Davis J McCarthy

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Gordon K SmythDivision Head, Bioinformatics, Walter and Eliza Hall Institute of Medical ResearchVerified email at wehi.edu.au
Mark D. RobinsonAssociate Professor of Statistical Genomics, University of ZurichVerified email at imls.uzh.ch
John MarioniEMBL-EBIVerified email at ebi.ac.uk
Aaron LunGenentech, Inc.Verified email at gene.com
Yunshun ChenLaboratory Head, Walter and Eliza Hall Institute of Medical ResearchVerified email at wehi.edu.au
Oliver StegleGerman Cancer Research Center (DKFZ) & EMBL HeidelbergVerified email at dkfz.de
Marc Jan BonderPostdoc & Team-leader, DKFZVerified email at dkfz.de
Sarah A. TeichmannWellcome Sanger Institute & University of CambridgeVerified email at cam.ac.uk
Wolfgang HuberEMBL - European Molecular Biology LaboratoryVerified email at embl.de
Florian BuettnerFrankfurt University/DKFZVerified email at med.uni-frankfurt.de
Kieran R CampbellTorontoVerified email at lunenfeld.ca
Anna SE CuomoPostdoctoral Researcher, Garvan Institute of Medical ResearchVerified email at garvan.org.au
Yuanhua HuangAssistant Professor, Univeristy of Hong KongVerified email at hku.hk
Daniel D SeatonScientific director, Computational biology, GSKVerified email at gsk.com
Manuel A. RivasAssistant Professor, Department of Biomedical Data Science, Stanford UniversityVerified email at stanford.edu
Peter HumburgStatistician, UNSWVerified email at unsw.edu.au
Kyle Jeffrie GaultonAssistant Professor, University of California San DiegoVerified email at ucsd.edu
Alexander KanapinSt Petersburg UniversityVerified email at spbu.ru
Daniel GaffneyDirectory, Therapeutics, Genomics plcVerified email at genomicsplc.com
Alicia OshlackPeter MacCallum Cancer CentreVerified email at petermac.org

Davis J McCarthy

Head, Bioinformatics and Cellular Genomics, St Vincent's Institute of Medical Research

Verified email at svi.edu.au - Homepage

Statistics Genetics Gene Expression


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edgeR: a Bioconductor package for differential expression analysis of digital gene expression data MD Robinson, DJ McCarthy, GK Smyth Bioinformatics 26 (1), 139-140, 2010	25308	2010
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	3605	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	1093	2013
The genetic architecture of type 2 diabetes C Fuchsberger, J Flannick, TM Teslovich, A Mahajan, V Agarwala, ... Nature 536 (7614), 41-47, 2016	993	2016
Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R DJ McCarthy, KR Campbell, ATL Lun, QF Wills Bioinformatics 33 (8), 1179-1186, 2017	842	2017
A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor ATL Lun, DJ McCarthy, JC Marioni F1000Research 5, 2016	842	2016
Testing significance relative to a fold-change threshold is a TREAT DJ McCarthy, GK Smyth Bioinformatics 25 (6), 765-771, 2009	522	2009
Classification of low quality cells from single-cell RNA-seq data T Ilicic, JK Kim, AA Kolodziejczyk, FO Bagger, DJ McCarthy, JC Marioni, ... Genome biology 17 (1), 1-15, 2016	424	2016
Eleven grand challenges in single-cell data science D Lähnemann, J Köster, E Szczurek, DJ McCarthy, SC Hicks, ... Genome biology 21 (1), 1-35, 2020	400	2020
Common genetic variation drives molecular heterogeneity in human iPSCs H Kilpinen, A Goncalves, A Leha, V Afzal, K Alasoo, S Ashford, S Bala, ... Nature 546 (7658), 370-375, 2017	398	2017
Factors influencing success of clinical genome sequencing across a broad spectrum of disorders JC Taylor, HC Martin, S Lise, J Broxholme, JB Cazier, A Rimmer, ... Nature genetics 47 (7), 717-726, 2015	319	2015
Detecting differential expression in RNA-sequence data using quasi-likelihood with shrunken dispersion estimates SP Lund, D Nettleton, DJ McCarthy, GK Smyth Statistical applications in genetics and molecular biology 11 (5), 2012	268	2012
Choice of transcripts and software has a large effect on variant annotation DJ McCarthy, P Humburg, A Kanapin, MA Rivas, K Gaulton, JB Cazier, ... Genome medicine 6 (3), 1-16, 2014	184	2014
Whole-genome sequencing of bladder cancers reveals somatic CDKN1A mutations and clinicopathological associations with mutation burden JB Cazier, SR Rao, CM McLean, AK Walker, BJ Wright, EEM Jaeger, ... Nature communications 5 (1), 1-13, 2014	150	2014
Benchmarking single-cell RNA-sequencing protocols for cell atlas projects E Mereu, A Lafzi, C Moutinho, C Ziegenhain, DJ McCarthy, ... Nature biotechnology 38 (6), 747-755, 2020	149	2020
Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression ASE Cuomo, DD Seaton, DJ McCarthy, I Martinez, MJ Bonder, ... Nature communications 11 (1), 1-14, 2020	122	2020
f-scLVM: scalable and versatile factor analysis for single-cell RNA-seq F Buettner, N Pratanwanich, DJ McCarthy, JC Marioni, O Stegle Genome biology 18 (1), 1-13, 2017	88	2017
Vireo: Bayesian demultiplexing of pooled single-cell RNA-seq data without genotype reference Y Huang, DJ McCarthy, O Stegle Genome biology 20 (1), 1-12, 2019	61	2019
Tutorial: guidelines for the computational analysis of single-cell RNA sequencing data TS Andrews, VY Kiselev, D McCarthy, M Hemberg Nature protocols 16 (1), 1-9, 2021	60	2021
Visualization of biomedical data SI O'Donoghue, BF Baldi, SJ Clark, AE Darling, JM Hogan, S Kaur, ... Annual Review of Biomedical Data Science 1, 275-304, 2018	59	2018

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