Dr Ulf Schmitz

Conjoint Senior Lecturer
Centenary Institute Cancer Medicine &
Cell Biology

Telephone +61 2 9565 6209

Website ResearchGate
Rakso Lab
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Biographical details


EDUCATION

01/2013 – 06/2015 Ph.D. (Dr.-Ing.) in Bioinformatics, Faculty of Computer Science and Electrical Engineering, University of Rostock, Germany.
1998 - 2003 Dipl.-Ing. (FH) in Multimedia Engineering at the University of Applied Sciences Wismar, Germany


ACADEMIC APPOINTMENTS

01/2016 to date Conjoint Senior Lecturer, Sydney Medical School, University of Sydney, Australia
07/2015 to date Research Officer
Gene & Stem Cell Therapy Program, Centenary Institute, Camperdown, NSW, Australia
11/2003 – 06/2015 Bioinformatician and Systems Engineer
Department of Systems Biology & Bioinformatics, University of Rostock, Germany

Research interests

I am designing integrative workflows combining various computational disciplines with experimentation to approach molecular biological and medical problems. These workflows are implemented and applied to identify and study molecular interactions, functional mechanisms of gene-regulation, cell signaling pathways and gene regulatory networks for the goal of getting deeper insights into disease emergence and progression with a focus on different cancer entities.

Current projects

Intron retention-mediated microRNA sponging in cancer

In a phylogenetic study of intron retention, we have identified a potential role of intron retaining transcripts to act as conserved microRNA sponges that are involved in the fine-tuning of global gene expression regulation (Schmitz et al., 2017). microRNAs have dozens to hundreds of targets and intron retention can affect hundreds or even thousands of expressed genes. Both microRNA-induced translation repression or target degradation and intron retention-induced nonsense-mediated decay are concurrent mechanisms of gene expression control. We have identified a significantly increased density of putative microRNA binding sites in retained introns and the 3' UTR sequences of intron-retaining genes. Therefore, we aim to systematically analyze concurrent and competitive gene expression regulation mechanisms, including intron retention-mediated microRNA sponging.
In this project, we will identify gene-regulatory network modules using a data integration approach to determine patterns of concerted post-transcriptional gene regulation. Toward this, we will integrate expression profiles of microRNAs and protein-coding genes with patterns of intron retention, predicted microRNA/gene interactions, transcription factor/gene interactions, and intron/microRNA interactions. For a selected sub-network we will construct a mathematical model of competitive post-transcriptional gene regulation. We will use this model to explain theimplications of aberrant gene expression regulation in human cancers.

Schmitz, Ulf, et al. "Intron retention enhances gene regulatory complexity in vertebrates." Genome biology 18.1 (2017): 216.

Awards and honours

  1. Travel Fellowship from the RNA Society (2018)
  2. Award of the Cancer Institute NSW Early Career Fellowship (2018)
  3. Award of an Honorary Adjunct Professorship at Chhattisgarh Swami Vivekanand Technical University (CSVTU), Bhilai, India (2017)
  4. Award of the honorary title ‘Conjoint Senior Lecturer’, Sydney Medical School, University of Sydney (2016)
  5. Award of the Peter Doherty Fellowship for Early Career Researchers, National Health & Medical Research Council (NHMRC), Australia (2016)
  6. Cure the Future Award of Scientific Excellence, Cure the Future Foundation, Australia (2016)
  7. Centenary Travel Award – International, Centenary Institute, Australia (2016)
  8. Joachim-Jungius Förderpreis, University of Rostock, Germany (2016)
  9. Travel scholarship for attending the German Conference on Bioinformatics 2014, Bielefeld, funded by DECHEMA, Germany (2014)
  10. Award for the “Model of the Month" in the BioModels database (http://tinyurl.com/y87q958x) (2014)
  11. Travel scholarship for attending the Systems Biology of Human Disease Conference 2014, Boston, USA, funded by the Federal Ministry of Education and Research (BMBF), Germany (2014)
  12. Faculty award for extraordinary work performance, Faculty of Computer Science and Electrical Engineering, Rostock, Germany (2013)
  13. Travel scholarship for attending the German Conference on Bioinformatics 2013, Göttingen, funded by DECHEMA, Germany (2013)
  14. Award for the best scientific contribution to the public image of the Faculty of Computer Science and Electrical Engineering, University of Rostock, Germany (2009)
  15. Scholarship for an internship at PASS IT Consulting P Ltd, Hyderabad, India, funded by the German Academic Exchange Service (DAAD), Germany (2002)

Selected grants

2018

  • Cooperating microRNAs for cancer therapy - a systems medicine approach; Schmitz U, Rasko J; Cancer Institute New South Wales/Early Career Fellowship.
  • New Initiatives in Basic and Applied Medical Research; Rasko J, Bailey C, Wong J, Schmitz U; Philip Bushell Foundation/Research Support.

