Publications

Found 287 results
2022
Heinzinger M, Littmann M, Sillitoe I, Bordin N, Orengo C, Rost B. Contrastive learning on protein embeddings enlightens midnight zone. NAR Genom Bioinform. 2022 ;4(2):lqac043.
Foley G, Mora A, Ross CM, Bottoms S, Sützl L, Lamprecht ML, Zaugg J, Essebier A, Balderson B, Newell R, et al. Engineering indel and substitution variants of diverse and ancient enzymes using Graphical Representation of Ancestral Sequence Predictions (GRASP). PLoS Comput Biol. 2022 ;18(10):e1010633.
Olenyi T, Marquet C, Heinzinger M, Kröger B, Nikolova T, Bernhofer M, Sändig P, Schütze K, Littmann M, Mirdita M, et al. LambdaPP: Fast and accessible protein-specific phenotype predictions. Protein Sci. 2022 :e4524.
Schütze K, Heinzinger M, Steinegger M, Rost B. Nearest neighbor search on embeddings rapidly identifies distant protein relations. Front Bioinform. 2022 ;2:1033775.
Bordin N, Dallago C, Heinzinger M, Kim S, Littmann M, Rauer C, Steinegger M, Rost B, Orengo C. Novel machine learning approaches revolutionize protein knowledge. Trends Biochem Sci. 2022 .
Weissenow K, Heinzinger M, Rost B. Protein language-model embeddings for fast, accurate, and alignment-free protein structure prediction. Structure. 2022 .
Lautenbacher L, Samaras P, Muller J, Grafberger A, Shraideh M, Rank J, Fuchs ST, Schmidt TK, The M, Dallago C, et al. ProteomicsDB: toward a FAIR open-source resource for life-science research. Nucleic Acids Res. 2022 ;50(D1):D1541-D1552.
Ilzhöfer D, Heinzinger M, Rost B. SETH predicts nuances of residue disorder from protein embeddings. Front Bioinform. 2022 ;2:1019597.
Bernhofer M, Rost B. TMbed: transmembrane proteins predicted through language model embeddings. BMC Bioinformatics. 2022 ;23(1):326.
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.
Marquet C, Heinzinger M, Olenyi T, Dallago C, Erckert K, Bernhofer M, Nechaev D, Rost B. Embeddings from protein language models predict conservation and variant effects. Hum Genet. 2021 .
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.
Littmann M, Heinzinger M, Dallago C, Weissenow K, Rost B. Protein embeddings and deep learning predict binding residues for various ligand classes. Sci Rep. 2021 ;11(1):23916.
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 .
2020
Lai J-S, Rost B, Kobe B, Boden M. Evolutionary model of protein secondary structure capable of revealing new biological relationships. Proteins. 2020 ;88(9):1251-1259.
Zaucha J, Heinzinger M, Tarnovskaya S, Rost B, Frishman D. Family-specific analysis of variant pathogenicity prediction tools. NAR Genom Bioinform. 2020 ;2(2):lqaa014.
Zaucha J, Heinzinger M, Kulandaisamy A, Kataka E, Salvádor ÓLlorian, Popov P, Rost B, M Gromiha M, Zhorov BS, Frishman D. Mutations in transmembrane proteins: diseases, evolutionary insights, prediction and comparison with globular proteins. Brief Bioinform. 2020 .
Qiu J, Bernhofer M, Heinzinger M, Kemper S, Norambuena T, Melo F, Rost B. ProNA2020 predicts protein-DNA, protein-RNA, and protein-protein binding proteins and residues from sequence. J Mol Biol. 2020 ;432(7):2428-2443.
Qiu J, Nechaev D, Rost B. Protein-protein and protein-nucleic acid binding residues important for common and rare sequence variants in human. BMC Bioinformatics. 2020 ;21(1):452.
Reeb J, Wirth T, Rost B. Variant effect predictions capture some aspects of deep mutational scanning experiments. BMC Bioinformatics. 2020 ;21(1):107.
Dallago C, Goldberg T, Andrade-Navarro MAngel, Alanis-Lobato G, Rost B. Visualizing Human Protein-Protein Interactions and Subcellular Localizations on Cell Images Through CellMap. Curr Protoc Bioinformatics. 2020 ;69(1):e97.
2019
Zhou N, Jiang Y, Bergquist TR, Lee AJ, Kacsoh BZ, Crocker AW, Lewis KA, Georghiou G, Nguyen HN, Hamid MNafiz, et al. The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens. Genome Biol. 2019 ;20(1):244.
Littmann M, Goldberg T, Seitz S, Boden M, Rost B. Correction to: Detailed prediction of protein sub-nuclear localization. BMC Bioinformatics. 2019 ;20(1):727.
Peeken JC, Bernhofer M, Spraker MB, Pfeiffer D, Devecka M, Thamer A, Shouman MA, Ott A, Nüsslin F, Mayr NA, et al. CT-based radiomic features predict tumor grading and have prognostic value in patients with soft tissue sarcomas treated with neoadjuvant radiation therapy. Radiother Oncol. 2019 .
Littmann M, Goldberg T, Seitz S, Boden M, Rost B. Detailed prediction of protein sub-nuclear localization. BMC Bioinformatics. 2019 ;20(1):205.
Scheibenreif L, Littmann M, Orengo C, Rost B. FunFam protein families improve residue level molecular function prediction. BMC Bioinformatics. 2019 ;20(1):400.
Miller M, Vitale D, Kahn PC, Rost B, Bromberg Y. funtrp: identifying protein positions for variation driven functional tuning. Nucleic Acids Res. 2019 ;47(21):e142.
Heinzinger M, Elnaggar A, Wang Y, Dallago C, Nechaev D, Matthes F, Rost B. Modeling aspects of the language of life through transfer-learning protein sequences. BMC Bioinformatics. 2019 ;20(1):723.
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.
2017
Dallago C, Goldberg T, Andrade-Navarro MAngel, Alanis-Lobato G, Rost B. CellMap visualizes protein-protein interactions and subcellular localization. F1000Res. 2017 ;6:1824.
Mahlich Y, Reeb J, Hecht M, Schelling M, De Beer TAndries Pe, Bromberg Y, Rost B. Common sequence variants affect molecular function more than rare variants?. Sci Rep. 2017 ;7(1):1608.
Hücker SM, Ardern Z, Goldberg T, Schafferhans A, Bernhofer M, Vestergaard G, Nelson CW, Schloter M, Rost B, Scherer S, et al. Discovery of numerous novel small genes in the intergenic regions of the Escherichia coli O157:H7 Sakai genome. PLoS One. 2017 ;12(9):e0184119.
Cejuela JMiguel, Bojchevski A, Uhlig C, Bekmukhametov R, Karn SKumar, Mahmuti S, Baghudana A, Dubey A, Satagopam VP, Rost B. nala: text mining natural language mutation mentions. Bioinformatics. 2017 .
2016
Goldberg T, Rost B, Bromberg Y. Computational prediction shines light on type III secretion origins. Sci Rep. 2016 ;6:34516.

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