We are hiring! Join our fantastic team of interdisciplinary, international researchers!

Funded PhD position – Computational modelling of host-microbiome co-metabolism
School of Medicine - NUI Galway and APC Microbiome, Cork.

The successful candidate will analyse metagenomic data in the context of microbial metabolic reconstructions to investigate in silico host-microbiome co-metabolism and predict personalised drug responses based on metagenomic data. The project involves the development of constraint-based modelling tools for host-microbiome metabolic modelling, integration of physiology-based pharmacokinetic models with the host-microbiome models, mining literature mining for relevant medical information.

Duties:

  • Acquire a profound understanding of key technologies and knowledge in computational systems biology, pharmacokinetic modelling, (medical) biochemistry, and bioinformatics.

  • Perform the research as defined by the PI and the funding source.

  • Contribute to the writing of scientific publications, progress reports, and grant applications.

  • Present at national and international conferences.

  • Acquire working skills in time and project management

  • Assist in the supervision of student projects and in teaching.

  • Participate in outreach activities, seminars and workshops for the development of scientific and transferable skills.

  • Actively collaborate in an interdisciplinary, international team.

  • Engage actively with international collaborators.

Qualifications/Skills required:

  • BSc/MSc (or equivalent) in Biochemistry, Microbiology, Bioinformatics, Computer Science, or related fields.

  • Strong interest in metabolism, biochemistry, and computational modelling.

  • Demonstrable skills/experience in programming and statistical data analysis

  • Excellent communication skills are required.

  • Excellent working knowledge of English is required.

  • High motivation and interest in interdisciplinary research are required.

  • Demonstrable experience in the constraint-based reconstruction and analysis approach is highly desirable.

  • Experience in metagenomic and metabolomic data analysis is highly desirable.

  • Experience in statistics and machine learning is desirable.

Stipend: €18,500 per annum

 

Start date: The position is available as soon as possible

To Apply:

Applications to include a covering letter, CV, a motivation letter, and the contact details of three referees should be sent, via e-mail (in word or PDF only) to Prof. Ines Thiele: e-mail

Please put reference NUIG-PhD-microbiome in the subject line of the e-mail application. Note only applications with the reference number in the subject will be considered.

 

The closing date for receipt of applications is 5.00 pm 23.05.2022

 
NUIG-RES 092-22 Research Assistant – Biomedical Data Curation for the Virtual Metabolic Human development School of Medicine.

Applications are invited from suitably qualified candidates for a full-time fixed-term position as a Research Assistant with the Molecular Systems Physiology Group, led by Prof. Ines Thiele, at the National University of Ireland, Galway.

This position is funded by an ERC grant and is immediately available to the contract end date of 30th April 2023, with the possibility of renewal.

The Virtual Metabolic Human (VMH) is a central and open-access resource for human metabolism with a focus on computational biology research applications in the context of interconnecting human and microbiome metabolism, nutrition, and disease information. The VMH is currently growing and diversifying its user base. Therefore, we are expanding the metabolic content of the resource for both human and microbial metabolism. Furthermore, we are dedicating efforts toward engaged research, which include the recently established series of fully digital undergraduate summer research programmes, MicroMaps and Virtuome. The VMH team composed of scientists from interdisciplinary backgrounds closely collaborates with a diverse range of stakeholders to further nurture VMH growth and foster research translation into digital health applications.

Job Description:

The successful candidate will assist with the VMH development, including expansion of biomedical data and support with engaged research endeavours.

Duties:

  • Actively participate as a member of the research team to assist with the VMH development.

  • Conduct literature and database searches and interpret and present the findings of the literature searches as appropriate.

  • Collect, analyse, document, curate, and implement new biomedical data sources into the VMH.

  • Assist with the organisation and delivery of engaged research endeavours, including student research programmes.

  • Contribute to the dissemination of research activities to a diverse range of internal and external stakeholders.

 

Qualifications/Skills required:

  • BSc in Statistics, Bioinformatics, Computer Science, Biochemistry, Microbiology, or related fields.

