Luyi Tian, Sara Tomei, Jaring Schreuder, Tom S Weber, Daniela Amann-Zalcenstein, Dawn S Lin, J. Tran, Cindy Audiger, Mathew Chu, Andrew Jarratt, Tracy Willson, Adrienne Hilton, Ee Shan Pang, Timothy Patton, Madison Kelly, Shian Su, Quentin Gouil, Peter Diakumis, M. Bahlo, Toby Sargeant, Lev M Kats, Philip D Hodgkin, M. Ritchie, Shalin H Naik, Meredith O’Keeffe. Clonal multi-omics reveals Bcor as a negative regulator of emergency dendritic cell development.. Immunity, 2021. doi: 10.1016/j.immuni.2021.03.012.
Stephane Chappaz, Charity W Law, Mark R Dowling, Kirstyn T Carey, Rachael M Lane, Linh H Ngo, Vihandha O Wickramasinghe, G. Smyth, M. Ritchie, Benjamin T Kile. Germline heterozygous mutations in Nxf1 perturb RNA metabolism and trigger thrombocytopenia and lymphopenia in mice.. Blood advances, 4, 1270-1283, 2020. doi: 10.1182/bloodadvances.2019001323.
Najoua Lalaoui, Delphine Merino, Goknur Giner, Francois Vaillant, Diep Chau, Lin Liu, Tobias Kratina, Bhupinder Pal, James R Whittle, Nima Etemadi, Jean Berthelet, Julius Grasel, Cathrine Hall, M. Ritchie, Matthias Ernst, G. Smyth, David L Vaux, Jane E Visvader, Geoffrey J Lindeman, John Silke, Julius Gräsel. Targeting triple-negative breast cancers with the Smac-mimetic birinapant.. Cell death and differentiation, 27, 2768-2780, 2020. doi: 10.1038/s41418-020-0541-0.
Charity W Law, Kathleen Zeglinski, Xueyi Dong, Monther Alhamdoosh, G. Smyth, M. Ritchie. A guide to creating design matrices for gene expression experiments.. F1000Research, 9, 1444, 2020. doi: 10.12688/f1000research.27893.1.
Charity W Law, Kathleen Zeglinski, Xueyi Dong, Monther Alhamdoosh, G. Smyth, M. Ritchie. A guide to creating design matrices for gene expression experiments.. F1000Research, 9, 1444, 2020. doi: 10.12688/f1000research.27893.1.
Luyi Tian, Xueyi Dong, Saskia Freytag, Kim-Anh Le Cao, Shian Su, Abolfazl JalalAbadi, Daniela Amann-Zalcenstein, Tom S Weber, Azadeh Seidi, Jafar S Jabbari, Shalin H Naik, M. Ritchie, Kim-Anh Lê Cao, K. Le-Cao. Benchmarking single cell RNA-sequencing analysis pipelines using mixture control experiments.. Nature methods, 16, 479-+, 2019. doi: 10.1038/s41592-019-0425-8.
Cyril Seillet, Kylie Luong, Julie Tellier, Nicolas Jacquelot, Rui Dong Shen, Peter Hickey, Verena C Wimmer, Lachlan Whitehead, Kelly Rogers, G. Smyth, Alexandra L Garnham, M. Ritchie, Gabrielle T Belz. The neuropeptide VIP confers anticipatory mucosal immunity by regulating ILC3 activity.. Nature immunology, 21, 168-+, 2019. doi: 10.1038/s41590-019-0567-y.
Luyi Tian, Xueyi Dong, Saskia Freytag, Kim-Anh Le Cao, Shian Su, Daniela Amann-Zalcenstein, Tom Weber, Azadeh Seidi, Shalin Naik, M. Ritchie, K. Le-Cao. scRNA-seq mixology: towards better benchmarking of single cell RNA-seq protocols and analysis methods. 433102, 2018. doi: 10.1101/433102.
Tian Luyi, Jaring Schreuder, Daniela Amann-Zalcenstein, J. Tran, Nikolce Kocovski, Shian Su, Peter Diakumis, M. Bahlo, Toby Sargeant, M. Ritchie, Philip Hodgkin, Shalin Naik. SIS-seq, a molecular 'time machine', connects single cell fate with gene programs. 403113, 2018. doi: 10.1101/403113.
Charity Law, Monther Alhamdoosh, Shian Su, Xueyi Dong, Luyi Tian, G. Smyth, M. Ritchie. RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR. 1408, 2018. doi: 10.12688/f1000research.9005.3.
Monther Alhamdoosh, Milica Ng, Nicholas J Wilson, Julie M Sheridan, Huy Huynh, M. Ritchie. Combining multiple tools outperforms individual methods in gene set enrichment analyses. Bioinformatics, 33, 414-424, 2017. doi: 10.1093/bioinformatics/btw623.
