Benoît Aliaga

Deaf PhD in epigenetics

DNA image

My curriculum vitæ

You can download the PDF version of my resume (curriculum vitæ).

Keywords

Evolution, genome, epigenome, G x E interaction, phenotypic plasticity, development and aging.

Education

2014-2018: PhD in Epigenetics at the IHPE lab, University of Perpignan, France

2011-2014: MSc in Environnemental Genomics, University of Perpignan, France

2011: BSc in Biology and Ecology, University of Perpignan, France

Fellowships

2014-2018: National Ph.D. grant for disabled graduate students (French Ministry of Education and Research)

Research experience

October 2014 - May 2018: PhD at the IHPE lab (University of Perpignan), Perpignan, France.

January - June 2014: Internship at the IHPE lab (University of Perpignan), Perpignan, France. Pan-species analysis of DNA methylation with bioinformatic tools under the supervision of Jan Bulla and Christoph Grunau

January - August 2013: Internship at the Department of Ecology and Evolution (University of Lausanne), Lausanne, Switzerland. Telomeres length, individual quality and fitness under the supervision of Pierre Bize

February - April 2012: Internship at the Ecobio lab (University of Rennes), Rennes, France. Reconstruction and assembly of ribosomal DNA (45S rDNA) in Spartines polyploidy under the supervision of Armel Salmon and Malika Aïnouche

May - July 2011: Internship at the Conseil Général des Pyrénées-Orientales, Perpignan, France. Pesticides and their impact on human health and the environment

July 2010: Internship in the Hygiene and Health Department of the city of Perpignan, France on Unhealthy Habitats in Perpignan

Skills and techniques

Bioinformatics: Galaxy

Programming languages: Bash, HTML5, CSS3 and I'm learning PHP, MySQL and Python

Biostatistics: R, JMP

Molecular Biology: DNA extraction, PCR, qPCR, molecular cloning, Tecan freedom evo

Parasitology: familiarized with the Schistosoma mansoni techniques (recovering eggs from liver and feces, miracidia and cercaria larva, infestation of mice or hamsters, In vitro sporocyst transformation).

Microbiology: general techniques

Text processing software: Word, Excel, Powerpoint, LibreOffice and Latex

Languages: French (mother tongue), English (B1 level), French Sign Language (fluent)

Leadership experience

Teaching

I taught during 64 hours:

  • Introduction to microbiology (practical works for 1st year undergraduates)
  • Animal physiology (practical works for 2nd year undergraduates)

Congress organisation

Administration works

I was a member of the IHPE lab group communication.

IHPE journal club presentation

During my PhD, I delivered several presentations during the IHPE journal club.

Yearly participation in science popularization days

Vice-President of a local association deaf and hearing impaired people (APIDA66)

Professional associations

Publications

You can download my articles in PDF-format . Otherwise, you can also find them in the journal's website.

Aliaga B., Bulla I., Mouahid G., Duval D., Grunau C. (2018) Universality of the DNA methylation codes in Eucaryotes. Scientific Reports. In press

Roquis D., Taudt A., Geyer K. K., Padalino G., Hoffmann K. F., Holroyd N., Berriman M., Aliaga B., Chaparro C., Grunau., Augusto R. (2018) Histone methylation changes are essential for life cycle progression in the human parasite Schistosoma mansoni. PLOS Pathogens.

Bulla I., Aliaga B., Lacal V., Bulla J., Grunau C., Chaparro C. (2017) Notos - a Galaxy tool to analyze CpN observed expected ratios for inferring DNA methylation types. BMC bioinformatics.

Fneich S., Theron A., Cosseau C., Rognon A., Aliaga B., Buard J., Duval., Aranciabia N., Boissier J., Roquis D., Mitta G., Grunau C. (2016) Epigenetic origin of adaptative phenotypic variants in the human blood-fluke Schistosoma mansoni. Epigenetics & Chromatin.

Boutte J., Aliaga B., Lima O., Ferreira de Carvalho J., Aïnouche A., Macas J., Rousseau-Gueutin M., Coriton O., Aïnouche M., Salmon A. (2016) Haplotype detection from next generation sequencing in high ploidy-level species: 45S rDNA genes copies in the hexaploid Spartina maritima. G3: Genes, Genomes, Genetics.

Oral presentations

B. Aliaga, I. Bulla, V. Lacal, J. Bulla, D. Duval, C. Grunau, C. Chaparro*. Predicting DNA methylation by means of CpGo/e ratios in the case of a pan-species study. CEMEB workshop epigenetics in ecology and evolution, April 4th 2016, Montpellier, France.*presented by Chaparro in my absence

B. Aliaga, D. Duval, C. Grunau. How to correlate the prediction of DNA methylation with experimental data: a statistical approach. Brainstorming workshop: Epigenetics & Mathematics, 28th-31th October 2015, Berlin, Germany.

B. Aliaga, D. Duval, K. Brehm, C. Grunau. Genome-wide comparison of chromatin structure changes in infective forms of parasitic flatworms. Interaction Micro-organismes Hôtes (IMH), 19th November 2014, Montpellier, France.

Posters

B. Aliaga, I. Bulla, G. Mouahid, D. Duval, C. Grunau. DNA methylation prediction in the gene body by means of CpGo/e ratios in a eukaryotic pan-species study. II Joint Congress on Evolutionary Biology, August 19th-22th 2018, Montpellier, France.

B. Aliaga, I. Bulla, V. Lacal, D. Duval, J. Bulla, C. Chaparro, C. Grunau. Predicting DNA methylation by means of CpGo/e ratios in the case of a pan-species study. Journées Ouvertes de Biologie, Informatique & Mathématiques (JOBIM), 28th-30th June 2016, Lyon, France.

B. Aliaga, V. Lacal, I. Bulla, D. Duval, J. Bulla, C. Grunau. A pan-species study of DNA methylation patterns by means of distributions of CpG o/e ratios. European Society for Evolutionary Biology (ESEB), 10th-14th August 2015, Lausanne, Switzerland.

J. Boutte, B. Aliaga, J. Ferreira de Carvalho, O. Lima, S. Coudouel, D. Naquin, P. Wincker, J. Poulain, C. Da Silva, M. Aïnouche and A. Salmon. Automatized detection of duplicated copies from NGS data: application to 45S rDNA and coding genes in hexaploid Spartina species (Poaceae). International Conference on Polyploidy, Hybridization, and Biodiversity (ICPHB), 7th-10th May 2012, Průhonice, Czech Republic.