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23/1/2012

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11/1/2012

Identified: New mechanism of tumoral cells reprogramation

A work published in Nature Medicine describes a new reprogrammation mechanism of the gene expression that turn into tumoral a health cell. The ICREA researcher Eduardo Eyras, head of the Regulatory Genomics Group at GRIB ( UPF-IMIM) have participated in this study.

One of the most relevant results of this study has been to establish that CPEB4 acts as a cell orchestra conductor which turns on hundreds of genes linked to tumoral growth.

The innovation is that it wouldn't be only the mutation of a concrete gene which would promote the tumor growth, but the expression in the incorrect place that "activates" hundreds of messenger molecules  (mARNs) that deliver the information contained in the genes to synthesize the proteins without these genes having been mutated.

Article Reference:

Ortiz-Zapater E, Pineda D, Martinez-Bosch N, Fernandez-Miranda G, Iglesias M, Alameda F, Moreno M, Elisiscovich C, Eyras E, Real FX, Mendez R, Navarro P. Key contribution of CPEB4-mediated translational control to cancer progression. Nat Med, 2011 Dec 4;18(1):83-90.

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22/12/2011

Join us at the XIth Spanish Symposium on Bioinformatics (JBI2012) in Barcelona

The XIth Spanish Symposium on Bioinformatics (JBI2012) will take place in January 23-25, 2012 at the Barcelona Biomedical Research Park (PRBB) in Barcelona (Spain) co-organised by the Spanish Institute of Bioinformatics and the Portuguese Bioinformatics Network

This year, the reference topic is “Genome Architecture, Annotation and Design” for which the conference will provide the opportunity to discuss the state of the art for the integration of the fields of biology, medicine and informatics.

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22/12/2011

Mutations caused by insertions of DNA short sequences are frequent than thought

The GRIB Evolutionary Genomics Research Group (UPF-IMIM) has described for the first time how insertions of one or more nucleotides in DNA are as common as deletions (the loss of a DNA fragment) in most mammals' genomes, in contrast to what was previously thought. The study has been based on a new algorithm, called Prank-F that makes better the detection of insertions.

"There has been little investigation in the past about the role of insertions and eliminations of DNA sequences, because they are difficult to study. Our work shows that insertions and eliminations are also important in the function of proteins," said Steve Laurie, IMIM researcher and the first author of the article.

The study has enabled a better estimate of the possible bias between deletions and insertions in different evolutionary periods. "We found that there was a systematic loss of DNA sequences in the ancestors of modern rodents due to an increase in deletions," explained Mar Albà, ICREA researcher at the IMIM and coordinator of the Evolutionary Genomics Group of GRIB (UPF-IMIM).

Article de referència:Sequence shortening in the rodent ancestor”. Steve Laurie, Macarena Toll-Riera, Núria Radó-Trilla, Mar Albà. Genome Research published on line November 29, 2011. Doi. 10.1101/gr.121897.111

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17/11/2011

INBIOMEDvision: Training Challenge 2012 - call for student applications is now open!

The INBIOMEDvision Training Challenge 2012 will take place in Monastery of Les Avellanes (Lleida, Spain) April 23rd – April 27th 2012. The call for student applications is now open! Application deadline is December 31st, 2011

The objective of this training activity is to promote the dialogue between disciplines, which is key for the future development of Biomedical Informatics.

The participants will spend the week in the Monastery of Les Avellanes, so that they can actually 'live' for a week on a research-driven environment. The INBIOMEDvision Training Challenge is organized by the EC FP7 funded Coordination and Support Action INBIOMEDvision that covers the participants’ expenses during the event.

If you are interested on this call please contact Maria Saarela, 

msaarela@imim.es (933160520)

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1/12/2011

Núria López-Bigas, Premi Nacional al Talent Jove 2011 per la qualitat i excel·lència en recerca

El Premi Nacional de Recerca en la modalitat de Talent Jove té una dotació econòmica de 10.000 euros i reconeix els joves investigadors que en la seva trajectòria professional han destacat per la qualitat i excel·lència del seu treball.

