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SignalP 4.0: discriminating signal peptides from transmembrane regions.
Petersen TN, Brunak S, von Heijne G, Nielsen H. Petersen TN, et al. Nat Methods. 2011 Sep 29;8(10):785-6. doi: 10.1038/nmeth.1701. Nat Methods. 2011. PMID: 21959131 No abstract available.
Improved prediction of signal peptides: SignalP 3.0.
Bendtsen JD, Nielsen H, von Heijne G, Brunak S. Bendtsen JD, et al. J Mol Biol. 2004 Jul 16;340(4):783-95. doi: 10.1016/j.jmb.2004.05.028. J Mol Biol. 2004. PMID: 15223320
Prediction of twin-arginine signal peptides.
Bendtsen JD, Nielsen H, Widdick D, Palmer T, Brunak S. Bendtsen JD, et al. BMC Bioinformatics. 2005 Jul 2;6:167. doi: 10.1186/1471-2105-6-167. BMC Bioinformatics. 2005. PMID: 15992409 Free PMC article.
Locating proteins in the cell using TargetP, SignalP and related tools.
Emanuelsson O, Brunak S, von Heijne G, Nielsen H. Emanuelsson O, et al. Nat Protoc. 2007;2(4):953-71. doi: 10.1038/nprot.2007.131. Nat Protoc. 2007. PMID: 17446895
Metagenomic species profiling using universal phylogenetic marker genes.
Sunagawa S, Mende DR, Zeller G, Izquierdo-Carrasco F, Berger SA, Kultima JR, Coelho LP, Arumugam M, Tap J, Nielsen HB, Rasmussen S, Brunak S, Pedersen O, Guarner F, de Vos WM, Wang J, Li J, Doré J, Ehrlich SD, Stamatakis A, Bork P. Sunagawa S, et al. Nat Methods. 2013 Dec;10(12):1196-9. doi: 10.1038/nmeth.2693. Epub 2013 Oct 20. Nat Methods. 2013. PMID: 24141494
A scored human protein-protein interaction network to catalyze genomic interpretation.
Li T, Wernersson R, Hansen RB, Horn H, Mercer J, Slodkowicz G, Workman CT, Rigina O, Rapacki K, Stærfeldt HH, Brunak S, Jensen TS, Lage K. Li T, et al. Nat Methods. 2017 Jan;14(1):61-64. doi: 10.1038/nmeth.4083. Epub 2016 Nov 28. Nat Methods. 2017. PMID: 27892958 Free PMC article.
A computational framework to integrate high-throughput '-omics' datasets for the identification of potential mechanistic links.
Pedersen HK, Forslund SK, Gudmundsdottir V, Petersen AØ, Hildebrand F, Hyötyläinen T, Nielsen T, Hansen T, Bork P, Ehrlich SD, Brunak S, Oresic M, Pedersen O, Nielsen HB. Pedersen HK, et al. Nat Protoc. 2018 Dec;13(12):2781-2800. doi: 10.1038/s41596-018-0064-z. Nat Protoc. 2018. PMID: 30382244
SignalP 5.0 improves signal peptide predictions using deep neural networks.
Almagro Armenteros JJ, Tsirigos KD, Sønderby CK, Petersen TN, Winther O, Brunak S, von Heijne G, Nielsen H. Almagro Armenteros JJ, et al. Nat Biotechnol. 2019 Apr;37(4):420-423. doi: 10.1038/s41587-019-0036-z. Epub 2019 Feb 18. Nat Biotechnol. 2019. PMID: 30778233
Prediction of lipoprotein signal peptides in Gram-negative bacteria.
Juncker AS, Willenbrock H, Von Heijne G, Brunak S, Nielsen H, Krogh A. Juncker AS, et al. Protein Sci. 2003 Aug;12(8):1652-62. doi: 10.1110/ps.0303703. Protein Sci. 2003. PMID: 12876315 Free PMC article.
Network biology concepts in complex disease comorbidities.
Hu JX, Thomas CE, Brunak S. Hu JX, et al. Nat Rev Genet. 2016 Oct;17(10):615-29. doi: 10.1038/nrg.2016.87. Epub 2016 Aug 8. Nat Rev Genet. 2016. PMID: 27498692 Review.
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