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State-of-the-art in membrane protein prediction.
Chen CP, Rost B. Chen CP, et al. Among authors: rost b. Appl Bioinformatics. 2002;1(1):21-35. Appl Bioinformatics. 2002. PMID: 15130854 Review.
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: rost b. 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.
HFSP: high speed homology-driven function annotation of proteins.
Mahlich Y, Steinegger M, Rost B, Bromberg Y. Mahlich Y, et al. Among authors: rost b. Bioinformatics. 2018 Jul 1;34(13):i304-i312. doi: 10.1093/bioinformatics/bty262. Bioinformatics. 2018. PMID: 29950013 Free PMC article.
nala: text mining natural language mutation mentions.
Cejuela JM, Bojchevski A, Uhlig C, Bekmukhametov R, Kumar Karn S, Mahmuti S, Baghudana A, Dubey A, Satagopam VP, Rost B. Cejuela JM, et al. Among authors: rost b. Bioinformatics. 2017 Jun 15;33(12):1852-1858. doi: 10.1093/bioinformatics/btx083. Bioinformatics. 2017. PMID: 28200120 Free PMC article.
FunFam protein families improve residue level molecular function prediction.
Scheibenreif L, Littmann M, Orengo C, Rost B. Scheibenreif L, et al. Among authors: rost b. BMC Bioinformatics. 2019 Jul 18;20(1):400. doi: 10.1186/s12859-019-2988-x. BMC Bioinformatics. 2019. PMID: 31319797 Free PMC article.
LocText: relation extraction of protein localizations to assist database curation.
Cejuela JM, Vinchurkar S, Goldberg T, Prabhu Shankar MS, Baghudana A, Bojchevski A, Uhlig C, Ofner A, Raharja-Liu P, Jensen LJ, Rost B. Cejuela JM, et al. Among authors: rost b. BMC Bioinformatics. 2018 Jan 17;19(1):15. doi: 10.1186/s12859-018-2021-9. BMC Bioinformatics. 2018. PMID: 29343218 Free PMC article.
Computational prediction shines light on type III secretion origins.
Goldberg T, Rost B, Bromberg Y. Goldberg T, et al. Among authors: rost b. Sci Rep. 2016 Oct 7;6:34516. doi: 10.1038/srep34516. Sci Rep. 2016. PMID: 27713481 Free PMC article.
Detailed prediction of protein sub-nuclear localization.
Littmann M, Goldberg T, Seitz S, Bodén M, Rost B. Littmann M, et al. Among authors: rost b. BMC Bioinformatics. 2019 Apr 23;20(1):205. doi: 10.1186/s12859-019-2790-9. BMC Bioinformatics. 2019. PMID: 31014229 Free PMC article.
An expanded evaluation of protein function prediction methods shows an improvement in accuracy.
Jiang Y, Oron TR, Clark WT, Bankapur AR, D'Andrea D, Lepore R, Funk CS, Kahanda I, Verspoor KM, Ben-Hur A, Koo da CE, Penfold-Brown D, Shasha D, Youngs N, Bonneau R, Lin A, Sahraeian SM, Martelli PL, Profiti G, Casadio R, Cao R, Zhong Z, Cheng J, Altenhoff A, Skunca N, Dessimoz C, Dogan T, Hakala K, Kaewphan S, Mehryary F, Salakoski T, Ginter F, Fang H, Smithers B, Oates M, Gough J, Törönen P, Koskinen P, Holm L, Chen CT, Hsu WL, Bryson K, Cozzetto D, Minneci F, Jones DT, Chapman S, Bkc D, Khan IK, Kihara D, Ofer D, Rappoport N, Stern A, Cibrian-Uhalte E, Denny P, Foulger RE, Hieta R, Legge D, Lovering RC, Magrane M, Melidoni AN, Mutowo-Meullenet P, Pichler K, Shypitsyna A, Li B, Zakeri P, ElShal S, Tranchevent LC, Das S, Dawson NL, Lee D, Lees JG, Sillitoe I, Bhat P, Nepusz T, Romero AE, Sasidharan R, Yang H, Paccanaro A, Gillis J, Sedeño-Cortés AE, Pavlidis P, Feng S, Cejuela JM, Goldberg T, Hamp T, Richter L, Salamov A, Gabaldon T, Marcet-Houben M, Supek F, Gong Q, Ning W, Zhou Y, Tian W, Falda M, Fontana P, Lavezzo E, Toppo S, Ferrari C, Giollo M, Piovesan D, Tosatto SC, Del Pozo A, Fernández JM, Maietta P, Valencia A, Tress ML, Benso A, Di Carlo S, Politano G, Savino A, Rehman HU, Re M, Mesiti M, Valentini G, Bargsten JW, van Dijk AD, Gemovic B, Glisic S, Perovic V, Veljkovic V, Veljkovic N, Almeida-E-Silva DC, Vencio RZ, Sharan M, Vogel J, Kansakar L, Zhang S, Vucetic S, Wang Z, Sternberg MJ, Wass MN, Huntley RP, Martin MJ, O'Donovan C, Robinson PN, Moreau Y, Tramontano A, Babbitt PC, Brenner SE, Linial M, Orengo CA, Rost B, Greene CS, Mooney SD, Friedberg I, Radivojac P. Jiang Y, et al. Among authors: rost b. Genome Biol. 2016 Sep 7;17(1):184. doi: 10.1186/s13059-016-1037-6. Genome Biol. 2016. PMID: 27604469 Free PMC article.
FreeContact: fast and free software for protein contact prediction from residue co-evolution.
Kaján L, Hopf TA, Kalaš M, Marks DS, Rost B. Kaján L, et al. Among authors: rost b. BMC Bioinformatics. 2014 Mar 26;15:85. doi: 10.1186/1471-2105-15-85. BMC Bioinformatics. 2014. PMID: 24669753 Free PMC article.
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