rost CV in German

Transcription

rost CV in German

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
Web
rost@in.tum.de
www.rostlab.org
rostlab.in.tum.de
Tel
Fax
+49-89-289-17-811
+49-89-289-19-414
Photo: © Echert & Heddergott, TUM
Unterlagen:
CV Burkhard Rost
TU München
Inhalt:
• Curriculum vitae
• Veröffentlichungen
printed Januar 10, 2011
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Burkhard Rost
CV
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Burkhard Rost
Tabulated CV
Tabellarischer Lebenslauf (Curriculum Vitae)
Datum:
Name:
Geschlecht:
Ehestand:
Staatsangehörigkeit:
Geburtsort:
Stelle:
Adresse:
Januar 10, 2011
Burkhard Rost
Männlich
Verheiratet, eine Tochter (geb. Dez. 2002)
Deutsch
Northeim, Niedersachsen, Germany
Ordinarius Bioinformatik
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
1980-1982
Oberschule, Herzberg, Niedersachsen
Wehrdienst in der Luftwaffe
1982-1985
10/1984
1985-1988
1985-1988
1986-1988
Thema:
Betreuer:
11/1988
12/1988
Studium der Physik an der Justus-Liebig-Universität Gießen
Vordiplom in Physik
Studium der Physik an der Ruprecht-Karls-Universität Heidelberg
Studium der Philosophie, Geschichte und Psychologie in Heidelberg
Diplomarbeit am Institut für Theoretische Physik in Heidelberg
'Learning algorithms for spin-glass-like neural networks'
Prof. Dr. Heinz Horner, Heidelberg
Vordiplom in Philosophie und Geschichte, Heidelberg
Diplom in Physik, Heidelberg
12/88-06/90
Thema:
Forschungsstipendium 'Stiftung Volkswagenwerk', Theor. Physik, Heidelberg
'Theoretical analysis of the possibilities of seismic and acoustical sensor
networks to verify arms control treaties for aircraft'
Forschungsprojekte in den USA (Princeton, Washington DC, MIT)
Doktorarbeit am EMBL, Heidelberg
Schreiben der Doktorarbeit
'Neural networks and evolution - prediction of protein secondary structure'
keiner ◊
Dr. rer. nat. (Doctor rerum naturarum) am Institut f. Theoretische Physik,
Ruprecht-Karl Universität Heidelberg
07-10/89
1990-1993
07/1993
Thema:
Betreuer:
07/1994
◊
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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Burkhard Rost
Tabulated CV
Stellen
1986-1988
12/88-06/90
07-10/1989
07/90- 1992
07/93-12/94
01/95-12/95
01/96- 04/98
05/98-11/98
12/98- 05/00
07/2000-2010
2004-2010
2002-2010
07/2005-2010
2006-2010
2006-2010
seit 06/2009
Assistent am Institut für Theoretische Physik, Heidelberg
Wissenschaftl. Mitarbeiter am Institut für Theoretische Physik, Heidelberg
Gastwissenschaftler an Instituten in den USA (Princeton, Union of
Concerned Scientists, MIT)
Gastwissenschaftler am EMBL Heidelberg
Wissenschaftlicher Mitarbeiter am EMBL Heidelberg
Wissenschaftlicher Mitarbeiter am EBI Hinxton, Cambridge, England
Wissenschaftlicher Mitarbeiter am EMBL Heidelberg
Wissenschaftler bei LION Biosciences Heidelberg
Professor (Assistant Prof.) an der Fakultät für Biochemie & Molekulare
Biophysik, Columbia Universität, Neu York, USA
Professor (Associate Prof.), Biochemie & Mol. Biophys., Columbia
Außerordentlicher Professor, Fakultät. für Medizinische Bioinformatik,
Columbia University
Mitarbeiter Center of Computational Biology and Bioinformatics (C2B2)
Feste Anstellung am Institut für Biochemie und Mol. Biophysik an der
Columbia Universität
Außerordentlicher Professor, Fakultät. für Pharmakologie, Columbia Univ.
Mitarbeiter Irving Center of Cancer Research, Columbia Univ.
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
1996-heute
2002-heute
2002-heute
2005-2006
2006
2007-heute
Programmkomittee der ISMB (Intelligent Systems for Molecular Biology)
Mitglied der ISCB (International Society for Computational Biology)
Board of Directors ISCB (International Society for Computational Biology)
Mitglied der NYAS (New York Academy of Sciences)
Vizepräsident ISCB (International Soc. for Computational Biology)
President Elect ISCB (International Society for Computational Biology)
Präsident der ISCB (International Society for Computational Biology)
Berufliche Erfahrungen
1992-heute
1995-heute
2001-heute
2005-2009
2006-heute
2006-heute
2009-heute
Über 500 Gutachten für peer-reviewed Zeitschriften (inkl. Nature, Science,
PNAS, Cell, EMBO J)
Über 50 Gutachten für Anträge von Wissenschaftlern und Instituten
(Österreich, Kanada, Dänemark, England, Deutschland, Israel, Italien,
Norwegen, Niederlande, Singapur, Spanien, Schweden, Schweiz, USA)
Gutachter für Anträge von NIH, NSF, European Community (EC), Welcome
Trust
Associate Editor von PLoS Computational Biology
Associate Editor von Bioinformatics
Associate Editor von Proteins: Structure, Function, and Bioinformatics
Deputy Editor von PLoS Computational Biology
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Burkhard Rost
2005-heute
2006-heute
2007-heute
2001-2006
2002, 2005
2004-2006
2005-2006
2002-2007
1999-2005
2004-heute
Tabulated CV
Editorial Board von FASEB (Vertreter der ISCB)
Editorial Board von Journal of Structural and Functional Genomics
Editorial Board von Bioinformatics and Biology Insights
Editorial Board von Journal of Medical Informatics
Editor for ISMB (Intelligent Systems for Molecular Biology) Proceedings
Editorial Board von Proteins: Structure, Function, and Bioinformatics
Editorial Board von Bioinformatics
Organisation der New York Computational Biology Society in der Neu York
Academy of Sciences
SAB von LION Biosciences, Heidelberg/Cambridge GB
Mitgründer, CEO von BioSof, Delaware, USA
Eingeladene Vorträge (138 in 20 Ländern)
12/1988
09/1989
10/1989
05/1990
09/1990
010/1990
London, England: Tagung zum Thema Rüstungskontrolle
Washington, DC, USA: Union of Concerned Scientists
Princeton, USA: Institute for Advanced Studies
Prag, CSFR: Tagung zum Thema Rüstungskontrolleʻ
Vienna, Österreich: Konferenz zum Thema Rüstungskontrolle
Mosbach, Germany: Konferenz zum Thema Rüstungskontrolle
06/1992
07/1992
11/1992
Elba, Italien: Konferenz: Neuronale Netzwerke
Turin, Italien: Konferenz: Protein Structure Prediction
Nijmegen, Niederlande: EU-Konferenz Sequence Analysis
06/1993
11/1993
Rennes, France: Workshop Secondary Structure Prediction
Kopenhagen, DK: Konferenz Protein Structure by Distance Analysis
01/1994
03/1994
04/1994
11/1994
11/1994
12/1994
Mauii, Hawaii, USA: HICCS Konferenz
Bologna, Italien: Konferenz Protein Structures
Kopenhagen, Dänemark: Mini-Symposium zum Thema Structure Prediction
Bielefeld, Germany: University
Asilomar, USA: CASP Konferenz (Critical Assessment of Structure
Prediction, CASP1)
06/1995
06/1995
10/1995
10/1995
11/1995
Cambridge, England: ISMB'95 (Tutorium)
Heidelberg, Germany: University
Brixen, Italien: Tagung zum Thema Protein Structures
IRBM Rom, Italien: Tagung Frontiers of protein structure prediction
Paris, Frankreich: Tagung Protein Structures and Drug Design
06/1996
08/1996
10/1996
11/1996
12/1996
St. Louis, USA: ISMB'96
Madrid, Spanien: CNB
Universität Heidelberg
Neu York, USA: Columbia Universität
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Burkhard Rost
Tabulated CV
12/1996
Asilomar, USA: UCSF
01/1997
02/1997
02/1997
03/1997
03/1997
06/1997
06/1997
07/1997
07/1997
07/1997
09/1997
09/1997
10/1997
11/1997
11/1997
12/1997
12/1997
12/1997
12/1997
Univ. Jerusalem, Israel: UNESCO-Workshop Sequence Analysis
Basel, Switzerland: CIBA-Geigy
EBI Hinxton, England: Tagung Protein Structure Prediction
Kopenhagen, Dänenmark: CBS
Neu York, USA: Columbia Universität
Berlin: Inst. für Theor. Biol.
