BIOINFORMATICS AND FUNCTIONAL GENOMICS
Head: Ana Conesa Cegarra (aconesa (at) ivia (dot) es)

 

Research Lines

(1) Functional Annotation

In this research activity we address the problem of the gene functional annotation and analysis in poorly characterized species. We have developed the software Blast2GO, a Bioinformatics tool for the functional annotation of novel sequences and their data mining in functional genomics studies. Blast2GO is a user friendly software, aimed at biologist users which allows a high-throughput evaluated annotation of DNA or protein sequences, in virtually any species, with Gene Ontology terms,InterPro identifiers, Enzyme Commission numbers (EC) and KEGG maps of metabolic pathways. The tool has different graphical and statistical functionalities for the study of the semantic meaning of groups of sequences, which has it application in transcriptomics projects, EST library analysis or comparison between organisms. This Project has been developed in collaboration with the group of Dra. Robles IBIME at the Polytechnic University of Valencia (UPV).
(More information available at www.blast2go.org www.blast2go.org)

TEAM:
PhD project: Stefan Gotz
Graduate Student: Damien Buatois
UPV Lecturer: Juan Miguel García

(2) Development of algorithms in transcriptomics

Within this research area we address the development of statistical algorithms for the analysis of time series microarray experiments and for data integration. This work is carried out in collaboration with the group of Dr. Ferrer (DEIO-UPV). Main research projects are:

- maSigPro: methodology and R package for the identification of significant gene expression profile changes. This method uses univariate methods with binary variables to model gene expression in time and find differences between series associated to diverse experimental conditions. [R package]

- ASCA-genes:. Adaptation of the ASCA methodology developed by Smilde and co-workers to the analysis of time series in transcriptomics. The method combines ANOVA and multivariate methods to identify main and secondary patters of gene expression associated to different experimental factors (time and treatments). Furthermore the approach includes a method for the selection of genes associated to the discovered patterns. [R code]

- MAASCA: Integration of ASCA-genes and maSigPro to the analysis of time series in transcriptomics. The approach applies the ASCA-genes method to filter expression signals based on the co-variation structure present in the data which is associated to the experimental factors, and applies secondly the method maSigPro to identity genes with a significant differential expression.

- N-way methods: On going project where the application of multidimensional multivariate methods is applied to the analysis, inference and integration of “omics” data, which includes experimental factors, measured variables (gene expression, metabolite levels or physiological factors) and a priori information (functional annotation).

TEAM:
PhD project: Maria José Nueda
PostDoc (N-way): Jose Manuel Prats

(3) Information Systems in Functional Genomics

Within this area we aim to provide computational solutions to the data storage needs of the data generated by different high-throughput projects on the functional genomics of Citrus species.

The main Project is CitrusBase, an information system where transcriptomics, sequence, and phenotypic data is stored and integrated. The main achievements in this Project up till now are the development of the database VICENTs, which hosts information on EST and BAC sequences generated at the Centro de Genómica (in collaboration with Dr. Terol), and the development of the software Vitamin, a bioinformatics tool for the annotation, analysis and management of phenotypic data in collections of biological material. This Project has funding from the Generalitat Valenciana and is done in a collaboration with Dr. Maldonado (IBIME-UPV)

TEAM:
PhD project: Oscar Sánchez
Graduate Student: Luis Marco
PostDoc: Jose Alberto Maldonado