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ArticlesPeer ReviewedFull Text
voom: precision weights unlock linear model analysis tools for RNA-seq read counts
Author / Creator:Law, Charity W ; Chen, Yunshun ; Shi, Wei ; Smyth, Gordon K
Publisher:England: BioMed Central Ltd
Journal title:Genome Biology (Online Edition), 2014-02, Vol.15 (2), p.R29-R29, Article R29
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Count-based differential expression analysis of RNA sequencing data using R and Bioconductor
Author / Creator:Anders, Simon ; McCarthy, Davis J ; Chen, Yunshun ; Okoniewski, Michal ; Smyth, Gordon K ; Huber, Wolfgang ; Robinson, Mark D
Publisher:London: Nature Publishing Group UK
Journal title:Nature protocols, 2013-09, Vol.8 (9), p.1765-1786
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Mammary tumour cells remodel the bone marrow vascular microenvironment to support metastasis
Author / Creator:Yip, Raymond K. H. ; Rimes, Joel S. ; Capaldo, Bianca D. ; Vaillant, François ; Mouchemore, Kellie A. ; Pal, Bhupinder ; Chen, Yunshun ; Surgenor, Elliot ; Murphy, Andrew J. ; Anderson, Robin L. ; Smyth, Gordon K. ; Lindeman, Geoffrey J. ; Hawkins, Edwin D. ; Visvader, Jane E.
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2021-11, Vol.12 (1), p.6920-6920, Article 6920
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From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline [version 2; peer review: 5 approved]
Author / Creator:Chen, Yunshun ; Lun, Aaron T. L ; Smyth, Gordon K
Publisher:England: F1000Research
Journal title:F1000 research, 2016, Vol.5, p.1438-1438
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Benchmarking cell type annotation methods for 10x Xenium spatial transcriptomics data
Author / Creator:Cheng, Jinming ; Jin, Xinyi ; Smyth, Gordon K. ; Chen, Yunshun
Publisher:England: BioMed Central Ltd
Journal title:BMC bioinformatics, 2025-01, Vol.26 (1), p.22-15, Article 22
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Construction of developmental lineage relationships in the mouse mammary gland by single-cell RNA profiling
Author / Creator:Pal, Bhupinder ; Chen, Yunshun ; Vaillant, François ; Jamieson, Paul ; Gordon, Lavinia ; Rios, Anne C. ; Wilcox, Stephen ; Fu, Naiyang ; Liu, Kevin He ; Jackling, Felicity C. ; Davis, Melissa J. ; Lindeman, Geoffrey J. ; Smyth, Gordon K. ; Visvader, Jane E.
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2017-11, Vol.8 (1), p.1627-14, Article 1627
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R code and downstream analysis objects for the scRNA-seq atlas of normal and tumorigenic human breast tissue
Author / Creator:Chen, Yunshun ; Pal, Bhupinder ; Lindeman, Geoffrey J. ; Visvader, Jane E. ; Smyth, Gordon K.
Publisher:London: Nature Publishing Group UK
Journal title:Scientific data, 2022-03, Vol.9 (1), p.96-96, Article 96
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Activation of stably silenced genes by recruitment of a synthetic de-methylating module
Author / Creator:Chan, Wing Fuk ; Coughlan, Hannah D. ; Chen, Yunshun ; Keenan, Christine R. ; Smyth, Gordon K. ; Perkins, Andrew C. ; Johanson, Timothy M. ; Allan, Rhys S.
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2022-09, Vol.13 (1), p.5582-5582, Article 5582
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Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR
Author / Creator:Chen, Yunshun ; Pal, Bhupinder ; Visvader, Jane E. ; Smyth, Gordon K.
Publisher:London: Faculty of 1000 Ltd
Journal title:F1000 research, 2017, Vol.6, p.2055
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Single cell transcriptome atlas of mouse mammary epithelial cells across development
Author / Creator:Pal, Bhupinder ; Chen, Yunshun ; Milevskiy, Michael J. G. ; Vaillant, François ; Prokopuk, Lexie ; Dawson, Caleb A. ; Capaldo, Bianca D. ; Song, Xiaoyu ; Jackling, Felicity ; Timpson, Paul ; Lindeman, Geoffrey J. ; Smyth, Gordon K. ; Visvader, Jane E.
Publisher:England: BioMed Central Ltd
Journal title:Breast cancer research : BCR, 2021-06, Vol.23 (1), p.69-69, Article 69
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Unraveling the timeline of gene expression: A pseudotemporal trajectory analysis of single-cell RNA sequencing data [version 2; peer review: 2 approved, 1 approved with reservations]
Author / Creator:Cheng, Jinming ; Smyth, Gordon K. ; Chen, Yunshun
Publisher:England: Faculty of 1000 Ltd
Journal title:F1000 research, 2023, Vol.12, p.684-684
