PhD Student
Transformation of Advanced
Medicines Manufacture (TRANS-AM)
Gene
therapies are a type of advanced medicine that represent exciting possibilities
to treat and potentially cure many life-altering and life-threatening diseases.
They also represent a huge growth area with several hundred currently in
various stages of development. Many of these are based on using recombinant
Adeno-associated virus (rAAV) as a delivery vector. If even a small portion of
them reach the market, current manufacturing and characterisation technologies
in the industry will struggle to deliver them economically and safely for
patients.
This
research program aims to provide innovative solutions to help overcome the
manufacturing challenges associated with producing rAAV and brings together
experts from two leading Irish institutions, NIBRT and UCD, and APC-VLE Ltd. (https://approcess.com/services/cell-and-gene-therapies)
- a leading Irish industrial partner - in an exciting 5-year collaborative
program.
We
are currently seeking applicants for two PhD projects as listed below. The
successful candidates will be based in either NIBRT or UCD and will also spend
some time on placements in the industrial partner.
We are seeking
ambitious, inquisitive and innovative individuals to join our multidisciplinary
research team. As part of a dynamic and collaborative environment, you will
contribute to breakthrough work that supports the scalable, efficient, and
high-quality production of viral vectors—laying the foundation for
next-generation treatments for genetic diseases. If you're excited by the
intersection of biotechnology, process development, and therapeutic innovation,
we’d love to hear from you.
The National Institute for Bioprocessing Research and
Training (‘NIBRT’) NIBRT is a Dublin-based global centre of excellence that provides training and research for the biopharmaceutical manufacturing industry. Founded through collaboration between leading Irish universities and funded by the Irish Government via IDA Ireland, NIBRT operates an 8,300 m² facility with over 100 staff, featuring pilot plants, research labs, and a dedicated space for early-stage biologics and advanced therapy development. NIBRT - National Institute for Bioprocessing Research and Training
UNIVERSITY COLLEGE
DUBLIN (UCD) - University College Dublin
Project 1: CRISPR library screening
to identify endogenous HEK293 genes that impact AAV production
Supervisors:
Prof. Niall Barron & Assoc. Prof. Colin Clarke
About the project:
A strategy that has proven very successful
in identifying the genetic basis of various
cellular phenotypes, including diseases
such as cancer, cellular behaviour in bioreactors and identifying viral
restriction factors, is the use of CRISPR library screens. These can be either
to knockout the genes expressed in a cell or to activate the expression of
silent genes. The advantage is that it is relatively unbiased and has the
potential to target every gene in the genome.
Aims and Objectives: In this project we will use this strategy in order to screen a
suspension-adapted HEK293 cell line for genes that contribute to or inhibit the
production of AAV gene therapy vectors. We will use a human CRISPR/guide RNA
library to create a HEK293 cell population within which every gene has been
targeted for deletion. We will select a sub-population
of cells with the highest and lowest level of AAV production and this
population of cells will be sequenced to identify which guide RNAs are
enriched, thereby identifying their target genes. The most impactful genes will
be validated by knocking out in parental HEK293 cells and then testing AAV
production yield after triple transfection.
Candidate profile: Applicants should hold or expect to receive an upper 2.1 or 1.1
degree in a relevant discipline. A cell biology/molecular biology background would
be ideal. Training will be provided in advanced methods and approaches in cell
and molecular biology required for successful completion of the programme. The
ability to work as part of a team, a strong interest in applied research,
motivation to learn new skills as well as excellent written and oral skills are
essential.
Example publications from the Lab:
·
Production of an Oncolytic
Adeno-Associated Virus Containing the Pro-Apoptotic TRAIL Gene Can Be Improved
by shRNA Interference. 2025 Int J Mol Sci. Link
·
Multiplex genome editing eliminates
lactate production without impacting growth rate in mammalian cells. 2025 Nat
Metab. Link
·
Detection of host cell
microprotein impurities in antibody drug products. 2024 Nature
Communications. Link
· A Direct Comparison of rAAV5 Variants Derived from the Baculovirus
Expression System Using LC-MS Workflows Demonstrates Key Differences in Overall
Production Yield, Product Quality and Vector Efficiency. 2024 Int J Mol Sci.
Link
How to apply:
Project 1 applicants should email: a cover
letter
(including your motivation statement outlining why you wish to do a PhD and why you are suited to this project), a CV,
and contact details for your academic
referees to careers@nibrt.ie
Informal enquiries to: niall.barron@nibrt.ie
Funding: Annual stipend of €25,000 plus fees for 4
years.
