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2018 Journal Article Synthetic microbe communities provide internal reference standards for metagenome sequencing and analysisHardwick, 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 |
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2018 Journal Article Machine learning annotation of human branchpointsSignal, 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 |
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2018 Journal Article Universal Alternative Splicing of Noncoding ExonsDeveson, 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 |
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2017 Journal Article Intergenic disease-associated regions are abundant in novel transcriptsBartonicek, 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 |
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2017 Journal Article Phosphoproteomic profiling reveals ALK and MET as novel actionable targets across synovial sarcoma subtypesFleuren, 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 |
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2017 Journal Article Long noncoding RNAs CUPID1 and CUPID2 mediate breast cancer risk at 11q13 by modulating the response to DNA damageBetts, 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 |
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2017 Journal Article Reference standards for next-generation sequencingHardwick, 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 |
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2017 Journal Article The dimensions, dynamics, and relevance of the mammalian noncoding transcriptomeDeveson, 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 |
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2017 Journal Article ANAQUIN: a software toolkit for the analysis of spike-in controls for next generation sequencingWong, 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 |
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2016 Journal Article Spliced synthetic genes as internal controls in RNA sequencing experimentsHardwick, 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 |
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2016 Journal Article Representing genetic variation with synthetic DNA standardsDeveson, 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 |
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2016 Journal Article Improved definition of the mouse transcriptome via targeted RNA sequencingBussotti, 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 |
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2015 Journal Article Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencingClark, 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 |
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2015 Journal Article Integrative analysis of 111 reference human epigenomesRoadmap 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 |
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2015 Journal Article Genome-wide discovery of human splicing branchpointsMercer, 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 |
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2014 Journal Article Extracellular vesicles from neural stem cells transfer IFN-γ via Ifngr1 to activate Stat1 signaling in target cellsCossetti, 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 |
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2014 Journal Article Targeted sequencing for gene discovery and quantification using RNA CaptureSeqMercer, 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 |
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2013 Journal Article Re-annotation of the Saccharopolyspora erythraea genome using a systems biology approachMarcellin, 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 |
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2013 Journal Article DNase I-hypersensitive exons colocalize with promoters and distal regulatory elementsMercer, 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 |
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2013 Journal Article Understanding the regulatory and transcriptional complexity of the genome through structureMercer, 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 |
