CV Burkhard Rost

Burkhard Rost CV

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BURKHARD ROST TUM Informatics/Bioinformatics i12 Boltzmannstrasse 3 (Rm 01.09.052) 85748 Garching/München, Germany & Dept. Biochemistry & Molecular Biophysics Columbia University New York, USA

Email [email protected] Tel +49-89-289-17-811 Web www.rostlab.org Fax +49-89-289-19-414

Photo: © Eckert & Heddergott, TUM

Document:

CV Burkhard Rost TU München Affiliation: Columbia University

TOC: • Tabulated curriculum vitae • Grants • List of publications

Highlights by numbers: • 186 invited talks in 29 countries (incl. TedX) • 250 publications (187 peer-review, 168 first/last author) • Google Scholar 2016/01: 30,502 citations, h-index=80, i10=179 • PredictProtein 1st Internet server in mol. biol. (since 1992) • 8 years ISCB President (International Society for Computational Biology) • 143 trained (29% female, 50% foreigners from 32 nations on 6 continents)

Brief narrative: Burkhard Rost obtained his doctoral degree (Dr. rer. nat.) from the Univ. of Heidelberg (Germany) in the field of theoretical physics. He began his research working on the thermo-dynamical properties of spin glasses and brain-like artificial neural networks. A short project on peace/arms control research sketched a simple, non-intrusive sensor networks to monitor aircraft (1988-1990). He entered the field of molecular biology at the European Molecular Biology Laboratory (EMBL, Heidelberg, Germany, 1990-1995), spent a year at the European Bioinformatics Institute (EBI, Hinxton, Cambridgshire, England, 1995), returned to the EMBL (1996-1998), joined the company LION Biosciences for a brief interim (1998), became faculty in the Medical School of Columbia University in 1998, and joined the TUM Munich to become an Alexander von Humboldt professor in 2009. In 1992, Dr. Rost developed the first Internet server for protein structure prediction (PredictProtein). Since, his group has contributed many highly used and original methods for the prediction of aspects of protein function and structure. His major contribution has been the combination of machine learning and evolutionary information. His academic research goal focuses on the development of top tools that can be applied in the context of analyzing entirely sequence organisms. Recently, has been focusing on the analysis of the effects of sequence variation and their implications for precision medicine and personalized health. Details: http://www.rostlab.org/

status Jan 19, 2016

Burkhard Rost Tabulated CV

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Tabulated Curriculum Vitae Date of preparation: Jan 19, 2016 Name: Burkhard Rost Gender: Male Marital Status: Married with one daughter (born Dec. 2002) Citizenship: German Birthplace: Northeim, Lower-Saxony, Germany Current position: Professor, Unit chair Address TUM, Department for Computer Sciences (Informatik)

Unit for Bioinformatics & Computational Biology (i12) Boltzmannstrasse 3, 85748 Garching/Munich, Germany tel.: +49-89-289-17-811 email: [email protected]

Education 1971-1980 High school, Herzberg, Lower-Saxony, Germany 1980-1982 Obligatory service in German air force

1982-1985 Study of physics at Justus-Liebig-University Gießen, Hessia, Germany 10/1984 Bachelor in physics 1985-1988 Study of physics at Ruprecht-Karls-University Heidelberg, Germany 1985-1988 Study of philosophy, history and psychology at Heidelberg University 1986-1988 Master thesis at the Institute of Theoretical Physics, Heidelberg Univ. Topic: 'Learning algorithms for spin-glass-like neural networks' Sponsor: Prof. Dr. Heinz Horner, Heidelberg 11/1988 Bachelor in philosophy and history, Heidelberg University 12/1988 Master in physics, Heidelberg University

12/88-06/90 Grant of the 'Stiftung Volkswagenwerk' (VW Foundation), Inst. Theor. Physics, Heidelberg

Topic: 'Theoretical analysis of the possibilities of seismic and acoustical sensor networks to verify arms control treaties for aircraft'

07-10/89 Research project in the USA (Princeton, Washington DC, MIT) 1990-1993 Completing studies in physics, Heidelberg Univ. and EMBL, Germany 07/1993 Writing PhD thesis Topic: 'Neural networks and evolution - prediction of protein secondary structure' Sponsor: none ◊ 07/1994 PhD in physics: Viva voce for Dr. rer. nat. (Doctor rerum naturarum) at

Institute for Theoretical Physics, Ruprecht-Karl University Heidelberg, Germany

◊ Over 600 years, Heidelberg University has allowed scholars to present a doctoral thesis on any

research subject independent of any sponsor. Apparently, I was the first who exercised this right over at least the last 60 years.


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Professional Positions 1986-1988 Assistant at Institute for Theoretical Physics, Heidelberg Univ., Germany 12/88-06/90 Research fellow at Inst. for Theoretical Physics, Heidelberg Univ. 07-10/1989 Visitor at Institutes in the USA (Princeton, U. of Concerned Scientists, MIT) 07/90- 1992 Visitor at EMBL Heidelberg, Germany 07/93-12/94 Research fellow at EMBL Heidelberg, Germany 01/95-12/95 Research fellow at EBI Hinxton, Cambridge, England 01/96- 04/98 Research fellow at EMBL Heidelberg, Germany 05/98-11/98 Researcher at LION Biosciences Heidelberg, Germany 12/98- 05/00 Assistant Professor at Department of Biochemistry and Molecular

Biophysics, Columbia University, New York, USA 07/2000-2010 Associate Professor at Dept. of Biochemistry & Mol. Biophys., Columbia 2004-2010 Affiliated Faculty, Dept. of Medical Bioinformatics, Columbia University 2002-2010 Faculty Center of Computational Biology and Bioinformatics (C2B2) 07/2005-2010 Tenure in Dept. of Biochemistry and Mol. Biophysics at Columbia University 2006-2010 Associated Faculty in the Department of Pharmacology at Columbia Univ. 2006-2010 Associated Faculty in the Irving Center of Cancer Research at Columbia since 06/2009 Alexander von Humboldt Professor in Department for Computer Sciences at

the TUM Munich, Germany since 06/2009 Fellow at the Institute for Advanced Studies, IAS-TUM, Germany since 02/2012 Affiliate Prof., Inst. Food & Plant Sciences WZW - Weihenstephan, Germany

Professional Organizations and Societies 1995-now Program Committee of ISMB (Intelligent Systems for Molecular Biology) 1996-now Member of ISCB (International Society for Computational Biology) 2002-now Board of Directors ISCB (International Society for Computational Biology) 2002-now Member of NYAS (New York Academy of Sciences) 2005-2006 Vice President ISCB (International Soc. for Computational Biology) 2006 President Elect of ISCB (International Society for Computational Biology) 2007-2014 President of the ISCB (International Society for Computational Biology)

Professional Experiences 1992-now Over 500 referee reports for peer-reviewed journals (including Nature,

Science, PNAS, Cell, EMBO J) 1995-now Over 50 reviews of grants from individuals and institutes (countries: Austria,

Canada, Denmark, England, Germany, Israel, Italy, Norway, Netherlands, Singapore, Spain, Sweden, Switzerland, USA); ad hoc panels for NIH and NSF, including role as chairman.

2001-now Ad-hoc panels for grants from the NIH, NSF and the European Community 2005-2009 Associate Editor of PLoS Computational Biology 2006-now Associate Editor of Bioinformatics 2006-now Associate Editor of Proteins: Structure, Function, and Bioinformatics 2009-now Deputy Editor of PLoS Computational Biology


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2005-now Editorial Board of FASEB (representative from ISCB) 2006-now Editorial Board of Journal of Structural and Functional Genomics 2007-now Editorial Board of Bioinformatics and Biology Insights 2001-2006 Editorial Board of Journal of Medical Informatics 2002, 2005 Editor for ISMB (Intelligent Systems for Molecular Biology) proceedings 2004-2006 Editorial Board of Proteins: Structure, Function, and Bioinformatics 2005-2006 Editorial Board of Bioinformatics 2002-2007 Organization of New York Computational Biology Society in the New York

Academy of Sciences 1999-2005 SAB for company LION Biosciences, Heidelberg/Cambridge UK 2004-now Co-founder, CEO of BioSof, Delaware, USA

Invited Talks (186 invited talks in 29 countries) 12/1988 London, England: Workshop on Arms Control 09/1989 Washington, DC, USA: Union of Concerned Scientists 10/1989 Princeton, USA: Institute for Advanced Studies 05/1990 Prague, CSFR: Workshop on Arms Control 09/1990 Vienna, Austria: Conference on Arms Control 010/1990 Mosbach, Germany: Conference on Arms Control

06/1992 Elba, Italy: Conference on Neural Networks 07/1992 Torino, Italy: Conference on Protein Structure Prediction 11/1992 Nijmegen, Netherlands: EU Conference on Sequence Analysis

06/1993 Rennes, France: Workshop on Secondary Structure Prediction 11/1993 Copenhagen, DK: Conf. on 'Protein Structure by Distance Analysis'

01/1994 Mauii, Hawaii, USA: HICCS Conference 03/1994 Bologna, Italy: Conference on Protein Structures 04/1994 Copenhagen, Denmark: Mini-symposium on structure prediction 11/1994 Bielefeld, Germany: University 11/1994 Copenhagen, DK: Conf. on 'Protein Structure by Distance Analysis' 12/1994 Asilomar, USA: CASP1

06/1995 Cambridge, England: ISMB'95 (Tutorial) 06/1995 Heidelberg, Germany: University 10/1995 Bressanone, Italy: Workshop on Protein Structures 10/1995 IRBM Rome, Italy: Workshop 'Frontiers of protein structure prediction' 11/1995 Paris, France: Workshop on Protein Structures and Drug Design

06/1996 St. Louis, USA: ISMB'96 08/1996 Madrid, Spain: CNB 10/1996 Heidelberg, Germany: University 11/1996 Copenhagen, Denmark: Protein Structure by Distance Analysis 12/1996 New York, USA: Columbia University 12/1996 Asilomar, USA: University of San Francisco


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01/1997 Jerusalem, Israel: UNESCO workshop on sequence analysis 02/1997 Basel, Switzerland: CIBA-Geigy 02/1997 EBI Hinxton, England: Workshop on protein structure prediction 03/1997 Copenhagen, Denmark: CBS University 03/1997 New York, USA: Columbia University 06/1997 Berlin, Germany: Inst. for Theor. Biol. 06/1997 Chalkidiki, Greece: ISMB'97 (Tutorial) 07/1997 EBI Hinxton, England: EMBO Workshop on protein sequence analysis 07/1997 San Sebastian, Spain: Proteins: integration of life's function 07/1997 Madrid, Spain: CNB 09/1997 Skövde, Sweden: Computing and Emergent Computation 09/1997 Vienna, Austria: Intern Conf on Molecular Structural Biology 10/1997 IRBM Rome, Italy: Frontiers of protein structure prediction 11/1997 Stockholm, Sweden: Pharmacia & Upjohn 11/1997 Stockholm, Sweden: Karolinska Inst. 12/1997 Paris, France: Pasteur Inst. 12/1997 Toulouse, France: INRA Inst. 12/1997 Toulouse, France: Elf Sanofi 12/1997 Basel, CH: Bioinformatics: from Exp. to Biol. Knowledge

03/1998 Marseille, France: Cancer Inst., INSERM/19CNRS 05/1998 Tallberg, Sweden: Annual meeting of Swedish Structural Biology 05/1998 Bad Honnef, Germany: Scientific Applications of Neural Nets 06/1998 New York, USA: Genome Centre, Workshop 10/1998 Cambridge, England: Newton Inst. Biomolecular Function and Evolution in

the Context of the Genome Project 10/1998 EBI, England: Methods for protein structure

07/1999 Havanna, Cuba: CIGB EMBO Workshop Bioinformatics 08/1999 Cambridge, England: Protein motifs and families 09/1999 Graz, Austria: International Meeting of Austrian Society for Genetics. 10/1999 Bologna, Italy: Protein sequence analysis in the genome era 11/1999 Atlanta, USA: In silico biology: sequence & structure & function

02/2000 Boston, USA: SGI Workshop: New Technologies for Discovery Research 02/2000 New York Structural Biology Society, USA 08/2000 Troy RPI, USA: Bioinformatics Workshop 08/2000 Madrid, Spain: Human Genome Workshop 08/2000 New York University, USA 10/2000 Heidelberg, Germany: LION's Bioinformatics 2000 12/2000 Asilomar, USA: CASP4

03/2001 Madrid, Spain: Workshop on structural genomics 03/2001 Madrid, Spain: CNB 04/2001 New York, USA: Rockefeller University 05/2001 New York, USA: New York Structural Biology Society


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05/2001 New York, USA: Columbia University, Dept. Biology 07/2001 Copenhagen, Denmark: DTH 07/2001 Heidelberg, Germany: University 09/2001 Il Ciocco, Italy: NATO summer school on bioinformatics (Talk, Teacher) 09/2001 IRBM Rome, Italy

01/2002 Breckenridge, USA: Keystone Symposium on Structural Genomics 04/2002 Madrid, Spain: Meeting on Bioinformatics and Computational Biology 04/2002 Basel, Switzerland: Talk at Biocenter Basel 05/2002 Erice, Italy: Summer school on structural biology 06/2002 San Diego, USA: 11th Annual Bioinformatics and Genome Research 06/2002 Rutgers University, USA: 'Northeast Structural Genomics Consortium Annual

Symposium' 07/2002 New York, USA: New York Academy of Sciences 08/2002 Edmonton, Canada: ISMB'2002 08/2002 Habanna, Cuba: Bioinformatica-Habana 10/2002 Lausanne, Switzerland: EPFL/Univ. Lausanne 11/2002 Toronto, Canada: Institute for Proteomics and Bioinformatics

02/2003 New York, USA: Fordham University 02/2003 Piscataway, USA: CABM, Rutgers University 02/2003 New York, USA: Manhattan College 05/2003 New York, USA: City College 10/2003 Bethesda, NIH, USA: Keynote at Workshop on Comparative modeling 11/2003 Bethesda, NIH, USA: Workshop on Target Selection in Structural Genomics 11/2003 Piscataway, USA: Rutgers University

02/2004 Ventura CA, USA: Gordon Conf. Structural, Functional & Evolutionary Genomics

06/2004 Heriman NY, USA: NESG Retreat - Arden House 07/2004 Zuerich, Switzerland: ETH 07/2004 Lausanne, Switzerland: EPFL 07/2004 Glasgow, Scotland: Meeting on data mining 07/2004 Glasgow, Scotland: Meeting on genome annotation 07/2004 Glasgow, Scotland: ISMB - Review of field 11/2004 Rome, Italy: La Sapienza University 11/2004 Washington DC, USA: Interntl. Conference on Structural Genomics (ICSG)

09/2005 Chicago, USA : Structural genomics workshop on target selection 11/2005 Piscataway, USA: RCSB workshop on homology modeling, Rutgers 12/2005 Bethesda, NIH, USA: Structural genomics workshop on target selection 12/2005 Paris, France: INRA, Univ. of Evry

01/2006 Munich, Germany: Seminar at TUM 02/2006 Keystone, USA: Keystone Meeting on structural genomics 05/2006 Piscataway, USA (Rutgers): Approaches to Predict Protein Function


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06/2006 Bethesda, NIH, USA: Target Selection for Structural Genomics 08/2006 Fortalezza, Brazil: SWISS-PROT 20 years

01/2007 Eilat, Israel: ECCB: 5th European Conf. for Comp. Biology 01/2007 Eilat, Israel: BIOSAPIENS Workshop on protein function prediction 07/2007 Vienna, Austria: SIG 3D 08/2007 Hong Kong, China: InCoB - 6th International Conference on Bioinformatics 04/2008 Princeton, USA: NESG retreat 05/2008 New Paltz, USA: Mohonk cBio Retreat 06/2008 Paris, France: Pasteur 07/2008 Toronto, Canada: ISMB Student Council 12/2008 Sardinia, Italy: CASP8

03/2009 San Francisco, USA: AMIA 05/2009 Berlin, Germany: Humboldt University 06/2009 Stockholm, Sweden: ISMB/ECCB 2009 12/2009 Bamako, Mali: Bioinformatics of African Pathogens

