Professor

Timothy Mercer

Email: 
Phone: 
+61 7 334 64300

Availability

Professor Timothy Mercer is:
Available for supervision

Qualifications

  • Doctor of Philosophy, The University of Queensland

Search Professor Timothy Mercer’s works on UQ eSpace

97 works between 2007 and 2025
All (97) Journal Article (91) Conference Publication (5) Other Outputs (1)

41 - 60 of 97 works

2018

Journal Article

Synthetic microbe communities provide internal reference standards for metagenome sequencing and analysis

Hardwick, Simon A., Chen, Wendy Y., Wong, Ted, Kanakamedala, Bindu S., Deveson, Ira W., Ongley, Sarah E., Santini, Nadia S., Marcellin, Esteban, Smith, Martin A., Nielsen, Lars K., Lovelock, Catherine E., Neilan, Brett A. and Mercer, Tim R. (2018). Synthetic microbe communities provide internal reference standards for metagenome sequencing and analysis. Nature Communications, 9 (1) 3096, 3096. doi: 10.1038/s41467-018-05555-0

Synthetic microbe communities provide internal reference standards for metagenome sequencing and analysis

2018

Journal Article

Machine learning annotation of human branchpoints

Signal, Bethany, Gloss, Brian S., Dinger, Marcel E. and Mercer, Tim R. (2018). Machine learning annotation of human branchpoints. Bioinformatics, 34 (6), 920-927. doi: 10.1093/bioinformatics/btx688

Machine learning annotation of human branchpoints

2018

Journal Article

Universal Alternative Splicing of Noncoding Exons

Deveson, Ira W., Brunck, Marion E., Blackburn, James, Tseng, Elizabeth, Hon, Ting, Clark, Tyson A., Clark, Michael B., Crawford, Joanna, Dinger, Marcel E., Nielsen, Lars K., Mattick, John S. and Mercer, Tim R. (2018). Universal Alternative Splicing of Noncoding Exons. Cell Systems, 6 (2), 245-255. doi: 10.1016/j.cels.2017.12.005

Universal Alternative Splicing of Noncoding Exons

2017

Journal Article

Intergenic disease-associated regions are abundant in novel transcripts

Bartonicek, N., Clark, M. B., Quek, X. C., Torpy, J. R., Pritchard, A. L., Maag, J. L. V., Gloss, B. S., Crawford, J., Taft, R. J., Hayward, N. K., Montgomery, G. W., Mattick, J. S., Mercer, T. R. and Dinger, M. E. (2017). Intergenic disease-associated regions are abundant in novel transcripts. Genome biology, 18 (241) 241, 241. doi: 10.1186/s13059-017-1363-3

Intergenic disease-associated regions are abundant in novel transcripts

2017

Journal Article

Phosphoproteomic profiling reveals ALK and MET as novel actionable targets across synovial sarcoma subtypes

Fleuren, Emmy D. G., Vlenterie, Myrella, Van Der Graaf, Winette T. A., Hillebrandt-Roeffen, Melissa H. S., Blackburn, James, Ma, Xiuquan, Chan, Howard, Magias, Mandy C., Van Erp, Anke, Van Houdt, Laurens, Cebeci, Sabri A. S., Van De Ven, Amy, Flucke, Uta E., Heyer, Erin E., Thomas, David M., Lord, Christopher J., Marini, Kieren D., Vaghjiani, Vijesh, Mercer, Tim R., Cain, Jason E., Wu, Jianmin, Versleijen-Jonkers, Yvonne M. H. and Daly, Roger J. (2017). Phosphoproteomic profiling reveals ALK and MET as novel actionable targets across synovial sarcoma subtypes. Cancer Research, 77 (16), 4279-4292. doi: 10.1158/0008-5472.CAN-16-2550

Phosphoproteomic profiling reveals ALK and MET as novel actionable targets across synovial sarcoma subtypes

2017

Journal Article

Long noncoding RNAs CUPID1 and CUPID2 mediate breast cancer risk at 11q13 by modulating the response to DNA damage

Betts, Joshua A., Moradi Marjaneh, Mahdi, Al-Ejeh, Fares, Lim, Yi Chieh, Shi, Wei, Sivakumaran, Haran, Tropee, Romain, Patch, Ann.-Marie, Clark, Michael B., Bartonicek, Nenad, Wiegmans, Adrian P., Hillman, Kristine M., Kaufmann, Susanne, Bain, Amanda L., Gloss, Brian S., Crawford, Joanna, Kazakoff, Stephen, Wani, Shivangi, Wen Shu W., Day, Bryan, Moller, Andreas, Cloonan, Nicole, Pearson,John, Brown, Melissa A., Mercer, Timothy R., Waddell, Nicola, Khanna, Kum Kum, Dray, Eloise, Dinger, Marcel E. ... French, Juliet D. (2017). Long noncoding RNAs CUPID1 and CUPID2 mediate breast cancer risk at 11q13 by modulating the response to DNA damage. American Journal of Human Genetics, 101 (2), 255-266. doi: 10.1016/j.ajhg.2017.07.007

