Yunshun Chen

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Gordon K SmythDivision Head, Bioinformatics, Walter and Eliza Hall Institute of Medical ResearchVerified email at wehi.edu.au
Mark D. RobinsonFull Professor of Statistical Genomics, University of ZurichVerified email at mls.uzh.ch
Davis J McCarthyHead, Bioinformatics and Cellular Genomics, St Vincent's Institute of Medical ResearchVerified email at svi.edu.au
Jane VisvaderThe Walter and Eliza Hall Institute of Medical ResearchVerified email at wehi.edu.au
Wei ShiProfessor, Monash UniversityVerified email at monash.edu
Geoffrey LindemanThe Walter and Eliza Hall Institute, Royal Melbourne Hospital and Peter MacCallum Cancer CentreVerified email at wehi.edu.au
Bhupinder PalLaboratory Head, Olivia Newton-John Cancer Research InstituteVerified email at onjcri.org.au
Charity W LawThe Walter and Eliza Hall Institute of Medical ResearchVerified email at wehi.edu.au
Aaron LunGenentech, Inc.Verified email at gene.com
Naiyang FUThe Walter and Eliza Hall Institute of Medical ResearchVerified email at wehi.edu.au
Xiaoyu SongWalter and Eliza Hall Institute of Medical ResearchVerified email at wehi.edu.au
Professor Tony PapenfussDeputy Director, Walter and Eliza Hall Institute of Medical ResearchVerified email at wehi.edu.au
Leon Di StefanoPostdoctoral Research Fellow, Murdoch Children's Research InstituteVerified email at mcri.edu.au
Caleb A Dawson, PhDThe Walter and Eliza Hall Institute of Medical ResearchVerified email at wehi.edu.au
Asselin-LabatThe Walter and Eliza Hall Institute of Medical ResearchVerified email at wehi.edu.au
Andreas StrasserThe Walter and Eliza Hall InstituteVerified email at wehi.edu.au
Kim Jacobson (publication names: Ki...Monash UniversityVerified email at monash.edu

Yunshun Chen

Laboratory Head, Walter and Eliza Hall Institute of Medical Research

Verified email at wehi.edu.au

RNA-Seq Single-cell Technology Differential expression Statistics Generalized linear models


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Voom: precision weights unlock linear model analysis tools for RNA-seq read counts CW Law, Y Chen, W Shi, GK Smyth Genome Biology 15 (2), R29, 2014	6204	2014
Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation DJ McCarthy, Y Chen, GK Smyth Nucleic acids research 40 (10), 4288-4297, 2012	5415	2012
Count-based differential expression analysis of RNA sequencing data using R and Bioconductor S Anders, DJ McCarthy, Y Chen, M Okoniewski, GK Smyth, W Huber, ... Nature protocols 8 (9), 1765-1786, 2013	1358	2013
From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline Y Chen, ATL Lun, GK Smyth F1000Research 5, 2016	1314	2016
It’s DE-licious: a recipe for differential expression analyses of RNA-seq experiments using quasi-likelihood methods in edgeR ATL Lun, Y Chen, GK Smyth Statistical Genomics, 391-416, 2016	441	2016
A single‐cell RNA expression atlas of normal, preneoplastic and tumorigenic states in the human breast B Pal, Y Chen, F Vaillant, BD Capaldo, R Joyce, X Song, VL Bryant, ... The EMBO journal 40 (11), e107333, 2021	305	2021
Differential Expression Analysis of Complex RNA-seq Experiments Using edgeR Y Chen, ATL Lun, GK Smyth Statistical Analysis of Next Generation Sequencing Data, 51-74, 2014	215	2014
Construction of developmental lineage relationships in the mouse mammary gland by single-cell RNA profiling B Pal, Y Chen, F Vaillant, P Jamieson, L Gordon, AC Rios, S Wilcox, N Fu, ... Nature communications 8 (1), 1-14, 2017	206	2017
Intraclonal plasticity in mammary tumors revealed through large-scale single-cell resolution 3d imaging AC Rios, BD Capaldo, F Vaillant, B Pal, R van Ineveld, CA Dawson, ... Cancer cell 35 (4), 618-632. e6, 2019	165	2019
edgeR: differential expression analysis of digital gene expression data User’s Guide Y Chen, D McCarthy, M Robinson, GK Smyth Bioconductor User’s Guide, 2014	146	2014
Barcoding reveals complex clonal behavior in patient-derived xenografts of metastatic triple negative breast cancer D Merino, TS Weber, A Serrano, F Vaillant, K Liu, B Pal, L Di Stefano, ... Nature communications 10 (1), 1-12, 2019	143	2019
statmod: Statistical modeling G Smyth, Y Hu, P Dunn, B Phipson, Y Chen R package version 1 (4), 17, 2013	115*	2013
Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR Y Chen, B Pal, JE Visvader, GK Smyth F1000Research 6, 2017	101	2017
edgeR v4: powerful differential analysis of sequencing data with expanded functionality and improved support for small counts and larger datasets Y Chen, L Chen, ATL Lun, PL Baldoni, GK Smyth Nucleic Acids Research 53 (2), gkaf018, 2025	92	2025
Mammary tumour cells remodel the bone marrow vascular microenvironment to support metastasis RKH Yip, JS Rimes, BD Capaldo, F Vaillant, KA Mouchemore, B Pal, ... Nature communications 12 (1), 1-17, 2021	77	2021
Calling differentially methylated regions from whole genome bisulphite sequencing with DMRcate TJ Peters, MJ Buckley, Y Chen, GK Smyth, CC Goodnow, SJ Clark Nucleic Acids Research, 2021	70	2021
c-Myb Regulates the T-Bet-Dependent Differentiation Program in B Cells to Coordinate Antibody Responses D Piovesan, J Tempany, A Di Pietro, I Baas, C Yiannis, K O’Donnell, ... Cell Reports 19 (3), 461-470, 2017	63	2017
Regulation of germinal center responses and B-cell memory by the chromatin modifier MOZ KL Good-Jacobson, Y Chen, AK Voss, GK Smyth, T Thomas, D Tarlinton Proceedings of the National Academy of Sciences 111 (26), 9585-9590, 2014	62	2014
edgeR: differential analysis of sequence read count data User’s Guide Y Chen, D McCarthy, M Ritchie, M Robinson, G Smyth, E Hall Accessed: Jul 8, 2020	55	2020
Lung Basal Stem Cells Rapidly Repair DNA Damage Using the Error-Prone Nonhomologous End-Joining Pathway CE Weeden, Y Chen, SB Ma, Y Hu, G Ramm, KD Sutherland, GK Smyth, ... PLOS Biology 15 (1), e2000731, 2017	53	2017

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