01/2010 Tegernsee, Germany: Ringberg meeting (Academia meets industry) 03/2010 Montevideo, Uruguay: ISCB-Latin America 04/2010 Starnberger See, Germany: IAS Retreat 04/2010 Weihenstephan, Germany: TUM/WZW 04/2010 Tegernsee, Germany: Machine Learning, Schloss Ringberg 05/2010 Garching, Germany: Lange Nacht der Wissenschaft/Kirchentag 05/2010 Bayreuth, Germany: University 07/2010 Martinsried, Germany: Max-Planck Inst. 07/2010 Boston, USA: ISMB 07/2010 New York, USA: City College 09/2010 Erice, Italy: Optimization, Machine Learning and Bioinformatics 09/2010 Gent, Belgium: ECCB 10/2010 San Diego, USA: UCSD 11/2010 Salzburg, Austria: Univ. 11/2010 Basel, Switzerland: Biocenter

01/2011 Madrid, Spain 03/2011 Cape Town, South Africa: ISCB-Africa/ASBCB 04/2011 Saarbruecken, Germany: Univ. / Max-Planck Inst. 04/2011 Leipzig, Germany: MPI Evolutionary Anthropology 05/2011 Tuebingen, Germany: Max-Planck Inst. 05/2011 Spitzingsee, Germany: GSISH/TUM 06/2011 Amsterdam, Netherlands 06/2011 Berlin, Germany 07/2011 Vienna, Austria: SIG 07/2011 Vienna, Austria: ISMB/ECCB 10/2011 Toulouse, France: Sanofi 12/2011 Kuala Lumpur, Malaysia: InCoB/ISCB-Asia


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12/2011 Luxembourg: BBC11: BeNeLux Bioinformatics

01/2012 Weihenstephan, Germany: WZW/TUM 01/2012 Munich, Germany: Helmholtz Zentrum 03/2012 Santiago, Chile: ISCB-Latin America 2 03/2012 Innsbruck, Austria: Genau Workshop 05/2012 Jerusalem, Israel: Hebrew Univ 05/2012 Tel Aviv, Israel: Univ 05/2012 Bar Ilan, Israel: Bar Ilan Univ 05/2012 Rehovot, Israel: Weizman Inst 06/2012 Stockholm, Sweden: Conf on Protein interactions 07/2012 Long Beach, USA: ISMB 09/2012 Basel, Switzerland: ECCB 10/2012 Potsdam, Germany: AGD: From genomes to networks 10/2012 Paris, France: Pasteur Inst 11/2012 New York, USA: New York Structural Biology Center 11/2012 Saarbruecken, Germany: Max-Planck Inst 12/2012 Shenzhen, China: ISCB-Asia/SCCG 2012

01/2013 Kiel, Germany: Inst. for Clinical Molecular Biology, Univ. Hospital 03/2013 Casablanca, Morocco: ISCB Africa ASBCB Conference on Bioinformatics 05/2013 Valencia, Spain: Next NGS Challenge 07/2013 Berlin, Germany: ISMB/ECCB 09/2013 Seoul, South Korea: ISCB-Asia/Translational Bioinformatics Conf. 10/2013 Luxembourg: Univ 11/2013 New York, USA: NYCOMPS annual

05/2014 Mainz, Germany: 30 years informatics 06/2014 Barcelona, Spain: NGS conference 07/2014 Boston, USA: ISMB 09/2014 Istanbul, Turkey: Bridging experiments and computations 10/2014 Belo Horizonte, Brazil: ISCB – Latin America 3 11/2014 New York, USA: NYCOMPS annual 12/2014 Tokyo, Japan: GIW & ISCB – Asia 4

03/2015 Dar es Salaam, Tanzania: ASBCB & ISCB-Africa 4 07/2015 Dublin, Ireland: ISMB/ECCB

Professional Award 2009-2015 Alexander von Humboldt Professorship, Germany 2012 Bat Sheva Fellowship, Israel


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Organization of International Scientific Meetings (48) 09/1990 Co-organizing 'The Second Workshop on Verification of Arms Reductions',

3-5 Sep. 1990, Vienna, Austria 06/1995 Program committee for 3rd ISMB, Cambridge, England 07/1996 Program committee for 4th ISMB, Halkidiki, Greece 02/1997 Organizing the workshop 'Methods for protein structure prediction - progress

and limitations' for Pharmaceutical Companies, 10-11 Feb., 1997, EBI Hinxton-Cambridge, England

07/1997 Program committee for 5th ISMB, St. Louis, USA 07/1998 Program committee for 6th ISMB, Montreal, Canada 08/1999 Organizing the workshop ‘Protein motifs and families in practice: Is protein

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

08/1999 Program committee for 7th ISMB, Heidelberg, Germany 10/1999 Program committee of the 2nd Bologna summer school on biotechnology

'Protein sequence analysis in the genome era', Bologna, Italy 07/2000 Program committee for 8th ISMB, San Diego, USA 12/2000 Co-organizing the CAFASP sessions at CASP meeting in Asilomar, CA 03/2001 Co-organizing bioinformatics competition of LION Biosciences, Boston 03/2001 Co-organizing Juan March workshop on structural genomics in Madrid,

Spain 07/2001 Program committee for 9th ISMB, Copenhagen, Denmark 02/2002 Program committee of the 3rd "International Meeting on Membrane proteins

in Bologna, Italy 06/2002 Program committee meeting on computational biology Manchester England 08/2002 Co-organizing 10th International Meeting on 'Intelligent Systems in Molecular

Biology' in Edmonton Canada (1500 participants; most important meeting in bioinformatics)

06/2003 Scientific Advisory Board, Editor, and Program Committee for 11th ISMB 2003 in Brisbane, Australia

11/2003 Co-organizing NIH workshop on 'Target selection for structural genomics' 06/2003 Scientific Advisory Board, Editor, and Program Committee for 12th ISMB

2004 in Glasgow, Scotland (>2,200 participants) 12/2004 Co-organizing meeting for the Critical Assessment of protein Structure

Prediction (CASP6) in Italy (most important meeting in the field of structure prediction)

06/2005 Co-Chair of Program Committee, Member of Scientific Advisory Board, and Editor for 13th ISMB 2005 in Detroit, USA (> 2500 participants expected)

12/2005 Co-organizing NIH workshop on ‘Target selection for structural genomics' 05/2006 Co-organizing CASP6.5 workshop (New York) 06/2006 Co-organizing NIH workshop on ‘Target selection and homology modeling’

(Bethesda, NIH) 12/2006 Co-organizing meeting for the Critical Assessment of protein Structure

Prediction (CASP7) in Asilomar, CA (most important meeting in the field of structure prediction)


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07/2007 ISMB/ECCB Vienna: Co-chair of 15th International Meeting on Intelligent Systems in Molecular Biology (ISMB) and Fifth European Conference of Computational Biology (ECCB) in Vienna Austria (most important meeting in bioinformatics), Chair of Highlight Track at ISMB/ECCB

07/2008 ISMB Toronto: Chair of 16th International Meeting on 'Intelligent Systems in Molecular Biology' (ISMB) in Toronto, Canada (most important meeting in bioinformatics in 2008), Chair of Highlights Track at ISMB 2008

12/2008 Co-organizing CASP8 in Sardinia, Italy 07/2009 ISMB/ECCB Stockholm: Scientific Organizing Committee & Chair of

Scientific Steering Committee 12/2009 Steering Committee for 1st ISCB-Africa/ASBCB, Bamako, Mali 03/2010 Steering Committee for 1st ISCB-Latin America, Montevideo, Uruguay 07/2010 ISMB 2010, Boston: Chair of Highlights Track & Chair of Scientific Steering

Committee 07/2011 Organizing Committee for SIG on Function Prediction (CAFA), Vienna 2011 07/2011 ISMB/ECCB 2011, Vienna, Austria: Chair of Meeting, Chair of Scientific

Steering Committee & Chair of Highlights Track 03/2011 Steering Committee for 2nd ISCB-Africa/ASBCB, Cape Town, South Africa 12/2011 Steering Committee for 1st ISCB-Asia/InCoB, Kuala Lumpur, Malaysia 03/2012 Steering Committee for 2nd ISCB-Latin America, Santiago, Chile 07/2012 ISMB 2012, Long Beach, USA: Chair of Meeting, Chair of Scientific Steering

Committee & Chair of Highlights Track 12/2012 Steering Committee for 2nd ISCB-Asia, Shenzhen, China 03/2013 Steering Committee for 3rd ISCB-Africa/ASBCB 4, Casablanca, Morocco 07/2013 ISMB/ECCB 2013, Berlin, Germany: Chair of Meeting, Chair of Scientific

Steering Committee & Chair of Highlights Track 10/2013 Steering Committee for TBC 2013 & 3rd ISCB-Asia, Seoul, South Korea 07/2014 ISMB 2014, Boston, USA: Scientific Steering Committee & Chair of

Highlights Track 10/2014 Steering Committee for 3rd ISCB-Latin America, Rio De Janeiro, Brazil 12/2014 Steering Committee for GIW 2013 & 4th ISCB-Asia, Tokyo, Japan 03/2015 Steering Committee for 4th ISCB-Africa & ASBCB 5, Dar es Salaam,

Tanzania 07/2015 ISMB/ECCB 2015, Dublin, Ireland: Scientific Steering Committee & Chair of

Highlights Track

Collaborations

Almost complete list of 809 co-authors (1993-2016) Mariam Abashidze, Thomas Abeel, Dominik Achten, Tom B Acton, Alexei A Adzhubei, Nadeem Ahmed, V Aidinis, JE Allen, Uwe Altermann, A Ambesi-Impiombato, Claus AF Andersen, Miguel A Andrade, Philip Angerer, C Angermuller, Sonja Ansorge, Christian Anthon, J Aoki, Rolf Apweiler, T Arakawa, James M Aramini, Chiara Ardiccioni, DL Armstrong, S Ashkenazi, H Ashkenazy, Zahra Assur, H S Atreya, RN Aturaliya, Florian Auer, E Auff, K B Avraham, Patricia C Babbitt, M Madan Babu, Timothy L Bailey, Amos Bairoch, VB Bajic, David Baker, Kinga Balasz, Pierre Baldi, Surajit Banerjee, M Bansal, Michael C Baran, C Barret, Geoff Barton, S Batalov, Alex Bateman, L Baxter, Niall Beard, KW Beisel, Adam Belachew, A Ben-Hur, Nir Ben-Tal, Jordi Benach, A Benet-Pages, Bonnie Berger, Karel Berka, Helen M Berman, Michael Bernhofer, T Bersano, Claudia Bertonati, Alexander Betz, P Bhat, Henry Bigelow, J Bjorne, Arianne Boehm, J Bohon, Dan Bolser, H Bono, Tim Booth, Peer Bork, M Bosnjak, Phil E Bourne, CJ ter Braak, Ana Bracic, T Braun, Stephen E Brenner, Anthony Bretaudeau, Jan Brezovsky, B