Chalkidiki, Griechenland: ISMB'97 (Tutorium)
EBI Hinxton, England: EMBO Workshop Protein Sequence Analysis
San Sebastian, Spanien: Tagung Proteins: integration of life's function
Madrid, Spanien: CNB
Skövde, Schweden: Konferenz Bio-Computing and Emergent Computation
Wien, Österreich: Intern. Conference on Molecular Structural Biology
IRBM Rom, Italien: Tagung Frontiers of protein structure prediction
Stockholm, Schweden: Pharmacia & Upjohn
Stockholm, Schweden: Karolinska Inst.
Paris, Frankreich: Pasteur Inst.
Toulouse, Frankreich: INRA Inst.
Toulouse, Frankreich: Elf Sanofi
Basel, CH: Symposium Bioinformatics: from Exp. to Biol. Knowledge
03/1998
05/1998
05/1998
06/1998
10/1998
10/1998
Marseille, Frankreich: Krebszentrum, INSERM/19CNRS
Tallberg, Schweden: Konf. Annual meeting of Swedish Structural Biology
Bad Honnef, Deutschland: Konf. Scientific Applications of Neural Nets
Neu York, USA: Tagung im Genomzentrum, Columbia Univ.
Cambridge, England: Newton Inst. Konf. Biomolecular Function and
Evolution in the Context of the Genome Project
EBI, England: Konf. ʻMethods for protein structureʼ
07/1999
08/1999
09/1999
10/1999
11/1999
Havanna, Kuba: CIGB EMBO Workshop Bioinformatics
Cambridge, England: EBI Workshop Protein motifs and families
Graz, Österreich: International Meeting of Austrian Society for Genetics
Bologna, Italien: Tagung Protein sequence analysis in the genome era
Atlanta, USA: Konf. In silico biology: sequence & structure & function
02/2000
02/2000
08/2000
08/2000
08/2000
10/2000
12/2000
Boston, USA: SGI Workshop New Technologies for Discovery Research
New York Structural Biology Society
Troy RPI, USA: Bioinformatics Workshop
Madrid, Spanien: Human Genome Workshop
Neu York Universität
Heidelberg, Deutschland: LION's Bioinformatics 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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Burkhard Rost
Tabulated CV
03/2001
04/2001
05/2001
05/2001
07/2001
07/2001
09/2001
09/2001
CNB Madrid, Spanien
Neu York, Rockefeller Universität
Neu York, New York Structural Biology Society
Neu York, Columbia Universität, Biologie
TU Kopenhagen, Dänemark
Heidelberg Universität, Deutschland
Il Ciocco, Italien: NATO Sommerschule Bioinformatics (Vortrag & Dozent)
IRBM Rom, Italien
01/2002
04/2002
04/2002
05/2002
06/2002
06/2002
07/2002
08/2002
08/2002
10/2002
11/2002
Keystone Symposium Structural Genomics, USA
Madrid, Spanien: Tagung Bioinformatics and Computational Biology
Basel, Schweiz: Vortrag im Bioczentrum Basel
Erice, Italien: Vortrag in der Sommerschule ʻStrukturbiologieʻ
San Diego, USA: 11th Annual Bioinformatics and Genome Research
Rutgers Univ., USA: Northeast Structural Genomics Consortium Annual
Symposium
New York Computational Biology Society, New York Academy of Sciences
Edmonton, Kanada: ISMB'2002
Havanna, Kuba: Bioinformatica-Habana
Lausanne, Schweiz, Universität Lausanne
Toronto, Kanada, Institute for Proteomics and Bioinformatics
02/2003
02/2003
02/2003
05/2003
10/2003
11/2003
11/2003
Neu York, Fordham Universität
CABM, Rutgers Univ., Piscataway, USA
Neu York, Manhattan College
Neu York, City College
Bethesda, NIH: Hauptredner auf dem Workshop Comparative modeling
Bethesda, NIH: Workshop Target Selection in Structural Genomics
Rutgers Univ., Piscataway, NJ
02/2004
06/2004
07/2004
07/2004
07/2004
07/2004
07/2004
11/2004
11/2004
Gordon Konferenz, Ventura CA: Structural, Functional & Evolutionary
Genomics
NESG Symposium, Arden House, Heriman, Neu York
ETH Zürich, Schweiz
EPFL Lausanne, Schweiz
Tagung zum Thema Data Mining, Glasgow, Scotland
Tagung zum Thema Genome Annotation, Glasgow, Scotland
ISMB Review of field, Glasgow, Scotland
Rom Universität, Italien
International Conference on Structural Genomics (ICSG), Washington DC
09/2005
11/2005
12/2005
12/2005
Structural-Genomics-Tagung zum Thema Target Selection (Chicago)
RCSB workshop zum Thema Homology Modeling (Rutgers)
Structural-Genomics-Tagung zum Thema Target Selection (NIH/Bethesda)
INRA, Univ. Evry, Paris, Frankreich
7
Burkhard Rost
Tabulated CV
01/2006
02/2006
05/2006
06/2006
08/2006
Seminar an der Technischen Universität München, Deutschland
Keystone Konferenz zum Thema Structural Genomics
DIMACS Tagung Approaches to Predict Protein Function (Rutgers)
NIH Tagung Target Selection for Structural Genomics (NIH/Bethesda)
SWISS-PROT 20 years (Fortalezza, Brasilien)
01/2007
01/2007
07/2007
08/2007
04/2008
05/2008
06/2008
07/2008
12/2008
Hauptredner der 5th European Conf. for Comp. Biology (ECCB, Eilat, Israel)
BIOSAPIENS Tagung zum Thema Protein Function Prediction (Eilat, Israel)
SIG 3D (Wien, Österreich)
Hauptredner auf InCoB - 6th International Conference on Bioinformatics
(Hong Kong, China)
NESG, Princeton
Mohonk cBio Symposium, New Paltz
Pasteur, Paris
ISMB Student Council, Toronto, Kanada
CASP8 Sardinien, Italien
03/2009
05/2009
06/2009
12/2009
AMIA, San Francisco, USA
Humboldt Universität, Berlin, Deutschland
ISMB/ECCB 2009, Stockholm, Schweden
Bioinformatics of African Pathogens, Bamako, Mali
01/2010
03/2010
04/2010
04/2010
05/2010
05/2010
07/2010
07/2010
07/2010
09/2010
09/2010
10/2010
11/2010
11/2010
Ringberg Tagung (Academia meets industry), Tegernsee, Deutschland
ISCB-Latin America, Montevideo, Uruguay
IAS Retreat, Starnberger See, Deutschland
Machine Learning, Schloss Ringberg, Tegernsee, Deutschland
Tag der Wissenschaft/Kirchentag, Garching, Deutschland