  • Strong interest in metabolism, biochemistry, and computational modelling.

  • Demonstrable skills/experience in biomedical research.

  • Experience in engaged research.

  • Excellent communication skills.

  • Excellent working knowledge of English.

  • High motivation and interest in interdisciplinary research.

  • Experience in biomedical data curation in a human and/or microbiome context.

  • Experience in biomedical data visualisation.

  • Experience in research communication.

Salary: Point 1 to Point 13 RA scale €27,380 to €36,786 per annum, pro-rata for shorter and/or part-time contracts (public sector pay policy rules pertaining to new entrants will apply). 

 

Start date: The position is available as soon as possible

To Apply:

Applications to include a cover letter, CV, a motivation letter, description of previous work experience,  and the contact details of three referees should be sent, via e-mail (in word or PDF only) to Dr. Cyrille Thinnes: e-mail.

Please put reference NUIG-RES 092-22 in the subject line of the e-mail application. Note only applications with the reference number in the subject will be considered.

 

The closing date for receipt of applications is 5.00 pm 23.05.2022

 
NUIG-RES 093-22 Research associate/Software engineer for the Virtual Metabolic Human database. School of Medicine

Applications are invited from suitably qualified candidates for a full-time fixed-term position as a Research Associate/Software engineer with the Molecular Systems Physiology Group, led by Prof. Ines Thiele, at the National University of Ireland, Galway.

This position is funded by an ERC grant and is immediately available to the contract end date of 30th April 2023, with the possibility of renewal.

This position is part of the ERC funded project BugTheDrug “Predicting the effects of gut microbiota and diet on an individual’s drug response and safety. The project aims at developing novel approaches that explicitly account for individual variations in drug response due to environmental influences, in addition to genetic variations. The human gut microbiota metabolises drugs and is modulated by diet, and it exhibits significant variation among individuals. However, the influence of the gut microbiota on drug failure or drug side effects is under-researched. In this project, we will combine whole-body, genome-scale molecular resolution modelling of human metabolism and human gut microbial metabolism with physiological, clinically relevant modelling of drug responses. In the course of the project, two pilot studies on human subjects will be carried out to illustrate that this innovative, versatile computational modelling framework can be used to stratify patients prior to drug prescription and to optimize drug bioavailability through personalized dietary intervention. This project will advance a mechanistic understanding of drug-microbiota-diet interactions and their contribution to individual drug responses. Moreover, the project will conceptually and technologically address the demand for novel approaches to the study of individual variability, thereby providing breakthrough support for progress in precision medicine.

The Virtual Metabolic Human (https://vmh.life) is a newly created resource that contains the most recent version of Recon, the global reconstruction of the human metabolic network, a gut microbiota resource of more than 800 reconstructions, information for more than 250 diseases and their connections with the human reconstruction, a gene-phenotype map for Leigh Syndrome to be used by clinicians, visualization of metabolic networks with ReconMaps, and a nutrition resource that allows researchers to model the metabolic effect of different diets. We are continuously expanding the database content and its links to biomedical and clinical information. The VMH targets researchers from all life science domains, including metabolomics, microbiome, and systems biomedicine.

Job Description:

The successful candidate will lead the continuous development of the VMH database interface.

Duties:

  • Maintain, expand, and improve the code base of the VMH database with a particular focus on data integration and visualization.

  • Respond to queries from the VMH user base.

  • Address open issues on the VMH.

  • Develop documentation and tutorials for the VMH.

  • Assist in writing documentation.

  • Integrate novel tools and applications into the VMH framework.

  • Acquire necessary background knowledge on metabolic reconstructions. 

  • Interact with national and international collaborators to ensure progress on the VMH development.

  • Participate in outreach activities, workshops, and tutorials demonstrating the VMH.

  • Assist in the maintenance of the group’s computing and software infrastructure.

