B. Rost

Yana Bromberg, Burkhard Rost, John Overton, 2009, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

Comprehensive in silico mutagenesis highlights functionally important residues in proteins

Burkhard Rost, Yana Bromberg, B. Rost, 2008, ECCB.

MSAViewer: interactive JavaScript visualization of multiple sequence alignments

Burkhard Rost, Ian Sillitoe, Suzanna Lewis, 2016, Bioinform..

Evolution and Neural Networks - Protein Secondary Structure Prediction Above 71% Accuracy

Burkhard Rost, Chris Sander, Reinhard Schneider, 1994, HICSS.

B. Rost, Christian Schaefer, Dominik Achten, 2012, BMC Genomics.

CATHe: detection of remote homologues for CATH superfamilies using embeddings from protein language models

B. Rost, C. Orengo, I. Sillitoe, 2022, bioRxiv.

End-to-end multitask learning, from protein language to protein features without alignments

Burkhard Rost, Michael Heinzinger, Ahmed Elnaggar, 2019, bioRxiv.

What’s in a name? Why these proteins are intrinsically disordered

Sonia Longhi, Burkhard Rost, Zoran Obradovic, 2013, Intrinsically disordered proteins.

Engineering indel and substitution variants of diverse and ancient enzymes using Graphical Representation of Ancestral Sequence Predictions (GRASP)

Burkhard Rost, Mikael Bodén, Julian Zaugg, 2019, bioRxiv.

LOC3D: annotate sub-cellular localization for protein structures

Burkhard Rost, Rajesh Nair, B. Rost, 2003, Nucleic Acids Res..

Inferring sub-cellular localization through automated lexical analysis

Burkhard Rost, Rajesh Nair, B. Rost, 2002, ISMB.

LocTree3 prediction of localization

Burkhard Rost, Tobias Hamp, Robert Greil, 2014, Nucleic Acids Res..

The 2.35 A structure of the TenA homolog from Pyrococcus furiosus supports an enzymatic function in thiamine metabolism.

B. Rost, G. Montelione, Jinfeng Liu, 2005, Acta crystallographica. Section D, Biological crystallography.

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

Tapio Salakoski, Feng Zhang, Paolo Fontana, 2019, Genome Biology.

An expanded evaluation of protein function prediction methods shows an improvement in accuracy

Tapio Salakoski, Paolo Fontana, Silvio C. E. Tosatto, 2016, Genome Biology.

SNPdbe: constructing an nsSNP functional impacts database

Christian Schaefer, Burkhard Rost, Yana Bromberg, 2011, Bioinform..

Prediction of DNA-binding residues from sequence

Burkhard Rost, Yanay Ofran, Venkatesh Mysore, 2007, ISMB/ECCB.

PROFbval: predict flexible and rigid residues in proteins

Avner Schlessinger, Burkhard Rost, Guy Yachdav, 2006, Bioinform..

Comparison of a molecular dynamics model with the X-ray structure of the N370S acid-beta-glucosidase mutant that causes Gaucher disease.

Marc N. Offman, B. Rost, J. Sussman, 2011, Protein engineering, design & selection : PEDS.

Structural genomics reveals EVE as a new ASCH/PUA‐related domain

Marco Punta, Weihong Zhou, Liang Tong, 2009, Proteins.

FreeContact: fast and free software for protein contact prediction from residue co-evolution

Burkhard Rost, Debora S. Marks, Thomas A. Hopf, 2014, BMC Bioinformatics.

Bioinformatics advances biology and medicine by turning big data troves into knowledge

Volker Heun, Burkhard Rost, Caroline C. Friedel, 2017, Informatik-Spektrum.

Sisyphus and prediction of protein structure

Burkhard Rost, Seán I. O'Donoghue, B. Rost, 1997, Comput. Appl. Biosci..

ProfPPIdb: Pairs of physical protein-protein interactions predicted for entire proteomes

Burkhard Rost, Tobias Hamp, Linh Tran, 2018, bioRxiv.

Natively Unstructured Loops Differ from Other Loops

Avner Schlessinger, Burkhard Rost, Jinfeng Liu, 2007, PLoS Comput. Biol..

