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* [[Machine learning]]
* [[Machine learning]]
* [[Evolution]]
* [[Evolution]]
* [[Protein structure prediction]]<ref>{{cite pmid| 23353650|noedit}}</ref>
* [[Protein structure prediction]]<ref>{{Cite journal
| last1 = Radivojac | first1 = P.
| last2 = Clark | first2 = W. T.
| last3 = Oron | first3 = T. R.
| last4 = Schnoes | first4 = A. M.
| last5 = Wittkop | first5 = T.
| last6 = Sokolov | first6 = A.
| last7 = Graim | first7 = K.
| last8 = Funk | first8 = C.
| last9 = Verspoor | first9 = K.
| last10 = Ben-Hur | first10 = A.
| last11 = Pandey | first11 = G.
| last12 = Yunes | first12 = J. M.
| last13 = Talwalkar | first13 = A. S.
| last14 = Repo | first14 = S.
| last15 = Souza | first15 = M. L.
| last16 = Piovesan | first16 = D.
| last17 = Casadio | first17 = R.
| last18 = Wang | first18 = Z.
| last19 = Cheng | first19 = J.
| last20 = Fang | first20 = H.
| last21 = Gough | first21 = J.
| last22 = Koskinen | first22 = P.
| last23 = Törönen | first23 = P.
| last24 = Nokso-Koivisto | first24 = J.
| last25 = Holm | first25 = L.
| last26 = Cozzetto | first26 = D.
| last27 = Buchan
| last29 = Jones | first29 = D. T.
| last30 = Limaye | first30 = B.
| last28 = Bryson | first28 = K.
| title = A large-scale evaluation of computational protein function prediction
| doi = 10.1038/nmeth.2340 | first27 = D. W. A.
| journal = Nature Methods
| volume = 10
| issue = 3
| pages = 221–227
| year = 2013
| pmid = 23353650
| pmc =3584181
}}</ref>
* [[Protein function prediction]]
* [[Protein function prediction]]
* [[Sequence analysis]]
* [[Sequence analysis]]
Line 98: Line 138:
| pmid = 10195279
| pmid = 10195279
| doi=10.1093/protein/12.2.85
| doi=10.1093/protein/12.2.85
}}</ref><ref>{{Cite journal | doi = 10.4016/31818.01| title = 20110621 - Protein Prediction 1 - Protein Structure - Burkhard Rost| year = 2011}}</ref><ref>{{cite pmid| 24068913|noedit}}</ref><ref name=rostlab>{{cite web|archiveurl=https://web.archive.org/web/20141221123054/https://rostlab.org/|url=https://rostlab.org|title=Welcome to the Rostlab|publisher=rostlab.org|archivedate=2014-12-21}}</ref>
}}</ref><ref>{{Cite journal | doi = 10.4016/31818.01| title = 20110621 - Protein Prediction 1 - Protein Structure - Burkhard Rost| year = 2011}}</ref><ref>{{Cite journal
| last1 = Bateman | first1 = A.
| authorlink1 = Alex Bateman
| last2 = Kelso | first2 = J.
| last3 = Mietchen | first3 = D.
| last4 = MacIntyre | first4 = G.
| last5 = Di Domenico | first5 = T. S.
| last6 = Abeel | first6 = T.
| last7 = Logan | first7 = D. W.
| last8 = Radivojac | first8 = P.
| last9 = Rost | first9 = B.
| authorlink9 = Burkhard Rost
| doi = 10.1371/journal.pcbi.1003242
| title = ISCB Computational Biology Wikipedia Competition
| journal = [[PLOS Computational Biology]]
| volume = 9
| issue = 9
| pages = e1003242
| year = 2013
| pmid = 24068913
| pmc = 3777890
}}</ref><ref name=rostlab>{{cite web|archiveurl=https://web.archive.org/web/20141221123054/https://rostlab.org/|url=https://rostlab.org|title=Welcome to the Rostlab|publisher=rostlab.org|archivedate=2014-12-21}}</ref>