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Loss of TAF8 causes TFIID dysfunction and p53-mediated apoptotic neuronal cell death
Author / Creator:El-Saafin, Farrah ; Bergamasco, Maria I. ; Chen, Yunshun ; May, Rose E. ; Esakky, Prabagaran ; Hediyeh-zadeh, Soroor ; Dixon, Mathew ; Wilcox, Stephen ; Davis, Melissa J. ; Strasser, Andreas ; Smyth, Gordon K. ; Thomas, Tim ; Voss, Anne K.
Publisher:London: Nature Publishing Group UK
Journal title:Cell death and differentiation, 2022-05, Vol.29 (5), p.1013-1027
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MCL‑1 safeguards activated hair follicle stem cells to enable adult hair regeneration
Author / Creator:Chin, Hui San ; Cheng, Jinming ; Hsu, Shih Han ; Lum, Guo Guang ; Zaldivia, Maria TK ; Nelameham, Sarmilla ; Guo, Fusheng ; Mallavarapu, Keerthana ; Jackling, Felicity C. ; Yang, Jicheng ; Tan, Jonathan S. L. ; Sampath, Prabha ; Barker, Nick ; Smyth, Gordon K. ; Lindeman, Geoffrey J. ; Strasser, Andreas ; Visvader, Jane E. ; Chen, Yunshun ; Chen, Ting ; Fu, Nai Yang
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2025-03, Vol.16 (1), p.2829-20, Article 2829
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Benchmarking spatial transcriptomics technologies with the multi-sample SpatialBenchVisium dataset
Author / Creator:Du, Mei R. M. ; Wang, Changqing ; Law, Charity W. ; Amann-Zalcenstein, Daniela ; Anttila, Casey J. A. ; Ling, Ling ; Hickey, Peter F. ; Sargeant, Callum J. ; Chen, Yunshun ; Ioannidis, Lisa J. ; Rajasekhar, Pradeep ; Yip, Raymond K. H. ; Rogers, Kelly L. ; Hansen, Diana S. ; Bowden, Rory ; Ritchie, Matthew E.
Publisher:England: BioMed Central Ltd
Journal title:Genome Biology, 2025-03, Vol.26 (1), p.77-77, Article 77
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Regulation of germinal center responses and B-cell memory by the chromatin modifier MOZ
Author / Creator:Good-Jacobson, Kim L. ; Chen, Yunshun ; Voss, Anne K. ; Smyth, Gordon K. ; Thomas, Tim ; Tarlinton, David
Publisher:United States: National Academy of Sciences
Journal title:Proceedings of the National Academy of Sciences - PNAS, 2014-07, Vol.111 (26), p.9585-9590
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In vivo genome‐editing screen identifies tumor suppressor genes that cooperate with Trp53 loss during mammary tumorigenesis
Author / Creator:Heitink, Luuk ; Whittle, James R. ; Vaillant, François ; Capaldo, Bianca D. ; Dekkers, Johanna F. ; Dawson, Caleb A. ; Milevskiy, Michael J. G. ; Surgenor, Elliot ; Tsai, Minhsuang ; Chen, Huei‐Rong ; Christie, Michael ; Chen, Yunshun ; Smyth, Gordon K. ; Herold, Marco J. ; Strasser, Andreas ; Lindeman, Geoffrey J. ; Visvader, Jane E.
Publisher:United States: John Wiley & Sons, Inc
Journal title:Molecular oncology, 2022-03, Vol.16 (5), p.1119-1131
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Single‐cell transcriptional atlas of human breast cancers and model systems
Author / Creator:Altman, Julia E. ; Olex, Amy L. ; Zboril, Emily K. ; Walker, Carson J. ; Boyd, David C. ; Myrick, Rachel K. ; Hairr, Nicole S. ; Koblinski, Jennifer E. ; Puchalapalli, Madhavi ; Hu, Bin ; Dozmorov, Mikhail G. ; Chen, X. Steven ; Chen, Yunshun ; Perou, Charles M. ; Lehmann, Brian D. ; Visvader, Jane E. ; Harrell, J. Chuck
Publisher:United States: John Wiley & Sons, Inc
Journal title:Clinical and translational medicine, 2024-10, Vol.14 (10), p.e70044-n/a
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Lung Basal Stem Cells Rapidly Repair DNA Damage Using the Error-Prone Nonhomologous End-Joining Pathway
Author / Creator:Weeden, Clare E. ; Chen, Yunshun ; Ma, Stephen B. ; Hu, Yifang ; Ramm, Georg ; Sutherland, Kate D. ; Smyth, Gordon K. ; Asselin-Labat, Marie-Liesse
Publisher:United States: Public Library of Science
Journal title:PLoS biology, 2017-01, Vol.15 (1), p.e2000731
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ArticlesPeer ReviewedFull Text
From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline [version 1; peer review: 5 approved]
Author / Creator:Chen, Yunshun ; Lun, Aaron T. L ; Smyth, Gordon K
Publisher:London: Faculty of 1000 Ltd
Journal title:F1000 research, 2016, Vol.5, p.1438
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Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR [version 2; peer review: 2 approved, 1 approved with reservations]
Author / Creator:Chen, Yunshun ; Pal, Bhupinder ; Visvader, Jane E ; Smyth, Gordon K
Publisher:England: F1000 Research Limited
Journal title:F1000 research, 2017, Vol.6, p.2055-2055
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Showing 1 to 20 of 32 results

