|
Burkhard Rost |
|
Email rost@columbia.edu
Web http://cubic.bioc.columbia.edu
Tel +1 (212) 305-4018
Fax +1 (212) 305-7932
Document:
CV Burkhard Rost
Columbia University
Contents:
¥ Tabulated curriculum vitae
¥ Grants
¥ List of publications
|
Burkhard Rost |
|
Email rost@columbia.edu
Web http://cubic.bioc.columbia.edu
Tel +1 (212) 305-4018
Fax +1 (212) 305-7932
Document:
CV Burkhard Rost
Columbia University
Contents:
¥ Tabulated curriculum vitae
¥ Grants
¥ List of publications
Date of preparation: April 1, 2004
Name: Burkhard Rost
Gender: Male
Citizenship: German
Birthplace: Northeim, Lower-Saxony, Germany
Current position: Associate Professor
Address Columbia University
Department of Biochemistry and Molecular Biophysics
650 West 168th Street, BB217
New York, N.Y. 10032
+1-212-305-4018 (fax: 7932), rost@columbia.edu
1971-1980 High school, Herzberg, Lower-Saxony, Germany
1980-1982 Obligatory service in German air force
1982-1985 Study of physics at Justus-Liebig-University Gie§en, Hessia, Germany
10/1984 Bachelor in physics
1985-1988 Study of physics at Ruprecht-Karls-University Heidelberg, Germany
1985-1988 Study of philosophy, history and psychology at Heidelberg University
1986-1988 Master thesis at the Institute of Theoretical Physics, Heidelberg Univ.
Topic: 'Learning algorithms for spin-glass-like neural networks'
Sponsor: Prof. Dr. Heinz Horner, Heidelberg
11/1988 Bachelor in philosophy and history, Heidelberg University
12/1988 Master in physics, Heidelberg University
12/88-6/90 Grant of the 'Stiftung Volkswagenwerk', Inst. Theor. Physics, Heidelberg
Topic: 'Theoretical analysis of the possibilities of seismic and acoustical sensor networks to verify arms control treaties for aircraft'
7-10/89 Research project in the USA (Princeton, Washington DC, MIT)
1990-1993 Completing studies in physics, Heidelberg Univ. and EMBL, Germany
7/1993 Writing PhD thesis
Topic: 'Neural networks and evolution - prediction of protein secondary structure'
Sponsor: none ˆ
7/1994 PhD in physics: Viva voce for Dr. rer. nat. (Doctor rerum naturarum) at Inst. for Theor. Physics, Ruprecht-Karl University Heidelberg, Germany
1986-1988 Assistant at Institute for Theoretical Physics, Heidelberg Univ., Germany
12/88-6/90 Research fellow at Inst. for Theoretical Physics, Heidelberg Univ.
7-10/1989 Visitor at Institutes in the USA (Princeton, Union of Concerned Scientists, MIT)
7/90- 1992 Visitor at EMBL Heidelberg, Germany
7/93-12/94 Research fellow at EMBL Heidelberg, Germany
1/95-12/95 Research fellow at EBI Hinxton, Cambridge, England
1/96- 4/98 Research fellow at EMBL Heidelberg, Germany
5/98-11/98 Researcher at LION Heidelberg, Germany
12/98- 5/00 Assistant Professor at Columbia University, Department of Biochemistry and Molecular Biophysics, New York, USA
since 6/00 Associate Professor at Columbia University
1995-now Program Committee of ISMB meetings (Intelligent Systems for Molecular Biology)
1996-now Member of ISCB (International Society for Computational Biology)
2002-now Board of Directors ISCB (International Society for Computational Biology)
2002-now Member of NYAS (New York Academy of Sciences)
1992-now Over 250 referee reports for peer-reviewed journals (including Nature, Science, Cell, EMBO J)
1995-now Over 40 referee reports on grants from individuals and institutes (countries: Austria, Canada, Denmark, England, Israel, Italy, Norway, Netherlands, Spain, Sweden, Switzerland, USA)
2001-2002 Ad-hoc panels for NIH grants
2001-now Editor Journal of Medical Informatics
2002-now Organisation of New York Computational Biology Society (NYCBS) in collaboration with Terry Gaasterland (Rockefeller University)
1999-now SAB for company LION Biosciences, Heidelberg/Cambridge UK/Cambridge USA/Cleveland/San Diego
12/1988 London, England: Workshop on Arms Control
9/1989 Washington, DC, USA: Union of Concerned Scientists
10/1989 Princeton, USA: Institute for Advanced Studies
5/1990 Prague, CSFR: Workshop on Arms Control
9/1990 Vienna, Austria: Conference on Arms Control
10/1990 Mosbach, Germany: Conference on Arms Control
6/1992 Elba, Italy: Conference on Neural Networks
7/1992 Torino, Italy: Conference on Protein Structure Prediction
11/1992 Nijmegen, Netherlands: EU Conference on Sequence Analysis
6/1993 Rennes, France: Workshop on Secondary Structure Prediction
11/1993 Copenhagen, DK: Conf. on 'Protein Structure by Distance Analysis'
1/1994 Mauii, Hawaii, USA: HICCS Conference
3/1994 Bologna, Italy: Conference on Protein Structures
4/1994 Copenhagen, Denmark: CBS Mini-symposium on structure prediction
11/1994 Bielefeld, Germany: University
11/1994 Copenhagen, DK: Conf. on 'Protein Structure by Distance Analysis'
12/1994 Asilomar, USA: Conf. on 'Critical Assessment of Structure Prediction'
6/1995 Cambridge, England: ISMB'95 (Tutorial)
6/1995 Heidelberg, Germany: University
10/1995 Bressanone, Italy: Workshop on Protein Structures
10/1995 IRBM Rome, Italy: Workshop 'Frontiers of protein structure prediction'
11/1995 Paris, France: Workshop on Protein Structures and Drug Design
6/1996 St. Louis, USA: ISMB'96
8/1996 Madrid, Spain: CNB
10/1996 Heidelberg, Germany: University
11/1996 Copenhagen, DK: Conf. on 'Protein Structure by Distance Analysis'
12/1996 New York, USA: Columbia University
12/1996 Asilomar, USA: University of San Francisco
1/1997 Univ. Jerusalem, Israel: UNESCO workshop on sequence analysis
2/1997 Basel, Switzerland: CIBA-Geigy
2/1997 EBI Hinxton, England: Workshop on protein structure prediction
3/1997 Copenhagen, Denmark: CBS University
3/1997 New York, USA: Columbia University
6/1997 Berlin, Germany: Inst. for Theor. Biol.
