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Boltzmannstrasse 3 (Rm
01.09.052) 85748 Garching/MŸnchen Germany & Dept. Biochemistry &
Molecular Biophysics Columbia University New York |
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Email rost@in.tum.de
Web www.rostlab.org
rostlab.in.tum.de
Tel +49-89-289-17-811
Fax +49-89-289-19-414
Document:
CV Burkhard
Rost
TU MŸnchen
Columbia
University
Contents:
¥
Tabulated curriculum vitae
¥
Grants
¥ List
of publications
printed September 26, 2011
Date of preparation: September 26, 2011
Name: Burkhard Rost
Gender: Male
Marital Status: Married with one daughter (born Dec. 2002)
Citizenship: German
Birthplace: Northeim, Lower-Saxony, Germany
Current position: Professor, Unit chair
Address TUM,
Department for Computer Sciences (Informatik)
Unit
for Bioinformatics & Computational Biology (i12)
Boltzmannstrasse
3, 85748 Garching/Munich, Germany
tel.:
+49-89-289-17-811
email:
assistant@rostlab.org (fast), rost@in.tum.de (slow)
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
12/88-06/90 Grant of the 'Stiftung Volkswagenwerk' (VW Foundation), Inst. Theor. Physics, Heidelberg
Topic: 'Theoretical analysis of the possibilities
of seismic and acoustical sensor networks to verify arms control treaties for
aircraft'
07-10/89 Research project in the USA (Princeton, Washington DC, MIT)
1990-1993 Completing studies in physics, Heidelberg Univ. and EMBL, Germany
07/1993 Writing PhD thesis
Topic: 'Neural networks and evolution - prediction
of protein secondary structure'
Sponsor: none ˆ
07/1994 PhD in physics: Viva voce for Dr. rer. nat. (Doctor rerum naturarum) at Institute for Theoretical Physics, Ruprecht-Karl University Heidelberg, Germany
1986-1988 Assistant at Institute for Theoretical Physics, Heidelberg Univ., Germany
12/88-06/90 Research fellow at Inst. for Theoretical Physics, Heidelberg Univ.
07-10/1989 Visitor at Institutes in the USA (Princeton, U. of Concerned Scientists, MIT)
07/90- 1992 Visitor at EMBL Heidelberg, Germany
07/93-12/94 Research fellow at EMBL Heidelberg, Germany
01/95-12/95 Research fellow at EBI Hinxton, Cambridge, England
01/96- 04/98 Research fellow at EMBL Heidelberg, Germany
05/98-11/98 Researcher at LION Biosciences Heidelberg, Germany
12/98- 05/00 Assistant Professor at Department of Biochemistry and Molecular Biophysics, Columbia University, New York, USA
07/2000-2010 Associate Professor at Dept. of Biochemistry & Mol. Biophys., Columbia
2004-2010 Affiliated Faculty, Dept. of Medical Bioinformatics, Columbia University
2002-2010 Faculty Center of Computational Biology and Bioinformatics (C2B2)
07/2005-2010 Tenure in Dept. of Biochemistry and Mol. Biophysics at Columbia University
2006-2010 Associated Faculty in the Department of Pharmacology at Columbia Univ.
2006-2010 Associated Faculty in the Irving Center of Cancer Research at Columbia
since 06/2009 Alexander von Humboldt Professor in Department for Computer Sciences at the TU Munich, Germany
1995-now Program Committee of ISMB (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)
2005-2006 Vice President ISCB (International Soc. for Computational Biology)
2006 President Elect of ISCB (International Society for Computational Biology)
2007-now President of the ISCB (International Society for Computational Biology)
1992-now Over 500 referee reports for peer-reviewed journals (including Nature, Science, PNAS, Cell, EMBO J)
1995-now Over 50 reviews of grants from individuals and institutes (countries: Austria, Canada, Denmark, England, Germany, Israel, Italy, Norway, Netherlands, Singapore, Spain, Sweden, Switzerland, USA); ad hoc panels for NIH and NSF, including role as chairman.
2001-now Ad-hoc panels for grants from the NIH, NSF and the European Community
2005-2009 Associate Editor of PLoS Computational Biology
2006-now Associate Editor of Bioinformatics
2006-now Associate Editor of Proteins: Structure, Function, and Bioinformatics
2009-now Deputy Editor of PLoS Computational Biology
2005-now Editorial Board of FASEB (representative from ISCB)
2006-now Editorial Board of Journal of Structural and Functional Genomics
2007-now Editorial Board of Bioinformatics and Biology Insights
2001-2006 Editorial Board of Journal of Medical Informatics
2002, 2005 Editor for ISMB (Intelligent Systems for Molecular Biology) proceedings
2004-2006 Editorial Board of Proteins: Structure, Function, and Bioinformatics
2005-2006 Editorial Board of Bioinformatics
2002-2007 Organization of New York Computational Biology Society in the New York Academy of Sciences
1999-2005 SAB for company LION Biosciences, Heidelberg/Cambridge UK
2004-now Co-founder, CEO of BioSof, Delaware, USA
12/1988 London, England: Workshop on Arms Control
09/1989 Washington, DC, USA: Union of Concerned Scientists
10/1989 Princeton, USA: Institute for Advanced Studies
05/1990 Prague, CSFR: Workshop on Arms Control
09/1990 Vienna, Austria: Conference on Arms Control
010/1990 Mosbach, Germany: Conference on Arms Control
06/1992 Elba, Italy: Conference on Neural Networks
07/1992 Torino, Italy: Conference on Protein Structure Prediction
11/1992 Nijmegen, Netherlands: EU Conference on Sequence Analysis
06/1993 Rennes, France: Workshop on Secondary Structure Prediction
11/1993 Copenhagen, DK: Conf. on 'Protein Structure by Distance Analysis'
01/1994 Mauii, Hawaii, USA: HICCS Conference
03/1994 Bologna, Italy: Conference on Protein Structures
04/1994 Copenhagen, Denmark: 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' (CASP1)
06/1995 Cambridge, England: ISMB'95 (Tutorial)
06/1995 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
06/1996 St. Louis, USA: ISMB'96
08/1996 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
01/1997 Univ. Jerusalem, Israel: UNESCO workshop on sequence analysis
02/1997 Basel, Switzerland: CIBA-Geigy
02/1997 EBI Hinxton, England: Workshop on protein structure prediction
03/1997 Copenhagen, Denmark: CBS University
03/1997 New York, USA: Columbia University
06/1997 Berlin, Germany: Inst. for Theor. Biol.
06/1997 Chalkidiki, Greece: ISMB'97 (Tutorial)
07/1997 EBI Hinxton, England: EMBO Workshop on protein sequence analysis
07/1997 San Sebastian, Spain: Workshop 'Proteins: integration of life's function'
07/1997 Madrid, Spain: CNB
09/1997 Skšvde, Sweden: Conf. 'Bio-Computing and Emergent Computation'
09/1997 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
03/1998 Marseille, France: Cancer Inst., INSERM/19CNRS
05/1998 Tallberg, Sweden: Conf. ÔAnnual meeting of Swedish Structural BiologyÕ
05/1998 Bad Honnef, Germany: Conf. ÔScientific Applications of Neural NetsÕ
06/1998 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
07/1999 Havanna, Cuba: CIGB EMBO Workshop ÔBioinformaticsÕ
08/1999 Cambridge, England: EBI Workshop. ÔProtein motifs and families inÕ
09/1999 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'
02/2000 Boston, USA: SGI Workshop 'New Technologies for Discovery Research'
02/2000 New York Structural Biology Society, USA
08/2000 Troy RPI, USA: Bioinformatics Workshop
08/2000 Madrid, Spain: Human Genome Workshop
08/2000 New York University, USA
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)
03/2001 Madrid, Spain: Workshop on structural genomics
03/2001 CNB Madrid, Spain
04/2001 New York, Rockefeller University, USA
05/2001 New York, New York Structural Biology Society, USA
05/2001 New York, Columbia University, Dept. Biology, USA
07/2001 Technical University Copenhagen, Denmark
07/2001 Heidelberg University, Germany
09/2001 Il Ciocco, Italy: NATO summer school on bioinformatics (Talk, Teacher)
09/2001 IRBM Rome, Italy
01/2002 Keystone Symposium on Structural Genomics, USA
04/2002 Madrid, Spain: Meeting on 'Bioinformatics and Computational Biology'
04/2002 Basel, Switzerland: Talk at Biocenter Basel
05/2002 Erice, Italy: Talk on predicting protein function at summer school on structural biology
06/2002 San Diego, USA: Ô11th Annual Bioinformatics and Genome Research'
06/2002 Rutgers University, USA: 'Northeast Structural Genomics Consortium Annual Symposium'
07/2002 New York Computational Biology Society, New York Academy of Sciences
08/2002 Edmonton, Canada: ISMB'2002
08/2002 Habanna, Cuba: 'Bioinformatica-Habana'
10/2002 Lausanne, Switzerland, University
11/2002 Toronto, Canada Institute for Proteomics and Bioinformatics
02/2003 New York, Fordham University, USA
02/2003 CABM, Rutgers University, Piscataway, USA
02/2003 New York, Manhattan College, USA
05/2003 New York, City College, USA
10/2003 Bethesda, NIH, USA: Keynote at Workshop on 'Comparative modeling'
11/2003 Bethesda, NIH, USA: Workshop on 'Target Selection in Structural Genomics'
11/2003 Rutgers University, Piscataway, NJ, USA
02/2004 Gordon Conference, Ventura CA, USA: Structural, Functional & Evolutionary Genomics
06/2004 NESG Retreat, Arden House, Heriman, New York, USA
07/2004 ETH Zuerich, Switzerland
07/2004 EPFL Lausanne, Switzerland
07/2004 Meeting on data mining, Glasgow, Scotland
07/2004 Meeting on genome annotation, Glasgow, Scotland
07/2004 ISMB ÒReview of fieldÓ, Glasgow, Scotland
11/2004 Rome University, Italy
11/2004 Interntl. Conference on Structural Genomics (ICSG), Washington DC, USA
09/2005 Structural genomics workshop on target selection (Chicago, USA)
11/2005 RCSB workshop on homology modeling (Rutgers, USA)
12/2005 Structural genomics workshop on target selection (NIH/Bethesda, USA)
12/2005 INRA, Univ. of Evry, Paris, France
01/2006 Seminar at Technical University Munich, Germany
02/2006 Keystone meeting on structural genomics, USA
05/2006 DIMACS workshop Approaches to Predict Protein Function (Rutgers, USA)
06/2006 NIH workshop Target Selection for Structural Genomics (NIH, USA)
