--- ------------------------------------------------------------ --- --- List of publications from CUBIC --- ------------------------------------------------------------ --- --- ------------------------------------------------------------ --- --- Papers published --- ------------------------------------------------------------ --- 1992 1. B Rost and C Sander (1992) Jury returns on structure prediction. Nature, 360, 540 2. B Rost and C Sander (1992) Exercising multi-layered networks on protein secondary structure. Neural Networks: From Biology to High Energy Physics, 3, 209-220 1993 3. T Meitinger, A Meindl, P Bork, B Rost, C Sander, M Haasemann and J Murken (1993) Molecular modelling of the Norrie disease protein predicts a cysteine knot growth factor tertiary structure. Nature Genetics, 5, 376-380 4. B Rost and G Vriend (1993) Neural networks in chemistry. CDA News, 8, 24-27 5. B Rost, C Sander and R Schneider (1993) Progress in protein structure prediction?. TIBS, 18, 120-123 6. B Rost and C Sander (1993) Improved prediction of protein secondary structure by use of sequence profiles and neural networks. Proceedings of the National Academy of Sciences, 90, 7558-7562 7. B Rost and C Sander (1993) Prediction of protein secondary structure at better than 70% accuracy. Journal of Molecular Biology, 232, 584-599 8. B Rost and C Sander (1993) Secondary structure prediction of all-helical proteins in two states. Protein Engineering, 6, 831-836 1994 9. L Holm, B Rost, C Sander, R Schneider and G Vriend (1994) Data based modeling of proteins. Statistical Mechanics, Protein Structure, and Protein Substrate Interactions, , 277-296 10. B Rost, C Sander and R Schneider (1994) PHD - an automatic server for protein secondary structure prediction. CABIOS, 10, 53-60 11. B Rost, C Sander and R Schneider (1994) Redefining the goals of protein secondary structure prediction. Journal of Molecular Biology, 235, 13-26 12. B Rost, C Sander and R Schneider (1994) Evolution and neural networks - protein secondary structure prediction above 71% accuracy. 27th Hawaii International Conference on System Sciences, 5, 385-394 13. B Rost and C Sander (1994) 1D secondary structure prediction through evolutionary profiles. in: 'Protein Structure by Distance Analysis' (eds. H Bohr and S Brunak), , 257-276 14. B Rost and C Sander (1994) Combining evolutionary information and neural networks to predict protein secondary structure. Proteins, 19, 55-72 15. B Rost and C Sander (1994) Conservation and prediction of solvent accessibility in protein families. Proteins, 20, 216-226 16. B Rost and C Sander (1994) Structure prediction of proteins - where are we now?. Current Opinion in Biotechnology, 5, 372-380 1995 17. B Rost and C Sander (1995) Protein structure prediction by neural networks. in: 'The handbook of brain theory and neural networks' (eds. M Arbib), , 772-775 18. B Rost and C Sander (1995) Progress of 1D protein structure prediction at last. Proteins, 23, 295-300 19. B Rost, R Casadio, P Fariselli and C Sander (1995) Prediction of helical transmembrane segments at 95% accuracy. Protein Science, 4, 521-533 20. B Rost (1995) Fitting 1-D predictions into 3-D structures. in: 'Protein folds: a distance based approach' (eds. H Bohr and S Brunak), , 132-151 21. B Rost (1995) TOPITS: Threading One-dimensional Predictions Into Three-dimensional Structures. Third International Conference on Intelligent Systems for Molecular Biology, , 314-321 1996 22. T Hubbard, A Tramontano, G Barton, D Jones, M Sippl, A Valencia, A Lesk, J Moult, B Rost, C Sander, R Schneider, A Lahm, R Leplae, C Buta , M Eisenstein, O Fjellström, H Floeckner, JG Grossmann, J Hansen, M Helmer-Citterich, FS Joergensen, A Marchler-Bauer, J