6/1997 Chalkidiki, Greece: ISMB'97 (Tutorial)
7/1997 EBI Hinxton, England: EMBO Workshop on protein sequence analysis
7/1997 San Sebastian, Spain: Workshop 'Proteins: integration of life's function'
7/1997 Madrid, Spain: CNB
9/1997 Skšvde, Sweden: Conf. 'Bio-Computing and Emergent Computation'
9/1997 Vienna, Austria: 'Intern. Conference on Molecular Structural Biology'
10/1997 IRBM Rome, Italy: Workshop 'Frontiers of protein structure prediction'
11/1997 Stockholm, Sweden: Pharmacia & Upjohn
11/1997 Stockholm, Sweden: Karolinska Inst.
12/1997 Paris, France: Pasteur Inst.
12/1997 Toulouse, France: INRA Inst.
12/1997 Toulouse, France: Elf Sanofi
12/1997 Basel, CH: Symposium ÔBioinformatics: from Exp. to Biol. KnowledgeÔ
3/1998 Marseille, France: Cancer Inst., INSERM/19CNRS
5/1998 Tallberg, Sweden: Conf. ÔAnnual meeting of Swedish Structural BiologyÕ
5/1998 Bad Honnef, Germany: Conf. ÔScientific Applications of Neural NetsÕ
6/1998 New York, USA: Genome Centre, Workshop
10/1998 Cambridge, England: Newton Inst. Conf. ÔBiomolecular Function and Evolution in the Context of the Genome ProjectÕ
10/1998 EBI, England: Conf. ÔMethods for protein structureÕ
7/1999 Havanna, Cuba: CIGB EMBO Workshop ÔBioinformaticsÕ
8/1999 Cambridge, England: EBI Workshop. ÔProtein motifs and families inÕ
9/1999 Graz, Austria: International Meeting of Austrian Society for Genetics.
10/1999 Bologna, Italy: Workshop ÔProtein sequence analysis in the genome eraÕ
11/1999 Atlanta, USA: Conf. 'In silico biology: sequence & structure & function'
2/2000 Boston, USA: SGI Workshop 'New Technologies for Discovery Research'
2/2000 New York Structural Biology Society
8/2000 Troy RPI, USA: Bioinformatics Workshop
8/2000 Madrid, Spain: Human Genome Workshop
8/2000 New York University
10/2000 Heidelberg, Germany: LION's Bioinformatics 2000
12/2000 Asilomar, USA: Invited session leader and two presentations at the fourth meeting on critical assessment of structure prediction (CASP4)
3/2001 Madrid, Spain: Workshop on structural genomics
3/2001 CNB Madrid, Spain
4/2001 New York, Rockefeller University
5/2001 New York, New York Structural Biology Society
5/2001 New York, Columbia University, Dept. Biology
7/2001 Technical University Copenhagen, Denmark
7/2001 Heidelberg University, Germany
9/2001 Il Ciocco, Italy: NATO summer school on bioinformatics (Talk, Teacher)
9/2001 IRBM Rome, Italy
1/2002 Keystone Symposium on Structural Genomics, USA
4/2002 Madrid, Spain: Meeting on 'Bioinformatics and Computational Biology'
4/2002 Basel, Switzerland: Talk at Biocenter Basel
5/2002 Erice, Italy: Talk on predicting protein function at summer school on structural biology
6/2002 San Diego, USA: 'Eleventh Annual Bioinformatics and Genome Research'
6/2002 Rutgers University, USA: 'Northeast Structural Genomics Consortium Annual Symposium'
7/2002 New York Computational Biology Society, New York Academy of Sciences
8/2002 Edmonton, Canada: ISMB'2002
8/2002 Habanna, Cuba: 'Bioinformatica-Habana'
10/2002 Lausanne, Switzerland, University
11/2002 Toronto, Canada Institute for Proteomics and Bioinformatics
2/2003 New York, Fordham University
2/2003 CABM, Rutgers University, Piscataway, USA
2/2003 New York, Manhattan College
5/2003 New York, City College
10/2003 Bethesda, NIH: Keynote at Workshop on 'Comparative modelling'
11/2003 Bethesda, NIH: Workshop on 'Target Selection in Structural Genomics'
11/2003 Rutgers University, Piscataway, NJ
02/2004 Gordon Conference, Ventura CA: Structural, Functional & Evolutionary Genomics
9/1990 Co-organising 'The Second Workshop on Verification of Arms Reductions', 3-5 Sep. 1990, Vienna, Austria
2/1997 Organising the workshop 'Methods for protein structure prediction - progress and limitations' for Pharmaceutical Companies, 10-11 Feb., 1997, EBI Hinxton-Cambridge, England
8/1999 Organising the workshop ÔProtein motifs and families in practice: Is protein function carved into sequence?Õ Aug 12-13, 1999, EBI Hinxton-Cambridge, England
10/1999 Program committee of the 2nd Bologna summer school on biotechnology 'Protein sequence analysis in the genome era', Bologna, Italy
12/2000 Co-organising CAFASP sessions at the CASP meeting in Asilomar, CA
03/2001 Co-organising bioinformatics competition of LION Biosciences, Boston
03/2001 Co-organising Juan March workshop on structural genomics in Madrid, Spain
02/2002 Program committee of the 3rd "International Meeting on Membrane proteins in Bologna, Italy
06/2002 Program committee meeting on computational biology Manchester England
08/2002 Co-organising 10th International Meeting on 'Intelligent Systems in Molecular Biology' in Edmonton Canada (1500 participants; most important meeting in bioinformatics)
