Unterlagen: CV Burkhard Rost TU München Inhalt - ROSTLAB.ORG

Burkhard Rost CV 

BURKHARD ROST 

International address: 

TUM Informatics/Bioinformatics i12 

Boltzmannstrasse 3 (Rm 01.09.052) 

85748 Garching/München 

Germany 

Deutsche Addresse: 

Technische Universität München 

Institut für Informatik, Lehrstuhl für Bioinformatik / i12 

Boltzmannstrasse 3 (Raum 01.09.052) 

85748 Garching/München 

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 

Unterlagen: 

Inhalt: 

CV Burkhard Rost 

TU München 

• Curriculum vitae 

• Veröffentlichungen 

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Photo: © Echert & Heddergott, TUM 

printed Januar 10, 2011

Burkhard Rost CV 

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Burkhard Rost Tabulated CV 

Tabellarischer Lebenslauf (Curriculum Vitae) 

Datum: Januar 10, 2011 

Name: Burkhard Rost 

Geschlecht: Männlich 

Ehestand: Verheiratet, eine Tochter (geb. Dez. 2002) 

Staatsangehörigkeit: Deutsch 

Geburtsort: Northeim, Niedersachsen, Germany 

Stelle: Ordinarius Bioinformatik 

Adresse: 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 (schnell), rost@in.tum.de (langsam) 

Ausbildung 

1971-1980 Oberschule, Herzberg, Niedersachsen 

1980-1982 Wehrdienst in der Luftwaffe 

1982-1985 Studium der Physik an der Justus-Liebig-Universität Gießen 

10/1984 Vordiplom in Physik 

1985-1988 Studium der Physik an der Ruprecht-Karls-Universität Heidelberg 

1985-1988 Studium der Philosophie, Geschichte und Psychologie in Heidelberg 

1986-1988 Diplomarbeit am Institut für Theoretische Physik in Heidelberg 

Thema: 'Learning algorithms for spin-glass-like neural networks' 

Betreuer: Prof. Dr. Heinz Horner, Heidelberg 

11/1988 Vordiplom in Philosophie und Geschichte, Heidelberg 

12/1988 Diplom in Physik, Heidelberg 

12/88-06/90 Forschungsstipendium 'Stiftung Volkswagenwerk', Theor. Physik, Heidelberg 

Thema: 'Theoretical analysis of the possibilities of seismic and acoustical sensor 

networks to verify arms control treaties for aircraft' 

07-10/89 Forschungsprojekte in den USA (Princeton, Washington DC, MIT) 

1990-1993 Doktorarbeit am EMBL, Heidelberg 

07/1993 Schreiben der Doktorarbeit 

Thema: 'Neural networks and evolution - prediction of protein secondary structure' 

Betreuer: keiner ◊ 

07/1994 Dr. rer. nat. (Doctor rerum naturarum) am Institut f. Theoretische Physik, 

Ruprecht-Karl Universität Heidelberg 

◊ Die Ruprecht-Karl Universität gestattet, jedem mit entsprechenden Qualifikationen Doktorarbeiten 

ohne Betreuer einzureichen. Als ich von diesem Recht Gebrauch machte, informierte mich die 

Fakultät der Physik und Astronomie, dass dies seit über 60 Jahren niemand mehr getan hatte. 

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Stellen 

1986-1988 Assistent am Institut für Theoretische Physik, Heidelberg 

12/88-06/90 Wissenschaftl. Mitarbeiter am Institut für Theoretische Physik, Heidelberg 

07-10/1989 Gastwissenschaftler an Instituten in den USA (Princeton, Union of 

Concerned Scientists, MIT) 

07/90- 1992 Gastwissenschaftler am EMBL Heidelberg 

07/93-12/94 Wissenschaftlicher Mitarbeiter am EMBL Heidelberg 

01/95-12/95 Wissenschaftlicher Mitarbeiter am EBI Hinxton, Cambridge, England 

01/96- 04/98 Wissenschaftlicher Mitarbeiter am EMBL Heidelberg 

05/98-11/98 Wissenschaftler bei LION Biosciences Heidelberg 

12/98- 05/00 Professor (Assistant Prof.) an der Fakultät für Biochemie & Molekulare 

Biophysik, Columbia Universität, Neu York, USA 

07/2000-2010 Professor (Associate Prof.), Biochemie & Mol. Biophys., Columbia 

2004-2010 Außerordentlicher Professor, Fakultät. für Medizinische Bioinformatik, 

Columbia University 

2002-2010 Mitarbeiter Center of Computational Biology and Bioinformatics (C2B2) 

07/2005-2010 Feste Anstellung am Institut für Biochemie und Mol. Biophysik an der 

Columbia Universität 

2006-2010 Außerordentlicher Professor, Fakultät. für Pharmakologie, Columbia Univ. 

2006-2010 Mitarbeiter Irving Center of Cancer Research, Columbia Univ. 

seit 06/2009 Alexander von Humboldt Professor in der Fakultät für Informatik an der TU 

München, Fellow im IAS (Inst. for Advanced Studies), TUM 

Berufsorganisationen und Gesellschaften 

1995-heute Programmkomittee der ISMB (Intelligent Systems for Molecular Biology) 

1996-heute Mitglied der ISCB (International Society for Computational Biology) 

2002-heute Board of Directors ISCB (International Society for Computational Biology) 

2002-heute Mitglied der NYAS (New York Academy of Sciences) 

2005-2006 Vizepräsident ISCB (International Soc. for Computational Biology) 

2006 President Elect ISCB (International Society for Computational Biology) 

2007-heute Präsident der ISCB (International Society for Computational Biology) 

Berufliche Erfahrungen 

1992-heute Über 500 Gutachten für peer-reviewed Zeitschriften (inkl. Nature, Science, 

PNAS, Cell, EMBO J) 

1995-heute Über 50 Gutachten für Anträge von Wissenschaftlern und Instituten 

(Österreich, Kanada, Dänemark, England, Deutschland, Israel, Italien, 

Norwegen, Niederlande, Singapur, Spanien, Schweden, Schweiz, USA) 