Univ. Bayreuth, Deutschland
Max-Planck Martinsried, Deutschland
ISMB Boston, USA
New York: City College, USA
Optimization, Machine Learning and Bioinformatics, Erice, Italien
ECCB Ghent, Belgien
UCSD, San Diego, USA
Salzburg, Österreich
Biozentrum, Basel, Schweiz
Organisation von Internationalen Wissenschaftlichen Tagungen (37)
09/1990
06/1995
07/1996
Mitveranstalter von The Second Workshop on Verification of Arms
Reductions, 3-5 Sep. 1990, Wien, Österreich
Programmkomittee der 3. ISMB (Intelligent Systems for Molecular Biology),
Cambridge, England
Programmkomittee der 4. ISMB, Halkidiki, Griechenland
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Burkhard Rost
02/1997
07/1997
07/1998
08/1999
08/1999
10/1999
07/2000
12/2000
03/2001
03/2001
07/2001
02/2002
06/2002
08/2002
06/2003
11/2003
06/2003
12/2004
06/2005
12/2005
05/2006
06/2006
12/2006
07/2007
Tabulated CV
Veranstalter des Workshops 'Methods for protein structure prediction progress and limitations' für Pharmaunternehmen, 10-11 Feb., 1997, EBI
Hinxton-Cambridge, England
Programmkomittee der 5. ISMB, St. Louis, USA
Programmkomittee der 6. ISMB, Montreal, Kanada
Veranstalter der Tagung Protein motifs and families in practice: Is protein
function carved into sequence? Aug 12-13, 1999, EBI Hinxton-Cambridge,
England
Programmkomittee der 7. ISMB, Heidelberg, Deutschland
Programmkomittee der 2. Bologna summer school on biotechnology: Protein
sequence analysis in the genome era, Bologna, Italien
Programmkomittee der 8. ISMB, San Diego, USA
Mitveranstalter der CAFASP Veranstaltung während der CASP (Critical
Assessment of Protein Structure Prediction) Tagung in Asilomar, CA
Mitveranstalter von Bioinformatik Wettbewerben der Fa. LION Biosciences,
Boston
Mitveranstalter des Juan-March-Workshops zum Thema ʻStructural
Genomicsʼ in Madrid, Spanien
Programmkomittee der 9. ISMB, Copenhagen, Dänemark
Programmkomittee des 3. "International Meeting on Membrane proteins” in
Bologna, Italien
Programmkomittee des Meetings zum Thema ʻComputational Biologyʼ,
Manchester, England
Mitveranstalter des 10. internationalen Meetings zum Thema 'Intelligent
Systems in Molecular Biology' in Edmonton, Kanada (1500 Teilnehmer; die
wichtigste Tagung für Bioinformatiker)
Wissenschaftlicher Beirat, Editor und Programmkomittee der 11. ISMB 2003
in Brisbane, Australien
Mitorganisation des NIH Workshops Target selection for structural genomics
Wissenschaftlicher Beirat, Editor und Programmkomittee der 12. ISMB 2004
in Glasgow, Schottland (>2,200 Teilnehmer)
Mitorganisation des Meetings ʻCritical Assessment of protein Structure
Predictionʼ (CASP6) in Italien (das wichtigste Meeting zum Thema ʻstructure
predictionʼ)
Co-Vorsitzender Programmkomittee, Mitglied des wissenschaftlichen Beirats
und Editor der 13. ISMB 2005 in Detroit, USA (> 2500 erwartete Teilnehmer)
Mitorganisation des NIH-Workshops ʻTarget selection for structural
genomics'
Mitorganisation des CASP6.5 Workshops (New York)
Mitorganisation des NIH-Workshops zum Thema ʻTarget selection and
homology modelingʼ (Bethesda, NIH)
Mitorganisation des Meetings ʻCritical Assessment of protein Structure
Predictionʼ (CASP7) in Asilomar, CA (das wichtigste Meeting zum Thema
ʻStructure Predictionʼ)
ISMB/ECCB Wien: Co-Vorsitzender des 15. International Meeting on
Intelligent Systems in Molecular Biology (ISMB) und der Fifth European
9
Burkhard Rost
07/2008
12/2008
07/2009
12/2009
03/2010
07/2010
07/2011
07/2011
03/2011
03/2012
Tabulated CV
Conference of Computational Biology (ECCB) in Wien, Österreich (das
wichtigste Meeting für Bioinformatiker), Chair of Highlight Track at
ISMB/ECCB
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
Mitorganisation von CASP8 in Sardinia, Italien
ISMB/ECCB Stockholm: Wissenschaftliches Organisationskomittee &
Vorsitzender des Wissenschaftlichen Lenkungsausschusses
Lenkungsausschuss der 1. ISCB-Africa/ASBCB, Bamako, Mali
Lenkungsausschuss der 1. ISCB-Latin America, Montevideo, Uruguay
ISMB 2010, Boston: Vorsitzender von Highlights Track & Vorsitzender des
Wissenschaftlichen Lenkungsausschusses
Organisationskomittee der SIG zum Thema Function Prediction, Wien 2011
ISMB/ECCB 2011, Wien, Österreich: Vorsitzender von Highlights Track &
Vorsitzender des Wissenschaftlichen Lenkungsausschusses
Lenkungsausschuss der 2. ISCB-Africa/ASBCB, Bamako, Mali
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 (BurnhamUCSD 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
10
Burkhard Rost
Tabulated CV
(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 MartiRenom (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
11/2009-heute
Qualifzierungsprüfung, Dept. Biochemie & Moleculare Biophysik, Columbia
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
2000-2003
2005-2008
2010-heute
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)
Lehren an der Medizinischen Fakultät, Columbia; Kurs Eukaryotes I (3
Kurse: 2000, 2001, 2002, 2003)
Semesterkurs Computational Biology II: Proteins: Sequence, Structure and
Networks an der Columbia University (in Zusammenarbeit mit Dr. Vitkup)
Zweisemestrige Vorlesung Protein Prediction 1+2 an der TUM (Jeder
Vortrag 2x2 SWS + 2 SWS Übung)
11
Burkhard Rost
2010-heute
2010 Sommer
2010/11
Tabulated CV
Oberseminar Bioinformatics & Computational Biology (jedes Semester, in
Zusammenarbeit mit Dr. Stefan Kramer)