06/2003 Scientific Advisory Board, Editor, and Program Committee for 11th ISMB 2003 in Brisbane, Australia
11/2003 Co-organising NIH workshop on 'Target selection for structural genomics'
06/2003 Scientific Advisory Board, Editor, and Program Committee for 12th ISMB 2004 in Glasgow, Scotland (over 2000 participants expected)
12/2004 Co-organising meeting for the Critical Assessment of protein Structure Prediction (CASP6) in Italy (most important meeting in the field of structure prediction)
1995-2004 Program Committee for ISMB meeting (Intelligent Systems for Molecular Biology; central meeting in computational biology/bioionformatics)
06/2003-now Qualifying exam Dept. Biochemistry & Molecular Biophysics, Columbia
1999-2004 Supervision of graduate students and co-organizing class-room work on bioinformatics in course 'Biophysics' taught by Ann McDermott, Chemistry, Columbia (4 courses: 1999, 2001, 2002, 2003)
2000-2003 Teaching at Medical Faculty, Columbia; course 'Eukaryotes I' (3 courses: 2000, 2001, 2002, 2003)
6/1995 Tutorial at ISMBÕ95 (International Conference on Intelligent Systems for Molecular Biology) in Cambridge, England
10/1995 Supervision of post-docs at the workshop 'Frontiers of protein structure prediction' at the IRBM in Rome, Italy
3/1997 Supervision of post-docs at a workshop at the CBS in Copenhagen (Denmark)
6/1997 Tutorial at ISMBÕ97 (International Conference on Intelligent Systems for Molecular Biology) in Chalkidiki, Greece
7/1997 Supervision of pre- and post-docs at the workshop (EMBO-course) 'Genome sequence analysis' at the EBI in Hinxton, England
7/1997 Teacher at the summer school 'Proteins: integration of life's function' in San Sebastian, Spain
10/1997 Supervision of post-docs at the 2nd workshop 'Frontiers of protein structure prediction' at the IRBM in Rome, Italy
7/1999 Supervision of pre- and post-docs at the workshop 'Bioinformatics' at the CIB in Havanna, Cuba
10/1997 Supervision of post-docs at the workshop 'Protein sequence analysis in the genome era' at the University of Bologna, Italy
9/2001 Teacher at a NATO summer school on bioinformatics in Il Ciocco, Italy
8/2002 Supervision of pre- and post-docs at the workshop 'Bioinformatics' at the CIB in Havanna, Cuba
1986-1988 Organisation of seminars in Theor. Physics, Heidelberg Univ., Germany
1989-1990 Lecture series on Arms control (I), Heidelberg University
1990 Lecture series on Arms control (II), Heidelberg Univ.
1986-1990 Courses on Physics and Arms control in extramural schools (Heidelberg, Mannheim, Frankfurt, Darmstadt)
1991-1995 Lectures, and supervision of courses for PhD students at EMBL Heidelberg
1992-1996 Course lectures on Protein structure prediction at Heidelberg Univ.
Name Graduation Current Affiliation
Yanay Ofran 02/2004 Columbia/Biochemistry
Jinfeng Liu 02/2004 Columbia/Biochemistry
Name University/Department Period
Rajesh Nair Columbia/Physics 1999-2003
Dariusz Przybylski Columbia/Physics 1999-2003
Henry Bigelow Columbia/Biochemistry 2000-2005
Andrew Kernytsky Columbia/Biochemistry 2001-2006
Sven Mika Columbia/Biochemistry 2002-2006
Yana Bromberg Columbia/Medical Inform. 2003-2007
Avner Schlessinger Columbia/Biochemistry 2003-2007
Name University/Department Date Group
Volker Eyrich Columbia/Chemistry 07/2001 Rich Friesner
Yun Zhang Columbia/Biology 10/2001 Marti Chalfie
Yuling An Columbia/Chemistry 07/2002 Rich Friesner
Chuck Duarte Columbia/Biochemistry 09/2002 Ann-Marie Pyle
Cathy S Gunther Rockefeller University 11/2002 Terry Gaasterland
Samuel K Handelman Columbia/Biology 10/2003 John Hunt
Trevor Siggers Columbia/Biochemistry 2005 Barry Honig
Oleg Trott Columbia/Biochemistry 2005 Arthur Palmer
Cinque Soto Columbia/Biochemistry 2005 Barry Honig
Christopher Tang Columbia/Biochemistry 2006 Barry Honig
Erroll Rueckert Columbia/Integrated 2006 Richard Axel
Marina Gimpelev Columbia/Biochemistry 2006 Barry Honig
Chen Peter Chien Columbia/MD,PhD 2006 Barry Honig
Murat Cokol Columbia/Biology 2006 Andrej Rzhetsky
Name University/Department Period
Murat Cokol Columbia/Biology Spring 2000
Trevor Siggers Columbia/Biochemistry Summer 2000
Hong Yu Columbia/Medical Inform. Summer 2000
Hepan Tan Columbia/Biochemistry Summer 2000
Enrique Tadique Bronx Highschool Summer 2000
Henry Bigelow Columbia/Biochemistry Spring 2001
Chen Peter Chien Columbia/MD-PhD Summer 2001
Seth Gale Columbia/Undergraduate Fall 2001
Andrew Kernytsky Columbia/Biochemistry Summer 2002
Avner Schlessinger Columbia/Biochemistry Summer 2002
Anthony J DeCostanzo Columbia/Pharmacology Fall 2002
Roman Trakhtenberg Columbia/Medical Inform. Winter 2002/2003
