OR

Browse By

Associate Professor Nathan Palpant

National Heart Foundation of Austra

Institute for Molecular Bioscience
n.palpant@uq.edu.au
+61 7 334 62054

Overview

Career Summary: 2009: PhD, University of Michigan, USA with training in cardiac physiology, modelling myocardial ischemia in vivo and in vitro, and development of therapeutic approaches for myocardial ischemia; 2009–2015: Postdoctoral Research Fellow, University of Washington, Institute for Stem Cell and Regenerative Medicine, USA with training in stem cell biology, genomics, genome editing, and cell therapeutics for ischemic heart disease; 2015–current: Group Leader, University of Queensland (UQ), Institute for Molecular Bioscience; 2022-current: Associate Professor, UQ; 2018–2021: National Heart Foundation Future Leader Fellow. Dr. Palpant’s research team has expertise in human stem cell biology, computational genomics, and cardiac physiology, which enables them to translate outcomes from cell biology and genomics to disease modelling, drug discovery, and preclinical modelling.

Research Interests

  • Developing new drugs for heart disease
    Our work aims to prevent organ damage associated with ischemic injuries of the heart. There are no drugs that prevent organ damage caused by these injuries, which ultimately leads to heart failure, making ischemic heart disease the leading cause of death worldwide. This project aims to identify new molecular targets coupled with development of a novel pharmacological inhibitors as novel therapeutics to promote rapid and more effective recovery following an acute cardiovascular event. Development of new cardiovascular drugs will address a major clinical area of unmet need, thereby decreasing mortality, improving recovery and quality-of-life for survivors, and drastically reducing the burden of these diseases. Conditions caused by obstruction of blood flow to the heart are the most common emergency manifestation of cardiovascular disease. Although acute reperfusion therapies have improved patient outcomes, mortality remains high and heart attacks are one of the largest attributable risks for heart failure (HF). Myocardial sensitivity to ischemia-reperfusion injury (IRI) therefore remains a primary point of vulnerability underlying cardiovascular disease, which is the leading cause of morbidity and mortality worldwide. Despite decades of preclinical therapeutic development, there are no drugs in clinical use that block the acute injury response to cardiac ischemia. My research group has discovered a new therapeutic drug to prevent injuries of the heart, a peptide (Hi1a) isolated from venom of the Fraser Island funnel-web spider. Hi1a is a safe and potent therapeutic that we have shown improves heart recovery after myocardial infarction (MI) and greatly enhances the performance of donor hearts procured for transplantation. These remarkable therapeutic properties stem from Hi1a’s ability to protect heart muscle cells from ischemic injury by inhibiting an ion channel known as acid-sensing ion channel 1a (ASIC1a). More broadly, my research program is advancing studies on Hi1a alongside development of other novel therapeutic drugs that reduce the scope and spread of organ injury to the heart after ischemic injuries. These research projects integrate information from diverse sources to establish rationale and mechanism including population statistical genetics methods (e.g. GWAS), CRISPR genetic perturbation studies in iPSCs, functional studies in cell models, and animal models of disease.
  • Building tools to predict how the genome controls cells
    This work focuses on development of disease-agnostic, high throughput and scalable functional genomics methods that integrate computational predictions and disease modelling to study mechanisms controlling cell differentiation and genetic causes of disease. Genome sequencing is a powerful tool for studying the biological basis of disease, yet out of millions of data points, finding the underlying cause of disease can be difficult. Current protocols for classifying variants from patient DNA data largely rely on prior knowledge about normal and abnormal gene variation contained in large public databases, known disease-causing gene panels, or identifying variants causing amino acid changes in proteins (which only comprise 2% of the genome). Despite these powerful approaches, studies indicate that classifying variants as pathogenic occurs in only a minority of cases and among variants reported in ClinVar, a public archive of relationships between human variation and phenotype, wherein a large proportion (37%) are classified as variants of unknown significance (VUS). New approaches are needed to improve variant prioritisation and classification from genetic data. My research group is developing unsupervised, genome-wide computational analysis methods to reveal genetic mechanisms of development and disease. For example, our recent work developed TRIAGE which uses epigenetic modification of DNA-binding histone proteins to identify regions of the genome that are critical determinants of cell decisions and functions. Using data from >800 cell types, we identified genomic “hot-spots” that, when mutated, are associated with diseases, including neurological and cardiovascular diseases, multi-organ syndromes, and cancer. Our data show that TRIAGE regions of the genome are enriched for pathological variants (especially those causing congenital diseases), intolerant to mutations, have significantly increased effects on complex trait phenotypes, and encode genes that are key determinants of cell differentiation and morphogenesis. This area of my program focuses four design criteria in developing and implementing computational tools to facilitate novel discovery in cells. Simplicity: We are building methods that help organise genomic information in an unsupervised manner across the human genome. These methods can be used to analyse orthogonal data (e.g. patient genetic data) to identify genetic causes of disease or development and/or reveal relationships between gene groups that inform programs controlling cell decisions and functions. Versatility: We aim to develop methods that can be used with any genomic data that maps to genes or a chromosomal address including analysis of patient genetic data or any genomic data type (GWAS, SNPs, RNAseq etc). Furthermore, these methods are ideal models to weight regions of the genome in genetic analysis tools such as polygenic risk scores or machine learning algorithms. Disease-agnostic: Using a systems level approach, these methods enable broad implementation in data analysis pipelines for any data sample from any cell, tissue, disease, or individual. Efficient functional screening: These prediction methods provide robust rationale for wet lab cell biology to functionally test novel hypotheses derived from computational prediction methods in functional genomics studies.
  • Harnessing control of stem cell decisions and functions
    Cell differentiation is a process involving the continuous coordination of gene expression programs that guide undifferentiated cells into specific, functional cell types. The mechanisms controlling cell differentiation are not well understood. Recent advances in stem cell biology and tissue engineering have highlighted this fundamental knowledge gap. For example, cells derived from pluripotent stem cells (iPSCs) are often heterogeneous, display physiological properties reminiscent of fetal cells and fail to fully mature towards an adult functional state. Our inability to accurately guide cell differentiation pathways currently limits the utility of iPSC-derived cell products in research, tissue engineering, and drug discovery. Despite these profound limitations, the stem cell market is forecasted to grow to nearly $6B USD by 2025. The anticipated impact of the stem cell sector is dependent on precision control of cell differentiation into cell types that model human physiology. Efforts to dissect cell differentiation mechanisms and recapitulate human development using iPSCs have encountered the following major challenges: 1) we lack fundamental understanding of human developmental biology, 2) we lack sufficient scale of data mapping gene expression changes controlling cell processes over time, 3) among the thousands of genes expressed in cells, we lack the ability to efficiently identify genes (especially non-transcription factors) responsible for guiding specific cell differentiation processes, and 4) we do not understand how and when to effectively perturb these specialised gene programs to customise cell differentiation decisions or functions. My group is developing the data, tools, and cell biology perturbation and phenotyping strategies to address these limitations, positioning us to establish new insights into cell biology of differentiation. Using our expertise in stem cell and cardiovascular developmental biology, we are studying how gene programs change as cells move across the cell developmental lineages and identifying genetic on/off switches that control cell choices and functions during differentiation.