08/2006 SWISS-PROT 20 years (Fortalezza, Brazil)
01/2007 Keynote at the 5th European Conf. for Comp. Biology (ECCB, Eilat, Israel)
01/2007 BIOSAPIENS Workshop on protein function prediction (Eilat, Israel)
07/2007 SIG 3D (Vienna, Austria)
08/2007 Keynote at InCoB - 6th International Conference on Bioinformatics (Hong Kong, China)
04/2008 NESG, Princeton, USA
05/2008 Mohonk cBio Retreat, New Paltz, USA
06/2008 Pasteur, Paris
07/2008 ISMB Student Council, Toronto, Canada
12/2008 CASP8 Sardinia, Italy
03/2009 AMIA, San Francisco, USA
05/2009 Humboldt University, Berlin, Germany
06/2009 ISMB/ECCB 2009, Stockholm, Sweden
12/2009 Bioinformatics of African Pathogens, Bamako, Mali
01/2010 Ringberg meeting (Academia meets industry), Tegernsee, Germany
03/2010 ISCB-Latin America, Montevideo, Uruguay
04/2010 IAS Retreat, Starnberger See, Germany
04/2010 TUM Weihenstephan, Germany
04/2010 Machine Learning, Schloss Ringberg, Tegernsee, Germany
05/2010 ÒLange Nacht der WissenschaftÓ/Kirchentag, Garching, Germany
05/2010 Univ. Bayreuth, Germany
07/2010 Max-Planck Martinsried, Germany
07/2010 ISMB Boston, USA
07/2010 New York: City College, USA
09/2010 Optimization, Machine Learning and Bioinformatics, Erice, Italy
10/2010 UCSD, San Diego, USA
11/2010 Salzburg, Austria
11/2010 Biocenter, Basel, Switzerland
01/2011 Madrid, Spain
03/2011 ISCB-Africa/ASBCB, Cape Town, South Africa
04/2011 Saarbruecken, Germany
056/2011 GSISH - Spitzingsee, Germany
07/2011 SIG, Vienna, Austria
07/2011 ISMB/ECCB Vienna, Austria
09/1990 Co-organizing 'The Second Workshop on Verification of Arms Reductions', 3-5 Sep. 1990, Vienna, Austria
06/1995 Program committee for 3rd ISMB, Cambridge, England
07/1996 Program committee for 4th ISMB, Halkidiki, Greece
02/1997 Organizing the workshop 'Methods for protein structure prediction - progress and limitations' for Pharmaceutical Companies, 10-11 Feb., 1997, EBI Hinxton-Cambridge, England
07/1997 Program committee for 5th ISMB, St. Louis, USA
07/1998 Program committee for 6th ISMB, Montreal, Canada
08/1999 Organizing the workshop ÔProtein motifs and families in practice: Is protein function carved into sequence?Õ Aug 12-13, 1999, EBI Hinxton-Cambridge, England
08/1999 Program committee for 7th ISMB, Heidelberg, Germany
10/1999 Program committee of the 2nd Bologna summer school on biotechnology 'Protein sequence analysis in the genome era', Bologna, Italy
07/2000 Program committee for 8th ISMB, San Diego, USA
12/2000 Co-organizing the CAFASP sessions at CASP meeting in Asilomar, CA
03/2001 Co-organizing bioinformatics competition of LION Biosciences, Boston
03/2001 Co-organizing Juan March workshop on structural genomics in Madrid, Spain
07/2001 Program committee for 9th ISMB, Copenhagen, Denmark
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-organizing 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-organizing NIH workshop on 'Target selection for structural genomics'
06/2003 Scientific Advisory Board, Editor, and Program Committee for 12th ISMB 2004 in Glasgow, Scotland (>2,200 participants)
12/2004 Co-organizing meeting for the Critical Assessment of protein Structure Prediction (CASP6) in Italy (most important meeting in the field of structure prediction)
06/2005 Co-Chair of Program Committee, Member of Scientific Advisory Board, and Editor for 13th ISMB 2005 in Detroit, USA (> 2500 participants expected)
12/2005 Co-organizing NIH workshop on ÔTarget selection for structural genomics'
05/2006 Co-organizing CASP6.5 workshop (New York)
06/2006 Co-organizing NIH workshop on ÔTarget selection and homology modelingÕ (Bethesda, NIH)
12/2006 Co-organizing meeting for the Critical Assessment of protein Structure Prediction (CASP7) in Asilomar, CA (most important meeting in the field of structure prediction)
07/2007 ISMB/ECCB Vienna: Co-chair of 15th International Meeting on Intelligent Systems in Molecular Biology (ISMB) and Fifth European Conference of Computational Biology (ECCB) in Vienna Austria (most important meeting in bioinformatics), Chair of Highlight Track at ISMB/ECCB
07/2008 ISMB Toronto: Chair of 16th International Meeting on 'Intelligent Systems in Molecular Biology' (ISMB) in Toronto, Canada (most important meeting in bioinformatics in 2008), Chair of Highlights Track at ISMB 2008
12/2008 Co-organizing CASP8 in Sardinia, Italy
07/2009 ISMB/ECCB Stockholm: Scientific Organizing Committee & Chair of Scientific Steering Committee
12/2009 Steering Committee for 1st ISCB-Africa/ASBCB, Bamako, Mali
03/2010 Steering Committee for 1st ISCB-Latin America, Montevideo, Uruguay
07/2010 ISMB 2010, Boston: Chair of Highlights Track & Chair of Scientific Steering Committee
07/2011 Organizing Committee for SIG on Function Prediction (CAFA), Vienna 2011
07/2011 ISMB/ECCB 2011, Vienna, Austria: Chair of Meeting, Chair of Scientific Steering Committee & Chair of Highlights Track
03/2011 Steering Committee for 2nd ISCB-Africa/ASBCB, Cape Town, South Africa
12/2012 Steering Committee for 1st ISCB-Asia/InCoB, Kuala Lumpur, Malaysia
03/2012 Steering Committee for 2nd ISCB-Latin America, Santiago, Chile
07/2012 ISMB 2012, Long Beach, USA: Chair of Meeting, Chair of Scientific Steering Committee & Chair of Highlights Track
03/2013 Steering Committee for 3rd ISCB-Africa/ASBCB, Tunis, Tunesia
03/2014 Steering Committee for 3rd ISCB-Latin America, Rio De Janeiro, Brazil
Tom Acton (Rutgers Univ. USA), Alexei Adzhubei (Oslo Norway), Claus AF Andersen (Siena Biotech Italy), Rolf Apweiler (EBI Hinxton England), JM Aramini (Rutgers Univ. USA), Cheryl Arrowsmith (Toronto Univ Canada), David Baker (Univ. of Washington USA), Pierre Baldi (UCI Irvine USA), N Ben-Tal (Tel Aviv Univ. Israel), J Benach (Columbia Univ. USA), Helen Berman (PDB-Rutgers USA), Phil Bourne (UCSD USA), S¿ren Brunak (TU Lyngby Denmark), Stephen Bryant (NCBI USA), Stephen Burley (SGX Parmaceuticals USA), Piero Carninici (RIKEN Japan), Phil Carter (Columbia Univ. USA), CP Chen (Columbia Univ. USA), Y Chiang (Rutgers USA), W Chiu (Baylor College Houston USA), B Cooper (Columbia Univ. USA), JR Cort (Rutgers Univ. USA), George DeTitta (Buffalo Univ. USA), Ronald Dunbrack (Inst. for Cancer Res. Philadelphia USA), N Ecols (Yale Univ. USA), Aled Edwards (Toronto Univ. Canada), Arne Elofsson (Stockholm Univ. Sweden), J Everett (Yale USA), Volker Eyrich (Schroedinger Inc. USA), Dani Fischer (Buffalo Univ. USA), Kryzsztof Fidelis (UC Davis USA), Andras Fiser (Albert Einstein New York USA), Paolo Frasconi (Univ. Firenze Italy), Joachim Frank (HMM Albany USA), Yoav Freund (UCSD USA), Rich Friesner (Columbia Univ. USA), Mark Gerstein (Yale Univ. USA), Mark Girvin (Albert Einstein New York USA), Janice Glasgow (Kingston Univ. Canada), Adam Godzik (Burnham-UCSD USA), Julian Gough (RIKEN Japan), Osvaldo Grana (CNB Madrid Spain), Eric Gouaux (Oregon Univ. USA), Hedi Hegyi (Columbia Univ. USA), Wayne Hendrickson (Columbia Univ. USA), Kim Henrick (EBI England), Bernard Heymann (NIAMS USA), Barry Honig (Columbia Univ. USA), Tim Hubbard (Sanger Inst. England), John Hunt (Columbia Univ. USA), Masayori Inouye (Rutgers Univ. USA), HV Jagadish (Ann Arbor USA), Andrzej Joachimiak (MSGC Argonne USA), David Jones (Univ. College London England), Igor Jurisica (Toronto Univ. Canada), Gail Kaiser (Columbia Univ. USA), Michael Kennedy (PNNL Richland USA), Andrew Kernytsky (Columbia Univ.), IYY Koh (Columbia Univ.), G Kornhaber (Yale Univ. USA), N Lan (Rutgers Univ. USA), Thomas Lengauer (MPI Saarbruekcen Germany), Michal Linial (Hebrew Univ. Jerusalem Israel), Jinfeng Liu (Columbia Univ. USA), James Love (New York Structur Biology Center-City College USA), Andrei Lupas (Max Planck Inst. Tuebingen Germany), MS Madhusudhan (UCSF USA), John Markley (Univ. Wisconsin-Madison USA), Robert M MacCallum (Stockholm Univ. Sweden), Roderick MacKinnon (Rockefeller Univ. USA), Filippo Mancia (Columbia Univ. USA), Richard Mann (Columbia Univ. USA), Hannah Margalit (Hebrew Univ. Jerusalem Israel), Mark Marti-Renom (UCSF San Francisco/Barcelona Spain), Ann McDermott (Columbia Univ. USA), Jill P Mesirov (Broad Inst. USA), Sven Mika (Columbia Univ. USA), Guy Montelione (Rutgers Univ. USA), John Moult (CARB Univ. Maryland USA), Diana Murray (Columbia Univ. USA), Rajesh Nair (FDA USA), E Narayanan (UCSF USA), Michael Nilges (Pasteur Paris France), Yanay Ofran (Bar-Ilan Univ. Israel), Christine Orengo (Univ. College London England), Arthur G Palmer (Columbia Univ. USA), Florencio Pazos (Madrid Spain), Israel Pecht (Weizmann Inst. Rehovot Israel), Gianlucca Pollastri (Dublin Ireland), Robert Powers (Nebraska Lincoln USA), Dariusz Przybylski (Columbia Univ. USA), Marco Punta (TUM Germany), Michael Rossmann (Purdue Univ. USA), Leszek Rychlewski (Warsaw Poland), Helen Saibil (Birkbeck College London England), Andrej Sali (UCSF San Francisco USA), Chris Sander (Whitehead Inst. Boston USA), Avner Schlessinger (UCSF USA), Reinhard Schneider (EMBL Heidelberg Germany), Peter Schuster (Vienna Univ. Austria), Torsten Schwede (Biozentrum Basel Switzerland), Larry Shapiro (Columbia Univ. USA), Daron Standley (PDB Japan), David States (Ann Arbor USA), Thomas Szyperski (Buffalo Univ. USA), Liang Tong (Columbia Univ. USA), Hepan Tan (Columbia Univ. USA), Dimitris Thanos (Athen Univ. Greece), Liang Tong (Columbia Univ.), Anna Tramontano (Univ. Rome Italy), Alfonso Valencia (CNB Madrid Spain), Gunnar von Heijne (Stockholm Univ. Sweden), Da-Neng Wang (New York Univ. USA), Kaz Wrzeszczynski (Cold Spring Harbor Labs USA), John Westbrook (PDB-Rutgers Univ. USA), Zeba Wunderlich (Rutgers Univ. USA), Ming Zhou (Columbia Univ. USA), Raphael Zidovetzki (Univ. of California Riverside USA).
