IHPE – CHAPARRO Cristian english

CristianIHPE UMR 5244
University of Perpignan via Domitia
52 Avenue Paul Alduy
F-66860 Perpignan Cedex FRANCE
Tel +33(0)4-68-66-20-50
Fax +33(0)4-68-66-22-81
email : cristian.chaparro@univ-perp.fr
POSITION: Engineer CNRS (Bioinformatician)
– Administration of HPC cluster
– Administration and maintenance of bioinformatics software including a local deployment of the Galaxy server
– Maintenance and evaluation of technical solutions for NGS data analysis
Researcher ID
et Publons
Research Gate
Google Scholar
Linked In
I’m interested in elucidating the dynamics by which transposable elements survive and reproduce inside their host genome. Through this dynamic the host genome is modified structurally as well as functionally and this aspect forms part of my interest as well.
 In order to understand the impacts that these elements have on the genome we have developed microarrays to identify the families that were transcriptionally active. Going a step further, I developed software to search for new insertions of elements starting from NGS resequencing data of Tos17 insertional mutants of rice.
 I have developed a series of tools to identify and annotate transposable elements, specially Retrotransposons, in genomes. These tools have been used in different plant genome sequencing projects like rice, cacao, maize, and the algae chondrus. I’ve also participated in de novo genome assembly projects of rice species like glaberrima and glumaepatula.
 I’m currently working on the identification and annotation of the transposable elements of the coral Pocillopora and searching for the possible role they might play in the primed resistance to heat stress.
 My expertise domain includes the development of algorithms for the analysis of NGS data, genome annotation, comparative genomics and differential expression analysis and visualization. I use tcl/tk, perl and python programming languages as well as the R software suite including the bioconductor set of packages for differential expression analysis. Within the NGS data analysis i’ve worked with several genome assemblers including Velvet, Soapdenovo, Abyss, Ray, Bambus, Mira, Zorro, Platanus, etc. Most recently I’m working with RNA-Seq analysis using different tools that are currently available like cufflinks, tophat, trinity, etc. I have a reasonable knowledge on web development and a solid base on cluster administration.
2003 – Doctorate in biotechnology
1996 – Agronomic Engineer
1995 – Bachelor in Agronomy
PUBLICATIONS in the lab with impact factor:link
PUBLICATIONS out of the lab or without impact factor:
– Kincaid-Smith J., Tracey A., Augusto R., Bulla I., Holroyd N., Rognon A., Rey O., Chaparro C., Oleaga A., Mas Coma S., Allienne J.F., Grunau C., Berriman M., Boissier J. and Toulza E. (2018) Whole genome sequencing and morphological analysis of the human-infecting schistosome emerging in Europe reveals a complex admixture between Schistosoma haematobium and Schistosoma bovis parasites. BioRxiv 387969 + The Lancet Infectious Disease
– Sow M.D., Le Gac A., Lafon-Placette C., Delaunay A., Le Jan I., Fichot R., Maury S., Mirouze M., Lanciano S., Tost J., Segura V., Chaparro C., Grunau C., Allona I., Le Provost G., Plomion C., Salse J., Ambroise C., Gribkova S. and Struass H.H. (2018) Clarifying the role of DNA methylation in tree phenotypic plasticity. FEBS Open Bio 8: 138 Meeting abstract P.03-003-W
– Rondon R., Grunau C., Fallet M., Charlemagne N., Sussarellu R., Chaparro C., Montagnani C., Mitta G., Bachère E., Akcha F. and Cosseau C. (2017) Effects of a parental exposure to diuron on Pacific oyster spat methylome. Environmental Epigenetics 3: dvx004