2001-heute Gutachter für Anträge von NIH, NSF, European Community (EC), Welcome 

Trust 

2005-2009 Associate Editor von PLoS Computational Biology 

2006-heute Associate Editor von Bioinformatics 

2006-heute Associate Editor von Proteins: Structure, Function, and Bioinformatics 

2009-heute Deputy Editor von PLoS Computational Biology 

4


2005-heute Editorial Board von FASEB (Vertreter der ISCB) 

2006-heute Editorial Board von Journal of Structural and Functional Genomics 

2007-heute Editorial Board von Bioinformatics and Biology Insights 

2001-2006 Editorial Board von Journal of Medical Informatics 

2002, 2005 Editor for ISMB (Intelligent Systems for Molecular Biology) Proceedings 

2004-2006 Editorial Board von Proteins: Structure, Function, and Bioinformatics 

2005-2006 Editorial Board von Bioinformatics 

2002-2007 Organisation der New York Computational Biology Society in der Neu York 

Academy of Sciences 

1999-2005 SAB von LION Biosciences, Heidelberg/Cambridge GB 

2004-heute Mitgründer, CEO von BioSof, Delaware, USA 

Eingeladene Vorträge (138 in 20 Ländern) 

12/1988 London, England: Tagung zum Thema Rüstungskontrolle 

09/1989 Washington, DC, USA: Union of Concerned Scientists 

10/1989 Princeton, USA: Institute for Advanced Studies 

05/1990 Prag, CSFR: Tagung zum Thema Rüstungskontrolleʻ 

09/1990 Vienna, Österreich: Konferenz zum Thema Rüstungskontrolle 

010/1990 Mosbach, Germany: Konferenz zum Thema Rüstungskontrolle 

06/1992 Elba, Italien: Konferenz: Neuronale Netzwerke 

07/1992 Turin, Italien: Konferenz: Protein Structure Prediction 

11/1992 Nijmegen, Niederlande: EU-Konferenz Sequence Analysis 

06/1993 Rennes, France: Workshop Secondary Structure Prediction 

11/1993 Kopenhagen, DK: Konferenz Protein Structure by Distance Analysis 

01/1994 Mauii, Hawaii, USA: HICCS Konferenz 

03/1994 Bologna, Italien: Konferenz Protein Structures 

04/1994 Kopenhagen, Dänemark: Mini-Symposium zum Thema Structure Prediction 

11/1994 Bielefeld, Germany: University 


12/1994 Asilomar, USA: CASP Konferenz (Critical Assessment of Structure 

Prediction, CASP1) 

06/1995 Cambridge, England: ISMB'95 (Tutorium) 

06/1995 Heidelberg, Germany: University 

10/1995 Brixen, Italien: Tagung zum Thema Protein Structures 

10/1995 IRBM Rom, Italien: Tagung Frontiers of protein structure prediction 

11/1995 Paris, Frankreich: Tagung Protein Structures and Drug Design 

06/1996 St. Louis, USA: ISMB'96 

08/1996 Madrid, Spanien: CNB 

10/1996 Universität Heidelberg 


12/1996 Neu York, USA: Columbia Universität 

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12/1996 Asilomar, USA: UCSF 

01/1997 Univ. Jerusalem, Israel: UNESCO-Workshop Sequence Analysis 

02/1997 Basel, Switzerland: CIBA-Geigy 

02/1997 EBI Hinxton, England: Tagung Protein Structure Prediction 

03/1997 Kopenhagen, Dänenmark: CBS 

03/1997 Neu York, USA: Columbia Universität 

06/1997 Berlin: Inst. für Theor. Biol. 

06/1997 Chalkidiki, Griechenland: ISMB'97 (Tutorium) 

07/1997 EBI Hinxton, England: EMBO Workshop Protein Sequence Analysis 

07/1997 San Sebastian, Spanien: Tagung Proteins: integration of life's function 

07/1997 Madrid, Spanien: CNB 

09/1997 Skövde, Schweden: Konferenz Bio-Computing and Emergent Computation 

09/1997 Wien, Österreich: Intern. Conference on Molecular Structural Biology 

10/1997 IRBM Rom, Italien: Tagung Frontiers of protein structure prediction 

11/1997 Stockholm, Schweden: Pharmacia & Upjohn 

11/1997 Stockholm, Schweden: Karolinska Inst. 

12/1997 Paris, Frankreich: Pasteur Inst. 

12/1997 Toulouse, Frankreich: INRA Inst. 

12/1997 Toulouse, Frankreich: Elf Sanofi 

12/1997 Basel, CH: Symposium Bioinformatics: from Exp. to Biol. Knowledge 

03/1998 Marseille, Frankreich: Krebszentrum, INSERM/19CNRS 

05/1998 Tallberg, Schweden: Konf. Annual meeting of Swedish Structural Biology 

05/1998 Bad Honnef, Deutschland: Konf. Scientific Applications of Neural Nets 

06/1998 Neu York, USA: Tagung im Genomzentrum, Columbia Univ. 

10/1998 Cambridge, England: Newton Inst. Konf. Biomolecular Function and 

Evolution in the Context of the Genome Project 

10/1998 EBI, England: Konf. ʻMethods for protein structureʼ 

07/1999 Havanna, Kuba: CIGB EMBO Workshop Bioinformatics 

08/1999 Cambridge, England: EBI Workshop Protein motifs and families 

09/1999 Graz, Österreich: International Meeting of Austrian Society for Genetics 

10/1999 Bologna, Italien: Tagung Protein sequence analysis in the genome era 

11/1999 Atlanta, USA: Konf. In silico biology: sequence & structure & function 

02/2000 Boston, USA: SGI Workshop New Technologies for Discovery Research 

02/2000 New York Structural Biology Society 

08/2000 Troy RPI, USA: Bioinformatics Workshop 

08/2000 Madrid, Spanien: Human Genome Workshop 

08/2000 Neu York Universität 

10/2000 Heidelberg, Deutschland: LION's Bioinformatics 2000 

12/2000 Asilomar, USA: Eingeladener Sitzungsleiter des vierten Meetings ʻCritical 

assessment of structure prediction (CASP4)ʻ, zwei Präsentationen 

03/2001 Madrid, Spanien: Workshop zum Thema Structural Genomics 

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03/2001 CNB Madrid, Spanien 

04/2001 Neu York, Rockefeller Universität 

05/2001 Neu York, New York Structural Biology Society 

05/2001 Neu York, Columbia Universität, Biologie 

07/2001 TU Kopenhagen, Dänemark 

07/2001 Heidelberg Universität, Deutschland 

09/2001 Il Ciocco, Italien: NATO Sommerschule Bioinformatics (Vortrag & Dozent) 

