Burkhard Rost

Orcid: 0000-0003-0179-8424

  • TU Munich, Faculty of Computer Science

According to our database1, Burkhard Rost authored at least 108 papers between 1992 and 2023.

Collaborative distances:



In proceedings 
PhD thesis 


Online presence:

On csauthors.net:


CAID prediction portal: a comprehensive service for predicting intrinsic disorder and binding regions in proteins.
Nucleic Acids Res., July, 2023

CATHe: detection of remote homologues for CATH superfamilies using embeddings from protein language models.
Bioinform., January, 2023

Ankh: Optimized Protein Language Model Unlocks General-Purpose Modelling.
CoRR, 2023

TMbed: transmembrane proteins predicted through language model embeddings.
BMC Bioinform., December, 2022

Engineering indel and substitution variants of diverse and ancient enzymes using Graphical Representation of Ancestral Sequence Predictions (GRASP).
PLoS Comput. Biol., October, 2022

ProtTrans: Toward Understanding the Language of Life Through Self-Supervised Learning.
IEEE Trans. Pattern Anal. Mach. Intell., 2022

ProteomicsDB: toward a FAIR open-source resource for life-science research.
Nucleic Acids Res., 2022

Nearest neighbor search on embeddings rapidly identifies distant protein relations.
Frontiers Bioinform., 2022

SETH predicts nuances of residue disorder from protein embeddings.
Frontiers Bioinform., 2022

PredictProtein - Predicting Protein Structure and Function for 29 Years.
Nucleic Acids Res., 2021

CodeTrans: Towards Cracking the Language of Silicone's Code Through Self-Supervised Deep Learning and High Performance Computing.
CoRR, 2021

Clustering FunFams using sequence embeddings improves EC purity.
Bioinform., 2021

Mutations in transmembrane proteins: diseases, evolutionary insights, prediction and comparison with globular proteins.
Briefings Bioinform., 2021

Validity of machine learning in biology and medicine increased through collaborations across fields of expertise.
Nat. Mach. Intell., 2020

ProtTrans: Towards Cracking the Language of Life's Code Through Self-Supervised Deep Learning and High Performance Computing.
CoRR, 2020

Variant effect predictions capture some aspects of deep mutational scanning experiments.
BMC Bioinform., 2020

Protein-protein and protein-nucleic acid binding residues important for common and rare sequence variants in human.
BMC Bioinform., 2020

Secondary Structure Prediction.
Proceedings of the Encyclopedia of Bioinformatics and Computational Biology - Volume 2, 2019

FunFam protein families improve residue level molecular function prediction.
BMC Bioinform., 2019

Correction to: Detailed prediction of protein sub-nuclear localization.
BMC Bioinform., 2019

Detailed prediction of protein sub-nuclear localization.
BMC Bioinform., 2019

Modeling aspects of the language of life through transfer-learning protein sequences.
BMC Bioinform., 2019

NLSdb - major update for database of nuclear localization signals and nuclear export signals.
Nucleic Acids Res., 2018

LocText: relation extraction of protein localizations to assist database curation.
BMC Bioinform., 2018

Correcting mistakes in predicting distributions.
Bioinform., 2018

HFSP: high speed homology-driven function annotation of proteins.
Bioinform., 2018

Bioinformatics advances biology and medicine by turning big data troves into knowledge.
Inform. Spektrum, 2017

nala: text mining natural language mutation mentions.
Bioinform., 2017

Bioinformatics Advances Biology and Medicine by Turning Big Data Troves into Knowledge.
Proceedings of the 50 Jahre Universitäts-Informatik in München, 2017

Predicted Molecular Effects of Sequence Variants Link to System Level of Disease.
PLoS Comput. Biol., 2016

Tools and data services registry: a community effort to document bioinformatics resources.
Nucleic Acids Res., 2016

MSAViewer: interactive JavaScript visualization of multiple sequence alignments.
Bioinform., 2016

ISCB Ebola Award for Important Future Research on the Computational Biology of Ebola Virus.
PLoS Comput. Biol., 2015

