Burkhard Rost
TUM Informatics/Bioinformatics i12

Boltzmannstrasse 3 (Rm 01.09.052)

85748 Garching/Mnchen, Germany

&

Dept. Biochemistry & Molecular Biophysics

Columbia University

New York, USA

Description: EH20100318019

Email      assistant@rostlab.org      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 Mnchen

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

 


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: assistant@rostlab.org

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 Gieen, 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

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

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)

Austria, Belgium, Brazil, Canada, Chile, China, Czech Republic, Cuba, Denmark, England, France, Germany, Greece, Israel, Italy, Luxembourg, Mali, Malaysia, Morocco, Netherlands, South Africa, South Korea, Spain, Sweden, Switzerland, Tanzania, Turkey, Uruguay, USA

12/1988               London, England: Workshop on Arms Control

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

10/1989               Princeton, USA: Institute for Advanced Studies

05/1990               Prague, CSFR: Workshop on Arms Control

09/1990               Vienna, Austria: Conference on Arms Control

010/1990             Mosbach, Germany: Conference on Arms Control

06/1992               Elba, Italy: Conference on Neural Networks

07/1992               Torino, Italy: Conference on Protein Structure Prediction

11/1992               Nijmegen, Netherlands: EU Conference on Sequence Analysis

06/1993               Rennes, France: Workshop on Secondary Structure Prediction

11/1993               Copenhagen, DK: Conf. on 'Protein Structure by Distance Analysis'

01/1994               Mauii, Hawaii, USA: HICCS Conference

03/1994               Bologna, Italy: Conference on Protein Structures

04/1994               Copenhagen, Denmark: Mini-symposium on structure prediction

11/1994               Bielefeld, Germany: University

11/1994               Copenhagen, DK: Conf. on 'Protein Structure by Distance Analysis'

12/1994               Asilomar, USA: 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

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               Skvde, 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

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

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

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

06/2015   xx

 

Scheduled:

 

Professional Award

2009-2015           Alexander von Humboldt Professorship, Germany

2012                    Bat Sheva Fellowship, Israel

Organization of International Scientific Meetings (48)

Last counted: dublin

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)

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)

Last included 250

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 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, 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), Sren 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), Igor Jurisica (Toronto Univ. Canada), Peter C Kahn (Rutgers Univ. New Brunswick USA), Janet Kelso (MPI Leipzig Germany), Michael Kennedy (Miami Univ. Oxford OH USA), Andrew Kernytsky (Columbia Univ.), Rick Lathrop (UCI Irvine USA), Thomas Lengauer (MPI Saarbruekcen Germany), Michal Linial (Hebrew Univ. Jerusalem Israel), James Love (Albert Einstein College New York USA), Andrei Lupas (Max Planck Inst. Tuebingen Germany), Filippo Mancia (Columbia Univ. USA), Richard Mann (Columbia Univ. USA), Hannah Margalit (Hebrew Univ. Jerusalem Israel), Scott Markel (Accelrys San Diego USA), Mark Marti-Renom (UCSF San Francisco/Barcelona Spain), Ann McDermott (Columbia Univ. USA), Thomas Meitinger (Helmholtz Munich Germany), Jill P Mesirov (Broad Inst. USA), Sven Mika (Columbia Univ. USA), Guy Montelione (Rutgers Univ. USA), Sean Mooney (Indiana Univ. Bloomington USA), John Moult (CARB Univ. Maryland USA), Diana Murray (Columbia Univ. USA), Rajesh Nair (FDA USA), E Narayanan (UCSF USA), Michael Nilges (Pasteur Paris France), Yanay Ofran (Bar-Ilan Univ. Israel), Christine Orengo (Univ. College London England), Arthur G Palmer (Columbia Univ. USA), Florencio Pazos (Madrid Spain), Israel Pecht (Weizmann Inst. Rehovot Israel), Gianlucca Pollastri (Dublin Ireland), Robert Powers (Nebraska Lincoln USA), Dariusz Przybylski (Columbia Univ. USA), Marco Punta (TUM Germany), 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), David States (Ann Arbor USA), Tim Strom (Helmholtz Munich Germany), Joel Sussman (Weizmann Inst. Rehovot Israel), Thomas Szyperski (Buffalo Univ. USA), Liang Tong (Columbia Univ. USA), Hepan Tan (Columbia Univ. USA), Dimitris Thanos (Athen Univ. Greece), Liang Tong (Columbia Univ.), Anna Tramontano (Univ. Rome Italy), Alfonso Valencia (CNB Madrid Spain), Gunnar von Heijne (Stockholm Univ. Sweden), Da-Neng Wang (New York Univ. USA), Gerrit Vriend (Nijmegen Univ. Netherlands), Kaz Wrzeszczynski (Cold Spring Harbor Labs USA), John Westbrook (PDB-Rutgers Univ. USA), Zeba Wunderlich (Rutgers Univ. USA), Ming Zhou (Columbia Univ. USA), Raphael Zidovetzki (Univ. of California Riverside USA).

