Publications

Found 287 results
2016
Ramilowski JA, Goldberg T, Harshbarger J, Kloppmann E, Lizio M, Satagopam VP, Itoh M, Kawaji H, Carninci P, Rost B, et al. Corrigendum: A draft network of ligand-receptor-mediated multicellular signalling in human. Nat Commun. 2016 ;7:10706.
Jiang Y, Oron TRonnen, Clark WT, Bankapur AR, D'Andrea D, Lepore R, Funk CS, Kahanda I, Verspoor KM, Ben-Hur A, et al. An expanded evaluation of protein function prediction methods shows an improvement in accuracy. Genome Biol. 2016 ;17(1):184.
Yachdav G, Wilzbach S, Rauscher B, Sheridan R, Sillitoe I, Procter J, Lewis SE, Rost B, Goldberg T. MSAViewer: interactive JavaScript visualization of multiple sequence alignments. Bioinformatics. 2016 .
Reeb J, Hecht M, Mahlich Y, Bromberg Y, Rost B. Predicted Molecular Effects of Sequence Variants Link to System Level of Disease. PLoS Comput Biol. 2016 ;12(8):e1005047.
Rost B, Radivojac P, Bromberg Y. Protein function in precision medicine: deep understanding with machine learning. FEBS Lett. 2016 .
Ardiccioni C, Clarke OB, Tomasek D, Issa HA, von Alpen DC, Pond HL, Banerjee S, Rajashankar KR, Liu Q, Guan Z, et al. Structure of the polyisoprenyl-phosphate glycosyltransferase GtrB and insights into the mechanism of catalysis. Nat Commun. 2016 ;7:10175.
Petrou VI, Herrera CM, Schultz KM, Clarke OB, Vendome J, Tomasek D, Banerjee S, Rajashankar KR, Dufrisne MBelcher, Kloss B, et al. Structures of aminoarabinose transferase ArnT suggest a molecular basis for lipid A glycosylation. Science. 2016 ;351(6273):608-12.
Bernhofer M, Kloppmann E, Reeb J, Rost B. TMSEG: Novel prediction of transmembrane helices. Proteins. 2016 .
Neuhaus K, Landstorfer R, Fellner L, Simon S, Schafferhans A, Goldberg T, Marx H, Ozoline ON, Rost B, Kuster B, et al. Translatomics combined with transcriptomics and proteomics reveals novel functional, recently evolved orphan genes in Escherichia coli O157:H7 (EHEC). BMC Genomics. 2016 ;17(1):133.
2015
Yachdav G, Goldberg T, Wilzbach S, Dao D, Shih I, Choudhary S, Crouch S, Franz M, García A, García LJ, et al. Anatomy of BioJS, an open source community for the life sciences. Elife. 2015 ;4.
O'Donoghue SI, Sabir KS, Kalemanov M, Stolte C, Wellmann B, Ho V, Roos M, Perdigão N, Buske FA, Heinrich J, et al. Aquaria: simplifying discovery and insight from protein structures. Nat Methods. 2015 ;12(2):98-9.
Hecht M, Bromberg Y, Rost B. Better prediction of functional effects for sequence variants. BMC Genomics. 2015 ;16 Suppl 8:S1.
Ramilowski JA, Goldberg T, Harshbarger J, Kloppman E, Lizio M, Satagopam VP, Itoh M, Kawaji H, Carninci P, Rost B, et al. A draft network of ligand-receptor-mediated multicellular signalling in human. Nat Commun. 2015 ;6:7866.
Vicedo E, Schlessinger A, Rost B. Environmental Pressure May Change the Composition Protein Disorder in Prokaryotes. PLoS One. 2015 ;10(8):e0133990.
Reeb J, Kloppmann E, Bernhofer M, Rost B. Evaluation of transmembrane helix predictions in 2014. Proteins. 2015 ;83(3):473-84.
Hamp T, Rost B. Evolutionary profiles improve protein-protein interaction prediction from sequence. Bioinformatics. 2015 .
Karp PD, Berger B, Kovats D, Lengauer T, Linial M, Sabeti P, Hide W, Rost B. ISCB Ebola Award for Important Future Research on the Computational Biology of Ebola Virus. F1000Res. 2015 ;4:12.
Karp PD, Berger B, Kovats D, Lengauer T, Linial M, Sabeti P, Hide W, Rost B. Message from the ISCB: ISCB Ebola award for important future research on the computational biology of Ebola virus. Bioinformatics. 2015 ;31(4):616-7.
Hamp T, Rost B. More challenges for machine-learning protein interactions. Bioinformatics. 2015 .
Vicedo E, Gasik Z, Dong Y-A, Goldberg T, Rost B. Protein disorder reduced in Saccharomyces cerevisiae to survive heat shock. F1000Res. 2015 ;4:1222.
Guo Y, Kalathur RC, Liu Q, Kloss B, Bruni R, Ginter C, Kloppmann E, Rost B, Hendrickson WA. Protein structure. Structure and activity of tryptophan-rich TSPO proteins. Science. 2015 ;347(6221):551-5.
Ison J, Rapacki K, Ménager H, Kalaš M, Rydza E, Chmura P, Anthon C, Beard N, Berka K, Bolser D, et al. Tools and data services registry: a community effort to document bioinformatics resources. Nucleic Acids Res. 2015 .
Perdigão N, Heinrich J, Stolte C, Sabir KS, Buckley MJ, Tabor B, Signal B, Gloss BS, Hammang CJ, Rost B, et al. Unexpected features of the dark proteome. Proc Natl Acad Sci U S A. 2015 .
2014
Feiglin A, Ashkenazi S, Schlessinger A, Rost B, Ofran Y. Co-expression and co-localization of hub proteins and their partners are encoded in protein sequence. Mol Biosyst. 2014 ;10(4):787-94.
