PhD Position in Bioinformatics and Genomics (KU Leuven Department of Human Genetics)

PHD POSITION IN BIOINFORMATICS AND GENOMICS KU Leuven and the Joint Research Centre (JRC) of the European Commission are inviting applications for PhD positions through the Collaborative Doctoral Partnership (CDP) scheme. The CDP scheme intends to enhance the science-policy link through strategic collaborations with higher education institutions characterized by research excellence and international reputation, in order to: - Train a new generation of doctoral graduates in science and technology with a focus on the science-policy interface, able to understand the research needs at different stages of the policy cycle, capable of providing scientific support to policy and of using transferable skills in science communication and knowledge management. - Co-develop, co-host and co-supervise doctoral studies between higher education institutions and the JRC. - Strengthen collaboration between the JRC and higher education institutions by promoting mutual enhancement of related skills and competences, combining existing knowledge and capacities, and enhancing networking in key scientific areas. Project Within the CDP scheme we offer a PhD position in Bioinformatics and Genomics. Next Generation Sequencing (NGS) technologies have become an indispensable tool in diagnostic laboratories. First, NGS panels have taken over Sanger sequencing in order to sequence at once all genes linked to a condition and improve diagnostic efficiency, while reducing time to diagnosis. However, targeted resequencing misses a significant proportion of causative genetic variants. Whole Genome Sequencing (WGS) is becoming affordable and is currently being implemented in a diagnostic setting. WGS will homogenize the wet lab workflow, offer a single test for all conditions, and ultimately decrease cost and time to diagnosis. However, several challenges remain to implement and routinize clinical whole genome sequencing. A first aim of the PhD is to implement, standardize and improve the algorithms for variant calling and, most importantly, to determine the quality parameters to allow for accurate genotype. Defining those parameters is paramount towards clinical implementation. In addition, to improve data analysis, a reference set of genomes is required. The student will explore different approaches to establish the best reference cohorts and training sets to improve genome variant mining. In the scope of this project, we aim to further extend and improve the existing frameworks both to provide the pipelines and the throughput required by the clinical applications. We will further develop cloud-based computing approaches. There will be a focus on identifying quality criteria for clinical WGS analysis. A second aim of the PhD is on data interpretation and data sharing. To allow for accurate variant interpretation data sharing is of utmost importance. However, privacy issues prohibit unlimited genomic data sharing. Currently, genomic variants are shared via both centralized and decentralized approaches. In this PhD we will explore methods to enable decentralized data sharing and explore how clinical records can be included in the data analysis processes. This is achieved by executing partial analyses locally and then aggregating the results centrally and passing only those results to the user. We are exploring methods to include phenotype information to the platform. The student will participate with those developments. Profile You have (or are near completion of) a Master in Bioinformatics, Computer Science, and/or genetics (or a related field). You have a motivated interest in research in computational biology. You work proactively and independently and have good communication skills. You have a very good knowledge of English, both spoken and written. You are highly motivated, ambitious and result-oriented. Offer We offer a four-year PhD position in collaboration with the Joint Research Centre (JRC) of the European Commission. The PhD research will be realized at the Joint Research Centre (JRC) in Ispra, Italy, for a period of up to 24 months and in Belgium (Leuven). We offer a competitive fellowship. While at the JRC in Ispra, you will get a contract as a grantholder Category 20 (for more info: https://ec.europa.eu/jrc/sites/jrcsh/files/jrc_grantholder_rules.pdf). General info on Ispra can be found at: https://ec.europa.eu/jrc/en/about/jrc-site/ispra https://ec.europa.eu/jrc/sites/jrcsh/files/jrc_living_in_ispra.pdf Interested? For more information please contact Prof. Joris Vermeesch (joris.vermeesch@kuleuven.be). The selection process is based on the CV, tests and interviews. It is composed of two phases, that is, a first selection is made by KU Leuven resulting in a short list of candidates and then a second selection is made by JRC. Candidates should at the start of the employment contract with JRC: Have the nationality of a Member State of the EU or a country associated to the Research Framework Programmes (Horizon2020). Candidates from other countries may also apply providing they have a residence and work permit in Italy. They will have to go through the security clearance before they can be granted the GH contract. Be enrolled in a PhD programme at KU Leuven. You can apply for this job no later than March 17, 2019 via the online application tool KU Leuven seeks to foster an environment where all talents can flourish, regardless of gender, age, cultural background, nationality or impairments. If you have any questions relating to accessibility or support, please contact us at diversiteit.HR@kuleuven.be. If you apply for this position please say you saw it on Bioloxy