Hauptseminar Bioinformatics & Computational Biology (Rost & Kramer
Gruppe)
Hauptseminar Bioinformatics & Computational Biology (Rost Gruppe)
Kurse an TUM (Rost Gruppe)
2010 Sommer
2010 Sommer
2010/11
2010/11
2010/11
Praktikum Bioinformatik Protein Structure and Function Analysis (Andrea
Schafferhans & Marco Punta)
Praktikum Bioinformatik Bioinformatics Lab (Laszlo Kajan & Markus
Schmidberger)
Vorlesung Computational Systems Biology (Shaila Rössle & Arthur Dong)
Seminar Presenting and Selling (Scientific Software) (Andrea Schafferhans)
Seminar Munich R course (Markus Schmidberger)
Kurse auf Meetings / Sommerkurse
06/1995
10/1995
03/1997
06/1997
07/1997
07/1997
10/1997
07/1999
10/1997
09/2001
08/2002
09/2010
Tutorium auf der ISMBʼ95 (International Conference on Intelligent Systems
for Molecular Biology) in Cambridge, England
Betreuung der post-docs auf dem Workshop Frontiers of protein structure
prediction am IRBM in Rom, Italien
Betreuung der post-docs auf dem Workshop an der CBS in Kopenhagen
(Dänemark)
Tutorium auf der ISMBʼ97 (International Conference on Intelligent Systems
for Molecular Biology) in Chalkidiki, Griechenland
Betreuung der pre- und post-docs auf dem Workshop (EMBO-course)
Genome sequence analysis am EBI in Hinxton, England
Lehrer während der Sommerschule Proteins: integration of life's function in
San Sebastian, Spanien
Betreuung der post-docs auf dem 2. Workshop Frontiers of protein structure
prediction at the IRBM in Rom, Italien
Betreuung der pre- und post-docs auf dem Workshop Bioinformatics im CIB
in Havanna, Kuba
Betreuung der post-docs auf dem Workshop Protein sequence analysis in
the genome era an der University of Bologna, Italien
Lehrer während der NATO-Sommerschule ʻBioinformatikʻ in Il Ciocco, Italien
Betreuung der pre- und post-docs auf dem Workshop Bioinformatics im CIB
in Havanna, Kuba
Sommerkurs zum Thema Optimization, Machine Learning and
Bioinformatics, Erice, Italien
Andere Lehrveranstaltungen
1986-1988
1989-1990
1990
Organisation der Seminare über Theor. Physik, Heidelberg Univ.,
Deutschland
Vortragsreihen zum Thema ʻRüstungskontrolleʻ (I), Heidelberg University
Vortragsreihen zum Thema ʻRüstungskontrolleʻ (II), Heidelberg Univ.
12
Burkhard Rost
1986-1990
1991-1995
1992-1996
Tabulated CV
Kurse
zum
Thema
ʻPhysikʻ
und
ʻRüstungskontrolleʻ in außeruniversitären Schulen (Heidelberg, Mannheim,
Frankfurt, Darmstadt)
Halten von Vorträgen und Betreuung der Lehrveranstaltungen für
Doktoranden im EMBL Heidelberg
Vortragsreihe ʻProtein structure predictionʻ an der Heidelberger Univ.
Studenten von meiner Gruppe, die den Doktortitel erlangt haben
Name
Yanay Ofran
Jinfeng Liu
Rajesh Nair
Dariusz Przybylski
Sven Mika
Yana Bromberg
Henry Bigelow
Avner Schlessinger
Andrew Kernytsky
Kaz O Wrzeszczynski
Ta-Tsen Soong
Dissertation
02/2004 (2000)
02/2004 (1999)
11/2004 (1999)
11/2004 (1999)
07/2006 (2002)
11/2006 (2003)
04/2007 (2001)
09/2007 (2003)
05/2008 (2001)
02/2009 (2001)
06/2009 (2005)
Affiliation für Dissertation
Columbia: Medical Informatics /C2B2
Columbia: Pharmacology/C2B2
Columbia: Physics/C2B2
Columbia: Physics/C2B2
Columbia: Biochemistry/C2B2
Columbia: Medical Informatics/C2B2
Columbia: Medical Informatics/C2B2
Doktoranden in meiner Gruppe
Name
Christian Schaefer
Tobias Hamp
Esmeralda Vicedo
Universität
TUM Munich
TUM Munich
TUM Munich
Zeitraum
2009-2012
2009-2012
2010-2012
Postdoktoranten in meiner Gruppe
Name
Affiliation
Marco Punta
TUM/IAS
Yu-An (Arthur) Dong
TUM: Bioinformatics
Laszlo Kajan
TUM: Bioinformatics
Edda Kloppmann
TUM: Bioinformatics
Mark Offman
TUM: Bioinformatics
Shruti Rastogi
Columbia: Biochemistry
Shaila Roessle-Blank
TUM: Bioinformatics
Andrea Schafferhans-Fuhrmann TUM
Markus Schmidberger
TUM: Bioinformatics
Mikhail Veshtort
In Gruppe seit
2002
2010/06
2008/04
2011/01
2010/07
2008/04
2010/07
2009/09
2010/01
2008/12
Technische Mitarbeiter in meiner Gruppe
Name
Timothy Karl
Guy Yachdav
Affiliation
TUM: Bioinformatics
13
In Gruppe seit
2010/05
2003
Burkhard Rost
Tabulated CV
Ehemalige Mitglieder meiner Gruppe
Name
Claus Andersen
Claudia Bertonati
Henry Bigelow
Yana Bromberg
Phil Carter
Volker Eyrich
Hedi Hegyi
Andrew Kernytsky
Ingrid Koh
Jinfeng Liu
Sven Mika
Eyal Mozes
Rajesh Nair
Yanay Ofran
Dariusz Przybylski
Megan Restuccia
Avner Schlessinger
Ta-Tsen Soong
Kaz O Wrzeszczynski
Zeitraum
2001-2002
2004-2006
2001-2007
2003-2009
2002-2004
1999-2005
2002-2004
2001-2008/10
2003-2006
1999-2007
2002-2006
2005-2008
1999-2008/08
2000-2007
1999-2007
2002-2005
2003-2008
2005-2009
2001-2009
Gegenwärtige Anstellung
Sr. Analyst, Siena Biotech., Italy
Staff, Univ. of Rome, Italy
Postdoc, Columbia Univ., New York, NY
Assistant Professor, Rutgers Univ., NJ
Univ. College, London
Sr. Analyst, Schroedinger Inc., New York, NY
Staff, Budapest Univ., Italy
Research Scientist, BROAD Inst. MIT, MA
Hongkong
Senior Research Scientist, Genentech, CA
Programmer, eSpeed Inc., New York, NY
Staff, Columbia Univ. Biology, NY
FDA (Federal Drag Agency), Bethesda, MD
Faculty, Bar-Ilan University, Israel
Senior Research Scientist, BROAD Inst. MIT, MA
Manager, Morgan & Stanley, New York, NY
Postdoc, UCSF, San Francisco, CA
Postdoc, Cornell Medical School, New York, NY
Postdoc, Cold Spring Harbor Laboratories, NY
Dissertations Ausschuss
Name
Yuling An
Chen Peter Chien
Murat Cokol
Chuck Duarte
Volker Eyrich
Marina Gimpelev
Cathy S Gunther
Samuel K Handelman
David Pincus
