ROSTLAB - Results / Papers (by Author)

Andersen Bigelow Bromberg Carter Chen Cokol Eyrich Hegyi Kernytsky Koh Liu Mika Mozes Nair Ofran Przybylski Punta Rost Schlessinger Soong Tan Wrzeszczynski Yachdav
Publication index - Sorted by year - Sorted by category - Collected abstracts
CAF Andersen (3): abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material

Automatic secondary structure assignment CAF Andersen, B Rost Methods Biochem Anal., 2003, 44:341-363 (abstr, web)
DSSPcont: continuous secondary structure assignments for proteins P Carter, CAF Andersen, B Rost Nucleic Acids Research, 2003, 31:3293-3295 (abstr, web, pdf)

Continuum secondary structure captures protein flexibility CAF Andersen, AG Palmer, S Brunak, B Rost Structure, 2002, 10:175-184 (abstr, web, pdf)
H Bigelow (5): abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material

Online tools for predicting integral membrane proteins H Bigelow, B Rost in: 'Proteomic analysis of membrane proteins: methods and protocols' (eds. MJ Peirce, R Wait), 2007, : Totowa, NJOnline tools for predicting integral membrane proteins: (abstr, web)
Membrane protein prediction methods M Punta, LR Forrest, H Bigelow, A Kernytsky, J Liu, B Rost Methods, 2007, 41:460-474 (pdf)

PROFtmb: a web server for predicting bacterial transmembrane beta barrel proteins H Bigelow, B Rost Nucleic Acids Research, 2006, 34:W186-188 (abstr, web, pdf)
Prediction of transmembrane beta-barrels for entire proteomes H Bigelow, D Petrey, J Liu, D Przybylski, B Rost Nucleic Acids Research, 2004, 32:2566-2577 (abstr, web, pdf)

Prediction of protein structure through evolution B Rost, J Liu, D Przybylski, R Nair, H Bigelow, KO Wrzeszczynski, Y Ofran in: 'Handbook of Chemoinformatics - from data to knowledge' (eds. J Gasteiger, T Engel), 2003, : WeinheimPrediction of protein structure through evolution:1789-1811
Y Bromberg (2): abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material

SNAP: predict effect of non-synonymous polymorphisms on function Y Bromberg, B Rost Nucleic Acids Research, 2007, 35:3823-3835 (abstr, web, pdf)
mlNODS: Split machine learning data sets using graphs Y Bromberg, B Rost CUBIC preprint, 2006, : New YorkmlNODS: Split machine learning data sets using graphs:submitted 2006_03_20
P Carter (4): abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material

The protein target list of the Northeast Structural Genomics Consortium Z Wunderlich, TB Acton, J Liu, G Kornhaber, J Everett, P Carter, N Lan, N Echols, M Gerstein, B Rost, GT Montelione Proteins: Structure, Function, and Bioinformatics, 2004, 56:181-187 (abstr, pdf)
DSSPcont: continuous secondary structure assignments for proteins P Carter, CAF Andersen, B Rost Nucleic Acids Research, 2003, 31:3293-3295 (abstr, web, pdf)

PEP: Predictions for Entire Proteomes P Carter, J Liu, B Rost Nucleic Acids Research, 2003, 31:410-413 (abstr, web, pdf)
NLSdb: database of nuclear localization signals R Nair, P Carter, B Rost Nucleic Acids Research, 2003, 31:397-399 (abstr, web)
CP Chen (3): abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material

Long membrane helices and short loops predicted less accurately CP Chen, B Rost Protein Science, 2002, Long membrane helices and short loops predicted less accurately:2766-2773 (abstr, web, pdf)
State-of-the-art in membrane prediction CP Chen, B Rost Applied Bioinformatics, 2002, 1:21-35 (abstr, web, pdf)

Transmembrane helix predictions revisited CP Chen, A Kernytsky, B Rost Protein Science, 2002, 11:2774-2791 (abstr, web, pdf)
M Cokol (1): abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material

Finding nuclear localisation signals M Cokol, R Nair, B Rost EMBO Reports, 2000, 1:411-415 (abstr, web, pdf)
V Eyrich (3): abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material