Research Impacts

Advancing stem cells toward clinical testing: Work by Dr Palpant on iPSC genome engineering and differentiation protocols led to him receiving the 2015 Young Investigator Award from the International Society for Heart Research. This work resulted in a licensed patent (US Patent 10,612,002; 2020) on derivation of hPSCs-endothelial cells. This patent and seminal studies on regenerating the mammalian heart with iPSC-derived heart muscle (Nature x2) formed the basis for Sana Biotechnology (USA; USD $700M series A VC investment in 2019). Dr Palpant has an ongoing collaboration with Sana CSO Professor Charles Murry (including publications and a 2017 UQ Global Strategy and Partnership Award) to advance discoveries for commercialisation by Sana.

Genomic innovation for drug discovery: Dr Palpant has been at the forefront of research into innovative genomics algorithms and sequencing methods. His work developing a computational method to identify genetic features controlling cells resulted in the Lorne Genome Millennium Science Award (2019) and led to current funded collaborations with HAYA Therapeutics (Switzerland; USD $16M series A VC investment, 2020), Merck (Germany), and ConcR (UK) resulting in >$600K in industry funding for early access to these discovery platforms.

New drug therapeutics for cardiovascular disease: Dr Palpant has led development of Hi1a as a novel cardiovascular drug. These discoveries stemmed from his expertise in using human pluripotent stem cell biology and disease modelling of acquired heart disease. This work was recognised by the Cardiac Society for Australia and New Zealand Ralph Reader Prize and resulted in a provisional patent on ASIC1a-knockout iPSCs (PAT-02408-US-01). The clinical impact of this work has resulted in a UQ spinout company, Infensa Bioscience to commercialise Hi1a for clinical testing. He is scientific co-founder and on the scientific advisory board of Infensa Bioscience.

