The Bioinformatics Department at CIPF has been providing microarray data analysis and consulting services for a long time. We have succeeded in bringing together a multidisciplinary team of biologists, statisticians and computer scientists, all of them important assets in any genomic data analysis. Babelomics software has been specifically developed for this purpose and is running in our 300 processor computer cluster. Many different genomic databases have also been combined and integrated into our bioinformatics tools and all of that is available for research.
We offer support in the interpretation of genomic data from different platforms, including microarrays and Next Generation Sequencing (NGS). Gene expression arrays or tiling arrays from different manufacturers (Affymetrix, Agilent, Illumina, etc.) can be analysed. Different NGS technologies (Roche 454, Solexa and ABI SOLiD) can also be analysed for different purposes (SNP discovery, RNA-Seq, Chip-Seq, etc.)
We can help you to understand gene expression by:
* Preprocessing of most popular microarray platforms: Affymetrix, Illumina, Agilent (including single-channel hybridization). Microarray Normalisation.
* Looking for differentially expressed genes in class comparison studies, time course analysis or survival experiments.
* Finding genes showing a coordinated pattern along samples. Gene clustering.
* Finding samples showing a similar pattern in their gene measurements. Clustering by samples (arrays or biological conditions).
Or making sense of your genomic data:
* Preprocessing your arrays and creating SNP calls.
* Discovering genetically different subpopulations in your data. Population Stratification Analysis in SNP Studies.
* Finding SNPs associated to a disease or a phenotype. Genomic Association Studies.
* Using the family or a pedigree structure as additional information. Linkage Analysis.
We have also extensive experience in class prediction:
* Developing and validating classification algorithms from gene expression measurements.
* Building up software for clinical class prediction based upon genomic data.
We are pioneers in analysing NGS data for different types of experiments which include (but are not restricted to):
* Genome resequencing and variation discovery and characterisation,
* Gene expression (RNA-seq)
* DNA-protein binding (Chip-seq)
* De novo sequencing of small and medium genomes (bacterias and small eukaryotes)
Our group has been a major developer of methods for integrating data base information with experimental information from high throughput experiments. Hence we have the tools and the expertise to:
* Confront your expression data to curated genomic databases using Gene Set Analysis techniques And functional profiling methods. Thus, by increasing the level of organisation of your experimental results and spotting functionally relevant characteristics in your samples.
* Link your SNP analysis results to database information and carry out Functional Interpretation of them relaying on genomic data bases.
Biology is not linear and recent bioinformatics is taking into accounting for that via network modeling of complex interactions. We can help you:
* Unravelling, within known biological pathways, the active sub-structures which are responsible for the biological changes in your experiment.
* Finding protein-protein interactions that are shown by your data to be significantly activated in your experiment.
As Bioinformatics is always developing you may find the following useful:
* Our experience in teaching and organising Genomic Data Analysis Training Courses.
* Our advice on how to set up (and configure) your bioinformatics laboratory.
Finally we are interested in computer science as much as in biological research so, do not hesitate to contact us for analysis services, consulting and, of course, for collaborations.