Publications

Found 16 results
Filters: Author is Bernhofer, Michael  [Clear All Filters]
2022
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.
Bernhofer M, Rost B. TMbed: transmembrane proteins predicted through language model embeddings. BMC Bioinformatics. 2022 ;23(1):326.
2021
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 .
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.
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.
2019
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 .
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 .
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.
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.
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
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.
2016
Bernhofer M, Kloppmann E, Reeb J, Rost B. TMSEG: Novel prediction of transmembrane helices. Proteins. 2016 .
2015
Reeb J, Kloppmann E, Bernhofer M, Rost B. Evaluation of transmembrane helix predictions in 2014. Proteins. 2015 ;83(3):473-84.
2014
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.