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Yunshun Chen, Lizhong Chen, Aaron T L Lun, Pedro L Baldoni, Gordon K Smyth

Liping Zhou, Zhentao Ma, Qingyun Liu, Qiangyong Li, Min Peng, Chunling Yang, Bin Zhang, Tiancong Chen, Yuliu Huang, Zhihong Zheng, Aiguo Huang, Xiuli Chen, Yueling Zhang, Xianliang Zhao, Yongzhen Zhao

Bin Cheng, Ronglu Yang, Hui Xu, Li Wang, Nan Jiang, Tingting Song, Changwu Dong

Bence Nagy, Zoltán Bognár, Timea Judit Csabai, Nóra Fekete, Edit Irén Buzás, Árpád Ferenc Kovács, Júlia Szekeres-Barthó, Éva Pállinger

Haimin Song, Huaiyu Zhou, Shaochun Yang, Chunming He

Boris P. Hejblum, Kalidou Ba, Rodolphe Thiébaut, Denis Agniel

Sang-Hee Lee, Sung-Je Moon, Seung Hee Woo, Gwangsook Ahn, Won Kon Kim, Chul-Ho Lee, Jung Hwan Hwang

Sonja Zehetmayer, Martin Posch, Alexandra Graf

Weitong Cui, Huaru Xue, Lei Wei, Jinghua Jin, Xuewen Tian, Qinglu Wang

Mengmei Yang, Mengdi Qi, Liangzi Xu, Pu Huang, Xu Wang, Jing Sun, Jiandong Shi, Yunzhang Hu

Marine Gauthier, Denis Agniel, Rodolphe Thiébaut, Boris P Hejblum

Josué Barrera-Redondo, Daniel Piñero, Luis E. Eguiarte

Goran Mitulović, Thomas Mohr, Marianne Koch

Dongdong Wang, Xiao Chen, Meng Fu, Hong Xu, Zhiping Li

Dongdong Wang, Xiao Chen, Meng Fu, Zhiping Li

Kimon Froussios, Nick J Schurch, Katarzyna Mackinnon, Marek Gierliński, Céline Duc, Gordon G Simpson, Geoffrey J Barton

Sally Badawi, Alexandre Paccalet, Zeina Harhous, Bruno Pillot, Lionel Augeul, Fabien Van Coppenolle, Joel Lachuer, Mazen Kurdi, Claire Crola Da Silva, Michel Ovize, Gabriel Bidaux

Craig P. Hersh, Ian M. Adcock, Juan C. Celedón, Michael H. Cho, David C. Christiani, Blanca E. Himes, Naftali Kaminski, Rasika A. Mathias, Deborah A. Meyers, John Quackenbush, Susan Redline, Katrina A. Steiling, Holly K. Tabor, Martin D. Tobin, Mark M. Wurfel, Ivana V. Yang, Gerard H. Koppelman

Stijn Hawinkel, Federico Mattiello, Luc Bijnens, Olivier Thas

Sophie Lamarre, Pierre Frasse, Mohamed Zouine, Delphine Labourdette, Elise Sainderichin, Guojian Hu, Véronique Le Berre-Anton, Mondher Bouzayen, Elie Maza

Junyan Liu, Ling Yang, Yuchao Hou, Thanapop Soteyome, Bingbing Zeng, Jianyu Su, Lin Li, Bing Li, Dingqiang Chen, Yanyan Li, Aiwu Wu, Mark E. Shirtliff, Janette M. Harro, Zhenbo Xu, Brian M. Peters

Tássia Mangetti Gonçalves, Luciana Correia de Almeida Regitano, James E. Koltes, Aline Silva Mello Cesar, Sónia Cristina da Silva Andrade, Gerson Barreto Mourão, Gustavo Gasparin, Gabriel Costa Monteiro Moreira, Elyn Fritz-Waters, James M. Reecy, Luiz Lehmann Coutinho

Samaneh K. Sarvestani, Steven A. Signs, Veronique Lefebvre, Stephen Mack, Ying Ni, Andrew Morton, Ernest R. Chan, Xiaoxia Li, Paul Fox, Angela Ting, Matthew F. Kalady, Michael Cruise, Jean Ashburn, Jennifer Stiene, Wei Lai, David Liska, Shao Xiang, Emina H. Huang

Aliaksei Z. Holik, Charity W. Law, Ruijie Liu, Zeya Wang, Wenyi Wang, Jaeil Ahn, Marie-Liesse Asselin-Labat, Gordon K. Smyth, Matthew E. Ritchie

Yixin H. Ye, Andrei Seleznev, Heather A. Flores, Megan Woolfit, Elizabeth A. McGraw

