“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”

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.

Gene kissing in the PRBB

Wouter de Laat was one of the developers of 4C, a technique highly used to find out DNA interactions between different regions within or between chromosomes. He came from the Hubrecht Institute in Utrecht, The Netherlands, to give a talk to the PRBB today, invited by Guillaume Filion, from the CRG. The room was packed, with more than 70 researchers ready to learn about how much function is actually within the genome structure. We learned about ‘gene kissing’ – or how genes functionally related but far away in a chromosome come close together during transcription. Interestingly, when de Laat and … Continue reading Gene kissing in the PRBB

From one to billions of cells – new techniques to understand our origins

The transition from single-celled organisms to multicellular animals (metazoans) is one of the most mysterious open questions in biology. To understand the mechanisms involved in this transition it is vital to study the closest unicellular relatives of metazoans. But the analyses on these protists have been severely limited by the lack of transgenesis tools and the difficulty in culturing these simple organisms. In this article published in Developmental Biology, the Multicellgenome lab the led by Iñaki Ruiz-Trillo at the IBE (CSIC-UPF) presents the first techniques of cell transformation and gene silencing developed in a close relative of metazoans, the ichthyosporean … Continue reading From one to billions of cells – new techniques to understand our origins

Improving the prediction of cancer causing mutations

Cancer is generally caused by a combination of many specific mutations, called drivers. But cancer cells contain many other mutations that are not the cause of the cancer, but rather a consequence (passenger mutations). Also, high-throughput genome projects are identifying a huge number of somatic variants. Which ones are cancer-causing? How to distinguish the needle in the haystack? A new computational method recently published in Genome Medicine by the research group led by Núria López-Bigas at the GRIB (UPF-IMIM), can help. Called transformed Functional Impact Score for Cancer (transFIC), it improves the assessment of the functional impact of tumor nonsynonymous … Continue reading Improving the prediction of cancer causing mutations

Studying how evolution has shaped our genome- Arcadi Navarro (UPF) explains

In this video you can hear Arcadi Navarro, from the Institute for Evolutionary Biology (IBE), a mixed centre from the CSIC and the Pompeu Fabra University (UPF). His group studies how evolution has shaped our genomes and those from other … Continue reading Studying how evolution has shaped our genome- Arcadi Navarro (UPF) explains

“It is a privilege to live off what you love”

An interview published in Ellipse, the monthly magazine of the PRBB. Mar Albà is a biologist who has moved from the lab to the computer and the analysis of the genome. After five years in England, she joined the UPF with a Ramon y Cajal contract, and since 2005 she is an ICREA Research Professor. Currently she coordinates the group of Evolutionary Genomics at the GRIB (IMIM/UPF) and the subject ‘Principles of Genome Bioinformatics’ at the master of Bioinformatics at the UPF. Since several months she has added motherhood to those tasks. What memories do you have from your PhD?  It … Continue reading “It is a privilege to live off what you love”

The colours of science

Science, in its day-to-day form, presents itself full of colours, as many as a painter’s palette and with the rainbow’s range of tonalities. The single nucleotide polymorphisms (SNPs) are the most common variations of the human genome. These small modifications are very useful in medical research of complex diseases and to develop new drugs. The SNPs present few variations between generations, a fact that allows us to follow the evolutionary processes in studies of population genetics. They are also used in some genetic tests, such as paternity tests or forensic analyses. The use of SNP arrays, seen in the image, … Continue reading The colours of science

Moving in, moving out

With more than 1,400 people working at the PRBB, the movement of researchers coming and going is constant. One of the most recent acquisitions is Eduard Sabidó, who has just arrived to be the new head of the CRG/UPF Proteomics Unit. Eduard is coming from the Swiss Federal Institute of Technology of Zurich (ETHZ)  and will be leading this core facility which offers service to the whole park and beyond. A new young group leader has also joined the CRG recently. The French molecular biologist Guillaume Filion (who, as we mentioned in an earlier post, is currently looking for a postdoc) was … Continue reading Moving in, moving out

The importance of being a highly conserved non-coding region

Yesterday Gill Bejerano (Stanford University) gave a talk at the PRBB in which he advocated the key role of highly conserved non-coding regions, in particular in the context of evolution. He explained there are only about 20,000 human genes, but more than 1,000,000 genome ‘switches’, short DNA regions which control which genes are expressed and at what levels. And the so-called ‘gene deserts’, areas of the genome with very few genes in them, are actually very rich in these conserved non-coding elements which act as cis-regulators of gene expression. So, as he said, perhaps more than gene deserts they should be … Continue reading The importance of being a highly conserved non-coding region