About

Research  / Background

Matt Field is an Associate Professor in Bioinformatics at James Cook University. He currently holds an NHMRC Emerging Leader II Fellowship and was recently awarded the Frank Fenner Early Career Fellowship for the highest scoring ECR applicant. A/Prof Field is a founder and co-director of the Centre for Tropical Bioinformatics and Molecular Biology and specialises in developing high-throughput bioinformatic analysis pipelines.

In the last five years Dr Field has published 50 peer reviewed publications in high impact journals such as Nature (x3), Cell, Science Advances (x2) and PNAS (x2), which have been cited over 6000 times. To date he has been a named investigator on $10 million in grants with >$2.5 million as sole CI.  He is a Chief Investigator for the Centre for Personalised Immunology, an NHMRC Centre of Research Excellence focused on bringing genomics and personalized medicine into routine clinical practice. He is also an associate editor for Human Genomics (Springer/Nature).

From 2010 to 2015 Dr Field worked as Senior Bioinformatics Manager at the Australian National University, developing software to uncover the underlying genetic cause of human diseases such as lupus, diabetes, and melanoma. During this time he developed a high-throughput variant detection pipeline which has analysed over 4000 exomes and 3000 genomes to date. He completed a PhD at ANU in medical science titled "Computational Analysis of Genetic Variation" with supervisor Chris Goodnow.

From 2004 to 2010 Dr Field worked as Assistant Bioinformatic Coordinator at the Genome Sciences Centre in Canada leading a group of bioinformaticians in a high-throughput research environment studying a variety of cancers. Prior to this, he completed two Bachelor of Science degrees in computer science and biology from the University of British Columbia.

HDR Opportunities

I would love to hear from aspiring bioinformaticians looking to complete a Masters or a PhD based in Cairns, gateway to the Great Barrier Reef and Daintree Rainforest. There are several projects available largely focused on the bioinformatics of genetic variation, precision medicine and immunology. 

For example, a PhD opportunity exists to work with leading immunologists and bioinformaticians across Australia in networks including the Centre for Personalised Immunology (https://www.cpi.org.au) and CIRCA (link). This project will utilise the latest in sequencing technologies (including single cell and long reads) to discover the genetic contribution to human immunological diseases. The candidate would help develop cutting edge bioinformatics workflows and through collaborations with the Garvan Institute of Medical Research and the Australian National University will contribute to the latest research in understanding the progression of auto-immune disease. This PhD project is suited to those with a background (or strong determination to advance) in bioinformatics, variant detection and workflow development. Experience with immunology and single cell technologies would be an asset.

 

Teaching
  • BC3203: Bioinformatics (Level 3; TSV)
  • BC5203: Advanced Bioinformatics (Level 5; TSV)
Interests
Research
  • Bioinformatics
  • Personalised Medicine
  • Immunogenomics
  • Disease Causing Variants
Experience
  • 2020 to present - Associate Professor, James Cook University (Cairns, Australia)
  • 2020 to present - Analysis Lead, Garvan Institue of Medical Research (Sydney, Australia)
  • 2018 to present - Co-director, Centre for Tropical Bioinformatics and Molecular Biology (Cairns, Australia)
  • 2010 to 2020 - Senior Bioinformatics Manager, Australian National University (Canberra, Australia)
  • 2016 to 2019 - Senior Bioinformatics Fellow, James Cook University (Cairns, Australia)
  • 2010 - Bioinformatics Software Development Team Leader, Biomatters (Auckland, New Zealand)
  • 2004 to 2010 - Assistant Bioinformatics Coordinator, Genome Sciences Centre (Vancouver, Canada)
Research Disciplines
Socio-Economic Objectives
Honours
Awards
  • 2022 - Dean's Award - Highest Research Productivity
  • 2020 - ECR Merit Allocation at National Computational Infrastructure
  • 2018 - James Cook University Rising Star
  • 2017 - Frank Fenner Early Career Fellowship
Fellowships
  • 2022 to 2026 - NHMRC Emerging Leader II
  • 2018 to 2021 - NHMRC CJ Martin
Memberships
  • 2021 - Australian Health Research Alliance (TAAHC)
  • 2019 - Executive member Australian Bioinformatics And Computational Biology Society
  • 2018 - American Society for Human Genetics
  • 2018 - Chair Bioinformatics Advisory Board QCIF
  • 2015 - International Society for Computational Biology
Publications

