Publications by Researcher: McCarthy, DJ

Year	Title	Author(s)
2016	Classification of low quality cells from single-cell RNA-seq data Genome Biol.	Ilicic, T Kim, JK Kolodziejczyk, AA Bagger, FO McCarthy, DJ Marioni, JC Teichmann, SA
2017	Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R Bioinformatics	McCarthy, DJ Campbell, KR Lun, ATL Wills, QF
2017	f-scLVM: scalable and versatile factor analysis for single-cell RNA-seq Genome Biol.	Buettner, F Pratanwanich, N McCarthy, DJ Marioni, JC Stegle, O
2019	Vireo: Bayesian demultiplexing of pooled single-cell RNA-seq data without genotype reference Genome Biology	Huang, YH McCarthy, DJ Stegle, O
2019	Method to Synchronize Cell Cycle of Human Pluripotent Stem Cells without Affecting Their Fundamental Characteristics Stem Cell Rep.	Yiangou, L Grandy, RA Morell, CM Tomaz, RA Osnato, A Kadiwala, J Muraro, D Garcia-Bernardo, J Nakanoh, S Bernard, WG Ortmann, D McCarthy, DJ Simonic, I Sinha, S Vallier, L
2020	Cardelino: computational integration of somatic clonal substructure and single-cell transcriptomes Nature Methods	McCarthy, DJ Rostom, R Huang, YH Kunz, DJ Danecek, P Bonder, MJ Hagai, T Lyu, RQ Wang, WY Gaffney, DJ Simons, BD Stegle, O Teichmann, SA
2020	Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression Nature Communications	Cuomo, ASE Seaton, DD McCarthy, DJ Martinez, I Bonder, MJ Garcia-Bernardo, J Amatya, S Madrigal, P Isaacson, A Buettner, F Knights, A Natarajan, KN Vallier, L Marioni, JC Chhatriwala, M Stegle, O
2020	Eleven grand challenges in single-cell data science Genome Biology	Lahnemann, D Koster, J Szczurek, E McCarthy, DJ Hicks, SC Robinson, MD Vallejos, CA Campbell, KR Beerenwinkel, N Mahfouz, A Pinello, L Skums, P Stamatakis, A Attolini, CSO Aparicio, S Baaijens, J Balvert, M de Barbanson, B Cappuccio, A Corleone, G Dutilh, BE Florescu, M Guryev, V Holmer, R Jahn, K Lobo, TJ Keizer, EM Khatri, I Kielbasa, SM Korbel, JO Kozlov, AM Kuo, TH Lelieveldt, BPF Mandoiu, II Marioni, JC Marschall, T Molder, F Niknejad, A Raczkowski, L Reinders, M de Ridder, J Saliba, AE Somarakis, A Stegle, O Theis, FJ Yang, H Zelikovsky, A McHardy, AC Raphael, BJ Shah, SRP Schonhuth, A
2020	Benchmarking single-cell RNA-sequencing protocols for cell atlas projects Nature Biotechnology	Mereu, E Lafzi, A Moutinho, C Ziegenhain, C McCarthy, DJ Alvarez-Varela, A Batlle, E Sagar Grun, D Lau, JK Boutet, SC Sanada, C Ooi, A Jones, RC Kaihara, K Brampton, C Talaga, Y Sasagawa, Y Tanaka, K Hayashi, T Braeuning, C Fischer, C Sauers, S Trefzer, T Conrad, C Adiconis, X Nguyen, LT Regev, A Levin, JZ Parekh, S Janjic, A Wange, LE Bagnoli, JW Enard, W Gut, M Sandberg, R Nikaido, I Gut, I Stegle, O Heyn, H
2021	Personalized genome structure via single gamete sequencing Genome Biology	Lyu, R Tsui, V McCarthy, DJ Crismani, W
2021	Optimizing expression quantitative trait locus mapping workflows for single-cell studies Genome Biology	Cuomo, ASE Alvari, G Azodi, CB McCarthy, DJ Bonder, MJ
2021	splatPop: simulating population scale single-cell RNA sequencing data Genome Biology	Azodi, CB Zappia, L Oshlack, A McCarthy, DJ