Associate Professor Timothy Mercer
Principal Research Fellow and GL
Australian Institute for Bioengineering and Nanotechnology
| Featured projects | Duration |
|---|---|
|
Using nanopore sequencing to test mRNA vaccine quality. Genome Innovation Hub Collaborative Project (UQ infrastructure) |
2022 |
Journal Articles
Gong, Binsheng, Li, Dan, Labaj, Pawel P., Pan, Bohu, Novoradovskaya, Natalia, Thierry-Mieg, Danielle, Thierry-Mieg, Jean, Chen, Guangchun, Bergstrom Lucas, Anne, Lococo, Jennifer S., Richmond, Todd A., Tseng, Elizabeth, Kusko, Rebecca, Happe, Scott, Mercer, Timothy R., Pabon-Pena, Carlos, Salmans, Michael, Tilgner, Hagen U., Xiao, Wenzhong, Johann, Donald J., Jones, Wendell, Tong, Weida, Mason, Christopher E., Kreil, David P. and Xu, Joshua (2024). Targeted DNA-seq and RNA-seq of reference samples with short-read and long-read sequencing. Scientific Data, 11 (1) 892. doi: 10.1038/s41597-024-03741-y
Signal, Brandon, Phipps, Andrew J., Giles, Katherine A., Huskins, Shannon N., Mercer, Timothy R., Robinson, Mark D., Woodhouse, Adele and Taberlay, Phillippa C. (2024). Ageing-Related Changes to H3K4me3, H3K27ac, and H3K27me3 in Purified Mouse Neurons. Cells, 13 (16) 1393, 1393. doi: 10.3390/cells13161393
Gunter, Helen M., Youlten, Scott E., Reis, Andre L. M., McCubbin, Tim, Madala, Bindu Swapna, Wong, Ted, Stevanovski, Igor, Cipponi, Arcadi, Deveson, Ira W., Santini, Nadia S., Kummerfeld, Sarah, Croucher, Peter I., Marcellin, Esteban and Mercer, Tim R. (2024). A universal molecular control for DNA, mRNA and protein expression. Nature Communications, 15 (1) 2480, 1-13. doi: 10.1038/s41467-024-46456-9
Williams, Thomas C., Kroukamp, Heinrich, Xu, Xin, Wightman, Elizabeth L. I., Llorente, Briardo, Borneman, Anthony R., Carpenter, Alexander C., Van Wyk, Niel, Meier, Felix, Collier, Thomas R. V., Espinosa, Monica I., Daniel, Elizabeth L., Walker, Roy S. K., Cai, Yizhi, Nevalainen, Helena K. M., Curach, Natalie C., Deveson, Ira W., Mercer, Timothy R., Johnson, Daniel L., Mitchell, Leslie A., Bader, Joel S., Stracquadanio, Giovanni, Boeke, Jef D., Goold, Hugh D., Pretorius, Isak S. and Paulsen, Ian T. (2023). Parallel laboratory evolution and rational debugging reveal genomic plasticity to S. cerevisiae synthetic chromosome XIV defects. Cell Genomics, 3 (11) 100379, 1-23. doi: 10.1016/j.xgen.2023.100379
Gunter, Helen M., Idrisoglu, Senel, Singh, Swati, Han, Dae Jong, Ariens, Emily, Peters, Jonathan R., Wong, Ted, Cheetham, Seth W., Xu, Jun, Rai, Subash Kumar, Feldman, Robert, Herbert, Andy, Marcellin, Esteban, Tropee, Romain, Munro, Trent and Mercer, Tim R. (2023). mRNA vaccine quality analysis using RNA sequencing. Nature Communications, 14 (1) 5663, 1-12. doi: 10.1038/s41467-023-41354-y
Mattick, John S., Amaral, Paulo P., Carninci, Piero, Carpenter, Susan, Chang, Howard Y., Chen, Ling-Ling, Chen, Runsheng, Dean, Caroline, Dinger, Marcel E., Fitzgerald, Katherine A., Gingeras, Thomas R., Guttman, Mitchell, Hirose, Tetsuro, Huarte, Maite, Johnson, Rory, Kanduri, Chandrasekhar, Kapranov, Philipp, Lawrence, Jeanne B., Lee, Jeannie T., Mendell, Joshua T., Mercer, Timothy R., Moore, Kathryn J., Nakagawa, Shinichi, Rinn, John L., Spector, David L., Ulitsky, Igor, Wan, Yue, Wilusz, Jeremy E. and Wu, Mian (2023). Long non-coding RNAs: definitions, functions, challenges and recommendations. Nature Reviews Molecular Cell Biology, 24 (6), 430-447. doi: 10.1038/s41580-022-00566-8
