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Burkhard Rost

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Burkhard Rost
BornJuly 11, 1961
Germany
Alma materUniversity of Heidelberg
Known forInternational Society for Computational Biology President, Computational Biology, Bioinformatics, Machine Learning, Protein structure prediction, Protein function prediction
SpouseKarima Djabali
AwardsAlexander von Humboldt Professor
Scientific career
Fieldscomputational biology, bioinformatics, biochemistry, molecular biophysics, evolutionary biology, structural biology
InstitutionsTechnical University of Munich
Doctoral advisorChris Sander
Doctoral studentsYana Bromberg, Jinfeng Liu, Yana Ofran, Avner Schlessinger

Professor Burkhard Rost, is a scientist currently heading the Unit for Computational Biology & Bioinformatics at the Department of Informatics of the Technical University of Munich [1]. Rost chairs the Study Section Bioinformatics Munich involving the TUM (Technical University of Munich) and the LMU (Ludwig Maximilian University of Munich) in Munich. Since 2007 Rost is the President of [www.iscb.org ISCB], the International Society for Computational Biology.

Career

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Burkhard Rost originally started his scientific career as theoretical physicist. After studying physics at the University of Giessen and physics, history, philosophy, and psychology at the University of Heidelberg, Professor Rost received his doctorate at the European Molecular Biology Laboratory (EMBL) in 1994. Following research internships at EMBL and the European Bioinformatics Institute in Cambridge (UK), in 1998, he became assistant a professor at the Department of Biochemistry and Molecular Biophysics in the College of Surgeons and Physicians of the CU Medical Center of Columbia University in the City of New York. In 2000, he became associate professor at Columbia University and in 2009 he accepted an appointment to the Chair of Bioinformatics at the Technical University of Munich. He is a member of the New York Academy of Sciences and has been President of ISCB, the International Society for Computational Biology since 2007. He has authored over 200 scientific publications with an ISI Hirsch index of 52 (2011).

Contributions to Computational Biology

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Professor Rost research has focused on combining Machine Learning and evolutionary information to predict aspects of critical importance to advance our understanding of evolution, protein structure and protein function. Examples of research carried out in his lab includes the prediction of enzymatic activity (ECGO), interaction partners (ISIS, DISIS, PiNAT), subcellular localization (LOCtree, LOCnet, PredictNLS), functional effects of point mutations/SNPs (SNAP), disordered regions (MD, NORSnet, Ucon), membrane spanning segments (PROF/PHDhtm), secondary structure (PROF/PHD, RePROF, DSSPcont), solvent accessibility (PROF/PHD, RePROF), internal residue-residue contacts (PROFcon) and the clustering of proteins into families (CHOP).

The current focus of the [www.rostlab.org Rostlab] is on predicting the effects of individual mutations mostly on the level of non-synonymous changes in coding regions, i.e. single nucleotide changes (or Single Nucleotide Polymorphisms that alter the amino acid sequence.

His group has been dedicated to making their tools available online as demonstrated through the first internet server for protein structure prediction and sequence analysis [2], [www.predictprotein.org PredictProtein], that was launched in 1992, and has been continuously in service ever since.

Organizational Work

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ISCB

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Rost has been President of the professional international organization in computational biology and bioinformatics , the International Society for Computational Biology (ISCB) since 2007. He will continue to serve until 2014.

Conferences

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Rost has co-chaired the largest annual meeting in computational biology ISMB, Intelligent Systems for Molecular Biology, in 2007 (Vienna), 2008 (Toronto), 2011 (Vienna), 2012 (Long Beach) [3]. He has initiated and been involved in the organization of several series of international conferences outside the usual northern hemisphere, namely the ISCB Africa (2010: Bamako, Mali; 2011: Cape Town, South Africa; 2013: Tunis, Tunisia) in cooperation with the [www.asbcb.org African Society for Computational Biology and Bioinformatics ASBCB], the ISCB Latin America (2010: Montevideo, Uruguay; 2012: Santiago de Chile, Chile; 2014: Rio de Janeiro, Brazil), and most recently the ISCB Asia (2011: Kuala Lumpur, Malaysia; 2012: Shen Zhen, China).

Rost has also been a co-organizer of the CASP Critical Assessment of protein Structure Prediction meetings from 2002-2008 (CASP4-CASP8).

Noteworthy Achievements

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Publications

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Excerpt from full publication list; direct link to more complete list below under PubMed.

