Benoît Aliaga

Deaf PhD in epigenetics

DNA image

My curriculum vitæ

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


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


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

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

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


2019: Wellcome Trust Sanger Institute for a course on Single Cell technologies and analysis

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

Research experiences

January 2019 - November 2019: Ingénieur de Recherche with Antoine Claessens at LPHI lab (University of Montpellier), Montpellier, France.

October 2014 - May 2018: PhD at the IHPE lab (University of Perpignan), Perpignan, France. With Christoph Grunau and David Duval

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

January - June 2011: Literature study on the LTR retrotransposons in plants with Eric Lasserre

Others professional experiences

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: RNA-seq, SNS-seq, HPC, Galaxy, Single Cell analysis

Programming languages: Bash, HTML5, CSS3, PHP, MySQL and Python

Biostatistics: R, JMP

Molecular Biology: DNA extraction, PCR, qPCR, molecular cloning, Tecan freedom evo, Bioanalyzer, Single Cell Technologies

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) in a L2 lab and Plasmodium falciparum cellular culture in a L3 lab.

Microbiology: general techniques

Miscroscopy: optical microscopes

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

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

Other: CNRS geslab software

Organization and leadership experience

2018: II Joint Congress on Evolutionary Biology (volunteer)

2018: Models in Ecology and Evolution seminar (scientific committee)

2015-2018: Member of the IHPE (Interaction Host Pathogen and Environment) lab group communication

2011-2018: Yearly participation in science popularization days

2015: University of Perpignan PhD student congress (scientific committee)

2011-2019: Vice-President of a local association for deaf and hearing-impaired people (APIDA 66)

2008-2019: APIDA 66 Member of the Board of Directors


2019: Population genetics, molecular evolution, bioinformatics and biostatistics (ParaFrap PhD South program)

2015-2016: Introduction to microbiology (practical works for 1st year undergraduates)

2015-2016: Animal physiology (practical works for 2nd year undergraduates)

Professional associations

Member of the European Society for Evolutionary Biology (ESEB)

Member of the Société Française de BioInformatique (SFBI)

Member of the Jeunes Bioinformaticiens de France


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. (2019) Universality of the DNA methylation codes in Eucaryotes. Scientific Reports.

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.


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.