By Professor Joseph Powell

Preprints

Chin VT; Muskovic W; McCloy RA; Neavin DR; Alquicira-Hernandez J; Arora H; Senabouth A; Keith P; Spenceley E; Murphy A; Kaczorowski D; Floros P; Earls P; Leavers B; Crawford J; Gallagher R; Powell JE, 2024, Protein Translation Dysregulation and Immune Cell Evasion Define Metastatic Clones in HPV-related Cancer of the Oropharynx, , http://dx.doi.org/10.1101/2024.04.15.589624

Rumker L; Sakaue S; Reshef Y; Kang JB; Yazar S; Alquicira-Hernandez J; Valencia C; Lagattuta KA; Mah-Som A; Nathan A; Powell JE; Loh P-R; Raychaudhuri S, 2023, Identifying genetic variants that influence the abundance of cell states in single-cell data., , http://dx.doi.org/10.1101/2023.11.13.566919

Greatbatch CJ; Lu Q; Hung S; Wing K; Liang H; Han X; Zhou T; Siggs OM; Mackey DA; Cook AL; Senabouth A; Liu G-S; Craig JE; MacGregor S; Powell JE; Hewitt AW, 2023, High throughput functional profiling of genes at intraocular pressure loci reveals distinct networks for glaucoma, , http://dx.doi.org/10.1101/2023.07.10.548340

Shen S; Werner T; Sun Y; Shim WJ; Lukowski S; Andersen S; Chiu HS; Xia D; Pham D; Su Z; Kim D; Yang P; Chen X; Tan MC; Powell JE; Tam PPL; Bodén M; Ho JWK; Nguyen Q; Palpant NJ, 2022, An integrated cell barcoding and computational analysis pipeline for scalable analysis of differentiation at single-cell resolution, , http://dx.doi.org/10.1101/2022.10.12.511862

Xue A; Yazar S; Neavin D; Powell JE, 2022, Pitfalls and opportunities for applying PEER factors in single-cell eQTL analyses, , http://dx.doi.org/10.1101/2022.08.02.502566

Maksimovic J; Shanthikumar S; Howitt G; Hickey PF; Ho W; Anttila C; Brown DV; Senabouth A; Kaczorowski D; Amann-Zalcenstein D; Powell JE; Ranganathan SC; Oshlack A; Neeland MR, 2022, Single-cell atlas of bronchoalveolar lavage from preschool cystic fibrosis reveals new cell phenotypes, , http://dx.doi.org/10.1101/2022.06.17.496207

Luecken M; Sikkema L; Strobl D; Zappia L; Madissoon E; Markov N; Zaragosi L-E; Ansari M; Arguel M-J; Apperloo L; Becavin C; Berg M; Chichelnitskiy E; Chung M-I; Collin A; Gay A; Kashani BH; Jain M; Kapellos T; Kole T; Mayr C; von Papen M; Peter L; Ramírez-Suástegui C; Schniering J; Taylor C; Walzthoeni T; Xu C; Bui L; de Donno C; Dony L; Guo M; Gutierrez A; Heumos L; Huang N; Río IID; Jackson N; Murthy PKL; Lotfollahi M; Tabib T; Talavera-Lopez C; Travaglini K; Wilbrey-Clark A; Worlock K; Yoshida M; Desai T; Rozenblatt-Rosen O; Falk C; Kaminski N; Krasnow M; Lafyatis R; Nikolic M; Powell J; Rajagopal J; Seibold M; Sheppard D; Shepherd D; Teichmann S; Tsankov A; Whitsett J; Xu Y; Banovich N; Barbry P; Duong T; Meyer K; Kropski J; Pe'er D; Schiller H; Tata PR; Schultze J; Berge MVD; Chen Y; Hagood J; Hassan A; Horvath P; Lundeberg J; Leroy S; Marquette C; Pryhuber G; Samakovlis C; Sun X; Ware L; Zhang K; Misharin A; Nawijn M; Theis F, 2022, An integrated cell atlas of the human lung in health and disease, , http://dx.doi.org/10.21203/rs.3.rs-1438584/v1