EVA: continuous automatic evaluation of protein structure prediction servers V Eyrich, MA Mart’-Renom, D Przybylski, A Fiser, F Pazos, A Valencia, A Sali, B Rost Bioinformatics, 2001, 17:1242-1243 (abstr, web, pdf)
EVA: large-scale analysis of secondary structure prediction B Rost, V Eyrich Proteins: Structure, Function, and Genetics, 2001, 45 Suppl 5:S192-S199 (abstr, web, pdf)

Simple jury predicts protein secondary structure best B Rost, P Baldi, G Barton, J Cuff, V Eyrich, D Jones, K Karplus, R King, M Ouali, G Pollastri, D Przybylski CUBIC preprint, 2001, Simple jury predicts protein secondary structure best:5 (abstr, web, pdf)
H Hegyi (1): abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material

Automatic target selection for structural genomics on eukaryotes J Liu, H Hegyi, TB Acton, GT Montelione, B Rost Proteins: Structure, Function, and Bioinformatics, 2004, 56:188-200 (abstr, web, pdf)
A Kernytsky (3): abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material

Membrane protein prediction methods M Punta, LR Forrest, H Bigelow, A Kernytsky, J Liu, B Rost Methods, 2007, 41:460-474 (pdf)
Static benchmarking of membrane helix predictions A Kernytsky, B Rost Nucleic Acids Research, 2003, 31:3642-3644 (abstr, web, pdf)

Transmembrane helix predictions revisited CP Chen, A Kernytsky, B Rost Protein Science, 2002, 11:2774-2791 (abstr, web, pdf)
IYY Koh (2): abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material

CAFASP3 in the spotlight of EVA VA Eyrich, IYY Koh, D Przybylski, O Gra–a, F Pazos, A Valencia, B Rost Proteins: Structure, Function, and Bioinformatics, 2003, 53 Suppl 6:548-560 (abstr, web, pdf)
EVA: evaluation of protein structure prediction servers IYY Koh, VA Eyrich, MA Marti-Renom, D Przybylski, MS Madhusudhan, E Narayanan, O Grana, A Valencia, A Sali, B Rost Nucleic Acids Research, 2003, 31:3311-3315 (abstr, web, pdf)
J Liu (26): abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material

Solution NMR structure of Escherichia coli ytfP expands the structural coverage of the UPF0131 protein domain family JM Aramini, YJ Huang, GV Swapna, JR Cort, PK Rajan, R Xiao, R Shastry, TB Acton, J Liu, B Rost, MA Kennedy, GT Montelione Proteins, 2007, 68:789-95 (pdf)
Novel leverage of structural genomics J Liu, GT Montelione, B Rost Nature Biotechnology, 2007, Novel leverage of structural genomics:in press (abstr, web, som)

Membrane protein prediction methods M Punta, LR Forrest, H Bigelow, A Kernytsky, J Liu, B Rost Methods, 2007, 41:460-474 (pdf)
Natively unstructured loops differ from other loops A Schlessinger, J Liu, B Rost PLoS Computational Biology, 2007, 3:e140 (abstr, web, som)

Distinguishing protein-coding from non-coding RNA through support vector machines J Liu, J Gough, B Rost PLoS Genetics, 2006, 2:e29; DOI: 10.1371/journal.pgen.0020029 (abstr, web, pdf)
The 2.35 A structure of the TenA homolog from Pyrococcus furiosus supports an enzymatic function in thiamine metabolism J Benach, WC Edstrom, I Lee, K Das, B Cooper, R Xiao, J Liu, B Rost, TB Acton, GT Montelione, JF Hunt Acta Crystallogr D Biol Crystallogr, 2005, 61:589-98 (pdf)

Solution structure of Archaeglobus fulgidis peptidyl-tRNA hydrolase (Pth2) provides evidence for an extensive conserved family of Pth2 enzymes in archea, bacteria, and eukaryotes R Powers, N Mirkovic, S Goldsmith-Fischman, TB Acton, Y Chiang, YJ Huang, L Ma, PK Rajan, JR Cort, MA Kennedy, J Liu, B Rost, B Honig, D Murray, GT Montelione Protein Science, 2005, 14:2849-61 (pdf)
Comparisons of NMR spectral quality and success in crystallization demonstrate that NMR and X-ray crystallography are complementary methods for small protein structure determination DA Snyder, Y Chen, NG Denissova, T Acton, JM Aramini, M Ciano, R Karlin, J Liu, P Manor, PA Rajan, P Rossi, GV Swapna, R Xiao, B Rost, J Hunt, GT Montelione J Am Chem Soc, 2005, 127:16505-11 (pdf)