PHD POSITION IN BIOINFORMATICS AND GENOMICS

KU Leuven and the Joint Research Centre (JRC) of the European Commission are inviting applications for PhD positions through the Collaborative Doctoral Partnership (CDP) scheme. The CDP scheme intends to enhance the science-policy link through strategic collaborations with higher education institutions characterized by research excellence and international reputation, in order to: - Train a new generation of doctoral graduates in science and technology with a focus on the science-policy interface, able to understand the research needs at different stages of the policy cycle, capable of providing scientific support to policy and of using transferable skills in science communication and knowledge management. - Co-develop, co-host and co-supervise doctoral studies between higher education institutions and the JRC. - Strengthen collaboration between the JRC and higher education institutions by promoting mutual enhancement of related skills and competences, combining existing knowledge and capacities, and enhancing networking in key scientific areas.

Project

Within the CDP scheme we offer a PhD position in Bioinformatics and Genomics.

Next Generation Sequencing (NGS) technologies have become an indispensable tool in diagnostic laboratories. First, NGS panels have taken over Sanger sequencing in order to sequence at once all genes linked to a condition and improve diagnostic efficiency, while reducing time to diagnosis. However, targeted resequencing misses a significant proportion of causative genetic variants. Whole Genome Sequencing (WGS) is becoming affordable and is currently being implemented in a diagnostic setting. WGS will homogenize the wet lab workflow, offer a single test for all conditions, and ultimately decrease cost and time to diagnosis. However, several challenges remain to implement and routinize clinical whole genome sequencing.

A first aim of the PhD is to implement, standardize and improve the algorithms for variant calling and, most importantly, to determine the quality parameters to allow for accurate genotype. Defining those parameters is paramount towards clinical implementation. In addition, to improve data analysis, a reference set of genomes is required. The student will explore different approaches to establish the best reference cohorts and training sets to improve genome variant mining. In the scope of this project, we aim to further extend and improve the existing frameworks both to provide the pipelines and the throughput required by the clinical applications. We will further develop cloud-based computing approaches. There will be a focus on identifying quality criteria for clinical WGS analysis.

A second aim of the PhD is on data interpretation and data sharing. To allow for accurate variant interpretation data sharing is of utmost importance. However, privacy issues prohibit unlimited genomic data sharing. Currently, genomic variants are shared via both centralized and decentralized approaches. In this PhD we will explore methods to enable decentralized data sharing and explore how clinical records can be included in the data analysis processes. This is achieved by executing partial analyses locally and then aggregating the results centrally and passing only those results to the user. We are exploring methods to include phenotype information to the platform. The student will participate with those developments.

Profile

You have (or are near completion of) a Master in Bioinformatics, Computer Science, and/or genetics (or a related field).
You have a motivated interest in research in computational biology.
You work proactively and independently and have good communication skills.
You have a very good knowledge of English, both spoken and written.
You are highly motivated, ambitious and result-oriented.

Offer

We offer a four-year PhD position in collaboration with the Joint Research Centre (JRC) of the European Commission.
The PhD research will be realized at the Joint Research Centre (JRC) in Ispra, Italy, for a period of up to 24 months and in Belgium (Leuven).
We offer a competitive fellowship. While at the JRC in Ispra, you will get a contract as a grantholder Category 20 (for more info: https://ec.europa.eu/jrc/sites/jrcsh/files/jrc_grantholder_rules.pdf).

General info on Ispra can be found at:
https://ec.europa.eu/jrc/en/about/jrc-site/ispra

https://ec.europa.eu/jrc/sites/jrcsh/files/jrc_living_in_ispra.pdf

Interested?

For more information please contact Prof. Joris Vermeesch (joris.vermeesch@kuleuven.be).

The selection process is based on the CV, tests and interviews. It is composed of two phases, that is, a first selection is made by KU Leuven resulting in a short list of candidates and then a second selection is made by JRC.

Candidates should at the start of the employment contract with JRC:

Have the nationality of a Member State of the EU or a country associated to the Research Framework Programmes (Horizon2020).
Candidates from other countries may also apply providing they have a residence and work permit in Italy. They will have to go through the security clearance before they can be granted the GH contract.
Be enrolled in a PhD programme at KU Leuven.

You can apply for this job no later than March 17, 2019 via the online application tool

KU Leuven seeks to foster an environment where all talents can flourish, regardless of gender, age, cultural background, nationality or impairments. If you have any questions relating to accessibility or support, please contact us at diversiteit.HR@kuleuven.be.

If you apply for this position please say you saw it on Bioloxy

Apply

All Jobs