Shoshana L Posy Columbia/Integrated Spring 2003
Shameek Biswas Columbia/Computer Sci. Summer 2003
Gabor Halasz Columbia/Integrated Summer 2003
Name From Period
Bastian Bruning Nijmegen, Netherlands Spring 2001
Phil Carter Imperial College, London Fall 2001
Seth Gale Columbia Fall 2001
Claus AF Andersen Copenhagen, Denmark Fall 2001/Spring 2002
Jackson Ng High school graduate Spring/Summer 2000
Enrique Tadique High school graduate Summer 2000
PI: Burkhard Rost
Period : August 2002
Agency: NSF
Total Dir Costs: $40 K Overhead 0
Title: ISMB'2002
Summary: Travel support for young participants of the ISMB 2002 meeting
PI: Burkhard Rost
Period : August 2002
Agency: DOE
Total Dir Costs: $35 K Overhead 0
Title: ISMB'2002
Summary: Travel support for young participants of the ISMB 2002 meeting
PI: Gaetano T. Montelione (Rutgers University)
Co-PI Burkhard Rost
Period: 10/01/00 to 31/10/05
Agency: NIH (P50 GM62413-01)
Ann Dir Costs: $180,000 Total (5 years) $750,000 Overhead (4 years) $580,000
Title: Structural genomics of eukaryotic model organisms
Summary: Goal of the pilot project in structural genomics (one of nine in the USA; of about 14 world-wide) to develop high-throughput techniques for large-scale structure determination. This project combines over 20 groups from 12 research institutions in the USA, Canada and Israel. Our particular task is the development of techniques that rationalize the automatic target selection, i.e. prioritize which proteins to pursue experimentally.
PI: Burkhard Rost
Period: 05/01/01 to 04/30/05
Agency: NIH (1 R01 GM63029-01)
Ann Dir Costs: $190,000 Total (4 years) $750,000 Overhead (4 years) $660,000
Title: Intruding into the midnight zone of protein sequence comparisons
Summary: The 'twilight zone' of protein sequence comparison is the region in which sequence similarity does not suffice to conclude, e.g., structural similarity. The vast majority of all protein pairs of similar structure populate a 'midnight zone', i.e., their sequences differ too much for sequence-based inferences. We proposed to refine, extend, and specialize methods combining sequence alignment, structure prediction and functional information. Goal is to unravel hidden similarities in entirely sequenced organisms by a reliable, automatic tool. Towards the end of our project, the sequences for most protein families realized by life will supposedly be available.
PI: Burkhard Rost
Period: 02/01/02 to 01/31/05
Agency: NSF (DBI-0131168)
Ann Dir Costs: $157,000 Total (3 years) $470,000 Overhead (4 years) $240,000
Title: Ab initio prediction of sub-cellular localization
Summary: The major goals of this project are to develop a system predicting the sub-cellular localization of a protein based on sequence alignments and signal peptide motifs. The ultimate objective is to combine a series of novel methods into a comprehensive system that we can use to automatically annotate genomes, in particular those of the fly and the subset of known human proteins. We expect to have our first comprehensive system for the major compartments available by fall 2003.
PI: Burkhard Rost
Period: 05/01/03 Ð 04/30/07
Agency: NIH/NLM (1 R01 LM07329-01 A1)
Ann Dir Costs: $175,000 Total (4 years) $900,000 Overhead (4 years) $770,000
Title: Improve predictions of structure and function by PredictProtein
Summary: The major objective is to improve the internet prediction server PredictProtein. The particular goals are to (1) implement technical improvements, (2) and to systematically combine the results from various methods.
PI: Burkhard Rost
Period: 05/01/03 Ð 04/30/07
Agency: NIH (1 R01 GM64633-01 A2)
Ann Dir Costs: $200,000 Total (4 years) $800,000 Overhead (4 years) $680,000
Title: Predict putative protein-protein interface segments at low resolution
Summary: Here, we propose to develop methods predicting interface segments, i.e. regions of residues consecutive in sequence that are in contact with other interface segments. Separate methods address internal and external interfaces. The basic means explored will be combinations of statistics and neural networks using evolutionary information as contained in multiple sequence alignments. The goal is a low-resolution prediction succeeding often enough to distinguish between internal and external interfaces to assist the design of experiments in molecular and medical biology. We focus on predicting interfaces from sequence.
PI: Barry Honig (Biochemistry, Columbia)
Co-PI: Burkhard Rost
Submitted: 03/01/01
Period: 09/01/01 to 08/31/03
Agency: NIH (5-P20-LM7276)
Ann Dir Costs: $20,000 Overhead 0
Summary: Grant supporting to prepare submitting a grant proposal to begin a center of excellence.
