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Computational Genomics
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Computational Genomics

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OVERVIEW

The main focus of our group is to decipher and understand the biology of genomes. Genomes, as the molecule of life, contain the necessary information for the development and evolution of living organisms. Despite this information is encoded in a four-letter code; it presents different levels of complexity. The comparison of genomic and derived sequences allows us to uncover the general rules and patterns that control and make life possible. Our research activity uses computational and experimental approaches to reach these goals by finding answers to specific molecular, evolutionary and biomedical questions.


RESEARCH DIRECTOR
ICREA
arrowTorrents Arenales, David (ICREA Research Professor)


OBJECTIVES


genomics torrentsCurrently, we have different research lines open:

- Identification and characterization of gene regulatory regions. Our goal is to understand how these regions evolve, and whether there are regular patterns and particular conservation levels depending on the nature and function of groups of eukaryotic genes, particularly within vertebrates. For this, we are first developing and then applying different computational tools to identify promoter regions and enhancers. Our approaches combine the use of sequence conservation at different levels: directly from alignments, through the mapping and evaluation of transcription factor binding boxes and, in collaboration with the group of Modesto Orozco of our department, also exploring the potential of the conservation of DNA structural properties in the prediction and characterization of these regulatory regions. All these analysis are also combined with experimental validation carried out within our group.  
-Analysis of regulatory regions in metagenomic data. Our goal is to determine and explore how the organisms associated to different environments control their gene expression. Our approach is based on the application of different prediction software and existing databases to identify promoter regions in bacteria and then compare them. As with the analysis of proteins, this study can highlight new pathways and strategies that might have an impact in ecology, evolution and biomedicine. Our group has a permanent collaborative activity with the group of Peer Bork (EMBL) for the analysis of metagenomic data at different levels. 
-Systems biology of complex diseases. In the context of a Collaborative Project supported by European Commission (MITIN, Grant Agreement no. HEALTHF4-2008-223450; http://mitin-fp7.eu/), we are developing the necessary methodology and tools to generate a computational framework for the study of complex diseases. In particular, we have started a pilot phase by modeling the insulin signaling pathway and the biology of the mitochondria, as well as the cross-talk between these two biological systems to analyze its implication in Diabetes and Obesity. On top of these research lines, our group is actively collaborating with a number of groups around the world by providing our expertise and tools. The unique computational environment where we are located, make us able to reach levels of comparison and analysis that allow answering more complex biological questions. 

 





PROJECTS/AREAS




PEOPLE
arrowDURAN, ELISA , RESIDENT STUDENT
arrowFERNANDEZ, LEYDEN , RESIDENT STUDENT
arrowGONZALEZ, SANTIAGO , JUNIOR RESEARCHER
arrowMERCADER, JOSEP MARIA , POSTDOC RESEARCHER
arrowMONCUNILL, VALENTI , RESEARCHER
arrowMONTSERRAT, BARBARA , RESEARCHER
arrowMONTSERRAT, PUIGGROS , RESEARCH SUPPORT ENGINEER
arrowPASTOR HOSTENCH, XAVIER , RESEARCHER
arrowPEREZ ANTONANZAS, ALBERTO , ASSOCIATE RESEARCHER
arrowTORRENTS ARENALES, DAVID , COMPUTATIONAL GENOMICS GROUP MANAGER


PUBLICATIONS AND COMMUNICATIONS


Publications

Journals

Carlos Quijano, Pavel Tomancak, Jesus Lopez-Marti, Mikita Suyama, Peer Bork, Marco Milan, David Torrents* and Miguel Manzanares*. Selective maintenance of Drosophila tandemly-arranged duplicated genes. Genome Biology, (Accepted Dec. 2008) , December 2008.

Casagrande F, Ratera M, Schenk AD, Chami M, Valencia E, Lopez JM, Torrents D, Engel A, Palacin M, Fotiadis D.. Projection structure of a member of the amino acid/polyamine/organocation transporter superfamily.. J Biol Chem. 283(48):33240-8. Epub 2008 Sep 25., , November 2008.

Goñi JR, Fenollosa C, Pérez A, Torrents D, Orozco M.. DNAlive: a tool for the physical analysis of DNA at the genomic scale.. Bioinformatics. 24(15):1731-2. Epub 2008 Jun 9., , August 2008.

Casals F, Ferrer-Admetlla A, Chillarón J, Torrents D, Palacín M, Bertranpetit J.. Is there selection for the pace of successive inactivation of the arpAT gene in primates?. J Mol Evol. 67(1):23-8. Epub 2008 Jun 20., , June 2008.

Goñi JR, Pérez A, Torrents D & Orozco M. . Determining promoter location based on DNA structure first principle calculations. Genome Biology, 8:R263, , December 2007.

Reig N, Del Rio C, Casagrande F, Ratera M, Gelpi JL, Torrents D, Henderson PJ, Xie H, Baldwin SA, Zorzano A, Fotiadis D, Palacin M.. Functional and Structural Characterization of the First Prokaryotic Member of the L-Amino Acid Transporter (LAT) Family: A MODEL FOR APC TRANSPORTERS.. J Biol Chem. 282(18):13270-81., , May 2007.

Suyama M, Torrents D, Bork P.. PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res, 34(Web Server issue):W609-12 , July 2006.

Suyama M, Harrington E, Bork P, Torrents D.. Identification and analysis of genes and pseudogenes within duplicated regions in the human and mouse genomes. PLoS Comput Biol, 2(6):e76 , July 2006.

