- PhD -

Molecular biologist, bioinformatician, data scientist

Nicolas GUILLEMIN

Experienced researcher - Genetics, genomics, bioinformatics and data sciences

Current position, from 2015

Faculty of Veterinary Medicine, University of Zagreb - Zagreb, CROATIA

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Establish a new laboratory of genomics

Molecular biology is a new research way in veterinary medicine in Croatia. Objective of the project is to finance, build and equip a new laboratory in molecular biology (proteomics and genomcis). I was recruited to this project as an expert in genomics and bioinformatics. I bring my experience and my skills to create experimental protocols in genomics, like DNA and RNA extractions, PCR and qPCR.

Project VetMedZg: ERA Chair FP7 - Upgrading the research performance in molecular medicine at the faculty of veterinary medicine, University of Zagreb

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Genomic laboratory before equipment 

Operational genomic laboratory

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Consultant in genomics

As an experienced researcher in genomics, I train different researchers from the Faculty to add and use genomics in their current research projects (DNA and RNA extraction, nucleic acids handling, PCR and qPCR). I worked notably with projects related with cancer and parasitology in dogs. I offered my support for different projects writing.

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Ressource person for bioinformatics and data analysis

I perform statistical and bioinformatics analysis for our laboratory experiments, but also for collaborators, which can be teams at the Faculty but also visitors from different countries (Brazil, UK, Iran). 

My aim is to transform raw data into understandable and usable knowledge.

In bioinformatics, I perform Gene Ontology analysis to better characterized complex phenotypes and diseases, and predict potential new markers. 

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Creation of a new diagnostics test

Answering an ask from the Department of Parasitology, I set up a new test to diagnose presence in blood of Babesia canis canis, a blood parasite in dogs which cause a potentially lethal disease, babesiosis. 

I designed a PCR-bases test which can diagnose presence of less than 1% parasitism rate of babesia in 2 hours, faster and more accuratly than microscopic identification and counting (which is he usual method used). Due to its specificity, this test can discriminate 2 closely related subspecies of babesia, Babesia canis canis and Babesia canis vogeli. This is an important feature as the 2 subspecies can be cured with different drugs.

Development of a statistical pipeline tool to quickly analyse thousands of proteomics data generated by LC-MS

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Our laboratory LC-MS generate thousands of peptides quantification on many different samples. I encoded a pipeline tool in R langage to manage and analyse such big data. This pipeline import data generated by LC-MS, calculate different descriptive statistics (fold change, mean, standard deviation, etc...) and finally identify peptides with significant changes of expression. The pipeline can be used for every kind of experimental plan, from 2 to an unlimited number of groups. In few seconds, the pipeline run the comlpete analyse of thousands of peptides data and export results into understandable tables. 

This pipeline has been used not only for our own researches in the laboratory VetMedZg, but also on our partners data. 

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Life and Earth Sciences teacher - High School

During the school year 2016-2017

French School of Zagreb, High School division - Zagreb, CROATIA

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Teacher in Life and Earth Sciences - High School 

I was contacted by the school to take in charge courses in Life and Earth Sciences for 5 high school students. The school has issues to find a french-speaking teacher for this thematic, and I was pleased to support French community in that way. During 1 school year, I tought to few teenager students. It was a wonderfull experience, as it change completly from my "routine" laboratory work. It also make me think differently, as I usually teach to established researchers. So I adapted myself to teach to teenagers. I organized some practical work in my laboratory to make my students discover what is research in molecular biology. At the end of the year, the only last-year graduation student in the group successfully validated his final exam in Life and Earth Sciences. I was happy to lead him to the success !

Research assistant 

2014

Saint-François d'Assise Hospital, CHUQ - Québec, CANADA

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Support for project submission - Bibliography and data analysis

My aim for this position was to provide a complete bibliography report on the utilization of antibiotics in primary care, and summarize statistics about such utilization. Using such data, I provided support for the submission of research projects about antibiotics in primary care. I also summarize data about elderly care. Thanks to this job, I discovered closely research in an hospital with thematics and problematics, directly applied to patients.

Post-doctoral researcher - Genetics and genomics

2011-2013

Center for Reproductive Biology Researches, University Laval - Québec, CANADA

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Establish a new methodology to identify genetic markers from genomics data generated by NGS

My post-doctoral aim was to create a analyse pipeline to identify genetic markers (SNP) of complex phenotype, by the application of genomics. The studied phenotype was the expression of a gene encoding the aromatase enzyme, essential component of female fertility, in dairy cattle.

