photo

Ulf Schmitz

Projects

18

Publications

63

Awards

8


Contact Details

Associate Professor- Bioinformatics
    Associate Dean, Research
      Associate Dean Research

      Biography

      Ulf is a computational biologist with training in bioinformatics and systems biology and more than 15 years of experience in analysing post-transcriptional gene regulation. His research interests focus on computational RNA biology and Systems Medicine.

      Ulf completed his PhD at the University of Rostock (Germany). In 2015, he joined the Centenary Institute in Sydney as a post-doctoral Research Officer in the Gene and Stem Cell Therapy Program. He later established the Computational Biomedicine Lab at the Centenary. He also holds an appointment as Conjoint Senior Lecturer at the University of Sydney (Faculty of Medicine & Health).

      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 58 research articles, 11 book chapters, and 4 books on this topic.

      Available HDR Student Projects

      Single-cell data analysis of hepatocellular carcinoma patient samples

      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

      Mathematical Modelling of Alternative Splicing and Transcriptomic Complexity

      Mathematical Modelling of Cell-Fate Determination

      Computational Biomedicine Lab

      group photo


      In the Computational Biomedicine Lab at James Cook University and the Centenary Institute (University of Sydney) computational biologists work hand-in-hand with molecular biologists integrating in silico, in vitro and in vivo approaches in advanced interdisciplinary research. We develop integrative systems medicine workflows along with tools and databases to identify and study interactions between RNAs and other molecules, functional mechanisms of gene regulation, cell signalling pathways and gene regulatory networks.

      Our goal is to achieve a deeper understanding of processes involved in disease emergence and progression, with a focus on cancer biology, and possible avenues for therapeutic interventions and optimised treatment schedules. Most projects involve the analysis of experimental high-throughput data (incl. (sc)RNA-seq, NanoString, DNA Methyl-Seq, ChIP-Seq, CLIP-seq, and more). Moreover, we use various mathematical formalisms to model the effects of environmental stimuli or pathogenic events on molecular interaction networks and signalling pathways. Using machine learning and computer simulation approaches, we predict disease progression and outcome as well as the effect of therapeutic agents on cellular survival and resistance mechanisms.

      Current Research Projects

      Portable long-read sequencing to diagnose Chronic Kidney Disease

      With the help of new seed funding from the Tropical Australian Academic Health Centre, we trial a portable, rapid, and targeted genomic test to find genetic variants that predispose people towards Chronik Kidney Disease. For more information see recent media coverage:

      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, Nucleic Acids Research 2022

      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

      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

      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.

      MicroRNAs as Cancer Biomarkers

      MicroRNAs are small molecules that play an important role in regulating gene expression. We have been exploring the potential of microRNAs as cancer biomarkers, as regulators of cancer genes and their role in immune cells. For more information about our work see recent media coverage:

      Research

      Projects

      Teaching

      Taught Modules
      Current JCU Research Students
      Developing a single-cell long-read sequencing data analysis pipeline for hepatocellular carcinoma patient samples
      Doctor of Philosophy (Medical, Molecular and Veterinary Sciences)
      Clinical Genomics in Kidney Transplantation;;
      Doctor of Philosophy (Health)
      Long-read Portable Sequencing and its application to diagnose Chronic Kidney Disease in North Queensland
      Master of Philosophy (Medical, Molecular and Veterinary Sciences)
      Clinical applications of genetic testing, sequencing and information to promote kidney health;;;;
      Doctor of Philosophy (Health)
      Computational approaches to Detect Genetic Variants at Single Cell resolution
      Doctor of Philosophy (Medical, Molecular and Veterinary Sciences)
      Pharmacogenomic Profiling of Mental Health Patients in the Philippine National Center for Mental Health
      Doctor of Philosophy (Medical, Molecular and Veterinary Sciences)
      Novel targets and strategies in the treatment of liver and oral pharyngeal cancer
      Doctor of Philosophy (Medical and Molecular Sciences)
      Developing a new treatment regime for hepatocellular carcinoma
      Doctor of Philosophy (Medical, Molecular and Veterinary Sciences)
      Analysing the role of chimeric transcripts in human cancers
      Doctor of Philosophy (Medical and Molecular Sciences)
      Insights into the molecular bases of coral-specific traits
      Doctor of Philosophy (Medical, Molecular and Veterinary Sciences)
      Investigating monocyte and NK derived MS genes by scSequencing, flow cytometry and cytotoxicity assays.
      Doctor of Philosophy (Medical, Molecular and Veterinary Sciences)
      Neural network based model for cell type-specific isoform expression pattern
      Master of Philosophy (Medical, Molecular and Veterinary Sciences)