==Career==
==Career==
Line 226: Line 288:
| pmid = 21471968
| pmid = 21471968
| pmc =3201810
| pmc =3201810
}}</ref> ''[[Science (journal)|Science]]'',<ref>{{cite pmid| 16141072|noedit}}</ref> ''[[PLOS Genetics]]''.<ref>{{cite pmid| 16683024|noedit}}</ref>
}}</ref> ''[[Science (journal)|Science]]'',<ref>{{Cite journal
| pmid = 16141072
| year = 2005
| author1 = Carninci
| first1 = P
| title = The transcriptional landscape of the mammalian genome
| journal = Science
| volume = 309
| issue = 5740
| pages = 1559-63
| last2 = Kasukawa
| first2 = T
| last3 = Katayama
| first3 = S
| last4 = Gough
| first4 = J
| authorlink4 = Julian Gough (scientist)
| last5 = Frith
| first5 = M. C.
| last6 = Maeda
| first6 = N
| last7 = Oyama
| first7 = R
| last8 = Ravasi
| first8 = T
| last9 = Lenhard
| first9 = B
| last10 = Wells
| first10 = C
| last11 = Kodzius
| first11 = R
| last12 = Shimokawa
| first12 = K
| last13 = Bajic
| first13 = V. B.
| last14 = Brenner | first14 = S. E. | authorlink14 = Steven E. Brenner
| last15 = Batalov
| first15 = S
| last16 = Forrest
| first16 = A. R.
| last17 = Zavolan
| first17 = M
| last18 = Davis
| first18 = M. J.
| last19 = Wilming
| first19 = L. G.
| last20 = Aidinis
| first20 = V
| last21 = Allen
| first21 = J. E.
| last22 = Ambesi-Impiombato
| first22 = A
| last23 = Apweiler
| first23 = R
| authorlink23 = Rolf Apweiler
| last24 = Aturaliya
| first24 = R. N.
| last25 = Bailey
| first25 = T. L.
| last26 = Bansal
| first26 = M
| last27 = Baxter
| first27 = L
| last28 = Beisel
| first28 = K. W.
| last29 = Bersano
| first29 = T
| last30 = Bono
| first30 = H
| display-authors = 29
| doi = 10.1126/science.1112014
}}</ref> ''[[PLOS Genetics]]''.<ref>{{Cite journal
| last1 = Liu | first1 = J.
| last2 = Gough | first2 = J. | authorlink2 =Julian Gough (scientist)
| last3 = Rost | first3 = B. |authorlink3 = Burkhard Rost
| doi = 10.1371/journal.pgen.0020029
| title = Distinguishing Protein-Coding from Non-Coding RNAs through Support Vector Machines
| journal = PLoS Genetics
| volume = 2
| issue = 4
| pages = e29
| year = 2006
| pmid = 16683024
| pmc =1449884
}}</ref>


===ISCB===
===ISCB===

Revision as of 08:09, 2 September 2015

Burkhard Rost
Burkhard Rost speaking
Born (1961-07-11) July 11, 1961 (age 62)
Germany
Alma materUniversity of Heidelberg[7]
Known for
SpouseKarima Djabali[citation needed]
AwardsAlexander von Humboldt Professor, ISCB Fellows Award[1]
Scientific career
Fields
Institutions
ThesisNeural networks and evolution - advanced prediction of protein secondary structure (1994)
Doctoral advisorChris Sander[7][8]
Doctoral students
Websitewww.rostlab.org

Burkhard Rost is a scientist leading the Department for Computational Biology & Bioinformatics at the Faculty of Informatics of the Technical University of Munich (TUM).[9] Rost chairs the Study Section Bioinformatics Munich involving the TUM and the Ludwig Maximilian University of Munich (LMU) in Munich. Since 2007 Rost has been the President of the International Society for Computational Biology (ISCB).[3][10][11][12][13][14][15][16]

Career

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, Rost received his PhD at the University Heidelberg for his work at the European Molecular Biology Laboratory (EMBL) in 1994.[7] 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 from 2007-2014. As of 2011, Rost has authored or co-authored over 200 scientific publications with an Google-Scholar h-index of 79.[3][10][11][12]

Research

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),[17] solvent accessibility (PROF/PHD, RePROF), internal residue-residue contacts (PROFcon) and the clustering of proteins into families (CHOP).[citation needed]

The his current focus 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, Predictprotein,[6] that was launched in 1992, and has been continuously in service ever since. Rost's work has been published in leading peer reviewed scientific journals including Nature,[8][18][19][20] Science,[21] PLOS Genetics.[22]

ISCB

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

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).[23] 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).[citation needed]

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

Awards and honors

Rost was awarded the Professorship of the Alexander von Humboldt Foundation in 2009. He was made a Fellow of the ISCB in 2015.[24]