Canson, Daffodil M., Dumenil, Troy, Parsons, Michael T., O'Mara, Tracy A., Davidson, Aimee L., Okano, Satomi, Signal, Bethany, Mercer, Tim R., Glubb, Dylan M. and Spurdle, Amanda B. (2023). Erratum: The splicing effect of variants at branchpoint elements in cancer genes (Genetics in Medicine (2022) 24(2) (398–409), (S109836002105348X), (10.1016/j.gim.2021.09.020)). Genetics in Medicine, 25 (1), 166-166. doi: 10.1016/j.gim.2022.11.015
Navone, Laura, Moffitt, Kaylee, Johnston, Wayne A., Mercer, Tim, Cooper, Crystal, Spann, Kirsten and Speight, Robert E. (2022). Bioengineered textiles with peptide binders that capture SARS-CoV-2 viral particles. Communications Materials, 3 (1) 54, 1-9. doi: 10.1038/s43246-022-00278-8
Mercer, Tim, Almond, Neil, Crone, Michael A., Chain, Patrick S. G., Deshpande, Alina, Eveleigh, Deepa, Freemont, Paul, Fuchs, Sebastien, Garlick, Russell, Huggett, Jim, Kammel, Martin, Li, Po-E, Milavec, Mojca, Marlowe, Elizabeth M., O’Sullivan, Denise M., Page, Mark, Pestano, Gary A., Suliman, Sara, Simen, Birgitte, Sninsky, John J., Sopchak, Lynne, Tato, Cristina M., Vallone, Peter M., Vandesompele, Jo, White, Thomas J., Zeichhardt, Heinz and Salit, Marc (2022). The Coronavirus Standards Working Group’s roadmap for improved population testing. Nature Biotechnology, 40 (11), 1563-1568. doi: 10.1038/s41587-022-01538-1
Gunter, Helen M., Youlten, Scott E., Madala, Bindu Swapna, Reis, Andre L. M., Stevanovski, Igor, Wong, Ted, Kummerfield, Sarah K., Deveson, Ira W., Santini, Nadia S., Marcellin, Esteban and Mercer, Tim R. (2022). Library adaptors with integrated reference controls improve the accuracy and reliability of nanopore sequencing. Nature Communications, 13 (1) 6437, 1-11. doi: 10.1038/s41467-022-34028-8
Mercer, Tim R., Munro, Trent and Mattick, John S. (2022). The potential of long noncoding RNA therapies. Trends in Pharmacological Sciences, 43 (4), 269-280. doi: 10.1016/j.tips.2022.01.008
Wei, Wei, Zhao, Qiongyi, Wang, Ziqi, Liau, Wei-Siang, Basic, Dean, Ren, Haobin, Marshall, Paul R., Zajaczkowski, Esmi L., Leighton, Laura J., Madugalle, Sachithrani U., Musgrove, Mason, Periyakaruppiah, Ambika, Shi, Jichun, Zhang, Jianjian, Mattick, John S., Mercer, Timothy R., Spitale, Robert C., Li, Xiang and Bredy, Timothy W. (2022). ADRAM is an experience-dependent long noncoding RNA that drives fear extinction through a direct interaction with the chaperone protein 14-3-3. Cell Reports, 38 (12) 110546, 110546. doi: 10.1016/j.celrep.2022.110546
Liu, Zhichao, Roberts, Ruth, Mercer, Timothy R., Xu, Joshua, Sedlazeck, Fritz J. and Tong, Weida (2022). Towards accurate and reliable resolution of structural variants for clinical diagnosis. Genome Biology, 23 (1) 68, 68. doi: 10.1186/s13059-022-02636-8
Canson, Daffodil M., Dumenil, Troy, Parsons, Michael T., O'Mara, Tracy A., Davidson, Aimee L., Okano, Satomi, Signal, Bethany, Mercer, Tim R., Glubb, Dylan M. and Spurdle, Amanda B. (2022). The splicing effect of variants at branchpoint elements in cancer genes. Genetics in Medicine, 24 (2), 398-409. doi: 10.1016/j.gim.2021.09.020
Reis, Andre L. M., Deveson, Ira W., Madala, Bindu Swapna, Wong, Ted, Barker, Chris, Xu, Joshua, Lennon, Niall, Tong, Weida, Mercer, Tim R. and on behalf of the SEQC2 Consortium (2022). Using synthetic chromosome controls to evaluate the sequencing of difficult regions within the human genome. Genome Biology, 23 (1) 19, 19. doi: 10.1186/s13059-021-02579-6
Anklam, Elke, Bahl, Martin Iain, Ball, Robert, Beger, Richard D, Cohen, Jonathan, Fitzpatrick, Suzanne, Girard, Philippe, Halamoda-Kenzaoui, Blanka, Hinton, Denise, Hirose, Akihiko, Hoeveler, Arnd, Honma, Masamitsu, Hugas, Marta, Ishida, Seichi, Kass, George EN, Kojima, Hajime, Krefting, Ira, Liachenko, Serguei, Liu, Yan, Masters, Shane, Marx, Uwe, McCarthy, Timothy, Mercer, Tim, Patri, Anil, Pelaez, Carmen, Pirmohamed, Munir, Platz, Stefan, Ribeiro, Alexandre JS, Rodricks, Joseph V ... Slikker Jr., William (2022). Emerging technologies and their impact on regulatory science. Experimental Biology and Medicine, 247 (1), 1-75. doi: 10.1177/15353702211052280