06/2003-2010 Qualifying exam Dept. Biochemistry & Molecular Biophysics, Columbia
11/2009-now Chair for Bachelor/Master Program on Bioinformatics, Munich, Germany
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)
2005-2008 Teaching full semester course Computational Biology II: Proteins: Sequence, Structure and Networks at Columbia University (in collaboration with Dr. Vitkup)
2010 summer Hauptseminar on Bioinformatics & Computational Biology (effort shared by Rost & Kramer groups)
06/1995 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
03/1997 Supervision of post-docs at a workshop at the CBS in Copenhagen (Denmark)
06/1997 Tutorial at ISMBÕ97 (International Conference on Intelligent Systems for Molecular Biology) in Chalkidiki, Greece
07/1997 Supervision of pre- and post-docs at the workshop (EMBO-course) Genome sequence analysis at the EBI in Hinxton, England
07/1997 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
07/1999 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
09/2001 Teacher at a NATO summer school on bioinformatics in Il Ciocco, Italy
08/2002 Supervision of pre- and post-docs at the workshop Bioinformatics at the CIB in Havanna, Cuba
09/2010 Course at Summer school for Optimization, Machine Learning and Bioinformatics, Erice, Italy
1986-1988 Organization 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 University:
Department Period
(expected graduation)
Christian Schaefer TUM Munich 2009-2012
Tobias Hamp TUM Munich 2009-2012
Esmeralda Vicedo TUM Munich 2010-2012
Name Affiliation In
lab since
Yu-An (Arthur) Dong TUM: Bioinformatics 2010/06
Laszlo Kajan TUM: Bioinformatics 2008/04
Edda Kloppmann TUM: Bioinformatics 2011/01
Mark Offman TUM: Bioinformatics 2010/07
Shaila Roessle-Blank TUM: Bioinformatics 2010/07
Andrea Schafferhans-Fuhrmann TUM 2009/09
Name Affiliation In
lab since
Guy Yachdav Columbia: Biochemistry 2003
Name University:
Department Period
Dominik Achten TUM: Comp. Sciences 2011
Juan Miguel Cejuela TUM: Comp. Sciences 2011
Tatyana Goldberg TUM: Comp. Sciences 2011
Maximilian Hecht TUM: Comp. Sciences 2011
Peter Hoenigschmid TUM: Comp. Sciences 2011
Yannick Mahlich TUM: Comp. Sciences 2011
Jonas Reeb TUM: Comp. Sciences 2011
Manfred Roos TUM: Comp. Sciences 2011
Stefan Seemayer TUM: Comp. Sciences 2011
Name Graduation
(begin) Affiliation
for thesis
Yanay Ofran 02/2004 (2000) Columbia: Medical Informatics /C2B2
Jinfeng Liu 02/2004 (1999) Columbia: Pharmacology/C2B2
Rajesh Nair 11/2004 (1999) Columbia: Physics/C2B2
Dariusz Przybylski 11/2004 (1999) Columbia: Physics/C2B2
Sven Mika 07/2006 (2002) Columbia: Biochemistry/C2B2
Yana Bromberg 11/2006 (2003) Columbia: Medical Informatics/C2B2
Henry Bigelow 04/2007 (2001) Columbia: Biochemistry/C2B2
Avner Schlessinger 09/2007 (2003) Columbia: Biochemistry/C2B2
Andrew Kernytsky 05/2008 (2001) Columbia: Biochemistry/C2B2
Kaz O Wrzeszczynski 02/2009 (2001) Columbia: Biochemistry/C2B2
Ta-Tsen Soong 06/2009 (2005) Columbia: Medical Informatics/C2B2
Name Group Current
Affiliation
Claus Andersen 2001-2002 Sr. Analyst, Siena Biotech., Italy
Claudia Bertonati 2004-2006 Staff, Univ. of Rome, Italy
Henry Bigelow 2001-2007 Postdoc, Columbia Univ., New York, NY
Yana Bromberg 2003-2010 Assistant Professor, Rutgers Univ., NJ
Phil Carter 2002-2004 Univ. College, London
Volker Eyrich 1999-2005 Sr. Analyst, Schroedinger Inc., New York, NY
Hedi Hegyi 2002-2004 Staff, Budapest Univ., Italy
Andrew Kernytsky 2001-2008 Research Scientist, BROAD Inst. MIT, MA
Ingrid Koh 2003-2006 ?
Jinfeng Liu 1999-2007 Senior Research Scientist, Genentech, CA
Michael Menden 2010-2011 PhD EBI, Cambridge, England
Sven Mika 2002-2006 Programmer, eSpeed Inc., New York, NY
Eyal Mozes 2005-2008 Staff, Columbia Univ. Biology, NY
Rajesh Nair 1999-2008 FDA (Federal Drag Agency), Bethesda, MD
Yanay Ofran 2000-2007 Faculty, Bar-Ilan University, Israel
Dariusz Przybylski 1999-2007 Senior Research Scientist, BROAD Inst. MIT, MA
Marco Punta 2002-2011 Senior Res. Scientist, Sanger Inst. Cambridge, UK
Shruti Rastogi 2008-2011 Postdoc, Columbia University, New York
Megan Restuccia 2002-2005 Manager, Morgan & Stanley, New York, NY
Avner Schlessinger 2003-2008 Postdoc, UCSF, San Francisco, CA
Markus Schmidberger 2010-2011 Group Leader Cloudnumber, Berlin, Germany
Ta-Tsen Soong 2005-2009 Postdoc, Cornell Medical School, New York, NY
Mikhail Veshtort 2008-2011 Sr. Res Scientist, Columbia Univ., New York, NY
Kaz O Wrzeszczynski 2001-2009 Postdoc, Cold Spring Harbor Laboratories, NY
Name University:
Department Date Group
Yuling An Columbia: Chemistry 07/2002 Rich Friesner
Chen Peter Chien Columbia: MD,PhD 12/2005 Barry Honig
Murat Cokol CU: Biomedical Informatics 05/2006 Andrej Rzhetsky
Chuck Duarte Columbia: Biochemistry 09/2002 Ann-Marie Pyle
Volker Eyrich Columbia: Chemistry 07/2001 Rich Friesner
Marina Gimpelev Columbia: Biochemistry 06/2004 Barry Honig
Cathy S Gunther Rockefeller University 11/2002 Terry Gaasterland
Samuel K Handelman Columbia: Biology 2008 John Hunt
David Pincus Columbia: Chemistry 09/2004 Rich Friesner
Erroll Rueckert Columbia: Integrated 2009 Richard Axel
Trevor Siggers Columbia: Biochemistry 11/2005 Barry Honig
Cinque Soto Columbia: Biochemistry 09/2007 Barry Honig
Hepan Tan Columbia: Biochemistry 02/2006 Wayne Hendrickson
Bahar Taneri Rockefeller University 04/2005 Terry Gaasterland
Christopher Tang Columbia: Biochemistry 06/2007 Barry Honig
Oleg Trott Columbia: Biochemistry 06/2004 Arthur Palmer
Yun Zhang Columbia: Biology 10/2001 Marti Chalfie
Name From Period
Claus AF Andersen Copenhagen, Denmark Fall 2001/Spring 2002
Shameek Biswas Columbia: Computer Sci. Summer 2003
Maina Bitar Brazil 2010-2011
Bastian Bruning Nijmegen, Netherlands Spring 2001
Joe Bylund Columbia: Integrated Spring 2008
Phil Carter Imperial College, London Fall 2001
Chen Peter Chien Columbia: MD-PhD Summer 2001
Murat Cokol Columbia: Biology Spring 2000
Anthony J DeCostanzo Columbia: Pharmacology Fall 2002
Seth Gale Columbia Fall 2001
Sarah Gilman Columbia, Computer Sc. Spring & Summer 2004
Dedan Githae Kenya: Nairobi 2010-2011
Gabor Halasz Columbia: Integrated Summer 2003
Laurence James Hunter College, CUNY Summer 2006
Andrew Kuziemko Columbia: Biochemistry Fall 2004
Wei Lim Columbia: Biomed. Engng. Summer 2005
Peng Liu Columbia: Medical Inform. Spring 2005
Alice Meier Bioinformatics Munich 2010-2011
Jackson Ng High school graduate Spring/Summer 2000
Bahar Moezi Columbia: Physics Summer 2005
Shoshana L Posy Columbia: Integrated Spring 2003
Doug Roberts-Wolfe Hampshire Summer 2006
Trevor Siggers Columbia: Biochemistry Summer 2000
Haitham Sobhy Bioinformatics Munich 2010-2011
Ta-tsen Soong Columbia: Medical Inform. Spring 2005
Enrique Tadique High school graduate Summer 2000
Hepan Tan Columbia: Biochemistry Summer 2000
Roman Trakhtenberg Columbia: Medical Inform. Winter 2002: 2003
Hong Yu Columbia: Medical Inform. Summer 2000
PI: Burkhard Rost
Period : 12/01/06-11/30/11
Agency: NIH (R01)
Effort: 15%
Ann Dir Costs: $250K (Total costs for entire grant: $1,250K)
Title: Comprehensive annotation of subcellular localization in entire proteomes
Summary: We propose the development of a comprehensive system that combines experimental resources with data mining techniques and novel prediction methods, with the objective of annotating the localization for all proteins in entirely sequenced eukaryotes with unprecedented detail and accuracy. Firstly, we propose the improvement over motif-based methods for secreted and nuclear proteins, as well as the extension of de novo predictions for the major compartments. Secondly, we plan to develop novel methods that predict the particular type of membrane into which an integral membrane protein is inserted (plasma, inner/outer nuclear, inner/outer mitochondrial, ER, Golgi, lysosome, chloroplast), and that predict minor eukaryotic compartments (ER, Golgi, lysosome), as well as sub-compartments such as Ònuclear matrix associatedÓ. Thirdly, we plan the integration of the new methods and experimental resources into a comprehensive system for which we already have a prototype.