Erroll Rueckert
Trevor Siggers
Cinque Soto
Hepan Tan
Christopher Tang
Bahar Taneri
Oleg Trott
Yun Zhang
Universität: Fakultät
Columbia: Chemistry
Columbia: MD,PhD
CU: Biomedical Informatics
Columbia: Chemistry
Rockefeller University
Columbia: Biology
Columbia: Chemistry
Columbia: Integrated
Rockefeller University
Columbia: Biology
Datum
07/2002
12/2005
05/2006
09/2002
07/2001
06/2004
11/2002
2008
09/2004
2009
11/2005
09/2007
02/2006
06/2007
04/2005
06/2004
10/2001
Bachelor/Master Studenten
Name
Michael Menden
University: Department
TUM: Informatik
14
Period
2010-2011
Gruppe
Rich Friesner
Barry Honig
Andrej Rzhetsky
Ann-Marie Pyle
Rich Friesner
Barry Honig
Terry Gaasterland
John Hunt
Rich Friesner
Richard Axel
Barry Honig
Barry Honig
Wayne Hendrickson
Barry Honig
Terry Gaasterland
Arthur Palmer
Marti Chalfie
Burkhard Rost
Tabulated CV
Rotation Studenten
Name
Murat Cokol
Trevor Siggers
Hong Yu
Hepan Tan
Enrique Tadique
Henry Bigelow
Chen Peter Chien
Seth Gale
Andrew Kernytsky
Avner Schlessinger
Anthony J DeCostanzo
Roman Trakhtenberg
Shoshana L Posy
Shameek Biswas
Gabor Halasz
Andrew Kuziemko
Peng Liu
Ta-tsen Soong
Bahar Moezi
Wei Lim
Joe Bylund
Universität: Fakultät
Columbia: Biology
Columbia: Medical Inform.
Bronx Highschool
Columbia: MD-PhD
Columbia: Undergraduate
Columbia: Pharmacology
Columbia: Computer Sci.
Columbia: Physics
Columbia: Biomed. Engng.
15
Zeitraum
03-05/2000
06-08/2000
06-08/2000
06-08/2000
06-08/2000
03-05/2001
06-08/2001
09-11/2001
06-08/2002
06-08/2002
09-11/2002
Winter 2002/2003
03-05/2003
06-08/2003
06-08/2003
09-11/2004
03-05/2005
03-05/2005
06-08/2005
06-08/2005
03-05/2008
Burkhard Rost
Grants
Drittmittel
Laufende Mittel
I.
PI:
Zeitraum :
Agentur:
Volumen:
Thema:
Burkhard Rost
12/01/06-11/30/11
NIH (R01) - USA
$250 Tsd. (Gesamtkosten: $1,250,000)
Comprehensive annotation of subcellular localization in entire proteomes
II.
PI:
Zeitraum:
Agentur:
Volumen:
Thema:
Burkhard Rost
06/01/09-05/31/15
Alexander von Humboldt Stiftung
750 Tsd € Gesamt (5 Jahre): 4,250 K € Overhead (5 Jahre): 750 K €
Alexander von Humboldt Professorship (AvH)
III.
PI:
Role:
Period:
Agency:
Volumen:
Thema:
Wayne Hendrickson
Co-PI
07/01/10 to 06/30/15
NIH (U54 GM75026)
$120 K
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
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.
II.
PI:
Period :
Agency:
Total Dir Costs:
Summary:
ISMB'2002
Burkhard Rost
August 2002
NSF
$40 K
Travel support for young participants of the ISMB 2002 meeting
III.
PI:
Period :
Agency:
ISMB'2002
Burkhard Rost
August 2002
DOE
16
Burkhard Rost
Grants
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)
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)
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
PI:
Burkhard Rost
Period:
05/01/03 – 04/30/07
Agency:
NIH/NLM (R01 LM07329)
17
Burkhard Rost
Grants
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)
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)
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)
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.
PI:
Submitted:
Meeting for Critical Assessment of protein Structure Prediction (CASP)
Burkhard Rost
12/15/03
18
Burkhard Rost
Grants
Period:
08/01/04 – 07/31/09
Agency:
NIH (1-R13-GM072354-01)
Effort:
5%
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
Publikationsliste
◊
Abschlussarbeiten
A.
B.
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 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.
*2.
*3.
4.
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.
B Rost (1991) Sensor Networks for Verifying Disarmament of Aircraft. Bochum: UVB
Universitätsverlag Brockmeyer, Book.
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.
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
Burkhard Rost
*10.
*11.
*12.
B Rost & C Sander (1993) Secondary structure prediction of all-helical proteins in
two states. Protein Engineering 6, 831-836.
B Rost, C Sander and R Schneider (1993) Progress in protein structure prediction?
TIBS 18, 120-123.
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
Burkhard Rost
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: BioComputing 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, S19S24.
*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
Burkhard Rost
*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) CAFASP1: 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.
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*55. D Przybylski & B Rost (2002) Alignments grow, secondary structure prediction
improves. Proteins 46, 195-205.
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CAF Andersen, AG Palmer, S Brunak & B Rost (2002) Continuum secondary
structure captures protein flexibility. Structure 10, 175-184.
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.
MA Marti-Renom, MS Madhusudhan, A Fiser, B Rost, A Sali (2002) Reliability of
assessment of protein structure prediction methods. Structure 10, 435-440.
B Rost (2002) Enzyme function less conserved than anticipated. J Mol Biol 318,
595-608.
B Rost (2002) Did evolution leap to create the protein universe? Curr Opin Struct
Biol 12, 409-416.
CP Chen & B Rost (2002) State-of-the-art in membrane protein prediction. Appl
J Liu & B Rost (2002) Target space for structural genomics revisited.
B Rost, B Honig & A Valencia (2002) Bioinformatics in structural genomics.