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Brokowski, Yana Bromberg, T Brucke, Soeren Brunak, Renato Bruni, V Brusic, Stephen H Bryant, K Bryson, DW Buchan, Michael J Buckley, C Bult, Stephen K Burley, FA Buske, Christiane Buta, M Camacho-Perez, Yu Cao, Piero Carninci, Phil Carter, Rita Casadio, Juan Miguel Cejuela, A Ceroni, Gianni Cesareni, AM Chalk, Mark R Chance, GA Chang, Chien Peter Chen, J Cheng, Y Chiang, M Chitale, KP Chiu, Piotr Chmura, JJ Chou, S Choudhary, Alan Christoffels, M Ciano, C Ciccosanti, Laura Cizmadija, W T Clark, Oliver B Clarke, DR Clutterbuck, Murat Cokol, H M Colecraft, S Collins, L J Colwell, B Cooper, Frederik Coppens, Michael Cornell, M Corpas, J R Cort, D Cozzetto, S Crouch, ML Crowe, Gianmauro Cuccuru, James Cuff, Kellie Cunningham, R D'Mello, E Dalla, BP Dalrymple, David Dao, Kalyan Das, A Datta, Kristian Davidsen, MJ Davis, B de Bono, Victor de la Torre, Lluis Ribas de Pouplana, George T De Titta, G Della Gatta, Gianluca Della Vedova, NG Denissova, Mehabaw Getahun Derebe, BH Dessailly, F Dey, D Di Bernardo, B Di Camillo, Tomas Di Domenico, N Djuric, Kieu Trinh Do, Tunca Dogan, S Domke, Y Arthur Dong, Olivia Doppelt-Azeroual, T Down, ME Dumont, Roland L Dunbrack, S Dzeroski, T Eberlein, Nathaniel Echols, SH Eck, William C Edstrom, M Eichner, Miriam Eisenstein, A Eletsky, Arne Elofsson, Laura Emery, P Engstrom, S Erdin, Asli Ertekin, J Ertl, J Everett, Volker A Eyrich, M Fagiolini, Eduardo Fajardo, M Falda, H Fang, Piero Fariselli, G Faulkner, Ariel Feiglin, A Felies, Krzysztof Fidelis, Daniel Fischer, Andras Fiser, Ola Fjellstroem, CF Fletcher, Hannes Floeckner, T Foki, P Fontana, Farhad Forouhar, Alistair RR Forrest, BG Fox, Joachim Frank, M Franz, Paolo Frasconi, Rune Moellegaard Friborg, Iddo Friedberg, Martin C Frith, P Fromme, S Fukuda, T Fukushima, C Funk, M Furuno, S Futaki, Anthony H Futerman, Terry Gaasterland, CA Galea, A Garcia, M Gariboldi, Zofia Gasik, Elisabeth Gasteiger, Thomas Gatter, F Gatzmann, P Georgii-Hemming, Julia Gerke, Mark Gerstein, Thomas R Gingeras, C Ginter, Mark Girvin, Janice Glasgow, Brian S Gloss, A Godzik, T Gojobori, Tatyana Goldberg, Sharon Goldsmith-Fischman, Q Gong, Eric Gouaux, Julian Gough, E Graf, K Graim, Osvaldo Grana, RE Green, Robert Greil, SM Grimmond, Marie Grosjean, J Guenter Grossmann, Bjoern Gruening, BA Gruning, Ziqiang Guan, Y Guo, S Gustincich, Martina Haasemann, T Haliloglu, K Hamilton, Christopher J Hammang, Tobias Hamp, Samuel K Handelman, Jan Hansen, M Harbers, Jayson Harshbarger, A Harutyunyan, CS Hassler, M Hastreiter, D Haubenberger, Y Hayashi, Y Hayashizaki, M Hecht, Hedi Hegyi, Julian Heinrich, Manuela Helmer-Citterich, Katharina Hembach, Wayne A Hendrickson, Kim Henrick, TK Hensch, M Heron, M Herzog, Bernhard Heymann, W Hide, A A High, D Hill, Brandan Hillerich, N Hirokawa, Chi Kent Ho, M Hoins, Lisa Holm, LM Holtz, Barry Honig, Peter Honigschmid, Thomas A Hopf, CJ Hoppe, Paul Horton, C Hotzy, Lei Hu, Hua Huang, Tim Hubbard, DA Hume, L Huminiecki, John F Hunt, M Iacono, Hans Ienasescu, J Iida, K Ikeo, K Imamura, H Inamdar, Masayoiri Inouye, D Inupakutika, Vassilios Ioannidis, T Ishikawa, Jon Ison, Habon A Issa, Masayoshi Itoh, A Iwama, H V Jagadish, M Jakt, H Janjua, L Jaroszewski, Jonathan A Javitch, Martin Closter Jespersen, Mei Jiang, Rafael Jimenez, Xiangshu Jin, Andrzej Joachimiak, Vadim Joerdens, Flemming Steen Joergensen, U John, David Jones, EM Jorgensen, R Joshi, Igor Jurisica, Nick Juty, Peter Juvan, Venkataraman Kabaleeswaran, Peter C Kahn, C Kai, Laszlo Kajan, Matus Kalas, RC Kalathur, Maria Kalemanov, M Kanamori-Katayama, A Kanapin, Sreenivas Kanugula, Tim Karl, R Karlin, Peter D Karp, Kevin J Karplus, Rebecca Kassner, T Kasukawa, S Katayama, T Kato, M Katoh, R Katzenschlager, S Kaufmann, N Kawagashira, J Kawai, Hideya Kawaji, Y Kawasawa, T Kawashima, LA Kelley, Janet Kelso, Michael A Kennedy, Andrew Kernytsky, Michael Kiening, D Kihara, Ross King, H Kitamura, H Kitano, N Klopp, Edda Kloppmann, Brian Kloss, M Kluge, Maximilian Koch, R Kodzius, Ingrid YY Koh, M Kojima, G Kollias, S Kondo, H Konno, Gregory Kornhaber, P Koskinen, DM Kottmeier, A Kouranov, YA Kourmpetis, D Kovats, R Kralovics, SA Kranz, SPT Krishnan, Richard W Kriwacki, M Krol, D Krompass, A Kruger, Andriy Kryshtafovych, SK Kummerfeld, IV Kurochkin, Alexander P Kuzin, Armin Lahm, Camille Laibe, L Lan, C Landerer, LF Lareau, Richard H Lathrop, A Lauricella, E Lavezzo, D Lazarevic, D Lee, Rudolph L Leibel, Thomas Lengauer, B Lenhard, Raphael Leplae, Arthur Lesk, Elena J Levin, Suzanna Lewis, Jing-Woei Li, Luana Licata, Oliver Lichtarge, P Lichtner, B Limaye, Michal Linial, L Lipovich, Marco Lippi, AM Lisewski, ET Liu, S Liuni, Marina Lizio, Jessica Locke, Darren W Logan, Peter Longreen, James Love, JD Luff, J R Luft, J Ma, RM MacCallum, Roderic MacKinnon, Geoff Macintyre, M Madera, MS Madhusudhan, N Maeda, Melissa Maglaqui, Yannick Mahlich, MG Malkowski, Filippo Mancia, SK Manjari, P Manor, M Chiara Manzini, L Marchionni, Aron Marchler-Bauer, Fabien Mareuil, Scott Markel, John L Markley, Deborah S Marks, Russell Marsden, Marc A Marti-Renom, Erik Martinez-Hackert, Steven J Marygold, H Matsuda, S Matsuzawa, John S Mattick, Ann McDermott, Barbara J Morrison McKay, Peter McQuilton, S McWilliam, Alice Meier, J Meiler, Alfons Meindl, Thomas Meitinger, Herve Menager, C Mertes, Jill P Mesirov, Ivan Micetic, Daniel Mietchen, F Mignone, Sven Mika, H Miki, Gillian H Millburn, JL Mills, Milo Mirdita, N Mirkovic, A Mishra, J Mistry, S Miyake, B Mollenhauer, Steffen Moeller, Gaetano T Montelione, Sean D Mooney, Sebastien Moretti, Chris Morris, S Mottagui-Tabar, John Moult, Eyal Mozes, Nicola Mulder, Jan Murken, Diana Murray, Venkatesh Mysore, Rajesh Nair, Kentai Nakano, H Nakauchi, Eswar Narayanan, H Nasir, S Nathan, V Naumov, H Neely, Aleksandra Nenadic, U Neumaier, Pauline Ng, Henrik Nielsen, R Nilsson, N Ninomiya, S Nishiguchi, S Nishikawa, T Nishio, J Nokso-Koivisto, F Nori, C Nwosu, Sean I O'Donoghue, JC Obenauer, Mark N Offman, Yanay Ofran, O Ohara, M Okada, Y Okamura-Oho, Y Okazaki, Osvaldo Olmea, Christine Orengo, V Orlando, TR Oron, Angel R Ortiz, Joel Osuna, Mohammed Ouali, John Overton, Leah A Owens, R Oyama, A Paccanaro, Arthur G Palmer, Yaping Pan, G Pandey, KC Pang, P Panov, CG Park, Helen Parkinson, M Pasmanik-Chor, Andrea Passerini, WJ Pavan, G Pavesi, K Pawowski, CD Payne, F Pazos, Israel Pecht, Anthony E Pegg, Nelson Perdigao, Carolina Perez-Iratxeta, G Pesole, A Peters, Hedi Peterson, Donald Petrey, K Petrou, N Petrovsky, S Pettifer, S Piazza, U Pieper, D Piovesan, W Pirker, C Plessy, W Poewe, Gianluca Pollastri, Heather L Pond, Laura Ponting, Robert Powers, V Prade, S Presslauer, W Nicholson Price, Giuseppe Profiti, Dariusz Przybylski, Marco Punta, John Quackenbush, Matthias Quick, Predrag Radivojac, PA Rajan, Kanagalaghatta R Rajashankar, PJ Ralph, T A Ramelot, Jordan A Ramilowski, S Ranganathan, G Ransmayr, Kristoffer Rapacki, S Rastogi, T Ravasi, J Reeb, J Reed, D C Rees, G J Reichart, JF Reid, Astrid Reinhardt, E Reinthaler, Eva Reisinger, R Rentzsch, S Repo, Peter Rice, Lothar Richter, BZ Ring, M Ringwald, Shaila C Roessle, Arturo Rojo-Dominguez, SD Rokitta, Paolo Romano, AE Romero, Paolo Roncaglia, Manfred Roos, C Rosenmund, P Rossi, S C Rossle, Michael G Rossmann, B R Rost, Y Ruan, E Ruppin, L Rychlewski, Emil Rydza, T A Rynearson, P Sabeti, Kenneth S Sabir, Helen Saibil, Rabie Saidi, T Salakoski, Andrej Sali, Steven L Salzberg, A Sandelin, Chris Sander, D Sasaki, Venkata P Satagopam, B Sathyamoorthy, Vladimir Saudek, JM Sauder, Christian Schaefer, Andrea Schafferhans, Avner Schlessinger, Markus Schmidberger, C Schneider, AM Schnoes, EC Schulte, Peter Schuster, Veit Schwaemmle, Thorsten Schwede, Christian Schoenbach, Stefan Seemayer, Jayaraman Seetharaman, K Sekiguchi, CAM Semple, S Seno, K Seppi, L Sessa, Larry Shapiro, Seema Sharma, R Shastry, Hagit Shatkay, Y Sheng, Robert Sheridan, Karishma Shetty, W Shi, K Shibata, I Shih, H Shimada, K Shimokawa, T Shiraki, Steven A Siegelbaum, Keri Siggers, Beth Signal, Ian Sillitoe, I Silman, D Silva, B Sinclair, KK Singarapu,


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Manfred Sippl, Arne Skerra, N Skunca, CA Slaughter, A Sluijs, Callum Smith, T Smuc, DA Snyder, B Sohl-Kielczynski, A Sokolov, I Sommer, Ta-Tsen Soong, A Sorokoumov, ML Souza, S Sperling, Maria Maddalena Sperotto, S Spielberger, Daron M Standley, C Staniewski, A Starovolsky-Shitrit, David States, Raymund Stefancsik, M Steinegger, Michael J Sternberg, RC Stevens, Heinz Stockinger, David L Stokes, Christian Stolte, MH Stowell, Tim M Strom, Robert M Stroud, W Struhal, E Stupka, Shane Sturrock, K Sugiura, DK Sukumaran, M Sullivan, R Sultana, F Supek, Joel L Sussman, H Suzuki, SS Swaminathan, GVT Swapna, Thomas Szyperski, Bruce Tabor, M Tagami, John A Tainer, Y Takenaka, K Taki, AS Talwalkar, K Tammoja, Hepan Tan, S Tang, MS Taylor, RD Teasdale, J Tegner, Sarah A Teichmann, A S Thanki, S Thoms, W Tian, Y Tomaru, David Tomasek, Liam Tong, J Toomey, S Toppo, P Toronen, PD Tortell, Silvio C Tosatto, Anna Tramontano, C Trenkwalder, Michael L Tress, S Trimborn, T Trimbuch, I Troshani, Oleg Trott, Julie L Tubbs, HR Ueda, Paolo Uva, Christian Vaisse, Alfonso Valencia, DB Van de Waal, AD van Dijk, Erik van Nimwegen, Radka S Varekova, GD Vedova, Ceslovas Venclovas, E Venner, R Verardo, K Verspoor, Allegra Via, Esmeralda Vicedo, B Vieira, JM Villaveces, Carla Vinals, Desiree C von Alpen, P Von Dassow, S Vorberg, Gerrit Vriend, S Vucetic, Claes Wahlestedt, G Wainreb, K Waki, S Waldraff, D Wang, MN Wass, A Watahiki, S Watanabe, CL Wei, Benjamin Wellmann, C Wells, Jun Weng, John D Westbrook, MC Wiener, LG Wilming, Stefan Wilzbach, J Winkelmann, T Wittkop, S Wohlrab, E Wolf, A Wong, Kazimierz O Wrzeszczynski, Y Wu, Zeba Wunderlich, Rong Xiao,Guy Yachdav, K Yagi, H Yamanishi, H Yang, Sheng Ye, A Yeheskel, Bomina Yu, JM Yunes, E Zabarovsky, Federico Zambelli, M Zavolan, Adam Zemla, Li Zhao, Ming Zhou, S Zhu, Raphael Zidovetzki, J Zierer, A Zimmer, A Zimprich, P Ziveri, Yinong Zong,

Collaborators over last 5 years (according to NSF definition) Tom Acton (Rutgers Univ. USA), JM Aramini (Rutgers Univ. USA), Alex Bateman (EBI Hinxton England) Nir Ben-Tal (Tel Aviv Univ. Israel), Søren Brunak (TU Lyngby Denmark), Piero Carninici (RIKEN Japan), Iddo Friedberg (Miami Univ. Oxford OH USA), Tony Futerman (Weizmann Inst. Rehovot Israel), Terry Gaasterland (UCSD USA), Wayne Hendrickson (Columbia Univ. USA), Peter C Kahn (Rutgers Univ. New Brunswick USA), Janet Kelso (MPI Leipzig Germany), Michael Kennedy (Miami Univ. Oxford OH USA), Rick Lathrop (UCI Irvine USA), Thomas Lengauer (MPI Saarbruekcen Germany), Michal Linial (Hebrew Univ. Jerusalem Israel), Filippo Mancia (Columbia Univ. USA), Ann McDermott (Columbia Univ. USA), Thomas Meitinger (Helmholtz Munich Germany), Jill P Mesirov (Broad Inst. USA), Guy Montelione (Rutgers Univ. USA), Sean Mooney (Indiana Univ. Bloomington USA), John Moult (CARB Univ. Maryland USA), Rajesh Nair (FDA 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), Robert Powers (Nebraska Lincoln USA), Dariusz Przybylski (Columbia Univ. USA), Marco Punta (TUM Germany), Predrag Radivojac (Indiana Univ. Bloomington USA), 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), Tim Strom (Helmholtz Munich Germany), Joel Sussman (Weizmann Inst. Rehovot Israel), Thomas Szyperski (Buffalo Univ. USA), Liang Tong (Columbia Univ. USA), 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), Gerrit Vriend (Nijmegen Univ. Netherlands), Kaz Wrzeszczynski (Cold Spring Harbor Labs USA), John Westbrook (PDB-Rutgers Univ. USA), Ming Zhou (Columbia Univ. USA).

Departmental and University Committees 06/2003-2010 Qualifying exam Dept. Biochemistry & Molecular Biophysics, Columbia 11/2009-now Chair for Bachelor/Master Program on Bioinformatics, Munich, Germany


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Teaching Experiences

Courses taught at TUM – past/present

2010-now 6 summer semester lectures (incl. summer 2015): Protein Prediction I: Protein Structure at TUM (each lecture 2x2 hours + 2 hours exercises)

2010-now 4 winter semester lectures (incl. winter 2013/4): Protein Prediction II: Protein Function at TUM (each lecture 2x2 hours + 2 hours exercises)

2013-now 3 summer semester lectures (incl. summer 2015): Introduction to protein prediction for computer scientists: Structure at TUM (each lecture 2x2 hours + 2 hours exercises)

2013-now 2 winter semester lectures (incl. winter 2014): Introduction to protein prediction for computer scientists: Function at TUM (each lecture 2x2 hours + 2 hours exercises)

2010-now 10 seminars (incl. summer 2015): Oberseminar on Bioinformatics & Computational Biology (each semester)

2010-now Hauptseminar Bioinformatics & Computational Biology (2010 SS, 2010 WS, 2011 SS, 2011 WS, 2012 SS, 2012 WS, 2013 SS, 2013 WS, 2014 SS)

2012-now Proseminar Proteins and diseases (2012 SS, 2012 WS, 2014 WS) 2010-2014 5 summer courses: Practical Protein Structure and Function Analysis (led

by: Edda Kloppmann, Marc Ofman, Marco Punta, Andrea Schafferhans) 2013-now 3 summer semester courses (incl. summer 2015): Distributed data mining

lab at TUM (1x2 hours, with Lothar Richter) 2013-now 2 winter semester courses (incl. winter 2014): Introduction to programming

for bioinformaticians at TUM (1x3 hours, leader: Lothar Richter) 2015-now 1 summer semester courses: Bioinformatics resources at TUM (1x3+3

hours, leader: Lothar Richter) 2013-2015 3 block-courses: Javascript at TUM (20+20 hours, leaders: Guy Yachdav &

Lothar Richter) 2013-2015 2 block-courses: Patterns and anti-patterns at TUM (20+20 hours, leaders:

Guy Yachdav & Lothar Richter)

Courses taught at Columbia University & TUM - past

1999-2004 Supervision of graduate students and co-organizing class-room work on bioinformatics in course Biophysics taught by Ann McDermott, Chemistry, Columbia (4 courses: 1999, 2001, 2002, 2003)

2000-2003 4 course lectures: Teaching at Medical Faculty, Columbia; course Eukaryotes I (2000, 2001, 2002, 2003)

2005-2008 4 courses: Teaching full semester course Computational Biology II: Proteins: Sequence, Structure and Networks at Columbia University (2 in collaboration with Dennis Vitkup)

2009-2011 2 courses: Munich R course: Parallel Computing with R (2 winter courses with Markus Schmidberger)

2010-2013 4 summer courses: Practical Bioinformatics Lab (with Laszlo Kajan) 2010-2012 2 winter lectures: Computational Systems Biology (with Arthur Dong)


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2010-2011 Seminar Presenting and selling scientific software (with Andrea Schafferhans)

2011 Practical Simulation of a real-life Software Development project - Connecting the R language to the Clouds (with Markus Schmidberger)

Courses taught at meetings/summer-schools

06/1995 Tutorial at ISMB’95 (International Conference on Intelligent Systems for Molecular Biology) in Cambridge, England

10/1995 Supervision of post-docs at the workshop Frontiers of protein structure prediction at the IRBM in Rome, Italy

03/1997 Supervision of post-docs at a workshop at the CBS in Copenhagen (Denmark)

06/1997 Tutorial at ISMB’97 (International Conference on Intelligent Systems for Molecular Biology) in Chalkidiki, Greece

07/1997 Supervision of pre- and post-docs at the workshop (EMBO-course) Genome sequence analysis at the EBI in Hinxton, England

07/1997 Teacher at the summer school Proteins: integration of life's function in San Sebastian, Spain

10/1997 Supervision of post-docs at the 2nd workshop Frontiers of protein structure prediction at the IRBM in Rome, Italy

07/1999 Supervision of pre- and post-docs at the workshop Bioinformatics at the CIB in Havanna, Cuba

10/1997 Supervision of post-docs at the workshop Protein sequence analysis in the genome era at the University of Bologna, Italy

09/2001 Teacher at a NATO summer school on bioinformatics in Il Ciocco, Italy 08/2002 Supervision of pre- and post-docs at the workshop Bioinformatics at the CIB

in Havanna, Cuba 09/2010 Course at Summer school for Optimization, Machine Learning and

Bioinformatics, Erice, Italy 06/2013 MaxQuant Summer School, Max Planck Institute of Biochemistry,

Martinsried, Germany

Other courses taught

1986-1988 Organization of seminars in Theor. Physics, Heidelberg Univ., Germany 1989-1990 Lecture series on Arms control (I), Heidelberg University 1990 Lecture series on Arms control (II), Heidelberg Univ. 1986-1990 Courses on Physics and Arms control in extramural schools (Heidelberg,

Mannheim, Frankfurt, Darmstadt) 1991-1995 Lectures, and supervision of courses for PhD students at EMBL Heidelberg 1992-1996 Course lectures on Protein structure prediction at Heidelberg Univ.

