QCIF - Key Persons
Callum joined QCIF in June 2021 as a casual Data Scientist. He is working with the team to support QCIF Member researchers with statistical analysis and data visualisation using software such as Power BI and Python.
He is also currently continuing his role as an Assistant Research Technician for The University of Queensland's Molecular Dynamics Group and the UQ Faculty of Medicine's Research and Statistical Support Service, a position he has held since January 2021 at the former, and since February 2019 at the latter.
Callum has programming, data analytics and visualisation expertise, and a particular knowledge of data science within health research.
He is in his final year of studying dual Bachelor degrees in Science and Mathematics, majoring in Biophysics, Data Analytics and Operations Research.
Research Interests
Qualifications
Bachelor of Mathematics in Data Analytics and Operations Research, University of Queensland, 2021
Bachelor of Science in Biophysics, University of Queensland, 2021
Ahmed joined QCIF in January 2021 as a Senior Biostatistician. Currently, he has dual appointment with UQ Diamantina Institute (UQDI) and QCIF. Ahmed has a strong background in biostatistics and bioinformatics and has experience in microbiome, RNA-seq and single cell analysis.
Ahmed has produced non-traditional research outputs in terms of software packages, curated databases and web applications to help research communities utilise his methods. These include NucImport (doi: 10.48610/7bfd689), dLOCALMotif,(doi: 10.1093/bioinformatics/bts654) PredictPA (doi: 10.48610/a53d449), E.PATH (doi: 10.48610/ee3f1f2), E. PAGE (doi: 10.1101/2022.01.03.474848), GLACIER, WebCytometry, GSAO (doi: 10.48610/2c1d352) and scLOCATE.
At UQDI he became an integral part of the planning, delivery and analyses of existing and novel analytical tools for several data rich programs in the institute. He undertook data modelling for clinical trials of Rheumavax and DEN-181, and published this in the high-ranked, Science Trans Med.
He established two computational statistics and bioinformatics programs:
uncovering predictors of immune checkpoint blockade
developing screening tools to predict T1D at-risk children.
He has significant experience contributing to the peer review of NHMRC grant applications. To date, he has reviewed more than 100 grants. He has supervised or mentored 20 PhD/MSc/BSc/Hons students.
At QCIF, he continues his work of the last seven years providing biostatistics support to researchers at UQDI. He also supports QCIF's other Members and partners as well as help deliver QCIF's biostatistics training program.
Research Interests
Integrating multidimensional single-cell data
Developing annotation tools for single-cell RNAseq data
Spatial transcriptomics and proteomics
Bayesian Networks
Qualifications
PhD - University of Queensland, 2013
MSc Engineering - University of Engineering and Technology (Lahore, Pakistan), 2008
BSc Engineering - University of Engineering and Technology, (Lahore, Pakistan), 2006
Andrew joined QCIF in late 2021 as a Senior Biostatistician to help provide biostatistics support to QCIF Members and partners. At QCIF, Andrew delivers biostatistical consulting, statistical analysis, and programming, as well as workshops and training in R.
Andrew has previously worked for Queensland Health as a data analyst, in the private sector as a statistician and data scientist, and as a post-doctoral research fellow at The University of Queensland School of Mathematics and Physics. In addition to his statistical skills, Andrew has extensive experience with multiple programming languages and software development workflows.
Andrew is appointed to QCIF Bioinformatics through UQ's Centre for Health Services Research. He is part of the Research and Statistical Support Service led by Associate Professor Jason Ferris to provide support to the UQ Faculty of Medicine.
Research Interests
Machine learning
Scientific programming
Reproducible research
Population genetics
Biomedical research
Qualifications
PhD in Applied Statistics, University of Queensland, 2017
Bachelor of Arts (Honours I)-Mathematics, University of Queensland, 2011
Bachelor of Engineering, University of Queensland, 2010
Skills: Biostatistics, machine learning, programming and data modelling applied to biomedical and clinical research. Andrew joined QCIF in late 2021 as a Senior Biostatistician to help provide biostatistics support to QCIF Members and partners. At QCIF, Andrew delivers biostatistical consulting, statistical analysis, and programming, as well as workshops and training in R. …
Job Titles:
- Head of Biostatistics
- Member of the French Statistical Society
Anne joined QCIF in early 2014 as a Senior Biostatistician to provide research and clinical biostatistics competencies. As Head of Biostatistics since 2018, she manages the biostatistics team and its different clinics across Queensland for hospitals, research centres and universities, and provides support to researchers leading to collaborations and numerous publications in international journals.