Ng, Stanley W. K., Murphy, Tracy, King, Ian, Zhang, Tong, Mah, Michelle, Lu, Zhibin, Stickle, Natalie, Ibrahimova, Narmin, Arruda, Andrea, Mitchell, Amanda, Mai, Ming, He, Rong, Madala, Bindu Swapna, Viswanatha, David S., Dick, John E., Chan, Steven M. C., Virtanen, Carl, Minden, Mark D., Mercer, Timothy R., Stockley, Tracy L. and Wang, Jean C. Y. (2021). A clinical laboratory-developed LSC17 stemness score assay for rapid risk assessment of acute myeloid leukemia patients. Blood Advances, 6 (3), 1064-1073. doi: 10.1182/bloodadvances.2021005741
Mercer, Tim R., Xu, Joshua, Mason, Christopher E. and Tong, Weida (2021). The Sequencing Quality Control 2 study: establishing community standards for sequencing in precision medicine. Genome Biology, 22 (1) 306, 306. doi: 10.1186/s13059-021-02528-3
Mirzayi, Chloe, Renson, Audrey, Furlanello, Cesare, Sansone, Susanna-Assunta, Zohra, Fatima, Elsafoury, Shaimaa, Geistlinger, Ludwig, Kasselman, Lora J., Eckenrode, Kelly, van de Wijgert, Janneke, Loughman, Amy, Marques, Francine Z., MacIntyre, David A., Arumugam, Manimozhiyan, Azhar, Rimsha, Beghini, Francesco, Bergstrom, Kirk, Bhatt, Ami, Bisanz, Jordan E., Braun, Jonathan, Bravo, Hector Corrada, Buck, Gregory A., Bushman, Frederic, Casero, David, Clarke, Gerard, Collado, Maria Carmen, Cotter, Paul D., Cryan, John F., Demmer, Ryan T. ... Massive Analysis and Quality Control Society (2021). Reporting guidelines for human microbiome research: the STORMS checklist. Nature Medicine, 27 (11), 1885-1892. doi: 10.1038/s41591-021-01552-x
Fang, Li Tai, Zhu, Bin, Zhao, Yongmei, Chen, Wanqiu, Yang, Zhaowei, Kerrigan, Liz, Langenbach, Kurt, de Mars, Maryellen, Lu, Charles, Idler, Kenneth, Jacob, Howard, Zheng, Yuanting, Ren, Luyao, Yu, Ying, Jaeger, Erich, Schroth, Gary P., Abaan, Ogan D., Talsania, Keyur, Lack, Justin, Shen, Tsai-Wei, Chen, Zhong, Stanbouly, Seta, Tran, Bao, Shetty, Jyoti, Kriga, Yuliya, Meerzaman, Daoud, Nguyen, Cu, Petitjean, Virginie, Sultan, Marc ... Zheng, Yuanting (2021). Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing. Nature Biotechnology, 39 (9), 1151-1160. doi: 10.1038/s41587-021-00993-6
Xiao, Wenming, Ren, Luyao, Chen, Zhong, Fang, Li Tai, Zhao, Yongmei, Lack, Justin, Guan, Meijian, Zhu, Bin, Jaeger, Erich, Kerrigan, Liz, Blomquist, Thomas M., Hung, Tiffany, Sultan, Marc, Idler, Kenneth, Lu, Charles, Scherer, Andreas, Kusko, Rebecca, Moos, Malcolm, Xiao, Chunlin, Sherry, Stephen T., Abaan, Ogan D., Chen, Wanqiu, Chen, Xin, Nordlund, Jessica, Liljedahl, Ulrika, Maestro, Roberta, Polano, Maurizio, Drabek, Jiri, Vojta, Petr ... Shi, Leming (2021). Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing. Nature Biotechnology, 39 (9), 1141-1150. doi: 10.1038/s41587-021-00994-5
Troskie, Robin-Lee, Jafrani, Yohaann, Mercer, Tim R., Ewing, Adam D., Faulkner, Geoffrey J. and Cheetham, Seth W. (2021). Long-read cDNA sequencing identifies functional pseudogenes in the human transcriptome. Genome Biology, 22 (1) 146, 1-15. doi: 10.1186/s13059-021-02369-0
Mercer, Tim R. and Salit, Marc (2021). Testing at scale during the COVID-19 pandemic. Nature Reviews Genetics, 22 (7), 415-426. doi: 10.1038/s41576-021-00360-w
