Genome BioInformatics Research Lab

 IMIM * UPF * CRG * GRIB HOME PEOPLE * Josep F. Abril
 

MyPhoto

jabril @ ub.edu

Current Address

Planarian Lab
Dept. Genètica
Facultat de Biologia
Universitat de Barcelona
Av Diagonal, 645
08028 - Barcelona
Catalonia (Spain)

Phone: +34.934.034.795
Fax: +34.934.110.969

Previous Address

Genome
Bioinformatics Lab

GRIB @ UPF/IMIM/CRG
Passeig Marítim, 37-49
08003 - Barcelona

I graduated on 1998 in Biology (Bachelor's degree) by Universitat de Barcelona (UB). I've spent my last years as undergraduate collaborating with the laboratory of genome analysis at the Grup de Recerca en Informàtica Biomèdica (GRIB), under Dr. Roderic Guigó supervision. I obtained the Research competence and Advanced Studies Diploma (Diploma d'Estudis Avançats, DEA) on 2002 by Department of Experimental Sciences and Health (CEXS) of Universitat Pompeu Fabra (UPF). From late 1998, I stayed as a PhD student, under supervision of Dr. Roderic Guigó within the Genome Bioinformatics Lab at GRIB. I defended my PhD thesis, entitled "Comparative Analysis of Eukaryotic Gene Sequence Features", on May 18, 2005. On January 2006, I received a "Juan de la Cierva" post-doctoral fellowship and I moved to the lab of Dr. Emili Saló at the Genetics Department of the Faculty of Biology of the Universitat de Barcelona. On October 2006, I've got a lector position at that department.

Although I have a degree in Biology, I also like computers, so I have been introduced into Bioinformatics. Therefore, I consider myself as a Computational Biologist. My main research interest focuses on the computational analysis of the exonic structure of eukaryotic genes, its definition, evolution and association with genetic disorders. Gene-finding and the visualization of genomic annotations, along with the iIntegration of highthroughput ("omics") evidences are also within those interests.

I program in GNUawk, bash, PostScript, Perl and a little of C and R. Now I am also learning mySQL and PHP. I have also skills in LaTeX and HTML, including a little bit of Javascript and CSS. From 2000 to 2006, I've been in charge of the Genome Bioinformatics Lab web site. Nowadays, I'm running the Planarian Lab web site. I have developed several scripts and PostScript code to obtain graphical representations from genomic annotation data-sets. The most advanced are gff2ps and gff2aplot, both reading input as GFF format and producing a PS output plot. gff2ps was used to visualize different whole genome maps, including those for human, the fruitfly and the malaria mosquito. You can now access to their web pages from here.

I have been teaching assistant for the practicals of the Bioinformatics course taught at the fourth year of the curricula of the Faculty of Biology at the Universitat Pompeu Fabra, between 2001 and 2006. Additionally, I have taught an introductory perl course for the MSc on Bioinformatics for Health Sciences, co-directed by Universitat Pompeu Fabra and Universitat de Barcelona, in 2004. I've also lectured seminars on computational genomics for the training node of the Instituto Nacional de Bioinformatica (INB). I've participated in the organization and presentation of the Bioinformatics stand "Desxifrem i comparem Genomes" (Deciphering and comparing genomes) for the Fira Viu la Ciència Contemporània (FVCC'03, a popular science fair) organized by the Societat Catalana de Biologia, in Barcelona in May 2003. I was also one of the organizers and lecturers of the workshops on "Computational Analysis of DNA Sequences" by La Caixa, held in Barcelona (November 2003 and 2004, July 2005) and in Madrid (June 2004). I was invited speaker on the 4th meeting of the Sociedad Española de Genética held in El Escorial on October 2003.

As part of the Local Organizing Committee, I have been involved in the editorial management of paper contributions to the Computational Biology 2005 meeting (ECCB/JBI'05), held in Madrid, Spain (Sep. 28 to Oct. 1, 2005). I have also participated in the organization of the ENCODE Genome Annotation Assessment Project (EGASP'05) workshop, held at the Wellcome Trust Sanger Institute (May 6-7, 2005).


CONTENTS

 


SEMINARS & LECTURES GO TOP

 
Here you can find the slides I have prepared for our Seminars and Journal Club sessions. Some of them were made with LaTeX (so you can find the PS file), and some were written in HTML. In this case, you can find a central icon from which starts, by clicking on it, the "slide manager window" in a new browser window (those seminars have frames, ensure that your browser can deal with them).

The schedule of the forthcoming GBIL group seminars is available at the following link: http://genome.imim.es/~rcastelo/gsem/

PHOTO ALBUM GO TOP

 
These pages contain many photos from many places.

ISMB'99 @ Heidelberg (August 6-10, 1999)
4th SEG's meeting @ El Escorial, Madrid (September 8-10, 2003)
EGASP'05 Workshop @ Sanger Center (May 5-7, 2005)

I will append more if I have time...  ;^)

 
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