09/2001 IRBM Rom, Italien 

01/2002 Keystone Symposium Structural Genomics, USA 

04/2002 Madrid, Spanien: Tagung Bioinformatics and Computational Biology 

04/2002 Basel, Schweiz: Vortrag im Bioczentrum Basel 

05/2002 Erice, Italien: Vortrag in der Sommerschule ʻStrukturbiologieʻ 

06/2002 San Diego, USA: 11th Annual Bioinformatics and Genome Research 

06/2002 Rutgers Univ., USA: Northeast Structural Genomics Consortium Annual 

Symposium 

07/2002 New York Computational Biology Society, New York Academy of Sciences 

08/2002 Edmonton, Kanada: ISMB'2002 

08/2002 Havanna, Kuba: Bioinformatica-Habana 

10/2002 Lausanne, Schweiz, Universität Lausanne 

11/2002 Toronto, Kanada, Institute for Proteomics and Bioinformatics 

02/2003 Neu York, Fordham Universität 

02/2003 CABM, Rutgers Univ., Piscataway, USA 

02/2003 Neu York, Manhattan College 

05/2003 Neu York, City College 

10/2003 Bethesda, NIH: Hauptredner auf dem Workshop Comparative modeling 

11/2003 Bethesda, NIH: Workshop Target Selection in Structural Genomics 

11/2003 Rutgers Univ., Piscataway, NJ 

02/2004 Gordon Konferenz, Ventura CA: Structural, Functional & Evolutionary 

Genomics 

06/2004 NESG Symposium, Arden House, Heriman, Neu York 

07/2004 ETH Zürich, Schweiz 

07/2004 EPFL Lausanne, Schweiz 

07/2004 Tagung zum Thema Data Mining, Glasgow, Scotland 

07/2004 Tagung zum Thema Genome Annotation, Glasgow, Scotland 

07/2004 ISMB Review of field, Glasgow, Scotland 

11/2004 Rom Universität, Italien 

11/2004 International Conference on Structural Genomics (ICSG), Washington DC 

09/2005 Structural-Genomics-Tagung zum Thema Target Selection (Chicago) 

11/2005 RCSB workshop zum Thema Homology Modeling (Rutgers) 

12/2005 Structural-Genomics-Tagung zum Thema Target Selection (NIH/Bethesda) 

12/2005 INRA, Univ. Evry, Paris, Frankreich 

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01/2006 Seminar an der Technischen Universität München, Deutschland 

02/2006 Keystone Konferenz zum Thema Structural Genomics 

05/2006 DIMACS Tagung Approaches to Predict Protein Function (Rutgers) 

06/2006 NIH Tagung Target Selection for Structural Genomics (NIH/Bethesda) 

08/2006 SWISS-PROT 20 years (Fortalezza, Brasilien) 

01/2007 Hauptredner der 5 th European Conf. for Comp. Biology (ECCB, Eilat, Israel) 

01/2007 BIOSAPIENS Tagung zum Thema Protein Function Prediction (Eilat, Israel) 

07/2007 SIG 3D (Wien, Österreich) 

08/2007 Hauptredner auf InCoB - 6 th International Conference on Bioinformatics 

(Hong Kong, China) 

04/2008 NESG, Princeton 

05/2008 Mohonk cBio Symposium, New Paltz 

06/2008 Pasteur, Paris 

07/2008 ISMB Student Council, Toronto, Kanada 

12/2008 CASP8 Sardinien, Italien 

03/2009 AMIA, San Francisco, USA 

05/2009 Humboldt Universität, Berlin, Deutschland 

06/2009 ISMB/ECCB 2009, Stockholm, Schweden 

12/2009 Bioinformatics of African Pathogens, Bamako, Mali 

01/2010 Ringberg Tagung (Academia meets industry), Tegernsee, Deutschland 

03/2010 ISCB-Latin America, Montevideo, Uruguay 

04/2010 IAS Retreat, Starnberger See, Deutschland 

04/2010 Machine Learning, Schloss Ringberg, Tegernsee, Deutschland 

05/2010 Tag der Wissenschaft/Kirchentag, Garching, Deutschland 

05/2010 Univ. Bayreuth, Deutschland 

07/2010 Max-Planck Martinsried, Deutschland 

07/2010 ISMB Boston, USA 

07/2010 New York: City College, USA 

09/2010 Optimization, Machine Learning and Bioinformatics, Erice, Italien 

09/2010 ECCB Ghent, Belgien 

10/2010 UCSD, San Diego, USA 

11/2010 Salzburg, Österreich 

11/2010 Biozentrum, Basel, Schweiz 

Organisation von Internationalen Wissenschaftlichen Tagungen (37) 

09/1990 Mitveranstalter von The Second Workshop on Verification of Arms 

Reductions, 3-5 Sep. 1990, Wien, Österreich 

06/1995 Programmkomittee der 3. ISMB (Intelligent Systems for Molecular Biology), 