These are the most recent publications associated with this author. To see a detailed profile of all publications stored at JCU, visit ResearchOnline@JCU. Hover over Altmetrics badges to see social impact.

Journal Articles
More

ResearchOnline@JCU stores 84+ research outputs authored by A/Prof Matt Field from 2004 onwards.

Current Funding

Current and recent Research Funding to JCU is shown by funding source and project.

Commonwealth Department of Health - Medical Research Future Fund - Cardiovascular Health

Improving clinical pathways for abdominal aortic aneurysm through incorporating biomarkers

Indicative Funding
$1,000,000 over 3 years
Summary
20 million people worldwide have weakening of their main abdominal artery (abdominal aortic aneurysm; AAA) and are at high risk of both major adverse cardiovascular events (MACE) and AAA related events (AAA repair and rupture-related death). Most AAAs are identified at a small size when their risk of rupture is low. Management of small AAA focuses on repeat aortic imaging every 6 months to identify when the threshold diameter (50mm in women and 55mm in men) is reached for elective surgical AAA repair. Most small AAAs continue to grow in size and eventually undergo repair. No drugs have been shown to limit AAA growth and the clinical pathway focuses on identifying those needing surgery rather than medical management. There are no established means to individualise care. Our interviews with patients and health professionals indicate that the number one deficiency in current AAA management is the lack of individualising medical management to reduce the high incidence of MACE and AAA related events. Our international AAA alliance is uniquely placed due to our resources (biobank-registry) and IP (bioinformatics, clinical, engineering software, genomics, biomarkers, machine learning and pathogenesis) to addresses this unmet clinical need.
Investigators
Jon Golledge, Clare Arnott, Thomas Gasser, Rebecca Evans, Joseph Moxon, Matt Field, Jenna Pinchbeck, Aaron Drovandi, Dylan Morris, Svetha Venkatesh, Truyen Tran, Catherine Rush, Aletta Schutte, Robyn Clay-Williams and Geoffrey Jones (College of Medicine & Dentistry, The George Institute for Global Health, KTH Royal Institute of Technology, College of Public Health, Medical & Vet Sciences, Townsville Hospital and Health Service, Deakin University, University of New South Wales, Macquarie University and University of Otago)
Keywords
Prevention; Complications; Peripheral artery disease; Risk Factors

National Health & Medical Research Council - Investigator Grants

Developing Bioinformatics Capability to Diagnose Infectious Diseases using Clinical Metagenomics

Indicative Funding
$1,420,531 over 5 years
Summary
Current pathogen identification techniques are limited in terms of their speed, accuracy and inability to detect exotic pathogens. Using an unbiased metagenomic sequencing approach offers an improvement over current practice however supporting bioinformatics workflows are needed to support clinical implementation. This work can have enormous global reach with half the world?s population living in the tropics by 2050, many with limited healthcare options.
Investigators
Matt Field (Australian Institute of Tropical Health & Medicine)
Keywords
Clinical Metagenomics; Infectious Diseases

Wet Tropics Management Authority - Contract Research

Genomic tools for monitoring yellow crazy ants.