During her PhD, Anne collaborated with dermatologists and biologists from CERIES* to identify genes, and more specifically SNPs or SNP-SNP interactions, potentially involved in skin ageing. The new statistical methods for dimensionality reduction developed by Anne are particularly suited to select relevant information in large data sets.
Anne is a member of the French Statistical Society ("Société Française de Statistique" - SFdS).
Research Interests
Machine learning
Mixed-effects models
Dimensionality reduction techniques
Qualifications
PhD in Biostatistics, Conservatoire National des Arts et Métiers and CERIES* (France), 2013
MSc in Mathematical Engineering, Statistics and Economics, University of Bordeaux II (France), 2010
Cameron joined QCIF in June 2021 as a Bioinformatician based at USC to support the university's researchers and contribute to QCIF's involvement in national software platforms.
Job Titles:
- Senior Bioinformatician
- Software Carpentries Instructor
Delaney joined QCIF in late 2021 to assist the team with the analysis of next generation sequencing projects two days per week. Delaney is also the eResearch Analyst at our Member university, University of the Sunshine Coast, where she provides support to researchers in the STEM and cyber infrastructure space and hosts Hacky Hour every Wednesday.
Prior to her transition into professional roles, she was a Postdoctoral Research Fellow at the University of Queensland Centre for Clinical Research, using genomics combined with medical microbiology to further understand complex bacterial infections and aspects of their antimicrobial resistance, virulence, transmission and pathogenesis. Delaney's experience in next generation sequencing is varied and includes long and short read, metagenomic, comparative genomic and phylogenomic analysis from clinical, veterinary and environmental samples.
Delaney will also be assisting with the bioinformatics, biostatistics and biodata advisory service provided for researchers from QCIF Member institutions, including USC.
As a Software Carpentries instructor, Delaney's experience is also put to good use by helping other researchers upskill in this area.
Research Interests
Comparative genomics
Analysis of high-throughput sequencing data
Bacterial genomics and antimicrobial resistance
Phylogenomics
Qualifications
PhD in Molecular Microbiology, University of the Sunshine Coast, 2018
MSc Cell and Molecular Bioscience, Victoria University of Wellington (New Zealand), 2015
Bachelor of Biomedical Science majoring in Human Genetics and Molecular Pathology, Victoria University of Wellington (New Zealand), 2012
Skills: Next Generation Sequencing, Metagenomics, Comparative Genomics, Phylogenomics, Antimicrobial Resistance. Delaney joined QCIF in late 2021 to assist the team with the analysis of next generation sequencing projects two days per week. Delaney is also the eResearch Analyst at our Member university, University of the Sunshine Coast, where she provides support…
Job Titles:
- Director, Data Scientist
- Director: QCIF Bioinformatics and Data Science
Farah joined QCIF in early 2019 to help provide biostatistics support to QCIF Members and partners. In particular, Farah helps deliver biostatistics clinics for CHQ, USC, the University of Queensland's Faculty of Medicine, and Metro South Hospital and Health Service.
Farah is a physician by training with a background in clinical practice and healthcare management and holds a PhD from UQ's Faculty of Medicine, and a Master's degree in Healthcare Management from the Royal College of Surgeons (Ireland).
Her thesis focused on examining the relationship between obesity and mortality in individuals with Type 2 diabetes and hypertension. The models developed during her PhD provided evidence needed to convince policymakers to develop conscientious weight management guidelines for individuals with chronic conditions.
Her expertise is in the fields of data science, epidemiology and public health.