Gong, Binsheng, Li, Dan, Kusko, Rebecca, Novoradovskaya, Natalia, Zhang, Yifan, Wang, Shangzi, Pabón-Peña, Carlos, Zhang, Zhihong, Lai, Kevin, Cai, Wanshi, LoCoco, Jennifer S., Lader, Eric, Richmond, Todd A., Mittal, Vinay K., Liu, Liang-Chun, Johann, Donald J., Willey, James C., Bushel, Pierre R., Yu, Ying, Xu, Chang, Chen, Guangchun, Burgess, Daniel, Cawley, Simon, Giorda, Kristina, Haseley, Nathan, Qiu, Fujun, Wilkins, Katherine, Arib, Hanane, Attwooll, Claire ... Xu, Joshua (2021). Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions. Genome Biology, 22 (1) 109, 1-23. doi: 10.1186/s13059-021-02315-0
Deveson, Ira W., SEQC2 Oncopanel Sequencing Working Group, Gong, Binsheng, Lai, Kevin, LoCoco, Jennifer S., Richmond, Todd A., Schageman, Jeoffrey, Zhang, Zhihong, Novoradovskaya, Natalia, Willey, James C., Jones, Wendell, Kusko, Rebecca, Chen, Guangchun, Madala, Bindu Swapna, Blackburn, James, Stevanovski, Igor, Bhandari, Ambica, Close, Devin, Conroy, Jeffrey, Hubank, Michael, Marella, Narasimha, Mieczkowski, Piotr A., Qiu, Fujun, Sebra, Robert, Stetson, Daniel, Sun, Lihyun, Szankasi, Philippe, Tan, Haowen, Tang, Lin-ya ... Xu, Joshua (2021). Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology. Nature Biotechnology, 39 (9), 1115-1128. doi: 10.1038/s41587-021-00857-z
Madala, Bindu Swapna, Reis, Andre L. M., Deveson, Ira W., Rawlinson, William and Mercer, Tim R. (2021). Chimeric synthetic reference standards enable cross-validation of positive and negative controls in SARS-CoV-2 molecular tests. Scientific Reports, 11 (1) 2636, 1-8. doi: 10.1038/s41598-021-81760-0
Willey, James C., Morrison, Thomas, Austermiller, Brad, Crawford, Erin L., Craig, Daniel J., Blomquist, Thomas M., Jones, wendell D., Wali, Aminah, Lococo, Jennifer S., Haseley, Nathan, Richmond, Todd A., Novoradovskaya, Natalia, Kusko, Rebecca, Chen, Guangchun, Li, Quan-Zhen, Johann, Don, Deveson, Ira W., Mercer, Tim, Wu, Leihong and Xu, Joshua (2021). Advancing quality-control for NGS measurement of actionable mutations in circulating tumor DNA. SSRN Electronic Journal, 1 (7) 100106. doi: 10.2139/ssrn.3830017
Canson, Daffodil, Dumenil, Troy, Parsons, Michael, O’Mara, Tracy, Davidson, Aimee , Okano, Satomi , Signal, Bethany , Mercer, Tim, Glubb, Dylan and Spurdle, Amanda (2021). The Impact of Variants at Branchpoint Splicing Elements in Cancer Genes. SSRN Electronic Journal, 24 (2), 398-409. doi: 10.2139/ssrn.3933049
Heyer, Erin E., Deveson, Ira W., Wooi, Danson, Selinger, Christina I., Lyons, Ruth J., Hayes, Vanessa M., O’Toole, Sandra A., Ballinger, Mandy L., Gill, Devinder, Thomas, David M., Mercer, Tim R. and Blackburn, James (2020). Author Correction: Diagnosis of fusion genes using targeted RNA sequencing (Nature Communications, (2019), 10, 1, (1388), 10.1038/s41467-019-09374-9). Nature Communications, 11 (1) 1810, 1810. doi: 10.1038/s41467-020-15697-9
Reis, Andre L. M., Deveson, Ira W., Wong, Ted, Madala, Bindu Swapna, Barker, Chris, Blackburn, James, Marcellin, Esteban and Mercer, Tim R. (2020). A universal and independent synthetic DNA ladder for the quantitative measurement of genomic features. Nature Communications, 11 (1) 3609, 3609. doi: 10.1038/s41467-020-17445-5
Singh, Mandeep, Jackson, Katherine J. L., Wang, Jing J., Schofield, Peter, Field, Matt A., Koppstein, David, Peters, Timothy J., Burnett, Deborah L., Rizzetto, Simone, Nevoltris, Damien, Masle-Farquhar, Etienne, Faulks, Megan L., Russell, Amanda, Gokal, Divya, Hanioka, Asami, Horikawa, Keisuke, Colella, Alexander D., Chataway, Timothy K., Blackburn, James, Mercer, Tim R., Langley, David B., Goodall, D. Margaret, Jefferis, Roy, Gangadharan Komala, Muralikrishna, Kelleher, Anthony D., Suan, Dan, Rischmueller, Maureen, Christ, Daniel, Brink, Robert ... Reed, Joanne H. (2020). Lymphoma driver mutations in the pathogenic evolution of an iconic human autoantibody. Cell, 180 (5), 878-894.e19. doi: 10.1016/j.cell.2020.01.029