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

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)

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 ISMB95 (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 ISMB97 (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%)

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

Nations (32): Albania, Australia, Austria, Belarussia, Brazil, Canada, China, Denmark, Egypt, England, Germany, Greece, Hongkong, Hungary, India, Indonesia, Iran, Israel, Italy, Kazakhstan, Kenya, Macedonia, Netherlands, Pakistan, Poland, Rumania, Russia, Spain, Taiwan, Turkey, Vietnam, USA

Total number non-local: 72 (of 143)

 

NamesF (41): Ansari, Ansorge, Bakenecker, Bertonati, Bitar, Bromberg, Charu, Drabik, Christiane Gasperi, Gasik, Gembarzhevskaya, Gergen, Gilman, Goldberg, Hegyi, Iacob, Kalemanov, Rebecca Kassner, Edda Kloppmann, Linh Klose, Koh, Lin Yichun, Linh Tran, Link, Meier, Moezi, Nunes, Posy, Rastogi, Restuccia, Reisinger, Rssle-Blank, Schafferhans, Schelling, Schmidt x, Seeland x, Varshnay, Vicedo, Weise, Wolf, Yu

 

NamesM (102): Achten, Ahlborn, Andersen, Baghudana, Betz, Bernhofer, Bigelow, Biswas, Boeck x, Boidol, Bojchevski, Bruning, Bylund, Carstens x, Carter, Cejuela, Chien, Cislak, Cokol, Dallago, Dao, DeCostanzo, Domenico, Dong, Dubey, Eyrich, Gale, Galtesev, Girschick x, Githae, Halasz, Hamp, Hapfelmeier x, Hecht, Hirschbeck, Hoehn, Hoenigschmid, Hopf, James, Kajan, Karl, Kernytsky, Kiening, Kuziemko, Lim, Jinfeng Liu, Peng Liu, Mahlich, Mahmud, Menden, Mika, Milot, Mozes, Nair, Nechaev, Ng, Nguyen, Offman, Ofner, Ofran, Papadopoulos, Przybylski, Punga, Punta, Raedele, Raharja-Liu, Rahmani, Rauscher, Ravindra, Reeb, Rehan, Roberts-Wolfe, Roos, Satagopam, Schfer, Schlessinger, Schmidberger, Seitz, Shankar, Siggers, Sobhy, Soong, Sorokoumow, Spoeri, Steinegger, Sturm, Tadique, Tan, de Toro Martin, Trakhtenberg, Uhlig, Veshtort, Vinchumar, Wagner, Wei, Weininger, Wellmann, Wicker x, Wieland x, Wilzbach, Wrzeszczynski, Yachdav

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 Bck 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 Schfer                   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

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

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

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 2011

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

Doug Roberts-Wolfe           M    USA                         Hampshire                                                                     Summer 2006

Shaila Rssle-Blank             F     Brazil                       LRZ Munich, Germany                                           2010-2012

Christian Schfer                   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

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

 

UNCLEAR (MS/BS/IDP)

 

 

 


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 pending

 

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                                                                                                       

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

 

iv.                        Center of excellence in bioinformatics

PI:                        Barry Honig (Biochemistry, Columbia)

Role:                    Co-PI

Period:                 09/01/01 to 08/31/03

Agency:               NIH (5-P20-LM7276)

Ann Dir Costs:     $20,000                                                                                                   

Summary:            Fund to prepare grant proposal to begin a center of excellence.

