|
2021 Journal Article Reporting guidelines for human microbiome research: the STORMS checklistMirzayi, 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 |
|
2021 Journal Article Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencingFang, 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 |
|
2021 Journal Article Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencingXiao, 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 |
|
2021 Journal Article Long-read cDNA sequencing identifies functional pseudogenes in the human transcriptomeTroskie, 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 |
|
2021 Journal Article Testing at scale during the COVID-19 pandemicMercer, 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 |
|
2021 Journal Article Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regionsGong, 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 |
|
2021 Journal Article Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncologyDeveson, 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 |
|
2021 Journal Article Chimeric synthetic reference standards enable cross-validation of positive and negative controls in SARS-CoV-2 molecular testsMadala, 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 |
|
2021 Journal Article The Impact of Variants at Branchpoint Splicing Elements in Cancer GenesCanson, 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 |
|
2021 Journal Article Advancing quality-control for NGS measurement of actionable mutations in circulating tumor DNAWilley, 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 |
|
2020 Journal Article 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 |
|
2020 Journal Article A universal and independent synthetic DNA ladder for the quantitative measurement of genomic featuresReis, 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 |
|
2020 Journal Article Lymphoma driver mutations in the pathogenic evolution of an iconic human autoantibodySingh, 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 |
|
2019 Journal Article Chiral DNA sequences as commutable controls for clinical genomicsDeveson, 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 |
|
2019 Journal Article Diagnosis of fusion genes using targeted RNA sequencingHeyer, 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 |
|
2019 Journal Article Use of synthetic DNA spike-in controls (sequins) for human genome sequencingBlackburn, 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 |
|
2019 Journal Article TMPRSS2-ERG fusions linked to prostate cancer racial health disparities: a focus on AfricaBlackburn, 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 |
|
2019 Journal Article Targeted, high-resolution RNA sequencing of non-coding genomic regions associated with neuropsychiatric functionsHardwick, 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 |
|
2019 Journal Article Natural and regenerated saltmarshes exhibit similar soil and belowground organic carbon stocks, root production and soil respirationSantini, 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 |
|
2019 Journal Article Crizotinib and surgery for long-term disease control in children and adolescents with ALK-positive inflammatory myofibroblastic tumorsTrahair, 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 |
