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
Yunshun ChenUniversity of Melbourne, Walter and Eliza Hall Institute of Medical ResearchVerified email at wehi.edu.au
Aaron LunGenentech, Inc.Verified email at gene.com
Oliver StegleGerman Cancer Research Center (DKFZ) & EMBL HeidelbergVerified 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
Marc Jan BonderPostdoc & Team-leader, DKFZVerified email at dkfz.de
Kieran R CampbellTorontoVerified email at lunenfeld.ca
Florian BuettnerFrankfurt University/DKFZVerified email at med.uni-frankfurt.de
Anna SE CuomoResearch Associate, Wellcome Sanger InstituteVerified email at sanger.ac.uk
Yuanhua HuangAssistant Professor, Univeristy of Hong KongVerified email at hku.hk
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 D SeatonScientific Leader, Human genetics, GSKVerified email at gsk.com
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	20690	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	2892	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, 2013	1020	2013
The genetic architecture of type 2 diabetes C Fuchsberger, J Flannick, TM Teslovich, A Mahajan, V Agarwala, ... Nature 536 (7614), 41-47, 2016	848	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	624	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	603	2016
Testing significance relative to a fold-change threshold is a TREAT DJ McCarthy, GK Smyth Bioinformatics 25 (6), 765-771, 2009	455	2009
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	321	2017
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	319	2016
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	277	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	240	2012
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	214	2020
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	169	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	123	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	88	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	66	2017
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	58	2020
NOX1 loss-of-function genetic variants in patients with inflammatory bowel disease T Schwerd, RV Bryant, S Pandey, M Capitani, L Meran, JB Cazier, J Jung, ... Mucosal immunology 11 (2), 562-574, 2018	39	2018
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	34	2019
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	33	2018

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