      Activities

      Associations
      Awards
      Employment

      Output

      Schmitz, Ulf (2023) Overview of Computational and Experimental Methods to Identify Tissue-Specific M. New York, NY, USA: [DOI] ...
      Other Publication ResearchOnline@JCU
      Lai, Xin; Schmitz, Ulf; Vera, Julio (2022) The Role of MicroRNAs in Cancer Biology and Therapy from . [DOI] ...
      Other Publication ResearchOnline@JCU
      Schmitz, Ulf; Wolkenhauer, Olaf; Vera-González, Julio (2022) Systems Biology of MicroRNAs in Cancer. [Edited Publication] [DOI] ...
      Other Publication ResearchOnline@JCU
      Schmitz, Ulf; Monteuuis, Geoffray; Petrova, Veronika; Shah, Jaynish S.; Rasko, John E.J. (2021) Comp. Lon...
      Other Publication ResearchOnline@JCU
      Schmitz, Ulf; Gupta, Shailendra K.; Vera, Julio; Wolkenhauer, Olaf (2019) Computational approaches i. Amsterdam, The Netherland...
      Other Publication ResearchOnline@JCU
      Amirkhah, Raheleh; Meshkin, Hojjat Naderi; Farazmand, Ali; Rasko, John E.J.; Schmitz, Ulf (2017) Com. Ne...
      Other Publication ResearchOnline@JCU
      Amirkhah, Raheleh; Farazmand, Ali; Wolkenhauer, Olaf; Schmitz, Ulf (2016) RNA systems biology for ca. New York, NY, USA: [DOI ...
      Other Publication ResearchOnline@JCU
      Schmitz, Ulf; Wolkenhauer, Olaf (2016) Systems medicine. New York, USA: [Edited Publication] [DOI] ...
      Other Publication ResearchOnline@JCU
      Julio Vera; Olaf Wolkenhauer; Ulf Schmitz (2014) Cancer Systems Biology: Current Achievements in - O. [DOI] ...
      Other Publication ResearchOnline@JCU
      Dorney, Ryley; Dhungel, Bijay P.; Rasko, John E.J.; Hebbard, Lionel; Schmitz, Ulf (2023) 'Recent Adv. Briefing, 24 (1)...
      Journal Publication ResearchOnline@JCU
      Oehler, Josphine B.; Wright, Helen; Stark, Zornitza; Mallett, Andrew; Schmitz, Ulf (2023) 'The appli. Human G, 17 . ...
      Journal Publication ResearchOnline@JCU
      Wong, Alex C.H.; Wong, Justin J.-L.; Rasko, John E.J.; Schmitz, Ulf (2023) 'SpliceWiz: Interactive a. Briefings in Bioinform, 25 (1). [DOI] ...
      Journal Publication ResearchOnline@JCU
      Gillman, Rhys; Field, Matt A.; Schmitz, Ulf; Karamatic, Rozemary; Hebbard, Lionel (2023) 'Identifyin. Computat, 21 :50...
      Journal Publication ResearchOnline@JCU
      Thavaneswaran, Subotheni; Kansara, Maya; Lin, Frank; Espinoza, David; Grady, John P.; Lee, Chee Khoo...
      Journal Publication ResearchOnline@JCU
      Wu, Siyuan; Schmitz, Ulf (2023) 'Single-cell and long-read sequencing to enhance modelling of splici. Computational and Structural Biotechnology Journal, 21 :2373-2380. [DOI] ...
      Journal Publication ResearchOnline@JCU
      Sadeghi, Mehdi; Karimi, Mohammad Reza; Karim, Amir Hossein; Farshbaf, Nafiseh Ghorbanpour; Barzegar,...
      Journal Publication ResearchOnline@JCU
      Wong, Justin J.L.; Schmitz, Ulf (2022) 'Intron retention: importance, challenges, and opportunities'. Trends in Genetics, 38 (8):789-792. [DOI] ...
      Journal Publication ResearchOnline@JCU
      Karimi, Mohammad Reza; Karimi, Amir Hossein; Abolmaali, Shamsozoha; Mehdi, Sadeghi; Schmitz, Ulf (20...
      Journal Publication ResearchOnline@JCU
      Shah, Jaynish S.; Milevskiy, Michael J.G.; Petrova, Veronika; Au, Amy Y.M.; Wong, Justin J.L.; Visva...
      Journal Publication ResearchOnline@JCU
      Petrova, Veronika; Song, Renhua; DEEP Consortium, ; Nordström, Karl J.V.; Walter, Jörn; Wong, Justin...
      Journal Publication ResearchOnline@JCU
