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

Get it right, keep it clean, make a record

Keeping detailed records of your research and taking the right decisions when analysing your data is easier said than done. Yet, despite its importance, researchers often receive no formal training in these and other issues key to scientific integrity. The PRBB Good Scientific Practice Working Group – formed by members of all the centres at the park, including myself – run a survey at the PRBB last year in which improper record keeping was the most relevant (mis)behaviour identified by scientists at the park, with over 40% of the 521 respondents saying they had “sometimes or often” noticed it.  Several surveys … Continue reading Get it right, keep it clean, make a record

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

About Linux, Freedom and Science

Today we recover this post “Why Linux is awesome” by CRG researcher Guillaume Fillion in his blog “The grand locus“. He explains his personal experience with this operating system, what he has learned by using Linux and why, in his own words “it has made me a better scientist”. Curious? Read the full post! We’ll tell you the take-home message: “Following my experience of using Linux, I believe that freedom and openness lead to knowledge and competence“. Continue reading About Linux, Freedom and Science

Your very own cancer avatar

Fátima Al-Shahrour, from the CNIO in Madrid, came last week to the PRBB to give a talk entitled “Bioinformatics challenges for personalized medicine”. She explained what they do at her Translational Bioinformatics Unit in the Clinical Research Programme. And what they do is both exciting and promising. They start with a biopsy of a tumour from a cancer patient who has relapsed after some initial treatment – they concentrate mostly in pancreatic cancer, but it would work with any, in principle. From this sample, they derive cell lines, but also – and they are quite unique in this – they … Continue reading Your very own cancer avatar

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

“Personalised medicine and Big Pharma need bioinformatics”

David Searls retired three years ago from his position as senior Vice President of Bioinformatics in GlaxoSmithKline. Since then, this computer scientist who spent 16 years in academia and 19 years in industry has gone back to his theoretical studies on linguistic analysis of biological sequences. He was invited to the PRBB and talked to us about drugs and computers. This interview was published in Ellipse, the monthly magazine of the PRBB. What part does bioinformatics have in drug development?  It is an essential step along the way. This is because not only drug discovery, but all biology, has become, since the … Continue reading “Personalised medicine and Big Pharma need bioinformatics”

“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