Publication Impact Metrics: Dr Palpant's expertise in pluripotent stem cell biology, cardiac muscle cells, and genomics has resulted in publications cited 7-fold higher than the field average (Topic E 4031 FWCI of 7.37, SciVal). His research has been featured on the ABC, Newsweek, The Guardian, and The Washington Post.

Professional Standing: Since 2019, Dr Palpant has been involved in national initiatives including as co-chair of the Queensland Cardiovascular Research Network and advisory member of the Precision Medicine Flagship for the Australian Cardiovascular Alliance. His expertise is reflected in his role on the steering committee for the Australian Functional Genomics Network. Dr Palpant has given seminars and presentations throughout Australia, USA, Europe, Singapore, China, and Japan. He reviews for journals including Science, Nature Methods, Cell Stem Cell, and JCI Insights.

Qualifications

  • Doctor of Philosophy, University of Michigan

Publications

  • Journal Article: Organization of gene programs revealed by unsupervised analysis of diverse gene–trait associations

    Mizikovsky, Dalia, Naval Sanchez, Marina, Nefzger, Christian M, Cuellar Partida, Gabriel and Palpant, Nathan J (2022). Organization of gene programs revealed by unsupervised analysis of diverse gene–trait associations. Nucleic Acids Research, 50 (15) e87, 1-12. doi: 10.1093/nar/gkac413

  • Journal Article: Integrating single-cell genomics pipelines to discover mechanisms of stem cell differentiation

    Shen, Sophie, Sun, Yuliangzi, Matsumoto, Maika, Shim, Woo Jun, Sinniah, Enakshi, Wilson, Sean B., Werner, Tessa, Wu, Zhixuan, Bradford, Stephen T., Hudson, James, Little, Melissa H., Powell, Joseph, Nguyen, Quan and Palpant, Nathan J. (2021). Integrating single-cell genomics pipelines to discover mechanisms of stem cell differentiation. Trends in Molecular Medicine, 27 (12), 1135-1158. doi: 10.1016/j.molmed.2021.09.006

  • Journal Article: Therapeutic inhibition of acid sensing ion channel 1a recovers heart function after ischemia-reperfusion injury

    Redd, Meredith A., Scheuer, Sarah E., Saez, Natalie J., Yoshikawa, Yusuke, Chiu, Han Sheng, Gao, Ling, Hicks, Mark, Villanueva, Jeanette E., Joshi, Yashutosh, Chow, Chun Yuen, Cuellar-Partida, Gabriel, Peart, Jason N., See Hoe, Louise E., Chen, Xiaoli, Sun, Yuliangzi, Suen, Jacky Y., Hatch, Robert J., Rollo, Ben, Xiao, Di, Alzubaidi, Mubarak A.H., Maljevic, Snezana, Quaife-Ryan, Gregory A., Hudson, James E., Porrello, Enzo R., White, Melanie Y., Cordwell, Stuart J., Fraser, John F., Petrou, Steven, Reichelt, Melissa E. ... Palpant, Nathan J. (2021). Therapeutic inhibition of acid sensing ion channel 1a recovers heart function after ischemia-reperfusion injury. Circulation, 144 (12), 947-960. doi: 10.1161/circulationaha.121.054360

  • Journal Article: scGPS: determining cell states and global fate potential of subpopulations

    Thompson, Michael, Matsumoto, Maika, Ma, Tianqi, Senabouth, Anne, Palpant, Nathan J., Powell, Joseph E. and Nguyen, Quan (2021). scGPS: determining cell states and global fate potential of subpopulations. Frontiers in Genetics, 12 666771, 666771. doi: 10.3389/fgene.2021.666771

  • Journal Article: Single cell eQTL analysis identifies cell type-specific genetic control of gene expression in fibroblasts and reprogrammed induced pluripotent stem cells

    Neavin, Drew, Nguyen, Quan, Daniszewski, Maciej S., Liang, Helena H., Chiu, Han Sheng, Wee, Yong Kiat, Senabouth, Anne, Lukowski, Samuel W., Crombie, Duncan E., Lidgerwood, Grace E., Hernández, Damián, Vickers, James C., Cook, Anthony L., Palpant, Nathan J., Pébay, Alice, Hewitt, Alex W. and Powell, Joseph E. (2021). Single cell eQTL analysis identifies cell type-specific genetic control of gene expression in fibroblasts and reprogrammed induced pluripotent stem cells. Genome Biology, 22 (1) 76, 1-19. doi: 10.1186/s13059-021-02293-3

  • Journal Article: Conserved epigenetic regulatory logic infers genes governing cell identity

