ProfessorGreg Neely

Project Opportunities

1. Project title: Functional genomic characterization of “irukandji” venom
Project summary: Carukia Barnesi is a tiny Australian jellyfish that inhabit the northern waters of Australia. Stings from this jellyfish cause Irukandji syndrome, a potentially fatal condition involving extreme pain, cardiac dysfunction, and an impending sense of doom. In this project we will use new gene editing and functional genomic techniques to characterize how this jellyfish causes Irukandji syndrome and use this information to design rational venom antidotes.

This opportunity/project is part of the Faculty of Science Australian Research Council (ARC) Scholarship scheme and is now advertised on the Scholarship Office website. Applications are open and will close on 18 January 2026.

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2. Project Title: Conserved Regulatory Genes in Neurodevelopment 

Summary of opportunity:

The present project aims to utilize the promising combination of 3D organoid technology and CRISPR genome editing, which will allow us to examine the roles of several conserved genes involved in neurodevelopmental regulation, in order to better understand human neuronal development at the molecular level. Investigating these mechanisms can not only shed light on human brain development, but also lead to new treatments for neurological diseases. 

A complimentary scholarship for this project may be available through a competitive process. To find out more, refer to the Faculty of Science Postgraduate Research Excellence Award and contact Associate Professor Greg Neely directly.

Program type

PHD

Opportunity synopsis:

Insight into the roles of conserved regulatory genes will provide a strong frame work for the understanding of developmental and morphogenic characteristics related to neurodevelopmental disorders. To examine the role of our candidate genes in neurodevelopment, we intend to utilize CRISPR genome-editing to knockout conserved neuronal regulator genes in human-derived 3D brain organoids. This will enable us to assay the functional roles of the respective genes during neurodevelopment by examining cell morphology and phenotype, neuronal firing activity and synaptic connectivity of an intact tissue. The proposed research aspires to understand paramount mechanisms in human neurodevelopment as well as in neurodegeneration.

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3. Project Title: New functional CRISPR screens

Summary

CRISPR genome editing has revolutionized how we do basic research. This technique can be scaled up so we can assess the role of each human gene in virtually any biological process. One of the major limitations of this technique is that the primary endpoint for these kinds of screens is cell survival. We have made progress in developing new more functional screens to evaluate cellular signal transduction responses at the genome scale. This project involves further developing and applying these new genome scale technologies to investigate major human disease pathways. This work will also be designed to quickly lead to new medicine. 

A complimentary scholarship for this project may be available through a competitive process. To find out more, refer to the Faculty of Science Postgraduate Research Excellence Award and contact Professor Greg Neely directly.

Research location: Charles Perkins Center

Program type

PHD

Synopsis

Evaluating human cellular responses functionally and at the genome scale has only recently been possible. This project is flexible and involves developing and using new genome editing technologies to investigate cellular responses to pain, inflammation, growth factors, neuropeptides, or other medically relevant stimuli using functional readouts. The techniques employed for this project will include CRISPR genome editing, cellular and molecular biology, synthetic virus design and generation, fluorescent activated cell sorting, lipid nanoparticle delivery of RNA, and potentially human stem cell derived organoids and / or animal studies.

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4. Project Title: New RNA medicines for major human diseases

Summary

The success of the COVID-19 vaccine has unlocked a new category of medicine, where we can identify and then deliver human genes that control disease as RNA-based medicines. We have established these systems and are now in the preclinical development phase to make new RNA based medicines. This project will involve designing and testing human or synthetic genes to help treat major human diseases, with a focus on neuroscience, immunity, or lung function. This project is designed to quickly lead to new medicine. 

A complimentary scholarship for this project may be available through a competitive process. To find out more, refer to the Faculty of Science Postgraduate Research Excellence Award and contact Professor Greg Neely directly.

Research location: Charles Perkins Center

Program type

PHD

Synopsis

Most successfully drugs act by inhibiting protein function. The ability to efficiently and safely deliver RNA therapeutically changes this, and now we can also specifically activate pathways therapeutically. In this project, we combine genomic and functional genomics techniques with new RNA technologies to quickly design and test new RNA medicines. We are looking at targeting a number of major human diseases, and there is some flexibility here depending on the specific interest of the student. The techniques employed for this project include advanced bioinformatic analysis of large human data sets, cellular and molecular biology, fluorescent activated cell sorting, lipid nanoparticle delivery of RNA, and human stem cell derived organoids and / or animal studies.