Project 3: PAT Applications for
Monitoring AAV Production
Supervisors:
Dr Jonathan Bones
This project aims to develop
process analytical technologies (PAT) for monitoring AAV production during cell
culture. PAT is widely used for monitoring chemical synthesis and has gained
traction for monitoring manufacturing processes of biopharmaceuticals such as
recombinant proteins and monoclonal antibodies. PAT for AAV remains a challenge
due to the size and complexity of AAV and their lower expression rates when
compared to more standard recombinant proteins.
Here, we aim to explore a
variety of analytical methods, inline, online and atline, facilitated by
automated sampling, as potential PAT approaches for monitoring AAV production
in small scale bioreactors. As part of the project, you will run these reactors
to generate AAV and combine this with the deployment of various spectroscopic
methods or other integrated analytical techniques. As these measurements are
expected to generate considerable volumes of data, you will also develop
strategies for the management and analysis of the data using various
statistical approaches with a view to understanding how we can ultimately use
PAT for advanced process control.
This exciting project offers a
mix of molecular biology, cell culture, automation, advanced analytics and data
analytics. We are looking for candidates that are interested in these areas and
who have a desire to better understand how processes work and to use their
combined skills to push for improvement in process performance.
Candidate profile: Applicants should hold or expect to receive an upper 2.1 or 1.1
degree in a relevant discipline such as analytical science, analytical
chemistry, bioanalytical science, biotechnology or chemical engineering.
Experience with statistical analysis, particularly multivariate statistics and
data modelling would be an advantage. Training will be provided in additional
aspects of biology required for successful completion of the programme. The
ability to work as part of a team, an interest in industrially focused
research, motivation to learn new skills as well as excellent written and oral
skills is also desirable.
How to apply:
Project 3 applicants should email a covering letter,
a motivation statement as well as outlining why you would like to do a PhD to careers@nibrt.ie.
You
will also need to forward a copy of your CV along with your academic
referees.
Informal enquiries to: Jonathan.bones@nibrt.ie
Funding: Annual stipend of €25,000 plus fees for 4
years.
Transformation of Advanced
Medicines Manufacture (TRANS-AM)
Gene
therapies are a type of advanced medicine that represent exciting possibilities
to treat and potentially cure many life-altering and life-threatening diseases.
They also represent a huge growth area with several hundred currently in
various stages of development. Many of these are based on using recombinant
Adeno-associated virus (rAAV) as a delivery vector. If even a small portion of
them reach the market, current manufacturing and characterisation technologies
in the industry will struggle to deliver them economically and safely for
patients.
This
research program aims to provide innovative solutions to help overcome the
manufacturing challenges associated with producing rAAV and brings together
experts from two leading Irish institutions, NIBRT and UCD, and APC-VLE Ltd. (https://approcess.com/services/cell-and-gene-therapies)
- a leading Irish industrial partner - in an exciting 5-year collaborative
program.
We
are currently seeking applicants for two PhD projects as listed below. The
successful candidates will be based in either NIBRT or UCD and will also spend
some time on placements in the industrial partner.
We are seeking
ambitious, inquisitive and innovative individuals to join our multidisciplinary
research team. As part of a dynamic and collaborative environment, you will
contribute to breakthrough work that supports the scalable, efficient, and
high-quality production of viral vectors—laying the foundation for
next-generation treatments for genetic diseases. If you're excited by the
intersection of biotechnology, process development, and therapeutic innovation,
we’d love to hear from you.
The National Institute for Bioprocessing Research and
Training (‘NIBRT’) NIBRT is a Dublin-based global centre of excellence that provides training and research for the biopharmaceutical manufacturing industry. Founded through collaboration between leading Irish universities and funded by the Irish Government via IDA Ireland, NIBRT operates an 8,300 m² facility with over 100 staff, featuring pilot plants, research labs, and a dedicated space for early-stage biologics and advanced therapy development. NIBRT - National Institute for Bioprocessing Research and Training
UNIVERSITY COLLEGE
DUBLIN (UCD) - University College Dublin
Project 1: CRISPR library screening
to identify endogenous HEK293 genes that impact AAV production
Supervisors:
Prof. Niall Barron & Assoc. Prof. Colin Clarke
About the project:
A strategy that has proven very successful
in identifying the genetic basis of various
cellular phenotypes, including diseases
such as cancer, cellular behaviour in bioreactors and identifying viral
restriction factors, is the use of CRISPR library screens. These can be either
to knockout the genes expressed in a cell or to activate the expression of
silent genes. The advantage is that it is relatively unbiased and has the
potential to target every gene in the genome.