    Shim, Woo Jun, Sinniah, Enakshi, Xu, Jun, Vitrinel, Burcu, Alexanian, Michael, Andreoletti, Gaia, Shen, Sophie, Sun, Yuliangzi, Balderson, Brad, Boix, Carles, Peng, Guangdun, Jing, Naihe, Wang, Yuliang, Kellis, Manolis, Tam, Patrick P L, Smith, Aaron, Piper, Michael, Christiaen, Lionel, Nguyen, Quan, Bodén, Mikael and Palpant, Nathan J. (2020). Conserved epigenetic regulatory logic infers genes governing cell identity. Cell Systems, 11 (6), 625-639.e13. doi: 10.1016/j.cels.2020.11.001

  • Journal Article: Genotype-free demultiplexing of pooled single-cell RNA-seq

    Xu, Jun, Falconer, Caitlin, Nguyen, Quan, Crawford, Joanna, McKinnon, Brett D., Mortlock, Sally, Senabouth, Anne, Andersen, Stacey, Chiu, Han Sheng, Jiang, Longda, Palpant, Nathan J., Yang, Jian, Mueller, Michael D., Hewitt, Alex W., Pébay, Alice, Montgomery, Grant W., Powell, Joseph E. and Coin, Lachlan J. M. (2019). Genotype-free demultiplexing of pooled single-cell RNA-seq. Genome Biology, 20 (1) 290, 290. doi: 10.1186/s13059-019-1852-7

  • Journal Article: Single-cell transcriptomic analysis of cardiac differentiation from human PSCs reveals HOPX-dependent cardiomyocyte maturation

    Friedman, Clayton E., Nguyen, Quan, Lukowski, Samuel W., Helfer, Abbigail, Chiu, Han Sheng, Miklas, Jason, Levy, Shiri, Suo, Shengbao, Han, Jing-Dong Jackie, Osteil, Pierre, Peng, Guangdun, Jing, Naihe, Baillie, Greg J., Senabouth, Anne, Christ, Angelika N., Bruxner, Timothy J., Murry, Charles E., Wong, Emily S., Ding, Jun, Wang, Yuliang, Hudson, James, Ruohola-Baker, Hannele, Bar-Joseph, Ziv, Tam, Patrick P.L., Powell, Joseph E. and Palpant, Nathan J. (2018). Single-cell transcriptomic analysis of cardiac differentiation from human PSCs reveals HOPX-dependent cardiomyocyte maturation. Cell Stem Cell, 23 (4), 586-598. doi: 10.1016/j.stem.2018.09.009

  • Journal Article: Single-cell RNA-seq of human induced pluripotent stem cells reveals cellular heterogeneity and cell state transitions between subpopulations

    Nguyen, Quan H., Lukowski, Samuel W., Chiu, Han Sheng, Senabouth, Anne, Bruxner, Timothy J.C., Christ, Angelika N., Palpant, Nathan J. and Powell, Joseph E. (2018). Single-cell RNA-seq of human induced pluripotent stem cells reveals cellular heterogeneity and cell state transitions between subpopulations. Genome Research, 28 (7), 1053-1066. doi: 10.1101/gr.223925.117

  • Conference Publication: Genetic networks modulating cell fate specification and contributing to cardiac disease risk in hiPSC-derived cardiomyocytes at single cell resolution

    Nguyen, Quan H., Lukowski, Samuel W., Chiu, Han S., Friedman, Clayton E., Senabouth, Anne, Crowhurst, Liam, Bruxner, Timothy J. C., Christ, Angelika N., Hudson, James, Ding, Jun, Bar-Joseph, Ziv, Tam, Patrick P. L., Palpant, Nathan J. and Powell, Joseph E. (2018). Genetic networks modulating cell fate specification and contributing to cardiac disease risk in hiPSC-derived cardiomyocytes at single cell resolution. Human Genome Meeting 2018, Yokohama, Japan, 12-15 March 2018. London, United Kingdom: Henry Stewart Publications LLP. doi: 10.1186/s40246-018-0138-6

  • Journal Article: Generating high-purity cardiac and endothelial derivatives from patterned mesoderm using human pluripotent stem cells

    Palpant, Nathan J., Pabon, Lil, Friedman, Clayton E., Roberts, Meredith, Hadland, Brandon, Zaunbrecher, Rebecca J., Bernstein, Irwin, Zheng, Ying and Murry, Charles E. (2017). Generating high-purity cardiac and endothelial derivatives from patterned mesoderm using human pluripotent stem cells. Nature Protocols, 12 (1), 15-31. doi: 10.1038/nprot.2016.153

  • Journal Article: Human embryonic-stem-cell-derived cardiomyocytes regenerate non-human primate hearts