Heyer, Erin E., Deveson, Ira W., Wooi, Danson, Selinger, Christina I., Lyons, Ruth J., Hayes, Vanessa M., O’Toole, Sandra A., Ballinger, Mandy L., Gill, Devinder, Thomas, David M., Mercer, Tim R. and Blackburn, James (2019). Diagnosis of fusion genes using targeted RNA sequencing. Nature Communications, 10 (1) 1388, 1-12. doi: 10.1038/s41467-019-09374-9
Deveson, Ira W., Madala, Bindu Swapna, Blackburn, James, Barker, Chris, Wong, Ted, Barton, Kirston M., Smith, Martin A., Watkins, D. Neil and Mercer, Tim R. (2019). Chiral DNA sequences as commutable controls for clinical genomics. Nature Communications, 10 (1) 1342, 1-13. doi: 10.1038/s41467-019-09272-0
Blackburn, James, Vecchiarelli, Stefano, Heyer, Erin E., Patrick, Sean M., Lyons, Ruth J., Jaratlerdsiri, Weerachai, van Zyl, Smit, Bornman, M. S. Riana, Mercer, Tim R. and Hayes, Vanessa M. (2019). TMPRSS2-ERG fusions linked to prostate cancer racial health disparities: a focus on Africa. Prostate, 79 (10), 1191-1196. doi: 10.1002/pros.23823
Blackburn, James, Wong, Ted, Madala, Bindu Swapna, Barker, Chris, Hardwick, Simon A., Reis, Andre L. M., Deveson, Ira W. and Mercer, Tim R. (2019). Use of synthetic DNA spike-in controls (sequins) for human genome sequencing. Nature Protocols, 14 (7), 2119-2151. doi: 10.1038/s41596-019-0175-1
Hardwick, Simon A., Bassett, Samuel D., Kaczorowski, Dominik, Blackburn, James, Barton, Kirston, Bartonicek, Nenad, Carswell, Shaun L., Tilgner, Hagen U., Loy, Clement, Halliday, Glenda, Mercer, Tim R., Smith, Martin A. and Mattick, John S. (2019). Targeted, high-resolution RNA sequencing of non-coding genomic regions associated with neuropsychiatric functions. Frontiers in Genetics, 10 (APR) 309. doi: 10.3389/fgene.2019.00309
Santini, Nadia S., Lovelock, Catherine E., Hua, Quan, Zawadzki, Atun, Mazumder, Debashish, Mercer, Tim R., Muñoz-Rojas, Miriam, Hardwick, Simon A., Madala, Bindu Swapna, Cornwell, William, Thomas, Torsten, Marzinelli, Ezequiel M., Adam, Paul, Paul, Swapan and Vergés, Adriana (2019). Natural and regenerated saltmarshes exhibit similar soil and belowground organic carbon stocks, root production and soil respiration. Ecosystems, 22 (8), 1803-1822. doi: 10.1007/s10021-019-00373-x
Trahair, Toby, Gifford, Andrew J., Fordham, Ashleigh, Mayoh, Chelsea, Fadia, Mitali, Lukeis, Robyn, Wood, Andrew C., Valvi, Santosh, Walker, Roderick D., Blackburn, James, Heyer, Erin E., Mercer, Tim R., Barbaric, Draga, Marshall, Glenn M. and MacKenzie, Karen L. (2019). Crizotinib and surgery for long-term disease control in children and adolescents with ALK-positive inflammatory myofibroblastic tumors. JCO Precision Oncology, 3 (3), 1-11. doi: 10.1200/PO.18.00297
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Mercer, Tim R. and Mattick, John S. (2013). Structure and function of long noncoding RNAs in epigenetic regulation. Nature Structural & Molecular Biology, 20 (3), 300-307. doi: 10.1038/nsmb.2480
Liu, Ganqiang, Mercer, Timothy R., Shearwood, Anne-Marie J., Siira, Stefan J., Hibbs, Moira E., Mattick, John S., Rackham, Oliver and Filipovska, Aleksandra (2013). Mapping of mitochondrial RNA-protein interactions by digital RNase footprinting. Cell Reports, 5 (3), 839-848. doi: 10.1016/j.celrep.2013.09.036
Marcellin, Esteban, Mercer, Tim R., Licona-Cassani, Cuauhtemoc, Palfreyman, Robin W., Dinger, Marcel E., Steen, Jennifer A., Mattick, John S. and Nielsen, Lars K. (2013). Saccharopolyspora erythraea's genome is organised in high-order transcriptional regions mediated by targeted degradation at the metabolic switch. BMC Genomics, 14 (1) 15, 15.1-15.9. doi: 10.1186/1471-2164-14-15