II.
PI: Burkhard Rost
Period: 06/01/09 to 05/31/15
Agency: Alexander von Humboldt Foundation, Germany
Ann Dir Costs: 750 K Û Total (5 years): 4,250 K Û Overhead (5 years): 750 K Û
Title: Alexander von Humboldt Professorship (AvH)
Summary: This grant provides the infrastructure for building up our research and teaching at the TUM in Munich, Germany.
III.
PI: Wayne Hendrickson
Role: Co-PI
Period: 07/01/10 to 06/30/15
Agency: NIH (U54 GM75026)
Ann Dir Costs: $120 K
Title: Structural Genomics of Membrane Proteins (NYCOMPS)
Summary: This grant supports the New York Structural Biology Center. Dr. W.A. Hendrickson (Columbia University) is the P.I. for this project. It aims to develop and apply structural genomics approaches to structure determination for membrane proteins. Our group is responsible for the target selection in this project.
i. Theoretical
analysis of the possibilities of seismic and acoustical sensor networks to
verify arms control treaties for aircraft
PI: Burkhard Rost
Period : 12/88-6/90
Agency: Foundation Volkswagenwerg, Germany
Total Dir Costs: $15 K
Summary: Funding for research project on arms control.
PI: Burkhard Rost
Period : August 2002
Agency: NSF
Total Dir Costs: $40 K
Summary: Travel support for young participants of the ISMB 2002 meeting
iii. ISMB'2002
PI: Burkhard Rost
Period : August 2002
Agency: DOE
Total Dir Costs: $35 K
Summary: Travel support for young participants of the ISMB 2002 meeting
iv. Center
of excellence in bioinformatics
PI: Barry Honig (Biochemistry, Columbia)
Role: Co-PI
Period: 09/01/01 to 08/31/03
Agency: NIH (5-P20-LM7276)
Ann Dir Costs: $20,000
Summary: Fund to prepare grant proposal to begin a center of excellence.
v. Structural
genomics of eukaryotic model organisms
PI: Gaetano T. Montelione (Rutgers University)
Role: Co-PI
Period: 10/01/00 to 31/10/05
Agency: NIH (P50 GM62413)
Ann Dir Costs: $180,000 Total (5 years) $750,000 Overhead (4 years) $580,000
Summary: Goal of the pilot project in structural genomics (one of nine in the USA; of about 14 world-wide) was to develop high-throughput techniques for large-scale structure determination. This project combined over 20 groups from 12 research institutions in the USA, Canada and Israel. Our particular task was the development of techniques that rationalize the automatic target selection, i.e. prioritize which proteins to pursue experimentally.
vi. Intruding
into the midnight zone of protein sequence comparisons
PI: Burkhard Rost
Period: 05/01/01 to 04/30/05
Agency: NIH (R01 GM63029)
Ann Dir Costs: $190,000 Total (4 years) $750,000 Overhead (4 years) $660,000
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 refined, extended, and specialized methods combining sequence alignment, structure prediction and functional information.
vii. Ab initio prediction of
sub-cellular localization
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
Summary: The major goals of this project were to develop a system predicting the sub-cellular localization of a protein based on sequence alignments and signal peptide motifs. The ultimate objective was to combine a series of novel methods into a comprehensive system that we can use to automatically annotate entire proteomes.
viii. Improve
predictions of structure and function by PredictProtein
PI: Burkhard Rost
Period: 05/01/03 – 04/30/07
Agency: NIH/NLM (R01 LM07329)
Ann Dir Costs: $175,000 Total (4 years) $900,000 Overhead (4 years) $770,000
Summary: The major objective was to improve the Internet prediction server PredictProtein. The specific aims were to (1) implement technical improvements, (2) and to systematically combine the results from various methods. In particular, we worked on the improvement of methods that identify transmembrane segments from sequence.
ix. Predict
putative protein-protein interface segments at low resolution
PI: Burkhard Rost
Period: 05/01/03 – 04/30/07
Agency: NIH (R01 GM64633-01)
Ann Dir Costs: $200,000 Total (4 years) $800,000 Overhead (4 years) $680,000
Summary: We developed methods predicting interface segments, i.e. regions of residues consecutive in sequence that are in contact with other interface segments. Separate methods addressed internal and external interfaces.
x. MAGNet: center for the analysis of multiscale genomic and
cellular network
PI: Andrea Califano (Bio-Medical Informatics, Columbia)
Role: Project leader
Period: 10/01/05 to 09/30/10
Agency: NIH (U54-GM072980)
Ann Dir Costs: $220,000 Overhead $120,000
Summary: Grant proposal to begin a National Center of Excellence. Preliminarily, we proposed to build a center that provides software to other scientists. For the first two years, I acted as the coordinator of Core II proposals (biological applications of algorithms), and project leader for one of the seven main projects that proposed to integrate methods for the prediction of protein structure and function. The project was supposed to focus on the combination of related resources that already exist in the labs of various center members and on making these methods available through common interfaces.
xi. Improve
predictions of structure and function by PredictProtein
PI: Burkhard Rost
Period: 04/01/07 – 03/31/10
Agency: NIH/NLM (2 R01 LM07329)
Ann Dir Costs: $175,000 Total (4 years) $900,000 Overhead (4 years) $770,000
Summary: The major objective was to improve the Internet prediction server PredictProtein (PP). By 2008, this server had been used over 2 million times by over 30,000 researchers from 106 countries. The scientific solutions address two related tasks pertaining to protein function prediction. The first was to predict the effect of amino acid substitutions. We developed novel machine learning-based methods to distinguish between mutations that effect structure, or function, or have no apparent phenotype. The second major task was the identification of natively unstructured regions and their functional classification. Proteins that do not adopt regular structures in isolation are increasingly becoming an important research area; they may provide a key to the evolution of complexity from proka- to eukaryotes. We developed machine learning-based identifications of features specific to this important class of molecules. All new methods have been made available through PredictProtein.
xii. Meeting
for Critical Assessment of protein Structure Prediction (CASP)
PI: Burkhard Rost
Period: 08/01/04 – 07/31/09
Agency: NIH (1-R13-GM072354-01)
Ann Dir Costs: $45,000 Total (5 years) $194,447 Overhead $0
Summary: This grant funded 3 consecutive CASP meetings that have evolved into the major event in the structure prediction field. Note that this grant neither covered any salaries, nor any expenses for my group.
xiii. Structural
genomics of eukaryotic model organisms
PI: Gaetano T. Montelione (Rutgers University)
Role: Co-PI
Period: 07/01/05 to 06/30/10
Agency: NIH (U54 GM074958-01)
Ann Dir Costs: $150,000 Total (5 years) $750,000 Overhead (5 years) $580,000
Title: Structural genomics of eukaryotic model organisms
Summary: Goal was the large-scale experimental determination of protein structures. This project combined over 20 groups from 12 research institutions in the USA and Canada. Our particular task was the development of techniques that rationalized the automatic target selection, i.e. prioritize which proteins to pursue experimentally and to cluster proteins into dynamic families with annotations of function.
xiv. Structural
genomics for membrane proteins (NYCOMPS)
PI: Wayne Hendrickson
Role: Co-PI
Period: 09/01/05 to 08/31/10
Agency: NIH (U54 GM75026)
Ann Dir Costs: $200 K Total (5 years) $500,000 Overhead (5 years) $300,000
Summary: Our development center in structural genomics (NYCOMPS: New York Consortium for Membrane Protein Structural genomics) investigated to which extent experimental high-throughput determination of 3D structures for membrane proteins is feasible. In order to achieve this, the center established a pipeline for high-throughput expression and purification. Our group was responsible for target selection. In particular, we clustered membrane proteins using existing methods. The project has been continued into a second five-year phase (see Grants active).
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. Doctoral (PhD) Thesis, Dept. of Physics and Astronomy, Heidelberg University.
*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.
1992 (2)
*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.
1993 (6)
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 cystine knot growth factor tertiary structure. Nature Genetics 5, 376-380.
*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.
1994 (8)
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.
1995 (5)
*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.
1996 (6)
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.
*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, iratxeta 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.
1997 (6)
*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. B Rost (1997) Better 1D predictions by experts with machines. Proteins Suppl. 1, 192-197.
1998 (4)
*38. MA Andrade, SI O'Donoghue & B Rost (1998) Adaptation of protein surfaces to subcellular location. J Mol Biol 276, 517-525.
*39. B Rost (1998) Marrying structure and genomics. Structure 6, 259-263.
*40. B Rost (1998) Protein structure prediction in 1D, 2D, and 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.
1999 (6)
*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.
2000 (2)
*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.
2001 (5)
*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.
2002 (15)
*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. 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.
2003 (24)
*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, membrane 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) Role of 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 Let 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 representative protein sequence 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: continuous secondary structure assignments for proteins, Nucl Acids Res 31, 3293-3295.
*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.
2004 (15)
*94. R Nair & B Rost (2004) Annotating protein function through lexical analysis. AI Magazine 25, 45-56.
95. J Glasgow, I Jurisica & B Rost (2004) AI and Bioinformatics. AI Magazine 25, 7-8 (editorial).
*96. J Liu & B Rost (2004) CHOP proteins into structural domain-like fragments. Proteins 55, 678-688.
*97. H Bigelow, D Petrey, J Liu, D Przybylski & B Rost (2004) Predicting transmembrane beta-barrels in proteomes. Nucl Acids Res 32, 2566-2577.
*98. KO Wrzeszczynski & B Rost (2004) Annotating proteins from Endoplasmic Reticulum and Golgi apparatus in eukaryotic proteomes. Cellular and Mol Life Sciences 61, 1341-1353.
*99. B Rost, G Yachdav & J Liu (2004) The PredictProtein server. Nucl Acids Res, 32, W321-W326.
*100. R Nair & B Rost (2004) LOCnet and LOCtarget: Sub-cellular localization for structural genomics targets. Nucl Acids Res 32, W517-W521.