Personnel in numbers PhD students trained in our lab 26 ( 5 Female=19%) Master students trained in our lab 39 ( 10 Female =26%) Bachelor students trained in our lab 23 ( 8 Female =35%)


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Others trained in our lab 79 ( 24 Female =31%) Sum trained in my lab: 143: 29% women, 50% foreigners from 32 nations on 6 continents

Postdocs currently in my group Name Nation Affiliation In lab since Edda Kloppmann F Germany TUM: Bionformatics/Informatics 2011/01 Lothar Richter M Germany TUM: Bionformatics/Informatics 2011 Andrea Schafferhans F Germany TUM: Bionformatics/Informatics 2009/09 Guy Yachdav M Israel TUM: Bionformatics/Informatics 2003

Technical staff currently in my group Name Nation Affiliation In lab since Inga Weise F Germany TUM: Bioinformatics 2015 Timothy Karl M USA TUM: Bioinformatics 2010

PhD students (alphabetically; x marks external): 27 – 5 women Name Nation Affiliation for thesis Period Henry Bigelow M USA Columbia: Biochem./C2B2 2001-04/2007 Matthias Böck x M Germany TUM: Inf. 2011-12/2015 Yana Bromberg F USA Columbia: Med. Inf./C2B2 2003-11/2006 Simeon Carstens x M Germany TUM: Inf./Bioinf. & Pasteur Paris 2013-03/2016 Juan Miguel Cejuela M Spain TUM Munich 2012-2017 Tobias Girschick x M Germany TUM: Inf./Bioinformatics 2011-06/2014 Tatyana Goldberg F Kazakhstan TUM Munich 2012-05/2016 Tobias Hamp M Germany TUM: Inf./Bioinformatics 2009-06/2014 Andreas Hapfelmeier x M Germany TUM: Inf. 2011-12/2015 Maximilian Hecht M Germany/Italy TUM Munich 2012-12/2015 Thomas Hopf M Germany TUM Munich/HMS Boston 2012-02/2016 Andrew Kernytsky M USA Columbia: Biochem./C2B2 2001-05/2008 Jinfeng Liu M China Columbia: Pharmacology/C2B2 1999-02/2004 Sven Mika M Germany Columbia: Biochem./C2B2 2002-07/2006 Rajesh Nair M India Columbia: Physics/C2B2 1999-11/2004 Yanay Ofran M Israel Columbia: Med. Inf. /C2B2 2000-02/2004 Dariusz Przybylski M Poland Columbia: Physics/C2B2 1999-11/2004 Venkata P Satagopam M India TUM: Inf. & Luxembourg 2010-2016 Christian Schäfer M Germany TUM: Inf./Bioinf. 2009-01/2013 Avner Schlessinger M Israel Columbia: Biochem./C2B2 2003-09/2007 Jana Schmidt x F Germany TUM: Inf./Bioinf. 2010-12/2013 Madeleine Seeland x F Germany TUM: Inf./Bioinformatics 2011-08/2014 Ta-Tsen Soong M Taiwan Columbia: Med. Inf./C2B2 2005-06/2009 Esmeralda Vicedo F Spain TUM Munich 2010-2016 Kaz O Wrzeszczynski M Poland Columbia: Biochem./C2B2 2001-02/2009 Joerg Wicker x M Germany TUM: Inf./Bioinformatics 2009-08/2013 Thomas Wieland x M Austria TUM: Inf./Bioinformatics 2012-10/2015 Guy Yachdav M Israel TUM: Inf./Bioinformatics 2014-07/2015

Master students (alphabetically; x marks external): 39 – 10 women Name Nation Affiliation for thesis Graduation Dominik Achten M Germany TUM Inf. / Bioinf. Munich 10/2011 Bernhard Ahlborn M Germany TUM Inf. / Bioinf. Munich 11/2013 Sonja Ansorge F Germany TUM Inf. / Bioinf. Munich 08/2015


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Ashish Baghudana M India TUM Inf. / Bioinf. Munich 12/2015 Alexander Betz M Germany TUM Inf. / Bioinf. Munich 05/2015 Michael Bernhofer M Germany TUM Inf. / Bioinf. Munich 02/2014 Ariane Boehm F Germany TUM Inf. 01/2015 Jonathan Boidol M Germany TUM Inf. / Bioinf. Munich 11/2013 Aleksandar Bojchevski M Macedonia TUM Inf. 01/2016 Juan Miguel Cejuela M Spain TUM Inf. / Bioinf. Munich 07/2012 S. Tanzeem H. Charu F Bangladesh TUM Inf. / Bioinf. Munich xx/2016 Aleksander Cislak M Poland TUM Inf. 08/2015 David Dao M Hongkong TUM Inf. 12/2012 Ankit Dubey M India TUM Inf. 01/2015 Tatyana Goldberg F Kazakhstan TUM Inf. / Bioinf. Munich 10/2011 Maximilian Hecht M Germany/Italy TUM Inf. / Bioinf. Munich 10/2011 Veit Hoehn M Germany TUM Inf. / Bioinf. Munich 11/2012 Peter Hoenigschmid M Germany TUM Inf. / Bioinf. Munich 08/2012 Thomas Hopf M Germany TUM Inf. / Bioinf. Munich 03/2012 Diana Iacob F Germany TUM Inf. / Bioinf. Munich 02/2014 Rebecca Kassner F Germany TUM Inf. / Bioinf. Munich 02/2015 Michael Kiening M Germany TUM Inf. / Bioinf. Munich 05/2013 Hossain Mahmud M Pakistan TUM Inf. 11/2015 Vivian Mai Linh Klose F Germany TUM Inf. / Bioinf. Munich 10/2012 Verena Link F Germany TUM Inf. / Bioinf. Munich 11/2012 Yannick Mahlich M Germany TUM Inf. / Bioinf. Munich 07/2014 Michael Menden M Germany TUM Inf. / Bioinf. Munich 04/2011 Dinh Nguyen M Vietnam TUM Inf. 02/2015 Sven Punga M Germany TUM Inf. / Bioinf. Munich 2016 Johannes Raedele M Germany TUM Inf. / Bioinf. Munich 07/2015 Kujtim Rahmani M Macedonia TUM Inf. 12/2014 Benedikt Rauscher M Germany TUM Inf. / Bioinf. Munich 07/2015 Jonas Reeb M Germany TUM Inf. / Bioinf. Munich 03/2014 Eva Reisinger F Germany TUM Inf. / Bioinf. Munich 01/2013 Sebastian Seitz M Germany TUM Inf. 01/2015 Shrikant Vinchumar M India TUM Inf. 04/2015 Robert Wagner M Germany TUM Inf. / Bioinf. Munich 01/2015 Benjamin Wellmann M Germany TUM Inf. / Bioinf. Munich 05/2012 Silvana Wolf F Germany TUM Inf. / Bioinf. Munich 01/2015

Bachelor students (alphabetically; x marks external): 17 - 4 women) Name Nation Affiliation for thesis Graduation Meshal Ansari F India TUM Inf. / Bioinf. Munich 09/2015 Susanne Bakenecker F Germany TUM Inf. / Bioinf. Munich 02/2014 Christiane Gasperi F Italy TUM Inf. / Bioinf. Munich 12/2012 Caroline Gergen F Germany TUM Inf. xx/2016 Peter Maxim. Hirschbeck M Germany TUM Inf. 09/2012 Diana Iacob F Rumania TUM Inf. / Bioinf. Munich 02/2014 Maria Kalemanov F Russia TUM Inf. / Bioinf. Munich 10/2012 Yannick Mahlich M Germany TUM Inf. / Bioinf. Munich 10/2011 Mirdita Milot M Albania TUM Inf. / Bioinf. Munich 04/2014 Andre Ofner M Germany TUM Inf. / Bioinf. Munich 08/2015 Nikolaos Papadopoulos M Greece TUM Inf. / Bioinf. Munich 11/2013 Pandu Raharja-Liu M Indonesia TUM Inf. / Bioinf. Munich 12/2015 Jonas Reeb M Germany TUM Inf. / Bioinf. Munich 09/2011 Manfred Roos M Germany TUM Inf. / Bioinf. Munich 11/2013


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Maria Schelling F Germany TUM Inf. / Bioinf. Munich 09/2014 Yann Spoeri M G/France TUM Inf. / Bioinf. Munich 06/2014 Martin Steinegger M Germany TUM Inf. / Bioinf. Munich 06/2012 Gregor Sturm M Germany TUM Inf. / Bioinf. Munich 02/2015 Carsten Uhlig M Germany TUM Inf. / Bioinf. Munich 01/2016 Shen Wei M China TUM Inf. / Bioinf. Munich 04/2012 Maximilian Weininger M Germany TUM Inf. 09/2015 Sebastian Wilzbach M Germany TUM Inf. / Bioinf. Munich 2014 Silvana Wolf F Germany TUM Inf. / Bioinf. Munich 01/2015

Others trained (alphabetically, incl. PhD, excl. BS/MS): 79 – 24 women Name Nation Current Affiliation (last known) Period Mohamed Ahmed M Egypt Unknown Summer 2015 Claus Andersen M Denmark Sr. Analyst, Siena Biotech., Italy 2001-2002 Claudia Bertonati F Italy Staff, Univ. of Rome, Italy 2004-2006 Henry Bigelow M USA Scientist, Amgen, San Francisco, USA 2001-2007 Shameek Biswas M India Columbia Univ, New York, USA Summer 2003 Maina Bitar F Brazil Postdoc Sydney, Australia 2010-2011 Yana Bromberg F USA Professor, Rutgers Univ., NJ, USA 2003-2010 Bastian Bruning M Netherlands Nijmegen, Netherlands Spring 2001 Joe Bylund M USA Columbia Univ, New York, USA Spring 2008 Phil Carter M England Univ. College, London 2002-2004 S. Tanzeem H. Charu F Bangladesh Student, TUM, Germany 2011-2012 Chen Peter Chien M China Sr. Scientist, Cold Spring Harbor Summer 2001 Murat Cokol M Turkey Prof. Sabanci Univ, Istanbul, Turkey Spring 2000 Christian Dallago M Italy Student, TUM, Germany Fall 2015 David Dao M Hongkong Student, MIT, Boston, USA 12/2012 Anthony J DeCostanzo M USA Columbia Univ, New York, USA Fall 2002 Carlo Di Domenico M Italy Student, TUM, Germany Sumer-Fall 2015 Yu-An (Arthur) Dong M China Shanghai Univ., China 2010-2013 Marlena Drabik F Poland Poland 2010-2014 Volker Eyrich M Germany Sr. Analyst, Schroedinger Inc., New York 1999-2005 Seth Gale M USA Columbia Univ, New York, USA Fall 2001 Alexander Galtesev M Russia Student, TUM, Germany 10/2015 Zofia Gasik F Poland Univ Warsaw, Poland Winter 2012 Yulia Gembarzhevskaya F Russia Student, TUM, Germany Spring 2016 Julia Gerke F Germany Student, TUM, Germany 2011-2012 Sarah Gilman F USA Columbia Univ, New York, USA Summer 2004 Dedan Githae M Kenya Int. Livestock Research Inst., Kenya 2010-2011 Gabor Halasz M Hungary Columbia Univ, New York, USA Summer 2003 Tobias Hamp M Germany Illumina, Cambridge, England 2010-2015 Jana Hapfelmeier F Germany Analyst, Gesundheitsforen Leipzig, Germ 2010-12/2013 Maximilian Hecht M Germany/Italy Analyst, Amazon, Germany 2012-12/2015 Hedi Hegyi F Hungary Staff, Budapest Univ., Italy 2002-2004 Barbara Hummel F Germany Student, TUM, Germany Summer 2010 Laurence James M USA Hunter College, CUNY Summer 2006 Laszlo Kajan M Hungary Poland 2008-2013 Andrew Kernytsky M USA Sr. Scientist, Agios Inc., USA 2001-2008 Ingrid Koh F Hongkong Sr. Scientist, Singapore Univ. 2003-2006 Andrew Kuziemko M USA Columbia Univ, New York, USA Fall 2004 Wei Lim M China Columbia Univ, New York, USA Summer 2005 Yichun Lin F China Student, TUM, Germany Fall 2015 Jinfeng Liu M China Sr. Res. Scientist, Genentech, CA 1999-2007


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Peng Liu M China Columbia Univ, New York, USA Spring 2005 Alice Meier F Germany Student, LMU, Germany 2010-2011 Michael Menden M Germany PhD EBI, Cambridge, England 2010-2011 Sven Mika M Germany eSpeed Inc., New York, NY 2002-2006 Bahar Moezi F Turkey Columbia Univ, New York, USA Summer 2005 Eyal Mozes M Israel Staff, Columbia Univ. Biology, NY 2005-2008 Rajesh Nair M India FDA, Bethesda, MD 1999-2008 Dmitrij Nechaev M Russia Student, TUM, Germany Fall 2015 Jackson Ng M USA High school graduate Summer 2000 Miriam Nunes F Brazil Brazil Winter 2012 Marc Offman M Germany Sr. Analyst, Iteratec, Munich, Germany 2010-2012 Yanay Ofran M Israel Professor, Bar-Ilan University, Israel 2000-2007 Shoshana L Posy F USA Columbia Univ, New York, USA Spring 2003 Dariusz Przybylski M Poland Sr. Res. Scientist, BROAD Inst. MIT 1999-2007 Marco Punta M Italy Sr. Res. Scientist, CNRS, Paris 2002-2011 Shruti Rastogi F India Postdoc, Columbia University, New York 2008-2011 Vikram Ravindra M India Student, TUM, Germany Summer 2013 Mohad Rehan M India Aligarh Muslim Univ, India Winter 2011Megan Restuccia F USA Manager, Morgan & Stanley, New York 2002-2005 Doug Roberts-Wolfe M USA Hampshire Summer 2006 Shaila Rössle-Blank F Brazil LRZ Munich, Germany 2010-2012 Christian Schäfer M Germany Siemens Nuernberg, Germany 2009-2013 Avner Schlessinger M Israel Professor, Mount Sinai, New York, USA 2003-2008 Markus Schmidberger M Germany Gr Ldr Cloudnumber, Berlin, Germany 2010-2011 Madhukar SP Shankar M India Student, TUM, Germany Summer 2015 Trevor Siggers M Canada Professor, Boston Univ, USA Summer 2000 Haitham Sobhy M Egypt Bioinformatics Munich 2010-2011 Ta-Tsen Soong M Taiwan Postdoc, Cornell Med, New York, USA 2005-2009 Aleksandr Sorokoumow M Russia Student, TUM, Germany 2013-2014 Enrique Tadique M USA High school graduate, New York, USA Summer 2000 Hepan Tan M China Columbia Univ, New York, USA Summer 2000 Juan de Toro Martin M Spain Univ Complutense, Spain Fall 2011 Linh Tran F China Student, TUM, Germany Summer 2015 Monika Varshney F India Student, TUM, Germany Winter 2015 Mikhail Veshtort M Bellarussia Sr. Res Scientist, MIT, Boston, USA 2008-2011 Kaz O Wrzeszczynski M Poland Gr Ldr, Genome Inst. New York, USA 2001-2009 Guy Yachdav M Israel Analyst, New York, USA 2003-2015 Hong Yu F China Columbia Univ, New York, USA Summer 2000