Prediction of transmembrane beta-barrels for entire proteomes H Bigelow, D Petrey, J Liu, D Przybylski, B Rost Nucleic Acids Research, 2004, 32:2566-2577 (abstr, web, pdf)
Automatic target selection for structural genomics on eukaryotes J Liu, H Hegyi, TB Acton, GT Montelione, B Rost Proteins: Structure, Function, and Bioinformatics, 2004, 56:188-200 (abstr, web, pdf)

CHOP proteins into structural domains J Liu, B Rost Proteins: Structure, Function, and Bioinformatics, 2004, 55:678-688 (abstr, web, pdf)
CHOP: parsing proteins into structural domains J Liu, B Rost Nucleic Acids Research, 2004, 32:W569-W571 (abstr, web, pdf)

Sequence-based prediction of protein domains J Liu, B Rost Nucleic Acids Research, 2004, 32:3522-3530 (abstr, web, pdf)
1H, 13C and 15N assignments for the Archaeglobus fulgidis protein AF2095 R Powers, TB Acton, Y Chiang, PK Rajan, JR Cort, MA Kennedy, J Liu, L Ma, B Rost, GT Montelione Journal of Biomolecular NMR, 2004, 30:107-108 (pdf)

The PredictProtein server B Rost, G Yachdav, J Liu Nucleic Acids Research, 2004, 32:W321-W326 (abstr, web, pdf)
The protein target list of the Northeast Structural Genomics Consortium Z Wunderlich, TB Acton, J Liu, G Kornhaber, J Everett, P Carter, N Lan, N Echols, M Gerstein, B Rost, GT Montelione Proteins: Structure, Function, and Bioinformatics, 2004, 56:181-187 (abstr, pdf)

Solution NMR structure of the 30S ribosomal protein S28E from Pyrococcus horikoshii JM Aramini, YJ Huang, JR Cort, S Goldsmith-Fischman, R Xiao, LY Shih, CK Ho, J Liu, B Rost, B Honig, MA Kennedy, TB Acton, GT Montelione Protein Science, 2003, 12:2823-2830 (abstr, pdf)
PEP: Predictions for Entire Proteomes P Carter, J Liu, B Rost Nucleic Acids Research, 2003, 31:410-413 (abstr, web, pdf)

Domains, motifs, and clusters in the protein universe J Liu, B Rost Current Opinion in Chemical Biology, 2003, 7:5-11 (abstr, web, pdf)
NORSp: predictions of long regions without regular secondary structure J Liu, B Rost Nucleic Acids Research, 2003, 31:3833-3835 (abstr, web, pdf)

Automatic prediction of protein function B Rost, J Liu, R Nair, KO Wrzeszczynski, Y Ofran Cellular and Molecular Life Sciences, 2003, 60:2637-2650 (abstr, web, pdf)
Prediction of protein structure through evolution B Rost, J Liu, D Przybylski, R Nair, H Bigelow, KO Wrzeszczynski, Y Ofran in: 'Handbook of Chemoinformatics - from data to knowledge' (eds. J Gasteiger, T Engel), 2003, : WeinheimPrediction of protein structure through evolution:1789-1811

The PredictProtein server B Rost, J Liu Nucleic Acids Research, 2003, 31:3300-3304 (abstr, web, pdf)
Loopy proteins appear conserved in evolution J Liu, H Tan, B Rost Journal of Molecular Biology, 2002, 322:53-64 (abstr, web, pdf)

Target space for structural genomics revisited J Liu, B Rost Bioinformatics, 2002, 18:922-933 (abstr, web, pdf)
Comparing function and structure between entire proteomes J Liu, B Rost Protein Science, 2001, 10:1970-1979 (abstr, web, pdf)
S Mika (5): abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material

Protein-protein interactions more conserved within species than across species S Mika, B Rost PLoS Computational Biology, 2006, 2:e79 (abstr, web, pdf, som)
NMPdb: database of nuclear matrix proteins S Mika, B Rost Nucleic Acids Research, 2005, 33:D160-163 (abstr, web, pdf)

NLProt: extracting protein names and sequences from papers S Mika, B Rost Nucleic Acids Research, 2004, 32:W634-W637 (abstr, web, pdf)
Protein names peeled precisely off free text S Mika, B Rost Bioinformatics, 2004, 20:I241-I247 (abstr, web, pdf)