Xiaogang Cui, Brett Marshall, Ning Shi, Shi-You Chen, Romdhane Rekaya, Hong-Xiang Liu

Shan Shan Liu, Wen Hui Zhu, Qing Hui Zhi, Jia Liu, Yan Wang, Huan Cai Lin

Yunshun Chen, Aaron T. L. Lun, Gordon K. Smyth

Mingliang Zhang, Feng Wei, Kai Guo, Zhen Hu, Yuyang Li, Guosheng Xie, Yanting Wang, Xiwen Cai, Liangcai Peng, Lingqiang Wang

Taewon Lee, Robert R. Delongchamp, Wonkuk Kim, Robert J. Shmookler Reis

Li-Fang Chu, Ning Leng, Jue Zhang, Zhonggang Hou, Daniel Mamott, David T. Vereide, Jeea Choi, Christina Kendziorski, Ron Stewart, James A. Thomson

Yunshun Chen, Aaron T. L. Lun, Gordon K. Smyth

Lu Gan, Rong Di, Yuehui Chao, Liebao Han, Xingwu Chen, Chao Wu, Shuxia Yin

Nicholas J. Schurch, Pietá Schofield, Marek Gierliński, Christian Cole, Alexander Sherstnev, Vijender Singh, Nicola Wrobel, Karim Gharbi, Gordon G. Simpson, Tom Owen-Hughes, Mark Blaxter, Geoffrey J. Barton

Chun Chen, Huong Le, Chetan T. Goudar

C. Sehwan Park, Amandine Valomon, Hans Welzl

Guoqiang Yi, Jingwei Yuan, Huijuan Bi, Wei Yan, Ning Yang, Lujiang Qu

Yet Nguyen, Dan Nettleton, Haibo Liu, Christopher K. Tuggle

Craig Monger, Paul S. Kelly, Clair Gallagher, Martin Clynes, Niall Barron, Colin Clarke