Cruickshank, Mark N., Karimi, Mahdad, Mason, Rhonda L., Fenwick, Emily, Mercer, Tim, Tsao, Betty P., Boackle, Susan A. and Ulgiati, Daniela (2012). Transcriptional effects of a lupus-associated polymorphism in the 5' untranslated region (UTR) of human complement receptor 2 (CR2/CD21). Molecular Immunology, 52 (3-4), 165-173. doi: 10.1016/j.molimm.2012.04.013
Rackham, Oliver, Mercer, Timothy R. and Filipovska, Aleksandra (2012). The human mitochondrial transcriptome and the RNA-binding proteins that regulate its expression. Wiley Interdisciplinary Reviews. RNA, 3 (5), 675-695. doi: 10.1002/wrna.1128
Mercer, Tim R., Gerhardt, Daniel J., Dinger, Marcel E., Crawford, Joanna, Trapnell, Cole, Jeddeloh, Jeffrey A., Mattick, John S. and Rinn, John L. (2012). Targeted RNA sequencing reveals the deep complexity of the human transcriptome. Nature Biotechnology, 30 (1), 99-104. doi: 10.1038/nbt.2024
Rackham, Oliver, Shearwood, Anne-Marie J., Mercer, Tim R., Davies, Stefan M. K., Mattick, John S. and Filipovska, Aleksandra (2011). Long noncoding RNAs are generated from the mitochondrial genome and regulated by nuclear-encoded proteins. RNA, 17 (12), 2085-2093. doi: 10.1261/rna.029405.111
Thiagarajan, Rathi D., Cloonan, Nicole, Gardiner, Brooke B., Mercer, Tim R., Kolle, Gabriel, Nourbaksh, Ehsan, Wani, Shivangi, Tang, Dave, Krishnan, Keerthana, Georgas, Kylie M., Rumballe, Bree A., Chiu, Han S., Steen, Jason A., Mattick, John S., Little, Melissa H. and Grimmond, Sean M. (2011). Refining transcriptional programs in kidney development by integration of deep RNA-sequencing and array-based spatial profiling. BMC Genomics, 12 (1) 441, 441-1-441-16. doi: 10.1186/1471-2164-12-441
Lopez Sanchez, Maria I. G., Mercer, Tim R., Davies, Stefan M. K., Shearwood, Anne-Marie J., Nygard, Karoline K. A., Richman, Tara R., Mattick, John S., Rackham, Oliver and Filipovska, Aleksandra (2011). RNA processing in human mitochondria. Cell Cycle, 10 (17), 2904-2916. doi: 10.4161/cc.10.17.17060
Mercer, Tim R., Neph, Shane, Dinger, Marcel E., Crawford, Joanna, Smith, Martin A., Shearwood, Anne-Marie J., Haugen, Eric, Bracken, Cameron P., Rackham, Oliver, Stamatoyannopoulos, John A., Filipovska, Aleksandra and Mattick, John S. (2011). The human mitochondrial transcriptome. Cell, 146 (4), 645-658. doi: 10.1016/j.cell.2011.06.051
Bracken, Cameron P., Szubert, Jan M., Mercer, Tim R., Dinger, Marcel E., Thomson, Daniel W., Mattick, John S., Michael, Michael Z. and Goodall, Gregory J. (2011). Global analysis of the mammalian RNA degradome reveals widespread miRNA-dependent and miRNA-independent endonucleolytic cleavage. Nucleic Acids Research, 39 (13), 5658-5668. doi: 10.1093/nar/gkr110
Askarian-Amiri, Marjan E., Crawford, Joanna, French, Juliet D., Smart, Chanel E., Smith, Martin A., Clark, Michael B., Ru, Kelin, Mercer, Tim R., Thompson, Ella R., Lakhani, Sunil R., Vargas, Ana C., Campbell, Ian G., Brown, Melissa A., Dinger, Marcel E. and Mattick, John S. (2011). SNORD-host RNA Zfas1 is a regulator of mammary development and a potential marker for breast cancer. RNA, 17 (5), 878-891. doi: 10.1261/rna.2528811
Mercer, Tim R., Wilhelm, Dagmar, Dinger, Marcel E., Solda, Giulia, Korbie, Darren J., Glazov, Evgeny A., Truong, Vy, Schwenke, Maren, Simons, Cas, Matthaei, Klaus I., Saint, Robert, Koopman, Peter and Mattick, John S. (2011). Expression of distinct RNAs from 3′ untranslated regions. Nucleic Acids Research, 39 (6), 2393-2403. doi: 10.1093/nar/gkq1158