UniqueProt: creating representative protein sequence sets S Mika, B Rost Nucleic Acids Research, 2003, 31:3789-3791 (abstr, web, pdf)
E Mozes (1): abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material

Create and assess protein networks through molecular characteristics of individual proteins Y Ofran, G Yachdav, E Mozes, T-t Soong, R Nair, B Rost Bioinformatics, 2006, 22:e402-7 (abstr, web, pdf)
R Nair (14): abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material

Predicting protein subcellular localization using intelligent systems R Nair, B Rost in: 'In Silico Technology in Drug Target Identification and Validation' (eds. D Leon, S Markel), 2007, Predicting protein subcellular localization using intelligent systems: (abstr, web)
Create and assess protein networks through molecular characteristics of individual proteins Y Ofran, G Yachdav, E Mozes, T-t Soong, R Nair, B Rost Bioinformatics, 2006, 22:e402-7 (abstr, web, pdf)

Mimicking cellular sorting improves prediction of subcellular localization R Nair, B Rost Journal of Molecular Biology, 2005, 348:85-100 (abstr, web, pdf)
Annotating protein function through lexical analysis R Nair, B Rost AI Magazine, 2004, 25:45-56 (abstr, web)

LOCnet and LOCtarget: Sub-cellular localization for structural genomics targets R Nair, B Rost Nucleic Acids Research, 2004, 32:W517-W521 (abstr, web, pdf)
Better prediction of sub-cellular localization by combining evolutionary and structural information R Nair, B Rost Proteins: Structure, Function, and Bioinformatics, 2003, 53:917-930 (abstr, web, pdf)

LOC3D: annotate sub-cellular localization for protein structures R Nair, B Rost Nucleic Acids Research, 2003, 31:3337-3340 (abstr, web, pdf)
NLSdb: database of nuclear localization signals R Nair, P Carter, B Rost Nucleic Acids Research, 2003, 31:397-399 (abstr, web)

Automatic prediction of protein function B Rost, J Liu, R Nair, KO Wrzeszczynski, Y Ofran Cellular and Molecular Life Sciences, 2003, 60:2637-2650 (abstr, web, pdf)
Prediction of protein structure through evolution B Rost, J Liu, D Przybylski, R Nair, H Bigelow, KO Wrzeszczynski, Y Ofran in: 'Handbook of Chemoinformatics - from data to knowledge' (eds. J Gasteiger, T Engel), 2003, : WeinheimPrediction of protein structure through evolution:1789-1811

Inferring sub-cellular localisation through automated lexical analysis R Nair, B Rost Bioinformatics, 2002, 18:S78-S86 (abstr, web, pdf)
Sequence conserved for sub-cellular localization R Nair, B Rost Protein Science, 2002, 11:2836-2847 (abstr, web, pdf)

Surface profiles predict sub-cellular localisation R Nair, B Rost CUBIC preprint, 2001, Surface profiles predict sub-cellular localisation: (abstr, pdf)
Finding nuclear localisation signals M Cokol, R Nair, B Rost EMBO Reports, 2000, 1:411-415 (abstr, web, pdf)
Y Ofran (12): abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material

ISIS: Interaction Sites Identified from Sequence Y Ofran, B Rost Bioinformatics, 2007, 23:e13-16 (abstr, web, pdf)
Prediction of DNA-binding residues from sequence Y Ofran, V Mysore, B Rost Bioinformatics, 2007, 23:i347-i353 (abstr, web, pdf)

Protein-protein interaction hot spots carved into sequences Y Ofran, B Rost PLoS Computational Biology, 2007, 3:e119 (abstr, web, pdf)
Create and assess protein networks through molecular characteristics of individual proteins Y Ofran, G Yachdav, E Mozes, T-t Soong, R Nair, B Rost Bioinformatics, 2006, 22:e402-7 (abstr, web, pdf)

Epitome: Database of structure-inferred antigenic epitopes A Schlessinger, Y Ofran, G Yachdav, B Rost Nucleic Acids Research, 2006, 34:D777-780 (abstr, web, pdf)
Beyond annotation transfer by homology: novel protein function prediction methods that can assist drug discovery Y Ofran, M Punta, R Schneider, B Rost Drug Discovery Today, 2005, 10:1475-1482 (pdf)