 

v.                         Structural genomics of eukaryotic model organisms

PI:                        Gaetano T. Montelione (Rutgers University)

Role:                    Co-PI

Period:                 10/01/00 to 31/10/05

Agency:               NIH (P50 GM62413)

Ann Dir Costs:     $180,000    Total (5 years) $750,000      Overhead (4 years) $580,000

Summary:            Goal of the pilot project in structural genomics (one of nine in the USA; of about 14 world-wide) was to develop high-throughput techniques for large-scale structure determination. This project combined over 20 groups from 12 research institutions in the USA, Canada and Israel. Our particular task was the development of techniques that rationalize the automatic target selection, i.e. prioritize which proteins to pursue experimentally.

 

vi.                        Intruding into the midnight zone of protein sequence comparisons

PI:                        Burkhard Rost

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

Agency:               NIH (R01 GM63029)

Ann Dir Costs:     $190,000    Total (4 years) $750,000      Overhead (4 years) $660,000

Summary:            The 'twilight zone' of protein sequence comparison is the region in which sequence similarity does not suffice to conclude, e.g., structural similarity. The vast majority of all protein pairs of similar structure populate a 'midnight zone', i.e., their sequences differ too much for sequence-based inferences. We refined, extended, and specialized methods combining sequence alignment, structure prediction and functional information.

 

vii.                       Ab initio prediction of sub-cellular localization

PI:                        Burkhard Rost

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

Agency:               NSF (DBI-0131168)

Ann Dir Costs:     $157,000    Total (3 years) $470,000      Overhead (4 years) $240,000

Summary:            The major goals of this project were to develop a system predicting the sub-cellular localization of a protein based on sequence alignments and signal peptide motifs. The ultimate objective was to combine a series of novel methods into a comprehensive system that we can use to automatically annotate entire proteomes.

 

viii.                      Improve predictions of structure and function by PredictProtein

PI:                        Burkhard Rost

Period:                 05/01/03 – 04/30/07

Agency:               NIH/NLM (R01 LM07329)

Ann Dir Costs:     $175,000    Total (4 years) $900,000      Overhead (4 years) $770,000

Summary:            The major objective was to improve the Internet prediction server PredictProtein. The specific aims were to (1) implement technical improvements, (2) and to systematically combine the results from various methods. In particular, we worked on the improvement of methods that identify transmembrane segments from sequence.

 

ix.                        Predict putative protein-protein interface segments at low resolution

PI:                        Burkhard Rost

Period:                 05/01/03 – 04/30/07

Agency:               NIH (R01 GM64633-01)

Ann Dir Costs:     $200,000    Total (4 years) $800,000      Overhead (4 years) $680,000

Summary:            We developed methods predicting interface segments, i.e. regions of residues consecutive in sequence that are in contact with other interface segments. Separate methods addressed internal and external interfaces.

 

x.                         MAGNet: center for the analysis of multiscale genomic and cellular network

PI:                        Andrea Califano (Bio-Medical Informatics, Columbia)

Role:                    Project leader

Period:                 10/01/05 to 09/30/10

Agency:               NIH (U54-GM072980)

Ann Dir Costs:     $220,000                                                                  Overhead $120,000

Summary:            Grant proposal to begin a National Center of Excellence. Preliminarily, we proposed to build a center that provides software to other scientists. For the first two years, I acted as the coordinator of Core II proposals (biological applications of algorithms), and project leader for one of the seven main projects that proposed to integrate methods for the prediction of protein structure and function. The project was supposed to focus on the combination of related resources that already exist in the labs of various center members and on making these methods available through common interfaces.

