Genís Parra web page --- Ian Korf Lab. Genome Center. UC Davis

   

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Hi, welcome to my web page, I am researcher focusing 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.

I did my Ph.D. under the supervision of Dr. Roderic Guigo at the Universitat Pompeu Fabra. Then, I moved to Davis where I am focus in gene prediction and gene definition in different model organism. I am a post doc in Ian Korf lab at the UC Davis Genome Center.

My email: genparra(at)ucdavis.edu

CONTENTS

Reseach Interest GO TOP

 
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.

My research seeks to understand structure and function in genomic DNA. My final goal would be to understand how genes are defined and to generate a complete biological model: from promoter recognition to the translation to protein. Some of the main topics I am interested within this frame are:

  • Gene Prediction -- Despite roughly 20 years of research, gene prediction algorithms cannot accurately derive a proteome from a genome. I have been working in the developing of the gene finding program geneid and now I am colaborating in developing SNAP.
  • Comparative Genomics -- What can we learn from all the available genomic sequences? I have been working in using this information to predict coding regions. I developed the comparative extension of geneid program called SGP2. But I still think that we can use comparative genomics to solve a lot of interesting problems.
  • Splicing -- In a sense, all my interests are fueled by a curiosity about how intron and exons are defined and recognized. Splice enhancers, silencers, donors and acceptors... how all this information is integrated and how different is from species to species.
  • Evolution of the signals that define genes -- The fact that individual parameter files for each species perform better that general models work better than generic gene finding. This implies that gene signals and structure in each species are adapted, enabling the cell to appropriate transcription and translation for each genome. I am interested in learning about the differences of gene definition among eukaryotes.


PUBLICATIONS GO TOP

 

  • Articles:

    • G. Parra, K. Bradnam, Z. Ning, T. Keane and I. Korf
      "Assessing the gene space in draft genomes."
      Nucleic Acid Research, 37: 289-297 (2009) [Abstract]  

    • A.B. Rose, T. Effersi, G. Parra and I. Korf
      "Promoter-proximal introns in Arabidopsis thaliana are enriched in dispersed signals that elevate gene expression."
      Plant Cell, 20:543-551 (2008) [Abstract]   [Full Text]   [In brief]  

    • B. Cantarel, I. Korf, S. Robb, G. Parra, E. Ross, B. Moore, C. Holt, A. Sanchez and M. Yandell
      "MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes."
      Genome Research, 18: 188-196 (2008)   [Abstract]   [Full Text]  

    • G. Parra, K. Bradnam and I. Korf
      "CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes."
      Bioinformatics, 23: 1061-1067 (2007)   [Abstract]   [Full Text]  

    • G. Parra, A. Reymond, N. Dabbouseh, E.T. Dermitzakis, R. Castelo, T.M. Thompson, S.E. Antonarakis and R. Guigó
      "Tandem chimerism as a means to increase protein complexity in the human genome."
      Genome Research, 19(8):475-484 (2006)   [Abstract]   [From the cover]   [PubMed]

    • E. Eyras, A. Reymond, R. Castelo, J.M. Bye, F. Camara, P. Flicek, E.J. Huckle, G. Parra, D.D. Shteynberg, C. Wyss, J. Rogers, S.E. Antonarakis, E. Birney, R. Guigó and M.R. Brent
      "Gene finding in the chicken genome."
      BMC Bioinformatics, 6(1):131 (2005)   [Abstract]   [BMC Open Access Article PDF]   [PubMed]

    • R. Castelo, A. Reymond, C. Wyss, F. Câmara, G. Parra, S.E. Antonarakis, R. Guigó and E. Eyras
      "Comparative gene finding in chicken indicates that we are closing in on the set of multi-exonic widely-expressed human genes."
      Nucleic Acid Research, 33(6):1935-1939 (2005)   [Abstract]   [NAR Open Access Article PDF]   [Supplementary Material]

    • N. López-Bigas, B. Audit, C. Ouzounis, G. Parra and R. Guigó
      "Are splicing mutations the most frequent cause of hereditary disease ?"
      FEBS Letters, 579(9):1900-3 (2005)   [Abstract]   [PubMed]

    • K. Szafranski, R. Lehmann, G. Parra, R. Guigó and G. Glöckner
      "Gene Organization Features in A/T-Rich Organisms."
      Journal of Molecular Evolution, 60(1):90-98 (2005)   [Abstract]   [Full Text]

    • International Chicken Genome Sequencing Consortium
      "Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution."
      Nature, 432(7018):695-716 (2004)   [Abstract]   [Full Text]

    • Tetraodon Genome Sequencing Consortium
      "Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype."
      Nature, 431(7011):946-957 (2004)   [Abstract]   [Full Text]

    • 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.
      "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 and 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:

    • G. Parra, K. Bradnam and I. Korf
      "Gene prediction on naked genomes."
      CSHL - The biology of genomes, Hixton, UK (2005) [1.5Mb gzipped PDF file]

    • G. Parra, A. Reymond, N. Dabbouseh, E.T. Dermitzakis, R. Castelo, T.M. Thompson, S.E. Antonarakis, and R. Guigó
      "Tandem chimerism in the human genome."
      CSHL - Genome Informatics , Hixton, UK (2004) [1.5Mb gzipped PDF file]

    • 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]


  • Ph.D. dissertation:

    • "Computational Identification of Genes: ab initio and comparative approaches."
      Ph.D. Thesis, Departament de Ciéncies Experimentals i de la Salut at Universitat Pompeu Fabra, 2004.
      [6 Mb PDF file]