nlopez

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About nlopez

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So far nlopez has created 41 blog entries.

Open position for a Research Associate

By | February 28th, 2017|Categories: Jobs|

We are searching for highly motivated and experienced researcher with expertise in Genetics, Epigenetics, Molecular and Cell Biology, with a strong peer-reviewed publication record and professional references. The [...]

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. […]

Practical Workshop on “Cancer Omics Data Integration” in Heidelberg

By | January 21st, 2014|Categories: Meetings/Conferences|Tags: |

Since last year I am participating in the COST Action BM1204 titled “An integrated European platform for pancreas cancer research: from basic science to clinical and public health interventions for a rare disease”, and in particular in its Work Group focus on “Omics Data Integration”.   As part of this Work Group, we have prepared a training workshop that will take place in Heidelberg, Germany on February 14, from 1-5pm. The covered topics fit into a series of workshops that will be organized within this COST Action. […]

Our research explained in a short video

By | October 29th, 2013|Categories: BG News|Tags: |

The University Pompeu Fabra has produced a video in which we explain in brief our research. We recorded three versions of the video, one in Catalan, one in Spanish and one in English. The videos are distributed through the UPF youtube channel. I leave you here with the English version of the video. For the Catalan version follow this link. And this link for the Spanish version.     […]

My slides on: Identification of cancer drivers across tumor types

By | October 25th, 2013|Categories: BG News|Tags: , , , |

Yesterday I gave a talk at the PRBB Computational Genomics Seminars Series. In that talk I summarized our work of this year in the lab. Basically, we have developed methods to identify cancer driver genes and we have applied them to thousands of tumor resequenced genomes. Here, I leave you the slides, and I summarize the talk below.   […]

The Cancer Genome Atlas Pan-Cancer Project

By | September 27th, 2013|Categories: BG News|Tags: , , , , |

Yesterday the paper describing TCGA Pan-Cancer Project was published in Nature Genetics. We’ve had the opportunity to participate in this exciting project and here I would like to explain our experience and contribution to it.   We have been interested for quite a while in the study of patterns of genomics alterations in cancer across tumor types. Thus a project like the TCGA Pan-Cancer provided a unique opportunity to apply our tools and expertise to a unique collection of data.   In the past few years we have developed computational methodologies to identify cancer drivers by analyzing the patterns of somatic mutations across tumors (i.e OncodriveFM and OncodriveCLUST) as well as tools to facilitate the visual exploration of multidimensional cancer genomics datasets (i.e. Gitools, IntOGen, see our review on this topic if you are interested in this), we now had the opportunity to apply those tools to TCGA Pan-Cancer data. […]

How to identify functional genetic variants in cancer genomes?

By | August 2nd, 2013|Categories: BG News, BioinfoTips|Tags: , |

The possibility to rapidly and inexpensively sequence tumor genomes is opening important new avenues for cancer research. One of the main objectives when sequencing tumor genomes is to identify the somatic alterations that have a relevant role in developing and maintaining the cancer phenotype. However the analysis of this data is hindered by the large number of mutations detected in tumors (often in the order of thousands) and the large molecular heterogeneity observed between tumor samples. As part of the International Cancer Genome Consortium (ICGC), during the last 2-3 years I have been co-leading (together with Lincoln Stein) a working group focused on discussing how to analyze this data. The group is formed by 48 Members from 10 different countries, and we have held one teleconference nearly every month. We have now written the results of these discussions in a perspective manuscript that has been published in the current issue of Nature Methods. […]