PI: Burkhard Rost
Submitted: 12/15/03
Period: 07/01/04 Ð 06/30/09
Agency: NIH (1-R13-GM072354-01)
Ann Dir Costs: $45,000 Total (5 years) $225,000
Title: Meeting for Critical Assessment of protein Structure Prediction (CASP)
Summary: This grant will cover the funding needed for the next 3 CASP meetings that have evolved to the major event in the structure prediction field.
PI: Barry Honig (Biochemistry, Columbia)
Project leader: Burkhard Rost
Submitted: 01/22/04
Period: 09/01/04 to 08/31/09
Agency: NIH ()
Ann Dir Costs: $200,000 Overhead $120,000
Summary: Grant proposal to begin a national center of excellence.
Estimated Total Budget from 1999-future, i.e. covered by grants $5,844,000
Estimated Total Revenue for Columbia University 1999-future $3,644,534
2002: Total Budget $982,224
2002: Salaries $625,216
2002: Equipment, etc. (estimate) $357,008
2002: Estimated total overhead for Columbia University $331,612
A. B Rost (1988) Lernalgorithmen fŸr verdŸnnte Spin-glas-artige Neuronale Netzwerke (Learning algorithms for spin-glass-like neural networks). Master Thesis, Inst. for Theoretical Physics, Heidelberg University, Germany.
B. B Rost (1993) Neural networks and evolution - advanced prediction of protein secondary structure. PhD Thesis, Dep. of Physics and Astronomy, Heidelberg Univ.
* 1. B Rost (1990) Report on conventional weapons. In 'Verification and arms control implications for European security', HG Brauch (ed.) Mosbach, Germany: AFES Press, 120-122.
* 2. B Rost (1991) Sensor Networks for Verifying Disarmament of Aircraft. Bochum: UVB UniversitŠtsverlag Brockmeyer, Book.
* 3. B Rost (1992) Aircraft Monitoring by Automatic Sensor Networks. In 'Verification at Vienna. Monitoring Reductions of Conventional Armed Forces', J Altmann, H Graaf, PM Lewis, and P Markl (eds.). Philadelphia et al.: Gordon & Breach, 179-187.
4. JLA Altmann, W Baus, A DeVolpi, B Gonsior, J Grin, J Hanousek, V JournŽ, W Kaiser, J Klinger, P Lewis, J M‡lek, J Matousek, M Pospisil, B Rost, V Rudajev, I Sabo & P Stein (1993) Ground Vibration, Acoustic Waves and Magnetic Disturbances Produced by Land Vehicles of the North-Atlantic Treaty Organization - Results of the 1989 Measurements of Baumholder, FRG. Bochum: UVB UniversitŠtsverlag Brockmeyer.
* 5. B Rost & Sander (1992) Jury returns on structure prediction. Nature 360, 540.
* 6. B Rost & C Sander (1992) Exercising multi-layered networks on protein secondary structure. In 'Neural Networks: From Biology to High Energy Physics', O Benhar, S Brunak, P DelGiudice, and M Grandolfo (eds.) Elba, Italy: International Journal of Neural Systems, 209-220.
7. T Meitinger, A Meindl, P Bork, B Rost, C Sander, M Haasemann & J Murken (1993) Molecular modelling of the Norrie disease protein predicts a cysteine knot growth factor tertiary structure. Nature Genetics 5, 376-380.
* 8. B Rost & C Sander (1993) Prediction of protein secondary structure at better than 70% accuracy. J Mol Biol 232, 584-599.
* 9. B Rost & C Sander (1993) Improved prediction of protein secondary structure by use of sequence profiles and neural networks. PNAS 90, 7558-7562.
* 10. B Rost & C Sander (1993) Secondary structure prediction of all-helical proteins in two states. Protein Engineering 6, 831-836.
* 11. B Rost, C Sander and R Schneider (1993) Progress in protein structure prediction? TIBS 18, 120-123.
* 12. B Rost & G Vriend (1993) Neural networks in chemistry. CDA News 8, 24-27.
13. L Holm, B Rost, C Sander, R Schneider & G Vriend (1994) Data based modeling of proteins. In 'Statistical Mechanics, Protein Structure, and Protein Substrate Interactions', Doniach, S (eds.) New York: Plenum Press, 277-296.
* 14. B Rost & C Sander (1994) Structure prediction of proteins - where are we now? Cur Opin Biotech 5, 372-380.
* 15. B Rost & C Sander (1994) 1D secondary structure prediction through evolutionary profiles. In 'Protein Structure by Distance Analysis', H Bohr and S Brunak (eds.) Amsterdam, Oxford, Washington: IOS Press, 257-276.
* 16. B Rost & C Sander (1994) Combining evolutionary information and neural networks to predict protein secondary structure. Proteins 19, 55-72.
* 17. B Rost & C Sander (1994) Conservation and prediction of solvent accessibility in protein families. Proteins 20, 216-226.
* 18. B Rost, C Sander & R Schneider (1994) Evolution and neural networks - protein secondary structure prediction above 71% accuracy. In '27th Hawaii International Conference on System Sciences', L Hunter (ed.) Wailea, Hawaii; Los Alamitos, CA: IEEE Society Press, 385-394.
* 19. B Rost, C Sander & R Schneider (1994) PHD - an automatic server for protein secondary structure prediction. CABIOS 10, 53-60.
* 20. B Rost, C Sander & R Schneider (1994) Redefining the goals of protein secondary structure prediction. J Mol Biol 235, 13-26.
* 21. B Rost (1995) Fitting 1-D predictions into 3-D structures. In 'Protein folds: a distance based approach', H Bohr and S Brunak (eds.) Boca Raton, FL: CRC Press, 132-151.
