Development of annotation guidelines for gene regulation corpus development, named entiry recognition of transcription factos and target genes, relation extraction of regulatory events from text, recognition of experimental methods for transcriptional regulation detection, literature triage, document classification.
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Biocuration activities related to the identification of mammalian sequence-specific DNA binding transcription factors (DbTFs) based on Gene Ontology (GO) Molecular Function (MF) terms;
Refactoring of the structure of the GO MF Ontology specifically related to
transcription factor activity (in collaboration with Astrid Lægreid and GO members)
Refactoring of the PSI-MI Controlled Vocabulary to add new terms describing transcription-related causal interactions for the CausalTAB (PSI-MITAB 2.8) (preprint paper at bioRxiv here)
Revamping of the TFCheckpoint database (still under construction; new version will be soon available)
Text-mining of DbTF-TG causal interactions from biomedical literature (in collaboration with Martin Krallinger from the Spanish National Cancer Research Centre (CNIO) and Barcelona Supercomputing Center (BSC)
Development of MICAST: Minimum Information for Causality Statements.
Expertise in data sharing and standardisation.
Took part in a Ljubljana meeting. Presented on interaction of genetic variants and transcription factor binding sites.
Development of CausalTAB, a common standard for the representation and dissemination of signalling data.
Trainer at GREEKC training hackathon in Lisbon.
Developer for WP2 (JASPAR //jaspar.genereg.net/).
Help the community in the development of REST interfaces for their resources.
Contribution of causal ontology development.
A key aspect of this Cost Action is the inter-connection of multiple resources dedicated to the study of gene expression regulation. To achieve this goal, the scientific community needs to address the need of interoperability between the multiple existing resources. We are currently involved in the development of the ReMap database (processing and storing ChIP-seq dataset to create a catalogue of cis-regulatory regions in human) and the JASPAR database. We foresee that these resources as well as other resources related to gene regulation (such as the RSAT tools, the Eukaryotic Promoter Database, cis-Regulon) should be inter-connected to allow the scientific community to leverage the power of these multiple resources.
This COST action will strengthen existing collaborations and create new ones for the analyses of gene expression regulation (e.g. with Dr. Jacques van Helden, Dr. Benoît Ballester, Dr. Stein Aerts).
Until now, I just participated at the Lisbon training school. But, I am hoping to contribute to creating standards and interoperability of gene regulation tools and resources.