*101. J Liu & B Rost (2004) CHOP: parsing proteins into structural domains. Nucl Acids Res 32, W569-W571.
*102. S Mika & B Rost (2004) NLProt: extracting protein names and sequences from papers. Nucl Acids Res 32, W634-W637.
*103. J Liu, H Hegyi, TB Acton, GT Montelione & B Rost (2004) Automatic target selection for structural genomics on eukaryotes. Proteins 56, 188-200.
104. Z Wunderlich, TB Acton, J Liu, G Kornhaber, J Everett, P Carter, N Lan, N Echols, M Gerstein, B Rost, & GT Montelione (2004) The protein target list of the Northeast Structural Genomics Consortium. Proteins 56, 181-187.
*105. J Liu & B Rost (2004) Sequence-based prediction of protein domains. Nucl Acids Res 32,3522-3530.
*106. S Mika & B Rost (2004) Protein names precisely peeled off free text. Bioinformatics 20 Suppl 1, I241-I247.
*107. D Przybylski & B Rost (2004) Improving fold recognition without folds. J Mol Biol 341, 255-269.
108. R Powers, TB Acton, Y Chiang, PK Rajan, JR Cort, MA Kennedy, J Liu, L Ma, B Rost & GT Montelione (2004) 1H, 13C and 15N assignments for the Archaeglobus fulgidis protein AF2095. J Biomol NMR 30, 107-108.
2005 (16)
*109. Y Ofran & B Rost (2005) Predictive methods using protein sequence. In 'Bioinformatics' AD Baxevanis & F Ouelette (eds.) New York: Wiley, 197-222.
*110. S Mika & B Rost (2005) NMPdb: database of nuclear matrix proteins. Nucl Acids Res 33, D160-D163.
*111. B Rost (2005) How to use protein 1D structure predicted by PROFphd. In ÔThe Proteomics Protocols HandbookÕ JE Walker (ed.) Totowa: Humana Press, 875-901.
*113. M Punta & B Rost (2005) Protein folding rates estimated from contact predictions. J Mol Biol 348, 507-512.
114. J Benach, WC Edstrom, I Lee, K Das, B Cooper, R Xiao, J Liu, B Rost, TB Acton, GT Montelione & JF Hunt (2005) The 2.35 A structure of the TenA homolog from Pyrococcus furiosus supports an enzymatic function in thiamine metabolism. Acta Crystallogr D Biol Crystallogr 61, 589-598.
115. O Grana, VA Eyrich, F Pazos, B Rost & A Valencia (2005) EVAcon: a protein contact prediction evaluation service. Nucleic Acids Res 33, W347-351.
*116. HV Jagadish, D States & B Rost (2005) ISMB 2005. Bioinformatics 21 Suppl 1, i1-i2.
*117. M Punta & B Rost (2005) PROFcon: novel prediction of long-range contacts. Bioinformatics 21, 2960-2968.
*118. A Schlessinger & B Rost (2005) Protein flexibility and rigidity predicted from sequence. Proteins 61, 115-126.
119. The FANTOM Consortium, P Carninci, T Kasukawa, S Katayama, J Gough, MC Frith, N Maeda, R Oyama, T Ravasi, B Lenhard, C Wells, R Kodzius, K Shimokawa, VB Bajic, SE Brenner, S Batalov, ARR Forrest, M Zavolan, MJ Davis, LG Wilming, V Aidinis, JE Allen, A Ambesi-Impiombato, R Apweiler, RN Aturaliya, TL Bailey, M Bansal, L Baxter, KW Beisel, T Bersano, H Bono, AM Chalk, KP Chiu, V Choudhary, A Christoffels, DR Clutterbuck, ML Crowe, E Dalla, BP Dalrymple, B deBono, G DellaGatta, D diBernardo, T Down, P Engstrom, M Fagiolini, G Faulkner, CF Fletcher, T Fukushima, M Furuno, S Futaki, M Gariboldi, P Georgii-Hemming, TR Gingeras, T Gojobori, RE Green, S Gustincich, M Harbers, Y Hayashi, TK Hensch, N Hirokawa, D Hill, L Huminiecki, M Iacono, K Ikeo, A Iwama, T Ishikawa, M Jakt, A Kanapin, M Katoh, Y Kawasawa, J Kelso, H Kitamura, H Kitano, G Kollias, SPT Krishnan, A Kruger, SK Kummerfeld, IV Kurochkin, LF Lareau, D Lazarevic, L Lipovich, J Liu, S Liuni, S McWilliam, M MadanBabu, M Madera, L Marchionni, H Matsuda, S Matsuzawa, H Miki, F Mignone, S Miyake, K Morris, S Mottagui-Tabar, N Mulder, N Nakano, H Nakauchi, P Ng, R Nilsson, S Nishiguchi, S Nishikawa, F Nori, O Ohara, Y Okazaki, V Orlando, KC Pang, WJ Pavan, G Pavesi, G Pesole, N Petrovsky, S Piazza, J Reed, JF Reid, BZ Ring, M Ringwald, B Rost, Y Ruan, SL Salzberg, A Sandelin, C Schneider, C Schšnbach, K Sekiguchi, CAM Semple, S Seno, L Sessa, Y Sheng, Y Shibata, H Shimada, K Shimada, D Silva, B Sinclair, S Sperling, E Stupka, K Sugiura, R Sultana, Y Takenaka, K Taki, K Tammoja, SL Tan, S Tang, MS Taylor, J Tegner, SA Teichmann, HR Ueda, E vanNimwegen, R Verardo, CL Wei, K Yagi, H Yamanishi, E Zabarovsky, S Zhu, A Zimmer, W Hide, C Bult, SM Grimmond, RD Teasdale, ET Liu, V Brusic, J Quackenbush, C Wahlestedt, JS Mattick, DA Hume, C Kai, D Sasaki, Y Tomaru, S Fukuda, M Kanamori-Katayama, M Suzuki, J Aoki, T Arakawa, J Iida, K Imamura, M Itoh, T Kato, H Kawaji, N Kawagashira, T Kawashima, M Kojima, S Kondo, H Konno, K Nakano, N Ninomiya, T Nishio, M Okada, C Plessy, K Shibata, T Shiraki, S Suzuki, M Tagami, K Waki, A Watahiki, Y Okamura-Oho, H Suzuki, J Kawai and Y Hayashizaki (2005) The transcriptional landscape of the mammalian genome. Science 309, 1559-1563.
*120. Y Ofran, M Punta, R Schneider & B Rost (2005) Beyond annotation transfer by homology: novel protein-function prediction methods that can assist drug discovery. Drug Disc Today 10, 1475-1482.
121. R Powers, N Mirkovic, D Murray, S Goldsmith-Fischman, TB Acton, Y Chiang, R Paranji, JR Cort, JY Huang, MA Kennedy, J Liu, L Ma, B Rost & GT Montelione (2005) Solution structure of Archaeglobus fulgidis Peptidyl-tRNA hydrolase (Pth2) provides evidence for an extensive conserved family of Pth2 enzymes in archea, bacteria and eukaryotes. Protein Science 14,2849-2861.
122. 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 (2005) Comparisons of NMR spectral quality and success in crystallization demonstrate that NMR and X-ray crystallography are complementary methods for small protein structure determination. J Am Chem Soc 127, 16505-16511
123. J Moult, K Fidelis, T Hubbard, B Rost & A Tramontano (2006) Critical assessment of methods of protein structure prediction (CASP) - round VI. Proteins 61, 3-7.
124. O Grana, D Baker, RM MacCallum, J Meiler, M Punta, B Rost, ML Tress & A Valencia (2006) CASP6 assessment of contact prediction. Proteins 61, 214-224.
2006 (8)
*125. A Schlessinger, Y Ofran, G Yachdav & B Rost (2006) Epitome: Database of structure-inferred antigenic epitopes. Nucleic Acids Res 34, D777-D780.
*126. J Liu, J Gough & B Rost (2006) Distinguishing protein-coding from non-coding RNA through support vector machines. PLoS Genetics 2 (4):e29, DOI: 10.1371/journal.pgen.0020029.
*127. A Schlessinger, G Yachdav & B Rost (2006) PROFbval: predict flexible and rigid residues in proteins. Bioinformatics 22, 891-893.
*128. S Mika & B Rost (2006) Protein–protein interactions more conserved within species than across species. PLoS Comp Biol 2, e79.
*129. Y Ofran, G Yachdav, E Mozes, T Soong & B Rost (2006) Create and assess protein networks through molecular characteristics of individual proteins. Bioinformatics (ISMB Proceedings), 22: e402-e407.
*130. H Bigelow & B Rost (2006) PROFtmb: A web server for predicting bacterial transmembrane beta barrel proteins. Nucleic Acids Res 34, W186-188.
131. A Passerini, M Punta, A Ceroni, B Rost & P Frasconi (2006) Identifying cysteines and histidines in transition metal binding sites by a two-stage support vector machines - neural networks approach. Proteins 22, 305-316.
132. HM Berman, SK Burley, W Chiu, A Sali, A Adzhubei, PE Bourne, SH Bryant, RL Dunbrack, Jr., K Fidelis, J Frank, A Godzik, K Henrick, A Joachimiak, B Heymann, D Jones, JL Markley, J Moult, GT Montelione, C Orengo, MG Rossmann, B Rost, H Saibil, T Schwede, DM Standley and JD Westbrook (2006) Outcome of a workshop on archiving structural models of biological macromolecules. Structure 14, 1211-1217.
2007 (13)
*133. Y Ofran & B Rost (2007) ISIS: Interaction Sites Identified from Sequence. Bioinformatics (ECCBÕ2006), 23, e13-e16.
*134. M Punta, LR Forrest, H Bigelow, A Kernytsky, J Liu & B Rost (2007) Membrane protein prediction methods. Methods, 41, 460-474.
*135. D Przybylski & B Rost (2007) Consensus sequences improve PSI-BLAST through mimicking profile-profile alignments. Nucleic Acids Res 35, 2238-2246, doi:10.1093/nar/gkm107.
136. JM Aramini, YJ Huang, GV Swapna, JR Cort, PK Rajan, R Xiao, R Shastray, TB Acton, J Liu, B Rost, MA Kennedy > Montelione (2007) Solution NMR structure of Escherichia coli ytfP expands the structural coverage of the UPF0131 protein domain family. Proteins 68, 789-795.
*137. T Lengauer, BJ Morrison McKay & B Rost (2007) ISMB/ECCB 2007: The premier conference on computational biology. PLoS CB 3, e96.
*140. T Lengauer, B Rost & P Schuster (2007) ISMB/ECCB 2007. Bioinformatics (Editorial) 23, i1-i4.