      Alharbi, Adel B.; Schmitz, Ulf; Bailey, Charles G.; Rasko, John E.J. (2021) 'CTCF as a regulator of . Nucleic Acids Researc, 49 (14):7825-7838. ...
      Journal Publication ResearchOnline@JCU
      Bailey, Charles G.; Gupta, Shailendra; Metierre, Cynthia; Amarasekera, Punkaja M.S.; O'Young, Patric...
      Journal Publication ResearchOnline@JCU
      Dhungel, Bijay P.; Monteuuis, Geoffray; Giardina, Caroline; Tabar, Mehdi S.; Feng, Yue; Metierre, Cy...
      Journal Publication ResearchOnline@JCU
      Monteuuis, Geoffray; Schmitz, Ulf; Petrova, Veronika; Kearney, Padraic S.; Rasko, John E.J. (2020) '....
      Journal Publication ResearchOnline@JCU
      Alharbi, Adel B.; Schmitz, Ulf; Marshall, Amy D.; Vanichkina, Darya; Nagarajah, Rajini; Vellozzi, Me...
      Journal Publication ResearchOnline@JCU
      Schmitz, Ulf; Shah, Jaynish S.; Dhungel, Bijay P.; Monteuuis, Geoffray; Luu, Phuc-Loi; Petrova, Vero...
      Journal Publication ResearchOnline@JCU
      Emran, Abdullah Al; Nsengimana, Jérémie; Punnia-Moorthy, Gaya; Schmitz, Ulf; Gallagher, Stuart J.; N...
      Journal Publication ResearchOnline@JCU
      Aghajani, Marra Jai; Yang, Tao; Schmitz, Ulf; James, Alexander; McCafferty, Charles Eugenio; de Souz...
      Journal Publication ResearchOnline@JCU
      Green, Immanuel D.; Pinello, Natalia; Song, Renhua; Lee, Quitin; Halsted, James M.; Kwok, Chau-To; W...
      Journal Publication ResearchOnline@JCU
      Monteuuis, Geoffray; Wong, Justin J.L.; Bailey, Charles G.; Schmitz, Ulf; Rasko, John E.J. (2019) 'T. ...
      Journal Publication ResearchOnline@JCU
      Naderi-Meshkin, Hojjat; Lai, Xin; Amirkhah, Raheleh; Vera, Julio; Rasko, John E.J.; Schmitz, Ulf (20...
      Journal Publication ResearchOnline@JCU
      Amirkhah, Raheleh; Naderi-Meshkin, Hojjat; Shah, Jaynish S.; Dunne, Philip D.; Schmitz, Ulf (2019) '....
      Journal Publication ResearchOnline@JCU
      Lai, Xin; Eberhardt, Martin; Schmitz, Ulf; Vera, Julio (2019) 'Systems biology-based investigation o. Nucleic Acids Research, 47 (15):7753-7766. [DOI] ...
      Journal Publication ResearchOnline@JCU
      Vanichkina, Darya P.; Schmitz, Ulf; Wong, Justin J.-L.; Rasko, John E.J. (2018) 'Challenges in defin. Seminars in Cell , 75 :40-49. [DO ...
      Journal Publication ResearchOnline@JCU
      Lai, Xin; Gupta, Shailendra K.; Schmitz, Ulf; Marquardt, Stephan; Knoll, Susanne; Spitschak, Alf; Wo...
      Journal Publication ResearchOnline@JCU
      Rajasekhar, Magha; Schmitz, Ulf; Flamant, Stephane; Wong, Justin J.-L.; Bailey, Charles G.; Ritchie,...
      Journal Publication ResearchOnline@JCU
      Khan, Faiz M.; Marquardt, Stephan; Gupta, Shailendra K.; Knoll, Susanne; Schmitz, Ulf; Spitschak, Al...
      Journal Publication ResearchOnline@JCU
      Marshall, A.D.; Bailey, C.G.; Champ, K.; Vellozzi, M.; O'Young, P.; Metierre, C.; Feng, Y.; Thoeng, ...
      Journal Publication ResearchOnline@JCU
      Schmitz, Ulf; Pinello, Natalia; Jia, Fangzhi; Alasmari, Sultan; Ritchie, William; Keightley, Maria-C...
      Journal Publication ResearchOnline@JCU
      Sadeghi, Mehdi; Ranjbar, Bijan; Ganjalikhany, Mohamad Reza; Khan, Faiz M.; Schmitz, Ulf; Wolkenhauer...
      Journal Publication ResearchOnline@JCU
      Gupta, Shailendra K.; Jaitly, Tanushree; Schmitz, Ulf; Schuler, Gerold; Wolkenhauer, Olaf; Vera, Jul...
      Journal Publication ResearchOnline@JCU
      Edwards, Christopher R.; Ritchie, William; Wong, Justin J-L.; Schmitz, Ulf; Middleton, Robert; An, X...