Predictive methods using protein sequence Y Ofran, B Rost in: 'Bioinformatics' (eds. AD Baxevanis, BF Ouellette), 2005, : New YorkPredictive methods using protein sequence:197-222 (pdf)
Rescue for statistical tests in high-throughput biology Y Ofran, B Rost CUBIC preprint, 2004, : New YorkRescue for statistical tests in high-throughput biology:

Analysing six types of protein-protein interfaces Y Ofran, B Rost Journal of Molecular Biology, 2003, 325:377-387 (abstr, web, pdf)
Predict protein-protein interaction sites from local sequence information Y Ofran, B Rost FEBS Letters, 2003, 544:236-239 (abstr, web, pdf)

Automatic prediction of protein function B Rost, J Liu, R Nair, KO Wrzeszczynski, Y Ofran Cellular and Molecular Life Sciences, 2003, 60:2637-2650 (abstr, web, pdf)
Prediction of protein structure through evolution B Rost, J Liu, D Przybylski, R Nair, H Bigelow, KO Wrzeszczynski, Y Ofran in: 'Handbook of Chemoinformatics - from data to knowledge' (eds. J Gasteiger, T Engel), 2003, : WeinheimPrediction of protein structure through evolution:1789-1811
D Przybylski (11): abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material

Consensus sequences improve PSI-BLAST through mimicking profile-profile alignments D Przybylski, B Rost Nucleic Acids Research, 2007, 35:2238-2246 (abstr, web, pdf, som)
Predicting simplified features of protein structure D Przybylski, B Rost in: 'Bioinformatics - From Genomes to Therapies' (eds. T Lengauer), 2007, : WeinheimPredicting simplified features of protein structure:in press (abstr, web)

Prediction of transmembrane beta-barrels for entire proteomes H Bigelow, D Petrey, J Liu, D Przybylski, B Rost Nucleic Acids Research, 2004, 32:2566-2577 (abstr, web, pdf)
Improving fold recognition without folds D Przybylski, B Rost Journal of Molecular Biology, 2004, 341:255-269 (abstr, web, pdf)

CAFASP3 in the spotlight of EVA VA Eyrich, IYY Koh, D Przybylski, O Gra–a, F Pazos, A Valencia, B Rost Proteins: Structure, Function, and Bioinformatics, 2003, 53 Suppl 6:548-560 (abstr, web, pdf)
EVA: evaluation of protein structure prediction servers IYY Koh, VA Eyrich, MA Marti-Renom, D Przybylski, MS Madhusudhan, E Narayanan, O Grana, A Valencia, A Sali, B Rost Nucleic Acids Research, 2003, 31:3311-3315 (abstr, web, pdf)

Prediction of protein structure through evolution B Rost, J Liu, D Przybylski, R Nair, H Bigelow, KO Wrzeszczynski, Y Ofran in: 'Handbook of Chemoinformatics - from data to knowledge' (eds. J Gasteiger, T Engel), 2003, : WeinheimPrediction of protein structure through evolution:1789-1811
Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles G Pollastri, D Przybylski, B Rost, P Baldi Proteins: Structure, Function, and Bioinformatics, 2002, 47:228-235 (pdf)

Alignments grow, secondary structure prediction improves D Przybylski, B Rost Proteins: Structure, Function, and Bioinformatics, 2002, 46:195-205 (abstr, web, pdf)
EVA: continuous automatic evaluation of protein structure prediction servers V Eyrich, MA Mart’-Renom, D Przybylski, A Fiser, F Pazos, A Valencia, A Sali, B Rost Bioinformatics, 2001, 17:1242-1243 (abstr, web, pdf)

Simple jury predicts protein secondary structure best B Rost, P Baldi, G Barton, J Cuff, V Eyrich, D Jones, K Karplus, R King, M Ouali, G Pollastri, D Przybylski CUBIC preprint, 2001, Simple jury predicts protein secondary structure best:5 (abstr, web, pdf)
M Punta (7): abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material

Membrane protein prediction methods M Punta, LR Forrest, H Bigelow, A Kernytsky, J Liu, B Rost Methods, 2007, 41:460-474 (pdf)
Natively unstructured regions in proteins identified from contact predictions A Schlessinger, M Punta, B Rost Bioinformatics, 2007, Natively unstructured regions in proteins identified from contact predictions:in press (abstr, web, pdf, som)

