From reads to regions: a Bioconductor workflow to detect differential binding in ChIP-seq data [version 1; referees: 2 approved, 1 approved with reservations] by Aaron T. L. Lun, Gordon K. Smyth

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Unraveling the timeline of gene expression: A pseudotemporal trajectory analysis of single-cell RNA sequencing data [version 2; peer review: 1 approved, 2 approved with reservation... by Jinming Cheng, Gordon K. Smyth, Yunshun Chen

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Benchmarking cell type annotation methods for 10x Xenium spatial transcriptomics data by Jinming Cheng, Xinyi Jin, Gordon K. Smyth, Yunshun Chen

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qtQDA: quantile transformed quadratic discriminant analysis for high-dimensional RNA-seq data by Necla Koçhan, G. Yazgi Tutuncu, Gordon K. Smyth, Luke C. Gandolfo, Göknur Giner

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RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR [version 2; referees: 3 approved] by Charity W. Law, Monther Alhamdoosh, Shian Su, Gordon K. Smyth, Matthew E. Ritchie

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KAT6B overexpression rescues embryonic lethality in homozygous null KAT6A mice restoring vitality and normal lifespan by Maria. I. Bergamasco, Yuqing Yang, Alexandra L. Garnham, Bilal N. Sheikh, Gordon K. Smyth, Anne. K. Voss, Tim Thomas

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Activation of stably silenced genes by recruitment of a synthetic de-methylating module by Wing Fuk Chan, Hannah D. Coughlan, Yunshun Chen, Christine R. Keenan, Gordon K. Smyth, Andrew C. Perkins, Timothy M. Johanson, Rhys S. Allan

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Publisher Correction: Modeling group heteroscedasticity in single-cell RNA-seq pseudo-bulk data by Yue You, Xueyi Dong, Yong Kiat Wee, Mhairi J. Maxwell, Monther Alhamdoosh, Gordon K. Smyth, Peter F. Hickey, Matthew E. Ritchie, Charity W. Law

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Modeling group heteroscedasticity in single-cell RNA-seq pseudo-bulk data by Yue You, Xueyi Dong, Yong Kiat Wee, Mhairi J. Maxwell, Monther Alhamdoosh, Gordon K. Smyth, Peter F. Hickey, Matthew E. Ritchie, Charity W. Law

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Genome-wide analysis reveals no evidence of trans chromosomal regulation of mammalian immune development. by Timothy M Johanson, Hannah D Coughlan, Aaron T L Lun, Naiara G Bediaga, Gaetano Naselli, Alexandra L Garnham, Leonard C Harrison, Gordon K Smyth, Rhys S Allan

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Proteomic and metabolomic analyses of the human adult myocardium reveal ventricle-specific regulation in end-stage cardiomyopathies by Benjamin Hunter, Mengbo Li, Benjamin L. Parker, Yen Chin Koay, Dylan J. Harney, Evangeline Pearson, Jacob Cao, Gavin T. Chen, Oneka Guneratne, Gordon K. Smyth, Mark Larance, John F. O’Sullivan, Sean Lal

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Hormone-responsive progenitors have a unique identity and exhibit high motility during mammary morphogenesis by Caleb A. Dawson, Michael J.G. Milevskiy, Bianca D. Capaldo, Raymond K.H. Yip, Xiaoyu Song, François Vaillant, Lexie Prokopuk, Felicity C. Jackling, Gordon K. Smyth, Yunshun Chen, Geoffrey J. Lindeman, Jane E. Visvader

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Self-maintenance of zonal hepatocytes during adult homeostasis and their complex plasticity upon distinct liver injuries by Chow Hiang Ang, Philip Arandjelovic, Jinming Cheng, Jicheng Yang, Fusheng Guo, Yuanquan Yu, Sarmilla Nelameham, Lachlan Whitehead, Jiangtao Li, David L. Silver, Nick Barker, Jane E. Visvader, Pierce K.H. Chow, Gordon K. Smyth, Yunshun Chen, David M. Virshup, Nai Yang Fu