 

xi.                        Improve predictions of structure and function by PredictProtein

PI:                        Burkhard Rost

Period:                 04/01/07 – 03/31/10

Agency:               NIH/NLM (2 R01 LM07329)

Ann Dir Costs:     $175,000    Total (4 years) $900,000      Overhead (4 years) $770,000

Summary:            The major objective was to improve the Internet prediction server PredictProtein (PP). By 2008, this server had been used over 2 million times by over 30,000 researchers from 106 countries. The scientific solutions address two related tasks pertaining to protein function prediction. The first was to predict the effect of amino acid substitutions. We developed novel machine learning-based methods to distinguish between mutations that effect structure, or function, or have no apparent phenotype. The second major task was the identification of natively unstructured regions and their functional classification. Proteins that do not adopt regular structures in isolation are increasingly becoming an important research area; they may provide a key to the evolution of complexity from proka- to eukaryotes. We developed machine learning-based identifications of features specific to this important class of molecules. All new methods have been made available through PredictProtein.

 

xii.                       Meeting for Critical Assessment of protein Structure Prediction (CASP)

PI:                        Burkhard Rost

Period:                 08/01/04 – 07/31/09

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

Ann Dir Costs:     $45,000      Total (5 years) $194,447                                 Overhead $0

Summary:            This grant funded 3 consecutive CASP meetings that have evolved into the major event in the structure prediction field. Note that this grant neither covered any salaries, nor any expenses for my group.

 

xiii.                      Structural genomics of eukaryotic model organisms

PI:                        Gaetano T. Montelione (Rutgers University)

Role:                    Co-PI

Period:                 07/01/05 to 06/30/10

Agency:               NIH (U54 GM074958-01)

Ann Dir Costs:     $150,000    Total (5 years) $750,000      Overhead (5 years) $580,000

Title:                     Structural genomics of eukaryotic model organisms

Summary:            Goal was the large-scale experimental determination of protein structures. This project combined over 20 groups from 12 research institutions in the USA and Canada. Our particular task was the development of techniques that rationalized the automatic target selection, i.e. prioritize which proteins to pursue experimentally and to cluster proteins into dynamic families with annotations of function.

 

xiv.                      Structural genomics for membrane proteins (NYCOMPS)

PI:                        Wayne Hendrickson

Role:                    Co-PI

Period:                 09/01/05 to 08/31/10

Agency:               NIH (U54 GM75026)

Ann Dir Costs:     $200 K        Total (5 years) $500,000        Overhead (5 years) $300,000

Summary:            Our development center in structural genomics (NYCOMPS: New York Consortium for Membrane Protein Structural genomics) investigated to which extent experimental high-throughput determination of 3D structures for membrane proteins is feasible. In order to achieve this, the center established a pipeline for high-throughput expression and purification. Our group was responsible for target selection. In particular, we clustered membrane proteins using existing methods. The project has been continued into a second five-year phase (see Grants active).

 

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.

 


List of publications

Theses

   A.      B Rost (1988) Lernalgorithmen fr verdnnte 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 Universittsverlag 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 Journ, W Kaiser, J Klinger, P Lewis, J Mlek, 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 Universittsverlag 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.

   *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 Fjellstrm, 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.) Skvde, Sweden: World Scientific, 87-101.

   *33.  B Rost (1997) NN which predicts protein secondary structure. In 'Handbook of Neural Computation', E Fiesler and R Beale (eds.) New York: Oxford Univ. Press, G4.1.

   *34.  B Rost (1997) Protein structures sustain evolutionary drift. Folding & Design 2, S19-S24.

   *35.  B Rost & SI O'Donoghue (1997) Sisyphus and prediction of protein structure. Bioinformatics 13, 345-356.