Research Interests
Conventional and network meta-analysis
Machine learning
Longitudinal and survival analyses
Confirmatory and exploratory factor analysis
Epidemiology
Qualifications
PhD, Faculty of Medicine, University of Queensland, 2019
Masters in Healthcare Management, 2007
Bachelor of Medicine and Bachelor of Surgery, 2000
Job Titles:
- Scientific Business Analyst, Australian BioCommons
Job Titles:
- Head of Computational Biology at QCIF Bioinformatics
Dr Gareth Price is Head of Computational Biology at QCIF Bioinformatics. Gareth has 20 years' experience as a Bioinformatician and Genomics Scientist. His expertise spans experimental design, assay performance, data quality control, data analysis and data interpretation, involving a variety of model organisms from microorganisms, fruit flies, mice to humans as well as non-model organisms with limited genome information.
In his role, Gareth manages the diverse spectrum of researcher-led questions involving life science data, provides training in genomic data analysis, as well as leading Galaxy Australia as Service Manager.
Qualifications
PhD in site-directed mutagenesis and protein Chemistry: structural and functional analysis of the Mixed Lineage Kinase 2 (University of Melbourne).
More than 10 years' experience in running laboratories utilising microarray and NGS technologies to address a variety of human and human pathogen related conditions.
Job Titles:
- Scientist at the Queensland Institute of Medical Research
- Senior Bioinformatician
Igor joined QCIF in early 2019. He looks after user support for Galaxy Australia and provides bioinformatics support to our Members.
Igor Makunin was trained as a genetics and molecular biologist. In 2003, he switched to comparative genomics and non-coding RNA, and gradually migrated from the wet lab work into bioinformatics and analysis of high-throughput sequencing data.
Igor has worked as a scientist at the Queensland Institute of Medical Research, The University of Queensland, Institute of Cytology and Genetics (Novosibirsk, Russia), the University of Geneva and the University of Cambridge.
He has more than 40 publications in peer-reviewed journals including Science, Genome Research, Genome Biology and Evolution, Molecular Biology and Evolution, BMC Genomics, Genetics, and Human Molecular Genetics.
Research Interests
Comparative genomics
Analysis of high-throughput sequencing data
Qualifications
PhD in Biology (1996)
Job Titles:
- Bioinformatician, Platform Developer and System Administrator
- Platform Developer and System Administrator
Justin also participates in bioinformatics tutoring at JCU and is the point of contact for JCU researchers to the QCIF Bioinformatics service. Prior to joining QCIF, Justin worked as a bioinformatician at JCU, developing a clinical cancer genomics pipeline and as a bioinformatics tutor.
He has a Bachelor of Computer Science (Hons) from Charles Darwin University and a PhD in modelling and simulation of gene expression and morphogenesis applied to electronic circuit generation from the Queensland University of Technology. He has a strong background in Linux, dev ops, high-performance computing, programming and open-source software.
Before joining JCU, he was employed as a Senior Research Support Specialist in QUT's High Performance Computing and Research Support Group. There, he worked closely with researchers in biology and bioinformatics in particular, helping them achieve their research outcomes by providing high-performance computing, eResearch, programming and other computational assistance.
His postdoctoral work was in intelligent transport systems with QUT's Centre for Accident Research and Road Safety (CARRS-Q). He has also worked in several research assistant positions in machine learning and autonomous robotics and tutored in a wide range of computational subjects.
Research Interests
Modelling and simulation of biological systems
Biologically-inspired hardware and software
Artificial Life, Autonomous Systems, Machine Learning
Qualifications
B. Comp Sci (Hons), Charles Darwin University
Skills: Modelling and simulation of gene expression and morphogenesis, programming, dev ops, high-performance computing. James Cook University bioinformatician Dr Justin Lee joined QCIF in May 2020 to work on the Australian Apollo Service as Platform Developer and System Administrator. He is based at the Centre for Tropical…
Magda joined QCIF as a bioinformatician in February 2023 after a year-and-a-half of working as a Postdoctoral Research Fellow at The University of Queensland's Frazer Institute alongside Professor Di Yu. Her research was focused on developing a pipeline that will assess the strength of the binding of proteins involved in immunological processes.