Create and assess protein networks through molecular characteristics of individual proteins

Burkhard Rost, Yanay Ofran, Guy Yachdav, 2006, ISMB.

Comparisons of NMR spectral quality and success in crystallization demonstrate that NMR and X-ray crystallography are complementary methods for small protein structure determination.

James M Aramini, Gaetano T Montelione, David A Snyder, 2005, Journal of the American Chemical Society.

HFSP: high speed homology-driven function annotation of proteins

Burkhard Rost, Yana Bromberg, Yannick Mahlich, 2018, Bioinform..

Rising Accuracy of Protein Secondary Structure Prediction

Burkhard Rost, B. Rost, 2003 .

Data Based Modeling of Proteins

B. Rost, L. Holm, C. Sander, 1994 .

Alternative Protein-Protein Interfaces Are Frequent Exceptions

Burkhard Rost, Tobias Hamp, B. Rost, 2012, PLoS Comput. Biol..

Secondary structure assignment.

Burkhard Rost, Claus A F Andersen, C. A. Andersen, 2003, Methods of biochemical analysis.

Using genetic algorithms to select most predictive protein features

Burkhard Rost, Andrew Kernytsky, A. Kernytsky, 2009, Proteins.

Online tools for predicting integral membrane proteins.

Burkhard Rost, Henry R. Bigelow, Henry Bigelow, 2009, Methods in molecular biology.

Protein secondary structure appears to be robust under in silico evolution while protein disorder appears not to be

Christian Schaefer, Avner Schlessinger, Burkhard Rost, 2010, Bioinform..

DSSPcont: continuous secondary structure assignments for proteins

Burkhard Rost, Phil Carter, Claus A. F. Andersen, 2003, Nucleic Acids Res..

CAFASP3 in the spotlight of EVA

Alfonso Valencia, Florencio Pazos, Burkhard Rost, 2003, Proteins.

TOPITS: Threading One-Dimensional Predictions Into Three-Dimensional Structures

Burkhard Rost, B. Rost, 1995, ISMB.

Progress of 1D protein structure prediction at last

B Rost, C Sander, B. Rost, 1995, Proteins.

SARS‐CoV‐2 structural coverage map reveals viral protein assembly, mimicry, and hijacking mechanisms

Bosco K. Ho, B. Rost, S. O’Donoghue, 2021, Molecular systems biology.

LocText: relation extraction of protein localizations to assist database curation

Burkhard Rost, Lars Juhl Jensen, Aleksandar Bojchevski, 2018, BMC Bioinformatics.

Evaluation of transmembrane helix predictions in 2014

Burkhard Rost, Edda Kloppmann, Michael Bernhofer, 2015, Proteins.

CAFASP‐1: Critical assessment of fully automated structure prediction methods

D Fischer, B Rost, L Rychlewski, 1999, Proteins.

Physical protein–protein interactions predicted from microarrays

Burkhard Rost, Ta-tsen Soong, Kazimierz O. Wrzeszczynski, 2008, Bioinform..

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

Florian Matthes, Ahmed Elnaggar, Burkhard Rost, 2021, ArXiv.

Role of transmembrane domains in the functions of B- and T-cell receptors.

B. Rost, R. Zidovetzki, I. Pecht, 1998, Immunology letters.

ISMB/ECCB 2007 Conference Proceedings

Burkhard Rost, Thomas Lengauer, Peter Schuster, 2007 .

ISCB Public Policy Statement on Open Access to Scientific and Technical Research Literature

Burkhard Rost, Richard H Lathrop, B. Rost, 2011, PLoS Comput. Biol..

NMPdb: Database of Nuclear Matrix Proteins

Burkhard Rost, Sven Mika, B. Rost, 2004, Nucleic Acids Res..

NLProt: extracting protein names and sequences from papers

Burkhard Rost, Sven Mika, B. Rost, 2004, Nucleic Acids Res..

Protein names precisely peeled off free text

Burkhard Rost, Sven Mika, B. Rost, 2004, ISMB/ECCB.