Osuna, J Park, A Reinhardt, L Ribas de Pouplana, A Rojo-Dominguez, V Saudek, J Sinclair, S Sturrock, C Venclovas and C Vinals (1996) Update on protein structure prediction: results of the 1995 IRBM workshop. Folding & Design, 1, R55-R63 23. B Rost (1996) PHD: predicting one-dimensional protein structure by profile based neural networks. Methods in Enzymology, 266, 525-539 24. B Rost and C Sander (1996) Bridging the protein sequence-structure gap by structure predictions. Annual Review of Biophysics and Biomolecular Structure, 25, 113-136 25. B Rost and A Valencia (1996) Pitfalls of protein sequence analysis. Current Opinion in Biotechnology, 7, 457-461 26. B Rost, R Casadio and P Fariselli (1996) Refining neural network predictions for helical transmembrane proteins by dynamic programming. Fourth International Conference on Intelligent Systems for Molecular Biology, , 192-200 27. B Rost, R Casadio and P Fariselli (1996) Topology prediction for helical transmembrane proteins at 86% accuracy. Protein Science, 5, 1704-1718 1997 28. B Rost (1997) NN which predicts protein secondary structure. in: 'Handbook of Neural Computation' (eds. E Fiesler and R Beale), , G4.1 29. B Rost, R Schneider and C Sander (1997) Protein fold recognition by prediction-based threading. Journal of Molecular Biology, 270, 471-480 30. B Rost (1997) Learning from evolution to predict protein structure. BCEC97: Bio-Computing and Emergent Computation, , 87-101 31. B Rost and SI O'Donoghue (1997) Sisyphus and prediction of protein structure. Computer Applications in Biological Science, 13, 345-356 32. B Rost (1997) Protein structures sustain evolutionary drift. Folding & Design, 2, S19-S24 33. B Rost (1997) Better 1D predictions by experts with machines. Proteins, Suppl. 1, 192-197 1998 34. MA Andrade, SI O'Donoghue and B Rost (1998) Adaptation of protein surfaces to subcellular location. Journal of Molecular Biology, 276, 517-525 35. R Zidovetzki, B Rost and I Pecht (1998) The role of transmembrane domains in the functions of B- and T-cell receptors. Immunology Letters, 64, 97-107 36. B Rost (1998) Protein structure prediction in 1D, 2D, and 3D. in: 'The Encyclopaedia of Computational Chemistry' (eds. PvR Schleyer, NL Allinger, T Clark, J Gasteiger, PA Kollman, HF Schaefer III and PR Schreiner), 3, 2242-2255 37. B Rost (1998) Marrying structure and genomics. Structure, 6, 259-263 1999 38. A Zemla, C Venclovas, K Fidelis and B Rost (1999) A modified definition of SOV, a segment-based measure for protein secondary structure prediction assessment. Proteins, 34, 220-223 39. F Pazos, B Rost and A Valencia (1999) A platform for integrating threading results with protein family analyses. Bioinformatics, 15, 1062-1063 40. O Olmea, B Rost and A Valencia (1999) Effective use of sequence correlation and conservation in fold recognition. Journal of Molecular Biology, 293, 1221-1239 41. B Rost (1999) Twilight zone of protein sequence alignments. Protein Engineering, 12, 85-94 42. B Rost (1999) Evolution teaches neural networks. in: 'Scientific applications of neural nets' (eds. JW Clark, T Lindenau and ML Ristig), , 207-223 2000 43. M Cokol, R Nair and B Rost (2000) Finding nuclear localization signals. EMBO Reports, 1, 411-415 44. B Rost and C Sander (2000) Third generation prediction of secondary structure. in: 'Protein structure prediction: Methods and Protocols' (ed. D. Webster), Totowa, NJ: Humana Press, 71-95 2001 45. D Fischer, A Elofsson, L Rychlewski, F Pazos, A Valencia, B Rost, AR Ortiz and RLJ Dunbrack (2001) Cafasp2: The second critical assessment of fully automated structure prediction methods. Proteins, 45 Suppl 5, S171-183 46. VA Eyrich, MA Marti-Renom, MS Madhusudhan, A Fiser, F Pazos, A