Cambridge, England 

07/1996 Programmkomittee der 4. ISMB, Halkidiki, Griechenland 

8


02/1997 Veranstalter des Workshops 'Methods for protein structure prediction - 

progress and limitations' für Pharmaunternehmen, 10-11 Feb., 1997, EBI 

Hinxton-Cambridge, England 

07/1997 Programmkomittee der 5. ISMB, St. Louis, USA 

07/1998 Programmkomittee der 6. ISMB, Montreal, Kanada 

08/1999 Veranstalter der Tagung Protein motifs and families in practice: Is protein 

function carved into sequence? Aug 12-13, 1999, EBI Hinxton-Cambridge, 

England 

08/1999 Programmkomittee der 7. ISMB, Heidelberg, Deutschland 

10/1999 Programmkomittee der 2. Bologna summer school on biotechnology: Protein 

sequence analysis in the genome era, Bologna, Italien 

07/2000 Programmkomittee der 8. ISMB, San Diego, USA 

12/2000 Mitveranstalter der CAFASP Veranstaltung während der CASP (Critical 

Assessment of Protein Structure Prediction) Tagung in Asilomar, CA 

03/2001 Mitveranstalter von Bioinformatik Wettbewerben der Fa. LION Biosciences, 

Boston 

03/2001 Mitveranstalter des Juan-March-Workshops zum Thema ʻStructural 

Genomicsʼ in Madrid, Spanien 

07/2001 Programmkomittee der 9. ISMB, Copenhagen, Dänemark 

02/2002 Programmkomittee des 3. "International Meeting on Membrane proteins” in 

Bologna, Italien 

06/2002 Programmkomittee des Meetings zum Thema ʻComputational Biologyʼ, 

Manchester, England 

08/2002 Mitveranstalter des 10. internationalen Meetings zum Thema 'Intelligent 

Systems in Molecular Biology' in Edmonton, Kanada (1500 Teilnehmer; die 

wichtigste Tagung für Bioinformatiker) 

06/2003 Wissenschaftlicher Beirat, Editor und Programmkomittee der 11. ISMB 2003 

in Brisbane, Australien 

11/2003 Mitorganisation des NIH Workshops Target selection for structural genomics 

06/2003 Wissenschaftlicher Beirat, Editor und Programmkomittee der 12. ISMB 2004 

in Glasgow, Schottland (>2,200 Teilnehmer) 

12/2004 Mitorganisation des Meetings ʻCritical Assessment of protein Structure 

Predictionʼ (CASP6) in Italien (das wichtigste Meeting zum Thema ʻstructure 

predictionʼ) 

06/2005 Co-Vorsitzender Programmkomittee, Mitglied des wissenschaftlichen Beirats 

und Editor der 13. ISMB 2005 in Detroit, USA (> 2500 erwartete Teilnehmer) 

12/2005 Mitorganisation des NIH-Workshops ʻTarget selection for structural 

genomics' 

05/2006 Mitorganisation des CASP6.5 Workshops (New York) 

06/2006 Mitorganisation des NIH-Workshops zum Thema ʻTarget selection and 

homology modelingʼ (Bethesda, NIH) 

12/2006 Mitorganisation des Meetings ʻCritical Assessment of protein Structure 

Predictionʼ (CASP7) in Asilomar, CA (das wichtigste Meeting zum Thema 

ʻStructure Predictionʼ) 

07/2007 ISMB/ECCB Wien: Co-Vorsitzender des 15. International Meeting on 

Intelligent Systems in Molecular Biology (ISMB) und der Fifth European 

9


Conference of Computational Biology (ECCB) in Wien, Österreich (das 

wichtigste Meeting für Bioinformatiker), Chair of Highlight Track at 

ISMB/ECCB 

07/2008 ISMB Toronto: Vorsitzender des 16. internationalen Meetings 'Intelligent 

Systems in Molecular Biology' (ISMB) in Toronto, Kanada (das wichtigste 

Meeting im Bereich der Bioinformatik in 2008), Chair of Highlights Track at 

ISMB 2008 

12/2008 Mitorganisation von CASP8 in Sardinia, Italien 

07/2009 ISMB/ECCB Stockholm: Wissenschaftliches Organisationskomittee & 

Vorsitzender des Wissenschaftlichen Lenkungsausschusses 

12/2009 Lenkungsausschuss der 1. ISCB-Africa/ASBCB, Bamako, Mali 

03/2010 Lenkungsausschuss der 1. ISCB-Latin America, Montevideo, Uruguay 

07/2010 ISMB 2010, Boston: Vorsitzender von Highlights Track & Vorsitzender des 

Wissenschaftlichen Lenkungsausschusses 

07/2011 Organisationskomittee der SIG zum Thema Function Prediction, Wien 2011 

07/2011 ISMB/ECCB 2011, Wien, Österreich: Vorsitzender von Highlights Track & 

Vorsitzender des Wissenschaftlichen Lenkungsausschusses 

03/2011 Lenkungsausschuss der 2. ISCB-Africa/ASBCB, Bamako, Mali 

03/2012 Lenkungsausschuss der 2. ISCB-Latin America, Santiago, Chile 

Kollaborationen 

Kollaborationen über die letzten 5 Jahre (ausgenommen 2005 Science Publikation) 

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), Søren 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 

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(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). 

Universitätskomitees 

06/2003-2010 Qualifzierungsprüfung, Dept. Biochemie & Moleculare Biophysik, Columbia 

11/2009-heute Prüfungsausschussvorsitzender für Bachelor/Master/Diplom Program für 

Bioinformatik in München (LMU, TUM, Helmholtz, MPI) 

Erfahrungen in der Lehre 

Kurse an Columbia & TUM (Rost) 

1999-2004 Betreuung von Doktoranden und Mitorganisieren der Klassenarbeit zum 

Thema ʻBioinformatikʻ im Kurs Biophysik unterrichtet von Ann McDermott, 

Chemie, Columbia (4 Kurse: 1999, 2001, 2002, 2003) 

2000-2003 Lehren an der Medizinischen Fakultät, Columbia; Kurs Eukaryotes I (3 

Kurse: 2000, 2001, 2002, 2003) 

2005-2008 Semesterkurs Computational Biology II: Proteins: Sequence, Structure and 

Networks an der Columbia University (in Zusammenarbeit mit Dr. Vitkup) 

2010-heute Zweisemestrige Vorlesung Protein Prediction 1+2 an der TUM (Jeder 

Vortrag 2x2 SWS + 2 SWS Übung) 