    Chong, James J. H., Yang, Xiulan, Don, Creighton W., Minami, Elina, Liu, Yen-Wen, Weyers, Jill J., Mahoney, William M., Van Biber, Benjamin, Cook, Savannah M., Palpant, Nathan J., Gantz, Jay A., Fugate, James A., Muskheli, Veronica, Gough, G. Michael, Vogel, Keith W., Astley, Cliff A., Hotchkiss, Charlotte E., Baldessari, Audrey, Pabon, Lil, Reinecke, Hans, Gill, Edward A., Nelson, Veronica, Kiem, Hans-Peter, Laflamme, Michael A. and Murry, Charles E. (2014). Human embryonic-stem-cell-derived cardiomyocytes regenerate non-human primate hearts. Nature, 510 (7504), 273-277. doi: 10.1038/nature13233

  • Journal Article: Human ES-cell-derived cardiomyocytes electrically couple and suppress arrhythmias in injured hearts

    Shiba, Yuji, Fernandes, Sarah, Zhu, Wei-Zhong, Filice, Dominic, Muskheli, Veronica, Kim, Jonathan, Palpant, Nathan J., Gantz, Jay, Moyes, Kara W., Reinecke, Hans, Van Biber, Benjamin, Dardas, Todd, Mignone, John L., Izawa, Atsushi, Hanna, Ramy, Viswanathan, Mohan, Gold, Joseph D., Kotlikoff, Michael I., Sarvazyan, Narine, Kay, Matthew W., Murry, Charles E. and Laflamme, Michael A. (2012). Human ES-cell-derived cardiomyocytes electrically couple and suppress arrhythmias in injured hearts. Nature, 489 (7415), 322-325. doi: 10.1038/nature11317

View all Publications

Grants

View all Grants

Supervision

View all Supervision

Available Projects

  • Projects in Stem Cell Biology, Genomics, Cardiovascular Development, and Cell Therapeutics

    As outlined in the research interests of my lab, there are numerous projects available for students covering a range of topics. These projects are continuously changing. The following areas cover topics I use to develop projects for incoming students:

    - Use stem cells, genome engineering, and single cell RNA-sequencing to study how cells differentiate into cell types of the heart

    - Modify stem cells to generate cells with custom engineered functions to create synthetic cell states

    - Use bioinformatics approaches to analyse large scale genomic data to study what features of the genome control cell decisions

    - Study novel genes that control how heart cells respond to stress like ischemia and work with chemists to develop novel drugs that could be used to treat patients who have heart attacks

    - Use computational genomics and cell biology approaches to study how the heart adapts to extreme environments (like high altitude) to learn what genes control stress responses in cells.

    - Study the biology of how venoms of marine and terrestrial species impact heart function using cells, whole organ models, and animal models.

    Contact me for a discussion about current opportunities and specific projects available.

View all Available Projects

Publications

Featured Publications

  • Organization of gene programs revealed by unsupervised analysis of diverse gene–trait associations

    Mizikovsky, Dalia, Naval Sanchez, Marina, Nefzger, Christian M, Cuellar Partida, Gabriel and Palpant, Nathan J (2022). Organization of gene programs revealed by unsupervised analysis of diverse gene–trait associations. Nucleic Acids Research, 50 (15) e87, 1-12. doi: 10.1093/nar/gkac413

  • Integrating single-cell genomics pipelines to discover mechanisms of stem cell differentiation

    Shen, Sophie, Sun, Yuliangzi, Matsumoto, Maika, Shim, Woo Jun, Sinniah, Enakshi, Wilson, Sean B., Werner, Tessa, Wu, Zhixuan, Bradford, Stephen T., Hudson, James, Little, Melissa H., Powell, Joseph, Nguyen, Quan and Palpant, Nathan J. (2021). Integrating single-cell genomics pipelines to discover mechanisms of stem cell differentiation. Trends in Molecular Medicine, 27 (12), 1135-1158. doi: 10.1016/j.molmed.2021.09.006

  • Therapeutic inhibition of acid sensing ion channel 1a recovers heart function after ischemia-reperfusion injury