Identifying cysteines and histidines in transition-metal-binding sites using support vector machines and neural networks A Passerini, M Punta, A Ceroni, B Rost, P Frasconi Proteins: Structure, Function, and Bioinformatics, 2006, 65:305-316 (pdf)
CASP6 assessment of contact prediction O Grana, D Baker, RM Maccallum, J Meiler, M Punta, B Rost, ML Tress, A Valencia Proteins, 2005, 61:214-224 (pdf)

Beyond annotation transfer by homology: novel protein function prediction methods that can assist drug discovery Y Ofran, M Punta, R Schneider, B Rost Drug Discovery Today, 2005, 10:1475-1482 (pdf)
PROFcon: novel prediction of long-range contacts M Punta, B Rost Bioinformatics, 2005, 21:2960-2968 (abstr, web, pdf)

Protein folding rates estimated from contact predictions M Punta, B Rost Journal of Molecular Biology, 2005, 348:507-512 (web, pdf)
B Rost only single-author papers, here (21): abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material
Prediction of protein structure in 1D - Secondary structure, membrane regions, and solvent accessibility B Rost in: 'Structural Bioinformatics - 2nd Edition' (eds. PE Bourne, H Weissig), 2007, Prediction of protein structure in 1D - Secondary structure, membrane regions, and solvent accessibility: (abstr, web)

How to use protein 1D structure predicted by PROFphd B Rost in: 'The Proteomics Protocols Handbook' (eds. JE Walker), 2005, : Totowa NJHow to use protein 1D structure predicted by PROFphd:875-901
Neural networks predict protein structure: hype or hit? B Rost in: 'Artificial intelligence and heuristic methods in bioinformatics' (eds. P Frasconi, R Shamir), 2003, : AmsterdamNeural networks predict protein structure: hype or hit?:34-50 (abstr, web, pdf)

Prediction in 1D: secondary structure, membrane helices, and accessibility B Rost Methods Biochem Anal, 2003, 44:559-587 (abstr, web)

Rising accuracy of protein secondary structure prediction B Rost in: 'Protein structure determination, analysis, and modeling for drug discovery' (eds. D Chasman), 2003, : New YorkRising accuracy of protein secondary structure prediction:207-249 (abstr, web)

Did evolution leap to create the protein universe? B Rost Current Opinion in Structural Biology, 2002, 12:409-416 (abstr, web, pdf)
Enzyme function less conserved than anticipated B Rost Journal of Molecular Biology, 2002, 318:595-608 (abstr, web, pdf)
Protein secondary structure prediction continues to rise B Rost Journal of Structural Biology, 2001, 134:204-218 (abstr, web, pdf)

Evolution teaches neural networks B Rost in: 'Scientific applications of neural nets' (eds. JW Clark, T Lindenau, ML Ristig), 1999, : HeidelbergEvolution teaches neural networks:207-223 (abstr, web, pdf)

Short yeast ORFs: expressed protein or not? B Rost CUBIC preprint, 1999, Short yeast ORFs: expressed protein or not?: (web)
Twilight zone of protein sequence alignments B Rost Protein Engineering, 1999, 12:85-94 (abstr, web, pdf)

Marrying structure and genomics B Rost Structure, 1998, 6:259-263 (abstr, web, pdf)
Protein structure prediction in 1D, 2D, and 3D B Rost in: 'The Encyclopaedia of Computational Chemistry' (eds. PvR Schleyer, NL Allinger, T Clark, J Gasteiger, PA Kollman, HF Schaefer III, PR Schreiner), 1998, 3:2242-2255 (abstr, web, pdf)
Better 1D predictions by experts with machines B Rost Proteins: Structure, Function, and Genetics, 1997, Suppl. 1:192-197 (abstr, web, pdf)

Learning from evolution to predict protein structure B Rost in: 'BCEC97: Bio-Computing and Emergent Computation' (eds. B Olsson, D Lundh, A Narayanan), 1997, : Skšvde, SwedenLearning from evolution to predict protein structure:87-101 (abstr, web, pdf)
NN which predicts protein secondary structure B Rost in: 'Handbook of Neural Computation' (eds. E Fiesler, R Beale), 1997, : New YorkNN which predicts protein secondary structure:G4.1 (abstr, pdf)
Protein structures sustain evolutionary drift B Rost Folding & Design, 1997, 2:S19-S24 (abstr, web, pdf)