Neavin D; Senabouth A; Hang Lee JT; Ripoll A; Franke L; Prabhakar S; Ye CJ; McCarthy DJ; Melé M; Hemberg M; Powell JE, 2022, Demuxafy: Improvement in droplet assignment by integrating multiple single-cell demultiplexing and doublet detection methods, , http://dx.doi.org/10.1101/2022.03.07.483367

Grimm L; Mason E; Yu O; Dudczig S; Panara V; Chen T; Bower NI; Paterson S; Okuda K; Galeano MR; Kobayashi S; Senabouth A; Lagendijk AK; Powell J; Smith KA; Koltowska K; Hogan BM, 2022, Single cell analysis of lymphatic endothelial cell fate specification and differentiation during zebrafish development, , http://dx.doi.org/10.1101/2022.02.10.479999

Phipson B; Sim CB; Porrello ER; Hewitt AW; Powell J; Oshlack A, 2021, propeller: testing for differences in cell type proportions in single cell data, , http://dx.doi.org/10.1101/2021.11.28.470236

Patel B; Kleeman SO; Neavin D; Powell J; Baskozos G; Ng M; Ahmed W-U-R; Bennett DL; Schmid A; Furniss D; Wiberg A, 2021, DIRC3-IGFBP5 is a shared genetic risk locus and therapeutic target for carpal tunnel syndrome and trigger finger, , http://dx.doi.org/10.1101/2021.10.07.21264697

Senabouth A; Daniszewski M; Lidgerwood GE; Liang HH; Hernández D; Mirzaei M; Zhang R; Han X; Neavin D; Rooney L; Sanchez IL; Gulluyan L; Paulo JA; Clarke L; Kearns LS; Gnanasambandapillai V; Chan C-L; Nguyen U; Steinmann AM; Zekanovic R; Farbehi N; Gupta VK; Mackey DA; Bylsma G; Verma N; MacGregor S; Guymer RH; Powell JE; Hewitt AW; Pébay A, 2021, Transcriptomic and proteomic retinal pigment epithelium signatures of age-related macular degeneration, , http://dx.doi.org/10.1101/2021.08.19.457044

Neavin DR; Steinmann AM; Chiu HS; Daniszewski MS; Moutinho C; Chan C-L; Tyebally M; Gnanasambandapillai V; Lam CE; Nguyen U; Hernández D; Lidgerwood GE; Hewitt AW; Pébay A; Palpant NJ; Powell JE, 2021, Village in a dish: a model system for population-scale hiPSC studies, , http://dx.doi.org/10.1101/2021.08.19.457030

Muskovic W; Powell JE, 2021, DropletQC: improved identification of empty droplets and damaged cells in single-cell RNA-seq data, , http://dx.doi.org/10.1101/2021.08.02.454717

Daniszewski MS; Senabouth A; Liang HH; Han X; Lidgerwood GE; Hernández D; Sivakumaran P; Clarke JE; Lim SY; Lees JG; Rooney L; Gulluyan L; Souzeau E; Graham SL; Chan C-L; Nguyen U; Farbehi N; Gnanasambandapillai V; McCloy RA; Clarke L; Kearns L; Mackey DA; Craig JE; MacGregor S; Powell JE; Pébay A; Hewitt AW, 2021, Retinal ganglion cell-specific genetic regulation in primary open angle glaucoma, , http://dx.doi.org/10.1101/2021.07.14.452417

Talenti A; Powell J; Hemmink JD; Cook EAJ; Wragg D; Jayaraman S; Paxton E; Ezeasor C; Obishakin ET; Agusi ER; Tijjani A; Marshall K; Fisch A; Ferreira B; Qasim A; Chaudhry UN; Wiener P; P. T; Morrison LJ; Connelley T; Prendergast J, 2021, A cattle graph genome incorporating global breed diversity, , http://dx.doi.org/10.1101/2021.06.23.449389

Wilson SB; Howden SE; Vanslambrouck JM; Dorison A; Alquicira-Hernandez J; Powell JE; Little MH, 2021, DevKidCC allows for robust classification and direct comparisons of kidney organoid datasets, , http://dx.doi.org/10.1101/2021.01.20.427346

