Is perfect genome assembly possible? Yes, says Gene Myers.

According to Gene Myers (near) perfect genome assembly is within reach for any organism of your choice. Time will tell if he’s right, but being an influential bioinformatician who has made key contributions in sequence comparison algorithms such as BLAST, whole-genome shotgun sequencing and genome assembling, one will think he knows what he’s talking about! In a conference at the PRBB auditorium today, he explained to a mixed audience of biologists and computer scientists how, after a few years dedicated to other issues (mostly image analysis), he was now coming back to sequencing with great excitement. The reason: PacBio RSII. This sequencing device is able to produce very … Continue reading Is perfect genome assembly possible? Yes, says Gene Myers.

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

Genomic high-throughput sequencing data: what to trust

Does your research imply having to deal with a huge amount of high-throughput data? Are you worried about the interpretation of your Illumina sequencing data? Illumina’s Genome Analyzer (GA) and HiSeq instruments are currently the most widely used sequencing devices. If you use them or are thinking of using them, you might be interested in having a look at the latest paper coming from Heinz Himmelbauer and his colleagues at the CRG ultrasequencing unit and published in Genome Biology. Find out about the errors and biases they report to make sure your data analysis is of the highest quality! Reference: Minoche AE, … Continue reading Genomic high-throughput sequencing data: what to trust

Mike Snyder: “It’s naïve to just look at one thing, we have to look at many levels”

Michael Snyder is the director of the Yale Center for Genomics and Proteomics, as well as Professor at Yale University. He studies protein function and regulatory networks using global approaches and high-throughput technologies, such as genomics and proteomics. During his visit to the PRBB he told us about the latest insights into human variation. What are the pros and cons of high-throughput technologies? There’s no question they are helping us advance in our knowledge. With genomics or proteomics experiments we discover things we would not have discovered by studying individual genes, and we have learned some basic principles out of … Continue reading Mike Snyder: “It’s naïve to just look at one thing, we have to look at many levels”

Protein coding genes exhibit low splicing variability within populations

Despite all having the same DNA content, each cell is different. The phenotypic differences observed between cells depend on the differences in the RNA transcript content of the cell. And this variability of transcript abundance is the result of gene expression variability, which has been studied for many years and is usually measured using DNA arrays, but also of alternative splicing variability. Indeed, changes in splicing ratios, even without changes in overall gene expression, can have important phenotypic effects. However, little is known about the variability of alternative splicing amongst individuals and populations. Taking advantage of the popular use of … Continue reading Protein coding genes exhibit low splicing variability within populations

CRG Symposium “Computational Biology of Molecular sequences”, part 3

On the second day of the conference, some more interesting talks at the “Computational Biology of Molecular sequences” X CRG Symposium taking place at the PRBB Conference Hall. I will focus on one talk of each of the sessions (genome regulation, RNA analysis and genome annotation), although all were very interesting! Ron Shamir (Tel Aviv University) presented Amadeus, a software platform for genome-scale detection of known and novel motifs in DNA sequences, and explained some of the findings they have done with it. He also presented his new book “Bioinformatics for biologists”, which will surely be very useful for many biologists drowning … Continue reading CRG Symposium “Computational Biology of Molecular sequences”, part 3