A quality assessment using curated protein families.

Trachana K, Larsson TA, Powell S, Chen WH, Doerks T, Muller J, Bork P

2011 Oct 19; 33(10): 769-80. Epub 2011 Aug 19; PubMed: 21853451.

2010 1 publication(s).

39.

eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations.

Muller J, Szklarczyk D, Julien P, Letunic I, Roth A, Kuhn M, Powell S, von Mering C, Doerks T, Jensen LJ, Bork P

Nucleic Acids Res.

2010 Jan 9; 38: D190-5. Epub 2009 Nov 9; PubMed: 19900971.

2009 4 publication(s).

38.

Transcriptome complexity in a genome-reduced bacterium.

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

2009 Nov 27; 326(5957): 1268-71. PubMed: 19965477.

37.

STRING 8--a global view on proteins and their functional interactions in 630 organisms.

Jensen LJ, Kuhn M, Stark M, Chaffron S, Creevey CJ, Muller J, Doerks T, Julien P, Roth A, Simonovic M, Bork P, von Mering C

Nucleic Acids Res.

2009 Jan 21; 37: D412-6. Epub 2008 Oct 21; PubMed: 18940858.

36.

SMART 6: recent updates and new developments.

Letunic I, Doerks T, Bork P

Nucleic Acids Res.

2009 Jan 31; 37: D229-32. Epub 2008 Oct 31; PubMed: 18978020.

35.

Discovering functional novelty in metagenomes: examples from light-mediated processes.

Singh AH, Doerks T, Letunic I, Raes J, Bork P

2009 Jan 10; 191(1): 32-41. Epub 2008 Oct 10; PubMed: 18849420.

2008 3 publication(s).

34.

A computational screen for type I polyketide synthases in metagenomics shotgun data.

Foerstner KU, Doerks T, Creevey CJ, Doerks A, Bork P

2008; 3(10): e3515. PubMed: 18953415.

33.

A Nitrile Hydratase in the Eukaryote Monosiga brevicollis.

Foerstner KU, Doerks T, Muller J, Raes J, Bork P

2008; 3(12): e3976. PubMed: 19096720.

32.

eggNOG: automated construction and annotation of orthologous groups of genes.

Jensen LJ, Julien P, Kuhn M, von Mering C, Muller J, Doerks T, Bork P

Nucleic Acids Res.

2008 Jan 16; 36: D250-4. Epub 2007 Oct 16; PubMed: 17942413.

2007 4 publication(s).

31.

Target-specific requirements for enhancers of decapping in miRNA-mediated gene silencing.

Eulalio A, Rehwinkel J, Stricker M, Huntzinger E, Yang SF, Doerks T, Dorner S, Bork P, Boutros M, Izaurralde E

2007 Oct 15; 21(20): 2558-70. Epub 2007 Sep 27; PubMed: 17901217.

30.

Quantitative assessment of protein function prediction from metagenomics shotgun sequences.

Harrington ED, Singh AH, Doerks T, Letunic I, von Mering C, Jensen LJ, Raes J, Bork P

Proc Natl Acad Sci U S A.

2007 Aug 28; 104(35): 13913-8. Epub 2007 Aug 23; PubMed: 17717083.

29.

Quantitative Phylogenetic Assessment of Microbial Communities in Diverse Environments.

von Mering C, Hugenholtz P, Raes J, Tringe SG, Doerks T, Jensen LJ, Ward N, Bork P

2007 Feb 23; 315(5815): 1126-30. Epub 2007 Feb 1; PubMed: 17272687. Media echos.

28.

STRING 7--recent developments in the integration and prediction of protein interactions.

von Mering C, Jensen LJ, Kuhn M, Chaffron S, Doerks T, Krüger B, Snel B, Bork P

Nucleic Acids Res.

2007 Jan 10; 35: D358-62. Epub 2006 Nov 10; PubMed: 17098935.

2006 3 publication(s).

27.

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

2006 Jul 15; 20(14): 1885-98. Epub 2006 Jun 30; PubMed: 16815998.

26.

Computational characterization of multiple Gag-like human proteins.