Nieto P; Elosua-Bayes M; Trincado JL; Marchese D; Massoni-Badosa R; Salvany M; Henriques A; Mereu E; Moutinho C; Ruiz S; Lorden P; Chin VT; Kaczorowski D; Chan C-L; Gallagher R; Chou A; Planas-Rigol E; Rubio-Perez C; Gut I; Piulats JM; Seoane J; Powell JE; Batlle E; Heyn H, 2020, A Single-Cell Tumor Immune Atlas for Precision Oncology, , http://dx.doi.org/10.1101/2020.10.26.354829

Alquicira-Hernandez J; Powell JE, 2020, Nebulosa recovers single cell gene expression signals by kernel density estimation, , http://dx.doi.org/10.1101/2020.09.29.315879

Alquicira-Hernandez J; Powell JE; Phan TG, 2020, No evidence that plasmablasts transdifferentiate into developing neutrophils in severe COVID-19 disease, , http://dx.doi.org/10.1101/2020.09.27.312538

Neavin D; Nguyen Q; Daniszewski MS; Liang HH; Chiu HS; Senabouth A; Lukowski SW; Crombie DE; Lidgerwood GE; Hernández D; Vickers JC; Cook AL; Palpant NJ; Pébay A; Hewitt AW; Powell JE, 2020, Single cell eQTL analysis identifies cell type-specific genetic control of gene expression in fibroblasts and reprogrammed induced pluripotent stem cells, , http://dx.doi.org/10.1101/2020.06.21.163766

Engel JA; Lee HJ; Williams CG; Kuns R; Olver S; Lansink LIM; Soon MSF; Andersen SB; Powell JE; Svensson V; Teichmann SA; Hill GR; Varelias A; Koyama M; Haque A, 2020, Single-cell transcriptomics of allo-reactive CD4⁺ T cells over time reveals divergent fates during gut GVHD, , http://dx.doi.org/10.1101/2020.03.08.978239

Cobos FA; Alquicira-Hernandez J; Powell J; Mestdagh P; De Preter K, 2020, Comprehensive benchmarking of computational deconvolution of transcriptomics data, , http://dx.doi.org/10.1101/2020.01.10.897116

Lidgerwood GE; Senabouth A; Smith-Anttila CJA; Gnanasambandapillai V; Kaczorowski DC; Amann-Zalcenstein D; Fletcher EL; Naik SH; Hewitt AW; Powell JE; Pébay A, 2019, Transcriptomic Profiling of Human Pluripotent Stem Cell-Derived Retinal Pigment Epithelium Over Time, , http://dx.doi.org/10.1101/842328

van der Wijst MGP; de Vries DH; Groot HE; Trynka G; Hon C-C; Nawijn MC; Idaghdour Y; van der Harst P; Ye CJ; Powell J; Theis FJ; Mahfouz A; Heinig M; Franke L, 2019, Single-cell eQTLGen Consortium: a personalized understanding of disease, , http://dx.doi.org/10.48550/arxiv.1909.12550

Xu J; Falconer C; Nguyen Q; Crawford J; McKinnon BD; Mortlock S; Pébay A; Hewitt AW; Senabouth A; Andersen S; Palpant N; Chiu HS; Montgomery GW; Powell J; Coin L, 2019, Genotype-free demultiplexing of pooled single-cell RNA-seq, , http://dx.doi.org/10.1101/570614

Senabouth A; Andersen S; Shi Q; Shi L; Liu P; Jiang F; Zhang W; Wing K; Daniszewski M; Lukowski SW; Hung SSC; Nguyen Q; Fink L; Beckhouse A; Jiang H; Pébay A; Hewitt AW; Powell JE, 2019, Comparative performance of the BGI and Illumina sequencing technology for single-cell RNA-sequencing, , http://dx.doi.org/10.1101/552588

Wang H; Zhang F; Zeng J; Wu Y; Kemper KE; Xue A; Zhang M; Powell JE; Goddard ME; Wray NR; Visscher PM; McRae AF; Yang J, 2019, Genotype-by-environment interactions inferred from genetic effects on phenotypic variability in the UK Biobank, , http://dx.doi.org/10.1101/519538

