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

De novo genes: starting to solve the mystery of their origins

  A new collaboration amongst scientists at different centres at the PRBB, with Mar Albà from the IMIM as leading author, has come up with a new mechanism for explaining the formation of de novo genes. Although commonly new genes arise by gene duplication and diversification of the copy, some genes appear in genomic regions which did not previously contain any gene, as compared with other species. How do these genes originate from nothing? In a preprint submitted to arXiv.org the authors propose – based on transcriptomic comparisons between humans and three other mammals – that first new regulatory motifs/promoters appeared in … Continue reading De novo genes: starting to solve the mystery of their origins

“Without 3D information it is very difficult to understand how the genome works”

Marc A. Marti-Renom is interested in three-dimensional structures. After eight years in the US dedicated to the world of proteins, the biophysicist returned to his native country, first Valencia and then Barcelona, to specialise in RNA and DNA folding. In 2006 he set up his own group, which today is divided between the CNAG, where there are ten people, and the CRG, where there are two. “We do the experimental part, the sample preparation, here in the CRG, and the sequencing and analysis happens in the CNAG”, he explains. For his research he requires a large sequencing and computing capacity, … Continue reading “Without 3D information it is very difficult to understand how the genome works”

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

Anniversary CRG Symposium: from genomics to cell biology

Next October 18 and 19, the CRG will be celebrating its annual Symposium. This year it is especially relevant, since this research centre is celebrating its 10th Anniversary. The symposium will focus on the latest and most important advances in genomics but also in genetics, molecular and cell biology, or biotechnology. Several scientists in the international arena, such as Angus LAMOND (Wellcome Trust Centre for Gene Regulation and Expression, Dundee, UK), Tom MANIATIS (Columbia University, New York, US), or Iain MATTAJ (EMBL Heidelberg, Germany) will showcase the achievements of the CRG in the last 10 years in these fields. You … Continue reading Anniversary CRG Symposium: from genomics to cell biology

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