Thesis committee (alphabetically) Name University: Department Date Group Yuling An Columbia: Chemistry 07/2002 Rich Friesner Kai Christian Bader TUM inf. 01/2013 Manfred Broy Chen Peter Chien Columbia: MD,PhD 12/2005 Barry Honig Andrey Chursov TUM: WZW 10/2013 Dmitrij Frishman Murat Cokol CU: Biomedical Informatics 05/2006 Andrej Rzhetsky Fabian Denbsky TUM: WZW 03/2014 Dmitrij Frishman Chuck Duarte Columbia: Biochemistry 09/2002 Ann-Marie Pyle Thilo Eissler TUM: Informatics 10/2012 Arndt Bode 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


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Andreas Naegele TUM: INF/Siemens 03/2013 Thomas A Runkler David Pincus Columbia: Chemistry 09/2004 Rich Friesner Johannes Rest TUM: WZW 12/2014 Dmitrij Frishman Erroll Rueckert Columbia: Integrated 2009 Richard Axel Trevor Siggers Columbia: Biochemistry 11/2005 Barry Honig Cinque Soto Columbia: Biochemistry 09/2007 Barry Honig Hepan Tan Columbia: Biochemistry 02/2006 Wayne Hendrickson Bahar Taneri Rockefeller University 04/2005 Terry Gaasterland Christopher Tang Columbia: Biochemistry 06/2007 Barry Honig Oleg Trott Columbia: Biochemistry 06/2004 Arthur Palmer Yun Zhang Columbia: Biology 10/2001 Marti Chalfie

Previously visiting faculty (alphabetically) Name From Period Timothy Angelotti Stanford U, USA 03/2013-01/2014 Mikael Boden U Queensland, Australia 12/2013-02/2014 Yana Bromberg Rutgers Univ, USA 05/2015-08/2015 Paul Horten AIST Tokyo, Japan 11/2011-12/2011

Burkhard Rost Grants

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Grants

Grants active I. PI: Burkhard Rost Period: 06/01/09 to 05/31/15 Agency: Alexander von Humboldt Foundation, Germany Ann Dir Costs: 750 K € Total (5 years): 4,250 K € Overhead (5 years): 750 K € Title: Alexander von Humboldt Professorship (AvH) Summary: This grant provides the infrastructure for building up our research and teaching at the TUM in Munich, Germany. II. PI: Wayne Hendrickson Role: Co-PI Period: 07/01/10 to 06/30/15 Agency: NIH (U54 GM75026) Ann Dir Costs: $120 K Title: Structural Genomics of Membrane Proteins (NYCOMPS) Summary: This grant supports the New York Structural Biology Center. Dr. W.A. Hendrickson (Columbia University) is the P.I. for this project. It aims to develop and apply structural genomics approaches to structure determination for membrane proteins. Our group is responsible for the target selection in this project.

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. ISMB'2002 PI: Burkhard Rost Period : August 2002 Agency: NSF Total Dir Costs: $40 K Summary: Travel support for young participants of the ISMB 2002 meeting iii. ISMB'2002 PI: Burkhard Rost Period : August 2002 Agency: DOE Total Dir Costs: $35 K


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Summary: Travel support for young participants of the ISMB 2002 meeting iv. Center of excellence in bioinformatics PI: Barry Honig (Biochemistry, Columbia) Role: Co-PI Period: 09/01/01 to 08/31/03 Agency: NIH (5-P20-LM7276) Ann Dir Costs: $20,000 Summary: Fund to prepare grant proposal to begin a center of excellence. v. Structural genomics of eukaryotic model organisms PI: Gaetano T. Montelione (Rutgers University) Role: Co-PI Period: 10/01/00 to 31/10/05 Agency: NIH (P50 GM62413) Ann Dir Costs: $180,000 Total (5 years) $750,000 Overhead (4 years) $580,000 Summary: Goal of the pilot project in structural genomics (one of nine in the USA; of about 14 world-wide) was to develop high-throughput techniques for large-scale structure determination. This project combined over 20 groups from 12 research institutions in the USA, Canada and Israel. Our particular task was the development of techniques that rationalize the automatic target selection, i.e. prioritize which proteins to pursue experimentally. vi. Intruding into the midnight zone of protein sequence comparisons PI: Burkhard Rost Period: 05/01/01 to 04/30/05 Agency: NIH (R01 GM63029) Ann Dir Costs: $190,000 Total (4 years) $750,000 Overhead (4 years) $660,000 Summary: The 'twilight zone' of protein sequence comparison is the region in which sequence similarity does not suffice to conclude, e.g., structural similarity. The vast majority of all protein pairs of similar structure populate a 'midnight zone', i.e., their sequences differ too much for sequence-based inferences. We refined, extended, and specialized methods combining sequence alignment, structure prediction and functional information. vii. Ab initio prediction of sub-cellular localization PI: Burkhard Rost Period: 02/01/02 to 01/31/05 Agency: NSF (DBI-0131168) Ann Dir Costs: $157,000 Total (3 years) $470,000 Overhead (4 years) $240,000 Summary: The major goals of this project were to develop a system predicting the sub-cellular localization of a protein based on sequence alignments and signal peptide motifs. The ultimate objective was to combine a series of novel methods into a comprehensive system that we can use to automatically annotate entire proteomes. viii. Improve predictions of structure and function by PredictProtein PI: Burkhard Rost Period: 05/01/03 – 04/30/07 Agency: NIH/NLM (R01 LM07329) Ann Dir Costs: $175,000 Total (4 years) $900,000 Overhead (4 years) $770,000 Summary: The major objective was to improve the Internet prediction server PredictProtein. The specific aims were to (1) implement technical improvements, (2) and to


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systematically combine the results from various methods. In particular, we worked on the improvement of methods that identify transmembrane segments from sequence. ix. Predict putative protein-protein interface segments at low resolution PI: Burkhard Rost Period: 05/01/03 – 04/30/07 Agency: NIH (R01 GM64633-01) Ann Dir Costs: $200,000 Total (4 years) $800,000 Overhead (4 years) $680,000 Summary: We developed methods predicting interface segments, i.e. regions of residues consecutive in sequence that are in contact with other interface segments. Separate methods addressed internal and external interfaces. x. MAGNet: center for the analysis of multiscale genomic and cellular network PI: Andrea Califano (Bio-Medical Informatics, Columbia) Role: Project leader Period: 10/01/05 to 09/30/10 Agency: NIH (U54-GM072980) Ann Dir Costs: $220,000 Overhead $120,000 Summary: Grant proposal to begin a National Center of Excellence. Preliminarily, we proposed to build a center that provides software to other scientists. For the first two years, I acted as the coordinator of Core II proposals (biological applications of algorithms), and project leader for one of the seven main projects that proposed to integrate methods for the prediction of protein structure and function. The project was supposed to focus on the combination of related resources that already exist in the labs of various center members and on making these methods available through common interfaces. xi. Improve predictions of structure and function by PredictProtein PI: Burkhard Rost Period: 04/01/07 – 03/31/10 Agency: NIH/NLM (2 R01 LM07329) Ann Dir Costs: $175,000 Total (4 years) $900,000 Overhead (4 years) $770,000 Summary: The major objective was to improve the Internet prediction server PredictProtein (PP). By 2008, this server had been used over 2 million times by over 30,000 researchers from 106 countries. The scientific solutions address two related tasks pertaining to protein function prediction. The first was to predict the effect of amino acid substitutions. We developed novel machine learning-based methods to distinguish between mutations that effect structure, or function, or have no apparent phenotype. The second major task was the identification of natively unstructured regions and their functional classification. Proteins that do not adopt regular structures in isolation are increasingly becoming an important research area; they may provide a key to the evolution of complexity from proka- to eukaryotes. We developed machine learning-based identifications of features specific to this important class of molecules. All new methods have been made available through PredictProtein. xii. Meeting for Critical Assessment of protein Structure Prediction (CASP) PI: Burkhard Rost Period: 08/01/04 – 07/31/09 Agency: NIH (1-R13-GM072354-01) Ann Dir Costs: $45,000 Total (5 years) $194,447 Overhead $0


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Summary: This grant funded 3 consecutive CASP meetings that have evolved into the major event in the structure prediction field. Note that this grant neither covered any salaries, nor any expenses for my group. xiii. Structural genomics of eukaryotic model organisms PI: Gaetano T. Montelione (Rutgers University) Role: Co-PI Period: 07/01/05 to 06/30/10 Agency: NIH (U54 GM074958-01) Ann Dir Costs: $150,000 Total (5 years) $750,000 Overhead (5 years) $580,000 Title: Structural genomics of eukaryotic model organisms Summary: Goal was the large-scale experimental determination of protein structures. This project combined over 20 groups from 12 research institutions in the USA and Canada. Our particular task was the development of techniques that rationalized the automatic target selection, i.e. prioritize which proteins to pursue experimentally and to cluster proteins into dynamic families with annotations of function. xiv. Structural genomics for membrane proteins (NYCOMPS) PI: Wayne Hendrickson Role: Co-PI Period: 09/01/05 to 08/31/10 Agency: NIH (U54 GM75026) Ann Dir Costs: $200 K Total (5 years) $500,000 Overhead (5 years) $300,000 Summary: Our development center in structural genomics (NYCOMPS: New York Consortium for Membrane Protein Structural genomics) investigated to which extent experimental high-throughput determination of 3D structures for membrane proteins is feasible. In order to achieve this, the center established a pipeline for high-throughput expression and purification. Our group was responsible for target selection. In particular, we clustered membrane proteins using existing methods. The project has been continued into a second five-year phase (see Grants active). xv. Comprehensive annotation of subcellular localization in entire proteomes PI: Burkhard Rost Period : 12/01/06-11/30/11 Agency: NIH (R01) Effort: 15% Ann Dir Costs: $250K (Total costs for entire grant: $1,250K) Summary: We developed a comprehensive system that combines experimental resources with data mining techniques and novel prediction methods, with the objective of annotating the localization for all proteins in entirely sequenced eukaryotes with unprecedented detail and accuracy. In particular, we developed LOCdb, a database of annotations of subcellular localization in Homo sapiens and Arabidopsis thaliana, and LOCtree2, a method that predicts localization for bacteria and eukaryotes more accurately and more comprehensively than previously existing tools.

Burkhard Rost List of publications

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List of publications ◊ Theses 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.

Publications on Arms Control *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.

Publications on Computational Biology and Bioinformatics 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.

*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.

◊ Group members in bold letters; journals underlined; asterisk marks first/senior author publications;

peer-reviewed publications marked by solid gray bar on left.


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*17. B Rost & C Sander (1994) Conservation and prediction of solvent accessibility in protein families. Proteins 20, 216-226.

*18. B Rost, C Sander & R Schneider (1994) Evolution and neural networks - protein secondary structure prediction above 71% accuracy. In '27th Hawaii International Conference on System Sciences', L Hunter (ed.) Wailea, Hawaii; Los Alamitos, CA: IEEE Society Press, 385-394.

*19. B Rost, C Sander & R Schneider (1994) PHD - an automatic server for protein secondary structure prediction. CABIOS 10, 53-60.

*20. B Rost, C Sander & R Schneider (1994) Redefining the goals of protein secondary structure prediction. J Mol Biol 235, 13-26.

1995 (5) *21. B Rost (1995) Fitting 1-D predictions into 3-D structures. In 'Protein folds: a distance based approach', H

Bohr and S Brunak (eds.) Boca Raton, FL: CRC Press, 132-151. *22. B Rost (1995) TOPITS: Threading One-dimensional Predictions Into Three-dimensional Structures. In 'Third

International Conference on Intelligent Systems for Molecular Biology', C Rawlings, D Clark, R Altman, L Hunter, T Lengauer, and S Wodak (eds.) Cambridge, England: Menlo Park, CA: AAAI Press, 314-321.

*23. B Rost, R Casadio, P Fariselli & C Sander (1995) Prediction of helical transmembrane segments at 95% accuracy. Protein Science 4, 521-533.

*24. B Rost & C Sander (1995) Progress of 1D protein structure prediction at last. Proteins 23, 295-300. *25. B Rost & C Sander (1995) Protein structure prediction by neural networks. In 'The handbook of brain theory

and neural networks', M Arbib (ed.) Cambridge, MA: Bradford Books/The MIT Press, 772-775. 1996 (6) 26. T Hubbard, A Tramontano, G Barton, D Jones, M Sippl, A Valencia, A Lesk, J Moult, B Rost, C Sander, R

Schneider, A Lahm, R Leplae, C Buta, M Eisenstein, O 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 prediction-based threading. J Mol Biol

270, 471-480. *37. B Rost (1997) Better 1D predictions by experts with machines. Proteins Suppl. 1, 192-197. 1998 (4) *38. MA Andrade, SI O'Donoghue & B Rost (1998) Adaptation of protein surfaces to subcellular location. J Mol

Biol 276, 517-525. *39. B Rost (1998) Marrying structure and genomics. Structure 6, 259-263.


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*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.

*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 ‘Scientific applications of neural nets’, JW Clark, T

Lindenau, and ML Ristig (eds.) Heidelberg: Springer, 207-223. 45. O Olmea, B Rost. & A Valencia (1999) Effective use of sequence correlation and conservation in fold

recognition. J Mol Biol 293, 1221-1231. 46. D Fischer, C Barret, K Bryson, A Elofsson, A Godzik, D Jones, KJ Karplus, LA Kelley, RM MacCallum, K

Pawowski, B Rost, L Rychlewski & M Sternberg (1999) CAFASP-1: critical assessment of fully automated structure prediction methods. Proteins Suppl 3, 209-21.

47. F Pazos, B Rost & A Valencia (1999) A platform for integrating threading results with protein family analyses. Bioinformatics 15, 1062-1063.

2000 (2) *48. B Rost & C Sander (2000) Third generation prediction of secondary structure. Meth Mol Biol 143, 71-95. *49. M Cokol, R Nair & B Rost (2000) Finding nuclear localization signals. EMBO Reports 1, 411-415. 2001 (5) *50. B Rost (2001) Protein secondary structure prediction continues to rise. J Struct Biol 134, 204-218. *51. J Liu & B Rost (2001) Comparing function and structure between entire proteomes. Protein Science 10,

1970-1979. *52. V Eyrich, MA Marti-Renom, D Przybylski, A Fiser, F Pazos, A Valencia, A Sali & B Rost (2001) EVA:

continuous automatic evaluation of protein structure prediction servers. Bioinformatics 17, 1242-1243. 53. D Fischer, A Elofsson, L Rychlewski, F Pazos, A Valencia, B Rost, AR Ortiz & RL Dunbrack (2001)

CAFASP2: the second critical assessment of fully automated structure prediction methods. Proteins 45 (S5), 171-183.

*54. B Rost & V Eyrich (2001) EVA: large-scale analysis of secondary structure prediction. Proteins. Proteins 45 (S5), 192-199.

2002 (15) *55. D Przybylski & B Rost (2002) Alignments grow, secondary structure prediction improves. Proteins 46, 195-

205. *56. CAF Andersen, AG Palmer, S Brunak & B Rost (2002) Continuum secondary structure captures protein

flexibility. Structure 10, 175-184. 57. G Pollastri, D Przybylski, B Rost & P Baldi (2002) Improving the prediction of protein secondary structure in

three and eight classes using recurrent neural networks and profiles. Proteins 47, 228-235. 58. MA Marti-Renom, MS Madhusudhan, A Fiser, B Rost, A Sali (2002) Reliability of assessment of protein

structure prediction methods. Structure 10, 435-440. *59. B Rost (2002) Enzyme function less conserved than anticipated. J Mol Biol 318, 595-608. *60. B Rost (2002) Did evolution leap to create the protein universe? Curr Opin Struct Biol 12, 409-416. *61. CP Chen & B Rost (2002) State-of-the-art in membrane protein prediction. Appl Bioinformatics 1, 21-35. *62. J Liu & B Rost (2002) Target space for structural genomics revisited. Bioinformatics 18, 922-933. *63. B Rost, B Honig & A Valencia (2002) Bioinformatics in structural genomics. Bioinformatics (Editorial) 18,

897-898. *64. J Glasgow & B Rost (2002) ISMB 2002. Bioinformatics (Editorial) 18 Suppl 1, S1 *65. R Nair & B Rost (2002) Inferring sub-cellular localization through automated lexical analysis.