Mercer, Tim R., Dinger, Marcel E., Bracken, Cameron P., Kolle, Gabriel, Szubert, Jan M., Korbie, Darren J., Askarian-Amiri, Marjan E., Gardiner, Brooke B., Goodall, Gregory J., Grimmond, Sean M. and Mattick, John S. (2010). Regulated post-transcriptional RNA cleavage diversifies the eukaryotic transcriptome. Genome Research, 20 (12), 1639-1650. doi: 10.1101/gr.112128.110
Taft, Ryan, Simons, Cas, Nahkuri, Satu, Oey, Harald, Korbie, Darren J., Mercer, Timothy R., Holst, Jeff, Ritchie, William, Wong, Justin J-L., Rasko, John E. J., Rokhsar, Daniel S., Degnan, Bernard M. and Mattick, John S. (2010). Nuclear-localized tiny RNAs are associated with transcription initiation and splice sites in metazoans. Nature Structural and Molecular Biology, 17 (8), 1030-1035. doi: 10.1038/nsmb.1841
Lai, John, Lehman, Melanie L., Dinger, Marcel E., Hendy, Stephen C., Mercer, Tim R., Seim, Inge, Lawrence, Mitchell G., Mattick, John S., Clements, Judith A. and Nelson, Colleen C. (2010). A variant of the KLK4 gene is expressed as a cis sense-antisense chimeric transcript in prostate cancer cells. RNA, 16 (6), 1156-1166. doi: 10.1261/rna.2019810
Mercer, Tim R., Qureshi, Irfan A., Gokhan, Solen, Dinger, Marcel E., Li, Guangyu, Mattick, John S. and Mehler, Mark F. (2010). Long noncoding RNAs in neuronal-glial fate specification and oligodendrocyte lineage maturation. BMC Neuroscience, 11 (1) 14, 1-15. doi: 10.1186/1471-2202-11-14
Dinger, M. E., Amaral, P. A., Mercer, T. R. and Mattick, J. S. (2009). Pervasive transcription of the eukaryotic genome: functional indices and conceptual implications. Briefings in Functional Genomics and Proteomics, 8 (6) elp038, 407-423. doi: 10.1093/bfgp/elp038
Taft, R. J., Pang, K. C., Mercer, T. R., Dinger, M and Mattick, J. S. (2009). Non-coding RNAs: regulators of disease. Journal of Pathology, 220 (2), 126-139. doi: 10.1002/path.2638
Pang, K. C., Dinger, M. E., Mercer, T. R., Malquori, L, Grimmond, S. M., Chen, W. S. and Mattick, J. S. (2009). Genome-wide identification of long noncoding RNAs in CD8(+) T cells. Journal of Immunology, 182 (12), 7738-7748. doi: 10.4049/jimmunol.0900603
Mercer, T. R., Dinger, M. E. and Mattick, J. S. (2009). Long non-coding RNAs: insights into functions. Nature Reviews Genetics, 10 (3), 155-159. doi: 10.1038/nrg2521
Dinger, M. E., Pang, K. C., Mercer, T. R., Crowe, M. L., Grimmond, S. M. and Mattick, J. S. (2009). NRED: a database of long noncoding RNA expression. Nucleic Acids Research, 37 (SUPPL. 1), D122-D126. doi: 10.1093/nar/gkn617
Mattick, J. S, Amaral, P. P., Dinger, M. E., Mercer, T. R. and Mehler, M. F. (2009). RNA regulation of epigenetic processes. BioEssays, 31 (1), 51-59. doi: 10.1002/bies.080099
Dinger, Marcel E., Pang, Ken C., Mercer, Tim R. and Mattick, John S. (2008). Differentiating protein-coding and noncoding RNA: Challenges and ambiguities. PLoS Computational Biology, 4 (11) e1000176, e1000176.1-e1000176.5. doi: 10.1371/journal.pcbi.1000176
Mercer, T. R., Dinger, M. E., Mariani J., Kosik, K . S., Mehler, M. F. and Mattick, J. S. (2008). Noncoding RNAs in long term memory formation. Neuroscientist, 14 (5), 434-445. doi: 10.1177/1073858408319187
Dinger, Marcel E., Amaral, Paulo P., Mercer, Tim R, Pang, Ken C., Bruce, Stephen J., Gardiner, Brooke B., Askarian-Amiri, Marjan E., Ru, Kelin, Solda, Giulia, Simons, Cas, Sunkin, Susan M., Crowe, Mark L., Grimmond, Sean M, Perkins, Andrew C. and Mattick, John S. (2008). Long Noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. Genome Research, 18 (9), 1433-1445. doi: 10.1101/gr.078378.108
Amaral, Paulo, Dinger, Marcel, Mattick, John, Mehler, Mark and Mercer, Tim (2008). RNA control of epigenetic processes. Australian Biochemist, 39 (2), 4-8.