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2010-heute Oberseminar Bioinformatics & Computational Biology (jedes Semester, in 

Zusammenarbeit mit Dr. Stefan Kramer) 

2010 Sommer Hauptseminar Bioinformatics & Computational Biology (Rost & Kramer 

Gruppe) 

2010/11 Hauptseminar Bioinformatics & Computational Biology (Rost Gruppe) 

Kurse an TUM (Rost Gruppe) 

2010 Sommer Praktikum Bioinformatik Protein Structure and Function Analysis (Andrea 

Schafferhans & Marco Punta) 

2010 Sommer Praktikum Bioinformatik Bioinformatics Lab (Laszlo Kajan & Markus 

Schmidberger) 

2010/11 Vorlesung Computational Systems Biology (Shaila Rössle & Arthur Dong) 

2010/11 Seminar Presenting and Selling (Scientific Software) (Andrea Schafferhans) 

2010/11 Seminar Munich R course (Markus Schmidberger) 

Kurse auf Meetings / Sommerkurse 

06/1995 Tutorium auf der ISMBʼ95 (International Conference on Intelligent Systems 

for Molecular Biology) in Cambridge, England 

10/1995 Betreuung der post-docs auf dem Workshop Frontiers of protein structure 

prediction am IRBM in Rom, Italien 

03/1997 Betreuung der post-docs auf dem Workshop an der CBS in Kopenhagen 

(Dänemark) 

06/1997 Tutorium auf der ISMBʼ97 (International Conference on Intelligent Systems 

for Molecular Biology) in Chalkidiki, Griechenland 

07/1997 Betreuung der pre- und post-docs auf dem Workshop (EMBO-course) 

Genome sequence analysis am EBI in Hinxton, England 

07/1997 Lehrer während der Sommerschule Proteins: integration of life's function in 

San Sebastian, Spanien 

10/1997 Betreuung der post-docs auf dem 2. Workshop Frontiers of protein structure 

prediction at the IRBM in Rom, Italien 

07/1999 Betreuung der pre- und post-docs auf dem Workshop Bioinformatics im CIB 

in Havanna, Kuba 

10/1997 Betreuung der post-docs auf dem Workshop Protein sequence analysis in 

the genome era an der University of Bologna, Italien 

09/2001 Lehrer während der NATO-Sommerschule ʻBioinformatikʻ in Il Ciocco, Italien 

08/2002 Betreuung der pre- und post-docs auf dem Workshop Bioinformatics im CIB 

in Havanna, Kuba 

09/2010 Sommerkurs zum Thema Optimization, Machine Learning and 

Bioinformatics, Erice, Italien 

Andere Lehrveranstaltungen 

1986-1988 Organisation der Seminare über Theor. Physik, Heidelberg Univ., 

Deutschland 

1989-1990 Vortragsreihen zum Thema ʻRüstungskontrolleʻ (I), Heidelberg University 

1990 Vortragsreihen zum Thema ʻRüstungskontrolleʻ (II), Heidelberg Univ. 

12


1986-1990 Kurse zum Thema ʻPhysikʻ und 

ʻRüstungskontrolleʻ in außeruniversitären Schulen (Heidelberg, Mannheim, 

Frankfurt, Darmstadt) 

1991-1995 Halten von Vorträgen und Betreuung der Lehrveranstaltungen für 

Doktoranden im EMBL Heidelberg 

1992-1996 Vortragsreihe ʻProtein structure predictionʻ an der Heidelberger Univ. 

Studenten von meiner Gruppe, die den Doktortitel erlangt haben 

Name Dissertation Affiliation für Dissertation 

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 

Doktoranden in meiner Gruppe 

Name Universität Zeitraum 

Christian Schaefer TUM Munich 2009-2012 

Tobias Hamp TUM Munich 2009-2012 

Esmeralda Vicedo TUM Munich 2010-2012 

Postdoktoranten in meiner Gruppe 

Name Affiliation In Gruppe seit 

Marco Punta TUM/IAS 2002 

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 

Shruti Rastogi Columbia: Biochemistry 2008/04 

Shaila Roessle-Blank TUM: Bioinformatics 2010/07 

Andrea Schafferhans-Fuhrmann TUM 2009/09 

Markus Schmidberger TUM: Bioinformatics 2010/01 

Mikhail Veshtort Columbia: Biochemistry 2008/12 

Technische Mitarbeiter in meiner Gruppe 

Name Affiliation In Gruppe seit 

Timothy Karl TUM: Bioinformatics 2010/05 

Guy Yachdav Columbia: Biochemistry 2003 

13


Ehemalige Mitglieder meiner Gruppe 

Name Zeitraum Gegenwärtige Anstellung 

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 2003-2009 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 2001-2008/10 Research Scientist, BROAD Inst. MIT, MA 