Aims and Objectives: In this project we will use this strategy in order to screen a
suspension-adapted HEK293 cell line for genes that contribute to or inhibit the
production of AAV gene therapy vectors. We will use a human CRISPR/guide RNA
library to create a HEK293 cell population within which every gene has been
targeted for deletion. We will select a sub-population
of cells with the highest and lowest level of AAV production and this
population of cells will be sequenced to identify which guide RNAs are
enriched, thereby identifying their target genes. The most impactful genes will
be validated by knocking out in parental HEK293 cells and then testing AAV
production yield after triple transfection.
Candidate profile: Applicants should hold or expect to receive an upper 2.1 or 1.1
degree in a relevant discipline. A cell biology/molecular biology background would
be ideal. Training will be provided in advanced methods and approaches in cell
and molecular biology required for successful completion of the programme. The
ability to work as part of a team, a strong interest in applied research,
motivation to learn new skills as well as excellent written and oral skills are
essential.
Example publications from the Lab:
·
Production of an Oncolytic
Adeno-Associated Virus Containing the Pro-Apoptotic TRAIL Gene Can Be Improved
by shRNA Interference. 2025 Int J Mol Sci. Link
·
Multiplex genome editing eliminates
lactate production without impacting growth rate in mammalian cells. 2025 Nat
Metab. Link
·
Detection of host cell
microprotein impurities in antibody drug products. 2024 Nature
Communications. Link
· A Direct Comparison of rAAV5 Variants Derived from the Baculovirus
Expression System Using LC-MS Workflows Demonstrates Key Differences in Overall
Production Yield, Product Quality and Vector Efficiency. 2024 Int J Mol Sci.
Link
How to apply:
Project 1 applicants should email: a cover
letter
(including your motivation statement outlining why you wish to do a PhD and why you are suited to this project), a CV,
and contact details for your academic
referees to careers@nibrt.ie
Informal enquiries to: niall.barron@nibrt.ie
Funding: Annual stipend of €25,000 plus fees for 4
years.
Project 3: PAT Applications for
Monitoring AAV Production
Supervisors:
Dr Jonathan Bones
This project aims to develop
process analytical technologies (PAT) for monitoring AAV production during cell
culture. PAT is widely used for monitoring chemical synthesis and has gained
traction for monitoring manufacturing processes of biopharmaceuticals such as
recombinant proteins and monoclonal antibodies. PAT for AAV remains a challenge
due to the size and complexity of AAV and their lower expression rates when
compared to more standard recombinant proteins.
Here, we aim to explore a
variety of analytical methods, inline, online and atline, facilitated by
automated sampling, as potential PAT approaches for monitoring AAV production
in small scale bioreactors. As part of the project, you will run these reactors
to generate AAV and combine this with the deployment of various spectroscopic
methods or other integrated analytical techniques. As these measurements are
expected to generate considerable volumes of data, you will also develop
strategies for the management and analysis of the data using various
statistical approaches with a view to understanding how we can ultimately use
PAT for advanced process control.
This exciting project offers a
mix of molecular biology, cell culture, automation, advanced analytics and data
analytics. We are looking for candidates that are interested in these areas and
who have a desire to better understand how processes work and to use their
combined skills to push for improvement in process performance.
Candidate profile: Applicants should hold or expect to receive an upper 2.1 or 1.1
degree in a relevant discipline such as analytical science, analytical
chemistry, bioanalytical science, biotechnology or chemical engineering.
Experience with statistical analysis, particularly multivariate statistics and
data modelling would be an advantage. Training will be provided in additional
aspects of biology required for successful completion of the programme. The
ability to work as part of a team, an interest in industrially focused
research, motivation to learn new skills as well as excellent written and oral
skills is also desirable.
How to apply:
Project 3 applicants should email a covering letter,
a motivation statement as well as outlining why you would like to do a PhD to careers@nibrt.ie.
You
will also need to forward a copy of your CV along with your academic
referees.
Informal enquiries to: Jonathan.bones@nibrt.ie
Funding: Annual stipend of €25,000 plus fees for 4
years.