 

Qualifications/Skills required:

  • BSc or MSc in Bioinformatics, Computer Science, or related fields.

  • 4+ years’ experience in MySQL, Javascript, Python, D3.js.

  • Excellent communication skills are required.

  • Excellent working knowledge of English is required.

  • High motivation and interest in interdisciplinary work are required.

  • Experience with Sencha and/or ExtJs is desirable.

  • Experience with Matlab.

  • Experience with clinical data is desirable.

  • Experience with RedCap and Transmart is desirable.

  • Working knowledge of metabolic reconstructions and constraint-based modelling is of advantage.

  • Programming experience in other languages is of advantage (R, Python).

  • Experience as a system administrator is desirable.

Salary:  Point 1 – Point 10 PDR €39,523– €51,035 per annum, pro-rata for shorter and/or part-time contracts (public sector pay policy rules pertaining to new entrants will apply). 

 

Start date: The position is available as soon as possible.

To Apply:

Applications to include a cover letter, CV, a motivation letter, description of previous work experience,  and the contact details of three referees should be sent, via e-mail (in word or PDF only) to Dr. Cyrille Thinnes: e-mail.

Please put reference NUIG-RES 093-22 in the subject line of the e-mail application. Note only applications with the reference number in the subject will be considered.

 

The closing date for receipt of applications is 5.00 pm 23.05.2022

 
NUIG RES 091-22 Postdoctoral Researcher in Computational Modelling of Human Drug Metabolism

Applications are invited from suitably qualified candidates for a full-time fixed-term position as a Postdoctoral Researcher/ in the Molecular Physiology Research group, led by Prof. Ines Thiele, at the National University of Ireland, Galway.

This position is funded by European Research Council (ERC) and is available from the earliest possible start date May 2022, to the contract end date of April 31st, 2023, with the option of extension.

 

This position is part of the ERC funded project BugTheDrug “Predicting the effects of gut microbiota and diet on an individual’s drug response and safety. The project aims at developing novel approaches that explicitly account for individual variations in drug response due to environmental influences, in addition to genetic variations. The human gut microbiota metabolises drugs and is modulated by diet, and it exhibits significant variation among individuals. However, the influence of the gut microbiota on drug failure or drug side effects is under-researched. In this project, we will combine whole-body, genome-scale molecular resolution modelling of human metabolism and human gut microbial metabolism with physiological, clinically relevant modelling of drug responses. In the course of the project, two pilot studies on human subjects will be carried out to illustrate that this innovative, versatile computational modelling framework can be used to stratify patients prior to drug prescription and to optimize drug bioavailability through personalized dietary intervention. This project will advance a mechanistic understanding of drug-microbiota-diet interactions and their contribution to individual drug responses. Moreover, the project will conceptually and technologically address the demand for novel approaches to the study of individual variability, thereby providing breakthrough support for progress in precision medicine.

Job Description:

The successful candidate will develop pharmacokinetic models of human drug metabolism and integrate them with constraint-based models of human metabolism.

Duties:

  • Development of drug-specific kinetic models (PBPK models).

  • Integration of the PBPK models with constraint-based models of human metabolism.

  • Analysis of the hybrid computational models.

  • Interaction with international collaborators.

  • Writing of writing scientific papers, reports, and grant applications.

 

Qualifications/Skills required:

  • PhD in Bioinformatics, Computer Science, or related fields.

  • Demonstrable expertise in kinetic modelling (e.g., ODE based models).

  • Experience with programming in Matlab.

  • Excellent communication skills are required.

  • Excellent working knowledge of English is required.

  • High motivation and interest in interdisciplinary work are required.

  • Experience in PBPK modelling.

  • Experience in constraint-based metabolic modelling (COBRA toolbox).

  • Knowledge of human drug metabolism.

  • Working knowledge of statistical methods and tools is of advantage.

  • Programming experience in other languages is of advantage (Julia, R, Python).

Salary:  Point 1 – Point 10 PDR €39,522– €51,036 per annum, pro-rata for shorter and/or part-time contracts (public sector pay policy rules pertaining to new entrants will apply).

