Publications

Found 276 results
2021
Littmann M, Bordin N, Heinzinger M, Schütze K, Dallago C, Orengo C, Rost B. Clustering FunFams using sequence embeddings improves EC purity. Bioinformatics. 2021 .
Littmann M, Heinzinger M, Dallago C, Olenyi T, Rost B. Embeddings from deep learning transfer GO annotations beyond homology. Sci Rep. 2021 ;11(1):1160.
Dallago C, Schütze K, Heinzinger M, Olenyi T, Littmann M, Lu AX, Yang KK, Min S, Yoon S, Morton JT, et al. Learned Embeddings from Deep Learning to Visualize and Predict Protein Sets. Curr Protoc. 2021 ;1(5):e113.
Bernhofer M, Dallago C, Karl T, Satagopam V, Heinzinger M, Littmann M, Olenyi T, Qiu J, Schütze K, Yachdav G, et al. PredictProtein - Predicting Protein Structure and Function for 29 Years. Nucleic Acids Res. 2021 ;49(W1):W535-W540.
Heinzinger M, Dallago C, Rost B. Protein matchmaking through representation learning. Cell Syst. 2021 ;12(10):948-950.
Elnaggar A, Heinzinger M, Dallago C, Rehawi G, Yu W, Jones L, Gibbs T, Feher T, Angerer C, Steinegger M, et al. ProtTrans: Towards Cracking the Language of Lifes Code Through Self-Supervised Deep Learning and High Performance Computing. IEEE Trans Pattern Anal Mach Intell. 2021 ;PP.
O'Donoghue SI, Schafferhans A, Sikta N, Stolte C, Kaur S, Ho BK, Anderson S, Procter JB, Dallago C, Bordin N, et al. SARS-CoV-2 structural coverage map reveals viral protein assembly, mimicry, and hijacking mechanisms. Mol Syst Biol. 2021 ;17(9):e10079.
Marot-Lassauzaie V, Goldberg T, Armenteros JJuan Almag, Nielsen H, Rost B. Spectrum of Protein Location in Proteomes Captures Evolutionary Relationship Between Species. J Mol Evol. 2021 .
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.

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