Long noncoding RNAs CUPID1 and CUPID2 mediate breast cancer risk at 11q13 by modulating the response to DNA damage

2017

Journal Article

Reference standards for next-generation sequencing

Hardwick, Simon A., Deveson, Ira W. and Mercer, Tim R. (2017). Reference standards for next-generation sequencing. Nature Reviews Genetics, 18 (8), 473-484. doi: 10.1038/nrg.2017.44

Reference standards for next-generation sequencing

2017

Journal Article

The dimensions, dynamics, and relevance of the mammalian noncoding transcriptome

Deveson, Ira W., Hardwick, Simon A., Mercer, Tim R. and Mattick, John S. (2017). The dimensions, dynamics, and relevance of the mammalian noncoding transcriptome. Trends in Genetics, 33 (7), 464-478. doi: 10.1016/j.tig.2017.04.004

The dimensions, dynamics, and relevance of the mammalian noncoding transcriptome

2017

Journal Article

ANAQUIN: a software toolkit for the analysis of spike-in controls for next generation sequencing

Wong, Ted, Deveson, Ira W., Hardwick, Simon A. and Mercer, Tim R. (2017). ANAQUIN: a software toolkit for the analysis of spike-in controls for next generation sequencing. Bioinformatics, 33 (11), 1723-1724. doi: 10.1093/bioinformatics/btx038

ANAQUIN: a software toolkit for the analysis of spike-in controls for next generation sequencing

2016

Journal Article

Spliced synthetic genes as internal controls in RNA sequencing experiments

Hardwick, Simon A., Chen, Wendy Y., Wong, Ted, Deveson, Ira W., Blackburn, James, Andersen, Stacey B., Nielsen, Lars K., Mattick, John S. and Mercer, Tim R. (2016). Spliced synthetic genes as internal controls in RNA sequencing experiments. Nature Methods, 13 (9), 792-798. doi: 10.1038/nmeth.3958

Spliced synthetic genes as internal controls in RNA sequencing experiments

2016

Journal Article

Representing genetic variation with synthetic DNA standards

Deveson, Ira W., Chen, Wendy Y., Wong, Ted, Hardwick, Simon A., Andersen, Stacey B., Nielsen, Lars K., Mattick, John S. and Mercer, Tim R. (2016). Representing genetic variation with synthetic DNA standards. Nature Methods, 13 (9), 784-791. doi: 10.1038/nmeth.3957

Representing genetic variation with synthetic DNA standards

2016

Journal Article

Improved definition of the mouse transcriptome via targeted RNA sequencing

Bussotti, Giovanni, Leonardi, Tommaso, Clark, Michael B., Mercer, Tim R., Crawford, Joanna, Malquori, Lorenzo, Notredame, Cedric, Dinger, Marcel E., Mattick, John S. and Enright, Anton J. (2016). Improved definition of the mouse transcriptome via targeted RNA sequencing. Genome Research, 26 (5), 705-716. doi: 10.1101/gr.199760.115

Improved definition of the mouse transcriptome via targeted RNA sequencing

2015

Journal Article

Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing

Clark, Michael B., Mercer, Tim R., Bussotti, Giovanni, Leonardi, Tommaso, Haynes, Katelin R., Crawford, Joanna, Brunck, Marion E., Cao, Kim-Anh Le, Thomas, Gethin P., Chen, Wendy Y., Taft, Ryan J., Nielsen, Lars K., Enright, Anton J., Mattick, John S. and Dinger, Marcel E. (2015). Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing. Nature Methods, 12 (4), 339-342. doi: 10.1038/nmeth.3321

Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing

2015

Journal Article

Integrative analysis of 111 reference human epigenomes

Roadmap Epigenomics Consortium, Kundaje, Anshul, Meuleman, Wouter, Ernst, Jason, Bilenky, Misha, Yen, Angela, Heravi-Moussavi, Alireza, Kheradpour, Pouya, Zhang, Zhizhuo, Wang, Jianrong, Ziller, Michael J., Amin, Viren, Whitaker, John W., Schultz, Matthew D., Ward, Lucas D., Sarkar, Abhishek, Quon, Gerald, Sandstrom, Richard S., Eaton, Matthew L., Wu, Yi-Chieh, Pfenning, Andreas R., Wang, Xinchen, Claussnitzer, Melina, Liu, Yaping, Coarfa, Cristian, Harris, R. Alan, Shoresh, Noam, Epstein, Charles B., Gjoneska, Elizabeta ... Kellis, Manolis (2015). Integrative analysis of 111 reference human epigenomes. Nature, 518 (7539), 317-330. doi: 10.1038/nature14248

Integrative analysis of 111 reference human epigenomes

2015

Journal Article

Genome-wide discovery of human splicing branchpoints

Mercer, Tim R., Clark, Michael B., Anderson, Stacey B., Brunck, Marion E., Haerty, Wilifried, Crawford, Joanna, Taft, Ryan J., Nielsen, Lars K., Dinger, Marcel E. and Mattick, John S. (2015). Genome-wide discovery of human splicing branchpoints. Genome Research, 25 (2), 290-303. doi: 10.1101/gr.182899.114