  • E Kloppmann, M Punta and B Rost (2012) Structural genomics plucks high-hanging membrane proteins. Curr Opin Struct Biol May 21, 601-602. Kloppmann, E.; Punta, M.; Rost, B. (2012). "Structural genomics plucks high-hanging membrane proteins". Current Opinion in Structural Biology. 22 (3): 326–32. doi:10.1016/j.sbi.2012.05.002. PMC 3400333. PMID 22622032.
  • T Hopf, LJ Colwell, R Sheridan, B Rost, C Sander and DS Marks (2012) Three-dimensional structures of membrane proteins from genomic sequencing. Cell May 9 online. Hopf, T. A.; Colwell, L. J.; Sheridan, R.; Rost, B.; Sander, C.; Marks, D. S. (2012). "Three-Dimensional Structures of Membrane Proteins from Genomic Sequencing". Cell. 149 (7): 1607–1621. doi:10.1016/j.cell.2012.04.012. PMC 3641781. PMID 22579045.
  • C Schaefer, A Meier, B Rost and Y Bromberg (2012) SNPdbe: Constructing an nsSNP functional impacts database. Bioinformatics 28, 601-602. Schaefer, C.; Meier, A.; Rost, B.; Bromberg, Y. (2011). "SNPdbe: Constructing an nsSNP functional impacts database". Bioinformatics. 28 (4): 601–602. doi:10.1093/bioinformatics/btr705. PMC 3278761. PMID 22210871.
  • M Punta & B Rost (2005) PROFcon: novel prediction of long-range contacts. Bioinformatics 21, 2960-2968. Punta, M.; Rost, B. (2005). "PROFcon: Novel prediction of long-range contacts". Bioinformatics. 21 (13): 2960–2968. doi:10.1093/bioinformatics/bti454. PMID 15890748.
  • A Schlessinger & B Rost (2005) Protein flexibility and rigidity predicted from sequence. Proteins 61, 115-126. Schlessinger, A.; Rost, B. (2005). "Protein flexibility and rigidity predicted from sequence". Proteins: Structure, Function, and Bioinformatics. 61 (1): 115–126. doi:10.1002/prot.20587. PMID 16080156.
  • R Nair & B Rost (2005) Mimicking cellular sorting improves prediction of subcellular localization. J Mol Biol 348, 85-100. Nair, R.; Rost, B. (2005). "Mimicking Cellular Sorting Improves Prediction of Subcellular Localization". Journal of Molecular Biology. 348 (1): 85–100. doi:10.1016/j.jmb.2005.02.025. PMID 15808855.
  • M Punta & B Rost (2005) Protein folding rates estimated from contact predictions. J Mol Biol 348, 507-512. Punta, M.; Rost, B. (2005). "Protein Folding Rates Estimated from Contact Predictions". Journal of Molecular Biology. 348 (3): 507–512. doi:10.1016/j.jmb.2005.02.068. PMID 15826649.
  • Y Ofran & B Rost (2003) Analysing six types of protein-protein interfaces. J Mol Biol 325, 377-387. Ofran, Y.; Rost, B. (2003). "Analysing six types of protein-protein interfaces". Journal of Molecular Biology. 325 (2): 377–387. doi:10.1016/s0022-2836(02)01223-8. PMID 12488102.
  • B Rost (2002) Did evolution leap to create the protein universe? Curr Opin Struct Biol 12, 409-416. Rost, B. (2002). "Did evolution leap to create the protein universe?". Current Opinion in Structural Biology. 12 (3): 409–416. doi:10.1016/s0959-440x(02)00337-8. PMID 12127462.
  • B Rost (2002) Enzyme function less conserved than anticipated. J Mol Biol 318, 595-608. Rost, B. (2002). "Enzyme Function Less Conserved than Anticipated". Journal of Molecular Biology. 318 (2): 595–608. doi:10.1016/S0022-2836(02)00016-5. PMID 12051862.