Sam Benidt, Dan Nettleton

2025	edgeR v4: powerful differential analysis of sequencing data with expanded functionality and improved support for small counts and larger datasets Nucleic Acids Research Yunshun Chen, Lizhong Chen, Aaron T L Lun, Pedro L Baldoni, Gordon K Smyth
2025	Shrimp Shapes a Nitrite Tolerance Trait via Regulating Autophagy and Apoptosis International Journal of Molecular Sciences Liping Zhou, Zhentao Ma, Qingyun Liu, Qiangyong Li, Min Peng, Chunling Yang, Bin Zhang, Tiancong Chen, Yuliu Huang, Zhihong Zheng, Aiguo Huang, Xiuli Chen, Yueling Zhang, Xianliang Zhao, Yongzhen Zhao
2025	Peripheral Blood miRNA Expression in Patients with Essential Hypertension in the Han Chinese Population in Hefei, China Biochemical Genetics Bin Cheng, Ronglu Yang, Hui Xu, Li Wang, Nan Jiang, Tingting Song, Changwu Dong
2025	Effects of light exposure during IVF: transcriptomic analysis of murine embryos and embryo-derived EVs Frontiers in Immunology Bence Nagy, Zoltán Bognár, Timea Judit Csabai, Nóra Fekete, Edit Irén Buzás, Árpád Ferenc Kovács, Júlia Szekeres-Barthó, Éva Pállinger
2024	Combining mendelian randomization analysis and network toxicology strategy to identify causality and underlying mechanisms of environmental pollutants with glioblastoma: A study of Methyl-4-hydroxybenzoate Ecotoxicology and Environmental Safety Haimin Song, Huaiyu Zhou, Shaochun Yang, Chunming He
2024	Neglecting the impact of normalization in semi-synthetic RNA-seq data simulations generates artificial false positives Genome Biology Boris P. Hejblum, Kalidou Ba, Rodolphe Thiébaut, Denis Agniel
2023	CrebH protects against liver injury associated with colonic inflammation via modulation of exosomal miRNA Cell & Bioscience Sang-Hee Lee, Sung-Je Moon, Seung Hee Woo, Gwangsook Ahn, Won Kon Kim, Chul-Ho Lee, Jung Hwan Hwang
2022	Impact of adaptive filtering on power and false discovery rate in RNA-seq experiments BMC Bioinformatics Sonja Zehetmayer, Martin Posch, Alexandra Graf
2021	High heterogeneity undermines generalization of differential expression results in RNA-Seq analysis Human Genomics Weitong Cui, Huaru Xue, Lei Wei, Jinghua Jin, Xuewen Tian, Qinglu Wang
2021	Differential host circRNA expression profiles in human lung epithelial cells infected with SARS-CoV-2 Infection, Genetics and Evolution Mengmei Yang, Mengdi Qi, Liangzi Xu, Pu Huang, Xu Wang, Jing Sun, Jiandong Shi, Yunzhang Hu
2020	dearseq: a variance component score test for RNA-seq differential analysis that effectively controls the false discovery rate NAR Genomics and Bioinformatics Marine Gauthier, Denis Agniel, Rodolphe Thiébaut, Boris P Hejblum
2020	Genomic, Transcriptomic and Epigenomic Tools to Study the Domestication of Plants and Animals: A Field Guide for Beginners Frontiers in Genetics Josué Barrera-Redondo, Daniel Piñero, Luis E. Eguiarte
2020	Lower Urinary Tract Dysfunction - From Evidence to Clinical Practice Goran Mitulović, Thomas Mohr, Marianne Koch
2019	Tacrolimus increases the expression level of the chemokine receptor CXCR2 to promote renal fibrosis progression International Journal of Molecular Medicine Dongdong Wang, Xiao Chen, Meng Fu, Hong Xu, Zhiping Li
2019	Transcriptomics analysis of sirolimus treatment in lupus nephritis Molecular Medicine Reports Dongdong Wang, Xiao Chen, Meng Fu, Zhiping Li
2019	How well do RNA-Seq differential gene expression tools perform in a complex eukaryote? A case study inArabidopsis thaliana Bioinformatics Kimon Froussios, Nick J Schurch, Katarzyna Mackinnon, Marek Gierliński, Céline Duc, Gordon G Simpson, Geoffrey J Barton
2019	A Dynamic Transcriptional Analysis Reveals IL-6 Axis as a Prominent Mediator of Surgical Acute Response in Non-ischemic Mouse Heart Frontiers in Physiology Sally Badawi, Alexandre Paccalet, Zeina Harhous, Bruno Pillot, Lionel Augeul, Fabien Van Coppenolle, Joel Lachuer, Mazen Kurdi, Claire Crola Da Silva, Michel Ovize, Gabriel Bidaux
2019	High-Throughput Sequencing in Respiratory, Critical Care, and Sleep Medicine Research. An Official American Thoracic Society Workshop Report Annals of the American Thoracic Society Craig P. Hersh, Ian M. Adcock, Juan C. Celedón, Michael H. Cho, David C. Christiani, Blanca E. Himes, Naftali Kaminski, Rasika A. Mathias, Deborah A. Meyers, John Quackenbush, Susan Redline, Katrina A. Steiling, Holly K. Tabor, Martin D. Tobin, Mark M. Wurfel, Ivana V. Yang, Gerard H. Koppelman
2019	A broken promise: microbiome differential abundance methods do not control the false discovery rate Briefings in Bioinformatics Stijn Hawinkel, Federico Mattiello, Luc Bijnens, Olivier Thas
2018	Optimization of an RNA-Seq Differential Gene Expression Analysis Depending on Biological Replicate Number and Library Size Frontiers in Plant Science Sophie Lamarre, Pierre Frasse, Mohamed Zouine, Delphine Labourdette, Elise Sainderichin, Guojian Hu, Véronique Le Berre-Anton, Mondher Bouzayen, Elie Maza
