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Our paper demonstrating that proteins bound to DNA impair Nucleotide Excision Repair published in Nature

By | April 14th, 2016|Categories: BG News|Tags: , , |

I am very happy to announce that our manuscript describing the increased mutation rate in Transcription Factor Binding Sites (TFBS) in melanomas and lung tumors has been published in today's issue of Nature. In the manuscript we demonstrate that this accumulation is due to the impairment of Nucleotide Excision Repair (NER) activity by proteins bound to DNA.

ERC-consolidator granted to our lab to find noncoding cancer drivers

By | February 4th, 2016|Categories: BG News|

We are happy to announce that our lab has been awarded an European Research Council Consolidator Grant. ERC-consolidator grants are designed “To fund top researchers of any nationality and age, with over 7 and up to 12 years of experience after PhD, and a scientific track record showing great promise. The sole evaluation criterion for this grants: scientific excellence of researcher and research proposal” 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. If you are interested in working in our lab stay tuned: we will open Postdoc positions soon to work on the ERC project. Just have a look below at what we intend to do within the project in the coming five years. […]

New IntOGen web to explore driver genes across cancer types

By | March 17th, 2015|Categories: BG News|Tags: , , , , |

Coinciding with the publication of our latest paper, on Monday (9 March 2015) (See blog post) we have crafted a new IntOGen interface which presents the results of the analysis of somatic mutations across almost 7000 cancer samples from 28 different cancer types to identify driver genes. […]

In silico prescription of anticancer drugs to cohorts of 28 tumor types reveals novel targeting opportunities

By | March 9th, 2015|Categories: BG News|

We are pleased to announce the publication of our 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.   Targeted therapies exploit tumor vulnerabilities offered by specific cancer alterations. However, not all  genomic alterations are equally relevant for a given tumor individual. Tumors are more dependent on alterations directly involved in their development and maintenance, namely driver alterations. These represent good options to develop targeted therapies. In this paper we describe an in silico prescription approach to obtain the landscape of targeted drugs against cancer driver alterations, composed of three main steps. […]

How to generate mutation distribution and frequency plots?

By | December 19th, 2014|Categories: BG News, BioinfoTips|Tags: , , , |

Let’s plot some mutations! Easy, right? For our next iteration of the IntOGen database, we wanted to add figures that represent the mutation distribution across the protein sequence. And we found ourselves, just as others, in the situation, that we know that there are solutions, but none is available for us to incorporate in the web portal. We would like to produce plots that describe the mutation frequency data, are aesthetically pleasing and easily understood. The Mutation Mapper at the cBioPortal does a great job already and provides a web service. Additionally we’d like to reflect different consequence types in the same position. Thus we decided to give the all-so-famous D3 (Data Driven Documents)  a go. It’s a blast to use and in a couple of days we had our first plots as a generic library. […]

OncodriveROLE predicts activating and loss of function cancer driver genes

By | August 26th, 2014|Categories: BG News|Tags: , , , , , , |

We are pleased to announce that the Oncodrive methods family has a new member: OncodriveROLE, an approach to classify cancer drivers into loss of function and activating roles. OncodriveROLE joins and complements the previously developed methods that identify cancer driver genes from the list of somatic mutations in cohort of tumors (OncodriveCLUST and OncodriveFM). Cancer driver genes come in two main flavors: those that contain driver alterations which cause the loss of function (LoF) of the gene product (for instance, in tumor suppressor genes like TP53 or CDKN2A), and those with driver alterations that increase or change the activity or function of the protein product, such as oncogenes like PIK3CA or BRAF. Distinguishing between these two classes of driver genes is very important to understand tumorigenesis in patients and has profound implications for therapeutic decision making and for the development of targeted drugs. […]

Molecular subtypes of human cancer

By | August 7th, 2014|Categories: BG News|Tags: , , |

Cancers are typically classified depending on their tissue of origin. However, novel large-scale genomic studies are providing more detailed molecular characterizations of tumors, and thus bring about the possibility of a more accurate classification based on their molecular profiling. Recently, our group has participated in the pan-cancer integrated subtypes study, published online today in Cell, in which a molecular taxonomy of cancer has been addressed by using the comprehensive multi-platform assays provided by the TCGA consortium for 12 diverse cancer types. This study represents an unprecedented effort to classify cancer by refining the molecular portrait of human malignancies. […]