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Staff at EMBL

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Publications

Total: 51 publication(s)

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, Hurt E, Carlomagno T, Gavin AC, Barabas O, Müller CW, van Noort V, Beck M, Bork P. (2014)
An integrated approach for genome annotation of the eukaryotic thermophile Chaetomium thermophilum.
Nucleic Acids Res. doi:10.1093/nar/gku1147
Europe PMC | doi

Letunic I, Doerks T, Bork P. (2014)
SMART: recent updates, new developments and status in 2015.
Nucleic Acids Res. doi:10.1093/nar/gku949
Europe PMC | doi


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, Colinge J. (2013)
Experimental characterization of the human non-sequence-specific nucleic acid interactome
Genome Biol. 14(7):R81. doi:10.1186/gb-2013-14-7-r81
Europe PMC | doi


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, Bandapalli OR, Kulozik AE. (2012)
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. 157(2):180-187. doi:10.1111/j.1365-2141.2012.09028.x
Europe PMC | doi

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

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. (2012)
eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges
Nucleic Acids Res. 40(Database issue):D284-9. doi:10.1093/nar/gkr1060
Europe PMC | doi

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


2011

Creevey CJ, Muller J, Doerks T, Thompson JD, Arendt D, Bork P. (2011)
Identifying single copy orthologs in Metazoa
PLoS Comput. Biol. 7(12):e1002269. doi:10.1371/journal.pcbi.1002269
Europe PMC | doi

Trachana K, Larsson TA, Powell S, Chen WH, Doerks T, Muller J, Bork P. (2011)
Orthology prediction methods: a quality assessment using curated protein families
Bioessays 33(10):769-780. doi:10.1002/bies.201100062
Europe PMC | doi

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. (2011)
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored
Nucleic Acids Res. 39(Database issue):D561-8. doi:10.1093/nar/gkq973
Europe PMC | doi

Creevey CJ, Doerks T, Fitzpatrick DA, Raes J, Bork P. (2011)
Universally distributed single-copy genes indicate a constant rate of horizontal transfer
PLoS ONE 6(8):e22099. doi:10.1371/journal.pone.0022099
Europe PMC | doi


2010

Muller J, Szklarczyk D, Julien P, Letunic I, Roth A, Kuhn M, Powell S, von Mering C, Doerks T, Jensen LJ, Bork P. (2010)
eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations
Nucleic Acids Res. 38(Database issue):D190-5. doi:10.1093/nar/gkp951
Europe PMC | doi


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, Serrano L. (2009)
Transcriptome complexity in a genome-reduced bacterium
Science 326(5957):1268-1271. doi:10.1126/science.1176951
Europe PMC | doi

Singh AH, Doerks T, Letunic I, Raes J, Bork P. (2009)
Discovering functional novelty in metagenomes: examples from light-mediated processes
J. Bacteriol. 191(1):32-41. doi:10.1128/jb.01084-08
Europe PMC | doi

Letunic I, Doerks T, Bork P. (2009)
SMART 6: recent updates and new developments
Nucleic Acids Res. 37(Database issue):D229-32. doi:10.1093/nar/gkn808
Europe PMC | doi

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. (2009)
STRING 8--a global view on proteins and their functional interactions in 630 organisms
Nucleic Acids Res. 37(Database issue):D412-6. doi:10.1093/nar/gkn760
Europe PMC | doi


2008

Jankun J, Doerks T, Aleem AM, Lysiak-Szydłowska W, Skrzypczak-Jankun E. (2008)
Do human lipoxygenases have a PDZ regulatory domain?
Curr. Mol. Med. 8(8):768-773. doi:10.2174/156652408786733757
Europe PMC | doi

Foerstner KU, Doerks T, Creevey CJ, Doerks A, Bork P. (2008)
A computational screen for type I polyketide synthases in metagenomics shotgun data
PLoS ONE 3(10):e3515. doi:10.1371/journal.pone.0003515
Europe PMC | doi

Foerstner KU, Doerks T, Muller J, Raes J, Bork P. (2008)
A nitrile hydratase in the eukaryote Monosiga brevicollis
PLoS ONE 3(12):e3976. doi:10.1371/journal.pone.0003976
Europe PMC | doi

Jensen LJ, Julien P, Kuhn M, von Mering C, Muller J, Doerks T, Bork P. (2008)
eggNOG: automated construction and annotation of orthologous groups of genes
Nucleic Acids Res. 36(Database issue):D250-4. doi:10.1093/nar/gkm796
Europe PMC | doi