Indicative Funding
$16,295 over 2 years
Summary
This project will establish protocols and baseline data for ddRAD-seq based sequencing of yellow crazy ants. In this phase of the project, we will sequence 200 individuals from historical infestations and develop tools to assess genetic relatedness among infestations. Baseline data established in this project will be used to help trace the origin of future infestations as well as improve our understanding of genetic diversity and gene flow in yellow crazy ants in Queensland.
Investigators
Matt Field, Megan Higgie, Ira Cooke and Lori Lach (College of Public Health, Medical & Vet Sciences and College of Science & Engineering)
Keywords
Yellow Crazy Ants; Invasive Species Monitoring; Anoplolepis gracilipes; Genomics; Genetic relatedness; biosecurity

Townsville Hospital and Health Service - SERTA Research Capacity Grant

Improving outcomes for patients with muscle wasting disease and liver cancer - SERTA Capacity Research Grant.

Indicative Funding
$140,000 over 2 years
Summary
The funding of a Research Assistant and the performance of work by the Research Assistant in connection with a program of work undertaken by the Cancer and Metabolism Group within the College of Public Health, Medicine and Veterinary Science aimed at improving outcomes for patients with muscle wasting disease and liver cancer.
Investigators
Pankaj Saxena, Lionel Hebbard, Jaishankar Raman, Rozemary Karamatic, Matan Ben David, Craig McFarlane, Ulf Schmitz, Matt Field and Miriam Wankell in collaboration with Shaurya Jhamb, Eun Jin Sun, Zaeem Ahmed, Rhys Gillman and Ryley Dorney (Townsville Hospital and Health Service, College of Public Health, Medical & Vet Sciences and College of Medicine & Dentistry)
Keywords
Sarcopenia; Hepatocellular Carcinoma; Liver Cancer

Townsville Hospital and Health Service - Study Education Research Trust Account (SERTA)

Establishing the North Queensland Liver Tumour Library: Improving HCC detection and treatment.

Indicative Funding
$50,000 over 2 years (administered by Townsville Hospital and Health Service)
Summary
The project will provide certain data on the usefulness of using liquid biopsy to diagnose HCC in Rural, regional and Remote patients, identify new liquid biopsy targets and test a new therapeutic approach to treat HCC.
Investigators
Rozemary Karamatic, Matan Ben David, Pankaj Saxena, Lionel Hebbard, Craig McFarlane, Ulf Schmitz, Matt Field and Miriam Wankell in collaboration with Shaurya Jhamb, Eun Jin Sun, Zaaem Ahmed, Rhys Gillman and Ryley Dorney (Townsville Hospital and Health Service, College of Public Health and Medical & Vet Sciences)
Keywords
Liquid biopsy; Hepatocellular Carcinoma; Liver Cancer

Tour de Cure - PhD Scholarship

Precision Hepatocellular Carcinoma Treatment Using Synthetic Lethality

Indicative Funding
$10,000 over 1 year
Summary
Hepatocellular carcinoma (HCC) is a major cause of cancer-related mortality. Current therapies for HCC show little efficacy due to extensive heterogeneity in the disease and a lack of corresponding patient-tailored treatment options. The purpose of this project is to validate various bioinformatic approaches to identifying personalised cancer driver genes and methods of targeting them through synthetic lethality. An integrated pipeline will be developed for the simple identification of therapeutics from sequencing of tissue biopsies. Finally, patient-derived organoids matched with patient-specific sequencing information will be used to validate this pipeline, building an important foundation for the future of personalised treatment.
Investigators
Rhys Gillman, Lionel Hebbard, Matt Field and Ulf Schmitz (College of Public Health and Medical & Vet Sciences)
Keywords
Liver Cancer; Genetics; Synthetic Lethality; Bioinformatics; Precision Medicine