*141. Y Ofran, V Mysore & B Rost (2007) Prediction of DNA-binding residues from sequence. Bioinformatics (ISMB Proceedings) 23, i347-353.
*143. J Liu, GT Montelione & B Rost (2007) Novel leverage of structural genomics. Nature Biotech 25,849-851.
*144. A Schlessinger, M Punta & B Rost (2007) Natively unstructured regions in proteins identified from contact predictions. Bioinformatics 23, 2376-2384.
145. J Moult, K Fidelis, A Kryshtafovych, B Rost, T Hubbard & A Tramontano (2007) Critical assessment of methods of protein structure prediction - Round VII. Proteins 69(S8), 3-9.
2008 (14)
146. KK Singarapu, R Xiao, T Acton, B Rost, GT Montelione & T Szyperski (2008) NMR structure of the peptidyl-tRNA hydrolase domain from Pseudomonas syringae expands the structural coverage of the hydrolysis domains of class 1 peptide chain release factors. Proteins 71, 1027-1031.
147. JM Aramini, S Sharma, YJ Huang, GV Swapna, CK Ho, K Shetty, K Cunningham, LC Ma, L Zhao, LA Owens, M Jiang, R Xiao, J Liu, MC Baran, TB Acton, B Rost & GT Montelione (2008) Solution NMR structure of the SOS response protein YnzC from Bacillus subtilis. Proteins 72, 526-530.
148. O Trott, K Siggers, B Rost & AG Palmer, 3rd (2008) Protein conformational flexibility prediction using machine learning. J Magn Reson 192, 37-47.
*149. M Linial, JP Mesirov, BJ Morrison McKay & B Rost (2008) ISMB 2008 Toronto. PLoS Comp Biol 4, e1000094.
*150. R Nair & B Rost (2008) Predicting protein subcellular localization using intelligent systems. Methods in Mol Biol 484, 435-463.
*151. Y Bromberg & B Rost (2008) Comprehensive in silico mutagenesis highlights functionally important residues in proteins. Bioinformatics (ECCB Proceedings) 24, i207-i212.
152. M Lippi, A Passerini, M Punta, B Rost & P Frasconi (2008) MetalDetector: a web server for predicting metal binding sites and disulfide bridges in proteins from sequence. Bioinformatics 24, 2094-2095.
153. JM Aramini, P Rossi, YJ Huang, L Zhao, M Jiang, M Maglaqui, R Xiao, J Locke, R Nair, B Rost, TB Acton, M Inouye & GT Montelione (2008) Solution NMR structure of the NlpC/P60 domain of lipoprotein Spr from Escherichia coli: structural evidence for a novel cysteine peptidase catalytic triad. Biochemistry 47, 9715-9717.
*154. D Przybylski & B Rost (2008) Powerful fusion: PSI-BLAST and consensus sequences. Proteins 24, 1987-1993.
*155. Y Ofran, A Schlessinger & B Rost (2008) Automated Identification of Complementarity Determining Regions (CDRs) reveals peculiar characteristics of CDRs and B cell epitopes. J Immunology 181, 6230-6235.
*156. Y Bromberg & B Rost (2008) SNAP predicts effect of mutations on protein function. Bioinformatics 24, 2397-2398.
*157. T-T Soong, KO Wrzeszczynski & B Rost (2008) Physical protein-protein interactions predicted from microarrays. Bioinformatics 15, 2608-2614.
*158. M Punta & B Rost (2008) Building a neural network for predicting protein features. In ÔApplication of Artificial Neural Networks to Chemistry and BiologyÕ D Livingston (ed.) Totowa: Humana Pres Methods Mol Biol 458, 203-230.
*159. D Przybylski & B Rost (2008) Predicting simplified features of proteins structure. In ÔBioinformatics – From Genomes to TherapiesÕ T Lengauer (ed.) Weinheim: Wiley-VCH, 261-295.
2009
(20)
*160. KO Wrzeszczynski & B Rost (2009) Cell cycle kinases predicted from conserved biophysical properties. Proteins 74, 655-668.
161. P Rossi, JM Aramini, R Xiao, CX Chen, C Nwosu, LA Owens, M Maglaqui, R Nair, M Fischer, TB Acton, B Honig, B Rost & GT Montelione (2009) Structural elucidation of the Cys-His-Glu-Asn proteolytic relay in the secreted CHAP domain enzyme from the human pathogen Staphylococcus saprophyticus. Proteins 74, 515-519.
162. CA Galea, AA High, JC Obenauer, A Mishra, CG Park, M Punta, A Schlessinger, J Ma, B Rost, CA Slaughter and RW Kriwacki (2009) Large-Scale analysis of thermostable, mammalian proteins provides insights into the intrinsically disordered proteome. J Proteome Res 8, 211-226.
163. WN Price 2nd, Y Chen, SK Handelman, H Neely, P Manor, R Karlin, R Nair, J Liu, M Baran, J Everett, SN Tong, F Forouhar, SS Swaminathan, T Acton, R Xiao, JR Luft, A Lauricella, GT DeTitta, B Rost, GT Montelione and JF Hunt (2009) Understanding the physical properties that control protein crystallization by analysis of large-scale experimental data. Nature Biotech 27, 51-57.
*164. A Schlessinger, M Punta, G Yachdav, L Kajan & B Rost (2009) Improved disorder prediction by combination of orthogonal approaches. PLoS ONE 4, doi:10.1371/journal.pone.0004433.
*165. R Nair, J Liu, T-T Soong, TB Acton, J Everett, A Kouranov, A Fiser, A Godzik, L Jaroszewski, C Orengo, GT Montelione & B Rost (2009) Structural genomics is the largest contributor of novel structural leverage. J Structural Functional Genomics 10:181-191.
*166. C Bertonati, M Punta, M Fischer, G Yachdav, F Forouhar, W Zhou, AP Kuzin, J Seetharaman, M Abashidze, TA Ramelot, MA Kennedy, JR Cort, A Belachew, JF Hunt, L Tong, GT Montelione & B Rost (2009) Structural genomics reveals EVE as a new ASCH/PUA-related domain. Proteins 75, 760-773.
167. G Liu, F Forouhar, A Eletsky, HS Atreya, JM Aramini, R Xiao, YJ Huang, M Abashidze, J Seetharaman, J Liu, B Rost, T Acton, GT Montelione, JF Hunt and T Szyperski (2009) NMR and X-RAY structures of human E2-like ubiquitin-fold modifier conjugating enzyme 1 (UFC1) reveal structural and functional conservation in the metazoan UFM1-UBA5-UFC1 ubiquination pathway. J Struct Funct Genomics 10, 127-136.
*168. Y Bromberg, G Yachdav, Y Ofran, R Schneider & B Rost (2009) New in protein structure and function annotation: hotspots, single nucleotide polymorphisms and the Deep Web. Curr Opin Drug Discov Devel 12, 408-419.
*169. A Kernytsky & B Rost (2009) Using genetic algorithms to select most predictive protein features. Proteins 75, 75-88.
170. BH Dessailly, R Nair, L Jaroszewski, JE Fajardo, A Kouranov, D Lee, A Fiser, A Godzik, B Rost & C Orengo (2009) PSI-2: Structural Genomics to Cover Protein Domain Family Space. Structure 17, 869-881.
*171. Y Bromberg & B Rost (2009) Correlating protein function and stability through the analysis of single amino acid substitutions. BMC Bioinformatics 10 Suppl 8, S8.
172. J Moult, K Fidelis, A Kryshtafovych, B Rost & A Tramontano (2009) Critical assessment of methods of protein structure prediction-Round VIII. Proteins 77(S9), 1-4.
*173. H Bigelow & B Rost (2009) Online tools for predicting integral membrane proteins. Methods Mol Biol 528, 3-23
174. A Eletsky, DK Sukumaran, R Xiao, TB Acton, B Rost, GT Montelione & T Szyperski (2009) NMR structure of protein YvyC from Bacillus subtilis reveals unexpected structural similarity between two PFAM families. Proteins 76, 1037-1041.
175. D Cozzetto, A Kryshtafovych, K Fidelis, J Moult, B Rost, & A Tramontano (2009) Evaluation of template-based models in CASP8 with standard measures. Proteins 77(S9), 18-28.
*177. M Punta, J Love, S Handelman, JF Hunt, L Shapiro, WA Hendrickson & B Rost (2009) Structural genomics target selection for the New York consortium on membrane protein structure. J Structural & Functional Genomics 10, 779-784.
*178. B Rost (2009) Prediction of protein structure in 1D – Secondary structure, membrane regions, and solvent accessibility. In ÔStructural BioinformaticsÕ P Bourne & J Gu (eds.) Wiley, 679-714.
*179. CAF Andersen & B Rost (2009) Secondary structure assignment. In ÔStructural BioinformaticsÕ P Bourne & J Gu (eds.) Wiley, 459-484.
2010 (8)
181. KK Singarapu, JL Mills, R Xiao, T Acton, M Punta, M Fischer, B Honig, B Rost, GT Montelione & T Szyperski (2010) Solution NMR structures of proteins VPA0419 from Vibrio paraheemolyticus and yiiS from Shigella flexneri provide structural coverage for protein domain family PFAM04175. Proteins 78, 779-784.
182. JM Aramini, JL Tubbs, S Kanugula, P Rossi, A Ertekin, M Maglaqui, K Hamilton, CT Ciccosanti, M Jiang, R Xiao, TT Soong, Rost B, TB Acton, JK Everett, AE Pegg, JA Tainer > Montelione (2010) Structural basis of O6-alkylguanine recognition by a bacterial alkyltransferase-like DNA repair protein. J Biol Chem 285, 13736-41.
*183. S Rastogi & B Rost (2010) Bioinformatics predictions of localization and targeting. Methods Mol Biol 619, 285-305.
184. J Love, F Mancia, L Shapiro, M Punta, Rost B, M Girvin, DN Wang, M Zhou, JF Hunt, T Szyperski, E Gouaux, R MacKinnon, A McDermott, B Honig, M Inouye, G Montelione & W Hendrickson (2010) The New York Consortium on Membrane Protein Structure (NYCOMPS): a high-throughput platform for structural genomics of integral membrane proteins. J Struct Funct Genomics 11, 191-199.
185. Y Tang, R Xiao, C Ciccosanti, H Janjua, DY Lee, JK Everett, GV Swapna, TB Acton, B Rost & GT Montelione (2010) Solution NMR structure of Lin0431 protein from Listeria innocua reveals high structural similarity with domain II of bacterial transcription antitermination protein NusG. Proteins 78, 2563-2568.