Selected publications

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Journals

  • Vanichkina, D., Schmitz, U., Wong, J., Rasko, J. (2018). Challenges in defining the role of intron retention in normal biology and disease. Seminars in Cell and Developmental Biology, 75, 40-49. [More Information]
  • Rajasekhar, M., Schmitz, U., Flamant, S., Wong, J., Bailey, C., Ritchie, W., Holst, J., Rasko, J. (2018). Identifying microRNA determinants of human myelopoiesis. Scientific Reports, 8(1), 7264. [More Information]
  • Lai, X., Gupta, S., Schmitz, U., Marquardt, S., Knoll, S., Spitschak, A., Wolkenhauer, O., Putzer, B., Vera, J. (2018). MiR-205-5p and miR-342-3p cooperate in the repression of the E2F1 transcription factor in the context of anticancer chemotherapy resistance. Theranostics, 8(4), 1106-1120. [More Information]
  • Amirkhah, R., Meshkin, H., Farazmand, A., Rasko, J., Schmitz, U. (2017). Computational and experimental identification of tissue-specific MicroRNA targets. Methods in Molecular Biology (Clifton N.J.), 1580, 127-147. [More Information]
  • Marshall, A., Bailey, C., Champ, K., Vellozzi, M., O�Young, P., Metierre, C., Feng, Y., Thoeng, A., Richards, A., Schmitz, U., Biro, M., Anderson, L., Rasko, J., et al (2017). CTCF genetic alterations in endometrial carcinoma are pro-tumorigenic. Oncogene, 36(29), 4100-4110. [More Information]
  • Schmitz, U., Pinello, N., Jia, F., Alasmari, S., Ritchie, W., Keightley, M., Shini, S., Lieschke, G., Wong, J., Rasko, J. (2017). Intron retention enhances gene regulatory complexity in vertebrates. Genome Biology, 18(1), 1-15. [More Information]
  • Khan, F., Marquardt, S., Gupta, S., Knoll, S., Schmitz, U., Spitschak, A., Engelmann, D., Vera, J., Wolkenhauer, O., P�tzer, B. (2017). Unraveling a tumor type-specific regulatory core underlying E2F1-mediated epithelial-mesenchymal transition to predict receptor protein signatures. Nature Communications, 8(1), 1-15. [More Information]
  • Edwards, C., Ritchie, W., Wong, J., Schmitz, U., Middleton, R., An, X., Mohandas, N., Rasko, J., Blobel, G. (2016). A dynamic intron retention program in the mammalian megakaryocyte and erythrocyte lineages. Blood, 127(17), e24-e34. [More Information]
  • Sadeghi, M., Ranjbar, B., Ganjalikhany, M., Khan, F., Schmitz, U., Wolkenhauer, O., Gupta, S. (2016). MicroRNA and transcription factor gene regulatory network analysis reveals key regulatory elements associated with prostate cancer progression. PloS One, 11(12), 1-19. [More Information]
  • Wong, J., Au, A., Gao, D., Pinello, N., Kwok, C., Thoeng, A., Lau, K., Gordon, J., Schmitz, U., Feng, Y., Nguyen, T., Middleton, R., Bailey, C., Holst, J., Rasko, J., Ritchie, W. (2016). RBM3 regulates temperature sensitive miR-142-5p and miR-143 (thermomiRs), which target immune genes and control fever. Nucleic Acids Research, 44(6), 2888-2897. [More Information]
  • Schmitz, U., Naderi-Meshkin, H., Gupta, S., Wolkenhauer, O., Vera, J. (2016). The RNA world in the 21st century-a systems approach to finding non-coding keys to clinical questions. Briefings in bioinformatics, 17(3), 380-392. [More Information]
  • Wolfien, M., Rimmbach, C., Schmitz, U., Jung, J., Krebs, S., Steinhoff, G., David, R., Wolkenhauer, O. (2016). TRAPLINE: a standardized and automated pipeline for RNA sequencing data analysis, evaluation and annotation. BMC Bioinformatics, 17(1), 1-11. [More Information]
  • Amirkhah, R., Farazmand, A., Irfan-Maqsood, M., Wolkenhauer, O., Schmitz, U. (2015). The role of microRNAs in the resistance to colorectal cancer treatments. Cellular and Molecular Biology, 61(6), 17-23. [More Information]