Townsville Hospital and Health Service - SERTA Research Capacity Grant

Improving outcomes for patients with muscle wasting disease and liver cancer

Indicative Funding
$135,439 over 2 years
Summary
This application is to provide support for an experienced research assistant to perform laboratory work with human tissues. The interdisciplinary project involves TUH surgeons, junior medical staff, JCU/AITHM researchers, medical and HDR students; and pursues two themes to develop better diagnostics and treatments for patients with (i) the muscle wasting disease sarcopenia, and (ii) hepatocellular carcinoma (HCC). Human ethics for the collection and culturing of human muscle cells and HCCs has been approved by THHS and JCU committees. The Research Program focus is to sequence DNA of the primary muscle cells and HCCs, and use state of the art bioinformatics to identify and characterise novel biomarkers and molecular targets that drive sarcopenia and HCC progression. This will support the development of patient-focussed therapeutic approaches and provide better health care outcomes for North Queenslanders.
Investigators
Pankaj Saxena, Jaishankar Raman, Rozemary Karamatic, Matan Ben David, Lionel Hebbard, Craig McFarlane, Ulf Schmitz, Matt Field and Miriam Wankell (Townsville Hospital and Health Service, College of Public Health and Medical & Vet Sciences)
Keywords
Sarcopenia; Hepatocellular Carcinoma; Liver Cancer

Tropical Australian Academic Health Centre Limited - Research Seed Grants

Using portable long-read sequencing to diagnose Chronic Kidney Disease in regional North QLD Using portable long-read sequencing to diagnose Chronic Kidney Disease in regional North Using portable long-read sequencing to diagnose Chronic Kidney Disease

Indicative Funding
$50,000 over 2 years
Summary
This project addresses the early diagnosis of genetic predispositions for Chronic Kidney Disease (CKD), which poses an increasing burden on the North Queensland population and unequally affects the Indigenous Australian peoples. We will develop a mobile diagnostic pipeline that allows a rapid and cost-efficient screening for genetic CKD predispositions and circulating biomarkers using a targeted, DNA/RNA long-read sequencing approach.
Investigators
Ulf Schmitz, Andrew Mallett, Matt Field, Paul Horwood, Helen Wright, Chirag Patel, Ira Cooke and Ben Lundie (College of Public Health, Medical & Vet Sciences, College of Medicine & Dentistry, College of Healthcare Sciences, Queensland Clinical Genetics Service and Pathology Queensland)
Keywords
long-read sequencing; Nanopore; Chronic Kidney Disease; Genetic Testing; targeted sequencing; transcriptomic complexity

Tropical Australian Academic Health Centre Limited - Research Seed Grants

Precision medicine for North Queensland Liver Cancer Patients.

Indicative Funding
$50,000 over 2 years
Summary
Hepatocellular carcinoma (HCC) is an aggressive and poorly treated liver cancer that is rapidly increasing in incidence in North Queensland. Most patients are ineligible to have their cancer surgically removed, and new systemic therapeutics only extend patient lives by six to eight months. Thus, new treatment approaches are urgently required. Through the collaboration of surgeons, scientists and bioinformaticians we are developing Precision Medicine for North Queensland Liver Cancer Patients. Using bioinformatics and three dimensional culture models we will trial novel therapeutic approaches. This research will rapidly lead to new therapeutic approaches to treat HCC.
Investigators
Lionel Hebbard, Pranavan Palamuthusingam, Craig McFarlane and Matt Field (College of Public Health, Medical & Vet Sciences, Townsville Hospital and Health Service and Australian Institute of Tropical Health & Medicine)
Keywords
Cancer; Cancer Stem Cell; Organoids

Tropical Australian Academic Health Centre Limited - Microfunding Scheme

Bayesian disease mapping to identify the high-risk population within North Queensland and interventional program for oral cancer prevention.

Indicative Funding
$19,500 over 2 years
Summary
Oral cancer 5-year survival rates have remained less than 50% for several decades, despite significant improvements in treatment. This is primarily due to patients generally presenting late with advanced stages of the disease. Consequently, in many cases, oral cancer is incurable or requires extensive life-changing surgery and chemo-radiotherapy. Early diagnosis through targeted screening of high-risk population groups would result in more favourable survival rates and treatment outcomes. The aim of this project is to identify specific, local populations in Northern Queensland at increased risk of developing oral cancer with a view to developing a target screening program for oral cancers.
Investigators
Peter Thomson, Dileep Sharma, Matt Field, Poornima Ramamurthy and Yousef Abdalla (College of Medicine & Dentistry, College of Public Health, Medical & Vet Sciences and Cairns and Hinterland Hospital and Health Service)
Keywords
Bayesian Disease Mapping; Oncology

Tropical Australian Academic Health Centre Limited - Contract Research

Can portable genome sequencing provide a rapid, comprehensive, point-of-care diagnostic test for Far North Queensland hospitals and healthcare centres?