Võsa U; Claringbould A; Westra H-J; Bonder MJ; Deelen P; Zeng B; Kirsten H; Saha A; Kreuzhuber R; Kasela S; Pervjakova N; Alvaes I; Fave M-J; Agbessi M; Christiansen M; Jansen R; Seppälä I; Tong L; Teumer A; Schramm K; Hemani G; Verlouw J; Yaghootkar H; Sönmez R; Brown A; Kukushkina V; Kalnapenkis A; Rüeger S; Porcu E; Kronberg-Guzman J; Kettunen J; Powell J; Lee B; Zhang F; Arindrarto W; Beutner F; Brugge H; Dmitreva J; Elansary M; Fairfax BP; Georges M; Heijmans BT; Kähönen M; Kim Y; Knight JC; Kovacs P; Krohn K; Li S; Loeffler M; Marigorta UM; Mei H; Momozawa Y; Müller-Nurasyid M; Nauck M; Nivard M; Penninx B; Pritchard J; Raitakari O; Rotzchke O; Slagboom EP; Stehouwer CDA; Stumvoll M; Sullivan P; Hoen PACT; Thiery J; Tönjes A; van Dongen J; van Iterson M; Veldink J; Völker U; Wijmenga C; Swertz M; Andiappan A; Montgomery GW; Ripatti S; Perola M; Kutalik Z; Dermitzakis E; Bergmann S; Frayling T; van Meurs J; Prokisch H; Ahsan H; Pierce B; Lehtimäki T; Boomsma D; Psaty BM; Gharib SA; Awadalla P; Milani L; Ouwehand W; Downes K; Stegle O; Battle A; Yang J; Visscher PM; Scholz M; Gibson G; Esko T; Franke L, 2018, Unraveling the polygenic architecture of complex traits using blood eQTL metaanalysis, , http://dx.doi.org/10.1101/447367

Lukowski SW; Lo CY; Sharov A; Nguyen QH; Fang L; Hung SSC; Zhu L; Zhang T; Nguyen T; Senabouth A; Jabbari JS; Welby E; Sowden JC; Waugh HS; Mackey A; Pollock G; Lamb TD; Wang P-Y; Hewitt AW; Gillies M; Powell JE; Wong RCB, 2018, Generation of human neural retina transcriptome atlas by single cell RNA sequencing, , http://dx.doi.org/10.1101/425223

Alquicira-Hernández J; Sathe A; Ji HP; Nguyen Q; Powell JE, 2018, scPred: Cell type prediction at single-cell resolution, , http://dx.doi.org/10.1101/369538

De Smit E; Lukowski SW; Anderson L; Senabouth A; Dauyey K; Song S; Wyse B; Wheeler L; Chen CY; Cao K; Yuen AWT; Shuey N; Clarke L; Sanchez IL; Hung SSC; Pébay A; Mackey DA; Brown MA; Hewitt AW; Powell JE, 2018, Longitudinal expression profiling of CD4+ and CD8+ cells in patients with active to quiescent Giant Cell Arteritis, , http://dx.doi.org/10.1101/243493

Friedman CE; Nguyen Q; Lukowski SW; Chiu HS; Helfer A; Miklas J; Suo SS; Jackie Han J-D; Osteil P; Peng G; Jing N; Baillie GJ; Senabouth A; Christ AN; Bruxner TJ; Murry CE; Wong ES; Ding J; Wang Y; Hudson J; Ruohola-Baker H; Bar-Joseph Z; Tam PPL; Powell JE; Palpant NJ, 2017, Analysis of cardiac differentiation at single cell resolution reveals a requirement of hypertrophic signaling for HOPX transcription, , http://dx.doi.org/10.1101/229294

Nguyen QH; Lukowski SW; Chiu HS; Friedman CE; Senabouth A; Crowhurst L; Bruxmer TJC; Christ AN; Palpant NJ; Powell JE, 2017, Determining cell fate specification and genetic contribution to cardiac disease risk in hiPSC-derived cardiomyocytes at single cell resolution, , http://dx.doi.org/10.1101/229336