2018

  • Vanichkina, D., Schmitz, U., Wong, J., Rasko, J. (2018). Challenges in defining the role of intron retention in normal biology and disease. Seminars in Cell and Developmental Biology, 75, 40-49. [More Information]
  • Rajasekhar, M., Schmitz, U., Flamant, S., Wong, J., Bailey, C., Ritchie, W., Holst, J., Rasko, J. (2018). Identifying microRNA determinants of human myelopoiesis. Scientific Reports, 8(1), 7264. [More Information]
  • Lai, X., Gupta, S., Schmitz, U., Marquardt, S., Knoll, S., Spitschak, A., Wolkenhauer, O., Putzer, B., Vera, J. (2018). MiR-205-5p and miR-342-3p cooperate in the repression of the E2F1 transcription factor in the context of anticancer chemotherapy resistance. Theranostics, 8(4), 1106-1120. [More Information]

2017

  • Amirkhah, R., Meshkin, H., Farazmand, A., Rasko, J., Schmitz, U. (2017). Computational and experimental identification of tissue-specific MicroRNA targets. Methods in Molecular Biology (Clifton N.J.), 1580, 127-147. [More Information]
  • Marshall, A., Bailey, C., Champ, K., Vellozzi, M., O�Young, P., Metierre, C., Feng, Y., Thoeng, A., Richards, A., Schmitz, U., Biro, M., Anderson, L., Rasko, J., et al (2017). CTCF genetic alterations in endometrial carcinoma are pro-tumorigenic. Oncogene, 36(29), 4100-4110. [More Information]
  • Schmitz, U., Pinello, N., Jia, F., Alasmari, S., Ritchie, W., Keightley, M., Shini, S., Lieschke, G., Wong, J., Rasko, J. (2017). Intron retention enhances gene regulatory complexity in vertebrates. Genome Biology, 18(1), 1-15. [More Information]
  • Khan, F., Marquardt, S., Gupta, S., Knoll, S., Schmitz, U., Spitschak, A., Engelmann, D., Vera, J., Wolkenhauer, O., P�tzer, B. (2017). Unraveling a tumor type-specific regulatory core underlying E2F1-mediated epithelial-mesenchymal transition to predict receptor protein signatures. Nature Communications, 8(1), 1-15. [More Information]

2016

  • Edwards, C., Ritchie, W., Wong, J., Schmitz, U., Middleton, R., An, X., Mohandas, N., Rasko, J., Blobel, G. (2016). A dynamic intron retention program in the mammalian megakaryocyte and erythrocyte lineages. Blood, 127(17), e24-e34. [More Information]
  • Sadeghi, M., Ranjbar, B., Ganjalikhany, M., Khan, F., Schmitz, U., Wolkenhauer, O., Gupta, S. (2016). MicroRNA and transcription factor gene regulatory network analysis reveals key regulatory elements associated with prostate cancer progression. PloS One, 11(12), 1-19. [More Information]
  • Wong, J., Au, A., Gao, D., Pinello, N., Kwok, C., Thoeng, A., Lau, K., Gordon, J., Schmitz, U., Feng, Y., Nguyen, T., Middleton, R., Bailey, C., Holst, J., Rasko, J., Ritchie, W. (2016). RBM3 regulates temperature sensitive miR-142-5p and miR-143 (thermomiRs), which target immune genes and control fever. Nucleic Acids Research, 44(6), 2888-2897. [More Information]
  • Schmitz, U., Naderi-Meshkin, H., Gupta, S., Wolkenhauer, O., Vera, J. (2016). The RNA world in the 21st century-a systems approach to finding non-coding keys to clinical questions. Briefings in bioinformatics, 17(3), 380-392. [More Information]
  • Wolfien, M., Rimmbach, C., Schmitz, U., Jung, J., Krebs, S., Steinhoff, G., David, R., Wolkenhauer, O. (2016). TRAPLINE: a standardized and automated pipeline for RNA sequencing data analysis, evaluation and annotation. BMC Bioinformatics, 17(1), 1-11. [More Information]

2015

  • Amirkhah, R., Farazmand, A., Irfan-Maqsood, M., Wolkenhauer, O., Schmitz, U. (2015). The role of microRNAs in the resistance to colorectal cancer treatments. Cellular and Molecular Biology, 61(6), 17-23. [More Information]

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