Sébastien Guizard (Roslin Institute)
Sébastien Guizard is a postdoc researcher at Roslin Institute, in Edinburgh (United Kingdom). His task in GENE-SWitCH project is to detect and locate genes in the genome by using long-read sequencing techniques in order to obtain the genome sequence. This will be helpful to define a landscape of gene expression in farmed pigs and chickens.
Fanny Mollandin (INRAE)
Fanny Mollandin is a PhD student at INRAE, the French National Research Institute of Agriculture. She's got a background in Mathematics and her PhD research, about the development of statistical models, aims to deliver new knowledge about the functional genomes of pigs and chickens to enhance the sustainability of farmer animal production.
Jani de Vos (Wageningen University)
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After finishing the MSc in Animal Breeding and Genetics at the University of Pretoria in South Africa, Jani de Vos started her PhD at Wageningen University (WU) in The Netherlands in July 2019. The GENE-SWitCH project had captured her attention a few months before when she saw the PhD position available at WU. From there it was a happy journey to begin this PhD, and her work is under the supervision of Dr. Ole Madsen and Prof. Dr. Martien Groenen. |
Becoming a scientist (bioinformatics and epigenomics) within the GENE-SWitCH project
Branches of this PhD
This PhD is a part of the WP2 of GENE-SWitCH, where development of standardized bioinformatics pipelines is one of the objectives. These pipelines will be used for the analyses of data from the project to predict regulatory elements as well as tissue and species specific patterns of gene regulation and comparisons between tissues and species. This PhD combines the field of bioinformatics and (epi)genomics. Using a bioinformatics approach, we can develop pipelines for the analysis of methylation data. Such pipelines can be used to analyze raw data and receive useful results (figures, statistics and graphs). Regulatory elements in the genomes of pig and chicken in specific tissues during different phases of fetal development are not fully understood. The activation status of these elements may vary between tissues as well as during the different developmental stages. The identification of the regulatory elements controlling the genome during the different stages of development in both species contributes to the identification of the switches that differentiate the different phases; especially as some of these elements may be undetectable or inactive in adults. Comparable developmental stages in pigs and chickens will be investigated, enabling a functional comparison and enabling studying the evolution of these elements.
Process of developing in bioinformatics and epigenomics
One of my first steps was attending a bioinformatics and a genomics course within the first 6 months of my PhD which was a good kick-start for learning new skills. During the COVID-19 pandemic, together with colleagues in our group, a python learning group was formed. This provided an opportunity to learn new basic python concepts such as loops, conditional statements and dictionaries. This has now expanded to studying an advanced book on python skills and has greatly helped in my development of coding skills. Further training in using a workflow manager (Nextflow) has been very beneficial for the development of the pipeline and understanding how to ‘glue’ different processes and sub-processes together. The next and hopefully final challenge is to pack the pipeline into a format that can be transferred between different computer systems. This will be done with so-called containers. Containers are very useful for a pipeline as tools used within the pipeline are stored here. This provides another way of standardizing data analysis (version of tools), as well as ease of use. A diagram of the strategy of developing the pipeline is shown in the figure. Data from the project is already arriving and the prospect of starting the analyses and unravelling the genomes of these species is an exciting prospect!
This PhD is a part of the WP2 of GENE-SWitCH, where development of standardized bioinformatics pipelines is one of the objectives. These pipelines will be used for the analyses of data from the project to predict regulatory elements as well as tissue and species specific patterns of gene regulation and comparisons between tissues and species. This PhD combines the field of bioinformatics and (epi)genomics. Using a bioinformatics approach, we can develop pipelines for the analysis of methylation data. Such pipelines can be used to analyze raw data and receive useful results (figures, statistics and graphs). Regulatory elements in the genomes of pig and chicken in specific tissues during different phases of fetal development are not fully understood. The activation status of these elements may vary between tissues as well as during the different developmental stages. The identification of the regulatory elements controlling the genome during the different stages of development in both species contributes to the identification of the switches that differentiate the different phases; especially as some of these elements may be undetectable or inactive in adults. Comparable developmental stages in pigs and chickens will be investigated, enabling a functional comparison and enabling studying the evolution of these elements.
Process of developing in bioinformatics and epigenomics
One of my first steps was attending a bioinformatics and a genomics course within the first 6 months of my PhD which was a good kick-start for learning new skills. During the COVID-19 pandemic, together with colleagues in our group, a python learning group was formed. This provided an opportunity to learn new basic python concepts such as loops, conditional statements and dictionaries. This has now expanded to studying an advanced book on python skills and has greatly helped in my development of coding skills. Further training in using a workflow manager (Nextflow) has been very beneficial for the development of the pipeline and understanding how to ‘glue’ different processes and sub-processes together. The next and hopefully final challenge is to pack the pipeline into a format that can be transferred between different computer systems. This will be done with so-called containers. Containers are very useful for a pipeline as tools used within the pipeline are stored here. This provides another way of standardizing data analysis (version of tools), as well as ease of use. A diagram of the strategy of developing the pipeline is shown in the figure. Data from the project is already arriving and the prospect of starting the analyses and unravelling the genomes of these species is an exciting prospect!
Figure: For the development of this pipeline, I will expand an
already existing pipeline (yellow block) to be more robust and
produce further results relevant for the GENE-SWitCH project
(blue block).
Further reading and listening:
- Klemm SL et al (2019) Chromatin accessibility and the regulatory epigenome. Nat Rev Genet. 20:207-220 (review)
- Nature Podcast Extra: Epigenetics
GENE-SWitCH Interview with Jani de Vos, PhD student at Wageningen University
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The GENE-SWitCH project has received funding from the European Union’s Horizon 2020 research and innovation program under Grant Agreement No 817998. This publication reflects the views only of the author, and the European Union cannot be held responsible for any use which may be made of the information contained therein. |