Radiomics in radiooncology - Challenging the medical physicist.

Daniel Cremers, Burkhard Rost, Fridtjof Nüsslin, 2018, Physica medica : PM : an international journal devoted to the applications of physics to medicine and biology : official journal of the Italian Association of Biomedical Physics.

Combining multimodal imaging and treatment features improves machine learning‐based prognostic assessment in patients with glioblastoma multiforme

Fridtjof Nüsslin, Benedikt Wiestler, Burkhard Rost, 2018, Cancer medicine.

Epitome: database of structure-inferred antigenic epitopes

Avner Schlessinger, Burkhard Rost, Yanay Ofran, 2005, Nucleic Acids Res..

NLSdb: database of nuclear localization signals

Burkhard Rost, Phil Carter, Rajesh Nair, 2003, Nucleic Acids Res..

Annotating Protein Function through Lexical Analysis

Burkhard Rost, Rajesh Nair, B. Rost, 2004, AI Mag..

Critical assessment of methods of protein structure prediction—Round VII

Anna Tramontano, Krzysztof Fidelis, Andriy Kryshtafovych, 2007, Proteins.

Protein folding rates estimated from contact predictions.

Marco Punta, Burkhard Rost, B. Rost, 2005, Journal of molecular biology.

Mutations in transmembrane proteins: diseases, evolutionary insights, prediction and comparison with globular proteins

Dmitrij Frishman, M. Michael Gromiha, Petr Popov, 2020, Briefings Bioinform..

Evolution and neural networks/spl minus/protein secondary structure prediction above 71% accuracy

B. Rost, C. Sander, R. Schneider, 1994, 1994 Proceedings of the Twenty-Seventh Hawaii International Conference on System Sciences.

Neural Networks Predict Protein Structure and Function

Marco Punta, Burkhard Rost, B. Rost, 2009, Artificial Neural Networks.

Secondary Structure Prediction

Burkhard Rost, Jonas Reeb, B. Rost, 2019, Encyclopedia of Bioinformatics and Computational Biology.

Prediction in 1D: secondary structure, membrane helices, and accessibility.

Burkhard Rost, B. Rost, 2003, Methods of biochemical analysis.

EVAcon: a protein contact prediction evaluation service

Burkhard Rost, Alfonso Valencia, Florencio Pazos, 2005, Nucleic Acids Res..

Establishment of an interdisciplinary workflow of machine learning-based Radiomics in sarcoma patients

Daniel Cremers, Burkhard Rost, Fridtjof Nüsslin, 2017 .

Protein–Protein Interactions More Conserved within Species than across Species

Burkhard Rost, Sven Mika, B. Rost, 2006, PLoS Comput. Biol..

EVA: Large‐scale analysis of secondary structure prediction

Volker A. Eyrich, B Rost, V A Eyrich, 2001, Proteins.

Static benchmarking of membrane helix predictions

Burkhard Rost, Andrew Kernytsky, A. Kernytsky, 2003, Nucleic Acids Res..

Structural genomics plucks high-hanging membrane proteins.

Marco Punta, Burkhard Rost, Edda Kloppmann, 2012, Current opinion in structural biology.

The Protein Structure Initiative

Burkhard Rost, Christine A. Orengo, Adam Godzik, 2010 .

Novel leverage of structural genomics

Jinfeng Liu, Gaetano T Montelione, Burkhard Rost, 2007, Nature Biotechnology.

Structural genomics is the largest contributor of novel structural leverage

Burkhard Rost, Jinfeng Liu, Ta-Tsen Soong, 2009, Journal of Structural and Functional Genomics.

Powerful fusion: PSI-BLAST and consensus sequences

Burkhard Rost, Dariusz Przybylski, B. Rost, 2008, Bioinform..

Tools and data services registry: a community effort to document bioinformatics resources

Silvio C. E. Tosatto, Anthony Bretaudeau, Burkhard Rost, 2015, Nucleic Acids Res..

Evolutionary profiles improve protein-protein interaction prediction from sequence

Burkhard Rost, Tobias Hamp, B. Rost, 2015, Bioinform..