186. G Wainreb, H Ashkenazy, Y Bromberg, A Starovolsky-Shitrit, T Halioglu, E Ruppin, KB Avraham, B Rost & N Ben-Tal (2010) MuD: an interactive web server for the prediction of non-neutral substitutions using protein structural data. NAR 38, W523-W528.
187. YH Chen, L Hu, M Punta, R Bruni, B Hillerich, B Kloss, B Rost , J Love, SA Siegelbaum & WA Hendrickson (2010) Homologue structure of the SLAC1 anion channel for closing stomata in leaves. Nature 28, 1074-1080.
2011 (9)
*188. S Rastogi & B Rost (2011) LocDB: experimental annotations of localization for Homo sapiens and Arabidopsis thaliana. NAR 39, D230-234.
189. Y Yang, TA Ramelot, JR Cort, D Wang, C Ciccosanti, K Hamilton, R Nair, Rost B, TB Acton, R Xiao, JK Everett, GT Montelione & MA Kennedy (2011) Solution NMR structure of photosystem II reaction center protein Psb28 from Synechocystis sp. Strain PCC 6803. Proteins 79, 340-344.
190. Y Cao, X Jin, H Huang, MG Derebe, EJ Levin, V Kabaleeswaran, Y Pan, M Punta, J Love, J Weng, M Quick, S Ye, B Kloss, R Bruni, E Martinez-Hackert, WA Hendrickson, B Rost, JA Javitch, KR Rajashankar, Y Jiang and M Zhou (2011) Crystal structure of a potassium ion transporter, TrkH. Nature 471, 336-340.
191. RH Lathrop & B Rost (2011) ISCB Public Policy Statement on Open Access to Scientific and Technical Research Literature. PLoS Comput Biol 7, e1002014.
192. RH Lathrop & B Rost (2011) ISCB Public Policy Statement on Open Access to Scientific and Technical Research Literature. Bioinformatics 27, 291-294.
*193. A Schlessinger, C Schaefer, E Vicedo, M Schmidberger, M Punta, B Rost (2011) Protein disorder - a breakthrough invention of evolution? Current Opinion in Structural Biology, 21: 412-418.
194. W Shi, M Punta, J Bohon, JM Sauder, R DÕMello, M Sullivan, J Toomey, D Abel, M Lippi, A Passerini, P Frasconi, SK Burley, B Rost, MR Chance (2011) Characterization of metalloproteins by high-throughput X-ray absorption spectroscopy. Genome Res. 21: 898-907.
195. Y Cao, X Jin, EJ Levin, H Huang, Y Zong, M Quick, J Weng, Y Pan, J Love, M Punta, B Rost, WA Hendrickson, JA Javitch, KR Rajashankar and M Zhou (2011) Crystal structure of a phosphorylation-coupled saccharide transporter. Nature 473 (7345): 50-54.
196. A Zimprich, A Benet-Pages, W Struhal, E Graf, SH Eck, MN Offman, D Haubenberger, S Spielberger, EC Schulte, P lichtner, SC Rossle, N Klopp, E Wolf, K Seppi, W Pirker, S Presslauer, B Mollenhauer, R Katzenschlager, T Foki, C Hotzy, E Reinthaler, A Harutyunyan, R Kralovics, A Peters, F Zimprich, T Bruecke, W Poewe, C Trenkwalder, B Rost, G Ransmayr, J Winkelmann, T Meitinger and TM Strom (2011) A mutation in VPS35, encoding a subunit of the retromer complex, causes late-onset Parkinson disease. Am J Hum Genet 89: 168-175.
197. MN Offman, M Krol, B Rost, I Silman, JL Sussman and AH Futerman (2011) Comparison of a molecular dynamics model with the X-ray structure of the N30S acid-(beta)-glucosidase mutant that causes Gaucher disease. Prot Eng vol: 50-54.
E1. B Rost: Protein fold recognition by
merging 1D structure prediction and sequence alignments. Preprint; 1996;
www.rostlab.org/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; www.rostlab.org/papers/pre1997_ismb/
E3. B Rost, SI O'Donoghue and C Sander:
Midnight zone of protein structure evolution. Preprint; 1998; www.rostlab.org/papers/pre1998_midnight/
E4. B Rost:
Short yeast ORFs: expressed protein or not? Preprint;
1999; www.rostlab.org/papers/1999_globe/
E5. B Rost:
Neural networks for protein structure prediction: hype or hit? Preprint;
1999; www.rostlab.org/papers/pre1999_tics/
E6. B Rost and R Schneider: Pedestrian guide to analysing sequence databases. Preprint;
1999; www.rostlab.org/papers/1999_pedestrian/
E7. R Nair and B Rost: Surface profiles predict
sub-cellular localisation. Preprint; 2001; www.rostlab.org/papers/2001_loci_surface/
E8. B Rost, P Baldi, G Barton, J
Cuff, VA Eyrich, D Jones, K Karplus, R King, G Pollastri and D Przybylski: Simple jury predicts protein secondary structure best. Preprint;
2001; www.rostlab.org/papers/2001_sec_jury/
E9. B Rost, J Liu, D Przybylski, R Nair, KO Wrzeszczynski, H Bigelow and Y Ofran: Predict protein structure and function through evolutionary information. Preprint; 2002; www.rostlab.org/papers/2002_rev_chem/
E10. G Yachdav, Y Ofran, S Gilman, E Mozes, Y Yemini and B Rost: GeneTegrate: a platform for integrating biology. Demo, Short presentation and Poster at ISMB 2005, Detroit, USA.
W1. B Rost & J Liu: PredictProtein: Service for sequence analysis and protein structure prediction. Service (first internet server for protein structure prediction; one of the first in molecular biology); $root/predictprotein/
W2. VA Eyrich & B Rost: META-PP: Single-page interface to validated sequence analysis services. Service; $root/predictprotein/submit_meta.html
W3. IYY Koh, VA Eyrich, MA Mart’-Renom, D Przybylski, MS Madhusudhan, E Narayanan, O Gra–a, A Valencia, A Sali & B Rost: EVA: Evaluation of automatic protein structure prediction servers. Service; $root/eva/
W4. R Nair & B Rost: PredictNLS: Prediction and analysis of nuclear localization signals. Service; $root/services/predictNLS/
W5. P Carter, CAF Andersen & B Rost: DSSPcont: Continuous assignment of protein secondary structure. Service and database; URL: $root/services/DSSPcont/
W6. S Mika & B Rost: UniqueProt: Creating sequence-unique protein databases. Service; $root/services/uniqueprot/
W7. J Liu & B Rost: NORSp: Prediction of NOn-Regular Secondary Structure (NORS). Service; $root/services/NORSp/
W8. A Kernytsky & B Rost: TMH-bench: Evaluate new methods for membrane helix structure prediction. Service; $root/services/tmh_benchmark/
W9. P Carter, J Liu & B Rost: PEP: Predictions for entire proteomes. Database; $root/db/PEP/
W10. R Nair & B Rost: NLSdb: Database of nuclear localization signals. Database; $root/db/NLSdb/
W11. KO Wrzeszczynski & B Rost: CellCycleDB: Archive of proteins involved in cell cycle control. Database; $root/services/CellCycleDB/
W12. R Nair & B Rost: LOC3d: Database of predicted sub-cellular localization for eukaryotic PDB chains. Database; $root/db/LOC3d/
W13. R Nair & B Rost: LOChom: Database of sub-cellular localization predictions based on sequence homology. Database; $root/db/LOChom/
W14. S Mika & B Rost: NLProt: Extracting protein names and sequences from scientific papers. Service; $root/services/NLProt/
W15. R Nair & B Rost: LOCtarget: Prediction of sub-cellular localization for targets in structural genomics. Database; $root/services/LOCtarget/
W16. KO Wrzeszczynski & B Rost: ERGolgiDB: Archive of proteins from endoplasmic reticulum and Golgi apparatus. Database; $root/services/ERGolgiDB/
W17. R Nair & B Rost: LOCnet: De novo prediction of sub-cellular localization and prediction. Service; $root/services/LOCnet/
W18. H Bigelow & B Rost: PROFtmb: Predictions of transmembrane beta barrels. Service; $root/services/PROFtmb/
W19. M Punta & B Rost: PROFcon08: Predictions of inter-residue contacts. Service; $root/services/PROFcon08/
W20. J Liu & B Rost: CHOP: Chopping proteins into structural domains. Service; $root/services/CHOP/
W21. A Schlessinger, Y Ofran, G Yachdav & B Rost: Epitome: Database of structure-inferred antigenic epitopes. Database/Service; $root/services/epitome/
W22. G Yachdav, Y Ofran, R Nair, T-T Soong, E Mozes & B Rost: PiNat: Protein Interaction Annotation Tool. Database/Service; $root/services/pinat/
W23. G Yachdav, Y Ofran, & B Rost: ISIS: protein-protein Interaction Sites Identified from Sequence. Service; $root/services/isis/
W24. G Yachdav, Y Ofran, & B Rost: DISIS: DNA-protein Interaction Sites Identified from Sequence. Service; $root/services/disis/
W25. G Yachdav, D Przybylski & B Rost: ConBlast: Consensus Sequence PSI-BLAST. Database/Service; $root/services/conblast/ (under construction)
W26. G Yachdav, Yana Bromberg & B Rost: SNAP: Screening of Non-Acceptable non-synonymous Polymorphisms. Service; $root/services/snap/
W27. G Yachdav, A Schlessinger & B Rost: NORSnet: Prediction of disorder by identification of regions with NO Regular Secondary structure by neural networks. Service; $root/services/norsnet/
W28. G Yachdav, A Schlessinger, M Punta & B Rost: Ucon: Prediction of disorder by identification of natively Unstructured regions through CONtacts. Service; $root/services/ucon/ (under construction)
W29. G Yachdav, A Schlessinger, M Punta, J Liu & B Rost: MD: Meta-Disorder prediction. Service; $root/services/md/ (under construction)
Peer-reviewed: 143 First/Last author: 139
Original Peer-reviewed: 130 First author: 31
Reviews: 29 Single author: 21
Book chapters: 27 Last author: 88
Conference Proceedings: 12
Editorials: 8 Books: 1
Count Noii Quote Last
12 months Total Impact Factor
1) #8 1993 JMB 232, 584-599 43 2201 122.3
2) #16 1994 Proteins 19, 55-72 10 1190 70.0
3) #27 1996 Meth Enzymol 266, 525-539 24 990 66.0
4) #119 2005 Science 309 1559-1563 120 770 154.0