   *36.  B Rost, R Schneider and C Sander (1997) Protein fold recognition by prediction-based threading. J Mol Biol 270, 471-480.

   *37.  B Rost (1997) Better 1D predictions by experts with machines. Proteins Suppl. 1, 192-197.

 

1998 (4)

   *38.  MA Andrade, SI O'Donoghue & B Rost (1998) Adaptation of protein surfaces to subcellular location. J Mol Biol 276, 517-525.

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

   *40.  B Rost (1998) Protein structure prediction in 1D, 2D, and 3D. In 'The Encyclopaedia of computational chemistry' P von Ragu 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.

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

 

2003 (24)

   *70.  Y Ofran & B Rost (2003) Analysing six types of protein-protein interfaces. J Mol Biol 325, 377-387.

   *71.  CAF Andersen & B Rost (2003) Automatic secondary structure assignment. Methods Biochem Anal 44, 341-363.

   *72.  B Rost (2003) Prediction in 1D: secondary structure, membrane helices and accessibility. Methods Biochem Anal 44, 559-587.

   *73.  P Carter, J Liu & B Rost (2003) PEP: Predictions for entire proteomes. Nucl Acids Res 31, 410-413.

   *74.  R Nair, P Carter & B Rost (2003) NLSdb: database of nuclear localization signals. Nucl Acids Res 31, 397-399.

   *75.  J Liu & B Rost (2003) Domains, motifs, and clusters in the protein universe. Curr Opin Chem Biol 7, 5-11.

   *76.  B Rost (2003) Rising accuracy of protein secondary structure prediction. In 'Protein structure determination, analysis, and modeling for drug discovery', D Chasman (ed.) New York: Dekker, 207-249.

   77.    R Zidovetzki, B Rost, Don L Armstrong & I Pecht (2003) Role of transmembrane domains in the functions of Fc receptors. J Biophysical Chemistry 15, 555-575.

   *78.  Y Ofran & B Rost (2003) Predict protein-protein interaction sites from local sequence information. FEBS Let 544, 236-239.

   *79.  B Rost (2003) Neural networks predict protein structure: hype or hit? In 'Artificial intelligence and heuristic methods in bioinformatics' P Frasconi and R Shamir (eds.) Amsterdam: IOS Press, 34-50.

   *80.  KO Wrzeszczynski & B Rost (2003) Cataloguing proteins in cell cycle control. In 'Cell cycle checkpoint control protocols' H Lieberman (ed.) Totowa: Humana Press, 219-233.

   *81.  B Rost, J Liu, D Przybylski, R Nair, H Bigelow, K Wrzeszczynski & Y Ofran (2003) Predicting protein structure through evolution. In 'Chemoinformatics - From Data to Knowledge' J Gasteiger & T Engel (eds.) New York: Wiley, 1789-1811.

   *82.  B Rost & J Liu (2003) The PredictProtein server. Nucl Acids Res 31, 3300-3304.

   *83.  J Liu & B Rost (2003) NORSp: predictions of long regions without regular secondary structure. Nucl Acids Res 31, 3833-3835.

   *84.  R Nair & B Rost (2003) LOC3D: annotate sub-cellular localization for protein structures. Nucl Acids Res 31, 3337-3340.

   *85.  S Mika & B Rost (2003) UniqueProt: creating representative protein sequence sets. Nucl Acids Res 31, 3789-3791.

   *86.  A Kernytsky & B Rost (2003) Static benchmarking of membrane helix predictions. Nucl Acids Res 31, 3642-3644.

   *87.  IYY Koh, VA Eyrich, MA Mart-Renom, D Przybylski, MS Madhusudhan, E Narayanan, O Graa, 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 Graa, 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.