More challenges for machine-learning protein interactions

Burkhard Rost, Tobias Hamp, B. Rost, 2015, Bioinform..

Crystal structure of fatty acid-binding protein-like Ycf58 from Thermosynecoccus elongatus. Northeast Structural Genomics Consortium target TeR13.

B. Rost, G. Montelione, M. Baran, 2007 .

Better 1D predictions by experts with machines

B Rost, B. Rost, 1997, Proteins.

Large-scale analysis of thermostable, mammalian proteins provides insights into the intrinsically disordered proteome.

Avner Schlessinger, Marco Punta, Burkhard Rost, 2009, Journal of proteome research.

An estimated 5% of new protein structures solved today represent a new Pfam family

Marco Punta, Jaina Mistry, Burkhard Rost, 2013, Acta crystallographica. Section D, Biological crystallography.

Corrigendum: A draft network of ligand-receptor-mediated multicellular signalling in human

Jordan A. Ramilowski, B. Rost, Piero Carninci, 2016, Nature Communications.

UniqueProt: creating representative protein sequence sets

Burkhard Rost, Sven Mika, B. Rost, 2003, Nucleic Acids Res..

Evaluation of template‐based models in CASP8 with standard measures

Burkhard Rost, Anna Tramontano, Domenico Cozzetto, 2009, Proteins.

tagtog: interactive and text-mining-assisted annotation of gene mentions in PLOS full-text articles

Burkhard Rost, Steven J. Marygold, Gillian H. Millburn, 2014, Database J. Biol. Databases Curation.

Detailed prediction of protein sub-nuclear localization

Burkhard Rost, Mikael Bodén, Sebastian Seitz, 2019, BMC Bioinformatics.

Protein–protein and protein-nucleic acid binding residues important for common and rare sequence variants in human

Burkhard Rost, Jiajun Qiu, Dmitrii Nechaev, 2020, BMC Bioinform..

Predicted Molecular Effects of Sequence Variants Link to System Level of Disease

Burkhard Rost, Yana Bromberg, Maximilian Hecht, 2016, PLoS Comput. Biol..

LocDB: experimental annotations of localization for Homo sapiens and Arabidopsis thaliana

Burkhard Rost, Shruti Rastogi, B. Rost, 2010, Nucleic Acids Res..

META-PP: single interface to crucial prediction servers

Burkhard Rost, Volker A. Eyrich, B. Rost, 2003, Nucleic Acids Res..

SARS-CoV-2 structural coverage map reveals state changes that disrupt host immunity

Bosco K. Ho, B. Rost, S. O’Donoghue, 2020, bioRxiv.

Bridging the protein sequence-structure gap by structure predictions.

B Rost, C Sander, B. Rost, 1996, Annual review of biophysics and biomolecular structure.

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

Burkhard Rost, Paolo Frasconi, Andrea Passerini, 2008, Bioinform..

InCoB celebrates its tenth anniversary as first joint conference with ISCB-Asia

Tin Wee Tan, Janet Kelso, Shoba Ranganathan, 2011, BMC Genomics.

Crystal structure of a potassium ion transporter TrkH

B. Rost, J. Javitch, M. Punta, 2010, Nature.

CAFASP2: The second critical assessment of fully automated structure prediction methods

Roland L. Dunbrack, D Fischer, B Rost, 2001, Proteins.

PredictProtein—an open resource for online prediction of protein structural and functional features

B. Rost, C. Sander, N. Ben-Tal, 2014, Nucleic Acids Res..

Tools and data services registry: a community effort to document bioinformatics resources

Silvio C. E. Tosatto, Radka Svobodová Vareková, Victor de la Torre, 2015, Nucleic Acids Res..

Anatomy of BioJS, an open source community for the life sciences

Burkhard Rost, Devasena Inupakutika, Manuel Corpas, 2015, eLife.

Critical assessment of methods of protein structure prediction (CASP)—Round 6

B. Rost, T. Hubbard, A. Tramontano, 2005, Proteins.

LocTree3 prediction of localization

Kieu Trinh Do, Katharina M. Hembach, B. Rost, 2014, Nucleic Acids Res..