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5. Project Title: Using Directed Evolution to design and evaluate new synthetic proteins

Summary

Evolution has led to protein function being highly optimized for specific context. As we start to use the products of evolution in new contexts, we find our current tools can be suboptimal. To address this issue, we have developed a synthetic, viral based approach to drive further evolution of existing proteins to give them new abilities that can be useful for research or medicine. This project involves applying our globally unique mammalian directed evolution platform to design and characterize new synthetic proteins and also further develop directed evolution technologies that allow us to generate new biology. These approaches can be used to generate new genome editing tools, or to design new proteins that can be used as medicines.

A complimentary scholarship for this project may be available through a competitive process. To find out more, refer to the Faculty of Science Postgraduate Research Excellence Award and contact Professor Greg Neely directly.

Research location: Charles Perkins Center

Program type

PHD

Synopsis

Directed evolution involves generating synthetic circuits where a protein that evolves a new or enhanced activity has an advantage over other proteins that do not have this new trait. This approach is powerful, but until recently has been limited to use in bacterial systems. We have developed a mammalian version of this system, and using this, we can evolve proteins that have new abilities within the mammalian cell. We are using this approach to enhance CRISPR tools, and we are also using this approach to evolve human genes to be used as more potent medicines. The techniques employed in this project include viral-based directed evolution, cellular and molecular biology, CRISPR, fluorescent activated cell sorting, and likely human stem cell derived organoids and / or animal studies.

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5. Project Title: Genomic investigation of poisonous plants and animals to develop new antidotes or medicines

Summary

There are many venomous plants and animals in our environment, and for the majority of these, we do not have effective ways to treat envenoming or poisonings. We have a long standing interest in using new genomic and CRISPR-based techniques to define how these venoms hurt us, and then use this information to generate new venom antidotes. Our overall goal is to develop a small number of universal venom antidotes that can block the effects of most poisonous venoms. We would also like to use venom components themselves as new medicines, and we have developed new functional genomic approaches to find new bioactive molecules we can then functionally investigate using pooled CRISPR approaches.

A complimentary scholarship for this project may be available through a competitive process. To find out more, refer to the Faculty of Science Postgraduate Research Excellence Award and contact Professor Greg Neely directly.

Research location: Charles Perkins Center

Program type

PHD

Synopsis

Directed evolution involves generating synthetic circuits where a protein that evolves a new or enhanced activity has an advantage over other proteins that do not have this new trait. This approach is powerful, but until recently has been limited to use in bacterial systems. We have developed a mammalian version of this system, and using this, we can evolve proteins that have new abilities within the mammalian cell. We are using this approach to enhance CRISPR tools, and we are also using this approach to evolve human genes to be used as more potent medicines. The techniques employed in this project include viral-based directed evolution, cellular and molecular biology, CRISPR, fluorescent activated cell sorting, and likely human stem cell derived organoids and / or animal studies.

----------Current Research Projects----------

We currently have several honors or PhD projects available in the lab.

#1. Genes and Neural Circuits Controling Pain Perception

Summary: This project involves combining human genomics data for chronic pain disease with high throughput behavioral genomics techniques in fruit fly in order to better understand how chronic pain develops after injury.

This project will involve using high throughput genetics and genomics approaches to better understand how animals become sensitized to pain after injury. The project will involve use of fruit fly behavioral genetics techniques, and potentially bioinformatics, transgenic mice or human stem cells, and the successful applicant will be trained in these techniques.

#2. Lifespan Extension

Summary: This project will combine human genomics with behavioral genetic and molecular biology in order to characterize new pathways that can extend lifespan and preserve cognitive function with age.

This project involves testing human genomics data on longevity to find new genes that can extend lifespan in the fruit fly. We focus on genes that when targeted specifically in the brain, can extend lifespan while also preserve cognitive function with age. We have identified 40 new targets that can extend lifespan, and the project will involve working on some of these new lifespan extending genes. Project will involve lifespan assays, behavioral genetics, molecular biology, and electrophysiology, and the successful candidate will be trained in all of these techniques.

#3. Whole genome CRISPR screening

Summary: This project will involve new whole genome CRISPR editing strategies, coupled with bioinformatics analysis, to identify the complete molecular mechanism of action for relevant human drugs or disease genes.

Recently CRISPR-based approaches have revolutionized functional genomics techniques. We have set up new whole genome CRISPR screening, and using this technique we have defined the molecular mechanism of action for over 20 relevant human drugs or venoms from deadly Australian creatures. This project involves working with our functional genomics team to continue these efforts. The successful candidate will learn state of the art whole genome CRISPR screening, as well as advanced molecular biology and potentially also basic bioinformatics analysis.