 

Start date: The position is available as soon as possible.

To Apply:

Applications to include a cover letter, CV, a motivation letter, description of previous work experience,  and the contact details of three referees should be sent, via e-mail (in word or PDF only) to Dr. Cyrille Thinnes: e-mail.

Please put reference NUIG-RES 091-22 in the subject line of the e-mail application. Note only applications with the reference number in the subject will be considered.

 

The closing date for receipt of applications is 5.00 pm 23.05.2022

 
NUIG RES 090-22 Postdoctoral Researcher in Chemoinformatics

Applications are invited from suitably qualified candidates for a full-time fixed-term position as a Postdoctoral Researcher/ in the Molecular Physiology Research group, led by Prof. Ines Thiele, at the National University of Ireland, Galway.

This position is funded by European Research Council (ERC) and is available from the earliest possible start date May 2022, to the contract end date of April 31st, 2023, with the option of extension.

 

This position is part of the ERC funded project BugTheDrug “Predicting the effects of gut microbiota and diet on an individual’s drug response and safety. The project aims at developing novel approaches that explicitly account for individual variations in drug response due to environmental influences, in addition to genetic variations. The human gut microbiota metabolises drugs and is modulated by diet, and it exhibits significant variation among individuals. However, the influence of the gut microbiota on drug failure or drug side effects is under-researched. In this project, we will combine whole-body, genome-scale molecular resolution modelling of human metabolism and human gut microbial metabolism with physiological, clinically relevant modelling of drug responses. In the course of the project, two pilot studies on human subjects will be carried out to illustrate that this innovative, versatile computational modelling framework can be used to stratify patients prior to drug prescription and to optimize drug bioavailability through personalized dietary intervention. This project will advance a mechanistic understanding of drug-microbiota-diet interactions and their contribution to individual drug responses. Moreover, the project will conceptually and technologically address the demand for novel approaches to the study of individual variability, thereby providing breakthrough support for progress in precision medicine.

Job Description:

The successful candidate will develop chemoinformatic approaches for human metabolism.

 

Duties:

  • Development of chemoinformatic approaches for the efficient formulation of metabolic reactions.

  • Integration of the metabolic reactions with constraint-based models of human metabolism.

  • Interaction with international collaborators.

  • Writing of writing scientific papers, reports, and grant applications.

 

Qualifications/Skills required:

  • PhD in Chemistry, Biochemistry, Biology, or related fields.

  • Demonstrable expertise in chemoinformatics.

  • Experience with programming (e.g., Matlab).

  • Excellent communication skills are required.

  • Excellent working knowledge of English is required.

  • High motivation and interest in interdisciplinary work are required.

  • Experience in constraint-based metabolic modelling (COBRA toolbox).

  • Knowledge of human and microbial metabolism.

  • Working knowledge of statistical methods and tools is of advantage.

Salary:  Point 1 – Point 10 PDR €39,522– €51,036 per annum, pro-rata for shorter and/or part-time contracts (public sector pay policy rules pertaining to new entrants will apply).

 

Start date: The position is available as soon as possible.

To Apply:

Applications to include a cover letter, CV, a motivation letter, description of previous work experience,  and the contact details of three referees should be sent, via e-mail (in word or PDF only) to Dr. Cyrille Thinnes: e-mail.

Please put reference NUIG-RES 090-22 in the subject line of the e-mail application. Note only applications with the reference number in the subject will be considered.

 

The closing date for receipt of applications is 5.00 pm 23.05.2022

 

We are actively looking for highly motivated researchers to join our international, interdisciplinary, and dynamic team.

Openings may be available for

- Master students

- PhD students

- Postdoctoral fellows

- Software engineers

Applications can be sent directly to Prof. Ines Thiele: ines.thiele(at)nuigalway.ie and should contain a detailed CV and a cover letter detailing the researcher's interest in our research and for joining our research group.