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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 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.

Nucleic Acids Res. 2014 Dec 16;42(22):13525-33. doi: 10.1093/nar/gku1147. Epub 2014 Nov 14.


A phylogeny-based benchmarking test for orthology inference reveals the limitations of function-based validation.

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

PLoS One. 2014 Nov 4;9(11):e111122. doi: 10.1371/journal.pone.0111122. eCollection 2014.


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

Letunic I, Doerks T, Bork P.

Nucleic Acids Res. 2015 Jan;43(Database issue):D257-60. doi: 10.1093/nar/gku949. Epub 2014 Oct 9.


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

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.

Genome Biol. 2013 Jul 31;14(7):R81. doi: 10.1186/gb-2013-14-7-r81.


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.


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.

Br J Haematol. 2012 Apr;157(2):180-7. doi: 10.1111/j.1365-2141.2012.09028.x. Epub 2012 Feb 1.


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. doi: 10.1371/journal.pcbi.1002269. Epub 2011 Dec 1.


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;40(Database issue):D284-9. doi: 10.1093/nar/gkr1060. Epub 2011 Nov 16.


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.


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

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

Bioessays. 2011 Oct;33(10):769-80. doi: 10.1002/bies.201100062. Epub 2011 Aug 19.


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

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

PLoS One. 2011;6(8):e22099. doi: 10.1371/journal.pone.0022099. Epub 2011 Aug 5.


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;39(Database issue):D561-8. doi: 10.1093/nar/gkq973. Epub 2010 Nov 2.


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.

Science. 2009 Nov 27;326(5957):1268-71. doi: 10.1126/science.1176951.


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;38(Database issue):D190-5. doi: 10.1093/nar/gkp951. Epub 2009 Nov 9.


A nitrile hydratase in the eukaryote Monosiga brevicollis.

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

PLoS One. 2008;3(12):e3976. doi: 10.1371/journal.pone.0003976. Epub 2008 Dec 19.


Do human lipoxygenases have a PDZ regulatory domain?

Jankun J, Doerks T, Aleem AM, Lysiak-Szydłowska W, Skrzypczak-Jankun E.

Curr Mol Med. 2008 Dec;8(8):768-73. Review.


SMART 6: recent updates and new developments.

Letunic I, Doerks T, Bork P.

Nucleic Acids Res. 2009 Jan;37(Database issue):D229-32. doi: 10.1093/nar/gkn808. Epub 2008 Oct 31.


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

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

PLoS One. 2008;3(10):e3515. doi: 10.1371/journal.pone.0003515. Epub 2008 Oct 27.


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

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.

Nucleic Acids Res. 2009 Jan;37(Database issue):D412-6. doi: 10.1093/nar/gkn760. Epub 2008 Oct 21.


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

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

J Bacteriol. 2009 Jan;191(1):32-41. doi: 10.1128/JB.01084-08. Epub 2008 Oct 10. Review.

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