Bioinformatics 18 Suppl 1 (ISMB Proceedings), S78-S86. *66. J Liu, H Tan & B Rost (2002) Loopy proteins appear conserved in evolution. J Mol Biol 322, 53-64. *67. CP Chen, A Kernytsky & B Rost (2002) Transmembrane helix predictions revisited. Protein Science 11,

2774-2791. *68. R Nair & B Rost (2002) Sequence conserved for sub-cellular localization. Protein Science 11, 2836-2847.


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*69. CP Chen & B Rost (2002) Long membrane helices and short loops predicted less accurately. Protein Science 11, 2766-2773.

2003 (24) *70. Y Ofran & B Rost (2003) Analysing six types of protein-protein interfaces. J Mol Biol 325, 377-387. *71. CAF Andersen & B Rost (2003) Automatic secondary structure assignment. Methods Biochem Anal 44,

341-363. *72. B Rost (2003) Prediction in 1D: secondary structure, membrane helices and accessibility. Methods Biochem

Anal 44, 559-587. *73. P Carter, J Liu & B Rost (2003) PEP: Predictions for entire proteomes. Nucl Acids Res 31, 410-413. *74. R Nair, P Carter & B Rost (2003) NLSdb: database of nuclear localization signals. Nucl Acids Res 31, 397-

399. *75. J Liu & B Rost (2003) Domains, motifs, and clusters in the protein universe. Curr Opin Chem Biol 7, 5-11. *76. B Rost (2003) Rising accuracy of protein secondary structure prediction. In 'Protein structure determination,

analysis, and modeling for drug discovery', D Chasman (ed.) New York: Dekker, 207-249. 77. R Zidovetzki, B Rost, Don L Armstrong & I Pecht (2003) Role of transmembrane domains in the functions of

Fc receptors. J Biophysical Chemistry 15, 555-575. *78. Y Ofran & B Rost (2003) Predict protein-protein interaction sites from local sequence information. FEBS Let

544, 236-239. *79. B Rost (2003) Neural networks predict protein structure: hype or hit? In 'Artificial intelligence and heuristic

methods in bioinformatics' P Frasconi and R Shamir (eds.) Amsterdam: IOS Press, 34-50. *80. KO Wrzeszczynski & B Rost (2003) Cataloguing proteins in cell cycle control. In 'Cell cycle checkpoint

control protocols' H Lieberman (ed.) Totowa: Humana Press, 219-233. *81. B Rost, J Liu, D Przybylski, R Nair, H Bigelow, K Wrzeszczynski & Y Ofran (2003) Predicting protein

structure through evolution. In 'Chemoinformatics - From Data to Knowledge' J Gasteiger & T Engel (eds.) New York: Wiley, 1789-1811.

*82. B Rost & J Liu (2003) The PredictProtein server. Nucl Acids Res 31, 3300-3304. *83. J Liu & B Rost (2003) NORSp: predictions of long regions without regular secondary structure. Nucl Acids

Res 31, 3833-3835. *84. R Nair & B Rost (2003) LOC3D: annotate sub-cellular localization for protein structures. Nucl Acids Res 31,

3337-3340. *85. S Mika & B Rost (2003) UniqueProt: creating representative protein sequence sets. Nucl Acids Res 31,

3789-3791. *86. A Kernytsky & B Rost (2003) Static benchmarking of membrane helix predictions. Nucl Acids Res 31,

3642-3644. *87. IYY Koh, VA Eyrich, MA 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. Nucl Acids Res 31, 3308-3310.

*89. P Carter, CAF Andersen, B Rost (2003) DSSPcont: continuous secondary structure assignments for proteins, Nucl Acids Res 31, 3293-3295.

*90. R Nair & B Rost (2003) Better prediction of sub-cellular localization by combining evolutionary and structural information. Proteins 53, 917-930.

*91. VA Eyrich, IYY Koh, D Przybylski, O 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.

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.


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*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 ‘The Proteomics Protocols

Handbook’ JE Walker (ed.) Totowa: Humana Press, 875-901. *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. Bioinformatics 21, 2960-

2968. *118. A Schlessinger & B Rost (2005) Protein flexibility and rigidity predicted from sequence. Proteins 61,

115-126. 119. The FANTOM Consortium, P Carninci, T Kasukawa, S Katayama, J Gough, MC Frith, N Maeda, R Oyama, T

Ravasi, B Lenhard, C Wells, R Kodzius, K Shimokawa, VB Bajic, SE Brenner, S Batalov, ARR Forrest, M Zavolan, MJ Davis, LG Wilming, V Aidinis, JE Allen, A Ambesi-Impiombato, R Apweiler, RN Aturaliya, TL Bailey, M Bansal, L Baxter, KW Beisel, T Bersano, H Bono, AM Chalk, KP Chiu, V Choudhary, A Christoffels, DR Clutterbuck, ML Crowe, E Dalla, BP Dalrymple, B deBono, G DellaGatta, D diBernardo, T Down, P Engstrom, M Fagiolini, G Faulkner, CF Fletcher, T Fukushima, M Furuno, S Futaki, M Gariboldi, P Georgii-Hemming, TR Gingeras, T Gojobori, RE Green, S Gustincich, M Harbers, Y Hayashi, TK Hensch, N Hirokawa, D Hill, L Huminiecki, M Iacono, K Ikeo, A Iwama, T Ishikawa, M Jakt, A Kanapin, M Katoh, Y Kawasawa, J Kelso, H Kitamura, H Kitano, G Kollias, SPT Krishnan, A Kruger, SK Kummerfeld, IV Kurochkin, LF Lareau, D Lazarevic, L Lipovich, J Liu, S Liuni, S McWilliam, M MadanBabu, M Madera, L Marchionni, H Matsuda, S Matsuzawa, H Miki, F Mignone, S Miyake, K Morris, S Mottagui-Tabar, N Mulder, N Nakano, H Nakauchi, P Ng, R Nilsson, S Nishiguchi, S Nishikawa, F Nori, O Ohara, Y Okazaki, V Orlando, KC Pang, WJ Pavan, G Pavesi, G Pesole, N Petrovsky, S Piazza, J Reed, JF Reid, BZ Ring, M Ringwald, B Rost, Y Ruan, SL Salzberg, A Sandelin, C Schneider, C 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,


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D Sasaki, Y Tomaru, S Fukuda, M Kanamori-Katayama, M Suzuki, J Aoki, T Arakawa, J Iida, K Imamura, M Itoh, T Kato, H Kawaji, N Kawagashira, T Kawashima, M Kojima, S Kondo, H Konno, K Nakano, N Ninomiya, T Nishio, M Okada, C Plessy, K Shibata, T Shiraki, S Suzuki, M Tagami, K Waki, A Watahiki, Y Okamura-Oho, H Suzuki, J Kawai and Y Hayashizaki (2005) The transcriptional landscape of the mammalian genome. Science 309, 1559-1563.

*120. Y Ofran, M Punta, R Schneider & B Rost (2005) Beyond annotation transfer by homology: novel protein-function prediction methods that can assist drug discovery. Drug Disc Today 10, 1475-1482.

121. R Powers, N Mirkovic, D Murray, S Goldsmith-Fischman, TB Acton, Y Chiang, R Paranji, JR Cort, JY Huang, MA Kennedy, J Liu, L Ma, B Rost & GT Montelione (2005) Solution structure of Archaeglobus fulgidis Peptidyl-tRNA hydrolase (Pth2) provides evidence for an extensive conserved family of Pth2 enzymes in archea, bacteria and eukaryotes. Protein Science 14,2849-2861.

122. DA Snyder, Y Chen, NG Denissova, T Acton, JM Aramini, M Ciano, R Karlin, J Liu, P Manor, PA Rajan, P Rossi, GV Swapna, R Xiao, B Rost, J Hunt & GT Montelione (2005) Comparisons of NMR spectral quality and success in crystallization demonstrate that NMR and X-ray crystallography are complementary methods for small protein structure determination. J Am Chem Soc 127, 16505-16511

123. J Moult, K Fidelis, T Hubbard, B Rost & A Tramontano (2006) Critical assessment of methods of protein structure prediction (CASP) - round VI. Proteins 61, 3-7.

124. O Grana, D Baker, RM MacCallum, J Meiler, M Punta, B Rost, ML Tress & A Valencia (2006) CASP6 assessment of contact prediction. Proteins 61, 214-224.

2006 (8) *125. A Schlessinger, Y Ofran, G Yachdav & B Rost (2006) Epitome: Database of structure-inferred antigenic

epitopes. Nucleic Acids Res 34, D777-D780. *126. J Liu, J Gough & B Rost (2006) Distinguishing protein-coding from non-coding RNA through support

vector machines. PLoS Genetics 2 (4):e29, DOI: 10.1371/journal.pgen.0020029. *127. A Schlessinger, G Yachdav & B Rost (2006) PROFbval: predict flexible and rigid residues in proteins.

Bioinformatics 22, 891-893. *128. S Mika & B Rost (2006) Protein–protein interactions more conserved within species than across species.

PLoS Comp Biol 2, e79. *129. Y Ofran, G Yachdav, E Mozes, T Soong & B Rost (2006) Create and assess protein networks through

molecular characteristics of individual proteins. Bioinformatics (ISMB Proceedings), 22: e402-e407. *130. H Bigelow & B Rost (2006) PROFtmb: A web server for predicting bacterial transmembrane beta barrel

proteins. Nucleic Acids Res 34, W186-188. 131. A Passerini, M Punta, A Ceroni, B Rost & P Frasconi (2006) Identifying cysteines and histidines in transition

metal binding sites by a two-stage support vector machines - neural networks approach. Proteins 22, 305-316.

132. HM Berman, SK Burley, W Chiu, A Sali, A Adzhubei, PE Bourne, SH Bryant, RL Dunbrack, Jr., K Fidelis, J Frank, A Godzik, K Henrick, A Joachimiak, B Heymann, D Jones, JL Markley, J Moult, GT Montelione, C Orengo, MG Rossmann, B Rost, H Saibil, T Schwede, DM Standley and JD Westbrook (2006) Outcome of a workshop on archiving structural models of biological macromolecules. Structure 14, 1211-1217.

2007 (13) *133. Y Ofran & B Rost (2007) ISIS: Interaction Sites Identified from Sequence. Bioinformatics (ECCB’2006),

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 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.


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*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.

153. JM Aramini, P Rossi, YJ Huang, L Zhao, M Jiang, M Maglaqui, R Xiao, J Locke, R Nair, B Rost, TB Acton, M Inouye & GT Montelione (2008) Solution NMR structure of the NlpC/P60 domain of lipoprotein Spr from Escherichia coli: structural evidence for a novel cysteine peptidase catalytic triad. Biochemistry 47, 9715-9717.

*154. D Przybylski & B Rost (2008) Powerful fusion: PSI-BLAST and consensus sequences. Proteins 24, 1987-1993.

*155. Y Ofran, A Schlessinger & B Rost (2008) Automated Identification of Complementarity Determining Regions (CDRs) reveals peculiar characteristics of CDRs and B cell epitopes. J Immunology 181, 6230-6235.

*156. Y Bromberg & B Rost (2008) SNAP predicts effect of mutations on protein function. Bioinformatics 24, 2397-2398.

*157. T-T Soong, KO Wrzeszczynski & B Rost (2008) Physical protein-protein interactions predicted from microarrays. Bioinformatics 15, 2608-2614.

*158. M Punta & B Rost (2008) Building a neural network for predicting protein features. In ‘Application of Artificial Neural Networks to Chemistry and Biology’ 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 ‘Bioinformatics – From Genomes to Therapies’ 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


31

Montelione and JF Hunt (2009) Understanding the physical properties that control protein crystallization by analysis of large-scale experimental data. Nature Biotech 27, 51-57.

*164. A Schlessinger, M Punta, G Yachdav, L Kajan & B Rost (2009) Improved disorder prediction by combination of orthogonal approaches. PLoS ONE 4, doi:10.1371/journal.pone.0004433.

*165. R Nair, J Liu, T-T Soong, TB Acton, J Everett, A Kouranov, A Fiser, A Godzik, L Jaroszewski, C Orengo, GT Montelione & B Rost (2009) Structural genomics is the largest contributor of novel structural leverage. J Structural Functional Genomics 10:181-191.

*166. C Bertonati, M Punta, M Fischer, G Yachdav, F Forouhar, W Zhou, AP Kuzin, J Seetharaman, M Abashidze, TA Ramelot, MA Kennedy, JR Cort, A Belachew, JF Hunt, L Tong, GT Montelione & B Rost (2009) Structural genomics reveals EVE as a new ASCH/PUA-related domain. Proteins 75, 760-773.

167. G Liu, F Forouhar, A Eletsky, HS Atreya, JM Aramini, R Xiao, YJ Huang, M Abashidze, J Seetharaman, J Liu, B Rost, T Acton, GT Montelione, JF Hunt and T Szyperski (2009) NMR and X-RAY structures of human E2-like ubiquitin-fold modifier conjugating enzyme 1 (UFC1) reveal structural and functional conservation in the metazoan UFM1-UBA5-UFC1 ubiquination pathway. J Struct Funct Genomics 10, 127-136.

*168. Y Bromberg, G Yachdav, Y Ofran, R Schneider & B Rost (2009) New in protein structure and function annotation: hotspots, single nucleotide polymorphisms and the Deep Web. Curr Opin Drug Discov Devel 12, 408-419.

*169. A Kernytsky & B Rost (2009) Using genetic algorithms to select most predictive protein features. Proteins 75, 75-88.

170. BH Dessailly, R Nair, L Jaroszewski, JE Fajardo, A Kouranov, D Lee, A Fiser, A Godzik, B Rost & C Orengo (2009) PSI-2: Structural Genomics to Cover Protein Domain Family Space. Structure 17, 869-881.

*171. Y Bromberg & B Rost (2009) Correlating protein function and stability through the analysis of single amino acid substitutions. BMC Bioinformatics 10 Suppl 8, S8.

172. J Moult, K Fidelis, A Kryshtafovych, B Rost & A Tramontano (2009) Critical assessment of methods of protein structure prediction-Round VIII. Proteins 77(S9), 1-4.

*173. H Bigelow & B Rost (2009) Online tools for predicting integral membrane proteins. Methods Mol Biol 528, 3-23

174. A Eletsky, DK Sukumaran, R Xiao, TB Acton, B Rost, GT Montelione & T Szyperski (2009) NMR structure of protein YvyC from Bacillus subtilis reveals unexpected structural similarity between two PFAM families. Proteins 76, 1037-1041.

175. D Cozzetto, A Kryshtafovych, K Fidelis, J Moult, B Rost, & A Tramontano (2009) Evaluation of template-based models in CASP8 with standard measures. Proteins 77(S9), 18-28.

*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 ‘Structural Bioinformatics’ P Bourne & J Gu (eds.) Wiley, 679-714.

*179. CAF Andersen & B Rost (2009) Secondary structure assignment. In ‘Structural Bioinformatics’ 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. 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.


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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 (13) *188. S Rastogi & B Rost (2011) LocDB: experimental annotations of localization for Homo sapiens and

Arabidopsis thaliana. NAR 39, D230-234. 189. Y Yang, TA Ramelot, JR Cort, D Wang, C Ciccosanti, K Hamilton, R Nair, Rost B, TB Acton, R Xiao, JK

Everett, GT Montelione & MA Kennedy (2011) Solution NMR structure of photosystem II reaction center protein Psb28 from Synechocystis sp. Strain PCC 6803. Proteins 79, 340-344.

190. Y Cao, X Jin, H Huang, MG Derebe, EJ Levin, V Kabaleeswaran, Y Pan, M Punta, J Love, J Weng, M Quick, S Ye, B Kloss, R Bruni, E Martinez-Hackert, WA Hendrickson, B Rost, JA Javitch, KR Rajashankar, Y Jiang and M Zhou (2011) Crystal structure of a potassium ion transporter, TrkH. Nature 471, 336-340.

191. RH Lathrop & B Rost (2011) ISCB Public Policy Statement on Open Access to Scientific and Technical Research Literature. PLoS Comput Biol 7, e1002014.

192. RH Lathrop & B Rost (2011) ISCB Public Policy Statement on Open Access to Scientific and Technical Research Literature. Bioinformatics 27, 291-294.