* 22. B Rost (1995) TOPITS: Threading One-dimensional Predictions Into Three-dimensional Structures. In 'Third International Conference on Intelligent Systems for Molecular Biology', C Rawlings, D Clark, R Altman, L Hunter, T Lengauer, and S Wodak (eds.) Cambridge, England: Menlo Park, CA: AAAI Press, 314-321.
* 23. B Rost, R Casadio, P Fariselli & C Sander (1995) Prediction of helical transmembrane segments at 95% accuracy. Protein Science 4, 521-533.
* 24. B Rost & C Sander (1995) Progress of 1D protein structure prediction at last. Proteins 23, 295-300.
* 25. B Rost & C Sander (1995) Protein structure prediction by neural networks. In 'The handbook of brain theory and neural networks', M Arbib (ed.) Cambridge, MA: Bradford Books/The MIT Press, 772-775.
26. 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 Fjellstršm, 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 & C Vinals (1996) Update on protein structure prediction: results of the 1995 IRBM workshop. Folding & Design 1, R55-R63.
* 27. B Rost (1996) PHD: predicting one-dimensional protein structure by profile based neural networks. Methods in Enzymology 266, 525-539.
* 28. B Rost, R Casadio & P Fariselli (1996) Refining neural network predictions for helical transmembrane proteins by dynamic programming. In 'Fourth International Conference on Intelligent Systems for Molecular Biology', D States, P Agarwal, T Gaasterland, L Hunter, and RF Smith (eds.) St. Louis, Menlo Park: AAAI Press, 192-200.
* 29. B Rost, R Casadio & P Fariselli (1996) Topology prediction for helical transmembrane proteins at 86% accuracy. Protein Science 5, 1704-1718.
* 30. B Rost & C Sander (1996) Bridging the protein sequence-structure gap by structure predictions. Ann Rev Biophys and Biomol Structure 25, 113-136.
* 31. B Rost & A Valencia (1996) Pitfalls of protein sequence analysis. Cur Op Biotech 7, 457-461.
* 32. B Rost (1997) Learning from evolution to predict protein structure. In 'BCEC97: Bio-Computing and Emergent Computation', B Olsson, D Lundh, and A Narayanan (eds.) Skšvde, Sweden: World Scientific, 87-101.
* 33. B Rost (1997) NN which predicts protein secondary structure. In 'Handbook of Neural Computation', E Fiesler and R Beale (eds.) New York: Oxford Univ. Press, G4.1.
* 34. B Rost (1997) Protein structures sustain evolutionary drift. Folding & Design 2, S19-S24.
* 35. B Rost & SI O'Donoghue (1997) Sisyphus and prediction of protein structure. Bioinformatics 13, 345-356.
* 36. B Rost, R Schneider and C Sander (1997) Protein fold recognition by prediction-based threading. J Mol Biol 270, 471-480.
* 37. MA Andrade, SI O'Donoghue & B Rost (1998) Adaptation of protein surfaces to subcellular location. J Mol Biol 276, 517-525.
* 38. B Rost (1998) Better 1D predictions by experts with machines. Proteins Suppl. 1, 192-197.
* 39. B Rost (1998) Marrying structure and genomics. Structure 6, 259-263.
* 40. B Rost (1998) Protein structure prediction in 1D, 2D, 3D. In 'The Encyclopaedia of computational chemistry' P von RaguŽ Schleyer, NL Allinger, T Clark, J Gasteiger, PA Kollman, HF Schaefer III, and PR Schreiner (eds.) Chichester: Wiley, 2242-2255.
* 41. R Zidovetzki, B Rost & I Pecht, (1998) The role of transmembrane domains in the functions of B- and T-cell receptors. Immunology Lett 64, 97-107.
* 42. B Rost (1999) Twilight zone of protein sequence alignments. Protein Engineering 12, 85-94.
* 43. A Zemla, C Venclovas, K Fidelis & B Rost (1999) A modified definition of SOV, a segment-based measure for protein secondary structure prediction assessment. Proteins 34, 220-223.
* 44. B Rost (1999) Evolution teaches neural networks. In ÔScientific applications of neural netsÕ, JW Clark, T Lindenau, and ML Ristig (eds.) Heidelberg: Springer, 207-223.
45. O Olmea, B Rost. & A Valencia (1999) Effective use of sequence correlation and conservation in fold recognition. J Mol Biol 293, 1221-1231.
46. D Fischer, C Barret, K Bryson, A Elofsson, A Godzik, D Jones, KJ Karplus, LA Kelley, RM MacCallum, K Pawowski, B Rost, L Rychlewski & M Sternberg (1999) CAFASP-1: critical assessment of fully automated structure prediction methods. Proteins Suppl 3, 209-21.
47. F Pazos, B Rost & A Valencia (1999) A platform for integrating threading results with protein family analyses. Bioinformatics 15, 1062-1063.
* 48. B Rost & C Sander (2000) Third generation prediction of secondary structure. Meth Mol Biol 143, 71-95.
* 49. M Cokol, R Nair & B Rost (2000) Finding nuclear localization signals. EMBO Reports 1, 411-415.
* 50. B Rost (2001) Protein secondary structure prediction continues to rise. J Struct Biol 134, 204-218.
* 51. J Liu & B Rost (2001) Comparing function and structure between entire proteomes. Protein Science 10, 1970-1979.
* 52. V Eyrich, MA Marti-Renom, D Przybylski, A Fiser, F Pazos, A Valencia, A Sali & B Rost (2001) EVA: continuous automatic evaluation of protein structure prediction servers. Bioinformatics 17, 1242-1243.