Chimpanzee Sequencing and Analysis Consortium (includes D. Torrents). Initial sequence of the chimpanzee genome and comparison with the human genome. Nature, 437(7055):69-87 , September 2005.

Hillier LW, ... Chromosomes 2 and 4 sequencing and analysis group (includes D. Torrents). Generation and annotation of the DNA sequences of human chromosomes 2 and 4. Nature, 434(7034):724-31 , July 2005.

Fernandez E, Torrents D, Zorzano A, Palacin M, Chillaron J.. Identification and functional characterization of a novel low affinity aromatic-preferring amino acid transporter (arpAT). One of the few proteins silenced during primate evolution. J Biol Chem., 280(19):19364-72 , May 2005.

Zdobnov EM, Campillos M, Harrington ED, Torrents D, Bork P.. Protein coding potential of retroviruses and other transposable elements in vertebrate genomes. Nucleic Acids Res, 33(3):946-54 , February 2005.

Suyama M, Torrents D, Bork P.. BLAST2GENE: a comprehensive conversion of BLAST output into independent genes and gene fragments. Bioinformatics, 20(12):1968-70 , December 2004.

International Chicken Genome Sequencing Consortium (inlcudes D. Torrents). Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature, 432(7018):695-716 , September 2004.

Rat Genome Sequencing Project Consortium (includes D. Torrents). Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature, 428(6982):493-521 , January 2004.

Torrents D, Suyama M, Zdobnov E, Bork P. A genome-wide survey of human pseudogenes. Genome Res., 13(12):2559-67 , October 2003.

Hillier LW, ... Chromosome 7 Sequencing and analysis group. (Inlcudes D. Torrents). The DNA sequence of human chromosome 7. Nature, 424(6945):157-64. , October 2003.

Waterston RH, Hillier LW, Fulton LA, Fulton RS, Graves TA, Pepin KH, Bork P, Suyama M, Torrents D, Chinwalla AT, Mardis ER, McPherson JD, Wilson RK.. The human genome: genes, pseudogenes, and variation on chromosome 7. Cold Spring Harb Symp Quant Biol., 68:13-22. Review , October 2003.

Fernandez E, Torrents D, Chillaron J, Martin Del Rio R, Zorzano A, Palacin M.. Basolateral LAT-2 has a major role in the transepithelial flux of L-cystine in the renal proximal tubule cell line OK.. J Am Soc Nephrol., 14(4):837-47.
, April 2003.

Mouse Genome Sequencing Consortium (includes D. Torrents) . Initial sequencing and comparative analysis of the mouse genome.. Nature, 420(6915):520-62. , May 2002.

Zdobnov EM, von Mering C, Letunic I, Torrents D, Suyama M, Copley RR, Christophides GK, Thomasova D, Holt RA, Subramanian GM, Mueller HM, Dimopoulos G, Law JH, Wells MA, Birney E, Charlab R, Halpern AL, Kokoza E, Kraft CL, Lai Z, Lewis S, Louis C, Barillas-Mury C, Nusskern D, Rubin GM, Salzberg SL, Sutton GG, Topalis P, Wides R, Wincker P, Yandell M, Collins FH, Ribeiro J, Gelbart WM, Kafatos FC, Bork P.. Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster.. Science, 298(5591):149-59. , April 2002.

Torras-Llort M, Torrents D, Soriano-Garcia JF, Gelpi JL, Estevez R, Ferrer R, Palacin M, Moreto M.. Sequential amino acid exchange across b(0,+)-like system in chicken brush border jejunum.. J Membr Biol., 180(3):213-20. , January 2001.

Mykkanen J, Torrents D, Pineda M, Camps M, Yoldi ME, Horelli-Kuitunen N, Huoponen K, Heinonen M, Oksanen J, Simell O, Savontaus ML, Zorzano A, Palacin M, Aula P.. Functional analysis of novel mutations in y(+)LAT-1 amino acid transporter gene causing lysinuric protein intolerance (LPI).. Hum Mol Genet., 9(3):431-8 , December 2000.

Feliubadalo L, Font M, Purroy J, Rousaud F, Estivill X, Nunes V, Reig N, Fernandez E, Estevez R, Pineda M, Torrents D, Camps M, Lloberas J, Zorzano A, Palacin M; International Cystinuria Consortium.. Non-type I cystinuria caused by mutations in SLC7A9, encoding a subunit (bo,+AT) of rBAT.. Nat Genet., 23(1):52-7 , September 1999.

Pineda M, Fernandez E, Torrents D, Estevez R, Lopez C, Camps M, Lloberas J, Zorzano A, Palacin M.. Identification of a membrane protein, LAT-2, that Co-expresses with 4F2 heavy chain, an L-type amino acid transport activity with broad specificity for small and large zwitterionic amino acids.. J Biol Chem., 274(28):19738-44., September 1999.

Torrents D, Mykkanen J, Pineda M, Feliubadalo L, Estevez R, de Cid R, Sanjurjo P, Zorzano A, Nunes V, Huoponen K, Reinikainen A, Simell O, Savontaus ML, Aula P, Palacin M. Identification of SLC7A7, encoding y+LAT-1, as the lysinuric protein intolerance gene. Nat Genet., 21(3):293-6 , March 1999.

Torrents D, Estevez R, Pineda M, Fernandez E, Lloberas J, Shi YB, Zorzano A, Palacin M. Identification and characterization of a membrane protein (y+L amino acid transporter-1) that associates with 4F2hc to encode the amino acid transport activity y+L. A candidate gene for lysinuric protein intolerance. J Biol Chem., 273(49):32437-45 , December 1998.

 
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