  • B Rost (1999) Twilight zone of protein sequence alignments. Protein Engineering 12, 85-94. Rost, B. (1999). "Twilight zone of protein sequence alignments". Protein Engineering. 12 (2): 85–94. doi:10.1093/protein/12.2.85. PMID 10195279.
  • B Rost (1998) Marrying structure and genomics. Structure 6, 259-263. Rost, B. (1998). "Marrying structure and genomics". Structure (London, England : 1993). 6 (3): 259–263. doi:10.1016/s0969-2126(98)00029-x. PMID 9551548.
  • MA Andrade, SI O'Donoghue & B Rost (1998) Adaptation of protein surfaces to subcellular location. J Mol Biol 276, 517-525. Andrade, M. A.; o’Donoghue, S. N. I.; Rost, B. (1998). "Adaptation of protein surfaces to subcellular location". Journal of Molecular Biology. 276 (2): 517–525. doi:10.1006/jmbi.1997.1498. PMID 9512720.
  • B Rost, R Schneider and C Sander (1997) Protein fold recognition by prediction-based threading. J Mol Biol 270, 471-480. Rost, B.; Schneider, R.; Sander, C. (1997). "Protein fold recognition by prediction-based threading". Journal of Molecular Biology. 270 (3): 471–480. doi:10.1006/jmbi.1997.1101. PMID 9237912.
  • B Rost (1997) Protein structures sustain evolutionary drift. Folding & Design 2, S19-S24. Rost, B. (1997). "Protein structures sustain evolutionary drift". Folding & Design. 2 (3): S19 – S24. doi:10.1016/s1359-0278(97)00059-x. PMID 9218962.
  • B Rost, C Sander & R Schneider (1994) PHD - an automatic server for protein secondary structure prediction. CABIOS 10, 53-60. Rost, B.; Sander, C.; Schneider, R. (1994). "PHD--an automatic mail server for protein secondary structure prediction". Computer Applications in the Biosciences : CABIOS. 10 (1): 53–60. doi:10.1093/bioinformatics/10.1.53. PMID 8193956.
  • B Rost & C Sander (1994) Conservation and prediction of solvent accessibility in protein families. Proteins 20, 216-226. Rost, B.; Sander, C. (1994). "Conservation and prediction of solvent accessibility in protein families". Proteins: Structure, Function, and Genetics. 20 (3): 216–226. doi:10.1002/prot.340200303. PMID 7892171.
  • B Rost & C Sander (1994) Combining evolutionary information and neural networks to predict protein secondary structure. Proteins 19, 55-72. Rost, B.; Sander, C. (1994). "Combining evolutionary information and neural networks to predict protein secondary structure". Proteins: Structure, Function, and Genetics. 19 (1): 55–72. doi:10.1002/prot.340190108. PMID 8066087.
  • B Rost & C Sander (1993) Prediction of protein secondary structure at better than 70% accuracy. J Mol Biol 232, 584-599. Rost, B.; Sander, C. (1993). "Prediction of Protein Secondary Structure at Better than 70% Accuracy". Journal of Molecular Biology. 232 (2): 584–599. doi:10.1006/jmbi.1993.1413. PMID 8345525.
  • B Rost & C Sander (1993) Improved prediction of protein secondary structure by use of sequence profiles and neural networks. PNAS 90, 7558-7562. Rost, B.; Sander, C. (1993). "Improved prediction of protein secondary structure by use of sequence profiles and neural networks". Proceedings of the National Academy of Sciences of the United States of America. 90 (16): 7558–7562. doi:10.1073/pnas.90.16.7558. PMC 47181. PMID 8356056.
  • 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. Meitinger, T.; Meindl, A.; Bork, P.; Rost, B.; Sander, C.; Haasemann, M.; Murken, J. (1993). "Molecular modelling of the Norrie disease protein predicts a cystine knot growth factor tertiary structure". Nature Genetics. 5 (4): 376–380. doi:10.1038/ng1293-376. PMID 8298646.
  • B Rost & Sander (1992) Jury returns on structure prediction. Nature 360, 540. Rost, B.; Sander, C. (1992). "Jury returns on structure prediction". Nature. 360 (6404): 540. doi:10.1038/360540b0. PMID 1281284.
  • B Rost (1991) Sensor Networks for Verifying Disarmament of Aircraft. Bochum: UVB Universitätsverlag Brockmeyer, Book.

References

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  1. ^ http://www.rostlab.org Rostlab web page
  2. ^ "Sequence analysis by electronic mail server". Trends in Biochemical Sciences: 267–268. July 1993.{{cite journal}}: CS1 maint: date and year (link)
  3. ^ "ISMB 2008 Toronto". PLOS Computational Biology: e1000094. June 2008.{{cite journal}}: CS1 maint: date and year (link)
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