Campillos M, Doerks T, Shah PK, Bork P

2006 Nov 15; 22(11): 585-9. Epub 2006 Sep 18; PubMed: 16979784.

25.

Toward automatic reconstruction of a highly resolved tree of life.

Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P

2006 Mar 3; 311(5765): 1283-7. PubMed: 16513982. Media echos.

2005 2 publication(s).

24.

Systematic association of genes to phenotypes by genome and literature mining.

Korbel JO, Doerks T, Jensen LJ, Perez-Iratxeta C, Kaczanowski S, Hooper SD, Andrade MA, Bork P

2005 May; 3(5): e134. Epub 2005 Apr 5; PubMed: 15799710. Media echos.

23.

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. Epub 2005 Jul 11; PubMed: 16008837.

2004 3 publication(s).

22.

Global analysis of bacterial transcription factors to predict cellular target processes.

Doerks T, Andrade MA, Lathe WC, von Mering C, Bork P

2004 Mar; 20(3): 126-31. PubMed: 15049306.

21.

Functional clues for hypothetical proteins based on genomic context analysis in prokaryotes.

Doerks T, von Mering C, Bork P

Nucleic Acids Res.

2004; 32(21): 6321-6. PubMed: 15576358.

20.

SMART 4.0: towards genomic data integration.

Letunic I, Copley RR, Schmidt S, Ciccarelli FD, Doerks T, Schultz J, Ponting CP, Bork P

Nucleic Acids Res.

2004 Jan 1; 32(Database issue): D142-4. PubMed: 14681379.

2002 6 publication(s).

19.

CASH--a beta-helix domain widespread among carbohydrate-binding proteins.

Ciccarelli FD, Copley RR, Doerks T, Russell RB, Bork P

Trends Biochem Sci.

2002 Feb; 27(2): 59-62. PubMed: 11852237.

18.

AMOP, a protein module alternatively spliced in cancer cells.

Ciccarelli FD, Doerks T, Bork P

Trends Biochem Sci.

2002 Mar; 27(3): 113-5. PubMed: 11893501.

17.

Protein domain analysis in the era of complete genomes.

Copley RR, Doerks T, Letunic I, Bork P

2002 Feb 20; 513(1): 129-34. PubMed: 11911892.

16.

Systematic identification of novel protein domain families associated with nuclear functions.

Doerks T, Copley RR, Schultz J, Ponting CP, Bork P

2002 Jan; 12(1): 47-56. PubMed: 11779830.

15.

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: 11943536.

14.

Recent improvements to the SMART domain-based sequence annotation resource.

Letunic I, Goodstadt L, Dickens NJ, Doerks T, Schultz J, Mott R, Ciccarelli F, Copley RR, Ponting CP, Bork P

Nucleic Acids Res.

2002 Jan 1; 30(1): 242-4. PubMed: 11752305.

2001 3 publication(s).

13.

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: 11246006.

12.

The Spir actin organizers are involved in vesicle transport processes.

Kerkhoff E, Simpson JC, Leberfinger CB, Otto IM, Doerks T, Bork P, Rapp UR, Raabe T, Pepperkok R

2001 Dec 11; 11(24): 1963-8. PubMed: 11747823.

11.

Initial sequencing and analysis of the human genome.