    Redd, Meredith A., Scheuer, Sarah E., Saez, Natalie J., Yoshikawa, Yusuke, Chiu, Han Sheng, Gao, Ling, Hicks, Mark, Villanueva, Jeanette E., Joshi, Yashutosh, Chow, Chun Yuen, Cuellar-Partida, Gabriel, Peart, Jason N., See Hoe, Louise E., Chen, Xiaoli, Sun, Yuliangzi, Suen, Jacky Y., Hatch, Robert J., Rollo, Ben, Xiao, Di, Alzubaidi, Mubarak A.H., Maljevic, Snezana, Quaife-Ryan, Gregory A., Hudson, James E., Porrello, Enzo R., White, Melanie Y., Cordwell, Stuart J., Fraser, John F., Petrou, Steven, Reichelt, Melissa E. ... Palpant, Nathan J. (2021). Therapeutic inhibition of acid sensing ion channel 1a recovers heart function after ischemia-reperfusion injury. Circulation, 144 (12), 947-960. doi: 10.1161/circulationaha.121.054360

  • scGPS: determining cell states and global fate potential of subpopulations

    Thompson, Michael, Matsumoto, Maika, Ma, Tianqi, Senabouth, Anne, Palpant, Nathan J., Powell, Joseph E. and Nguyen, Quan (2021). scGPS: determining cell states and global fate potential of subpopulations. Frontiers in Genetics, 12 666771, 666771. doi: 10.3389/fgene.2021.666771

  • Single cell eQTL analysis identifies cell type-specific genetic control of gene expression in fibroblasts and reprogrammed induced pluripotent stem cells

    Neavin, Drew, Nguyen, Quan, Daniszewski, Maciej S., Liang, Helena H., Chiu, Han Sheng, Wee, Yong Kiat, Senabouth, Anne, Lukowski, Samuel W., Crombie, Duncan E., Lidgerwood, Grace E., Hernández, Damián, Vickers, James C., Cook, Anthony L., Palpant, Nathan J., Pébay, Alice, Hewitt, Alex W. and Powell, Joseph E. (2021). Single cell eQTL analysis identifies cell type-specific genetic control of gene expression in fibroblasts and reprogrammed induced pluripotent stem cells. Genome Biology, 22 (1) 76, 1-19. doi: 10.1186/s13059-021-02293-3

  • Conserved epigenetic regulatory logic infers genes governing cell identity

    Shim, Woo Jun, Sinniah, Enakshi, Xu, Jun, Vitrinel, Burcu, Alexanian, Michael, Andreoletti, Gaia, Shen, Sophie, Sun, Yuliangzi, Balderson, Brad, Boix, Carles, Peng, Guangdun, Jing, Naihe, Wang, Yuliang, Kellis, Manolis, Tam, Patrick P L, Smith, Aaron, Piper, Michael, Christiaen, Lionel, Nguyen, Quan, Bodén, Mikael and Palpant, Nathan J. (2020). Conserved epigenetic regulatory logic infers genes governing cell identity. Cell Systems, 11 (6), 625-639.e13. doi: 10.1016/j.cels.2020.11.001

  • Genotype-free demultiplexing of pooled single-cell RNA-seq

    Xu, Jun, Falconer, Caitlin, Nguyen, Quan, Crawford, Joanna, McKinnon, Brett D., Mortlock, Sally, Senabouth, Anne, Andersen, Stacey, Chiu, Han Sheng, Jiang, Longda, Palpant, Nathan J., Yang, Jian, Mueller, Michael D., Hewitt, Alex W., Pébay, Alice, Montgomery, Grant W., Powell, Joseph E. and Coin, Lachlan J. M. (2019). Genotype-free demultiplexing of pooled single-cell RNA-seq. Genome Biology, 20 (1) 290, 290. doi: 10.1186/s13059-019-1852-7

  • Single-cell transcriptomic analysis of cardiac differentiation from human PSCs reveals HOPX-dependent cardiomyocyte maturation

    Friedman, Clayton E., Nguyen, Quan, Lukowski, Samuel W., Helfer, Abbigail, Chiu, Han Sheng, Miklas, Jason, Levy, Shiri, Suo, Shengbao, Han, Jing-Dong Jackie, Osteil, Pierre, Peng, Guangdun, Jing, Naihe, Baillie, Greg J., Senabouth, Anne, Christ, Angelika N., Bruxner, Timothy J., Murry, Charles E., Wong, Emily S., Ding, Jun, Wang, Yuliang, Hudson, James, Ruohola-Baker, Hannele, Bar-Joseph, Ziv, Tam, Patrick P.L., Powell, Joseph E. and Palpant, Nathan J. (2018). Single-cell transcriptomic analysis of cardiac differentiation from human PSCs reveals HOPX-dependent cardiomyocyte maturation. Cell Stem Cell, 23 (4), 586-598. doi: 10.1016/j.stem.2018.09.009

  • Single-cell RNA-seq of human induced pluripotent stem cells reveals cellular heterogeneity and cell state transitions between subpopulations

