quotations

Analyzing microarray data

A Cold Spring Harbour protocol based on Babelomics

Because there is no widely used software for analyzing RNA-seq data that has a graphical user interface, this protocol provides an example of analyzing microarray data using Babelomics. This analysis entails performing quantile normalization and then detecting differentially expressed genes associated with the transgenesis of a human oncogene c-Myc in mice.

Integrated gene set analysis for microRNA studies

RNA-Seq blog on gsa4mirna

 
Functional interpretation of miRNA expression data is currently done in a three step procedure: select differentially expressed miRNAs, find their target genes, and carry out gene set overrepresentation analysis Nevertheless, major limitations of this approach have already been described at the gene level, while some newer arise in the miRNA scenario.
Here, researchers from the

Publicado el primer catálogo de la variación genética de la población española sana

El Dr. Joaquín Dopazo, Director del Departamento de Genómica Computacional del Centro de Investigación Príncipe Felipe, ha elaborado un catálogo detallado de la variabilidad genética de la población española a partir de las secuencias de exomas (parte del genoma que codifica para proteínas) completos de 267 individuos representativos de la población española sana, obtenidas por el Dr.

Identifican mutaciones genéticas recurrentes en genes que podrían estar implicados en el origen de la leucemia

Una profesora del Departamento de Ciencias Biomédicas de la Universidad CEU Cardenal Herrera y miembro del Grupo de Investigación en Hematología y Hematoterapia del Hospital La Fe de Valencia, Mariam Ibáñez, en colaboración con José Carbonell del Departamento de Genómica Computacional del CIPF, liderado por el doctor Joaquín Dopazo, han logrado determinar un grupo de genes recurrentes que podrían estar implicados en el origen de la leucemia mieloide aguda.

PLoS Computation Biology highlights our paper on cancer drivers

Cancer Drivers, Protein Complex Prediction, and Crawling and Gliding Cells: the PLOS Comp Biol October Issue

 
Posted November 5, 2015 by bchadwick in Cancer, Cell biology, Community, Computational biology, Molecular biology, PLOS Computational Biology
Here are our highlights from October’s PLOS Computational Biology:
 
 
 

A Pan-Cancer Catal

'Big Data' used to identify new cancer driver genes

In a collaborative study led by Sanford Burnham Prebys Medical Discovery Institute (SBP), researchers have combined two publicly available 'omics' databases to create a new catalogue of 'cancer drivers'. Cancer drivers are genes that when altered, are responsible for cancer progression. The researchers used cancer mutation and protein structure databases to identify mutations in patient tumors that alter normal protein-protein interaction (PPI) interfaces.

‘Big Data’ Used to Identify New Cancer Driver Genes

Newswise — La Jolla, Calif., October 20, 2015 – In a collaborative study led by Sanford Burnham Prebys Medical Discovery Institute (SBP), researchers have combined two publicly available ‘omics’ databases to create a new catalogue of ‘cancer drivers’. Cancer drivers are genes that when altered, are responsible for cancer progression. The researchers used cancer mutation and protein structure databases to identify mutations in patient tumors that alter normal protein-protein interaction (PPI) interfaces.

Citrus History

An analysis of 34 chloroplast genomes reveals how and when modern fruit varieties evolved from a common ancestor.

The Scientist cites our paper: A

Dissecting deleterious mutation complexity. Nature Genetics Reviews highlights our Mol. Syst. Biol. interactome paper

Dissecting deleterious mutation complexity

Nature Reviews genetics highlights our paper "The role of the interactome in the maintenance of deleterious variability in human populations" by Garcia-Alonso et al., recently published in Mol.Syst Biol.

GenomeWeb quotes our collaborative paper on RNA-seq controls

GenomeWeb highlights our paper "A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium"  published online

GenomeWeb quotes our PATHiWAY software

PATHiWAYS has been cited in GenomeWeb
 
A number of papers in the new Web Server issue were related to NAR's theme of network and pathway analysis.

Babelomics cited in the Maniatis

The Babelomics suite of programs becomes a classic. Now is cited as a method in the last edition of Molecular Cloning, the popular Maniatis.

GenomeWeb quotes our VARIANT software

Our VARIANT software tool for assessing the possible pathological effect of variants found in deep

The Bulletin Electronique quotes our VARIANT software

Our VARIANT software tool for assessing the possible pathological effect of variants found in deep sequencing experiments has been quoted in the Bulletin Electronique, a observatory for   technological developments of the French Ministry of Foreign Affaires 

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