Flanders Institute for Biotechnology (VIB)

Four 4-year PhD studentships @ the Van de Peer Lab

VIB - Flanders Institute for Biotechnology

Ghent, Belgium

About the Lab

Four 4-year PhD studentships are available in the Van de Peer Lab (Bioinformatics and evolutionary genomics) at the VIB Center for Plant Systems Biology at Ghent University, Belgium.

The Van de Peer lab studies the evolution of (plant) genomes and in particular the importance of gene and genome duplication for evolution and adaptation. This is done mainly using computational approaches but more recently also using evolutionary experiments and through lab work.

More information can be found at our website at http://bioinformatics.psb.ugent.be/beg/.

1)One PhD student will conduct academic research (full-time) in the field of ‘evolve and resequence’ experiments and evolutionary genomics. Starting January 2020.

Project

The potential role of whole genome duplication (WGD) in evolution is controversial. Whereas some view WGD mainly as detrimental and an evolutionary ‘dead end’, there is growing evidence that the long-term establishment of polyploidy might be linked to environmental change, stressful conditions, or periods of extinction. However, despite much research, the mechanistic underpinnings of why and how polyploids might be able to outcompete non-polyploids at times of environmental upheaval remain elusive.

Different hypotheses have been proposed to explain how stressful conditions might promote the formation of polyploids, how polyploidization might confer fitness advantages, and how polyploids might adapt faster to a changing environment. Using a combination of long- and short-term evolution experiments on the greater duckweed Spirodela polyrhiza and whole genome (re)sequencing, we aim to test some of these hypotheses and to gain insights into the stabilization of a polyploid genome.

The project has several components, such as creating neoautopolyploid duckweed lineages with different genetic backgrounds, testing the immediate effects of WGD on the survival, fitness and the phenotype (and its plasticity) of duckweed in different environments, and studying the genomic stabilization, transcriptional dynamics and proteomic changes subsequent to WGD.

Profile of the candidate

  • The applicant should have a master’s degree in biology, bio-technology, bio-engineering (or equivalent) or will have obtained this degree by the start of appointment, which is January 2020.
  • A strong interest in evolutionary biology is required and experience in both experimental research and bioinformatics is preferred. The student needs to be dedicated to carry out long-term multidisciplinary research, which involves regular maintenance of duckweed cultures, some molecular work, as well as computational genomic analyses.
  • Basic knowledge of programming/scripting and statistics is required.
  • Very good command of the English language, and good communication skills, oral and in writing, are essential.

How to apply?

Motivated candidates are asked to apply online. Your application should include a detailed CV, a cover letter (max. 2 pages, including your research interests and motivation to apply) and contact information of two referees. All documents should be merged into a single PDF.

2) One PhD student will conduct academic research (full-time) in the field of network biology. Starting January 2020.

Project

Gene duplications and particularly whole genome duplications (WGDs) affect the structure of genomes and the encoded gene regulatory networks (GRNs). While redundancy facilitates the gradual evolution and rewiring of duplicated networks for adaptation in the longer term, the more complex structure of duplicated GRNs might also allow polyploids to explore a wider evolutionary landscape, providing short-term increased opportunity to adapt to novel, different, or rapidly changing environments. Through WGD, increased complexity, modularity and functional redundancy following WGD could help explain the different behavior of polyploids and non-polyploids under stable or challenging environments.

We want to develop a computational framework to study the effects of WGD on the structure of genomes and the underlying genetic networks in simulation. We want to investigate how duplicated networks affect evolvability of genomes and adaptation and evolution of their hosts.

The PhD work will involve scientific research in the domain of algorithms and graph-theory, specifically linked to the field of evolution.

Profile of the candidate

  • The applicant should have a master’s degree in bio-engineering, mathematics, physics or computer science (or equivalent) or will have obtained this degree by the start of appointment, which is January 2020.
  • A strong interest in – and some knowledge of – evolutionary biology is required.
  • The applicant should be proficient in programming and have proven (e.g. student project, master thesis, …) strong analytical skills for designing models and analyzing research results.
  • The applicant should be able to work independently and should have a strong feeling of responsibility.
  • Very good command of the English language, and good communication skills, oral and in writing, are essential.