    Nguyen, Quan H., Lukowski, Samuel W., Chiu, Han Sheng, Senabouth, Anne, Bruxner, Timothy J.C., Christ, Angelika N., Palpant, Nathan J. and Powell, Joseph E. (2018). Single-cell RNA-seq of human induced pluripotent stem cells reveals cellular heterogeneity and cell state transitions between subpopulations. Genome Research, 28 (7), 1053-1066. doi: 10.1101/gr.223925.117

  • Genetic networks modulating cell fate specification and contributing to cardiac disease risk in hiPSC-derived cardiomyocytes at single cell resolution

    Nguyen, Quan H., Lukowski, Samuel W., Chiu, Han S., Friedman, Clayton E., Senabouth, Anne, Crowhurst, Liam, Bruxner, Timothy J. C., Christ, Angelika N., Hudson, James, Ding, Jun, Bar-Joseph, Ziv, Tam, Patrick P. L., Palpant, Nathan J. and Powell, Joseph E. (2018). Genetic networks modulating cell fate specification and contributing to cardiac disease risk in hiPSC-derived cardiomyocytes at single cell resolution. Human Genome Meeting 2018, Yokohama, Japan, 12-15 March 2018. London, United Kingdom: Henry Stewart Publications LLP. doi: 10.1186/s40246-018-0138-6

  • Generating high-purity cardiac and endothelial derivatives from patterned mesoderm using human pluripotent stem cells

    Palpant, Nathan J., Pabon, Lil, Friedman, Clayton E., Roberts, Meredith, Hadland, Brandon, Zaunbrecher, Rebecca J., Bernstein, Irwin, Zheng, Ying and Murry, Charles E. (2017). Generating high-purity cardiac and endothelial derivatives from patterned mesoderm using human pluripotent stem cells. Nature Protocols, 12 (1), 15-31. doi: 10.1038/nprot.2016.153

  • Human embryonic-stem-cell-derived cardiomyocytes regenerate non-human primate hearts

    Chong, James J. H., Yang, Xiulan, Don, Creighton W., Minami, Elina, Liu, Yen-Wen, Weyers, Jill J., Mahoney, William M., Van Biber, Benjamin, Cook, Savannah M., Palpant, Nathan J., Gantz, Jay A., Fugate, James A., Muskheli, Veronica, Gough, G. Michael, Vogel, Keith W., Astley, Cliff A., Hotchkiss, Charlotte E., Baldessari, Audrey, Pabon, Lil, Reinecke, Hans, Gill, Edward A., Nelson, Veronica, Kiem, Hans-Peter, Laflamme, Michael A. and Murry, Charles E. (2014). Human embryonic-stem-cell-derived cardiomyocytes regenerate non-human primate hearts. Nature, 510 (7504), 273-277. doi: 10.1038/nature13233

  • Human ES-cell-derived cardiomyocytes electrically couple and suppress arrhythmias in injured hearts

    Shiba, Yuji, Fernandes, Sarah, Zhu, Wei-Zhong, Filice, Dominic, Muskheli, Veronica, Kim, Jonathan, Palpant, Nathan J., Gantz, Jay, Moyes, Kara W., Reinecke, Hans, Van Biber, Benjamin, Dardas, Todd, Mignone, John L., Izawa, Atsushi, Hanna, Ramy, Viswanathan, Mohan, Gold, Joseph D., Kotlikoff, Michael I., Sarvazyan, Narine, Kay, Matthew W., Murry, Charles E. and Laflamme, Michael A. (2012). Human ES-cell-derived cardiomyocytes electrically couple and suppress arrhythmias in injured hearts. Nature, 489 (7415), 322-325. doi: 10.1038/nature11317

Book

Book Chapter

  • Analysing genetic programs of cell differentiation to study cardiac cell diversification

    Wu, Zhixuan, Shen, Sophie, Sun, Yuliangzi, Werner, Tessa, Bradford, Stephen T. and Palpant, Nathan J. (2022). Analysing genetic programs of cell differentiation to study cardiac cell diversification. Advanced technologies in cardiovascular bioengineering. (pp. 125-167) edited by Jianyi Zhang and Vahid Serpooshan. Cham, Switzerland: Springer International Publishing. doi: 10.1007/978-3-030-86140-7_8

  • scIVA: single cell database and tools for interactive visualisation and analysis

    Crowhurst, Liam M., Mulay, Onkar, Palpant, Nathan and Nguyen, Quan H. (2021). scIVA: single cell database and tools for interactive visualisation and analysis. Practical guide to life science databases. (pp. 191-205) edited by Imad Abugessaisa and Takeya Kasukawa. Singapore: Springer. doi: 10.1007/978-981-16-5812-9_10