Bioinformatics (Editorial) 18, 897-898.
J Glasgow & B Rost (2002) ISMB 2002. Bioinformatics (Editorial) 18 Suppl 1, S1
R Nair & B Rost (2002) Inferring sub-cellular localization through automated lexical
analysis. Bioinformatics 18 Suppl 1 (ISMB Proceedings), S78-S86.
J Liu, H Tan & B Rost (2002) Loopy proteins appear conserved in evolution. J Mol
Biol 322, 53-64.
CP Chen, A Kernytsky & B Rost (2002) Transmembrane helix predictions revisited.
Protein Science 11, 2774-2791.
R Nair & B Rost (2002) Sequence conserved for sub-cellular localization. Protein
Science 11, 2836-2847.
CP Chen & B Rost (2002) Long membrane helices and short loops predicted less
accurately. Protein Science 11, 2766-2773.
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*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.
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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.
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.
Y Ofran & B Rost (2003) Predict protein-protein interaction sites from local sequence
information. FEBS Let 544, 236-239.
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.
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.
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.
B Rost & J Liu (2003) The PredictProtein server. Nucl Acids Res 31, 3300-3304.
J Liu & B Rost (2003) NORSp: predictions of long regions without regular secondary
structure. Nucl Acids Res 31, 3833-3835.
R Nair & B Rost (2003) LOC3D: annotate sub-cellular localization for protein
structures. Nucl Acids Res 31, 3337-3340.
S Mika & B Rost (2003) UniqueProt: creating representative protein sequence sets.
A Kernytsky & B Rost (2003) Static benchmarking of membrane helix predictions.
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.
VA Eyrich & B Rost (2003) META-PP: single interface to crucial prediction servers.
P Carter, CAF Andersen, B Rost (2003) DSSPcont: continuous secondary structure
assignments for proteins, Nucl Acids Res 31, 3293-3295.
R Nair & B Rost (2003) Better prediction of sub-cellular localization by combining
evolutionary and structural information. Proteins 53, 917-930.
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.
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.
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
Burkhard Rost
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*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
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R Nair & B Rost (2005) Mimicking cellular sorting improves prediction of subcellular
localization. J Mol Biol 348, 85-100.
M Punta & B Rost (2005) Protein folding rates estimated from contact predictions. J
Mol Biol 348, 507-512.
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.
O Grana, VA Eyrich, F Pazos, B Rost & A Valencia (2005) EVAcon: a protein
contact prediction evaluation service. Nucleic Acids Res 33, W347-351.
HV Jagadish, D States & B Rost (2005) ISMB 2005. Bioinformatics 21 Suppl 1, i1-i2.
M Punta & B Rost (2005) PROFcon: novel prediction of long-range contacts.
A Schlessinger & B Rost (2005) Protein flexibility and rigidity predicted from
sequence. Proteins 61, 115-126.
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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 OkamuraOho, H Suzuki, J Kawai and Y Hayashizaki (2005) The transcriptional landscape of the
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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.
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.
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
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demonstrate that NMR and X-ray crystallography are complementary methods for
small protein structure determination. J Am Chem Soc 127, 16505-16511
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.
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, 12111217.
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
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Escherichia coli ytfP expands the structural coverage of the UPF0131 protein domain
family. Proteins 68, 789-795.
T Lengauer, BJ Morrison McKay & B Rost (2007) ISMB/ECCB 2007: The premier
conference on computational biology. PLoS CB 3, e96.
Y Bromberg & B Rost (2007) SNAP: predict effect of non-synonymous
polymorphisms on function. Nucleic Acids Res 35, 3823-3835.
Y Ofran & B Rost (2007) Protein-protein interaction hotspots carved into sequences.
PLoS Computational Biology 3, e119.
T Lengauer, B Rost & P Schuster (2007) ISMB/ECCB 2007. Bioinformatics
(Editorial) 23, i1-i4.
Y Ofran, V Mysore & B Rost (2007) Prediction of DNA-binding residues from
sequence. Bioinformatics (ISMB Proceedings) 23, i347-353.
A Schlessinger, J Liu & B Rost (2007) Natively unstructured loops differ from other
loops. PLoS Comp Biol 3, e140.
J Liu, GT Montelione & B Rost (2007) Novel leverage of structural genomics. Nature
Biotech 25,849-851.
A Schlessinger, M Punta & B Rost (2007) Natively unstructured regions in proteins
identified from contact predictions. Bioinformatics 23, 2376-2384.
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.
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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.
D Przybylski & B Rost (2008) Powerful fusion: PSI-BLAST and consensus
sequences. Proteins 24, 1987-1993.
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.
Y Bromberg & B Rost (2008) SNAP predicts effect of mutations on protein function.
T-T Soong, KO Wrzeszczynski & B Rost (2008) Physical protein-protein
interactions predicted from microarrays. Bioinformatics 15, 2608-2614.
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.
D Przybylski & B Rost (2008) Predicting simplified features of proteins structure. In
ʻBioinformatics – From Genomes to Therapiesʼ T Lengauer (ed.) Weinheim: WileyVCH, 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
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Hunt, L Tong, GT Montelione & B Rost (2009) Structural genomics reveals EVE as a
new ASCH/PUA-related domain. Proteins 75, 760-773.
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.
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.
A Kernytsky & B Rost (2009) Using genetic algorithms to select most predictive
protein features. Proteins 75, 75-88.
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.
Y Bromberg & B Rost (2009) Correlating protein function and stability through the
analysis of single amino acid substitutions. BMC Bioinformatics 10 Suppl 8, S8.
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.
H Bigelow & B Rost (2009) Online tools for predicting integral membrane proteins.
Methods Mol Biol 528, 3-23
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.
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.
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.
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.
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.
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
Burkhard Rost
181.
182.
*183.
184.
185.
186.
187.
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.
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.
S Rastogi & B Rost (2010) Bioinformatics predictions of localization and targeting.
Methods Mol Biol 619, 285-305.
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.
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.
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, W523W528.
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.
E2.
E3.
B Rost: Protein fold recognition by merging 1D structure prediction and sequence
alignments. Preprint; 1996; www.rostlab.org/papers/pre1996_topits/
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/
B Rost, SI O'Donoghue and C Sander: Midnight zone of protein structure evolution.
Preprint; 1998; www.rostlab.org/papers/pre1998_midnight/
32
Burkhard Rost
E4.
E5.
E6.
E7.
E8.
E9.
E10.
B Rost: Short yeast ORFs: expressed protein or not? Preprint; 1999;
www.rostlab.org/papers/1999_globe/
B Rost: Neural networks for protein structure prediction: hype or hit? Preprint; 1999;
www.rostlab.org/papers/pre1999_tics/
B Rost and R Schneider: Pedestrian guide to analysing sequence databases.
Preprint; 1999; www.rostlab.org/papers/1999_pedestrian/
R Nair and B Rost: Surface profiles predict sub-cellular localisation. Preprint; 2001;
www.rostlab.org/papers/2001_loci_surface/
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/
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/
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.
