Andreas Prlic - CV
| place of birth: | Salzburg |
| nationality: | Austrian |
| e-mail: | andreas.prlic@gmail.com |
Employment
- 2008 - now Senior Scientist at the PDB database
at University of California, San Diego, CA, USA.
-
2004 - 2008 Research Associate with Tim Hubbard
at the Wellcome Trust Sanger Institute, Hinxton, Cambridge, U.K.
working on the BioSapiens and eFamily projects. - 1999-2003 Research Assistent with Manfred Sippl
at Center of Applied Molecular Engineering, University of Salzburg, Austria - 2000-2003 Bioinformatics Consultant for ProCeryon Bioinformatics
- 2000-2003 Teaching at University of Salzburg- different Lectures and Courses
Education
- 1999-2003 Ph.D. student in group of Manfred Sippl
Center of Applied Molecular Engineering, University of Salzburg
Title: WILMA - a platform for the automated annotation of protein sequences [more] - 1997- 1999 Diploma thesis in group of Manfred Sippl.
Center of Applied Molecular Engineering, University of Salzburg
Title: Deriving substitution matrices for amino acids and secondary structure [more] - 1992 - 1999 studies in biology / genetics with special focus on bioinformatics
University of Salzburg
Projects
- BioJava - Project leader, maintainer of the protein structure modules, release coordinator
- SPICE - Data integration from genome to protein structure, based on the Distributed Annotation System (DAS). e.g. mapping SNPs on protein structure. SPICE is a browser for protein sequences, structures and their annotations. [more]
- DAS registration server - a repository of available DAS servers. Currently more than 250 DAS sources from ~40 groups worldwide are available. [more]
- SISYPHUS multiple structure alignments of proteins with non-trivial relationships. [website]
- WILMA - platform for automated annotation of protein sequences [more]
- Amino acid substitution matrices [more]
Languages
- German
- English
- Croatian
Computer Skills
- open source projects:
- BioJava - Project leader
- programming languages:
- relational database design, administration
MySQL - OSX, Linux, Windows
- various: GUIs (Java, Tk, HTML), SOAP, Apache, Tomcat, JSP, Ajax, Hibernate, JQuery, OpenID
Publications:
[pubmed]
[google scholar]
Integration of open access literature into the RCSB Protein Data Bank Using BioLit.
BMC Bioinformatics. 2010 Apr 29;11(1):220.
Prlic A, Martinez MA, Dimitropoulos D, Beran B, Yukich BT, Rose PW, Bourne PE, Fink JL.
[abstract] [ pubmed ]
Will widgets and semantic tagging change computational biology?
PLoS Comput Biol. 2010 Feb 26;6(2)
Bourne PE, Beran B, Bi C, Bluhm W, Dunbrack R, Prlic A, Quinn G, Rose P, Shah R, Tao W, Weitzner B, Yukich B.
[abstract]
[pdf]
[pubmed]
DASMI: exchanging, annotating and assessing molecular interaction data.
Bioinformatics. 2009 May 15;25(10):1321-8
Blankenburg H, Finn RD, Prlic A, Jenkinson AM, Ramirez F, Emig D, Schelhorn SE, Buech J, Lengauer T, Alrbecht M.
[abstract] [pdf] [pubmed]
The Protein Feature Ontology: A Tool for the Unification of Protein Feature Annotations
Bioinformatics. 2008 Dec 1;24(23):2767-72. Epub 2008 Oct 20
Gabrielle A. Reeves, Karen Eilbeck, Michele Magrane, Claire O'Donovan, Luisa Montecchi-Palazzi, Midori A. Harris, Sandra Orchard, Rafael C. Jimenez, Andreas Prlic, Tim J.P. Hubbard, Henning Hermjakob, and Janet M. Thornton
doi:10.1093/bioinformatics/btn528
[abstract] [pdf] [pubmed]
BioJava: an Open-Source Framework for Bioinformatics
Bioinformatics 2008 24(18):2096-2097
Richard CG Holland, Thomas A Down, Matthew Pocock, Andreas Prlic, David Huen, Keith James, Sylvain Foisy, Andreas Dräger, Andy Yates, Michael Heuer, and Mark J. Schreiber
doi:10.1093/bioinformatics/btn397
[abstract] [pdf] [pubmed]
Integrating biological data - the Distributed Annotation System
BMC Bioinformatics 2008, 9(Suppl 8):S3
Andrew M Jenkinson, Mario Albrecht, Ewan Birney, Hagen Blankenburg, Thomas Down, Robert D Finn, Henning Hermjakob, Tim JP Hubbard, Rafael C Jimenez, Philip Jones, Andreas Kahari, Eugene Kulesha, Jose R Macias, Gabrielle A Reeves, and Andreas Prlic
doi:10.1186/1471-2105-9-S8-S3
[abstract] [pdf] [pubmed]
Ensembl 2008
Nucleic Acids Res. Database Issue 2008
Flicek P, Aken BL, Beal K, Ballester B, Caccamo M, Chen Y, Clarke L, Coates G, Cunningham F, Cutts T, Down T, Dyer SC, Eyre T, Fitzgerald S, Fernandez-Banet J, Graf S, Haider S, Hammond M, Holland R, Howe KL, Howe K, Johnson N, Jenkinson A, Kahari A, Keefe D, Kokocinski F, Kulesha E, Lawson D, Longden I, Megy K, Meidl P, Overduin B, Parker A, Pritchard B, Prlic A, Rice S, Rios D, Schuster M, Sealy I, Slater G, Smedley D, Spudich G, Trevanion S, Vilella AJ, Vogel J, White S, Wood M, Birney E, Cox T, Curwen V, Durbin R, Fernandez-Suarez XM, Herrero J, Hubbard TJ, Kasprzyk A, Proctor G, Smith J, Ureta-Vidal A, Searle S.