Message from the ISCB: ISCB Ebola award for important future research on the computational biology of Ebola virus.
Bioinform., 2015

Evolutionary profiles improve protein-protein interaction prediction from sequence.
Bioinform., 2015

More challenges for machine-learning protein interactions.
Bioinform., 2015

PredictProtein - an open resource for online prediction of protein structural and functional features.
Nucleic Acids Res., 2014

LocTree3 prediction of localization.
Nucleic Acids Res., 2014

<i>HeatMapViewer</i>: interactive display of 2D data in biology.
F1000Research, 2014

FreeContact: fast and free software for protein contact prediction from residue co-evolution.
BMC Bioinform., 2014

tagtog: interactive and text-mining-assisted annotation of gene mentions in PLOS full-text articles.
Database J. Biol. Databases Curation, 2014

ISCB Computational Biology Wikipedia Competition.
PLoS Comput. Biol., 2013

Homology-based inference sets the bar high for protein function prediction.
BMC Bioinform., 2013

ISCB: past-present perspective for the International Society for Computational Biology.
Bioinform., 2013

Alternative Protein-Protein Interfaces Are Frequent Exceptions.
PLoS Comput. Biol., 2012

SNPdbe: constructing an nsSNP functional impacts database.
Bioinform., 2012

Paving the future: finding suitable ISMB venues.
Bioinform., 2012

LocTree2 predicts localization for all domains of life.
Bioinform., 2012

ISCB Public Policy Statement on Open Access to Scientific and Technical Research Literature.
PLoS Comput. Biol., 2011

LocDB: experimental annotations of localization for <i>Homo sapiens</i> and <i>Arabidopsis thaliana</i>.
Nucleic Acids Res., 2011

Towards big data science in the decade ahead from ten years of InCoB and the 1st ISCB-Asia Joint Conference.
BMC Bioinform., 2011

MuD: an interactive web server for the prediction of non-neutral substitutions using protein structural data.
Nucleic Acids Res., 2010

Protein secondary structure appears to be robust under <i>in silico</i> evolution while protein disorder appears not to be.
Bioinform., 2010

Correlating protein function and stability through the analysis of single amino acid substitutions.
BMC Bioinform., 2009

Neural Networks Predict Protein Structure and Function.
Proceedings of the Artificial Neural Networks, 2009

ISMB 2008 Toronto.
PLoS Comput. Biol., 2008

Physical protein-protein interactions predicted from microarrays.
Bioinform., 2008

Powerful fusion: PSI-BLAST and consensus sequences.
Bioinform., 2008

MetalDetector: a web server for predicting metal-binding sites and disulfide bridges in proteins from sequence.
Bioinform., 2008

SNAP predicts effect of mutations on protein function.
Bioinform., 2008

Comprehensive <i>in silico</i> mutagenesis highlights functionally important residues in proteins.
Proceedings of the ECCB'08 Proceedings, 2008

Natively Unstructured Loops Differ from Other Loops.
PLoS Comput. Biol., 2007

Protein-Protein Interaction Hotspots Carved into Sequences.
PLoS Comput. Biol., 2007

ISMB/ECCB 2007: The Premier Conference on Computational Biology.
PLoS Comput. Biol., 2007

Natively unstructured regions in proteins identified from contact predictions.
Bioinform., 2007

ISIS: interaction sites identified from sequence.
Bioinform., 2007

Prediction of DNA-binding residues from sequence.
Proceedings of the Proceedings 15th International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB), 2007

Protein-Protein Interactions More Conserved within Species than across Species.
PLoS Comput. Biol., 2006

Epitome: database of structure-inferred antigenic epitopes.
Nucleic Acids Res., 2006

PROFtmb: a web server for predicting bacterial transmembrane beta barrel proteins.
Nucleic Acids Res., 2006