      Journal Publication ResearchOnline@JCU
      Wong, Justin J.-L.; Au, Amy Y.M.; Gao, Dada; Pinello, Natalia; Kwok, Chau-To; Thoeng, Annora; Lau, K...
      Journal Publication ResearchOnline@JCU
      Wolfien, Markus; Rimmbach, Christian; Schmitz, Ulf; Jung, Julia Jeannine; Krebs, Stefan; Steinhoff, ...
      Journal Publication ResearchOnline@JCU
      Schmitz, Ulf; Naderi-Meshkin, Hojjat; Gupta, Shailendra K.; Wolkenhauer, Olaf; Vera, Julio (2016) 'T. ...
      Journal Publication ResearchOnline@JCU
      Amirkhah, Raheleh; Schmitz, Ulf; Linnebacher, Michael; Wolkenhauer, Olaf; Farazmand, Ali (2015) 'Mic. G,...
      Journal Publication ResearchOnline@JCU
      Amirkhah, Raheleh; Farazmand, Ali; Gupta, Shailendra K.; Ahmadi, Hamed; Wolkenhauer, Olaf; Schmitz, ...
      Journal Publication ResearchOnline@JCU
      Amirkhah, R.; Farazmand, A.; Irfan-Maqsood, M.; Wolkenhauer, O.; Schmitz, U. (2015) 'The role of mic. 61 (6):17-23....
      Journal Publication ResearchOnline@JCU
      Schmitz, Ulf; Lai, Xin; Winter, Felix; Wolkenhauer, Olaf; Vera, Julio; Gupta, Shailendra (2014) 'Coo. N,...
      Journal Publication ResearchOnline@JCU
      Knoll, S.; Fürst, K.; Kowtharapu, B.; Schmitz, U.; Marquardt, S.; Wolkenhauer, O.; Martin, H.; Pütze...
      Journal Publication ResearchOnline@JCU
      Khan, Faiz M.; Schmitz, Ulf; Nikolov, Svetoslav; Engelmann, David; Pützer, Brigitte M.; Wolkenhauer,...
      Journal Publication ResearchOnline@JCU
      Lai, X.; Bhattacharya, A.; Schmitz, U.; Kunz, M.; Vera, J.; Wolkenhauer, O. (2013) 'A systems' biolo. BioMed Researc, 2013 . [DOI ...
      Journal Publication ResearchOnline@JCU
      Bhattacharya, A.; Schmitz, U.; Wolkenhauer, O.; Schönherr, M.; Raatz, Y.; Kunz, M. (2013) 'Regulatio. Oncogen, 32 :3...
      Journal Publication ResearchOnline@JCU
      Vera, Julio; Schmitz, Ulf; Lai, Xin; Engelmann, David; Khan, Faiz M.; Wolkenhauer, Olaf; Pützer, Bri...
      Journal Publication ResearchOnline@JCU
      Guebel, Daniel V.; Schmitz, Ulf; Wolkenhauer, Olaf; Vera, Julio (2012) 'Analysis of cell adhesion du. Molecular BioSystems, 8 :1230-1242. [DOI] ...
      Journal Publication ResearchOnline@JCU
      Alla, Vijay; Kowtharapu, Bhavani S.; Engelmann, David; Emmrich, Stephan; Schmitz, Ulf; Steder, Marc;...
      Journal Publication ResearchOnline@JCU
      Lai, Xin; Schmitz, Ulf; Gupta, Shailendra K.; Bhattacharya, Animesh; Kunz, Manfred; Wolkenhauer, Ola...
      Journal Publication ResearchOnline@JCU
      Gupta, Shailendra K.; Gupta, Shishir K.; Smita, Suchi; Srivastava, Mugdha; Lai, Xin; Schmitz, Ulf; R...
      Journal Publication ResearchOnline@JCU
      Gupta, Shishir K.; Srivastava, Mugdha; Akhoon, Bashir A.; Smita, Suchi; Schmitz, Ulf; Wolkenhauer, O...
      Journal Publication ResearchOnline@JCU
      Raasch, Peter; Schmitz, Ulf; Patenge, Nadja; Vera, Julio; Kreikemeyer, Bernd; Wolkenhauer, Olaf (201...
      Journal Publication ResearchOnline@JCU
      Nikolov, Svetoslav; Vera, Julio; Schmitz, Ulf; Wolkenhauer, Olaf (2010) 'A model-based strategy to i. Theory in Biosciences, 130 :55-69. [DOI] ...
      Journal Publication ResearchOnline@JCU
      Schultz, Julia; Koczan, Dirk; Schmitz, Ulf; Ibrahim, Saleh M.; Pilch, Dominik; Landsberg, Jenny; Kun...
      Journal Publication ResearchOnline@JCU
      Hoffrogge, Raimund; Beyer, Susanne; Hübner, Rayk; Mikkat, Stefan; Mix, Eilhard; Scharf, Christian; S...
      Journal Publication ResearchOnline@JCU