*193. A Schlessinger, C Schaefer, E Vicedo, M Schmidberger, M Punta, B Rost (2011) Protein disorder - a breakthrough invention of evolution? Current Opinion in Structural Biology, 21, 412-418.

194. W Shi, M Punta, J Bohon, JM Sauder, R D’Mello, M Sullivan, J Toomey, D Abel, M Lippi, A Passerini, P Frasconi, SK Burley, B Rost, MR Chance (2011) Characterization of metalloproteins by high-throughput X-ray absorption spectroscopy. Genome Res 21, 898-907.

195. Y Cao, X Jin, EJ Levin, H Huang, Y Zong, M Quick, J Weng, Y Pan, J Love, M Punta, B Rost, WA Hendrickson, JA Javitch, KR Rajashankar and M Zhou (2011) Crystal structure of a phosphorylation-coupled saccharide transporter. Nature 473, 50-54.

196. MN Offmann, M Krol, B Rost, I Silman, JL Sussman, AH Futerman (2011) Comparison of a molecular dynamics model with the X-ray structure of the N370S acid-beta-glucosidase mutant that causes Gaucher disease. Protein Eng Des & Sel 24, 773-775.

197. A Zimprich, A Benet-Pages, W Struhal, E Graf, SH Eck, MN Offman, D Haubenberger, S Spielberger, EC Schulte, P lichtner, SC Rossle, N Klopp, E Wolf, K Seppi, W Pirker, S Presslauer, B Mollenhauer, R Katzenschlager, T Foki, C Hotzy, E Reinthaler, A Harutyunyan, R Kralovics, A Peters, F Zimprich, T Bruecke, W Poewe, C Trenkwalder, B Rost, G Ransmayr, J Winkelmann, T Meitinger and TM Strom (2011) A mutation in VPS35, encoding a subunit of the retromer complex, causes late-onset Parkinson disease. Am J Hum Genet 89, 168-175.

198. WN Price 2nd, SK Handelman, JK Everett, SN Tong, A Bracic, JD Luff, V Naumov, T Acton, P Manor, R Xiao, B Rost, GT Montelione and JF Hunt (2011) Large-scale experimental studies show unexpected amino acid effects on protein expression and solubility in vivo in E. coli. Microbial informatics and experimentation 1, 6.

199. S Ranganathan, C Schoenbach, J Kelso, B Rost S Nathan & TW Tan (2011) Towards big data science in the decade ahead from ten years of InCoB and the 1st ISCB-Asia Joint Conference. BMC Bioinf 12 Suppl 13, S1.

200. C Schoenbach, TW Tan, J Kelso, B Rost S Nathan & S Ranganathan (2011) ICoB celebrates its tenth anniversary as first joint conference with ISCB-Asia. BMC Bioinf 12 Suppl 3, S1.

2012 (10) *201. C Schaefer, A Meier, B Rost and Y Bromberg (2012) SNPdbe: Constructing an nsSNP functional

impacts database. Bioinformatics 28, 601-602. 202. DA Snyder, JM Aramini, B Yu, YJ Huang, R Xiao, JR Cort, R Shastry, LC Ma, J Liu, Rost B, TB Acton, MA

Kennedy & GT Montelione (2012) Solution NMR structure of the ribosomal protein RP-L35Ae from Pyrococcus furiosus. Proteins 79, doi 10.1002/prot.24071.

*203. E Kloppmann, M Punta and B Rost (2012) Structural genomics plucks high-hanging membrane proteins. Curr Opin Struct Biol May 21, 601-602.


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204. T Hopf, LJ Colwell, R Sheridan, B Rost, C Sander and DS Marks (2012) Three-dimensional structures of membrane proteins from genomic sequencing. Cell 80, 1901-1906.

*205. C Schaefer, Y Bromberg, D Achten & B Rost (2012) Disease-related mutations predicted to impact protein function. BMC Genomics 13, S11 doi:10.1186/1471-2164-13-S4-S11.

*206. C Schaefer & B Rost (2012) Predict impact of single amino acid change upon protein structure. BMC Genomics 13, S4 doi:10.1186/1471-2164-13-S4-S4.

207. Z Wu, M Punta, R Xiao, TB Acton, B Sathyamoorthy, F Dey, M Fischer, A Skerra, B Rost, GT Montelione, T Szyperski (2012) NMR structure of lipoprotein YxeF from Bacillus subtilis reveals a calycin fold and distant homology with the lipocalin Blc from Escherichia coli. PLoS One 7, e37404.

208. B Rost, T Gaasterland, T Lengauer, M Linial, S Markel, BJ Morrison McKay, R Schneider, P Horton, J Kelso (2012) Paving the future: finding suitable ISMB venues. Bioinformatics 28, 2556-2559.

209. T Hamp, B Rost (2012) Alternative protein-protein interfaces are frequent exceptions. PLoS Comput Biol 8, e1002623. doi: 10.1371/journal.pcbi.1002623.

210. T Goldberg, T Hamp, B Rost (2012) LocTree2 predicts localization for all domains of life. Bioinformatics 28, i458-i465.

2013 (12) 211. U Pieper, A Schlessinger, E Kloppmann, GA Chang, JJ Chou, ME Dumont, BG Fox, P Fromme, WA

Hendrickson, MG Malkowski, DC Rees, DL Stokes, MH Stowell, MC Wiener, B Rost, RM Stroud, RC Stevens, A Sali (2013) Coordinating the impact of structural genomics on the human α-helical transmembrane proteome. Nat Struct Mol Biol 20, 135-138. doi: 10.1038/nsmb.2508.

212. P Radivojac, WT Clark, TR Oron, AM Schnoes, T Wittkop, A Sokolov, K Graim, C Funk, K Verspoor, A Ben-Hur, G Pandey, JM Yunes, AS Talwalkar, S Repo, ML Souza, D Piovesan, R Casadio, Z Wang, J Cheng, H Fang, J Gough, P Koskinen, P Törönen, J Nokso-Koivisto, L Holm, D Cozzetto, DW Buchan, K Bryson, DT Jones, B Limaye, H Inamdar, A Datta, SK Manjari, R Joshi, M Chitale, D Kihara, AM Lisewski, S Erdin, E Venner, O Lichtarge, R Rentzsch, H Yang, AE Romero, P Bhat, A Paccanaro, T Hamp, R Kaßner, S Seemayer, E Vicedo, C Schaefer, D Achten, F Auer, A Boehm, T Braun, M Hecht, M Heron, P Hönigschmid, TA Hopf, S Kaufmann, M Kiening, D Krompass, C Landerer, Y Mahlich, M Roos, J Björne, T Salakoski, A Wong, H Shatkay, F Gatzmann, I Sommer, MN Wass, MJ Sternberg, N Skunca, F Supek, M Bošnjak, P Panov, S Džeroski, T Smuc, YA Kourmpetis, AD van Dijk, CJ Braak, Y Zhou, Q Gong, X Dong, W Tian, M Falda, P Fontana, E Lavezzo, B Di Camillo, S Toppo, L Lan, N Djuric, Y Guo, S Vucetic, A Bairoch, M Linial, PC Babbitt, SE Brenner, C Orengo, B Rost, SD Mooney, I Friedberg (2013) A large-scale evaluation of computational protein function prediction. Nat Methods 10, 221-227. doi: 10.1038/nmeth.2340.

213. T Hamp, R Kassner, S Seemayer, E Vicedo, C Schaefer, D Achten, F Auer, A Boehm, T Braun, M Hecht, M Heron, P Hoenigschmid, TA Hopf, S Kaufmann, M Kiening, D Krompass, C Landerer, Y Mahlich, M Roos, B Rost (2013) Homology-based inference sets the bar high for protein function prediction. BMC Bioinformatics 14, S7.

214. T Hamp, T Goldberg, B Rost (2013) Accelerating the Original Profile Kernel. PLoS One 8, e68459. 215. J Mistry, E Kloppmann, B Rost and M Punta (2013) An estimated 5% of new protein structures solved today

represent a new Pfam family. Acta Crystallogr D Biol Crystallogr 69, 2186-2193. 216. A Bateman, J Kelso, D Mietchen, G Macintyre, T Di Domenico, T Abeel, DW Logan, P Radivojac and B Rost

(2013) ISCB computational biology Wikipedia competition. PLoS Comput Biol 9, e1003242. 217. AK Dunker, MM Babu, E Barbar, M Blackledge, SE Bondos, Z Dosztanyi, HJ Dyson, J Forman-Kay, M

Fuxtrieter, J Gsponer, K-H Han, DT Jones, S Longhi, SJ Metallo, K Nishikawa, R Nussinov, Z Obradovic, RV Pappu, B Rost, P Selenko, V Subramaniam, JL Sussman, P Tompa, VN Uversky (2013) Whats’ in a name? Why these proteins are intrinsically disordered. Intrinsically Disordered Proteins 1, e24157.

218. L Kajan, G Yachdav, E Vicedo, M Steinegger, M Mirdita, C Angermuller, A Bohm, S Domke, J Ertl, C Mertes, E Reisinger, C Staniewski and B Rost (2013) Cloud prediction of protein structure and function with PredictProtein for Debian. Biomed Res Int 2013, 398968.

219. Y Bromberg, PC Kahn and B Rost (2013) Neutral and weakly nonneutral sequence variants may define individuality. Proc Natl Acad Sci U S A 110, 14255-14260.

220. M Hecht, Y Bromberg and B Rost (2013) News from the protein mutability landscape. J Mol Biol 425, 3937-3948.

221. T Hamp, T Goldberg and B Rost (2013) Accelerating the Original Profile Kernel. PLoS ONE 8, e68459. 222. B Rost (2013) ISCB: past-present perspective for the International Society for Computational Biology.

Bioinformatics 15, 3243-3245.


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2014 (10) 223. B Rost (2014) ISCB: past-present perspective for the International Society for Computational Biology.

Bioinformatics 30, 143-145 224. A Feiglin, S Ashkenazi, A Schlessinger, B Rost and Y Ofran (2014) Co-expression and co-localization of hub

proteins and their partners are encoded in protein sequence. Mol Biosyst 10, 787-794. 225. L Kajan, TA Hopf, M Kalas, DS Marks and B Rost (2014) FreeContact: fast and free software for protein

contact prediction from residue co-evolution. BMC Bioinformatics 15, 85. 226. JM Cejuela, P McQuilton, L Ponting, SJ Marygold, R Stefancsik, GH Millburn, B Rost and C FlyBase (2014)

tagtog: interactive and text-mining-assisted annotation of gene mentions in PLOS full-text articles. Database (Oxford) 2014, bau033.

227. G Yachdav, M Hecht, M Pasmanik-Chor, A Yeheskel and B Rost (2014) HeatMapViewer: interactive display of 2D data in biology. F1000Res 3, 48.

228. Y Chang, R Bruni, B Kloss, Z Assur, E Kloppmann, B Rost, WA Hendrickson and Q Liu (2014) Structural basis for a pH-sensitive calcium leak across membranes. Science 344, 1131-1135.

229. A Schafferhans, B Rost (2014) Taking structure searches to the next dimension. Structure 22, 938-939. 230. G Yachdav, E Kloppmann, L Kajan, M Hecht, T Goldberg, T Hamp, P Honigschmid, A Schafferhans, M

Roos, M Bernhofer, L Richter, H Ashkenazy, M Punta, A Schlessinger, Y Bromberg, R Schneider, G Vriend, C Sander, N Ben-Tal and B Rost (2014) PredictProtein-an open resource for online prediction of protein structural and functional features. NAR 42, W337-43 doi:10.1093/nar/gku366.

231. T Goldberg, M Hecht, T Hamp, T Karl, G Yachdav, N Ahmed, U Altermann, P Angerer, S Ansorge, K Balasz, M Bernhofer, A Betz, L Cizmadija, KT Do, J Gerke, R Greil, V Joerdens, M Hastreiter, K Hembach, M Herzog, M Kalemanov, M Kluge, A Meier, H Nasir, U Neumaier, V Prade, J Reeb, A Sorokoumov, I Troshani, S Vorberg, S Waldraff, J Zierer, H Nielsen and B Rost (2014a) LocTree3 prediction of localization. NAR 42, W350-355 doi: 10.1093/nar/gku396.

232. T Yang, Q Liu, B Kloss, R Bruni, RC Kalathur, Y Guo, E Kloppmann, B Rost, HM Colecraft and WA Hendrickson (2014) Structure and selectivity in bestrophin ion channels. Science 346, 355-359.

2015 (15) 233. SI O'Donoghue, KS Sabir, M Kalemanov, C Stolte, B Wellmann, V Ho, M Roos, N Perdigao, FA Buske, J

Heinrich, B Rost and A Schafferhans (2015) Aquaria: simplifying discovery and insight from protein structures. Nat Methods 12, 98-99.

234. Y Guo, RC Kalathur, Q Liu, B Kloss, R Bruni, C Ginter, E Kloppmann, B Rost and WA Hendrickson (2015) Protein structure. Structure and activity of tryptophan-rich TSPO proteins. Science 347, 551-555.

235. PD Karp, B Berger, D Kovats, T Lengauer, M Linial, P Sabeti, W Hide and B Rost (2015) ISCB Ebola Award for Important Future Research on the Computational Biology of Ebola Virus. PLoS Comput Biol 11, e1004087.

236. PD Karp, B Berger, D Kovats, T Lengauer, M Linial, P Sabeti, W Hide and B Rost (2015) ISCB Ebola Award for Important Future Research on the Computational Biology of Ebola Virus. Bioinformatics 31, 616-617; e1004087.

237. J Reeb, E Kloppmann, M Bernhofer and B Rost (2015) Evaluation of transmembrane helix predictions in 2014. Proteins 83, 473-484; doi: 10.1002/prot.24749.

238. T Hamp and B Rost (2015) More challenges for machine-learning protein interactions. Bioinformatics 31, 1521-1525; doi: 10.1093/bioinformatics/btu857.

239. PD Karp, B Berger, D Kovats, T Lengauer, M Linial, P Sabeti, W Hide and B Rost (2015c) Message from the ISCB: ISCB Ebola award for important future research on the computational biology of Ebola virus. Bioinformatics pii: btv019.

240. T Hamp and B Rost (2015) Evolutionary profiles improve protein-protein interaction prediction from sequence. Bioinformatics 31, 1945-1950; doi: 10.1093/bioinformatics/btv077.

241. G Yachdav, T Goldberg, S Wilzbach, D Dao, I Shih, S Choudhary, S Crouch, M Franz, A Garcia, LJ Garcia, BA Gruning, D Inupakutika, I Sillitoe, AS Thanki, B Vieira, JM Villaveces, MV Schneider, S Lewis, S Pettifer, B Rost and M Corpas (2015) Anatomy of BioJS, an open source community for the life sciences. Elife 4; doi: 10.7554/eLife.07009.

242. M Hecht, Y Bromberg and B Rost (2015) Better prediction of functional effects for sequence variants. BMC Genomics 16 Suppl 8, S1; doi: 10.1186/1471-2164-16-S8-S1.

243. G Yachdav, T Goldberg, S Wilzbach, D Dao, I Shih, S Choudhary, S Crouch, M Franz, A Garcia, LJ Garcia, BA Gruning, D Inupakutika, I Sillitoe, AS Thanki, B Vieira, JM Villaveces, MV Schneider, S Lewis, S Pettifer, B Rost and M Corpas (2015) Anatomy of BioJS, an open source community for the life sciences. Elife 4; doi: 10.7554/eLife.07009.


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244. JA Ramilowski, T Goldberg, J Harshbarger, E Kloppman, M Lizio, VP Satagopam, M Itoh, H Kawaji, P Carninci, B Rost and AR Forrest (2015) A draft network of ligand-receptor-mediated multicellular signalling in human. Nat Commun 6, 7866; doi: 10.1038/ncomms8866.

245. E Vicedo, A Schlessinger and B Rost (2015) Environmental Pressure May Change the Composition Protein Disorder in Prokaryotes. PLoS One 10, e0133990. doi: 10.1371/journal.pone.0133990.