  • Methods for assessing the electromechanical integration of human pluripotent stem cell-derived cardiomyocyte grafts

    Zhu, Wei-Zhong, Filice, Dominic, Palpant, Nathan J. and Laflamme, Michael A. (2014). Methods for assessing the electromechanical integration of human pluripotent stem cell-derived cardiomyocyte grafts. Cardiac tissue engineering: methods and protocols. (pp. 229-247) edited by Radisci, Milica and Black III, Lauren D.. New York, NY United States: Springer New York. doi: 10.1007/978-1-4939-1047-2_20

  • Human dignity and the debate over early human embryos

    Palpant, Nathan J. and Holland, Suzanne (2013). Human dignity and the debate over early human embryos. Human dignity in bioethics: from worldviews to the public square. (pp. 239-263) New York, NY, United States: Routledge. doi: 10.4324/9780203075005

  • Human dignity in the throes?: An introduction to the volume

    Dilley, Stephen and Palpant, Nathan J. (2013). Human dignity in the throes?: An introduction to the volume. Human Dignity in Bioethics: From Worldviews to the Public Square. (pp. 3-18) New York, NY United States: Taylor and Francis. doi: 10.4324/9780203075005

Journal Article

Conference Publication

Grants (Administered at UQ)

PhD and MPhil Supervision

Current Supervision

  • Using genomic data and epigenetic annotations to identify genetic causes of cell differentiation

    Doctor Philosophy — Principal Advisor

    Other advisors:

  • Understanding genetic adaptation of the heart to extreme environments

    Doctor Philosophy — Principal Advisor

    Other advisors:

  • Determine the molecular basis of Wnt signaling control of heart field specification

    Doctor Philosophy — Principal Advisor

    Other advisors:

  • Single cell analysis of the developing heart

    Doctor Philosophy — Principal Advisor

    Other advisors:

  • The Role of Genetic Regulators of Cardiovascular Disease

    Doctor Philosophy — Principal Advisor

    Other advisors:

  • Cell death, inflammation, and macrophages in cardiac ischemia and metabolic disease

    Doctor Philosophy — Associate Advisor

    Other advisors:

  • Development of peptide drugs for treating stroke and heart attack

    Doctor Philosophy — Associate Advisor

    Other advisors:

  • The long-term cardiovascular complications of COVID-19

    Doctor Philosophy — Associate Advisor

    Other advisors:

  • Identifying the structure, function, and mechanism of action of cardiotoxic components in the venoms of box (Chironex fleckeri) and Irukandji (Carukia barnesi) jellyfish

    Doctor Philosophy — Associate Advisor

    Other advisors:

Completed Supervision

Possible Research Projects

Note for students: The possible research projects listed on this page may not be comprehensive or up to date. Always feel free to contact the staff for more information, and also with your own research ideas.

  • Projects in Stem Cell Biology, Genomics, Cardiovascular Development, and Cell Therapeutics

    As outlined in the research interests of my lab, there are numerous projects available for students covering a range of topics. These projects are continuously changing. The following areas cover topics I use to develop projects for incoming students:

    - Use stem cells, genome engineering, and single cell RNA-sequencing to study how cells differentiate into cell types of the heart

    - Modify stem cells to generate cells with custom engineered functions to create synthetic cell states

    - Use bioinformatics approaches to analyse large scale genomic data to study what features of the genome control cell decisions

    - Study novel genes that control how heart cells respond to stress like ischemia and work with chemists to develop novel drugs that could be used to treat patients who have heart attacks

    - Use computational genomics and cell biology approaches to study how the heart adapts to extreme environments (like high altitude) to learn what genes control stress responses in cells.

    - Study the biology of how venoms of marine and terrestrial species impact heart function using cells, whole organ models, and animal models.

    Contact me for a discussion about current opportunities and specific projects available.

This staff member is a UQ Expert for media in the following fields:

cardiovascular system, cardiovascular disease, bioengineering, heart disease, heart development, vascular development, heart regeneration, human pluripotent stem cells, genomics, genome engineering, stem cells, differentiation

They are happy to lend their expertise to your articles or broadcasts and share their research discoveries and insights with the community via media channels.

For additional assistance with story ideas, general advice and information or help with seeking further experts, please email the UQ Media Team or telephone (07) 3365 1120.

Links

ResearcherID: B-1641-2017

ORCID: 0000-0002-9334-8107

Scopus ID: 19934254600

Personal Profile: Link

Unit Links
Other Media

Related Resources

Similar Staff
Researchers in Associated Units
Fields of Research