Valencia, A Sali, and B. Rost (2001) EVA: continuous automatic evaluation of protein structure prediction servers. Bioinformatics, 17, 1242-1243 47. J Liu and B Rost (2001) Comparing function and structure between entire proteomes. Protein Science, 10, 1970-1979 48. B Rost (2001) Protein secondary structure prediction continues to rise. J Structural Biology, 134, 204-218 49. B Rost and VE Eyrich (2001) EVA: large-scale analysis of secondary structure prediction. Proteins, 45:S5, S192-199 2002 50. G Pollastri, D Przybylski, B Rost and P Baldi (2002) Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles. Proteins, 47, 228-235 51. MA Marti-Renom, MS Madhusudhan, A Fiser, B Rost and A Sali (2002) Reliability of assessment of protein structure prediction methods. Structure, 10, 435-440 52. B Rost, B Honig and A Valencia (2002) Bioinformatics in structural genomics. Bioinformatics, 18, 897 53. B Rost and J Glasgow (2002) ISMB 2002. Bioinformatics, 18:Suppl 1, S1 54. D Przybylski and B Rost (2002) Alignments grow, secondary structure prediction improves. Proteins, 46, 197-205 55. CAF Andersen, AG Palmer, S Brunak and B Rost (2002) Continuum secondary structure captures protein flexibility. Structure, 10, 175-185 56. CP Chen and B Rost (2002) State-of-the-art in membrane protein prediction. Applied Bioinformatics, 1, 21-35 57. J Liu and B Rost (2002) Target space for structural genomics revisited. Bioinformatics, 18, 922-933 58. R Nair and B Rost (2002) Inferring sub-cellular localization through automated lexical analysis. Bioinformatics, 18:Suppl 1, S78-S86 59. J Liu, H Tan and B Rost (2002) Loopy proteins appear conserved in evolution. J Mol Biol, 322, 53-64 60. CP Chen, A Kernytsky and B Rost (2002) Transmembrane helix predictions revisited. Protein Science, 11, 2774-2791 61. R Nair and B Rost (2002) Sequence conserved for sub-cellular localization. Protein Science, 11, 2836-2847 62. CP Chen and B Rost (2002) Long membrane helices and short loops predicted less accurately. Protein Science, 11, 2766-2773 63. B Rost (2002) Enzyme function less conserved than anticipated. J Mol Biol, 318, 595-608 64. B Rost (2002) Did evolution leap to create the protein universe?. Curr Opin Struc Biol, 12, 409-416 2003 65. R Zidovetzki, B Rost, DL Armstrong and I Pecht (2003) Transmembrane domains in the functions of Fc receptors. J Biophys Chem, 15, 555-575 66. 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 and GT Montelione (2003) Solution NMR structure of the 30S ribosomal protein S28E from Pyrococcus horikoshii. Prot Sci, 12, 2823-2830 67. R Nair, P Carter and B Rost (2003) NLSdb: database of nuclear localization signals. Nucl Acid Res, 322, 397-399 68. P Carter, J Liu and B Rost (2003) PEP: Predictions for Entire Proteomes. Nucl Acid Res, 31, 410-413 69. Y Ofran and B Rost (2003) Analysing six types of protein-protein interfaces. J Mol Biol, 325, 377-387 70. J Liu and B Rost (2003) Domains, motifs, and clusters in the protein universe. Curr Opinion Chem Biol, 7, 5-11 71. CAF Andersen and B Rost (2003) Secondary structure assignment. in: 'Structural Bioinformatics' (eds. P Bourne and H Weissig), New York: Wiley, 339-361 72. Y Ofran and B Rost (2003) Local sequence information can predict protein-protein interaction sites. FEBS Let, 544, 236-239 73. J Liu and B Rost (2003) NORSp: predictions of long regions without regular secondary structure. Nucl Acids Res, 31, 3833-3835 74. R Nair and B Rost (2003) LOC3D: annotate sub-cellular localization for protein structures. Nucl Acids Res, 31, 3337-3340 75. A Kernytsky and B Rost (2003) Static benchmarking of membrane helix predictions. Nucl Acids Res, 31, 3642-3644 76. S Mika and B Rost (2003) UniqueProt: creating sequence-unique protein