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Hi, welcome to my web page, I am a PhD. student focusing my
research on the computational modeling of DNA and gene prediction. I
was born in Barcelona in 1975, and I graduated at the
Facultat de Biologia of the
Universitat de Barcelona. Computer
science was always my favourite hobby, so I have been introduced into
Bioinformatics.
My email:
gparra(at)imim.es
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The main focus area of my research is genome sequence analysis of
either the human and any other available genome sequence. Current
projects in the group focus on novel gene prediction methodology, in
particular making use of comparative genome sequence data from related
species. We are also exploring ways to recognise conserved regulatory
sequences.
I am almost finishing my Ph.D. thesis on gene prediction and the
analysis of the mechanism of recognition and processing of eukariotic
genes.
• Gene prediction
I have worked in the "training" of geneid. In the context of geneid training means essentially computing PWMs for splice sites and start codons, deriving a model of coding, and building a gene model. GeneID for GASP1
• Gene prediction in Dictyostelium discoideum
• Syntenic gene prediction
- Articles:
- R. Guigó, E.T. Dermitzakis, P. Agarwal, C.P. Ponting, G. Parra, A. Reymond, J.F. Abril, E. Keibler, R. Lyle, C. Ucla, S.E. Antonarakis and M.R. Brent.
"Comparison of mouse and human genomes followed by experimental verification yields an estimated 1,019 additional genes."
Proc. Nat. Acad. Sci. 100(3):1140-1145 (2003) [ PubMed ]
[ Abstract ]
[ Full Text ]
- G. Parra, P. Agarwal, J.F. Abril, T. Wiehe, J.W. Fickett and R. Guigó.
"Comparative gene prediction in human and mouse."
Genome Research 13(1):108-117 (2003) [Abstract]
- Mouse Genome Sequencing Consortium (including G. Parra).
"Initial sequencing and comparative analysis of the mouse genome."
Nature 420(6915):520-562 (2002) [Abstract]
- G. Glökner, L. Eichinger, K. Szafranski, J.A. Pachebat, A.T. Bankier, P.H. Dear, R. Lehmann, C. Baumgart, G. Parra, J.F. Abril, R. Guigó, K. Kumpf, B. Tunggal, the Dictyostelium Genome Sequencing Consortium, E. Cox, M.A. Quail, M. Platzer, A. Rosenthal and A.A. Noegel.
"Sequence and Analysis of Chromosome 2 of Dictyostelium discoideum."
Nature 418(6893):79-85 (2002) [Abstract]
- G. Parra, E, Blanco, R. Guigó.
"geneid in Droshophila."
Genome Research,10, 511-515 (2000) [Abstract]
- Book Chapters:
- E. Blanco, G. Parra and R. Guigó.
"Using geneid to Identify Genes."
In A. D. Baxevanis and D. B. Davison, chief editors:
Current Protocols in Bioinformatics. Volume 1, Unit 4.3.
John Wiley & Sons Inc., New York, 2002. ISBN: 0-471-25093-7.
- Posters:
- J.F. Abril, M. Albà, E. Blanco, M. Burset, F. Câmara, S. Castellano, R. Castelo, O. Gonzalez, G. Parra and R. Guigó
"Understanding the Eukaryotic Genome Sequence."
Inaugural Symposium of the Center for Genomic Regulation, Barcelona, Spain (2002) [1.5Mb gzipped PDF file]
- E. Blanco, G. Parra, S. Castellano, J.F. Abril, M. Burset, X. Fustero, X. Messeguer and R. Guigó
"Gene Prediction in the Post-Genomic Era."
IX th ISMB, Copenhagen, Denmark (2001) [695Kb gzipped PostScript file]
- G. Glöckner, L. Eichinger, K. Szafranski, P. Dear, J. Pachebat, K. Kumpf, R. Lehmann, J.F. Abril, G. Parra, R. Guigó, B. Tunggal, E. Cox, M.A. Quail, M. Platzer, A. Rosenthal, A.A. Noegel and the Dictyostelium Genome Sequencing Consortium.
"Sequence and Analysis of Chromosome 2 from the Model Organism Dictyostelium discoideum."
CSHL - Genome Sequencing & Biology, New York, USA (2001) [ Link to Dictyostelium team at IMB-Jena ]
- J.F. Abril, E. Blanco, M. Burset, S. Castellano, X. Fustero, G. Parra and R. Guigó
"Genome Informatics Research Laboratory: Main Research Topics."
I st Jornadas de Bioinformática, Cartagena, Spain (2000) [1.2Mb gzipped PostScript file]
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