Publications

Found 202 results
Filters: Author is Rost, Burkhard  [Clear All Filters]
2018
Peeken JC, Goldberg T, Pyka T, Bernhofer M, Wiestler B, Kessel KA, Tafti PD, Nüsslin F, Braun AE, Zimmer C, et al. Combining multimodal imaging and treatment features improves machine learning-based prognostic assessment in patients with glioblastoma multiforme. Cancer Med. 2018 .
Marot-Lassauzaie V, Bernhofer M, Rost B. Correcting mistakes in predicting distributions. Bioinformatics. 2018 .
Schafferhans A, O'Donoghue SI, Heinzinger M, Rost B. Dark Proteins Important for Cellular Function. Proteomics. 2018 ;18(21-22):e1800227.
Schelling M, Hopf TA, Rost B. Evolutionary couplings and sequence variation effect predict protein binding sites. Proteins. 2018 .
Mahlich Y, Steinegger M, Rost B, Bromberg Y. HFSP: high speed homology-driven function annotation of proteins. Bioinformatics. 2018 ;34(13):i304-i312.
Cejuela JMiguel, Vinchurkar S, Goldberg T, Shankar MSollepura, Baghudana A, Bojchevski A, Uhlig C, Ofner A, Raharja-Liu P, Jensen LJuhl, et al. LocText: relation extraction of protein localizations to assist database curation. BMC Bioinformatics. 2018 ;19(1):15.
Bernhofer M, Goldberg T, Wolf S, Ahmed M, Zaugg J, Boden M, Rost B. NLSdb-major update for database of nuclear localization signals and nuclear export signals. Nucleic Acids Res. 2018 ;46(D1):D503-D508.
Tran L, Hamp T, Rost B. ProfPPIdb: Pairs of physical protein-protein interactions predicted for entire proteomes. PLoS One. 2018 ;13(7):e0199988.
Peeken JC, Bernhofer M, Wiestler B, Goldberg T, Cremers D, Rost B, Wilkens JJ, Combs SE, Nüsslin F. Radiomics in radiooncology - Challenging the medical physicist. Phys Med. 2018 ;48:27-36.
Sanghai ZAssur, Liu Q, Clarke OB, Belcher-Dufrisne M, Wiriyasermkul P, M Giese H, Leal-Pinto E, Kloss B, Tabuso S, Love J, et al. Structure-based analysis of CysZ-mediated cellular uptake of sulfate. Elife. 2018 ;7.
Cevost J, Vaillant C, Meyer S, Rost B. ThreaDNA: predicting DNA mechanics' contribution to sequence selectivity of proteins along whole genomes. Bioinformatics. 2018 ;34(4):609-616.
Peeken JC, Goldberg T, Knie C, Komboz B, Bernhofer M, Pasa F, Kessel KA, Tafti PD, Rost B, Nüsslin F, et al. Treatment-related features improve machine learning prediction of prognosis in soft tissue sarcoma patients. Strahlenther Onkol. 2018 ;194(9):824-834.
2016
Goldberg T, Rost B, Bromberg Y. Computational prediction shines light on type III secretion origins. Sci Rep. 2016 ;6:34516.
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 .

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