Dr Jose M Gonzalez

Former Senior Bioinformatician at the Sanger Institute


This person is a member of Sanger Institute Alumni.

Jose provides bioinformatics support to the HAVANA genome annotation team and coordinates the GENCODE data releases.

As a bioinformatician in the HAVANA team, I perform bespoke analyses to support the manual annotation of various vertebrate genomes. This work is mainly done in the context of the GENCODE project, which aims to produce a highly accurate reference gene annotation of the human and mouse genomes. One of my tasks involves importing and analysing transcriptomics experiment data and computational predictions, publicly available or generated by GENCODE collaborators, in order to find genomic regions where novel gene annotation can be introduced. GENCODE has been recently generating long read RNAseq data which has proved useful to improve the annotation of existing genes as well as to find novel genes, especially long non-coding RNA genes.

As GENCODE data coordinator I am responsible for maintaining and improving the GENCODE release pipeline, that has been adapted to the increasing complexity of release files over the last five years. I am also involved in updating the gencodegenes.org website and coordinating the GENCODE helpdesk, and contribute to the QC of the GENCODE gene set.

My background is in biology. During my PhD in molecular biology, as a wet lab scientist, I carried out work that led to developing the first infectious cDNA of the largest RNA virus genome at the time. Subsequently I moved on to the bioinformatics field, where I collaborated with experimental groups using protein sequence and structure analysis. Before joining the Sanger I was involved in the functional genomics analysis of the effect of virus infection on host cells.

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