PHD: predicting one-dimensional protein structure by profile based neural networks B Rost Methods in Enzymology, 1996, 266:525-539 (abstr, web, pdf)
Fitting 1-D predictions into 3-D structures B Rost in: 'Protein folds: a distance based approach' (eds. H Bohr, S Brunak, S Brunak), 1995, : Boca Raton, FloridaFitting 1-D predictions into 3-D structures:132-151 (abstr, pdf)
TOPITS: Threading One-dimensional Predictions Into Three-dimensional Structures B Rost in: 'Third International Conference on Intelligent Systems for Molecular Biology' (eds. C Rawlings, D Clark, R Altman, L Hunter, T Lengauer, S Wodak), 1995, : Cambridge, EnglandTOPITS: Threading One-dimensional Predictions Into Three-dimensional Structures:314-321 (abstr, pdf)

Neural networks and evolution - advanced prediction of protein secondary structure B Rost Thesis, 1993, Neural networks and evolution - advanced prediction of protein secondary structure:
A Schlessinger (5): abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material

Natively unstructured loops differ from other loops A Schlessinger, J Liu, B Rost PLoS Computational Biology, 2007, 3:e140 (abstr, web, som)
Natively unstructured regions in proteins identified from contact predictions A Schlessinger, M Punta, B Rost Bioinformatics, 2007, Natively unstructured regions in proteins identified from contact predictions:in press (abstr, web, pdf, som)

Epitome: Database of structure-inferred antigenic epitopes A Schlessinger, Y Ofran, G Yachdav, B Rost Nucleic Acids Research, 2006, 34:D777-780 (abstr, web, pdf)
PROFbval: predict flexible and rigid residues in proteins A Schlessinger, G Yachdav, B Rost Bioinformatics, 2006, 22:891-893 (abstr, web, pdf, som)

Protein flexibility and rigidity predicted from sequence A Schlessinger, B Rost Proteins: Structure, Function, and Bioinformatics, 2005, 61:115-126 (abstr, web, pdf)
T-T Soong (1): abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material

Create and assess protein networks through molecular characteristics of individual proteins Y Ofran, G Yachdav, E Mozes, T-t Soong, R Nair, B Rost Bioinformatics, 2006, 22:e402-7 (abstr, web, pdf)
H Tan (1): abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material

Loopy proteins appear conserved in evolution J Liu, H Tan, B Rost Journal of Molecular Biology, 2002, 322:53-64 (abstr, web, pdf)
KO Wrzeszczynski (4): abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material

Annotating proteins from Endoplasmic reticulum and Golgi apparatus in eukaryotic proteomes KO Wrzeszczynski, B Rost Cellular and Molecular Life Sciences, 2004, 61:1341-1353 (abstr, web)
Cataloguing proteins in cell cycle control KO Wrzeszczynski, B Rost Methods in Molecular Biology, 2004, 241:219-233 (abstr, web, pdf)

Automatic prediction of protein function B Rost, J Liu, R Nair, KO Wrzeszczynski, Y Ofran Cellular and Molecular Life Sciences, 2003, 60:2637-2650 (abstr, web, pdf)
Prediction of protein structure through evolution B Rost, J Liu, D Przybylski, R Nair, H Bigelow, KO Wrzeszczynski, Y Ofran in: 'Handbook of Chemoinformatics - from data to knowledge' (eds. J Gasteiger, T Engel), 2003, : WeinheimPrediction of protein structure through evolution:1789-1811
G Yachdav (4): abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material

Create and assess protein networks through molecular characteristics of individual proteins Y Ofran, G Yachdav, E Mozes, T-t Soong, R Nair, B Rost Bioinformatics, 2006, 22:e402-7 (abstr, web, pdf)
Epitome: Database of structure-inferred antigenic epitopes A Schlessinger, Y Ofran, G Yachdav, B Rost Nucleic Acids Research, 2006, 34:D777-780 (abstr, web, pdf)

PROFbval: predict flexible and rigid residues in proteins A Schlessinger, G Yachdav, B Rost Bioinformatics, 2006, 22:891-893 (abstr, web, pdf, som)
The PredictProtein server B Rost, G Yachdav, J Liu Nucleic Acids Research, 2004, 32:W321-W326 (abstr, web, pdf)