W2.
W3.
W4.
W5.
W6.
W7.
W8.
W9.
W10.
W11.
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/
VA Eyrich & B Rost: META-PP: Single-page interface to validated sequence
analysis services. Service; $root/predictprotein/submit_meta.html
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/
R Nair & B Rost: PredictNLS: Prediction and analysis of nuclear localization signals.
Service; $root/services/predictNLS/
P Carter, CAF Andersen & B Rost: DSSPcont: Continuous assignment of protein
secondary structure. Service and database; URL: $root/services/DSSPcont/
S Mika & B Rost: UniqueProt: Creating sequence-unique protein databases. Service;
$root/services/uniqueprot/
J Liu & B Rost: NORSp: Prediction of NOn-Regular Secondary Structure (NORS).
Service; $root/services/NORSp/
A Kernytsky & B Rost: TMH-bench: Evaluate new methods for membrane helix
structure prediction. Service; $root/services/tmh_benchmark/
P Carter, J Liu & B Rost: PEP: Predictions for entire proteomes. Database;
$root/db/PEP/
R Nair & B Rost: NLSdb: Database of nuclear localization signals. Database;
$root/db/NLSdb/
KO Wrzeszczynski & B Rost: CellCycleDB: Archive of proteins involved in cell cycle
control. Database; $root/services/CellCycleDB/
33
Burkhard Rost
W12.
W13.
W14.
W15.
W16.
W17.
W18.
W19.
W20.
W21.
W22.
W23.
W24.
W25.
W26.
W27.
W28.
W29.
R Nair & B Rost: LOC3d: Database of predicted sub-cellular localization for
eukaryotic PDB chains. Database; $root/db/LOC3d/
R Nair & B Rost: LOChom: Database of sub-cellular localization predictions based
on sequence homology. Database; $root/db/LOChom/
S Mika & B Rost: NLProt: Extracting protein names and sequences from scientific
papers. Service; $root/services/NLProt/
R Nair & B Rost: LOCtarget: Prediction of sub-cellular localization for targets in
structural genomics. Database; $root/services/LOCtarget/
KO Wrzeszczynski & B Rost: ERGolgiDB: Archive of proteins from endoplasmic
reticulum and Golgi apparatus. Database; $root/services/ERGolgiDB/
R Nair & B Rost: LOCnet: De novo prediction of sub-cellular localization and
prediction. Service; $root/services/LOCnet/
H Bigelow & B Rost: PROFtmb: Predictions of transmembrane beta barrels.
Service; $root/services/PROFtmb/
M Punta & B Rost: PROFcon08: Predictions of inter-residue contacts. Service;
$root/services/PROFcon08/
J Liu & B Rost: CHOP: Chopping proteins into structural domains. Service;
$root/services/CHOP/
A Schlessinger, Y Ofran, G Yachdav & B Rost: Epitome: Database of structureinferred antigenic epitopes. Database/Service; $root/services/epitome/
G Yachdav, Y Ofran, R Nair, T-T Soong, E Mozes & B Rost: PiNat: Protein
Interaction Annotation Tool. Database/Service; $root/services/pinat/
G Yachdav, Y Ofran, & B Rost: ISIS: protein-protein Interaction Sites Identified from
Sequence. Service; $root/services/isis/
G Yachdav, Y Ofran, & B Rost: DISIS: DNA-protein Interaction Sites Identified from
Sequence. Service; $root/services/disis/
G Yachdav, D Przybylski & B Rost: ConBlast: Consensus Sequence PSI-BLAST.
Database/Service; $root/services/conblast/ (under construction)
G Yachdav, Yana Bromberg & B Rost: SNAP: Screening of Non-Acceptable nonsynonymous Polymorphisms. Service; $root/services/snap/
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/
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)
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:
34
139
Burkhard Rost
Original Peer-reviewed:
Rezensionen:
Buchkapitel:
Tagungsberichte:
Leitartikel:
130
29
27
12
8
Erstautor:
Einzelautor:
Letztautor:
Bücher:
35
31
21
88
1
Burkhard Rost
Liste meiner am häufigsten zitierten Publikationen (Nummerierung wie oben)
Publikationen (Auszug i)
ii Zitat
Nr.
1)
2)
3)
#8
#16
#27
Quelle: ISI Index, August 2010
Letzten 12 Monate Gesamt Impact-Faktor
1993 JMB 232, 584-599
1994 Proteins 19, 55-72
1996 Meth Enzymol 266, 525-539
69
16
33
2158
1180
966
126.9
73.8
69.0
135
12
8
21
59
91
10
48
18
650
558
532
418
409
384
340
322
300
162.5
34.9
35.5
29.9
37.2
64.0
20.0
32.2
18.8
4) #119
5) #19
6) #23
7) #29
8) #42
9) #99
10) #9
11) #49
12) #17
2005 Science 309 1559-1563
1994 CABIOS 10, 53-60
1995 Protein Science 4, 521-533
1996 Protein Science 5, 1704-18
1999 Prot Engng 12, 85-94
2004 NAR 32, W321-W326 (PP 2/Yachdav)
1993 PNAS 90, 7558-7562
2000 EMBO Reports 1, 411-5
1994 Proteins 20, 216-226
13) #57
14) #50
15) #20
16) #70
17) #36
18) #43
19) #59
20) #112
21) #7
22) #67
23) #51
24) #52
25) #82
2002 Proteins 47, 228-235 (pollastri)
2001 J Structural Biology 134, 204-18
1994 JMB 235, 13-26
2003 JMB 325, 377-87 (ofran/six)
1997 JMB 270, 471-80
1999 Proteins 34, 220-3 (SOV)
2002 JMB 318, 595-608 (enzyme)
2005 JMB 348, 85-100 (LOCtree)
1993 Nature Genetics 5, 376-80
2002 Prot Sci 11, 2774-91 - TMH revisited
2001 Protein Science 10, 1970-9 - Proteomes
2001 Bioinformatics 17, 1242-3 - EVA
2003 NAR 31, 3300-4 (PP 1=Liu & rost)
33
16
10
22
6
13
21
31
2
13
15
8
4
293
221
187
164
164
141
137
124
114
113
108
104
101
36.6
24.6
11.7
23.4
12.6
12.8
17.1
24.8
6.7
14.1
12.0
11.6
14.4
26) #66
27) #78
28) #45
29) #11
30) #55
31) #87
32) #5
33) #145
34) #30
35) #123
36) #34
37) #83
2002 JMB 322, 53-64 - Loopy/NORS
2003 FEBS Letters 544, 236-9
1999 JMB 293, 1221-1239 (Olmea)
1993 TIBS 18, 120-123
2002 Proteins 46, 197-205 - Alignments grow
2003 NAR 31, 3311-3315 (EVA)
1992 Nature 360, 540
2007 Proteins 69, 3-9
1996 Ann Rev 25, 113-36
2005 Moult intro Proteins 61, 3-7
1996 Fold & Des 2, S19-S24
2003 NAR 31, 3833-5 (NORSp)
8
15
18
0
5
8
0
82
0
9
6
9
92
91
91
89
88
84
84
82
77
76
76
75
11.5
13.0
8.3
5.2
11.0
12.0
4.7
27.3
5.5
15.2
5.4
10.7
i
ii
Nur Veröffentlichung mit ≥30 Zitaten oder einem Impakt ≥10
Nummer aus der Publikationsliste (hohe Zahlen deuten neuere Veröffentlichungen an)
36
Burkhard Rost
Lfd.Nr.