References

  1. ^ Category:Fellows of the International Society for Computational Biology
  2. ^ Radivojac, P.; Clark, W. T.; Oron, T. R.; Schnoes, A. M.; Wittkop, T.; Sokolov, A.; Graim, K.; Funk, C.; Verspoor, K.; Ben-Hur, A.; Pandey, G.; Yunes, J. M.; Talwalkar, A. S.; Repo, S.; Souza, M. L.; Piovesan, D.; Casadio, R.; Wang, Z.; Cheng, J.; Fang, H.; Gough, J.; Koskinen, P.; Törönen, P.; Nokso-Koivisto, J.; Holm, L.; Cozzetto, D.; Buchan, D. W. A.; Bryson, K.; Jones, D. T.; Limaye, B. (2013). "A large-scale evaluation of computational protein function prediction". Nature Methods. 10 (3): 221–227. doi:10.1038/nmeth.2340. PMC 3584181. PMID 23353650.
  3. ^ a b c Burkhard Rost publications indexed by Google Scholar
  4. ^ 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.
  5. ^ 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.
  6. ^ a b c Rost, B.; Yachdav, G.; Liu, J. (2004). "The PredictProtein server". Nucleic Acids Research. 32 (Web Server issue): W321–W326. doi:10.1093/nar/gkh377. PMC 441515. PMID 15215403.
  7. ^ a b c Rost, Burkhard (1994). Neuronale Netzwerke und evolutionäre Information : verbesserte Vorhersage der Sekundärstruktur von Proteinen (PhD thesis). Heidelberg University. OCLC 311916999.
  8. ^ a b Rost, B.; Sander, C. (1992). "Jury returns on structure prediction". Nature. 360 (6404): 540. doi:10.1038/360540b0. PMID 1281284.
  9. ^ http://www.rostlab.org Rostlab web page
  10. ^ a b Burkhard Rost at DBLP Bibliography Server Edit this at Wikidata
  11. ^ a b Burkhard Rost publications indexed by Microsoft Academic
  12. ^ a b Burkhard Rost's publications indexed by the Scopus bibliographic database. (subscription required)
  13. ^ Rost, B. (1999). "Twilight zone of protein sequence alignments". Protein engineering. 12 (2): 85–94. doi:10.1093/protein/12.2.85. PMID 10195279.
  14. ^ "20110621 - Protein Prediction 1 - Protein Structure - Burkhard Rost". 2011. doi:10.4016/31818.01. {{cite journal}}: Cite journal requires |journal= (help)
  15. ^ Bateman, A.; Kelso, J.; Mietchen, D.; MacIntyre, G.; Di Domenico, T. S.; Abeel, T.; Logan, D. W.; Radivojac, P.; Rost, B. (2013). "ISCB Computational Biology Wikipedia Competition". PLOS Computational Biology. 9 (9): e1003242. doi:10.1371/journal.pcbi.1003242. PMC 3777890. PMID 24068913.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  16. ^ "Welcome to the Rostlab". rostlab.org. Archived from the original on 2014-12-21.
  17. ^ Rost, B. (1996). "PHD: Predicting one-dimensional protein structure by profile-based neural networks". Methods in enzymology. 266: 525–539. doi:10.1016/s0076-6879(96)66033-9. PMID 8743704.
  18. ^ Chen, Y. H.; Hu, L.; Punta, M.; Bruni, R.; Hillerich, B.; Kloss, B.; Rost, B.; Love, J.; Siegelbaum, S. A.; Hendrickson, W. A. (2010). "Homologue structure of the SLAC1 anion channel for closing stomata in leaves". Nature. 467 (7319): 1074–1080. doi:10.1038/nature09487. PMC 3548404. PMID 20981093.
  19. ^ Cao, Y; Jin, X; Huang, H; Derebe, M. G.; Levin, E. J.; Kabaleeswaran, V; Pan, Y; Punta, M; Love, J; Weng, J; Quick, M; Ye, S; Kloss, B; Bruni, R; Martinez-Hackert, E; Hendrickson, W. A.; Rost, B; Javitch, J. A.; Rajashankar, K. R.; Jiang, Y; Zhou, M (2011). "Crystal structure of a potassium ion transporter, TrkH". Nature. 471 (7338): 336–40. doi:10.1038/nature09731. PMC 3077569. PMID 21317882.
  20. ^ Cao, Y.; Jin, X.; Levin, E. J.; Huang, H.; Zong, Y.; Quick, M.; Weng, J.; Pan, Y.; Love, J.; Punta, M.; Rost, B.; Hendrickson, W. A.; Javitch, J. A.; Rajashankar, K. R.; Zhou, M. (2011). "Crystal structure of a phosphorylation-coupled saccharide transporter". Nature. 473 (7345): 50–54. doi:10.1038/nature09939. PMC 3201810. PMID 21471968.
  21. ^ Carninci, P; Kasukawa, T; Katayama, S; Gough, J; Frith, M. C.; Maeda, N; Oyama, R; Ravasi, T; Lenhard, B; Wells, C; Kodzius, R; Shimokawa, K; Bajic, V. B.; Brenner, S. E.; Batalov, S; Forrest, A. R.; Zavolan, M; Davis, M. J.; Wilming, L. G.; Aidinis, V; Allen, J. E.; Ambesi-Impiombato, A; Apweiler, R; Aturaliya, R. N.; Bailey, T. L.; Bansal, M; Baxter, L; Beisel, K. W.; Bersano, T; et al. (2005). "The transcriptional landscape of the mammalian genome". Science. 309 (5740): 1559–63. doi:10.1126/science.1112014. PMID 16141072.
  22. ^ Liu, J.; Gough, J.; Rost, B. (2006). "Distinguishing Protein-Coding from Non-Coding RNAs through Support Vector Machines". PLoS Genetics. 2 (4): e29. doi:10.1371/journal.pgen.0020029. PMC 1449884. PMID 16683024.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  23. ^ Linial, M.; Mesirov, J. P.; Morrison Mckay, B. J.; Rost, B. (2008). "ISMB 2008 Toronto". PLoS Computational Biology. 4 (6): e1000094. doi:10.1371/journal.pcbi.1000094. PMC 2427177. PMID 18584023.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  24. ^ "Meet the ISCB Fellows Class of 2015". International Society for Computational Biology. Archived from the original on 2015-02-20.

External links

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