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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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