doi:10.1093/nar/gkm988
[abstract] [pdf] [pubmed]
Integrating sequence and structural biology with DAS BMC Bioinformatics 2007, 8:333;
Andreas Prlic, Thomas A Down, Eugene Kulesha, Robert D Finn, Andreas Kahari and Tim J.P. Hubbard
[abstract] [pdf] [pubmed]
New tools and expanded data analysis capabilities at the protein structure prediction center
Proteins: Structure, Function, and Bioinformatics; 2007;69 Suppl 8:19-26.
Andriy Kryshtafovych, Andreas Prlic, Zinoviy Dmytriv, Pawel Daniluk, Maciej Milostan, Volker Eyrich, Tim Hubbard, Krzysztof Fidelis
[abstract] [pdf] [pubmed]
Ensembl 2007.
Nucleic Acids Res. Database Issue 2007
Hubbard TJ, Aken BL, Beal K, Ballester B, Caccamo M, Chen Y, Clarke L, Coates G, Cunningham F, Cutts T, Down T, Dyer SC, Fitzgerald S, Fernandez-Banet J, Graf S, Haider S, Hammond M, Herrero J, Holland R, Howe K, Howe K, Johnson N, Kahari A, Keefe D, Kokocinski F, Kulesha E, Lawson D, Longden I, Melsopp C, Megy K, Meidl P, Ouverdin B, Parker A, Prlic A, Rice S, Rios D, Schuster M, Sealy I, Severin J, Slater G, Smedley D, Spudich G, Trevanion S, Vilella A, Vogel J, White S, Wood M, Cox T, Curwen V, Durbin R, Fernandez-Suarez XM, Flicek P, Kasprzyk A, Proctor G, Searle S, Smith J, Ureta-Vidal A, Birney E.
[abstract] [pdf] [pubmed]
SISYPHUS - structural alignments for proteins with non-trivial relationships
Nucleic Acid Research Database Issue 2007 D253-D259
Antonina Andreeva, Andreas Prlic, Tim J. P. Hubbard and Alexey G. Murzin
[abstract] [pdf] [pubmed]
The Distributed Annotation System for Integration of Biological Data
Data Integration in the Life Sciences: Third International Workshop, DILS 2006. Proceedings
Andreas Prlic, Ewan Birney, Tony Cox, Thomas A. Down, Rob Finn, Stefan Graef, David Jackson, Andreas Kahari, Eugene Kulesha, Roger Pettett, James Smith, Jim Stalker, Tim J. P. Hubbard
Lecture Notes in Computer Science
Publisher: Springer Berlin / Heidelberg
ISSN: 0302-9743
Volume 4075 / 2006
Editors: Ulf Leser, Felix Naumann, Barbara Eckman
ISBN: 3-540-36593-1
DOI: 10.1007/11799511
Chapter: pp. 195 - 203
[abstract] [pdf]
Ensembl 2006.
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D556-61.
Birney E, Andrews D, Caccamo M, Chen Y, Clarke L, Coates G, Cox T, Cunningham F, Curwen V, Cutts T, Down T, Durbin R, Fernandez-Suarez XM, Flicek P, Graf S, Hammond M, Herrero J, Howe K, Iyer V, Jekosch K, Kahari A, Kasprzyk A, Keefe D, Kokocinski F, Kulesha E, London D, Longden I, Melsopp C, Meidl P, Overduin B, Parker A, Proctor G, Prlic A, Rae M, Rios D, Redmond S, Schuster M, Sealy I, Searle S, Severin J, Slater G, Smedley D, Smith J, Stabenau A, Stalker J, Trevanion S, Ureta-Vidal A, Vogel J, White S, Woodwark C, Hubbard TJ.
[abstract] [pdf] [pubmed]
Adding some SPICE to DAS
Bioinformatics. 2005 Volume 21, suppl_2 Pp. ii40-ii41
Prlic-A, Down-TA, Hubbard-TJP
[abstract] [pdf] [pubmed]
WILMA - platform for the annotation of protein sequences
Bioinformatics. 2004 Jan 1;20(1):127-8.
Prlic-A, Domingues-FS, Lackner-P, Sippl-MJ
[abstract] [pdf] [pubmed]
Assessment of the CASP4 Fold Recognition Category.
Proteins. 2001; 45 (S5): 55-67
Sippl-MJ, Lackner-P, Domingues-FS, Prlic-A, Malik-R, Andreeva-A, Wiederstein-M [abstract] [pdf] [pubmed]
Structure-derived substitution matrices for alignment of distantly related sequences.
Protein Eng. 2000 Aug;13(8):545-50
Prlic-A, Domingues-FS, Sippl-MJ
[abstract] [pdf] [pubmed]
Sustained performance of knowledge-based potentials in fold recognition.
Proteins. 1999;37(S3):112-20
Domingues-FS, Koppensteiner-WA, Jaritz-M, Prlic-A, Weichenberger-C, Wiederstein-M, Floeckner-H, Lackner-P, Sippl-MJ
[abstract] [pdf] [pubmed]
© Andreas Prlić 2010