Nuria López-Bigas, doctora en Biologia, professora d'investigació ICREA de la UPF i cap del laboratori de Genòmica Biomèdica del GRIB (IMIM-UPF) ha desenvolupat una impecable trajectòria en termes d'estades en centres internacionals de prestigi, finançament obtingut en convocatòries competitives, publicacions científiques en revistes d'alt impacte, i capacitat de captació i formació de col·laboradors. Entre els seus mèrits destaca el Career Development Award concedit pel Human Frontier Science Programme.

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The CBBL, awarded in the new edition of the “marató de TV3″ projects

The Computational Biochemistry and Biophysics Laboratory of GRIB has been awarded in the new edition of the “Marató de TV3” basic research projects call. The awarded project deals with the study of the modulation of microglia/macrophage response by targeting novel immune receptors regulating cell activation and phenotype, which will provide neuroprotection after acute CNS damage.

As public researchers we take this new challenge with renovated energy, and taking into account the individual contributions of many anonymous people we will put all our efforts to produce a succesful outcome of the project.

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Join us at the XI Jornadas de Bioinformática in Barcelona. Registration is now open!

We are only 15 days away from end of Early Registration ( and abstract submission  to the "XI Jornadas de Bioinformática", which is to be held at the PRBB in Barcelona between the 23rd and the 25th of January 2012 and organized by the Spanish Institut of Bioinformatics and the Portuguese Bioinformatics Network.

IMPORTANT DATES
• Early Registration deadline: 30th of November 2011
• Deadline for submission of papers and highlight proposals: 30th of November 2011
• Notification of acceptance: 30th of December 2011


Please, follow these links for details on how-to submit your work (http://jbi2012.org/?page_id=23) as well as the formatting instructions (http://jbi2012.org/?page_id=224).

We look forward to meeting all of you in Barcelona!

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18/10/2011

Pyicos: A versatile toolkit for the analysis of high-throughput sequencing data

This new tool framework, developed by the Regulatory Genomics Group of GRIB (IMIM-UPF), is used for the analysis of various data types following from experiments of RNA sequencing (RNA-Seq) as well as Chromatin immunoprecipitation (ChIP-Seq) or Cross-linking immunoprecipitation (CLIP-Seq). Pyicos is available at http://sourceforge.net/projects/pyicos/

Publication reference:  Althammer S, Gonzalez-Vallinas J, Ballare C, Beato M, Eyras E. Pyicos: A versatile toolkit for the analysis of high-throughput sequencing data. Bioinformatics. 2011 Oct 12. [Epub ahead of print]

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11/10/2011

Un estudi mostra que la temperatura controla el missatge genètic

L'splicing alternatiu, el mecanisme que permet a un gen codificar diferents proteïnes en funció de les necessitats de la cèl·lula, encara amaga molts secrets. Ha transformat la teoria inicial d'"un gen, una proteïna" però quina és la seva estratègia de control segueix sent, en gran part, un misteri.

Ara, un equip d'investigadors ha descobert una nova estratègia de control: la temperatura. L'equip, dirigit per Josep Vilardell, investigador ICREA a l'Institut de Biologia Molecular de Barcelona del CSIC i en el que participen Eduardo Eyras investigador ICREA i Mireya Plass, ambdós investigadors del Grup de Genòmica Computacional del GRIB (UPF-IMIM) , ha descobert que la temperatura afecta l'estructura de l'RNA i que, d'aquesta manera, controla quines parts de la seqüència genètica li interessa utilitzar.

Treball de referència: Meyer M, Plass M, Pérez-Valle J, Eyras E, Vilardell J. Deciphering 3'ss Selection in the Yeast Genome Reveals an RNA Thermosensor that Mediates Alternative Splicing",   Molecular Cell, 2011; Volum 43 (6): 1033-1039

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