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!

A tutorial on Burrows-Wheeler indexing methods

Guillaume Filion’s latest post is aimed at those wanting to understand the details of how the Burrows–Wheeler transform (an algorithm used in data compression) works. It may be of particular interest to those genomics researchers working on alignments, since, Filion says, the Burrows-Wheeler indexing is used to perform the seeding step of the DNA alignment problem, and it’s exceptionally well adapted to indexing the human genome. For those of you who are not afraid of the small mathematical details, you can see this “The grand locus” post here. Continue reading A tutorial on Burrows-Wheeler indexing methods

Open Science: not only a matter of outcomes, but also of processes

Post written by Toni Hermoso, bioinformatician at the CRG.   It’s been almost a decade since the term “Open Science” first appeared in Wikipedia. The page was created by Aaron Swartz and initially redirected to the “Open Access” entry. Some years later this young activist committed suicide as a result of the pressure from the judicial charges against him after having uploaded many privative licensed articles to the Internet. Parallel to these events, Creative Commons licenses, a set of recommendations intended to foster sharing in the digital world, became increasingly popular, and many novel publishing initiatives took advantage of them … Continue reading Open Science: not only a matter of outcomes, but also of processes

Cells have an alternative plan when energy is needed in the cell nucleus

All our cells require the small molecule; ATP, generated in the mitochondria to cover the energy required for cell metabolism, dynamics and growth. To a lower extent and particularly in cancer cells, ATP can also be generated in the cytoplasm from the energy gained during degradation of glucose. These sources of ATP are sufficient to cover the energetic needs of cells in normal conditions. However, in response to stress-inducing external signals or to extensive DNA damage, the cells need to globally reprogram their gene expression pattern, a process that requires extensive remodelling of chromatin to gain access to the regulatory … Continue reading Cells have an alternative plan when energy is needed in the cell nucleus

Leroy Hood: “Your genome does not control your destiny, just your potential”

More than 36 patents, 17 honorary degrees and 100 plus awards. This is the weight behind Lee Hood, one of only 15 people elected to all three US National Academies—of Science, Engineering and Medicine. Hood has also founded 15 biotech companies, as well as the Institute for Systems Biology in Seattle. A pioneer in the systems approach to biology and medicine, he came to the PRBB to talk about his vision for the future of medicine. How has biology changed in the last 50 years? There have been several paradigm changes in biology I have been involved in. The first … Continue reading Leroy Hood: “Your genome does not control your destiny, just your potential”

Science for All and All for Air Quality

Citizen Science is blooming. There’s a growing number of examples of research projects in which the general population can participate. In this post at the blog Health ISGlobal, the researcher Irene Eleta (CREAL) talks about some of these projects which are related to air pollution and that scientists at CREAL /ISGlobal are leading, such as CITI-SENSE.     Continue reading Science for All and All for Air Quality

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