Genome-wide discovery of human splicing branchpoints

2014

Journal Article

Extracellular vesicles from neural stem cells transfer IFN-γ via Ifngr1 to activate Stat1 signaling in target cells

Cossetti, Chiara, Iraci, Nunzio, Mercer, Tim R., Leonardi, Tommaso, Alpi, Emanuele, Drago, Denise, Alfaro-Cervello, Clara, Siani, Harpreet K., Davis, Matthew P., Schaeffer, Julia, Vega, Beatriz, Stefanini, Matilde, Zhao, CongJian, Muller, Werner, Garcia-Verdugo, Jose Manuel, Mathivanan, Suresh, Bachi, Angela, Enright, Anton J., Mattick, John S. and Pluchino, Stefano (2014). Extracellular vesicles from neural stem cells transfer IFN-γ via Ifngr1 to activate Stat1 signaling in target cells. Molecular Cell, 56 (2), 193-204. doi: 10.1016/j.molcel.2014.08.020

Extracellular vesicles from neural stem cells transfer IFN-γ via Ifngr1 to activate Stat1 signaling in target cells

2014

Journal Article

Targeted sequencing for gene discovery and quantification using RNA CaptureSeq

Mercer, Tim R., Clark, Michael B., Crawford, Joanna, Brunck, Marion E., Gerhardt, Daniel J., Taft, Ryan J., Nielsen, Lars K., Dinger, Marcel E. and Mattick, John S. (2014). Targeted sequencing for gene discovery and quantification using RNA CaptureSeq. Nature Protocols, 9 (5), 989-1009. doi: 10.1038/nprot.2014.058

Targeted sequencing for gene discovery and quantification using RNA CaptureSeq

2013

Journal Article

Re-annotation of the Saccharopolyspora erythraea genome using a systems biology approach

Marcellin, Esteban, Licona-Cassani, Cuauhtemoc, Mercer, Tim R., Palfreyman, Robin W. and Nielsen, Lars K. (2013). Re-annotation of the Saccharopolyspora erythraea genome using a systems biology approach. BMC Genomics, 14: Provisional (699) 699, 1-18. doi: 10.1186/1471-2164-14-699

Re-annotation of the Saccharopolyspora erythraea genome using a systems biology approach

2013

Journal Article

DNase I-hypersensitive exons colocalize with promoters and distal regulatory elements

Mercer, Tim R., Edwards, Stacey L., Clark, Michael B., Neph, Shane J., Wang, Hao, Stergachis, Andrew B., John, Sam, Sandstrom, Richard, Li, Guoliang, Sandhu, Kuljeet S., Ruan, Yijun, Nielsen, Lars K., Mattick, John S. and Stamatoyannopoulos, John A. (2013). DNase I-hypersensitive exons colocalize with promoters and distal regulatory elements. Nature Genetics, 45 (8), 852-859. doi: 10.1038/ng.2677

DNase I-hypersensitive exons colocalize with promoters and distal regulatory elements

2013

Journal Article

Understanding the regulatory and transcriptional complexity of the genome through structure

Mercer, Tim R. and Mattick, John S. (2013). Understanding the regulatory and transcriptional complexity of the genome through structure. Genome Research, 23 (7), 1081-1088. doi: 10.1101/gr.156612.113

Understanding the regulatory and transcriptional complexity of the genome through structure

Current funding

  • 2025 - 2028
    Improving Quality Control of mRNA Manufacture with Nanopore Sequencing
    ARC Linkage Projects
    Open grant
  • 2024 - 2029
    Building mRNA Cancer Vaccines for Australia.
    MRFF - National Critical Infrastructure Initiative
    Open grant
  • 2023 - 2028
    Translational ecosystem for clinical development of mRNA modalities (externally led by Southern RNA)
    Southern RNA PTY LTD
    Open grant
  • 2023 - 2025
    Base - NCRIS 2022 (administered by the Therapeutic Innovation Australia (TIA))
    Therapeutic Innovation Australia Limited
    Open grant
  • 2023 - 2028
    Building the next mRNA vaccines and therapies
    MRFF - National Critical Infrastructure Initiative
    Open grant
  • 2023 - 2027
    Building RNA therapies to re-program gene expression.
    NHMRC Investigator Grants
    Open grant

Past funding

  • 2024
    Conjugation of targeting protein moieties to non-viral vectors such as lipid nanoparticles (LNPs) (University College London administered UKRI BBSRC grant)
    University College London
    Open grant
  • 2023 - 2024
    Optimisation of mRNA production and purification using the AMBR15 and AMBRCF
    Innovation Connections
    Open grant
  • 2022 - 2024
    Building Synthetic DNA Controls for Oxford Nanopore Sequencing
    NHMRC Development Grant
    Open grant
  • 2011 - 2012
    Receptor-specific targeting of extracellular RNA to recipient cells
    UQ Early Career Researcher
    Open grant

Availability

Professor Timothy Mercer is:
Available for supervision

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Supervision history

Current supervision

Completed supervision

Enquiries

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