Amaral, P. P., Dinger, M. E., Mercer, T. R. and Mattick, J. S. (2008). The Eukaryotic genome as an RNA machine. Science, 319 (5871), 1787-1789. doi: 10.1126/science.1155472
Dinger, M. E., Mercer, T. R. and Mattick, J. S. (2008). RNAs as extracellular signaling molecules. Journal Of Molecular Endocrinology, 40 (4), 151-159. doi: 10.1677/JME-07-0160
Mercer, T. R., Dinger, M. E., Sunkin, S. M., Mehler, M. F. and Mattick, J. S. (2008). Specific expression of long noncoding RNAs in the mouse brain. Proceedings of the National Academy of Sciences of the United States of America, 105 (2), 716-721. doi: 10.1073/pnas.0706729105
Wu, Hui, Boackle, Susan A., Hanvivadhanakul, Punchong, Ulgiati, Daniela, Grossman, Jennifer M., Lee, Youngho, Shen, Nan, Abraham, Lawrence J., Mercer, Timothy R., Park, Elly, Hebert, Lee A., Rovin, Brad H., Birmingham, Dan J., Chang, Den-Ming, Chung, Jen Chen, McCurdy, Deborah, Badsha, Humeira M., Thong, Bernard Y. H., Chng, Hiok H., Arnett, Frank C., Wallace, Daniel J., Yu, C. Yung, Hahn, Bevra H., Cantor, Rita M. and Tsao, Betty P. (2007). Association of a common complement receptor 2 haplotype with increased risk of systemic lupus erythematosus. Proceedings of the National Academy of Sciences of the United States of America, 104 (10), 3961-3966. doi: 10.1073/pnas.0609101104
Conference Papers
Leonardi, Tommaso, Cossetti, Chiara, Iraci, Nunzio, Mercer, Tim, Mattick, John and Pluchino, Stefano (2012). The inflammatory fingerprint of Neural Stem Cells. 11th International Congress of Neuroimmunology (ISNI), Boston MA., United States, 4-8 November 2012. Amsterdam, The Netherlands: Elsevier.
Cossetti, Chiara, Mercer, Tim R., Alpi, Emanuele, Leonardi, Tommaso, Drago, Denise, Iraci, Nunzio, Alfaro-Cervello, Clara, Dinger, Marcel E., Dietmann, Sabine, Crawford, Joanna, Caddeo, Carla, Garcia Verdugo, Manuel, Bachi, Angela, Mattick, John S. and Pluchino, Stefano (2012). Neural stem cells sort protein and RNA cargoes for export with exosomes in response to inflammation. 11th International Congress of Neuroimmunology (ISNI), Boston MA., United States, 4-8 November 2012. Amsterdam, The Netherlands: Elsevier.
Marcellin Saldana, Esteban Stefane, Mercer, Timothy, Licona Cassani, Cuauthemoc and Nielsen, Lars K. (2011). Building Systems biology platforms for Actinobacteria. ISBA XVI, Puerto Vallarta, Mexico, 11-15 December 2011.
Marcellin, E., Mercer, T. R., Licona, C. and Nielsen, L. K. (2011). Systems biology for industrial microorganisms. XIV Congreso Nacional de Biotecnología y Bioingeniería, Queretaro, Mexico, 19-24 June 2011.
Mercer, Tim R., Dinger, Marcel E., Wilhelm, Dagmar E., Solda, Giulia S., Koopman, Peter A. and Mattick, John S. (2009). Regulated independent expression of 3' untranslated regions in mammals. 3rd Marie Curie-Genome Architecture in Relation to Disease Meeting (MC-GARD), Edinburgh Scotland, 01-05 April 2009.
Thesis
Mercer, Timothy (2008). Expression of long noncoding RNAs during mouse development. PhD Thesis, Institute for Molecular Bioscience, The University of Queensland. doi: 10.14264/177175