Ingrid Koh 2003-2006 Hongkong 

Jinfeng Liu 1999-2007 Senior Research Scientist, Genentech, CA 

Sven Mika 2002-2006 Programmer, eSpeed Inc., New York, NY 

Eyal Mozes 2005-2008 Staff, Columbia Univ. Biology, NY 

Rajesh Nair 1999-2008/08 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 

Megan Restuccia 2002-2005 Manager, Morgan & Stanley, New York, NY 

Avner Schlessinger 2003-2008 Postdoc, UCSF, San Francisco, CA 

Ta-Tsen Soong 2005-2009 Postdoc, Cornell Medical School, New York, NY 

Kaz O Wrzeszczynski 2001-2009 Postdoc, Cold Spring Harbor Laboratories, NY 

Dissertations Ausschuss 

Name Universität: Fakultät Datum Gruppe 

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 

Christopher Tang Columbia: Biochemistry 06/2007 Barry Honig 

Bahar Taneri Rockefeller University 04/2005 Terry Gaasterland 

Oleg Trott Columbia: Biochemistry 06/2004 Arthur Palmer 

Yun Zhang Columbia: Biology 10/2001 Marti Chalfie 

Bachelor/Master Studenten 

Name University: Department Period 

Michael Menden TUM: Informatik 2010-2011 

14


Rotation Studenten 

Name Universität: Fakultät Zeitraum 

Murat Cokol Columbia: Biology 03-05/2000 

Trevor Siggers Columbia: Biochemistry 06-08/2000 

Hong Yu Columbia: Medical Inform. 06-08/2000 

Hepan Tan Columbia: Biochemistry 06-08/2000 

Enrique Tadique Bronx Highschool 06-08/2000 

Henry Bigelow Columbia: Biochemistry 03-05/2001 

Chen Peter Chien Columbia: MD-PhD 06-08/2001 

Seth Gale Columbia: Undergraduate 09-11/2001 

Andrew Kernytsky Columbia: Biochemistry 06-08/2002 

Avner Schlessinger Columbia: Biochemistry 06-08/2002 

Anthony J DeCostanzo Columbia: Pharmacology 09-11/2002 

Roman Trakhtenberg Columbia: Medical Inform. Winter 2002/2003 

Shoshana L Posy Columbia: Integrated 03-05/2003 

Shameek Biswas Columbia: Computer Sci. 06-08/2003 

Gabor Halasz Columbia: Integrated 06-08/2003 

Andrew Kuziemko Columbia: Biochemistry 09-11/2004 

Peng Liu Columbia: Medical Inform. 03-05/2005 

Ta-tsen Soong Columbia: Medical Inform. 03-05/2005 

Bahar Moezi Columbia: Physics 06-08/2005 

Wei Lim Columbia: Biomed. Engng. 06-08/2005 

Joe Bylund Columbia: Integrated 03-05/2008 

15

Burkhard Rost Grants 

Laufende Mittel 

Drittmittel 

I. 

PI: Burkhard Rost 

Zeitraum : 12/01/06-11/30/11 

Agentur: NIH (R01) - USA 

Volumen: $250 Tsd. (Gesamtkosten: $1,250,000) 

Thema: Comprehensive annotation of subcellular localization in entire proteomes 

II. 


Zeitraum: 06/01/09-05/31/15 

Agentur: Alexander von Humboldt Stiftung 

Volumen: 750 Tsd € Gesamt (5 Jahre): 4,250 K € Overhead (5 Jahre): 750 K € 

Thema: Alexander von Humboldt Professorship (AvH) 

III. 

PI: Wayne Hendrickson 

Role: Co-PI 

Period: 07/01/10 to 06/30/15 

Agency: NIH (U54 GM75026) 

Volumen: $120 K 

Thema: Structural Genomics of Membrane Proteins (NYCOMPS) 

Grants completed 

I. Theoretical analysis of the possibilities of seismic and acoustical sensor 

networks to verify arms control treaties for aircraft 


Period : 12/88-6/90 

Agency: Foundation Volkswagenwerg, Germany 

Total Dir Costs: $15 K 

Summary: Funding for research project on arms control. 

II. ISMB'2002 


Period : August 2002 

Agency: NSF 


Summary: Travel support for young participants of the ISMB 2002 meeting 

III. ISMB'2002 


Period : August 2002 

Agency: DOE 

16



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 


Period: 05/01/01 to 04/30/05 

Agency: NIH (R01 GM63029) 


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 


Period: 02/01/02 to 01/31/05 

Agency: NSF (DBI-0131168) 


Summary: The major goals of this project were to develop a system predicting the subcellular 

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 


Period: 05/01/03 – 04/30/07 

Agency: NIH/NLM (R01 LM07329) 


17


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 


Period: 05/01/03 – 04/30/07 

Agency: NIH (R01 GM64633-01) 


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 


Period: 04/01/07 – 03/31/10 

Agency: NIH/NLM (2 R01 LM07329) 

Effort: 5% 


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) 


Submitted: 12/15/03 

18


Period: 08/01/04 – 07/31/09 

Agency: NIH (1-R13-GM072354-01) 

Effort: 5% 

Ann Dir Costs: $45,000 Total (5 years) $194,447 

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. 

19

Burkhard Rost List of publications 

Abschlussarbeiten 

Publikationsliste ◊ 

A. B Rost (1988) Lernalgorithmen für verdünnte 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. 

Publikationen zum Thema ʻRüstungskontrolleʼ 

*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 

Universitätsverlag 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 Journé, W 

Kaiser, J Klinger, P Lewis, J Málek, 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 Universitätsverlag 

Brockmeyer. 

Publikationen zum Thema ʻComputational Biology and Bioinformaticsʼ 

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. 

*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. 

◊ Gruppenmitglieder in Fettdruck; Journale unterstrichen; Sterne markieren Publikationen, auf denen 

ich Erst- oder Letztautor bin; “peer-reviewed” Publikationen sind durch graue Linien an der linken 

Marge markiert. 

20


*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 Threedimensional 

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. 

21


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 

Fjellström, H Floeckner, JG Grossmann, J Hansen, M Helmer-Citterich, FS 

Joergensen, A Marchler-Bauer, J Osuna, J Park, A Reinhardt, L Ribas de Pouplana, 

A Rojo-Dominguez, V Saudek, J Sinclair, S Sturrock, C Venclovas & 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, 

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.) 

Skövde, 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 predictionbased 

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 Ragué Schleyer, NL Allinger, T Clark, J Gasteiger, 

PA Kollman, HF Schaefer III, and PR Schreiner (eds.) Chichester: Wiley, 2242-2255. 

22


*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 ʻScientific applications of neural 

netsʼ, 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. 

23


*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 


*62. J Liu & B Rost (2002) Target space for structural genomics revisited. 


*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. 

24


*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. 


*86. A Kernytsky & B Rost (2003) Static benchmarking of membrane helix predictions. 


*87. IYY Koh, VA Eyrich, MA Martí-Renom, D Przybylski, MS Madhusudhan, E 

Narayanan, O Graña, 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. 


*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 Graña, 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 &GT 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. 

25


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 ʻThe 

Proteomics Protocols Handbookʼ JE Walker (ed.) Totowa: Humana Press, 875-901. 

