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!

Proteins bound to DNA impair Nucleotide Excision Repair

Congratulations to Núria López-Bigas at the GRIB (UPF-IMIM) for her lab’s latest paper in Nature describing why there’s an increased mutation rate in Transcription Factor Binding Sites (TFBS) in melanomas and lung tumors!!!! You can read more about the experience publishing this paper in this post from her lab’s blog, where she explains how, after a long process of reviewing, they felt they “had the responsibility to describe our finding as soon as possible to the community”, and decided to publish the manuscript in bioRxiv. Later on, the paper was accepted and published by Nature. Here’s for this success story! You can read the paper … Continue reading Proteins bound to DNA impair Nucleotide Excision Repair

The ERC recognises the excellence of PRBB researchers

The research group of Biomedical Genomics from the Research Programme on Biomedical Informatics (GRIB), led by Núria López-Bigas, has been awarded an European Research Council (ERC) Consolidator Grant. These grants are aimed at the development of innovative and excellent projects conducted by young postdoctoral researchers of a consolidated career between 7 and 12 years. The project that received the ERC, named “NONCODRIVERS” aims at identifying mutations involved in tumour development in non-coding regions. It is set to start in 2016 and to last for five years. You can read more about this here. The ERC has also recognized the work of another female … Continue reading The ERC recognises the excellence of PRBB researchers

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

“We are the interface between industry and academia” – Computer-assisted drug design lab

The Computer-Assisted Drug Design (CADD) laboratory of the GRIB is devoted to the area of drug design and development. Directed by Manuel Pastor, who started the group 10 years ago at the IMIM, it includes pharmacists, biologists, chemists, and a mathematician. “We also had a telecommunications engineer at one point. Our research needs experts in both science and programming”, justifies Pastor. The group’s interests are divided into three main areas. The first is methodological: they have written several programs marketed and are used by many pharmaceutical companies. The most recent one is Pentacle, which allows the creation of models relating … Continue reading “We are the interface between industry and academia” – Computer-assisted drug design lab

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

“It is a privilege to live off what you love”

An interview published in Ellipse, the monthly magazine of the PRBB. Mar Albà is a biologist who has moved from the lab to the computer and the analysis of the genome. After five years in England, she joined the UPF with a Ramon y Cajal contract, and since 2005 she is an ICREA Research Professor. Currently she coordinates the group of Evolutionary Genomics at the GRIB (IMIM/UPF) and the subject ‘Principles of Genome Bioinformatics’ at the master of Bioinformatics at the UPF. Since several months she has added motherhood to those tasks. What memories do you have from your PhD?  It … Continue reading “It is a privilege to live off what you love”

Sequence shortening in the rodent ancestor

A study led by the ICREA researcher Mar Albà, head of the evolutionary genomics research group at IMIM/UPF, clarified the evolution of insertion and deletion accumulation of DNA sequences in different primate and rodent branches. By using the algorithm Prank+F they have observed that, contrary to previous reports, the only branch with a marked deletion to insertion mutational bias, resulting in substantial sequence shortening, is the rodent ancestral branch. It also appears that protein sequences tolerate deletions better than insertions, resulting in an increase in the deletion to insertion ratio for coding sequences in all branches. These results were published … Continue reading Sequence shortening in the rodent ancestor

How to integrate your experimental data in a nice image

SVGmap is a configurable image browser for experimental data, a  new tool developed by the biomedical genomics group of the GRIB (UPF-IMIM) at the PRBB. According to the group “it is useful to create browsers for individualized high-quality images which change the color of some regions according to some values”.  It has recently been published in Bioinformatics. You can read more about it at Núria López-Bigas’ laboratory blog: http://bg.upf.edu/blog/ Continue reading How to integrate your experimental data in a nice image