53. D Fischer, A Elofsson, L Rychlewski, F Pazos, A Valencia, B Rost, AR Ortiz & RL Dunbrack (2001) CAFASP2: the second critical assessment of fully automated structure prediction methods. Proteins 45 (S5), 171-183.
* 54. B Rost & V Eyrich (2001) EVA: large-scale analysis of secondary structure prediction. Proteins. Proteins 45 (S5), 192-199.
* 55. D Przybylski & B Rost (2002) Alignments grow, secondary structure prediction improves. Proteins 46, 195-205.
* 56. CAF Andersen, AG Palmer, S Brunak & B Rost (2002) Continuum secondary structure captures protein flexibility. Structure 10, 175-184.
57. G Pollastri, D Przybylski, B Rost & 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.
58. MA Marti-Renom, MS Madhusudhan, A Fiser, B Rost, A Sali (2002) Reliability of assessment of protein structure prediction methods at CASP. Structure 10, 435-440.
* 59. B Rost (2002) Enzyme function less conserved than anticipated, J Mol Biol 318, 595-608.
* 60. B Rost (2002) Did evolution leap to create the protein universe? Curr Opin Struct Biol 12, 409-416.
* 61. CP Chen & B Rost (2002) State-of-the-art in membrane protein prediction. Appl Bioinformatics 1, 21-35.
* 62. J Liu & B Rost (2002) Target space for structural genomics revisited. Bioinformatics 18, 922-933.
* 63. B Rost, B Honig & A Valencia (2002) Bioinformatics in structural genomics. Bioinformatics (Editorial) 18, 897-898.
* 64. J Glasgow & B Rost (2002) ISMB 2002. Bioinformatics (Editorial) 18 Suppl 1, S1
* 65. R Nair & B Rost (2002) Inferring sub-cellular localization through automated lexical analysis. Bioinformatics 18 Suppl 1 (ISMB Proceedings), S78-S86.
* 66. J Liu, H Tan & B Rost (2002) Loopy proteins appear conserved in evolution. J Mol Biol 322, 53-64.
* 67. CP Chen, A Kernytsky & B Rost (2002) Transmembrane helix predictions revisited. Protein Science 11, 2774-2791.
* 68. R Nair & B Rost (2002) Sequence conserved for sub-cellular localization. Protein Science 11, 2836-2847.
* 69. CP Chen & B Rost (2002) Long membrane helices and short loops predicted less accurately. Protein Science 11, 2766-2773.
* 70. Y Ofran & B Rost (2003) Analysing six types of protein-protein interfaces. J Mol Biol 325, 377-387.
* 71. CAF Andersen & B Rost (2003) Automatic secondary structure assignment. Methods Biochem Anal 44, 341-363.
* 72. B Rost (2003) Prediction in 1D: secondary structure, transmembrane helices and accessibility. Methods Biochem Anal 44, 559-587.
* 73. P Carter, J Liu & B Rost (2003) PEP: Predictions for entire proteomes. Nucl Acids Res 31, 410-413.
* 74. R Nair, P Carter & B Rost (2003) NLSdb: database of nuclear localization signals. Nucl Acids Res 31, 397-399.
* 75. J Liu & B Rost (2003) Domains, motifs, and clusters in the protein universe. Curr Opin Chem Biol 7, 5-11.
* 76. B Rost (2003) Rising accuracy of protein secondary structure prediction. In 'Protein structure determination, analysis, and modeling for drug discovery', D Chasman (ed.) New York: Dekker, 207-249.
77. R Zidovetzki, B Rost, Don L Armstrong & I Pecht (2003) Transmembrane domains in the functions of Fc receptors. J Biophysical Chemistry 15, 555-575.
* 78. Y Ofran & B Rost (2003) Predict protein-protein interaction sites from local sequence information. FEBS Letters 544, 236-239.
* 79. B Rost (2003) Neural networks predict protein structure: hype or hit? In 'Artificial intelligence and heuristic methods in bioinformatics' P Frasconi and R Shamir (eds.) Amsterdam: IOS Press, 34-50.
* 80. KO Wrzeszczynski & B Rost (2003) Cataloguing proteins in cell cycle control. In 'Cell cycle checkpoint control protocols' H Lieberman (ed.) Totowa: Humana Press, 219-233.
* 81. B Rost, J Liu, D Przybylski, R Nair, H Bigelow, K Wrzeszczynski & Y Ofran (2003) Predicting protein structure through evolution. In 'Chemoinformatics - From Data to Knowledge' J Gasteiger & T Engel (eds.) New York: Wiley, 1789-1811.
* 82. B Rost & J Liu (2003) The PredictProtein server. Nucl Acids Res 31, 3300-3304.
* 83. J Liu & B Rost (2003) NORSp: predictions of long regions without regular secondary structure. Nucl Acids Res 31, 3833-3835.
* 84. R Nair & B Rost (2003) LOC3D: annotate sub-cellular localization for protein structures. Nucl Acids Res 31, 3337-3340.
* 85. S Mika & B Rost (2003) UniqueProt: creating sequence-unique protein data sets. Nucl Acids Res 31, 3789-3791.
* 86. A Kernytsky & B Rost (2003) Static benchmarking of membrane helix predictions. Nucl Acids Res 31, 3642-3644.
* 87. IYY Koh, VA Eyrich, MA Mart’-Renom, D Przybylski, MS Madhusudhan, E Narayanan, O Gra–a, A Valencia, A Sali & B Rost (2003) EVA: evaluation of protein structure prediction servers. Nucl Acids Res 31, 3311-3315.