26


*112. R Nair & B Rost (2005) Mimicking cellular sorting improves prediction of subcellular 

localization. J Mol Biol 348, 85-100. 

*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. 


*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 Schönbach, 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 

27


(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 (ECCBʼ2006), 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 &GT Montelione (2007) Solution NMR structure of 

28


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. 

*138. Y Bromberg & B Rost (2007) SNAP: predict effect of non-synonymous 

polymorphisms on function. Nucleic Acids Res 35, 3823-3835. 

*139. Y Ofran & B Rost (2007) Protein-protein interaction hotspots carved into sequences. 

PLoS Computational Biology 3, e119. 

*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. 

*142. A Schlessinger, J Liu & B Rost (2007) Natively unstructured loops differ from other 

loops. PLoS Comp Biol 3, e140. 

*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. 

29


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. 


*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 

ʻApplication of Artificial Neural Networks to Chemistry and Biologyʼ 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 

ʻBioinformatics – From Genomes to Therapiesʼ 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 

30


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. 

*176. Y Bromberg, J Overton, RL Leibel & B Rost (2009) In silico mutagenesis: a case 

study of the melanocortin 4 receptor. FASEB J 23, 3059-3069. 

*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 ʻStructural Bioinformaticsʼ P Bourne & J Gu 

(eds.) Wiley, 679-714. 

*179. CAF Andersen & B Rost (2009) Secondary structure assignment. In ʻStructural 

Bioinformaticsʼ P Bourne & J Gu (eds.) Wiley, 459-484. 

2010 (8) 

*180. C Schaefer, A Schlessinger & B Rost (2010) Protein secondary structure appears 

to be robust under in silico evolution while protein disorder appears not to be. 

Bioionformatics 26, 625-631. 

31


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 &GT 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 (2) 

*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. 

Preprints/Electronic material 

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/ 

32


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. 

Webservices ($root = www.rostlab.org) 

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 Martí-Renom, D Przybylski, MS Madhusudhan, E 

Narayanan, O Graña, 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/ 

33


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 structureinferred 

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 nonsynonymous 

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) 

Gesamtzahl der Publikationen 

Publikationstypen (einschl. in press): 

Peer-reviewed: 143 Erst-/Letztautor: 139 

34


Original Peer-reviewed: 130 Erstautor: 31 

Rezensionen: 29 Einzelautor: 21 

Buchkapitel: 27 Letztautor: 88 

Tagungsberichte: 12 

Leitartikel: 8 Bücher: 1 

35


Liste meiner am häufigsten zitierten Publikationen (Nummerierung wie oben) 

Publikationen (Auszug i ) Quelle: ISI Index, August 2010 

Nr. ii Zitat Letzten 12 Monate Gesamt Impact-Faktor 

1) #8 1993 JMB 232, 584-599 69 2158 126.9 

2) #16 1994 Proteins 19, 55-72 16 1180 73.8 

3) #27 1996 Meth Enzymol 266, 525-539 33 966 69.0 

4) #119 2005 Science 309 1559-1563 135 650 162.5 

5) #19 1994 CABIOS 10, 53-60 12 558 34.9 

6) #23 1995 Protein Science 4, 521-533 8 532 35.5 

7) #29 1996 Protein Science 5, 1704-18 21 418 29.9 

8) #42 1999 Prot Engng 12, 85-94 59 409 37.2 

9) #99 2004 NAR 32, W321-W326 (PP 2/Yachdav) 91 384 64.0 

10) #9 1993 PNAS 90, 7558-7562 10 340 20.0 

11) #49 2000 EMBO Reports 1, 411-5 48 322 32.2 

12) #17 1994 Proteins 20, 216-226 18 300 18.8 

13) #57 2002 Proteins 47, 228-235 (pollastri) 33 293 36.6 

14) #50 2001 J Structural Biology 134, 204-18 16 221 24.6 

15) #20 1994 JMB 235, 13-26 10 187 11.7 

16) #70 2003 JMB 325, 377-87 (ofran/six) 22 164 23.4 

17) #36 1997 JMB 270, 471-80 6 164 12.6 

18) #43 1999 Proteins 34, 220-3 (SOV) 13 141 12.8 

19) #59 2002 JMB 318, 595-608 (enzyme) 21 137 17.1 

20) #112 2005 JMB 348, 85-100 (LOCtree) 31 124 24.8 

21) #7 1993 Nature Genetics 5, 376-80 2 114 6.7 

22) #67 2002 Prot Sci 11, 2774-91 - TMH revisited 13 113 14.1 

23) #51 2001 Protein Science 10, 1970-9 - Proteomes 15 108 12.0 

24) #52 2001 Bioinformatics 17, 1242-3 - EVA 8 104 11.6 

25) #82 2003 NAR 31, 3300-4 (PP 1=Liu & rost) 4 101 14.4 

26) #66 2002 JMB 322, 53-64 - Loopy/NORS 8 92 11.5 

27) #78 2003 FEBS Letters 544, 236-9 15 91 13.0 

28) #45 1999 JMB 293, 1221-1239 (Olmea) 18 91 8.3 

29) #11 1993 TIBS 18, 120-123 0 89 5.2 

30) #55 2002 Proteins 46, 197-205 - Alignments grow 5 88 11.0 

31) #87 2003 NAR 31, 3311-3315 (EVA) 8 84 12.0 

32) #5 1992 Nature 360, 540 0 84 4.7 

33) #145 2007 Proteins 69, 3-9 82 82 27.3 

34) #30 1996 Ann Rev 25, 113-36 0 77 5.5 

35) #123 2005 Moult intro Proteins 61, 3-7 9 76 15.2 

36) #34 1996 Fold & Des 2, S19-S24 6 76 5.4 

37) #83 2003 NAR 31, 3833-5 (NORSp) 9 75 10.7 

i Nur Veröffentlichung mit ≥30 Zitaten oder einem Impakt ≥10 

ii Nummer aus der Publikationsliste (hohe Zahlen deuten neuere Veröffentlichungen an) 