Magda obtained her PhD from England's University of Kent where she was involved in projects dedicated to identifying protein function and variation. Her findings have contributed to an increased understanding of the mechanisms in which cancer cells develop resistance to various anti-cancer drugs as well as the fundamental cellular functions which were summarised in her manuscript "Environmental conditions shape the nature of a minimal bacterial genome" (Antczak M. et al. Nat. Commun. 2019, 15;10(1):3100).
Magda is interested in designing and implementing bioinformatical pipelines to advance medicine, especially involving more personalised treatments. She is passionate about programming, especially in Python, as well as data visualisation and science communication - she has vast experience designing training materials and presentations in an audience-adjusted manner. Magda is a lifelong learner, and as such, she gained broad experience in various areas of bioinformatics. This includes protein function and structure prediction, and processing of WES and single-cell RNA data to solve burning questions in medical science.
Research Interests
Design and implementation of bioinformatical pipelines
Molecular biology with applications to medicine
Data analysis and visualisation
Qualifications
PhD Student in Bioinformatics, University of Kent, UK, Oct. 2016 - Dec. 2020
MEng Financial Mathematics, Gdansk University of Technology, Poland, 2006 - 2011.
Skills: Programming, data analysis and visualisation, protein function prediction, protein structure prediction, whole-exome sequencing data analysis, single-cell RNA data analysis (emerging), cancer genomics, immunology, high-performance computing. Magda joined QCIF as a bioinformatician in February 2023 after a year-and-a-half of working as a Postdoctoral Research Fellow at The University of Queensland's Frazer Institute…
Job Titles:
- Training & Communications Officer, Australian BioCommons
Melissa joined QCIF in September 2020 as the Training and Communications Officer for the Australian BioCommons. This is a joint appointment with the University of Queensland's Research Computing Centre (RCC).
In this role Melissa works with a national network of bioinformatics experts and trainers to design, develop and organise bioinformatics-focused webinars and workshops. She joined the team from the European Bioinformatics Institute (EMBL-EBI) in Cambridge, UK, where she worked as a Scientific Training Officer managing the day-to-day running of EMBL-EBI's bioinformatics e-learning program..
Job Titles:
- Research Community Engagement
Job Titles:
- Software and Platform Services Manager, Australian BioCommons
Gavin has been involved in various commercial industry sectors including retail, manufacturing & travel/accommodation which complement his nine year tenure in research technology and life sciences at The University of Queensland.
Prominently, he led the EBI Mirror, National Computational Infrastructure Specialised Facility in Bioinformatics and The Bioinformatics Resource Australia-EMBL Australia initiatives which facilitated web services integration to high-performance computing pipelines with the outlook of lowering the barrier to entry for researcher access to computational analysis.
Gavin's focus is on service delivery by applying commercial mission critical methods in maintaining reliable, agile and transformational systems.
Qualifications
Graduate Diploma in Business Administration
Associate Diploma in Computing
Skills: Service delivery, Prince-II, ITIL applied to bioinformatics and research computing at scale. Gavin has been involved in various commercial industry sectors including retail, manufacturing & travel/accommodation which complement his nine year tenure in research technology and life sciences at The University of Queensland. Prominently, he…
Job Titles:
- Linux Systems Administrator
Skills: Programming (Linux and OpenStack), web development and cloud computing. John joined QCIF in December 2021. His primary discipline has been in web development, but has more recently seen cloud computing as integral in application delivery. John will build, support and head the ongoing maintenance of QCIF's QRIScloud restricted region.…
Justin joined the team in 2013. He has previously worked as a biometrician and biostatistician for CSIRO, the University of New England, and the Queensland Institute of Medical Research. He has also worked at the Queensland Department of Environment and Heritage Protection modelling climate change, and at Griffith University modelling koala GPS tracking data.
Linda has returned to the QCIF board - she was previously its longest-serving member. She stepped down in 2017 following her Griffith University promotion to Pro Vice Chancellor and Head of the Logan Campus, a role she left in early 2020. She has previously held executive information and technology (CIO) roles across a number of universities and is currently an Adjunct Professor and Executive in Residence at the Griffith Business School. Linda is committed to strengthening community partnerships to advance research and translate research into practise, and to positioning Queensland as an innovative and resilient region. She is engaged in a number of international and national initiatives aimed at leveraging innovative information technologies to make data, in all its forms, and research outputs FAIR (Findable, Accessible, Interoperable and Reusable). She is currently Chair of the ORCID board and Deputy Chair elect of Infoxchange. She was formerly on the Victorian Partnership for Advanced Computing board, a member of the NCRIS eResearch Advisory Committee, the Australasian Open Access Advisory Committee executive and chair of the Open Data Institute Australia.