How to apply?

Interested candidates should apply online. Your application should include a detailed CV, a cover letter (max. 2 pages, including your research interests and motivation to apply) and contact information of two referees. All documents should be merged into a single PDF.

3) One PhD student will conduct academic research (full-time) in the field of evolutionary genomics. Starting January 2020.

Project

Genomes are dynamic entities that change over time. An important mechanism by which genomes evolve novel functions is gene and genome duplication. However, not all cellular processes are equally malleable by evolution through gene duplication.

Studies in human genomes have revealed that certain genes might be intolerant to duplication, leading to human disease. Similarly, many genes in flowering plants appear preferentially as single copy in all angiosperm genomes sequenced. This is surprising given the duplication-rich history of the angiosperms. The basis of this intolerance for duplication remains unknown. A popular hypothesis is that duplication directly influences the amount of protein that gets produced and as such disturbs key pathways in which these ‘dosage-sensitive’ genes are involved.

Alternatively, putative mutations in the duplicate copy might interfere with the essential wild-type function of the corresponding single copy gene, as such promoting fast removal of duplicated copies from the genome.

In the current project, we will leverage the availability of large collections of omics data, to pinpoint key determinants underlying intolerance to duplication. Obtaining a deep understanding in a widespread evolutionary process such as gene duplication will have wide-ranging applications from understanding the role of duplication in adaptation to understanding how it can impact plant fitness.

Profile of the candidate

  • The applicant should have a master’s degree in biology, bio-technology, bio-engineering (or equivalent) or will have obtained this degree by the start of appointment, which is January 2020.
  • A strong interest in evolutionary biology is required and experience in bioinformatics is essential.
  • Good knowledge of programming/scripting and statistics is required. Very good command of the
  • English language, and good communication skills, oral and in writing, are essential.

How to apply?

Motivated candidates are asked to apply online. Your application should include a detailed CV, a cover letter (max. 2 pages, including your research interests and motivation to apply) and contact information of two referees. All documents should be merged into a single PDF.

4) One PhD student will conduct academic research (full-time) in the field of insect genomics and epigenetics. Starting January 2020.

Project

Economically devastating locust swarms result from an extreme type of ‘phenotypic plasticity’. Depending on population density, the locust genome can manifest as one of two very different phenotypic outcomes: a lone-living solitarious phase or a swarming gregarious phase. Gregarious behavior can arise within hours of crowding, and is soon consolidated to keep locust swarms together. Recent work strongly implicates epigenetic changes in neural DNA methylation in this consolidation.

We aim to unravel the role of DNA methylation in both the consolidation and the loss of gregarious behavior in desert locusts. We aim to bridge two seemingly unrelated research challenges: elucidating how social experiences accumulate over a lifetime to affect behavior; and finding novel ways for disbanding locust swarms by destabilizing consolidated swarming behavior.

This multidisciplinary project combines behavioral analyses with transcriptomics, methylomics, confocal brain imaging, advanced bioinformatics and manipulation of the methylation patterns to:

1) identify the genes that undergo changes in DNA methylation and expression upon crowding;

2) determine whether crowding and isolation engage the same molecular mechanisms;

3) compare DNA methylation between locusts and other organisms; and

4) destabilize the onset and maintenance of the swarming phenotype.

Profile of the candidate

  • The applicant should have a master’s degree in biology, bio-technology, bio-engineering (or equivalent) or will have obtained this degree by the start of appointment, which is January 2020.
  • A strong interest in genomics and in integrating different omics data is required.
  • Experience in bioinformatics and good knowledge of programming/scripting and statistics is essential.
  • Very good command of the English language, and good communication skills, oral and in writing, are essential.

How to apply?

Interested candidates should apply online. Your application should include a detailed CV, a cover letter (max. 2 pages, including your research interests and motivation to apply) and contact information of two referees. All documents should be merged into a single PDF.

Please apply via recruiter’s website.

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