See you soon, Computational Oncogenomics lab!

Núria López-Bigas started her lab on Computational Oncogenomics at the GRIB, within the PRBB, ten years ago. After a very successful decade, we are sad to see her leaving. We wish her all the best in her lab’s new adventure, and we hope the very fruitful interactions she has started with the different groups at the park will continue to prosper. In her last post on her blog, Núria says thanks to the GRIB, the UPF, the PRBB community and the PRBB Intervals programme… We want to say, thanks to you Núria, for the great research you have done and for … Continue reading See you soon, Computational Oncogenomics lab!

In-silico selection of targeted anti-cancer therapies

The Biomedical Genomics group led by Núria López-Bigas at the Pompeu Fabra Unviersity have recently published a paper in Cancer Cell describing the landscape of anti-cancer targeted therapeutic opportunities across a cohort of patients of twenty eight of the most prevalent cancers. They first looked for all the driver mutations (mutations that ’cause’ the cancer) for each individual cancer, then collected information on all the existing therapeutic agents that target those mutations, and finally, combining both datasets, came up with anti-cancer targeted drugs that could potentially benefit each patient. You can read more about this paper on their blog post. Coinciding with the publication of that paper, the … Continue reading In-silico selection of targeted anti-cancer therapies

Improving the prediction of cancer causing mutations

Cancer is generally caused by a combination of many specific mutations, called drivers. But cancer cells contain many other mutations that are not the cause of the cancer, but rather a consequence (passenger mutations). Also, high-throughput genome projects are identifying a huge number of somatic variants. Which ones are cancer-causing? How to distinguish the needle in the haystack? A new computational method recently published in Genome Medicine by the research group led by Núria López-Bigas at the GRIB (UPF-IMIM), can help. Called transformed Functional Impact Score for Cancer (transFIC), it improves the assessment of the functional impact of tumor nonsynonymous … Continue reading Improving the prediction of cancer causing mutations

Finding the genes underlying complex genetic diseases

Complex genetic disorders often involve multiple proteins interacting with each other, and pinpointing which of them are actually important for the disease is still challenging. Many computational approaches exploiting interaction network topology have been successfully applied to prioritize which individual genes may be involved in diseases, based on their proximity to known disease genes in the network. In a paper published in PLoS One, Baldo Oliva, head of the Structural bioinformatics group at the GRIB (UPF–IMIM)  and Emre Guney, have presented GUILD (Genes Underlying Inheritance Linked Disorders), a new genome-wide network-based prioritization framework. GUILD includes four novel algorithms that use protein-protein interaction data to predict gene-phenotype associations at genome-wide scale, … Continue reading Finding the genes underlying complex genetic diseases

“I’m working at what I’d always dreamed of” – Manuel Pastor, researcher on drug design

An interview published in Ellipse, the monthly magazine of the PRBB. Manuel Pastor, 45 and from Madrid, studied pharmacy at the University of Alcalà de Henares (Madrid), and after doing his PhD in the organic chemistry department went to Perugia in Italy for his postdoc. Self-taught computer expert and passionate about reading and the cinema, Pastor fell in love with medicines when he was little. Years later he has realised his dream as head of the research group for computer aided drug design at the GRIB (IMIM-UPF). When did you hear the call to science?  I’ve been passionate about medicines since … Continue reading “I’m working at what I’d always dreamed of” – Manuel Pastor, researcher on drug design

The next international conference on computational molecular biology, in April in Barcelona

RECOMB 2012, the 16th Annual International Conference on Research in Computational Molecular Biology, will take place in Barcelona on April 21-24, 2012. It is being organised by Roderic Guigó, from the CRG. Check out this video where he presents the meeting. The meeting will focus on the computational challenges arising from the extraordinary developments in high throughput technologies. You can check the updates on the speakers and the program on the conference website. As the organisers point out, the meeting overlaps with Sant Jordi (Saint George), on April 23, the patron of Catalonia, and one of the most important civic … Continue reading The next international conference on computational molecular biology, in April in Barcelona

Protein coding genes exhibit low splicing variability within populations

Despite all having the same DNA content, each cell is different. The phenotypic differences observed between cells depend on the differences in the RNA transcript content of the cell. And this variability of transcript abundance is the result of gene expression variability, which has been studied for many years and is usually measured using DNA arrays, but also of alternative splicing variability. Indeed, changes in splicing ratios, even without changes in overall gene expression, can have important phenotypic effects. However, little is known about the variability of alternative splicing amongst individuals and populations. Taking advantage of the popular use of … Continue reading Protein coding genes exhibit low splicing variability within populations

CRG Symposium “Computational Biology of Molecular sequences”, part 3

On the second day of the conference, some more interesting talks at the “Computational Biology of Molecular sequences” X CRG Symposium taking place at the PRBB Conference Hall. I will focus on one talk of each of the sessions (genome regulation, RNA analysis and genome annotation), although all were very interesting! Ron Shamir (Tel Aviv University) presented Amadeus, a software platform for genome-scale detection of known and novel motifs in DNA sequences, and explained some of the findings they have done with it. He also presented his new book “Bioinformatics for biologists”, which will surely be very useful for many biologists drowning … Continue reading CRG Symposium “Computational Biology of Molecular sequences”, part 3