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voom: precision weights unlock linear model analysis tools for RNA-seq read counts

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Count-based differential expression analysis of RNA sequencing data using R and Bioconductor

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Mammary tumour cells remodel the bone marrow vascular microenvironment to support metastasis

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From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline [version 2; peer review: 5 approved]

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Benchmarking cell type annotation methods for 10x Xenium spatial transcriptomics data

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Construction of developmental lineage relationships in the mouse mammary gland by single-cell RNA profiling

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R code and downstream analysis objects for the scRNA-seq atlas of normal and tumorigenic human breast tissue

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Activation of stably silenced genes by recruitment of a synthetic de-methylating module

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Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR

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Single cell transcriptome atlas of mouse mammary epithelial cells across development

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Unraveling the timeline of gene expression: A pseudotemporal trajectory analysis of single-cell RNA sequencing data [version 2; peer review: 2 approved, 1 approved with reservations]

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Loss of TAF8 causes TFIID dysfunction and p53-mediated apoptotic neuronal cell death

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MCL‑1 safeguards activated hair follicle stem cells to enable adult hair regeneration

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Benchmarking spatial transcriptomics technologies with the multi-sample SpatialBenchVisium dataset

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Regulation of germinal center responses and B-cell memory by the chromatin modifier MOZ

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In vivo genome‐editing screen identifies tumor suppressor genes that cooperate with Trp53 loss during mammary tumorigenesis

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Single‐cell transcriptional atlas of human breast cancers and model systems

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Lung Basal Stem Cells Rapidly Repair DNA Damage Using the Error-Prone Nonhomologous End-Joining Pathway

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From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline [version 1; peer review: 5 approved]

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Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR [version 2; peer review: 2 approved, 1 approved with reservations]

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