Kaján L, Hopf TA, Kalaš M, Marks DS, Rost B. FreeContact: fast and free software for protein contact prediction from residue co-evolution. BMC Bioinformatics. 2014 ;15:85.
Yachdav G, Hecht M, Pasmanik-Chor M, Yeheskel A, Rost B. HeatMapViewer: interactive display of 2D data in biology. F1000Res. 2014 ;3:48.
Rost B. ISCB: past-present perspective for the International Society for Computational Biology. Bioinformatics. 2014 ;30(1):143-5.
Goldberg T, Hecht M, Hamp T, Karl T, Yachdav G, Ahmed N, Altermann U, Angerer P, Ansorge S, Balasz K, et al. LocTree3 prediction of localization. Nucleic Acids Res. 2014 ;42(Web Server issue):W350-5.
Yachdav G, Kloppmann E, Kaján L, Hecht M, Goldberg T, Hamp T, Hönigschmid P, Schafferhans A, Roos M, Bernhofer M, et al. PredictProtein--an open resource for online prediction of protein structural and functional features. Nucleic Acids Res. 2014 ;42(Web Server issue):W337-43.
Chang Y, Bruni R, Kloss B, Assur Z, Kloppmann E, Rost B, Hendrickson WA, Liu Q. Structural basis for a pH-sensitive calcium leak across membranes. Science. 2014 ;344(6188):1131-5.
Yang T, Liu Q, Kloss B, Bruni R, Kalathur RC, Guo Y, Kloppmann E, Rost B, Colecraft HM, Hendrickson WA. Structure and selectivity in bestrophin ion channels. Science. 2014 ;346(6207):355-9.
Cejuela JMiguel, McQuilton P, Ponting L, Marygold SJ, Stefancsik R, Millburn GH, Rost B. tagtog: interactive and text-mining-assisted annotation of gene mentions in PLOS full-text articles. Database (Oxford). 2014 ;2014:bau033.
Schafferhans A, Rost B. Taking structure searches to the next dimension. Structure. 2014 ;22(7):938-9.
2013
Hamp T, Goldberg T, Rost B. Accelerating the Original Profile Kernel. PLoS One. 2013 ;8(6):e68459.
Kaján L, Yachdav G, Vicedo E, Steinegger M, Mirdita M, Angermüller C, Böhm A, Domke S, Ertl J, Mertes C, et al. Cloud prediction of protein structure and function with PredictProtein for Debian. Biomed Res Int. 2013 ;2013:398968.
Pieper U, Schlessinger A, Kloppmann E, Chang GA, Chou JJ, Dumont ME, Fox BG, Fromme P, Hendrickson WA, Malkowski MG, et al. Coordinating the impact of structural genomics on the human α-helical transmembrane proteome. Nat Struct Mol Biol. 2013 ;20(2):135-8.
Mistry J, Kloppmann E, Rost B, Punta M. An estimated 5% of new protein structures solved today represent a new Pfam family. Acta Crystallogr D Biol Crystallogr. 2013 ;69(Pt 11):2186-93.
Hamp T, Kassner R, Seemayer S, Vicedo E, Schaefer C, Achten D, Auer F, Boehm A, Braun T, Hecht M, et al. Homology-based inference sets the bar high for protein function prediction. BMC Bioinformatics. 2013 ;14 Suppl 3:S7.
Bateman A, Kelso J, Mietchen D, Macintyre G, Di Domenico T, Abeel T, Logan DW, Radivojac P, Rost B. ISCB computational biology Wikipedia competition. PLoS Comput Biol. 2013 ;9(9):e1003242.
Rost B. ISCB: past-present perspective for the International Society for Computational Biology. Bioinformatics. 2013 ;29(24):3243-5.
Radivojac P, Clark WT, Oron TRonnen, Schnoes AM, Wittkop T, Sokolov A, Graim K, Funk C, Verspoor K, Ben-Hur A, et al. A large-scale evaluation of computational protein function prediction. Nat Methods. 2013 ;10(3):221-7.
Bromberg Y, Kahn PC, Rost B. Neutral and weakly nonneutral sequence variants may define individuality. Proc Natl Acad Sci U S A. 2013 ;110(35):14255-60.
Hecht M, Bromberg Y, Rost B. News from the protein mutability landscape. J Mol Biol. 2013 ;425(21):3937-48.
2012
Hamp T, Rost B. Alternative protein-protein interfaces are frequent exceptions. PLoS Comput Biol. 2012 ;8(8):e1002623.
Schaefer C, Bromberg Y, Achten D, Rost B. Disease-related mutations predicted to impact protein function. BMC Genomics. 2012 ;13 Suppl 4:S11.
Goldberg T, Hamp T, Rost B. LocTree2 predicts localization for all domains of life. Bioinformatics. 2012 ;28(18):i458-i465.
Wu Y, Punta M, Xiao R, Acton TB, Sathyamoorthy B, Dey F, Fischer M, Skerra A, Rost B, Montelione GT, et al. NMR structure of lipoprotein YxeF from Bacillus subtilis reveals a calycin fold and distant homology with the lipocalin Blc from Escherichia coli. PLoS One. 2012 ;7(6):e37404.
Rost B, Gaasterland T, Lengauer T, Linial M, Markel S, McKay BJMorrison, Schneider R, Horton P, Kelso J. Paving the future: finding suitable ISMB venues. Bioinformatics. 2012 ;28(19):2556-9.
Schaefer C, Rost B. Predict impact of single amino acid change upon protein structure. BMC Genomics. 2012 ;13 Suppl 4:S4.
Schaefer C, Meier A, Rost B, Bromberg Y. SNPdbe: constructing an nsSNP functional impacts database. Bioinformatics. 2012 ;28(4):601-2.

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