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, Kann L, Lehoczky J, Levine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann N, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M, Gibbs RA, Muzny DM, Scherer SE, Bouck JB, Sodergren EJ, Worley KC, Rives CM, Gorrell JH, Metzker ML, Naylor SL, Kucherlapati RS, Nelson DL, Weinstock GM, Sakaki Y, Fujiyama A, Hattori M, Yada T, Toyoda A, Itoh T, Kawagoe C, Watanabe H, Totoki Y, Taylor T, Weissenbach J, Heilig R, Saurin W, Artiguenave F, Brottier P, Bruls T, Pelletier E, Robert C, Wincker P, Smith DR, Doucette-Stamm L, Rubenfield M, Weinstock K, Lee HM, Dubois J, Rosenthal A, Platzer M, Nyakatura G, Taudien S, Rump A, Yang H, Yu J, Wang J, Huang G, Gu J, Hood L, Rowen L, Madan A, Qin S, Davis RW, Federspiel NA, Abola AP, Proctor MJ, Myers RM, Schmutz J, Dickson M, Grimwood J, Cox DR, Olson MV, Kaul R, Raymond C, Shimizu N, Kawasaki K, Minoshima S, Evans GA, Athanasiou M, Schultz R, Roe BA, Chen F, Pan H, Ramser J, Lehrach H, Reinhardt R, McCombie WR, de la Bastide M, Dedhia N, Blöcker H, Hornischer K, Nordsiek G, Agarwala R, Aravind L, Bailey JA, Bateman A, Batzoglou S, Birney E, Bork P, Brown DG, Burge CB, Cerutti L, Chen HC, Church D, Clamp M, Copley RR, Doerks T, Eddy SR, Eichler EE, Furey TS, Galagan J, Gilbert JG, Harmon C, Hayashizaki Y, Haussler D, Hermjakob H, Hokamp K, Jang W, Johnson LS, Jones TA, Kasif S, Kaspryzk A, Kennedy S, Kent WJ, Kitts P, Koonin EV, Korf I, Kulp D, Lancet D, Lowe TM, McLysaght A, Mikkelsen T, Moran JV, Mulder N, Pollara VJ, Ponting CP, Schuler G, Schultz J, Slater G, Smit AF, Stupka E, Szustakowski J, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Wallis J, Wheeler R, Williams A, Wolf YI, Wolfe KH, Yang SP, Yeh RF, Collins F, Guyer MS, Peterson J, Felsenfeld A, Wetterstrand KA, Patrinos A, Morgan MJ, de Jong P, Catanese JJ, Osoegawa K, Shizuya H, Choi S, Chen YJ, Szustakowki J, International Human Genome Sequencing Consortium

2001 Feb 15; 409(6822): 860-921. PubMed: 11237011. Media echos.

2000 7 publication(s).

10.

Re-annotating the Mycoplasma pneumoniae genome sequence: adding value, function and reading frames.

Dandekar T, Huynen MA, Regula JT, Ueberle B, Zimmermann CU, Andrade MA, Doerks T, Sánchez-Pulido L, Snel B, Suyama M, Yuan YP, Herrmann R, Bork P

Nucleic Acids Res.

2000 Sep 1; 28(17): 3278-88. PubMed: 10954595.

9.

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: 10871881.

8.

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: 11050430.

7.

SMART: a web-based tool for the study of genetically mobile domains.

Schultz J, Copley RR, Doerks T, Ponting CP, Bork P

Nucleic Acids Res.

2000 Jan 1; 28(1): 231-4. PubMed: 10592234.

6.

More than 1,000 putative new human signalling proteins revealed by EST data mining.

Schultz J, Doerks T, Ponting CP, Copley RR, Bork P

2000 Jun; 25(2): 201-4. PubMed: 10835637.

5.

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 IC, Séraphin B, Wilm M, Bork P, Izaurralde E

2000 Apr; 6(4): 638-50. PubMed: 10786854.

4.

Prediction of structural domains of TAP reveals details of its interaction with p15 and nucleoporins.

Suyama M, Doerks T, Braun IC, Sattler M, Izaurralde E, Bork P

2000 Jul; 1(1): 53-8. PubMed: 11256625.

1999 1 publication(s).

3.

Domains in plexins: links to integrins and transcription factors.

Bork P, Doerks T, Springer TA, Snel B

Trends Biochem Sci.

1999 Jul; 24(7): 261-3. PubMed: 10390613.

1998 2 publication(s).

2.

Protein annotation: detective work for function prediction.

Doerks T, Bairoch A, Bork P

1998 Jun; 14(6): 248-50. PubMed: 9635409.

1.

Homology-based fold predictions for Mycoplasma genitalium proteins.

Huynen MA, Doerks T, Eisenhaber F, Orengo C, Sunyaev SR, Yuan YP, Bork P

1998 Jul 17; 280(3): 323-6. PubMed: 9665839.