246. N Perdigao, J Heinrich, C Stolte, KS Sabir, MJ Buckley, B Tabor, B Signal, BS Gloss, CJ Hammang, B Rost, A Schafferhans and SI O'Donoghue (2015) Unexpected features of the dark proteome. PNAS 112, 15898-15903 doi: 10.1073/pnas.1508380112.

247. E Vicedo, Z Gasik, YA Dong, T Goldberg and B Rost (2015) Protein disorder reduced in Saccharomyces cerevisiae to survive heat shock. F1000Res 4, 1222 doi: 10.12688/f1000research.7178.1.

2016 (3) 248. SI O'Donoghue, KS Sabir, M Kalemanov, C Stolte, B Wellmann, V Ho, M Roos, N Perdigao, FA Buske, J

Heinrich, B Rost and A Schafferhans (2015) Aquaria: simplifying discovery and insight from protein structures. Nat Methods 12, 98-99.

249.J Ison, K Rapacki, H Menager, M Kalas, E Rydza, P Chmura, C Anthon, N Beard, K Berka, D Bolser, T Booth, A Bretaudeau, J Brezovsky, R Casadio, G Cesareni, F Coppens, M Cornell, G Cuccuru, K Davidsen, GD Vedova, T Dogan, O Doppelt-Azeroual, L Emery, E Gasteiger, T Gatter, T Goldberg, M Grosjean, B Gruning, M Helmer-Citterich, H Ienasescu, V Ioannidis, MC Jespersen, R Jimenez, N Juty, P Juvan, M Koch, C Laibe, JW Li, L Licata, F Mareuil, I Micetic, RM Friborg, S Moretti, C Morris, S Moller, A Nenadic, H Peterson, G Profiti, P Rice, P Romano, P Roncaglia, R Saidi, A Schafferhans, V Schwammle, C Smith, MM Sperotto, H Stockinger, RS Varekova, SC Tosatto, V de la Torre, P Uva, A Via, G Yachdav, F Zambelli, G Vriend, B Rost, H Parkinson, P Longreen and S Brunak (2015) Tools and data services registry: a community effort to document bioinformatics resources. NAR 44:D38-47 doi:10.1093/nar/gkv1116.

250. Ardiccioni, OB Clarke, D Tomasek, HA Issa, DC von Alpen, HL Pond, S Banerjee, KR Rajashankar, Q Liu, Z Guan, C Li, B Kloss, R Bruni, E Kloppmann, B Rost, MC Manzini, L Shapiro, F Mancia (2016) Structure of the polyisoprenyl-phosphate glycosyltransferase GtrB and insights into the mechanism of catalysis. Nat Commun, 7, 10175 doi: 10.1038/ncomms10175.

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/ 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.

Web services ($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


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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/ W12. R Nair & B Rost: LOC3d: Database of predicted sub-cellular localization for eukaryotic PDB chains.

Database; $root/db/LOC3d/ W13. R Nair & B Rost: LOChom: Database of sub-cellular localization predictions based on sequence

homology. Database; $root/db/LOChom/ W14. S Mika & B Rost: NLProt: Extracting protein names and sequences from scientific papers. Service;

$root/services/NLProt/ W15. R Nair & B Rost: LOCtarget: Prediction of sub-cellular localization for targets in structural genomics.

Database; $root/services/LOCtarget/ W16. KO Wrzeszczynski & B Rost: ERGolgiDB: Archive of proteins from endoplasmic reticulum and Golgi

apparatus. Database; $root/services/ERGolgiDB/ W17. R Nair & B Rost: LOCnet: De novo prediction of sub-cellular localization and prediction. Service;

$root/services/LOCnet/ W18. H Bigelow & B Rost: PROFtmb: Predictions of transmembrane beta barrels. Service;

$root/services/PROFtmb/ W19. M Punta & B Rost: PROFcon08: Predictions of inter-residue contacts. Service;

$root/services/PROFcon08/ W20. J Liu & B Rost: CHOP: Chopping proteins into structural domains. Service; $root/services/CHOP/ W21. A Schlessinger, Y Ofran, G Yachdav & B Rost: Epitome: Database of structure-inferred antigenic

epitopes. Database/Service; $root/services/epitome/ W22. G Yachdav, Y Ofran, R Nair, T-T Soong, E Mozes & B Rost: PiNat: Protein Interaction Annotation Tool.

Database/Service; $root/services/pinat/ W23. G Yachdav, Y Ofran, & B Rost: ISIS: protein-protein Interaction Sites Identified from Sequence. Service;

$root/services/isis/ W24. G Yachdav, Y Ofran, & B Rost: DISIS: DNA-protein Interaction Sites Identified from Sequence. Service;

$root/services/disis/ W25. G Yachdav, D Przybylski & B Rost: ConBlast: Consensus Sequence PSI-BLAST. Database/Service;

$root/services/conblast/ (under construction) W26. G Yachdav, Yana Bromberg & B Rost: SNAP: Screening of Non-Acceptable non-synonymous

Polymorphisms. Service; $root/services/snap/ W27. G Yachdav, A Schlessinger & B Rost: NORSnet: Prediction of disorder by identification of regions with

NO Regular Secondary structure by neural networks. Service; $root/services/norsnet/ W28. G Yachdav, A Schlessinger, M Punta & B Rost: Ucon: Prediction of disorder by identification of natively

Unstructured regions through CONtacts. Service; $root/services/ucon/ (under construction) W29. G Yachdav, A Schlessinger, M Punta, J Liu & B Rost: MD: Meta-Disorder prediction. Service;

$root/services/md/ (under construction)


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Overall numbers of publications

Types of publications (incl. in press): Peer-reviewed: 187 First/Last author: 168 Original Peer-reviewed: 172 First author: 32 Reviews: 32 Single author: 21 Book chapters: 27 Last author: 117 Conference Proceedings: 13 Editorials: 18 Books: 1


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Most often quoted publications (ISI Nov 2015) # TCi TC12 Impact Quote 1 11814 1089 1181.4 2005 Science 309 1559-1563 2 2414 1089 109.7 1993 JMB 232, 584-599 3 1262 62 60.1 1994 Proteins 19, 55-72 4 1084 21 57.1 1996 Meth Enzymol 266, 525-539 5 776 24 70.5 2004 NAR 32, W321-W326 (PP 2/Yachdav) 6 681 74 42.6 1999 Prot Engng 12, 85-94 7 603 56 28.7 1994 CABIOS 10, 53-60 8 601 9 30.1 1995 Protein Science 4, 521-533 9 496 14 26.1 1996 Protein Science 5, 1704-18 10 462 21 30.8 2000 EMBO Reports 1, 411-5 11 427 27 32.8 2002 Proteins 47, 228-235 (pollastri) 12 388 27 18.5 1994 Proteins 20, 216-226 13 320 19 22.9 2001 J Structural Biology 134, 204-18 14 283 23 35.4 2007 NAR 35, 3823-3835 (SNAP) 15 268 108 22.3 2003 JMB 325, 377-87 (ofran/six) 16 222 17 22.2 2005 JMB 348, 85-100 (LOCtree) 17 222 14 10.6 1994 JMB 235, 13-26 (sov) 18 222 6 22.2 2005 JMB 348, 85-100 (LOCtree) 19 219 14 16.8 2002 JMB 318, 595-608 (enzyme) 20 219 16 13.7 1999 Proteins 34, 220-3 (SOV2) 21 185 16 10.3 1997 JMB 270, 471-80 22 160 5 11.4 2001 Protein Science 10, 1970-9 - Proteomes 23 154 10 11.8 2002 Prot Sci 11, 2774-91 - TMH revisited 24 147 24 18.4 2007 Proteins 69, 3-9 25 147 24 12.3 2003 FEBS Letters 544, 236-9 26 141 11 11.8 2003 NAR 31, 3300-4 (PP 1=Liu & rost) 27 140 9 6.4 1993 Nature Genetics 5, 376-80 28 138 3 10.6 2002 JMB 322, 53-64 - Loopy/NORS 29 133 7 9.5 2001 Bioinformatics 17, 1242-3 - EVA 30 132 6 16.5 2007 PLOS CB 3, 1169-1176 (hotspots) 31 131 40 8.2 1999 Proteins 209-217 (cafasp) 32 126 2 10.5 2003 CMLS 60, 2637-50 33 119 13 59.5 2013 Nat Meth 10, 221-7 (CAFA1) 34 117 59 39.0 2012 Cell 149, 1607-21 (Hopf1) 35 116 57 8.9 2002 Proteins 46, 197-205 - Alignments grow 36 115 4 7.2 1999 JMB 293, 1221-1239 (Olmea) 37 112 4 9.3 2003 NAR 31, 3311-3315 (EVA) 38 110 5 10.0 2004 NAR 32, 2566-2577 (PROFtmb) 39 108 7 18.0 2009 Proteins 77, 1-4 40 108 7 10.8 2005 Moult intro Proteins 61, 3-7 41 104 7 8.0 2002 Prot Sci 11, 2836-47 - localization 42 101 9 8.4 2003 NAR 31, 3833-5 (NORSp) 43 99 7 5.8 1998 JMB 276, 517-25 - andrade 44 98 5 8.2 2003 NAR 31, 397-99 (NLSdb) 45 98 10 5.2 1996 Fold & Des 2, S19-S24 46 96 4 12.0 2007 Bioinformatics 23, E13-E16 (ofran - sites) 47 0 31 0.0 2005 Bioinformatics 21 2960-2968 (PROFcon) 48 89 -36 4.0 1993 TIBS 18, 120-123 49 86 0 8.6 2005 Proteins 61 115-126 - PROFbval 50 84 13 4.4 1996 Ann Rev 25, 113-36 51 84 3 3.7 1992 Nature 360, 540 52 82 0 13.7 2009 PLOS One 4

i TC: Times Cited (from ISI), TC12: Times Cited over last 12 months, Impact: average impact factor,

i.e. TC/number of years, Quote: ‘X et al & Rost’ -> last author=Rost, ‘X et al’ -> other last author


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53 81 24 13.5 2009 Structure 17, 869-881 54 81 24 11.6 2008 Bioinformatics 24, 2397-2398 (snap server) 55 81 40 9.0 2007 Methods 41, 460-474 (punta - membrane pred) 56 80 22 6.7 2003 NAR 31, 3789-91 (uniqueProt) 57 78 7 6.0 2002 Applied Bioinf 1, 21-35 (Chen State-of-the-art membrane) 58 77 39 5.9 2002 Structure 10, 175-184 (DSSPcont) 59 0 0 0.0 1995 ISMB 60 70 35 11.7 2009 Nature Biotechnology 27, 51-57 (Price) 61 68 35 7.6 2006 PLOS CB 2, 698-709 - Mika/Interactions 62 68 10 6.8 2005 JMB 348 507-512 (folding rates) 63 67 9 3.4 1995 Proteins 23, 295-300 64 66 13 11.0 2009 Proteins 77, 18-28 (CASP8 measures Cozetto) 65 66 13 8.3 2007 Bioinformatics 23 2376-2384 (disocontact) 66 64 20 5.3 2003 Curr Opin Chem Biol 7, 5-11 67 63 4 3.7 1998 Structure 6, 259-63 (Marrying) 68 61 2 5.1 2003 Proteins 53, 917-30 - localization 69 60 30 4.6 2002 Structure 10, 435-40 (Marti-Renom) 70 59 30 5.9 2005 Drug Disc Today 10 1475-1482 71 59 9 4.5 2002 Bioinformatics 18, 922-933 72 57 7 5.7 2005 Proteins 61, 214-224 (Grana/CASP6/cont) 73 56 7 6.2 2006 PLOS Gen 2, 529-536 74 56 14 5.1 2004 NAR 32, 3522-3530 (CHOPnet) 75 55 2 6.1 2006 Bioinformatics 22, 891-893 (PROFbval server) 76 54 5 6.8 2007 PLOS CB 3, 1335-1346 77 53 14 8.8 2009 JSFG 10, 181-91 (Structural genomics) 78 52 26 10.4 2010 Nature 467, 1074-U157 (Chen, SLAC1) 79 52 26 4.3 2003 NAR 31, 3293-5 (DSSPcont) 80 51 5 4.6 2004 Proteins 56, 188-200 (NESG) 81 49 5 3.8 2002 Bioinformatics 18, 922-933 (Target space) 82 48 24 12.0 2011 Nature 471, 336 (Cao: TrkH) 83 48 24 2.2 1993 Protein Engineering 6, 831-836 84 47 2 4.3 2004 Proteins 55, 678-688 (CHOP) 85 45 4 11.3 2011 Curr Opin Str Biol 21, 412-18 (disorder) 86 45 22 5.6 2007 Nature Biotechnology 25, 850-853 87 45 7 4.5 2005 Snyder J Am Chem Soc 127, 16505-16511 88 44 7 4.0 2004 JMB 341, 255-269 (AGAPE) 89 44 5 2.4 1997 CABIOS/Bioinformatics 13, 345-56 90 43 0 5.4 2007 Bioinformatics 23, I347-I353 (DISIS) 91 43 21 4.8 2006 Proteins 65, 305-316 (Passerini, metal binding) 92 42 21 2.8 2000 Methods 143, 71-95 (3rd generation sec str) TCsum TCave Ave Impact All 247 publications (Nov 2015) 31,997 129 10.7 Rostlab publications reached an average per-year citation index (known as Impact Factor) of ~10.7 for all publications referenced by ISI; this is higher than the impact factor of, e.g., EMBO J and PNAS. The h-index (Herfindahl index/Hirsch number) is the number of publications h cited ≥h times. My h-index according to Google is 80 (Nov 2015) and 65 according to ISI (marked by black line). The difference largely originates from the fact that ISI neither includes proceedings nor book chapters, nor any of the other many modern media that often cite the type of work we do.


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Web servers and public resources Note all the following tools are published through our web site ◊: http://www.rostlab.org PredictProtein First and most widely used internet server for protein structure prediction that

currently combines over 20 methods developed by others (e.g. ASP, BLAST, ClustalX, COILS, CYSPRED, HMMer, MaxHom, ProDom, PROSITE, PSI-BLAST, SEG, SIFT) and over 20 methods developed by us (marked by asterisk; e.g. PHD<sec|acc|htm|psi*>, TOPITS*, AGAPE*, CHOP|CHOPnet*, DISIS*, ISIS*, LOC*<hom|key|net>, MD*, PredictNLS*, PROF*<con08|acc|sec|tmb>, NORSnet*, NORSp*, SNAP*, Ucon*).

AGAPE* Fold recognition without folds: Improved and generalized method for sequence-profile and profile-profile comparisons using sequence and predicted 1D structure (secondary structure and accessibility).

CellCycleDB Database collecting and annotating proteins involved in cell-cycle control CHOP/ CHOPnet*

Method chopping proteins into structural domain-like fragments and database for 62 entirely sequence proteomes.

CLUP* Database with clusters of CHOP* fragments. ConBLAST* Aligning proteins through consensus motifs – simple add-on to the popular

BLAST/PSI-BLAST methods. DISIS* Prediction of protein-DNA interactions. DSSPcont* Server and database for continuous secondary structure assignment from PDB files. Epitome* Database of structure-inferred antigenic epitopes. ERGolgiDB Archive of proteins from endoplasmic reticulum and Golgi apparatus. EVA* Server continuously evaluating structure prediction servers for: homology modeling

(done by Sali group at UCSF), fold recognition, prediction of secondary structure, and prediction of inter-residue contacts (done by Valencia group in Madrid).

GenTegrate* ISIS* Prediction of residues involved in external protein-protein interactions. LOCdb* Database with annotations of localization for all eukaryotic proteins in PDB

(LOC3D*), all structural genomics targets (LOCtarget*), and entirely sequenced prokaryotic and eukaryotic proteomes (not yet completed).

LOCtree* Combined system for the prediction of sub-cellular localization through homology-transfer (LOChom*), automated text analysis of SWISS-PROT keywords (LOCkey*), neural network-based (LOCnet*) and SVM-based predictions (LOCsvm*), and combinations of methods specialized on “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

◊ Tools developed in our group at Columbia University marked by asterisks.


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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.

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