data sets. Nucl Acids Res, 31, 3789-3791 77. VA Eyrich and B Rost (2003) META-PP: single crucial to prediction servers. Nucl Acids Res, 31, 3308-3310 78. P Carter, CAF Andersen and B Rost (2003) DSSPcont: continuous secondary structure assignments for proteins. Nucl Acids Res, 31, 3293-3295 79. IYY Koh, VA Eyrich, MA Mart’-Renom, D Przybylski, MS Madhusudhan, A Fiser, F Pazos, A Valencia, A Sali and B Rost (2003) EVA: evaluation of protein structure prediction servers. Nucl Acids Res, 31, 3311-3315 80. VA Eyrich, IYY Koh, D Przybylski, O Grana, F Pazos, A Valencia and B Rost (2003) CAFASP3 in the spotlight of EVA. Proteins, 53 S6, 548-560 81. R Nair and B Rost (2003) Better prediction of sub-cellular localization through evolution and structure. Proteins, 53, 917-930 82. KO Wrzeszczynski and B Rost (2003) Cataloguing proteins in cell cycle control. in: 'Cell cycle checkpoint control protocols' (ed. H Liebermann), Totowa: Humana Press, 219-233 83. B Rost (2003) Prediction In 1D: secondary structure, membrane helices, and accessibility. in: 'Structural Bioinformatics' (eds. P Bourne and H Weissig), New York: Wiley, 557-585 84. B Rost (2003) Rising accuracy of protein secondary structure prediction. in: 'Protein structure determination, analysis, and modeling for drug discovery' (ed. D Chasman), New York: Dekker, 207-249 85. B Rost (2003) Neural networks predict protein structure: hype or hit?. in: 'Artificial intelligence and heuristic methods for bioinformatics' (ed. P Frasconi), Amsterdam: IOS Press, 34-50 86. B Rost and J Liu (2003) The PredictProtein server. Nucl Acids Res, 31, 3300-3304 87. B Rost, J Liu, D Przybylski, R Nair, KO Wrzeszczynski, H Bigelow and Y Ofran (2003) Prediction of protein structure through evolution. in: 'Handbook of Chemoinformatics - From Data to Knowledge' (eds. J Gasteiger & T Engel), Weinheim: Wiley-VCH, 1789-1811 88. B Rost, J Liu, R Nair, KO Wrzeszczynski and Y Ofran (2003) Automatic prediction of protein function. Cellular Molecular Life Sciences, 12, 2637-2650 2004 89. J Glasgow, I Jurisica and B Rost (2004) AI and Bioinformatics. AI Magazine, 25, 7-8 90. R Nair and B Rost (2004) Annotating protein function through lexical analysis. AI Magazine, 25, 45-56 --- ------------------------------------------------------------ --- --- Papers pending --- ------------------------------------------------------------ --- 1. Z Wunderlich, TB Acton, J Liu, G Kornhaber, J Everett, P Carter, N Lan, N Echols, M Gerstein, B Rost and GT Montelione (2004) The Protein Target List of the Northeast Structural Genomics Consortium. Proteins, volxx, pages_xx 2. J Liu, H Hegyi, TB Acton, GT Montelione and B Rost (2004) Automatic target selection for structural genomics on eukaryotes. Proteins, volxx, in_press_pages_xx 3. J Liu and B Rost (2004) CHOP proteins into structural domains. Proteins, volxx, in_press_pages_xx 4. Y Ofran and B Rost (2004) Predictive methods using protein sequence. in: 'Bioinformatics' (eds. AD Baxevanis & F Ouelette), Wiley, pages_xx 5. KO Wrzeszczynski and B Rost (2004) Annotating proteins from Endoplasmic Reticulum and Golgi apparatus in eukaryotic proteomes. Cellular and Molecular Life Sciences, volxx, pages_xx 6. S Mika and B Rost (2004) Protein names peeled precisely off free text. Bioinformatics, volxx, pages_xx 7. H Bigelow, D Petrey, J Liu, D Przybylski and B Rost (2004) Predicting transmembrane beta-barrels for entire proteomes. NAR, volxx, pages_xx 8. S Mika and B Rost (2004) NLProt: extracting protein names and sequences from papers. Nucl Acids Res, volxx, pages_xx 9. R Nair and B Rost (2004) LOCnet and LOCtarget: Sub-cellular localization for structural genomics targets. Nucl Acids Res, volxx, pages_xx 10. J Liu and B