5) #19 1994 CABIOS 10, 53-60 8 566 33.3
6) #23 1995 Protein Science 4, 521-533 8 532 35.5
7) #99 2004 NAR 32, W321-W326 (PP 2/Yachdav) 89 473 67.6
8) #42 1999 Prot Engng 12, 85-94 38 447 37.3
9) #29 1996 Protein Science 5, 1704-18 15 433 29.9
10) #49 2000 EMBO Reports 1, 411-5 35 357 32.5
11) #9 1993 PNAS 90, 7558-7562 7 347 19.3
12) #17 1994 Proteins 20, 216-226 16 316 18.6
13) #57 2002 Proteins 47, 228-235 (pollastri) 22 315 35.0
14) #50 2001 J Structural Biology 134, 204-18 18 239 23.9
15) #20 1994 JMB 235, 13-26 6 193 11.4
16) #70 2003 JMB 325, 377-87 (ofran/six) 26 190 23.8
17) #36 1997 JMB 270, 471-80 5 169 12.1
18) #112 2005 JMB 348, 85-100 (LOCtree) 39 163 27.2
19) #43 1999 Proteins 34, 220-3 (SOV) 16 157 13.1
20) #59 2002 JMB 318, 595-608 (enzyme) 13 150 16.7
21) #67 2002 Prot Sci 11, 2774-91 - TMH revisited 7 120 13.3
22) #51 2001 Protein Science 10, 1970-9 - Proteomes 10 118 11.8
23) #7 1993 Nature Genetics 5, 376-80 2 116 6.4
24) #52 2001 Bioinformatics 17, 1242-3 - EVA 5 109 10.9
25) #82 2003 NAR 31, 3300-4 (PP 1=Liu & rost) 5 106 13.3
26) #78 2003 FEBS Letters 544, 236-9 14 105 13.1
27) #66 2002 JMB 322, 53-64 - Loopy/NORS 9 101 11.2
28) #145 2007 Proteins 69, 3-9 16 98 24.5
29) #45 1999 JMB 293, 1221-1239 (Olmea) 4 95 7.9
30) #55 2002 Proteins 46, 197-205 - Alignments grow 5 93 10.3
31) #11 1993 TIBS 18, 120-123 0 89 4.9
32) #87 2003 NAR 31, 3311-3315 (EVA) 4 88 11.0
33) #5 1992 Nature 360, 540 0 84 4.7
34) #123 2005 Moult intro Proteins 61, 3-7 5 81 13.5
35) #97 2004 NAR 32, 2566-2577 (PROFtmb) 16 81 11.6
36) #34 1996 Fold & Des 2, S19-S24 4 80 5.3
37) #93 2003 CMLS 60, 2637-50 10 78 9.8
38) #83 2003 NAR 31, 3833-5 (NORSp) 3 78 10.7
39) #30 1996 Ann Rev 25, 113-36 0 77 5.5
Count Noii Quote Last
12 months Total Impact Factor
40) #37 1998 JMB 276, 517-25 - andrade 8 74 5.7
41) #22 1995 ISMB 0 73 iii 12.2
42) #74 2003 NAR 31, 397-99 (NLSdb) 7 69 8.6
43) #138 2007 NAR 35, 3823-3835 24 66 16.5
44) #24 1995 Proteins 23, 295-300 0 64 4.0
45) #117 2005 Bioinformatics 21 2960-2968 (PROFcon) 5 60 10.0
46) #85 2003 NAR 31, 3789-91 (uniqueProt) 6 57 7.1
47) #39 1998 Structure 6, 259-63 1 56 4.3
48) #68 2002 Prot Sci 11, 2836-47 - localization 6 53 6.6
49) #118 2005 Proteins 61 115-126 - PROFbval 9 53 8.8
50) #75 2003 Curr Opin Chem Biol 7, 5-11 2 53 6.6
51) #56 2002 Structure 10, 175-184 4 52 5.8
52) #139 2007 PLOS CB 3, 1169-1176 (hotspots) 13 52 12.8
53) #105 2004 NAR 32, 3522-3530 (CHOPnet) 5 49 7.0
54) #128 2006 PLOS CB 2, 698-709 - Mika/Interactions 10 47 9.4
55) #113 2005 JMB 348 507-512 (folding rates) 6 45 7.5
56) #62 2002 Bioinformatics 18, 922-933 0 45 5.0
57) #58 2002 Structure 10, 435-440 (renom reliability) 3 43 4.8
58) #35 1997 CABIOS/Bioinformatics 13, 345-56 1 43 3.1
59) #90 2003 Proteins 53, 917-30 - localization 8 42 5.3
60) #10 1993 Protein Engineering 6, 831-836 0 41 2.4
61) #120 2005 Drug Disc Today 10 1475-1482 4 40 6.7
62) #103 2004 Proteins 56, 188-200 (NESG) 4 40 5.7
63) #89 2003 NAR 31, 3293-5 (DSSPcont) 7 40 5.0
64) #96 2004 Proteins 55, 678-688 (CHOP) 3 36 6.0
65) #171 2009 Proteins 77, 1-4 26 36 18.0
67) #134 2007 Methods 41, 460-474 9 36 7.2
Sum Average Citations
All 196 iv publications: 15,578 79
139 iv First/Last author papers listed 14,437 103
The h-index (Herfindahl index/Hirsch number) is the number of publications h cited ³h times. My h-index according to Google is 62 (Aug. 2010) and 52 according to ISI (Aug. 2010). The difference largely originates from the fact that ISI neither includes proceedings nor book chapters, nor any of the other many modern media that often cite the type of work we do.
Note all the following tools are published through our web site ˆ: http://www.rostlab.org
|
PredictProtein |
First and most widely used internet server for protein
structure prediction that currently combines over 20 methods developed by
others (e.g. ASP, BLAST, ClustalX, COILS, CYSPRED, HMMer, MaxHom, ProDom,
PROSITE, PSI-BLAST, SEG, SIFT) and over 20 methods developed by us (marked by
asterisk; e.g. PHD<sec|acc|htm|psi*>, TOPITS*, AGAPE*, CHOP|CHOPnet*,
DISIS*, ISIS*, LOC*<hom|key|net>, MD*, PredictNLS*,
PROF*<con08|acc|sec|tmb>, NORSnet*, NORSp*, SNAP*, Ucon*). |
|
AGAPE* |
Fold recognition without folds: Improved and
generalized method for sequence-profile and profile-profile comparisons using
sequence and predicted 1D structure (secondary structure and accessibility). |
|
CellCycleDB |
Database collecting and annotating proteins involved in
cell-cycle control |
|
CHOP/ CHOPnet* |
Method chopping proteins into structural domain-like
fragments and database for 62 entirely sequence proteomes. |
|
CLUP* |
Database with clusters of CHOP* fragments. |
|
ConBLAST* |
Aligning proteins through consensus motifs –
simple add-on to the popular BLAST/PSI-BLAST methods. |
|
DISIS* |
Prediction of protein-DNA interactions. |
|
DSSPcont* |
Server and database for continuous secondary structure
assignment from PDB files. |
|
Epitome* |
Database of structure-inferred antigenic epitopes. |
|
ERGolgiDB |
Archive of proteins from endoplasmic reticulum and Golgi
apparatus. |
|
EVA* |
Server continuously evaluating structure prediction
servers for: homology modeling (done by Sali group at UCSF), fold
recognition, prediction of secondary structure, and prediction of
inter-residue contacts (done by Valencia group in Madrid). |
|
GenTegrate* |
|
|
ISIS* |
Prediction of residues involved in external
protein-protein interactions. |
|
LOCdb* |
Database with annotations of localization for all
eukaryotic proteins in PDB (LOC3D*), all structural genomics targets
(LOCtarget*), and entirely sequenced prokaryotic and eukaryotic proteomes
(not yet completed). |
|
LOCtree* |
Combined system for the prediction of sub-cellular
localization through homology-transfer (LOChom*), automated text analysis of
SWISS-PROT keywords (LOCkey*), neural network-based (LOCnet*) and SVM-based
predictions (LOCsvm*), and combinations of methods specialized on Òshuttling
sequencesÓ (PredictNLS*, SignalP, ChloroP, ER_GolgiDB*). |
|
MD* |
MetaDisorder prediction – method to
predict natively unstructured/disordered regions through a combination of
original methods, including PROFbval, NORSnet, Ucon, IUpred, DISOpred.
|
|
META-PP* |
Common interface that simplifies the access to a
battery of high-quality public protein structure and function prediction
servers. |
|
NLProt* |
Automatic identification of protein names in scientific
literature. |
|
NLSdb* |
Database of nuclear localization and DNA-binding
motifs. |
|
NORSnet* |
Neural network based prediction of disordered/natively
unstructured regions dominated by loops in the non-bound state. |
|
NORSp* |
Prediction of long regions with no regular
secondary structure (NORS, i.e. almost no helix or strand over at
least 70 consecutive residues) and database with predictions for entire
proteomes. |
|
PEP* |
Database with alignments and predictions for 62
entirely sequenced proteomes (interfaced by the Sequence-Retrieval-System
SRS). |
|
PiNat* |
Protein interaction annotation tool combining a lookup
of experimental interactions with predictions and annotations of localization
and from the GeneOntology |
|
PredictNLS* |
Interactive assessment of selectivity and sensitivity
for nuclear localization signals. |
|
PROFacc* |
Improved prediction of solvent accessibility. |
|
PROFcon08* |
Prediction of inter-residue contacts (preliminary
version). |
|
PROFsec* |
Improved prediction of secondary structure. |
|
PROFtmb* |
Prediction of beta-membrane proteins. |
|
SNAP* |
Prediction of effects on protein function of SNPs
(non-synonymous single nucleotide polymorphism) |
|
TMH-bench* |
Static benchmark to test novel methods or propensity
scales (hydrophobicity indices) for membrane helix prediction. |
|
Ucon* |
Prediction of natively unstructured
(disordered) regions through the prediction of inter-residue contacts. |
|
UniqueProt* |
Creates representative subsets from a limited set of
protein sequences. |
ˆ Over 600 years, Heidelberg University has allowed scholars to present a doctoral thesis on any research subject independent of any sponsor. Apparently, I was the first who exercised this right over at least the last 60 years.
ˆ Group members in bold letters; journals underlined; asterisk marks first/senior author publications; peer-reviewed publications marked by solid gray bar on left.
i subset of publications with ³36 citations or citation index ³10, or that contribute to the H-factor
ii number used in publication list, i.e. higher numbers reveal more recent publications
ii number used in publication list, i.e. higher numbers reveal more recent publications
iii numbers from Feb 2001, no longer listed in ISI
iv averages compiled over ALL papers in Publication list; since many publications do not appear in ISI (too new, book chapters, computer science journals), the averages constitute lower bounds.
ˆ Tools developed in our group at Columbia University marked by asterisks.