   *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 Schnbach, K Sekiguchi, CAM Semple, S Seno, L Sessa, Y Sheng, Y Shibata, H Shimada, K Shimada, D Silva, B Sinclair, S Sperling, E Stupka, K Sugiura, R Sultana, Y Takenaka, K Taki, K Tammoja, SL Tan, S Tang, MS Taylor, J Tegner, SA Teichmann, HR Ueda, E vanNimwegen, R Verardo, CL Wei, K Yagi, H Yamanishi, E Zabarovsky, S Zhu, A Zimmer, W Hide, C Bult, SM Grimmond, RD Teasdale, ET Liu, V Brusic, J Quackenbush, C Wahlestedt, JS Mattick, DA Hume, C Kai, D Sasaki, Y Tomaru, S Fukuda, M Kanamori-Katayama, M Suzuki, J Aoki, T Arakawa, J Iida, K Imamura, M Itoh, T Kato, H Kawaji, N Kawagashira, T Kawashima, M Kojima, S Kondo, H Konno, K Nakano, N Ninomiya, T Nishio, M Okada, C Plessy, K Shibata, T Shiraki, S Suzuki, M Tagami, K Waki, A Watahiki, Y Okamura-Oho, H Suzuki, J Kawai and Y Hayashizaki (2005) The transcriptional landscape of the mammalian genome. Science 309, 1559-1563.

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

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

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

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

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

 

2006 (8)

   *125.    A Schlessinger, Y Ofran, G Yachdav & B Rost (2006) Epitome: Database of structure-inferred antigenic epitopes. Nucleic Acids Res 34, D777-D780.

   *126.    J Liu, J Gough & B Rost (2006) Distinguishing protein-coding from non-coding RNA through support vector machines. PLoS Genetics 2 (4):e29, DOI: 10.1371/journal.pgen.0020029.

   *127.    A Schlessinger, G Yachdav & B Rost (2006) PROFbval: predict flexible and rigid residues in proteins. Bioinformatics 22, 891-893.

   *128.    S Mika & B Rost (2006) Protein–protein interactions more conserved within species than across species. PLoS Comp Biol 2, e79.

   *129.    Y Ofran, G Yachdav, E Mozes, T Soong & B Rost (2006) Create and assess protein networks through molecular characteristics of individual proteins. Bioinformatics (ISMB Proceedings), 22: e402-e407.

   *130.    H Bigelow & B Rost (2006) PROFtmb: A web server for predicting bacterial transmembrane beta barrel proteins. Nucleic Acids Res 34, W186-188.

   131. A Passerini, M Punta, A Ceroni, B Rost & P Frasconi (2006) Identifying cysteines and histidines in transition metal binding sites by a two-stage support vector machines - neural networks approach. Proteins 22, 305-316.

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

 

2007 (13)

   *133.    Y Ofran & B Rost (2007) ISIS: Interaction Sites Identified from Sequence. Bioinformatics (ECCB2006), 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.

   *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. In In silico technology in drug target identification and validation D Leon & S Markel (eds.) Boca Raton, FL: CRC Press, 435-463.

   *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 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.

   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 DMello, 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.

   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 Trnen, 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 Kaner, S Seemayer, E Vicedo, C Schaefer, D Achten, F Auer, A Boehm, T Braun, M Hecht, M Heron, P Hnigschmid, TA Hopf, S Kaufmann, M Kiening, D Krompass, C Landerer, Y Mahlich, M Roos, J Bjrne, 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.

 

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.

   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

   W3.  IYY Koh, VA Eyrich, MA Mart-Renom, D Przybylski, MS Madhusudhan, E Narayanan, O Graa, 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)

 

Overall numbers of publications

Cumulative 1999-2008 (Columbia):

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

 

Xxbr:

Google 2016/01/20: total 30502; h-index 80, i10-index 179

ISI 2015/02/11

Results 256

Sum times cited 29798

Avg 116.4

h-index 64

 

 


Most often quoted publications (ISI Nov 2015)

#             TC[i]    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

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.  


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 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.

 

           

 



       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.

       Group members in bold letters; journals underlined; asterisk marks first/senior author publications; peer-reviewed publications marked by solid gray bar on left.

[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

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