36


Lfd.Nr. ii Zitat Letzten 12 Monate Gesamt Impact-Faktor 

38) #22 1995 ISMB 0 73 iii 12.2 

39) #93 2003 CMLS 60, 2637-50 21 68 9.7 

40) #37 1998 JMB 276, 517-25 - andrade 6 66 5.5 

41) #97 2004 NAR 32, 2566-2577 (PROFtmb) 14 65 10.8 

42) #24 1995 Proteins 23, 295-300 0 64 4.3 

43) #74 2003 NAR 31, 397-99 (NLSdb) 0 62 8.9 

44) #117 2005 Bioinformatics 21 2960-2968 (PROFcon) 13 55 11.0 

45) #39 1998 Structure 6, 259-63 0 55 4.6 

46) #68 2002 Prot Sci 11, 2836-47 - localization 6 53 6.6 

47) #85 2003 NAR 31, 3789-91 (uniqueProt) 6 51 7.3 

48) #75 2003 Curr Opin Chem Biol 7, 5-11 3 51 7.3 

49) #56 2002 Structure 10, 175-184 7 47 5.9 

50) #62 2002 Bioinformatics 18, 922-933 0 45 5.6 

51) #118 2005 Proteins 61 115-126 - PROFbval 13 44 8.8 

52) #105 2004 NAR 32, 3522-3530 (CHOPnet) 3 44 7.3 

53) #138 2007 NAR 35, 3823-3835 42 42 14.0 

54) #58 2002 Structure 10, 435-440 (renom reliability) 3 43 5.4 

55) #35 1997 CABIOS/Bioinformatics 13, 345-56 1 42 3.2 

56) #10 1993 Protein Engineering 6, 831-836 41 41 2.4 

57) #113 2005 JMB 348 507-512 (folding rates) 11 39 7.8 

58) #139 2007 PLOS CB 3, 1169-1176 (hotspots) 22 38 12.7 

59) #128 2006 PLOS CB 2, 698-709 - Mika/Interactions 12 37 9.3 

60) #120 2005 Drug Disc Today 10 1475-1482 6 36 7.2 

61) #103 2004 Proteins 56, 188-200 (NESG) 4 36 6.0 

62) #96 2004 Proteins 55, 678-688 (CHOP) 3 36 6.0 

63) #90 2003 Proteins 53, 917-30 - localiation 4 34 4.9 

64) #89 2003 NAR 31, 3293-5 (DSSPcont) 5 33 4.7 

65) #54 2001 Proteins 45, 192-199 5 33 3.7 

66) #124 2005 Proteins 61, 214-224 (Grana/CASP6/cont) 31 31 6.2 

67) #107 2004 JMB 341, 255-269 (AGAPE) 3 31 5.2 

89) #162 2009 Nature Biotechnology 27, 51-57 13 13 13.0 

93) #163 2009 PLOS One 4 12 12 12.0 

96) #169 2009 Structure 17, 869-881 11 11 11.0 

98) #171 2009 Proteins 77, 1-4 10 10 10.0 

Summe Durchschnittl. Zitierungen 

Alle 186 iv Publikationen: 14.315 77 

138 iv Erster/Letzter Autor (aufgelistete Papers) 12.069 88 

ii Nummer aus der Publikationsliste (hohe Zahlen deuten neuere Veröffentlichungen an) 

iii Zahlen von Feb. 2001, seitdem nicht mehr in ISI aufgeführt. 

iv Mittelwerte sind über ALLE Veröffentlichungen in der Publikationsliste berechnet; viele 

Veröffentlichungen sind nicht in ISI aufgeführt. 

37


Bemerkung: dies resultiert in einem mittleren pro-Jahr Index (ueblicherweise als Impaktfaktor 

bekannt) von ~12 fuer all meine Veroeffentlichungen, die in ISI gelistet sind. Dies ist hoeher 

als der Impaktfaktor von einigen der renomiertesten Fachzeitschriften in der Molekularbiolgie 

(z.B. EMBO J and PNAS). Veroeffentlichung aus den letzten Jahren (nach 1999) haben einen 

niedrigeren Mittelwert, bleiben aber immer noch ueber 10, d.h. die Pseudo Fachzeitschrift 

„Rost seit 1999“ wuerde immer noch in den Top 100 der 6066 ISI Zeitschriften rangieren. In 

der Tat sind die meisten meiner Veroeffentlichungen wesentlich mehr zitiert als der die top 

10% der Veroeffentlichungen in fast allen Zeitschriften, in denen ich veroeffentlicht habe. 

Der h-index (Herfindahl index/Hirsch Zahl) ist die Zahl von Veroeffentlichungen h die mehr als 

h-mal zitiert wurden. Mein h-index nach Google ist 58 (August 2010) and 48 nach ISI 

(August 2010). Der Unterschied resultiert im Wesentlichen daraus, dass ISI weder 

Proceedings noch Buchkapitel zählt, und ueberhaupt viele Zitate in modernen Medien von 

Wissenschaftlichen Arbeiten ignoriert. 

38


Webservers und öffentliche Ressourcen 

Bitte beachten Sie, dass die folgenden Tools auf unserer Website veröffentlicht 

werden ◊ : 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, TOPITS*, AGAPE*, CHOP|CHOPnet*, DISIS*, 

ISIS*, LOC*, MD*, PredictNLS*, PROF*, 

NORSnet*, NORSp*, SNAP*, Ucon*). 

AGAPE* Fold recognition without folds: Improved and generalized method for sequenceprofile 

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/ Method chopping proteins into structural domain-like fragments and database for 

CHOPnet* 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 homologytransfer 

(LOChom*), automated text analysis of SWISS-PROT keywords 

(LOCkey*), neural network-based (LOCnet*) and SVM-based predictions 

(LOCsvm*), and combinations of methods specialized on “shuttling sequences” 

(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 

◊ Alle mit Stern* markierten Tools sind im Rost Lab an der Columbia Univ. oder TUM entwickelt worden. 

39


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. 

40

Unterlagen: CV Burkhard Rost TU München Inhalt - ROSTLAB.ORG

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