2007

Eulalio A, Rehwinkel J, Stricker M, Huntzinger E, Yang SF, Doerks T, Dorner S, Bork P, Boutros M, Izaurralde E. (2007)
Target-specific requirements for enhancers of decapping in miRNA-mediated gene silencing
Genes Dev. 21(20):2558-2570. doi:10.1101/gad.443107
Europe PMC | doi

Harrington ED, Singh AH, Doerks T, Letunic I, von Mering C, Jensen LJ, Raes J, Bork P. (2007)
Quantitative assessment of protein function prediction from metagenomics shotgun sequences
Proc. Natl. Acad. Sci. U.S.A. 104(35):13913-13918. doi:10.1073/pnas.0702636104
Europe PMC | doi

von Mering C, Hugenholtz P, Raes J, Tringe SG, Doerks T, Jensen LJ, Ward N, Bork P. (2007)
Quantitative phylogenetic assessment of microbial communities in diverse environments
Science 315(5815):1126-1130. doi:10.1126/science.1133420
Europe PMC | doi

von Mering C, Jensen LJ, Kuhn M, Chaffron S, Doerks T, Krüger B, Snel B, Bork P. (2007)
STRING 7--recent developments in the integration and prediction of protein interactions
Nucleic Acids Res. 35(Database issue):D358-62. doi:10.1093/nar/gkl825
Europe PMC | doi


2006

Campillos M, Doerks T, Shah PK, Bork P. (2006)
Computational characterization of multiple Gag-like human proteins
Trends Genet. 22(11):585-589. doi:10.1016/j.tig.2006.09.006
Europe PMC | doi

Behm-Ansmant I, Rehwinkel J, Doerks T, Stark A, Bork P, Izaurralde E. (2006)
mRNA degradation by miRNAs and GW182 requires both CCR4:NOT deadenylase and DCP1:DCP2 decapping complexes
Genes Dev. 20(14):1885-1898. doi:10.1101/gad.1424106
Europe PMC | doi

Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P. (2006)
Toward automatic reconstruction of a highly resolved tree of life
Science 311(5765):1283-1287. doi:10.1126/science.1123061
Europe PMC | doi


2005

Korbel JO, Doerks T, Jensen LJ, Perez-Iratxeta C, Kaczanowski S, Hooper SD, Andrade MA, Bork P. (2005)
Systematic association of genes to phenotypes by genome and literature mining
PLoS Biol. 3(5):e134. doi:10.1371/journal.pbio.0030134
Europe PMC | doi

Tenhaken R, Doerks T, Bork P. (2005)
DCD - a novel plant specific domain in proteins involved in development and programmed cell death
BMC Bioinformatics 6:169. doi:10.1186/1471-2105-6-169
Europe PMC | doi


2004

Doerks T, Andrade MA, Lathe W 3rd, von Mering C, Bork P. (2004)
Global analysis of bacterial transcription factors to predict cellular target processes
Trends Genet. 20(3):126-131. doi:10.1016/j.tig.2004.01.006
Europe PMC | doi

Doerks T, von Mering C, Bork P. (2004)
Functional clues for hypothetical proteins based on genomic context analysis in prokaryotes
Nucleic Acids Res. 32(21):6321-6326. doi:10.1093/nar/gkh973
Europe PMC | doi

Letunic I, Copley RR, Schmidt S, Ciccarelli FD, Doerks T, Schultz J, Ponting CP, Bork P. (2004)
SMART 4.0: towards genomic data integration
Nucleic Acids Res. 32(Database issue):D142-4. doi:10.1093/nar/gkh088
Europe PMC | doi


2002

Doerks T, Huber S, Buchner E, Bork P. (2002)
BSD: a novel domain in transcription factors and synapse-associated proteins
Trends Biochem. Sci. 27(4):168-170. doi:10.1016/s0968-0004(01)02042-4
Europe PMC | doi

Ciccarelli FD, Doerks T, Bork P. (2002)
AMOP, a protein module alternatively spliced in cancer cells
Trends Biochem. Sci. 27(3):113-115. doi:10.1016/s0968-0004(01)02049-7
Europe PMC | doi

Ciccarelli FD, Copley RR, Doerks T, Russell RB, Bork P. (2002)
CASH--a beta-helix domain widespread among carbohydrate-binding proteins
Trends Biochem. Sci. 27(2):59-62. doi:10.1016/s0968-0004(01)02046-1
Europe PMC | doi