Rost (2004) Sequence-based prediction of protein domains. NAR, volxx, submitted_pages_xx 11. D Przybylski and B Rost (2004) Improving fold recognition without folds. JMB, volxx, submitted_pages_xx 12. M Punta and B Rost (2004) Toward good 2D predictions in proteins. FEBS, volxx, submitted_pages_xx 13. J Liu and B Rost (2004) CHOP: parsing proteins into structural domains. Nucl Acids Res, volxx, submitted_pages_xx 14. B Rost, G Yachdav and J Liu (2004) The PredictProtein server. Nucl Acids Res, volxx, in_press_pages 15. B Rost (2004) How to use protein 1D structure predicted by PROFphd. in: 'Proteomics Handbook' (ed. JM Walker), Methods in Molecular Biology, Humana Press, submitted_pages_xx --- ------------------------------------------------------------ --- --- Preprints and unpublished documents --- ------------------------------------------------------------ --- 1. B Rost (1996) Protein fold recognition by merging 1D structure prediction and sequence alignments. 2. B Rost (1997) Sisyphus and protein structure prediction. 5th International Conference on Intelligent Systems for Molecular Biology, , Tutorial 3. B Rost, S O'Donoghue and C Sander (1998) Midnight zone of protein structure evolution. 4. B Rost (1998) Short yeast ORFs: expressed protein or not?. Preprint CUBIC, 1999_1 5. B Rost (1999) Neural networks for protein structure prediction: hype or hit?. 6. B Rost and R Schneider (1999) Pedestrian guide to analysing sequence databases. in: 'Core techniques in biochemistry' (eds. K Ashman), , in press since 96... 7. R Nair and B Rost (2001) Surface profiles predict sub-cellular localisation. New York: Columbia University, Preprint CUBIC_2001_05, May 2001 8. B Rost, P Baldi, G Barton, J Cuff, VA Eyrich, D Jones, K Karplus, R King, G Pollastri and D Przybylski (2001) Simple jury predicts protein secondary structure best. New York: Columbia University, Preprint CUBIC_2001_10, Oct 2001 9. B Rost, J Liu, D Przybylski, R Nair, KO Wrzeszczynski, H Bigelow and Y Ofran (2002) Predict protein structure and function through evolutionary information. New York: Columbia University, Preprint CUBIC_2002_12, Dec 2002 --- ------------------------------------------------------------ --- --- WWW published documents --- ------------------------------------------------------------ --- 1. B Rost WWW (1996) Appendix to 'Protein fold recognition by prediction-based threading'. () 2. B Rost WWW (1996) Appendix to 'Topology prediction for helical transmembrane proteins at 86% accuracy'. () 3. B Rost WWW and R Schneider (1996) WWW services for sequence analysis. (http://cubic.bioc.columbia.edu/) 4. B Rost WWW (1996) Average conservation of 1D structure between remote homologues. (http://cubic.bioc.columbia.edu/~rost/Res/96/ConservationOf1D.html) 5. B Rost WWW (1996) Observed secondary structure content for 721 proteins. (http://cubic.bioc.columbia.edu/~rost/Res/96/SecStrContent.html) 6. B Rost WWW (1996) Accuracy of predicting buried helices by PHDsec. (http://cubic.bioc.columbia.edu/~rost/Res/96/PredBuriedHelices.html) 7. B Rost WWW (1996) 1D structure prediction for Chameleon (IgG binding domain of protein G). (http://cubic.bioc.columbia.edu/~rost/Res/96/PredChameleon.html) 8. B Rost WWW (1996) Expected prediction accuracy of PHD. (http://cubic.bioc.columbia.edu/~rost/Res/96/ExpAccuracyPHD.html) 9. B Rost WWW (1997) PredictProtein - internet prediction service. (http://cubic.bioc.columbia.edu/predictprotein/) 10. B Rost WWW (1998) Appendix to 'Twilight zone of protein sequence alignments'. (http://cubic.bioc.columbia.edu/papers/) 11. MA Andrade WWW, SI O'Donoghue and B Rost (1998) Appendix to 'Adaptation of protein surfaces to subcellular location'. (http://cubic.bioc.columbia.edu/papers/)