Job Titles:
- User Experience ( UX ) Designer
Madeline joined QCIF as a User Experience (UX) Designer in May 2020.
She works with QCIF's software and platform developers on projects, such as Galaxy Australia and the new web Apollo service for manual curation of genome annotation.
She also works on QCIF Members' web applications enabling researchers to expose their research data, such as TraDIS-vault.
Outside of her QCIF role, Madeline works with the World Bank Data and Evidence for Justice Reform (DE JURE) program. DE JURE aims to harness the potential of recent changes in data availability to establish a global data infrastructure for the justice sector, and through rigorous analysis and experimentation, expand the evidence base on the economics of justice reform.
She is currently studying a Postgraduate Certificate in Interaction Design at UQ and has a Bachelor of Business (Economics) from the Queensland University of Technology (QUT).
Research Interests
User Experience for public goods
Quadratic Voting
Web Design
Open Source
Augmented Reality
Qualifications
BBus in Economics, Queensland University of Technology, 2015
GradCert in Interaction Design, University of Queensland, ongoing
Skills: UX design and web development. Madeline joined QCIF as a User Experience (UX) Designer in May 2020. She works with QCIF's software and platform developers on projects, such as Galaxy Australia and the new web Apollo service for manual curation of genome annotation. She also works on QCIF…
Job Titles:
- Senior Health Informatician
Mark joined QCIF in November 2020 as a Senior Health Informatician to provide researchers with advice on sensitive data management and REDCap, a secure web application for building and managing online surveys and databases.
Mark will also join the project team behind the Secure eResearch Platform (SeRP). SeRP is a Monash University-led sensitive data platform QCIF is working on alongside other partners.
Mark was previously employed via Monash University as a database developer and systems administrator for Eastern Health.
He has practical experience with the management of large, multi-format, health data sets and the utilisation of these for research purposes by internal and external parties.
Prior to entering the health research field, Mark worked more than 10 years in Queensland state government in a broad range of research, policy and project management roles.
He holds degrees in Economics and Information Technology from QUT.
Skills: Informatics, sensitive data management, ReDCap, software development, systems administration and project management. Mark joined QCIF in November 2020 as a Senior Health Informatician to provide researchers with advice on sensitive data management and REDCap, a secure web application for building and managing online surveys and databases. Mark will also join…
Job Titles:
- Chief Information and Digital Officer at CQUniversity
Roy is Chief Information and Digital Officer at CQUniversity. His responsibilities include delivering real business and technical solutions for the whole of the university's activities in learning, teaching, research and corporate functions. He focuses on establishing innovation culture through effective partnerships with stakeholders and improving customer engagement, service delivery, governance and management of technology applications and solutions. Roy first joined CQUniversity in 2008 as Associate Director of Infrastructure Services and Support. Prior to that he was IT Director at Charles Darwin University from 2003-2008.
Job Titles:
- Biostatistician and Bioinformatician
Job Titles:
- Database and Systems Administrator
Job Titles:
- Associate Director of Platforms - Australian BioCommons
Skills: software engineering Peter Marendy joined QCIF in October 2021 as Head of Data Services. The Data Services team is an expansion of QCIF's BioData activities into other research domains, such as health, with a broader scope including the provision of managed services, such as platforms for sensitive data, as well as the development of dashboards and specialised research data portals. Peter has 20 years of software engineering experience across multiple domains in…
Job Titles:
- Senior Communications Officer
Job Titles:
- Windows Systems Administrator
Skills: Statistics, Econometrics After working with QCIF as a casual biostatistics training instructor for three years, William joined QCIF full-time in late March 2022 as a Gold Coast-based Junior Statistician. As a fully certified The Carpentries instructor, William will continue to assist QCIF with its training program for researchers, including providing…