About

Dr Schmitz joined James Cook University in July 2021. He is an Associate Professor in Bioinformatics at the Department of Molecular & Cell Biology, College of Public Health, Medical & Vet Sciences, and an NHMRC Emerging Leadership Fellow (2021-2025).

Ulf completed his PhD at the University of Rostock (Germany). In 2015, he joined the Centenary Institute (University of Sydney) as a post-doctoral Research Officer in the Gene and Stem Cell Therapy Program. In 2016, he was also appointed as Conjoint Senior Lecturer at the Faculty of Medicine & Health (University of Sydney). Before joining JCU, Ulf was Head of the Computational Biomedicine Lab at the Centenary Institute.

Ulf is a computational biologist with training in bioinformatics and systems biology and more than 12 years of experience in analysing post-transcriptional gene regulation. His research interests focus on computational RNA biology and Systems Medicine. Ulf and his team develop integrative workflows combining various computational disciplines with experimentation to address questions around non-coding RNAs, post-transcriptional gene regulation, and cancer biology. He has published 48 research articles, 9 book chapters, and 3 books on this topic. 

Research Projects

Alternative splicing and the epigenome in Chronic Myeloid Leukaemia

In this project, we are investigating gene regulatory processes in leukaemia. The third biggest cause of cancer death in all Australians is blood cancers (leukaemia), which are diagnosed 35 times each day. Using a multi-omics approach, we examine alternative splicing and epigenetic changes in blood samples from chronic myeloid leukaemia (CML) patients before and after treatment with tyrosine kinase inhibitors. Find out more: Schmitz et al, Cancers 2020

Cooperating microRNAs for cancer therapy

In this project, we use a systems medicine approach to find new avenues for overcoming chemotherapy resistance in aggressive tumour cells. Our results suggest that pairs of cooperating microRNAs could be used as potential RNA therapeutics to reduce E2F1-related chemoresistance. Find out more: Lai X, Gupta SK, Schmitz U et al, Theranostics 2018

 

Intron retention regulation in haematopoietic cells

There is growing evidence that alternative splicing, including intron retention (IR), is regulated on at least two levels: locally, through a network of interacting trans-acting splicing regulators with cis-acting regulatory elements, and globally, through the chromatin structure. In this project, we explore a global regulation of IR in haematopoietic cells – we use statistical analysis to better understand IR regulation using information derived from the epigenetic factors that govern chromatin organisation, namely nucleosome assembly, DNA methylation, and histone modifications. The main challenge here is to integrate multiple layers of ‘-omics’ into a single computational model which produces biologically interpretable results. Find out more: Petrova et al, bioRxiv 2021

 

Cross-talk between post-transcriptional gene regulation mechanisms

Combining computational predictions and in vitro assays, we elucidate the cross-talk between post-transcriptional gene regulation mechanisms. More specifically, we focus on interactions between microRNA molecules and intron-retaining mRNA transcripts and try to identify networks of interconnected gene regulation. Using a systems biology approach we will model competitive post-transcriptional gene regulation through iterative cycles of time-course experiments and model simulations.

 

Available HDR Student Projects

Portable long-read sequencing to diagnose Chronic Kidney Disease

Determining cellular gene isoform abundance from long-read RNA sequencing data

Mirtron synthesis and expression in leukemia

Alternative splicing-based subtyping of 5k leukaemia and lymphoma samples

Single-cell multi-omics data analysis to elucidate gene isoform regulation in Acute Myeloid Leukemia