Senabouth A; Lukowski SW; Alquicira Hernandez J; Andersen S; Mei X; Nguyen QH; Powell JE, 2017, ascend: R package for analysis of single cell RNA-seq data, , http://dx.doi.org/10.1101/207704

Daniszewski M; Senabouth A; Nguyen Q; Crombie DE; Lukowski SW; Kulkarni T; Zack DJ; Pébay A; Powell JE; Hewitt AW, 2017, Single Cell RNA Sequencing of stem cell-derived retinal ganglion cells, , http://dx.doi.org/10.1101/191395

McRae AF; Marioni RE; Shah S; Yang J; Powell JE; Harris SE; Gibson J; Henders AK; Bowdler L; Painter JN; Murphy L; Martin NG; Starr JM; Wray NR; Deary IJ; Visscher PM; Montgomery GW, 2017, Identification of 55,000 Replicated DNA Methylation QTL, , http://dx.doi.org/10.1101/166710

Zeng J; de Vlaming R; Wu Y; Robinson MR; Lloyd-Jones L; Yengo L; Yap C; Xue A; Sidorenko J; McRae AF; Powell JE; Montgomery GW; Metspalu A; Esko T; Gibson G; Wray NR; Visscher PM; Yang J, 2017, Widespread signatures of negative selection in the genetic architecture of human complex traits, , http://dx.doi.org/10.1101/145755

Wong ES; Chenoweth S; Blows M; Powell JE, 2017, Evidence for stabilizing selection at pleiotropic loci for human complex traits, , http://dx.doi.org/10.1101/126888

Nguyen QH; Lukowski SW; Chiu HS; Senabouth A; Bruxner TJC; Christ AN; Palpant NJ; Powell JE, 2017, Single-cell RNA-seq of human induced pluripotent stem cells reveals cellular heterogeneity and cell state transitions between subpopulations, , http://dx.doi.org/10.1101/119255

Zeng B; Lloyd-Jones LR; Holloway A; Marigorta UM; Metspalu A; Montgomery GW; Esko T; Brigham KL; Quyyumi AA; Idaghdour Y; Yang J; Visscher PM; Powell JE; Gibson G, 2016, Constraints on eQTL fine mapping in the presence of multi-site local regulation of gene expression, , http://dx.doi.org/10.1101/084293

Hung SSC; Chrysostomou V; Li F; Lim JKH; Wang J-H; Powell JE; Tu L; Daniszewski M; Lo C; Wong RC; Crowston JG; Pébay A; King AE; Bui BV; Liu G-S; Hewitt AW, 2016, AAV-mediated CRISPR/Cas gene editing of retinal cellsin vivo, , http://dx.doi.org/10.1101/039156

Tuong ZK; Lukowski SW; Nguyen QH; Chandra J; Zhou C; Gillinder K; Bashaw AA; Ferdinand JR; Stewart BJ; Teoh SM; Hanson SJ; Devitt K; Clatworthy MR; Powell JE; Frazer IH, A Model of Impaired Langerhans Cell Maturation Associated With HPV Induced Epithelial Hyperplasia, , http://dx.doi.org/10.2139/ssrn.3889711

Friedman CE; Nguyen Q; Lukowski SW; Helfer A; Chiu HS; Voges HK; Suo Suo S; Jackie Han J-D; Osteil P; Peng G; Jing N; Baillie GJ; Senabouth A; Christ AN; Bruxner TJ; Murry CE; Wong ES; Ding J; Wang Y; Hudson J; Bar-Joseph Z; Tam PPL; Powell JE; Palpant NJ, Cardiac Directed Differentiation Using Small Molecule WNT Modulation at Single-Cell Resolution, , http://dx.doi.org/10.2139/ssrn.3155757

Daniszewski M; Nguyen Q; Chy H; Singh V; Crombie D; Kulkarni T; Liang H; Lidgerwood G; Hernnndez D; Conquest A; Rooney L; Chevalier S; Andersen S; Senabouth A; Vickers J; Mackey D; Craig J; Laslett A; Hewitt A; Powell JE; PPbay A, Single Cell Profiling Identifies Key Pathways Expressed by iPSCs Cultured in Different Commercial Media, , http://dx.doi.org/10.2139/ssrn.3188388

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