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KAT6B overexpression in mice causes aggression, anxiety, and epilepsy by Maria I. Bergamasco, Ezgi Ozturk, Pablo M. Casillas-Espinosa, Alexandra L. Garnham, Waruni Abeysekera, Verena C. Wimmer, Pradeep Rajasekhar, Hannah K. Vanyai, Lachlan Whitehead, Marnie E. Blewitt, Kelly Rogers, Adam P. Vogel, Anthony J. Hannan, Gordon K. Smyth, Nigel C. Jones, Tim Thomas, Anne K. Voss

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Stem cell plasticity, acetylation of H3K14, and de novo gene activation rely on KAT7 by Andrew J. Kueh, Maria I. Bergamasco, Anna Quaglieri, Belinda Phipson, Connie S.N. Li-Wai-Suen, Ingrid M. Lönnstedt, Yifang Hu, Zhi-Ping Feng, Chris Woodruff, Rose E. May, Stephen Wilcox, Alexandra L. Garnham, Michael P. Snyder, Gordon K. Smyth, Terence P. Speed, Tim Thomas, Anne K. Voss

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Systemic inflammatory response syndrome triggered by blood-borne pathogens induces prolonged dendritic cell paralysis and immunosuppression by Mitra Ashayeripanah, Javier Vega-Ramos, Daniel Fernandez-Ruiz, Shirin Valikhani, Aaron T.L. Lun, Jason T. White, Louise J. Young, Atefeh Yaftiyan, Yifan Zhan, Linda Wakim, Irina Caminschi, Mireille H. Lahoud, Andrew M. Lew, Ken Shortman, Gordon K. Smyth, William R. Heath, Justine D. Mintern, Antoine Roquilly, Jose A. Villadangos

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Correction: TRAF2 regulates TNF and NF-κB signalling to suppress apoptosis and skin inflammation independently of Sphingosine kinase 1 by Nima Etemadi, Michael Chopin, Holly Anderton, Maria C Tanzer, James A Rickard, Waruni Abeysekera, Cathrine Hall, Sukhdeep K Spall, Bing Wang, Yuquan Xiong, Timothy Hla, Stuart M Pitson, Claudine S Bonder, Wendy Wei-Lynn Wong, Matthias Ernst, Gordon K Smyth, David L Vaux, Stephen L Nutt, Ueli Nachbur, John Silke

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TRAF2 regulates TNF and NF-κB signalling to suppress apoptosis and skin inflammation independently of Sphingosine kinase 1 by Nima Etemadi, Michael Chopin, Holly Anderton, Maria C Tanzer, James A Rickard, Waruni Abeysekera, Cathrine Hall, Sukhdeep K Spall, Bing Wang, Yuquan Xiong, Timothy Hla, Stuart M Pitson, Claudine S Bonder, Wendy Wei-Lynn Wong, Matthias Ernst, Gordon K Smyth, David L Vaux, Stephen L Nutt, Ueli Nachbur, John Silke

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High-dimensional mass cytometry identifies T cell and B cell signatures predicting reduced risk of Plasmodium vivax malaria by Lisa J. Ioannidis, Halina M. Pietrzak, Ann Ly, Retno A.S. Utami, Emily M. Eriksson, Stephanie I. Studniberg, Waruni Abeysekera, Connie S.N. Li-Wai-Suen, Dylan Sheerin, Julie Healer, Agatha M. Puspitasari, Dwi Apriyanti, Farah N. Coutrier, Jeanne R. Poespoprodjo, Enny Kenangalem, Benediktus Andries, Pak Prayoga, Novita Sariyanti, Gordon K. Smyth, Leily Trianty, Alan F. Cowman, Ric N. Price, Rintis Noviyanti, Diana S. Hansen

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Molecular profiling reveals features of clinical immunity and immunosuppression in asymptomatic P. falciparum malaria by Stephanie I Studniberg, Lisa J Ioannidis, Retno A S Utami, Leily Trianty, Yang Liao, Waruni Abeysekera, Connie S N Li‐Wai‐Suen, Halina M Pietrzak, Julie Healer, Agatha M Puspitasari, Dwi Apriyanti, Farah Coutrier, Jeanne R Poespoprodjo, Enny Kenangalem, Benediktus Andries, Pak Prayoga, Novita Sariyanti, Gordon K Smyth, Alan F Cowman, Ric N Price, Rintis Noviyanti, Wei Shi, Alexandra L Garnham, Diana S Hansen

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