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LocTree2 predicts localization for all domains of life.
Goldberg T, Hamp T, Rost B. Goldberg T, et al. Among authors: hamp t. Bioinformatics. 2012 Sep 15;28(18):i458-i465. doi: 10.1093/bioinformatics/bts390. Bioinformatics. 2012. PMID: 22962467 Free PMC article.
Accelerating the Original Profile Kernel.
Hamp T, Goldberg T, Rost B. Hamp T, et al. PLoS One. 2013 Jun 18;8(6):e68459. doi: 10.1371/journal.pone.0068459. Print 2013. PLoS One. 2013. PMID: 23825697 Free PMC article.
LocTree3 prediction of localization.
Goldberg T, Hecht M, Hamp T, Karl T, Yachdav G, Ahmed N, Altermann U, Angerer P, Ansorge S, Balasz K, Bernhofer M, Betz A, Cizmadija L, Do KT, Gerke J, Greil R, Joerdens V, Hastreiter M, Hembach K, Herzog M, Kalemanov M, Kluge M, Meier A, Nasir H, Neumaier U, Prade V, Reeb J, Sorokoumov A, Troshani I, Vorberg S, Waldraff S, Zierer J, Nielsen H, Rost B. Goldberg T, et al. Among authors: hamp t. Nucleic Acids Res. 2014 Jul;42(Web Server issue):W350-5. doi: 10.1093/nar/gku396. Epub 2014 May 21. Nucleic Acids Res. 2014. PMID: 24848019 Free PMC article.
Evolutionary profiles improve protein-protein interaction prediction from sequence.
Hamp T, Rost B. Hamp T, et al. Bioinformatics. 2015 Jun 15;31(12):1945-50. doi: 10.1093/bioinformatics/btv077. Epub 2015 Feb 4. Bioinformatics. 2015. PMID: 25657331
More challenges for machine-learning protein interactions.
Hamp T, Rost B. Hamp T, et al. Bioinformatics. 2015 May 15;31(10):1521-5. doi: 10.1093/bioinformatics/btu857. Epub 2015 Jan 12. Bioinformatics. 2015. PMID: 25586513
PredictProtein--an open resource for online prediction of protein structural and functional features.
Yachdav G, Kloppmann E, Kajan L, Hecht M, Goldberg T, Hamp T, Hönigschmid P, Schafferhans A, Roos M, Bernhofer M, Richter L, Ashkenazy H, Punta M, Schlessinger A, Bromberg Y, Schneider R, Vriend G, Sander C, Ben-Tal N, Rost B. Yachdav G, et al. Among authors: hamp t. Nucleic Acids Res. 2014 Jul;42(Web Server issue):W337-43. doi: 10.1093/nar/gku366. Epub 2014 May 5. Nucleic Acids Res. 2014. PMID: 24799431 Free PMC article.
Improving structure alignment-based prediction of SCOP families using Vorolign kernels.
Hamp T, Birzele F, Buchwald F, Kramer S. Hamp T, et al. Bioinformatics. 2011 Jan 15;27(2):204-10. doi: 10.1093/bioinformatics/btq618. Epub 2010 Nov 18. Bioinformatics. 2011. PMID: 21098432
Alternative protein-protein interfaces are frequent exceptions.
Hamp T, Rost B. Hamp T, et al. PLoS Comput Biol. 2012;8(8):e1002623. doi: 10.1371/journal.pcbi.1002623. Epub 2012 Aug 2. PLoS Comput Biol. 2012. PMID: 22876170 Free PMC article.
ProfPPIdb: Pairs of physical protein-protein interactions predicted for entire proteomes.
Tran L, Hamp T, Rost B. Tran L, et al. Among authors: hamp t. PLoS One. 2018 Jul 18;13(7):e0199988. doi: 10.1371/journal.pone.0199988. eCollection 2018. PLoS One. 2018. PMID: 30020956 Free PMC article.
Homology-based inference sets the bar high for protein function prediction.
Hamp T, Kassner R, Seemayer S, Vicedo E, Schaefer C, Achten D, Auer F, Boehm A, Braun T, Hecht M, Heron M, Hönigschmid P, Hopf TA, Kaufmann S, Kiening M, Krompass D, Landerer C, Mahlich Y, Roos M, Rost B. Hamp T, et al. BMC Bioinformatics. 2013;14 Suppl 3(Suppl 3):S7. doi: 10.1186/1471-2105-14-S3-S7. Epub 2013 Feb 28. BMC Bioinformatics. 2013. PMID: 23514582 Free PMC article.
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