* 88. VA Eyrich & B Rost (2003) META-PP: single interface to crucial prediction servers. Nucl Acids Res 31, 3308-3310.
* 89. P Carter, CAF Andersen, B Rost (2003) DSSPcont: a database of continuous secondary structure assignments for proteins, Nucl Acids Res 31, 3308-3310.
* 90. R Nair & B Rost (2003) Better prediction of sub-cellular localization by combining evolutionary and structural information. Proteins 53, 917-930.
* 91. VA Eyrich, IYY Koh, D Przybylski, O Gra–a, F Pazos, A Valencia & B Rost (2003) CAFASP3 in the spotlight of EVA. Proteins 53 S6, 548-560.
92. JM Aramini, YJ Huang, JR Cort, S Goldsmith-Fischman, R Xiao, L Shih, CK Ho, J Liu, B Rost, B Honig, MA Kennedy, TB Acton > Montelione (2003) Solution NMR structure of the 30S ribosomal protein S28E from Pyrococcus horikoshii. Protein Science 12, 2823-2830.
* 93. B Rost, J Liu, R Nair, K Wrzeszczynski & Y Ofran (2003) Automatic prediction of protein function. Cellular and Mol Life Sciences 60, 2637-2650.
* 94. R Nair & B Rost (2004) Annotating protein function through lexical analysis. AAAI Magazine special issue, in press.
* 95. J Liu, H Hegyi, TB Acton, GT Montelione & B Rost (2004) Automatic target selection for structural genomics on eukaryotes. Proteins , in press.
96. Z Wunderlich, TB Acton, J Liu, G Kornhaber, J Everett, P Carter, N Lan, N Ecols, Mark Gerstein, B Rost, & GT Montelione (2004) ZebaView: a web-based tool for organizing the protein target list of the Northeast Structural Genomics consortium. Proteins , in press.
* 97. J Liu & B Rost (2004) CHOP proteins into structural domains. Proteins in press.
* 98. B Rost (2004) How to use protein 1D structure predicted by PROFphd. Meth Mol Biol, in press.
* 99. B Rost, G Yachdav & J Liu (2004) The PredictProtein server. Nucl Acids Res, in press.
*100. Y Ofran & B Rost (2004) Predictive methods using protein sequence. In 'Bioinformatics' AD Baxevanis & F Ouelette (eds.) New York: Wiley, in press.
*101. KO Wrzeszczynski & B Rost (2004) Annotating proteins from Endoplasmic Reticulum and Golgi apparatus in eukaryotic proteomes. Cellular and Molecular Life Sciences 2004-01-06.
*102. S Mika & B Rost (2004) Protein names peeled precisely off free text. Bioinformatics , submitted 2004-01-09.
*103. M Punta & B Rost (2004) Toward good 2D predictions in proteins. Bioinformatics, submitted 2004-01-14.
*104. J Liu & B Rost (2004) Sequence-based prediction of protein domains. Nucl Acids Res, submitted 2004-01-20.
*105. H Bigelow, D Petrey, J Liu, D Przybylski & B Rost (2004) Predicting transmembrane beta-barrels for entire proteomes. Nucl Acids Res , submitted 2004-01-21.
*106. D Przybylski & B Rost (2004) Improving fold recognition without folds. J Molecular Biology , submitted 2004-02-03.
*107. S Mika & B Rost (2004) NLProt: extracting protein names and sequences from papers. Nucl Acids Res , submitted 2004-02-15.
*108. J Liu & B Rost (2004) CHOP: parsing proteins into structural domains. Nucl Acids Res, submitted 2004-02-14.
*109. R Nair & B Rost (2004) LOCnet and LOCtarget: Sub-cellular localization for structural genomics targets. Nucl Acids Res, submitted 2004-02-15.
110. R Powers, T Acton, Y Chiang, R Paranji, JR Cort, LC Ma, J Liu, B Rost, GT Montelione (2003) 1H, 13C and 15N Assignments for the Archaeglobus fulgidis Protein AF2095 Northeast Structural Genomics Consortium target GR4. Proteins in preparation.
*111. Y Ofran & B Rost (2004) Predicting protein-protein interfaces through evolution. PNAS , in preparation.
*112. S Mika & B Rost (2004) Cataloguing nuclear matrix proteins. Bioinformatics , in preparation.
*113. D Murray, J Liu, H Hegyi, TB Acton, S Goldsmith, B Honig, GT Montelione & B Rost (2004) Target selection strategy for Northeast Structural Genomics project. Proteins , in preparation.
*114. Y Ofran & B Rost (2004) Rescue for statistical tests in high-throughput biology. Science , in preparation.
*115. KO Wrzeszczynski, G Yachdav, P Carter & B Rost (2004) PredictCellCycle: identifying cell cycle control proteins. Bioinformatics, in preparation.
*116. A Schlessinger & B Rost (2004) Protein flexibility prediction from sequence, in preparation.
*117. P Carter & B Rost (2004) PEP: database for predictions of entire proteomes. Bioinformatics, in preparation
E1. B Rost: Protein fold recognition by merging 1D structure prediction and sequence alignments. Preprint; 1996; http://cubic.bioc.columbia.edu/papers/pre1996_topits/
E2. B Rost & SI O'Donoghue: Sisyphus and protein structure prediction. Fifth International Conference on Intelligent Systems for Molecular Biology; Tutorial; 1997; http://cubic.bioc.columbia.edu/papers/pre1997_ismb/
E3. B Rost, SI O'Donoghue and C Sander: Midnight zone of protein structure evolution. Preprint; 1998; http://cubic.bioc.columbia.edu/papers/pre1998_midnight/
E4. B Rost: Short yeast