Aliaksei Z Holik, C. Law, Ruijie Liu, Z. Wang, Jaeil Ahn, Marie-Liesse Asselin-Labat, G. Smyth, M. Ritchie. RNA-seq mixology: designing realistic control experiments to compare protocols and analysis methods. Nucleic Acids Research, 45, e30 (18pp), 2017. doi: 10.1093/nar/gkw1063.
Nai Yang Fu, Anne C Rios, Bhupinder Pal, C. Law, Paul Jamieson, Ruijie Liu, Francois Vaillant, Felicity Jackling, G. Smyth, Geoffrey J Lindeman, M. Ritchie, Jane E Visvader. Identification of quiescent and spatially restricted mammary stem cells that are hormone responsive. Nature Cell Biology, 19, 164-176, 2017. doi: 10.1038/ncb3471.
Marie-Liesse Asselin-Labat, Rishi Rampersad, Xia Xu, M. Ritchie, Jacob Michalski, Lingling Huang, Mark W Onaitis. High-LET Radiation Increases Tumor Progression in a K-Ras-Driven Model of Lung Adenocarcinoma. Radiation Research, 188, 562-570, 2017. doi: 10.1667/RR14794.1.
M Alhamdoosh, C. Law, L Tian, JM Sheridan, M. Ng, M. Ritchie. Easy and efficient ensemble gene set testing with EGSEA. F1000Research, 6, 2010, 2017. doi: 10.12688/f1000research.12544.1.
Cyril Seillet, Lisa A Mielke, Daniela B Amann-Zalcenstein, Shian Su, Jerry Gao, Francisca F Almeida, Wei Shi, M. Ritchie, Shalin H Naik, Nicholas D Huntington, Sebastian Carotta, Gabrielle T Belz. Deciphering the Innate Lymphoid Cell Transcriptional Program. Cell Reports, 17, 436-447, 2016. doi: 10.1016/j.celrep.2016.09.025.
G. Smyth, C. Law, M Alhamdoosh, S. Su, M. Ritchie. RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR. F1000Research, 5, 1408, 2016. doi: 10.12688/f1000research.9005.2.
Julie M Sheridan, M. Ritchie, Sarah A Best, Kun Jiang, Tamara J Beck, Francois Vaillant, Kevin Liu, Ross A Dickins, G. Smyth, Geoffrey J Lindeman, Jane E Visvader. A pooled shRNA screen for regulators of primary mammary stem and progenitor cells identifies roles for Asap1 and Prox1. BMC Cancer, 15, 221 (13pp), 2015. doi: 10.1186/s12885-015-1187-z.
Ruijie Liu, Aliaksei Z Holik, S. Su, Natasha Jansz, K. Chen, Huei San Leong, Marnie E Blewitt, Marie-Liesse Asselin-Labat, G. Smyth, M. Ritchie. Why weight? Modelling sample and observational level variability improves power in RNA-seq analyses. Nucleic Acids Research, 43, E97-U28, 2015. doi: 10.1093/nar/gkv412.
M. Ritchie, B. Phipson, Di Wu, Y. Hu, C. Law, Wei Shi, G. Smyth. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Research, 43, e47 (13pp), 2015. doi: 10.1093/nar/gkv007.
B Pal, T Bouras, W Shi, F Vaillant, JM Sheridan, NY Fu, K Breslin, K Jiang, M. Ritchie, M. Young, GJ Lindeman, G. Smyth, J Visvader. Global Changes in the Mammary Epigenome Are Induced by Hormonal Cues and Coordinated by Ezh2. Cell Reports, 3, 411-426, 2013. doi: 10.1016/j.celrep.2012.12.020.
F Vaillant, D Merino, L Lee, K Breslin, B Pal, M. Ritchie, G. Smyth, M Christie, LJ Phillipson, CJ Burns, GB Mann, JE Visvader, GJ Lindeman. Targeting BCL-2 with the BH3 Mimetic ABT-199 in Estrogen Receptor-Positive Breast Cancer. Cancer Cell, 24, 120-129, 2013. doi: 10.1016/j.ccr.2013.06.002.
GJ Lindeman, F Vaillant, D Merino, L Lee, K Breslin, B Pal, M. Ritchie, G. Smyth, M Christie, LJ Phillipson, CJ Burns, GB Mann, JE Visvader. Targeting BCL-2 with the BH3 mimetic ABT-199 in ER-positive breast cancer. Cancer Research, 73, P2-09-01 (2pp), 2013. doi: 10.1158/0008-5472.SABCS13-P2-09-01.
S Oakes, F Vaillant, E Lim, LX Lee, K Breslin, F Feleppa, S Deb, M. Ritchie, E Takano, T Ward, S Fox, D Generali, G. Smyth, A Strasser, DC Huang, J Visvader, GJ Lindeman. Sensitization of BCL-2-expressing breast tumors to chemotherapy by the BH3 mimetic ABT-737. Proceedings of the National Academy of Sciences of the United States of America, 109, 2766-2771, 2012. doi: 10.1073/pnas.1104778108.