Teaching
  • BC3203: Bioinformatics (Level 3; TSV)
  • BC5203: Advanced Bioinformatics (Level 5; TSV)
Interests
Professional
  • Mentoring Early Career Researchers
Research
  • RNA Biology
  • Cancer Biology
  • Bioinformatics
  • Systems Biology
Experience
  • 2021 to present - A/Prof, James Cook University (Townsville/Australia)
  • 2018 to present - Associate Faculty, Centenary Institute (Sydney/Australia)
  • 2015 to present - Conjoint Senior Lecturer, University of Sydney (Australia)
  • 2018 to 2021 - Senior Research Officer, Centenary Institute (Sydney/Australia)
  • 2018 to 2021 - Lab Head, Centenary Institute (Sydney/Australia)
  • 2015 to 2017 - Research Officer, Centenary Institute (Sydney/Australia)
  • 2003 to 2015 - Systems Engineer, University of Rostock (Germany)
Socio-Economic Objectives
Honours
Awards
  • 2020 - Travel Award - The CASS Foundation
  • 2020 - Centenary Recognition Award for Contribution to Centenary Life
  • 2016 - Cure the Future Award of Scientific Excellence, Cure the Future Foundation
  • 2016 - Joachim-Jungius Award for best PhD thesis at the University of Rostock, Germany
Fellowships
  • 2021 to 2025 - NHMRC Investigator (EL1)
  • 2018 to 2020 - Cancer Institute NSW Early Career Fellowship
  • 2018 to 2019 - Australia-India Strategic Research Fund (AISRF) Early and Mid-Career Fellowship, Australian Academy of Science
  • 2017 to 2019 - NHMRC Peter Doherty Fellowship for Early Career Researchers
Other
  • 2017 - Honorary Adjunct Professorship at Chhattisgarh Swami Vivekanand Technical University (CSVTU), Bhilai, India
  • 2016 - Conjoint Senior Lecturer, Sydney Medical School, University of Sydney
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
Book Chapters
More

ResearchOnline@JCU stores 25+ research outputs authored by A/PROF Ulf Schmitz from 2016 onwards.

Current Funding

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

National Health & Medical Research Council - Investigator Grants

Investigating post-transcriptional gene regulation in cancer

Indicative Funding
$577,910 over 4 years
Summary
In this project we willl employ integrative systems medicine approaches to generate a detailed mechanistic overview of multi-level cancer gene regulation and provide novel avenues for the treatment of aggressive tumours. We will determine patterns of gene regulation in leukaemia and test whether these patterns are predictive for disease outcome. We will devise strategies for the therapeutic interference with gene regulation to effectively sensitise aggressive tumours to chemotherapy and thereby diminish tumour cell populations and prevent relapse.
Investigators
Ulf Schmitz (College of Public Health and Medical & Vet Sciences)
Keywords
Bioinformatics; Breast Cancer; Gene Regulation; Computational Biology; Leukaemia; RNA biology

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

Cancer Council NSW - Project Grants

Deciphering cancer gene regulation

Indicative Funding
$404,943 over 4 years
Summary
In this project, we investigate regulatory processes in cancer, whereby the control of protein generation from DNA genetic code is disrupted. This process is referred to as intron retention (IR), a phenomenon, which allows ?junk? DNA to enter the cell. IR plays a critical role in cancer development, yet the mechanism of its involvement remains unresolved. We hypothesise that IR can significantly interfere with other forms of gene regulation via `cross-talk?. This introduces a distortion of gene regulation, which is amenable to therapeutic manipulation. Our enhanced understanding of gene-regulatory cross-talk will facilitate improved IR-directed therapies.
Investigators
Ulf Schmitz and Charles Bailey (College of Public Health, Medical & Vet Sciences and Centenary Institute of Cancer Medicine & Cell Biology)
Keywords
Bioinformatics; Breast Cancer; Gene Regulation; Computational Biology; Leukaemia; RNA biology
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
  • Investigating monocyte and NK derived MS genes by scSequencing, flow cytometry and cytotoxicity assays. (PhD , Secondary Advisor)
  • Analysing the role of chimeric transcripts in human cancers (PhD , Primary Advisor/AM/Adv)
  • Identification of viral versus bacterial triggers in immune cells from AECOPD patients (PhD , Secondary Advisor)
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
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Location
  • 142.302, The Science Place (Townsville campus)
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