Copley RR, Doerks T, Letunic I, Bork P. (2002)
Protein domain analysis in the era of complete genomes
FEBS Lett. 513(1):129-134. doi:10.1016/s0014-5793(01)03289-6
Europe PMC | doi

Letunic I, Goodstadt L, Dickens NJ, Doerks T, Schultz J, Mott R, Ciccarelli F, Copley RR, Ponting CP, Bork P. (2002)
Recent improvements to the SMART domain-based sequence annotation resource
Nucleic Acids Res. 30(1):242-244. doi:10.1093/nar/30.1.242
Europe PMC | doi

Doerks T, Copley RR, Schultz J, Ponting CP, Bork P. (2002)
Systematic identification of novel protein domain families associated with nuclear functions
Genome Res. 12(1):47-56. doi:10.1101/gr.203201
Europe PMC | doi


2001

Kerkhoff E, Simpson JC, Leberfinger CB, Otto IM, Doerks T, Bork P, Rapp UR, Raabe T, Pepperkok R. (2001)
The Spir actin organizers are involved in vesicle transport processes
Curr. Biol. 11(24):1963-1968. doi:10.1016/s0960-9822(01)00602-9
Europe PMC | doi

Doerks T, Copley R, Bork P. (2001)
DDT -- a novel domain in different transcription and chromosome remodeling factors
Trends Biochem. Sci. 26(3):145-146. doi:10.1016/s0968-0004(00)01769-2
Europe PMC | doi

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, International Human Genome Sequencing Consortium. (2001)
Initial sequencing and analysis of the human genome
Nature 409(6822):860-921. doi:10.1038/35057062
Europe PMC | doi


2000

Doerks T, Strauss M, Brendel M, Bork P. (2000)
GRAM, a novel domain in glucosyltransferases, myotubularins and other putative membrane-associated proteins
Trends Biochem. Sci. 25(10):483-485. doi:10.1016/s0968-0004(00)01664-9
Europe PMC | doi

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. (2000)
Re-annotating the Mycoplasma pneumoniae genome sequence: adding value, function and reading frames
Nucleic Acids Res. 28(17):3278-3288. doi:10.1093/nar/28.17.3278
Europe PMC | doi

Doerks T, Bork P, Kamberov E, Makarova O, Muecke S, Margolis B. (2000)
L27, a novel heterodimerization domain in receptor targeting proteins Lin-2 and Lin-7
Trends Biochem. Sci. 25(7):317-318. doi:10.1016/s0968-0004(00)01599-1
Europe PMC | doi

Suyama M, Doerks T, Braun IC, Sattler M, Izaurralde E, Bork P. (2000)
Prediction of structural domains of TAP reveals details of its interaction with p15 and nucleoporins
EMBO Rep. 1(1):53-58. doi:10.1093/embo-reports/kvd009
Europe PMC | doi

Schultz J, Doerks T, Ponting CP, Copley RR, Bork P. (2000)
More than 1,000 putative new human signalling proteins revealed by EST data mining
Nat. Genet. 25(2):201-204. doi:10.1038/76069
Europe PMC | doi

Stutz F, Bachi A, Doerks T, Braun IC, Séraphin B, Wilm M, Bork P, Izaurralde E. (2000)
REF, an evolutionary conserved family of hnRNP-like proteins, interacts with TAP/Mex67p and participates in mRNA nuclear export
RNA 6(4):638-650. doi:10.1017/s1355838200000078
Europe PMC | doi

Schultz J, Copley RR, Doerks T, Ponting CP, Bork P. (2000)
SMART: a web-based tool for the study of genetically mobile domains
Nucleic Acids Res. 28(1):231-234. doi:10.1093/nar/28.1.231
Europe PMC | doi


1999

Bork P, Doerks T, Springer TA, Snel B. (1999)
Domains in plexins: links to integrins and transcription factors
Trends Biochem. Sci. 24(7):261-263. doi:10.1016/s0968-0004(99)01416-4
Europe PMC | doi


1998

Huynen M, Doerks T, Eisenhaber F, Orengo C, Sunyaev S, Yuan Y, Bork P. (1998)
Homology-based fold predictions for Mycoplasma genitalium proteins
J. Mol. Biol. 280(3):323-326. doi:10.1006/jmbi.1998.1884
Europe PMC | doi

Doerks T, Bairoch A, Bork P. (1998)
Protein annotation: detective work for function prediction
Trends Genet. 14(6):248-250. doi:10.1016/s0168-9525(98)01486-3
Europe PMC | doi