2018	Transcriptomics Study on Staphylococcus aureus Biofilm Under Low Concentration of Ampicillin Frontiers in Microbiology Junyan Liu, Ling Yang, Yuchao Hou, Thanapop Soteyome, Bingbing Zeng, Jianyu Su, Lin Li, Bing Li, Dingqiang Chen, Yanyan Li, Aiwu Wu, Mark E. Shirtliff, Janette M. Harro, Zhenbo Xu, Brian M. Peters
2018	Gene Co-expression Analysis Indicates Potential Pathways and Regulators of Beef Tenderness in Nellore Cattle Frontiers in Genetics Tássia Mangetti Gonçalves, Luciana Correia de Almeida Regitano, James E. Koltes, Aline Silva Mello Cesar, Sónia Cristina da Silva Andrade, Gerson Barreto Mourão, Gustavo Gasparin, Gabriel Costa Monteiro Moreira, Elyn Fritz-Waters, James M. Reecy, Luiz Lehmann Coutinho
2018	Cancer-predicting transcriptomic and epigenetic signatures revealed for ulcerative colitis in patient-derived epithelial organoids Oncotarget Samaneh K. Sarvestani, Steven A. Signs, Veronique Lefebvre, Stephen Mack, Ying Ni, Andrew Morton, Ernest R. Chan, Xiaoxia Li, Paul Fox, Angela Ting, Matthew F. Kalady, Michael Cruise, Jean Ashburn, Jennifer Stiene, Wei Lai, David Liska, Shao Xiang, Emina H. Huang
2017	RNA-seq mixology: designing realistic control experiments to compare protocols and analysis methods Nucleic Acids Research Aliaksei Z. Holik, Charity W. Law, Ruijie Liu, Zeya Wang, Wenyi Wang, Jaeil Ahn, Marie-Liesse Asselin-Labat, Gordon K. Smyth, Matthew E. Ritchie
2017	Gut microbiota in Drosophila melanogaster interacts with Wolbachia but does not contribute to Wolbachia -mediated antiviral protection Journal of Invertebrate Pathology Yixin H. Ye, Andrei Seleznev, Heather A. Flores, Megan Woolfit, Elizabeth A. McGraw
2017	RNA-Seq analysis on chicken taste sensory organs: An ideal system to study organogenesis Scientific Reports Xiaogang Cui, Brett Marshall, Ning Shi, Shi-You Chen, Romdhane Rekaya, Hong-Xiang Liu
2017	Analysis of sucrose-induced small RNAs in Streptococcus mutans in the presence of different sucrose concentrations Applied Microbiology and Biotechnology Shan Shan Liu, Wen Hui Zhu, Qing Hui Zhi, Jia Liu, Yan Wang, Huan Cai Lin
2016	From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline F1000Research Yunshun Chen, Aaron T. L. Lun, Gordon K. Smyth
2016	A Novel FC116/BC10 Mutation Distinctively Causes Alteration in the Expression of the Genes for Cell Wall Polymer Synthesis in Rice Frontiers in Plant Science Mingliang Zhang, Feng Wei, Kai Guo, Zhen Hu, Yuyang Li, Guosheng Xie, Yanting Wang, Xiwen Cai, Liangcai Peng, Lingqiang Wang
2016	Use of p-value plots to diagnose and remedy problems with statistical analysis of microarray data Genes & Genomics Taewon Lee, Robert R. Delongchamp, Wonkuk Kim, Robert J. Shmookler Reis
2016	Single-cell RNA-seq reveals novel regulators of human embryonic stem cell differentiation to definitive endoderm Genome Biology Li-Fang Chu, Ning Leng, Jue Zhang, Zhonggang Hou, Daniel Mamott, David T. Vereide, Jeea Choi, Christina Kendziorski, Ron Stewart, James A. Thomson
2016	From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline F1000Research Yunshun Chen, Aaron T. L. Lun, Gordon K. Smyth
2016	De Novo Transcriptome Analysis for Kentucky Bluegrass Dwarf Mutants Induced by Space Mutation PLOS ONE Lu Gan, Rong Di, Yuehui Chao, Liebao Han, Xingwu Chen, Chao Wu, Shuxia Yin
2016	How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use? RNA Nicholas J. Schurch, Pietá Schofield, Marek Gierliński, Christian Cole, Alexander Sherstnev, Vijender Singh, Nicola Wrobel, Karim Gharbi, Gordon G. Simpson, Tom Owen-Hughes, Mark Blaxter, Geoffrey J. Barton
2015	An automated RNA-Seq analysis pipeline to identify and visualize differentially expressed genes and pathways in CHO cells Biotechnology Progress Chun Chen, Huong Le, Chetan T. Goudar
2015	Integrative Transcriptome Profiling of Cognitive Aging and Its Preservation through Ser/Thr Protein Phosphatase Regulation PLOS ONE C. Sehwan Park, Amandine Valomon, Hans Welzl
2015	In-Depth Duodenal Transcriptome Survey in Chickens with Divergent Feed Efficiency Using RNA-Seq PLOS ONE Guoqiang Yi, Jingwei Yuan, Huijuan Bi, Wei Yan, Ning Yang, Lujiang Qu
2015	Detecting Differentially Expressed Genes with RNA-seq Data Using Backward Selection to Account for the Effects of Relevant Covariates Journal of Agricultural, Biological, and Environmental Statistics Yet Nguyen, Dan Nettleton, Haibo Liu, Christopher K. Tuggle
2015	Towards next generation CHO cell biology: Bioinformatics methods for RNA‐Seq‐based expression profiling Biotechnology Journal Craig Monger, Paul S. Kelly, Clair Gallagher, Martin Clynes, Niall Barron, Colin Clarke
2015	SimSeq: a nonparametric approach to simulation of RNA-sequence datasets Bioinformatics Sam Benidt, Dan Nettleton
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