The University of Queensland

A universal molecular control for DNA, mRNA and protein expression

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, 2480. doi: 10.1038/s41467-024-46456-9

Parallel laboratory evolution and rational debugging reveal genomic plasticity to S. cerevisiae synthetic chromosome XIV defects

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, 100379. doi: 10.1016/j.xgen.2023.100379

mRNA vaccine quality analysis using RNA sequencing

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

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))

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

Long non-coding RNAs: definitions, functions, challenges and recommendations

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

Bioengineered textiles with peptide binders that capture SARS-CoV-2 viral particles

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

The Coronavirus Standards Working Group’s roadmap for improved population testing

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

Library adaptors with integrated reference controls improve the accuracy and reliability of nanopore sequencing

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

The potential of long noncoding RNA therapies

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

ADRAM is an experience-dependent long noncoding RNA that drives fear extinction through a direct interaction with the chaperone protein 14-3-3

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

Towards accurate and reliable resolution of structural variants for clinical diagnosis

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

The splicing effect of variants at branchpoint elements in cancer genes

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

Using synthetic chromosome controls to evaluate the sequencing of difficult regions within the human genome

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

Emerging technologies and their impact on regulatory science

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

A clinical laboratory-developed LSC17 stemness score assay for rapid risk assessment of acute myeloid leukemia patients

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

The Sequencing Quality Control 2 study: establishing community standards for sequencing in precision medicine

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

Reporting guidelines for human microbiome research: the STORMS checklist

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

Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing

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

Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing

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

Long-read cDNA sequencing identifies functional pseudogenes in the human transcriptome

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

Testing at scale during the COVID-19 pandemic

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

Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions

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

Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology

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

Chimeric synthetic reference standards enable cross-validation of positive and negative controls in SARS-CoV-2 molecular tests

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

Advancing quality-control for NGS measurement of actionable mutations in circulating tumor DNA

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

The Impact of Variants at Branchpoint Splicing Elements in Cancer Genes

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

Author Correction: Diagnosis of fusion genes using targeted RNA sequencing (Nature Communications, (2019), 10, 1, (1388), 10.1038/s41467-019-09374-9)

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

A universal and independent synthetic DNA ladder for the quantitative measurement of genomic features

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

Lymphoma driver mutations in the pathogenic evolution of an iconic human autoantibody

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

Chiral DNA sequences as commutable controls for clinical genomics

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

Diagnosis of fusion genes using targeted RNA sequencing

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

TMPRSS2-ERG fusions linked to prostate cancer racial health disparities: a focus on Africa

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

Use of synthetic DNA spike-in controls (sequins) for human genome sequencing

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

Targeted, high-resolution RNA sequencing of non-coding genomic regions associated with neuropsychiatric functions

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

Natural and regenerated saltmarshes exhibit similar soil and belowground organic carbon stocks, root production and soil respiration

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

Crizotinib and surgery for long-term disease control in children and adolescents with ALK-positive inflammatory myofibroblastic tumors

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Structure and function of long noncoding RNAs in epigenetic regulation

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

Mapping of mitochondrial RNA-protein interactions by digital RNase footprinting

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

Saccharopolyspora erythraea's genome is organised in high-order transcriptional regions mediated by targeted degradation at the metabolic switch

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

Transcriptional effects of a lupus-associated polymorphism in the 5' untranslated region (UTR) of human complement receptor 2 (CR2/CD21)

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

The human mitochondrial transcriptome and the RNA-binding proteins that regulate its expression

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

Targeted RNA sequencing reveals the deep complexity of the human transcriptome

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

Long noncoding RNAs are generated from the mitochondrial genome and regulated by nuclear-encoded proteins

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

Refining transcriptional programs in kidney development by integration of deep RNA-sequencing and array-based spatial profiling

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

RNA processing in human mitochondria

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

The human mitochondrial transcriptome

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

Global analysis of the mammalian RNA degradome reveals widespread miRNA-dependent and miRNA-independent endonucleolytic cleavage

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

SNORD-host RNA Zfas1 is a regulator of mammary development and a potential marker for breast cancer

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

Expression of distinct RNAs from 3′ untranslated regions

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

Regulated post-transcriptional RNA cleavage diversifies the eukaryotic transcriptome

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

Nuclear-localized tiny RNAs are associated with transcription initiation and splice sites in metazoans

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

A variant of the KLK4 gene is expressed as a cis sense-antisense chimeric transcript in prostate cancer cells

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

Long noncoding RNAs in neuronal-glial fate specification and oligodendrocyte lineage maturation

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

Pervasive transcription of the eukaryotic genome: functional indices and conceptual implications

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

Non-coding RNAs: regulators of disease

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

Genome-wide identification of long noncoding RNAs in CD8(+) T cells

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

Long non-coding RNAs: insights into functions

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

NRED: a database of long noncoding RNA expression

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

RNA regulation of epigenetic processes

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

Differentiating protein-coding and noncoding RNA: Challenges and ambiguities

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

Noncoding RNAs in long term memory formation

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

Long Noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation

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

RNA control of epigenetic processes

Amaral, Paulo, Dinger, Marcel, Mattick, John, Mehler, Mark and Mercer, Tim (2008). RNA control of epigenetic processes. Australian Biochemist, 39 (2), 4-8.

The Eukaryotic genome as an RNA machine

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

RNAs as extracellular signaling molecules

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

Specific expression of long noncoding RNAs in the mouse brain

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

Association of a common complement receptor 2 haplotype with increased risk of systemic lupus erythematosus

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

Neural stem cells sort protein and RNA cargoes for export with exosomes in response to inflammation

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.

The inflammatory fingerprint of Neural Stem Cells

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.

Building Systems biology platforms for Actinobacteria

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.

Systems biology for industrial microorganisms

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.

Regulated independent expression of 3' untranslated regions in mammals

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.

Expression of long noncoding RNAs during mouse development

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