PROFbval: predict flexible and rigid residues in proteins.
Bioinform., 2006

Create and assess protein networks through molecular characteristics of individual proteins.
Proceedings of the Proceedings 14th International Conference on Intelligent Systems for Molecular Biology 2006, 2006

NMPdb: Database of Nuclear Matrix Proteins.
Nucleic Acids Res., 2005

EVAcon: a protein contact prediction evaluation service.
Nucleic Acids Res., 2005

PROFcon: novel prediction of long-range contacts.
Bioinform., 2005

ISMB 2005 Organization.
Proceedings of the Proceedings Thirteenth International Conference on Intelligent Systems for Molecular Biology 2005, 2005

ISMB 2005.
Proceedings of the Proceedings Thirteenth International Conference on Intelligent Systems for Molecular Biology 2005, 2005

The PredictProtein server.
Nucleic Acids Res., 2004

LOCnet and LOCtarget: sub-cellular localization for structural genomics targets.
Nucleic Acids Res., 2004

NLProt: extracting protein names and sequences from papers.
Nucleic Acids Res., 2004

CHOP: parsing proteins into structural domains.
Nucleic Acids Res., 2004

Annotating Protein Function through Lexical Analysis.
AI Mag., 2004

AI and Bioinformatics.
AI Mag., 2004

Protein names precisely peeled off free text.
Proceedings of the Proceedings Twelfth International Conference on Intelligent Systems for Molecular Biology/Third European Conference on Computational Biology 2004, 2004

The PredictProtein server.
Nucleic Acids Res., 2003

LOC3D: annotate sub-cellular localization for protein structures.
Nucleic Acids Res., 2003

NLSdb: database of nuclear localization signals.
Nucleic Acids Res., 2003

UniqueProt: creating representative protein sequence sets.
Nucleic Acids Res., 2003

NORSp: predictions of long regions without regular secondary structure.
Nucleic Acids Res., 2003

EVA: evaluation of protein structure prediction servers.
Nucleic Acids Res., 2003

Static benchmarking of membrane helix predictions.
Nucleic Acids Res., 2003

META-PP: single interface to crucial prediction servers.
Nucleic Acids Res., 2003

PEP: Predictions for Entire Proteomes.
Nucleic Acids Res., 2003

DSSPcont: continuous secondary structure assignments for proteins.
Nucleic Acids Res., 2003

Bioinformatics in structural genomics - Editorial.
Bioinform., 2002

Target space for structural genomics revisited.
Bioinform., 2002

Inferring sub-cellular localization through automated lexical analysis.
Proceedings of the Tenth International Conference on Intelligent Systems for Molecular Biology, 2002

ISMB 2002
Proceedings of the Tenth International Conference on Intelligent Systems for Molecular Biology, 2002

EVA: continuous automatic evaluation of protein structure prediction servers.
Bioinform., 2001

A platform for integrating threading results with protein family analyses.
Bioinform., 1999

Sisyphus and prediction of protein structure.
Comput. Appl. Biosci., 1997

Learning from Evolution to Predict Protein Structure.
Proceedings of the Biocomputing and emergent computation: Proceedings of BCEC97, 1997

Refining Neural Network Predictions for Helical Transmembrane Proteins by Dynamic Programming.
Proceedings of the Fourth International Conference on Intelligent Systems for Molecular Biology, 1996

TOPITS: Threading One-Dimensional Predictions Into Three-Dimensional Structures.
Proceedings of the Third International Conference on Intelligent Systems for Molecular Biology, 1995

Neuronale Netzwerke und evolutionäre Information: verbesserte Vorhersage der Sekundärstruktur von Proteinen ; (abgefasst in Englisch).
PhD thesis, 1994

PHD - an automatic mail server for protein secondary structure prediction.
Comput. Appl. Biosci., 1994

Evolution and Neural Networks - Protein Secondary Structure Prediction Above 71% Accuracy.
Proceedings of the 27th Annual Hawaii International Conference on System Sciences (HICSS-27), 1994

Exercising Multi-Layered Networks on Protein Secondary Structure.
Int. J. Neural Syst., 1992