I quantified gene expression of this gene in 100 samples. Then I studied gene expression by a DNA micro-array to determine which genes could be related with a modification of the aromatase gene expression profile. After sequencing bovine genome by Illumina HiSeq on a reference population (N=1000) and alignment, I genotyped the 100 samples on the best candidates genes (from DNA micro-array experiment) to characterize their genome on specific positions (SNP).

To modelize aromatase gene expression profile in function of genotype content, I was inspiered by publications in human forensic science (determination of hair color by genetic markers). Then I calculated a prediction model and identify the best genetic markers related with the complex phetnotype (aromatase gene expression level).

Before the end of my post-doctoral internship, I set up this metholodology to identify genetic markers using genomics data, allowing a genomics laboratory to identify genetic markers. I also wrote protocol for genotyping, as I was the first to perform such experiment in the Research Center.

 

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Identification and validation of new genetic markers (SNP)

With the utlization of the methodology set up, I identified and validated genetic markers related with aromatase gene expression profile. Those SNPs were then validated in bulls, according to their daughters performances.

Some of those markers were completely unknown by the industry. Some were located in known QTL and so allow to precise coordinates of this region. 

In those two cases, my work identified new markers for dairy cattle indstry.

PhD student - Molecular physiology and genetics

2008-2010

Herbivore Research Unit, National Institute for Agricultural Researches (INRA) - Clermont-Ferrand-Theix, FRANCE

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Set up a new methodology for muscle protein quantification

At the beginning of my PhD, I needed a better methods (in terms of speed) than Western-Blot to quantity proteins in muscle. So I started to set up a new method to quickly quantify proteins, with at least the same accurac than Western-Blot. After 1 years of tests and improvments, I successfully publish a protocol of proteomics dot-blot. By the utlization of this technique, I was able to quantify proteins in hundred of muscle samples in few weeks, intead in 2 to 3 years as it should have been with Western-Blot. This technique changed completely my PhD results.

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Set up fluorescence detection of antibodies in the laboratory

When I started my PhD, the only detection system of antibodies used in the laboratory was chemiluminescence. When I was developing Dot-Blot protocol, it appear that I needed a better detection system in term of sensitivity and reproductibility. I was trained in the fluorescent detection system by a laboratory in human physiology, and bring the protocol back to my laboratory (with some adaptation to the equipment). This protocol is now a routine one in the laboratory.

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Set up a new statistical approach for the modelization of complex phenotype from proteomics data

Main aim of my PhD was to validate (or not) the relation of different muscle proteins with beef tenderness. For that, I calculated prediction models of beef tenderness score from proteomics data, using a dedicated methodology designed for this objective.

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Validation of proteins as biomarkers and pathway analysis of beef tenderness

Thanks to my PhD results, some proteins were validated as markers of beef tenderness. Going further, I performed bioinformatics analysis to decipher beef tenderness into cellular pathways. Using those analysis, I predicted 3 never-studied (in beef tenderness) proteins as potential new biomakers. Those proteins were validated few months after my PhD for their role in beef tenderness.

Master student internship - Microbiology and genetics

2006 - 2007

Laboratory of microbiology and genetics, University Nancy II - Nancy, France

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Design a new bacterial plasmid in Streptomyces ambofaciens

Aim of this internship was to design a new plasmid by molecular cloning and transform the soil bacteria Streptomyces ambofaciens with it.

During this internship (in alternance with Master courses), I successfully designed the required plasmid. Due to toxicity of the genetic construction for Escheriachia coli, I needed to transformed directly Streptomyces ambofaciens which is a more time-consuming process. I produced different strains of bacteria for laboratory collection.

I had working experiences in 3 different countries, on 2 continents. I worked with different people with different working philosophy, on different thematics and objectives. All those various and rich experiments forged the researcher I am today.

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A Gene Ontology analyse to decipher pathways implied in a dog infectious disease

Diagnostic by qPCR for the detection of Babesia canis canis in dog blood

Part of the developed script for LC-MS big data analyse

Volcano plot of protein fold changes and their associated p-values

Results of HRM genotyping - 3 different genotypes detected on 1 position

An example of DNA micro-array

Identification of significant (or not) SNPs related with studied phenotype

Volcano plot of more than 1000 gene expression data produced by DNA micro-array

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First Dot-Blot. This methodology saved 2-3 years of PhD.

Switching from chemiluminescence to fluorescence detection produced better results (sensibility, reproductibility)

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Functional interactome generated from my PhD results

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Predictive model for beef tenderness

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