Indicative Funding
$49,987 over 2 years
Summary
Respiratory disease, fevers, and sepsis are common in FNQ and treatment often requires admission to hospital. These infections have many different causes, and diagnosing them requires multiple tests that take weeks to perform. Consequently, patients are treated with broad-spectrum antibiotics before a pathogen is identified, leading to poorer outcomes for the patient and contributing to the spread of antibiotic-resistant infections. We will trial new genome sequencing technology as a point-of-care diagnostic test for fever, sepsis, and pneumonia at Cairns Hospital, and test the hypothesis that this approach will increase the proportion of infections that are diagnosed and reduce the time-to-diagnosis.
Investigators
John McBride, Cadhla Firth, Simon Smith, Joshua Hanson, Matt Field, Emma McBryde, John Miles, Damon Eisen and Christopher Heather (College of Medicine & Dentistry, Australian Institute of Tropical Health & Medicine and Queensland Health)
Keywords
Genomics; Healthcare; pathogens

National Health & Medical Research Council - Development Grant

Hookworm peptide therapeutic for oral treatment of IBD

Indicative Funding
$732,700 over 2 years
Summary
We intend to develop an orally delivered peptide that can modulate the immune system and be developed as a therapeutic for inflammatory bowel disease. We have identified a peptide, derived from a hookworm protein, that alleviates the clinical symptoms of experimental colitis when orally administered to mice. The peptide has bioactivity with human cells ex vivo and displays desirable drug-like properties. The aim of this project is to acquire further data on the mechanism of action and formulation conditions to facilitate formal product development prior to licensing and clinical trials.
Investigators
Alex Loukas, Norelle Daly, Paul Giacomin, John Miles, Roland Ruscher, Keith Dredge, Istvan Toth, Mariusz Skwarczynski, Matthew Moyle, Ashley Waardenberg, John Croese, Matt Field and Tony Rahman (Australian Institute of Tropical Health & Medicine, The University of Queensland and The Prince Charles Hospital)
Keywords
Inflammatory Bowel Disease; Peptide; therapeutic; Hookworm; Oral delivery
Supervision

Advisory Accreditation: I can be on your Advisory Panel as a Primary or Secondary Advisor.

These Higher Degree Research projects are either current or by students who have completed their studies within the past 5 years at JCU. Linked titles show theses available within ResearchOnline@JCU.

Current
  • Structural Variant analysis in Coral Populations of A. tenuis and A. digitifera and their role in Gene Flow, Adaptive Evolution and Diversification (Masters , Secondary Advisor)
  • Computational approaches to Detect Genetic Variants at Single Cell resolution (PhD , Primary Advisor)
  • Unravelling genomic patterns of population structure and fitness in the Australian koala (Phascolarctos cinereus) (PhD , Secondary Advisor)
  • Targeting DNA Repair in HCC through Synthetic Lethality (PhD , Secondary Advisor)
Completed
Collaboration

The map shows research collaborations by institution from the past 7 years.
Note: Map points are indicative of the countries or states that institutions are associated with.

  • 5+ collaborations
  • 4 collaborations
  • 3 collaborations
  • 2 collaborations
  • 1 collaboration
  • Indicates the Tropics (Torrid Zone)

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Email
Phone
Location
  • E4.110, Queensland Tropical Health Alliance (Cairns campus)
Advisory Accreditation
Primary Advisor
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