PROFtmb: a web server for predicting bacterial transmembrane beta barrel proteins

Burkhard Rost, Henry R. Bigelow, B. Rost, 2006, Nucleic Acids Res..

A platform for integrating threading results with protein family analyses

B. Rost, F. Pazos, Alfonso Valencia, 1999 .

PredictProtein—an open resource for online prediction of protein structural and functional features

B. Rost, C. Sander, N. Ben-Tal, 2014, Nucleic Acids Res..

MSAViewer: interactive JavaScript visualization of multiple sequence alignments

B. Rost, S. Lewis, I. Sillitoe, 2016, Bioinform..

Modeling aspects of the language of life through transfer-learning protein sequences

Burkhard Rost, Yu Wang, Florian Matthes, 2019, BMC Bioinformatics.

SNAP predicts effect of mutations on protein function

B. Rost, Y. Bromberg, Guy Yachdav, 2008, Bioinform..

Adaptation of protein surfaces to subcellular location.

B. Rost, M. Andrade, S. O’Donoghue, 1998, Journal of molecular biology.

FunFam protein families improve residue level molecular function prediction

Burkhard Rost, Christine Orengo, Maria Littmann, 2019, BMC Bioinformatics.

Supporting online material for: Clustering FunFams using sequence embeddings improves EC purity

B. Rost, C. Orengo, M. Heinzinger, 2021 .

Critical assessment of methods of protein structure prediction—Round VIII

B. Rost, A. Tramontano, K. Fidelis, 2009, Proteins.

Evaluation of template‐based models in CASP8 with standard measures

B. Rost, D. Cozzetto, A. Tramontano, 2009, Proteins.

A platform for integrating threading results with protein family analyses

B. Rost, A. Valencia, F. Pazos, 1999, Bioinform..

Evolutionary profiles improve protein-protein interaction prediction from sequence

B. Rost, Tobias Hamp, T. Hamp, 2015, Bioinform..

Homology-based inference sets the bar high for protein function prediction

Thomas A. Hopf, B. Rost, Tobias Hamp, 2013, BMC Bioinformatics.

CAID prediction portal: a comprehensive service for predicting intrinsic disorder and binding regions in proteins

Silvio C. E. Tosatto, M. Y. Lobanov, Md. Wasi Ul Kabir, 2023, Nucleic Acids Res..

Structural genomics is the largest contributor of novel structural leverage

B. Rost, A. Godzik, C. Orengo, 2009, Journal of Structural and Functional Genomics.

Structural genomics reveals EVE as a new ASCH/PUA‐related domain

B. Rost, G. Montelione, M. Punta, 2009, Proteins.

CHOP: parsing proteins into structural domains

Burkhard Rost, Jinfeng Liu, B. Rost, 2004, Nucleic Acids Res..

EVA: evaluation of protein structure prediction servers

B. Rost, A. Valencia, F. Pazos, 2003, Nucleic Acids Res..

Membrane protein prediction methods.

Henry R. Bigelow, A. Kernytsky, B. Rost, 2007, Methods.

News from the protein mutability landscape.

B. Rost, M. Hecht, Y. Bromberg, 2013, Journal of molecular biology.

Protein subcellular localization prediction using artificial intelligence technology.

B. Rost, R. Nair, 2008, Methods in molecular biology.

Supporting online material for: Protein embeddings and deep learning predict binding residues for various ligand classes

B. Rost, M. Heinzinger, Christian Dallago, 2021 .

University of Michigan Law School Scholarship Repository University of Michigan Law School Scholarship Repository

B. Rost, G. Montelione, T. Acton, 2022 .

The Aquila Digital Community The Aquila Digital Community

Silvio C. E. Tosatto, Karin M. Verspoor, David A. Lee, 2022 .

Neutral and weakly nonneutral sequence variants may define individuality

B. Rost, Y. Bromberg, P. Kahn, 2013, Proceedings of the National Academy of Sciences.

Cell cycle kinases predicted from conserved biophysical properties

B. Rost, K. Wrzeszczynski, 2009, Proteins.