M. Ritchie, Ruijie Liu, Benilton S Carvalho, Rafael A Irizarry, Australia and New Zealand Multiple Sclerosis Genetics Consortium (ANZgene), M. Bahlo, DR Booth, SA Broadley, MA Brown, SJ Foote, LR Griffiths, TJ Kilpatrick, J Lechner-Scott, P Moscato, VM Perreau, JP Rubio, J Stankovich, GJ Stewart, BV Taylor, J Wiley, G Clarke, MB Cox, PA Csurhes, P Danoy, JL Dickinson, K Drysdale, J Field, JM Greer, P Guru, J Hadler, E Hoban, BJ McMorran, CJ Jensen, LJ Johnson, R McCallum, M Merriman, A Polanowski, K Pryce, L Tajouri, L Whittock, EJ Wilkins, BL Browning, D Perera, H Butzkueven, WM Carroll, C Chapman, AG Kermode, M Marriott, D. Mason, RN Heard, MP Pender, M Slee, N Tubridy, E Willoughby. Comparing genotyping algorithms for Illumina's Infinium whole-genome SNP BeadChips.. BMC bioinformatics, 12, 68 (12pp), 2011. doi: 10.1186/1471-2105-12-68.
I Majewski, M. Ritchie, B. Phipson, J Corbin, M Pakusch, A Ebert, M Busslinger, H Koseki, Y. Hu, G. Smyth, W Alexander, D Hilton, M Blewitt. Opposing roles of polycomb repressive complexes in hematopoietic stem and progenitor cells. Blood, 116, 731-739, 2010. doi: 10.1182/blood-2009-12-260760.
C Hewitt, K Ling, T Merson, K Simpson, M. Ritchie, S King, M Pritchard, G. Smyth, T THOMAS, H Scott, A Voss. Gene Network Disruptions and Neurogenesis Defects in the Adult Ts1Cje Mouse Model of Down Syndrome. PLoS One, 5, e11561 (15pp), 2010. doi: 10.1371/journal.pone.0011561.
Wei Shi, Ashish Banerjee, M. Ritchie, Steve Gerondakis, G. Smyth. Illumina WG-6 BeadChip strips should be normalized separately. BMC Bioinformatics, 10, 372 (12pp), 2009. doi: 10.1186/1471-2105-10-372.
J. Silver, M. Ritchie, G. Smyth. Microarray background correction: maximum likelihood estimation for the normal-exponential convolution. Biostatistics, 10, 352-363, 2009. doi: 10.1093/biostatistics/kxn042.
Joelle Michaud, Ken M Simpson, Robert Escher, Karine Buchet-Poyau, Tim Beissbarth, Catherine Carmichael, M. Ritchie, Frederic Schuetz, Ping Cannon, M. Liu, Xiaofeng Shen, Yoshiaki Ito, Wendy H Raskind, Marshall S Horwitz, Motomi Osato, David R Turner, T. Speed, Maria Kavallaris, G. Smyth, Hamish S Scott, F Schütz. Integrative analysis of RUNX1 downstream pathways and target genes. BMC Genomics, 9, 363 (17pp), 2008. doi: 10.1186/1471-2164-9-363.
JP Dwyer, M. Ritchie, G. Smyth, S Harrap, L Delbridge, A Domenighetti, R di Nicolantonio. Myocardial gene expression associated with genetic cardiac hypertrophy in the absence of hypertension. Hypertension Research, 31, 941-955, 2008. doi: 10.1291/hypres.31.941.
C Huggins, A Domenighetti, M. Ritchie, N Khalil, J Favaloro, J Proietto, G. Smyth, S Pepe, L Delbridge. Functional and metabolic remodelling in GLUT4-deficient hearts confers hyper-responsiveness to substrate intervention. Journal of Molecular and Cellular Cardiology, 44, 270-280, 2008. doi: 10.1016/j.yjmcc.2007.11.020.
M. Ritchie, J. Silver, Alicia Oshlack, M. Holmes, Dileepa Diyagama, Andrew Holloway, G. Smyth. A comparison of background correction methods for two-colour microarrays. Bioinformatics, 23, 2700-2707, 2007. doi: 10.1093/bioinformatics/btm412.
M. Ritchie, D Diyagama, J Neilson, R van Laar, A Dobrovic, A Holloway, G. Smyth. Empirical array quality weights in the analysis of microarray data. BMC Bioinformatics, 7, 261, 2006. doi: 10.1186/1471-2105-7-261.
JP Dwyer, M. Ritchie, G. Smyth, LM Delbridge, AA Domenighetti, SB Harrap, R Di Nicolantonio. Differentially expressed genes in cardiac tissue from the hypertrophic heart rat. CLINICAL AND EXPERIMENTAL PHARMACOLOGY AND PHYSIOLOGY, 32, A13-A14, 2005.
AA Domenighetti, M. Ritchie, G. Smyth, T Pedrazzini, J Proietto, LMD Delbridge. Gene expression profiling reveals distinct sets of genes altered during hormonally and metabolically induced cardiac hypertrophies. JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY, 37, 303-304, 2004.