ii
38) #22
39) #93
40) #37
41) #97
42) #24
43) #74
44) #117
45) #39
46) #68
47) #85
48) #75
49) #56
50) #62
51) #118
52) #105
53) #138
54) #58
55) #35
56) #10
57) #113
58) #139
59) #128
60) #120
61) #103
62) #96
63) #90
64) #89
65) #54
66) #124
67) #107
89) #162
93) #163
96) #169
98) #171
Zitat
Letzten 12 Monate
1995 ISMB
2003 CMLS 60, 2637-50
1998 JMB 276, 517-25 - andrade
2004 NAR 32, 2566-2577 (PROFtmb)
1995 Proteins 23, 295-300
2003 NAR 31, 397-99 (NLSdb)
2005 Bioinformatics 21 2960-2968 (PROFcon)
1998 Structure 6, 259-63
2002 Prot Sci 11, 2836-47 - localization
2003 NAR 31, 3789-91 (uniqueProt)
2003 Curr Opin Chem Biol 7, 5-11
2002 Structure 10, 175-184
2002 Bioinformatics 18, 922-933
2005 Proteins 61 115-126 - PROFbval
2004 NAR 32, 3522-3530 (CHOPnet)
2007 NAR 35, 3823-3835
2002 Structure 10, 435-440 (renom reliability)
1997 CABIOS/Bioinformatics 13, 345-56
1993 Protein Engineering 6, 831-836
2005 JMB 348 507-512 (folding rates)
2007 PLOS CB 3, 1169-1176 (hotspots)
2006 PLOS CB 2, 698-709 - Mika/Interactions
2005 Drug Disc Today 10 1475-1482
2004 Proteins 56, 188-200 (NESG)
2004 Proteins 55, 678-688 (CHOP)
2003 Proteins 53, 917-30 - localiation
2003 NAR 31, 3293-5 (DSSPcont)
2001 Proteins 45, 192-199
2005 Proteins 61, 214-224 (Grana/CASP6/cont)
2004 JMB 341, 255-269 (AGAPE)
2009 Nature Biotechnology 27, 51-57
2009 PLOS One 4
2009 Structure 17, 869-881
2009 Proteins 77, 1-4
iv
Alle 186 Publikationen:
iv
138 Erster/Letzter Autor (aufgelistete Papers)
ii
iii
iv
0
21
6
14
0
0
13
0
6
6
3
7
0
13
3
42
3
1
41
11
22
12
6
4
3
4
5
5
31
3
13
12
11
10
Summe
14.315
12.069
Gesamt
73 iii
68
66
65
64
62
55
55
53
51
51
47
45
44
44
42
43
42
41
39
38
37
36
36
36
34
33
33
31
31
13
12
11
10
Impact-Faktor
12.2
9.7
5.5
10.8
4.3
8.9
11.0
4.6
6.6
7.3
7.3
5.9
5.6
8.8
7.3
14.0
5.4
3.2
2.4
7.8
12.7
9.3
7.2
6.0
6.0
4.9
4.7
3.7
6.2
5.2
13.0
12.0
11.0
10.0
Durchschnittl. Zitierungen
77
88
Nummer aus der Publikationsliste (hohe Zahlen deuten neuere Veröffentlichungen an)
Zahlen von Feb. 2001, seitdem nicht mehr in ISI aufgeführt.
Mittelwerte sind über ALLE Veröffentlichungen in der Publikationsliste berechnet; viele
Veröffentlichungen sind nicht in ISI aufgeführt.
37
Burkhard Rost
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
Burkhard Rost
Webservers und öffentliche Ressourcen
Bitte beachten Sie, dass die folgenden Tools auf unserer Website veröffentlicht
werden ◊: http://www.rostlab.org
PredictProtein
AGAPE*
CellCycleDB
CHOP/
CHOPnet*
CLUP*
ConBLAST*
DISIS*
DSSPcont*
Epitome*
ERGolgiDB
EVA*
GenTegrate*
ISIS*
LOCdb*
LOCtree*
MD*
META-PP*
NLProt*
NLSdb*
NORSnet*
NORSp*
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, PSIBLAST, 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*).
Fold recognition without folds: Improved and generalized method for sequenceprofile and profile-profile comparisons using sequence and predicted 1D structure
(secondary structure and accessibility).
Database collecting and annotating proteins involved in cell-cycle control
Method chopping proteins into structural domain-like fragments and database for
62 entirely sequence proteomes.
Database with clusters of CHOP* fragments.
Aligning proteins through consensus motifs – simple add-on to the popular
BLAST/PSI-BLAST methods.
Prediction of protein-DNA interactions.
Server and database for continuous secondary structure assignment from PDB files.
Database of structure-inferred antigenic epitopes.
Archive of proteins from endoplasmic reticulum and Golgi apparatus.
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).
Prediction of residues involved in external protein-protein interactions.
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).
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*).
MetaDisorder prediction – method to predict natively unstructured/disordered
regions through a combination of original methods, including PROFbval,
NORSnet, Ucon, IUpred, DISOpred.
Common interface that simplifies the access to a battery of high-quality public
protein structure and function prediction servers.
Automatic identification of protein names in scientific literature.
Database of nuclear localization and DNA-binding motifs.
Neural network based prediction of disordered/natively unstructured regions
dominated by loops in the non-bound state.
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
Burkhard Rost
PEP*
PiNat*
PredictNLS*
PROFacc*
PROFcon08*
PROFsec*
PROFtmb*
SNAP*
TMH-bench*
Ucon*
UniqueProt*
no helix or strand over at least 70 consecutive residues) and database with
predictions for entire proteomes.
Database with alignments and predictions for 62 entirely sequenced proteomes
(interfaced by the Sequence-Retrieval-System SRS).
Protein interaction annotation tool combining a lookup of experimental interactions
with predictions and annotations of localization and from the GeneOntology
Interactive assessment of selectivity and sensitivity for nuclear localization signals.
Improved prediction of solvent accessibility.
Prediction of inter-residue contacts (preliminary version).
Improved prediction of secondary structure.
Prediction of beta-membrane proteins.
Prediction of effects on protein function of SNPs (non-synonymous single
nucleotide polymorphism)
Static benchmark to test novel methods or propensity scales (hydrophobicity
indices) for membrane helix prediction.
Prediction of natively unstructured (disordered) regions through the prediction of
inter-residue contacts.
Creates representative subsets from a limited set of protein sequences.
40

rost CV in German

Transcription

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