Garvan-Weizmann Centre for Cellular Genomics (GWCCG) – Research


Myocyte-Specific Upregulation of ACE2 in Cardiovascular Disease: Implications for SARS-CoV-2-Mediated Myocarditis
Tucker, N. R.; Chaffin, M.; Bedi, K. C., Jr.; Papangeli, I.; Akkad, A. D.; Arduini, A.; Hayat, S.; Eraslan, G.; Muus, C.; Bhattacharyya, R. P.; Stegmann, C. M.; Human Cell Atlas Lung Biological, Network; Margulies, K. B.; Ellinor, P. T.; Human Cell Atlas Lung Biological Network Consortium, Members
CIRCULATION 142(7):708-710, 2020
The relationship between adrenocortical candidate gene expression and clinical response to hydrocortisone in patients with septic shock
Cohen, J.; Blumenthal, A.; Cuellar-Partida, G.; Evans, D. M.; Finfer, S.; Li, Q.; Ljungberg, J.; Myburgh, J.; Peach, E.; Powell, J.; Rajbhandari, D.; Rhodes, A.; Senabouth, A.; Venkatesh, B.
INTENSIVE CARE MEDICINE 47(9):974-983, 2021
PODNL1 Methylation Serves as a Prognostic Biomarker and Associates with Immune Cell Infiltration and Immune Checkpoint Blockade Response in Lower-Grade Glioma
Noor, H.; Zaman, A.; Teo, C.; Sughrue, M. E.
Single-Cell Immune Profiling in Coronary Artery Disease: The Role of State-of-the-Art Immunophenotyping With Mass Cytometry in the Diagnosis of Atherosclerosis
Kott, K. A.; Vernon, S. T.; Hansen, T.; de Dreu, M.; Das, S. K.; Powell, J.; Fazekas de St Groth, B.; Di Bartolo, B. A.; McGuire, H. M.; Figtree, G. A.
Journal of the American Heart Association 9(24):e017759, 2020
Single-cell transcriptomic analysis of cardiac differentiation from human PSCs reveals HOPX-dependent cardiomyocyte maturation
Friedman, C. E.; Nguyen, Q.; Lukowski, S. W.; Helfer, A.; Chiu, H. S.; Miklas, J.; Levy, S.; Suo, S.; Han, J. J.; Osteil, P.; Peng, G.; Jing, N.; Baillie, G. J.; Senabouth, A.; Christ, A. N.; Bruxner, T. J.; Murry, C. E.; Wong, E. S.; Ding, J.; Wang, Y.; Hudson, J.; Ruohola-Baker, H.; Bar-Joseph, Z.; Tam, P. P. L.; Powell, J. E.; Palpant, N. J.
Cell Stem Cell 23(4):586-598, 2018
Prevalence of Keratoconus Based on Scheimpflug Imaging: The Raine Study
Chan, E.; Chong, E. W.; Lingham, G.; Stevenson, L. J.; Sanfilippo, P. G.; Hewitt, A. W.; Mackey, D. A.; Yazar, S.
OPHTHALMOLOGY 128(4):515-521, 2021
Co-expression of calcium and hERG potassium channels reduces the incidence of proarrhythmic events
Ballouz, S.; Mangala, M. M.; Perry, M. D.; Heitmann, S.; Gillis, J. A.; Hill, A. P.; Vandenberg, J. I.
CARDIOVASCULAR RESEARCH 117(10):2216-2227, 2021
scGPS: Determining Cell States and Global Fate Potential of Subpopulations
Thompson, M.; Matsumoto, M.; Ma, T.; Senabouth, A.; Palpant, N. J.; Powell, J. E.; Nguyen, Q.
Frontiers in Genetics 12:666771, 2021
Phantom epistasis between unlinked loci
Hemani, G.; Powell, J. E.; Wang, H.; Shakhbazov, K.; Westra, H. J.; Esko, T.; Henders, A. K.; McRae, A. F.; Martin, N. G.; Metspalu, A.; Franke, L.; Montgomery, G. W.; Goddard, M. E.; Gibson, G.; Yang, J.; Visscher, P. M.
NATURE 596(7871):E1-E3, 2021
Transcriptomics and single-cell RNA-sequencing
Chambers, D. C.; Carew, A. M.; Lukowski, S. W.; Powell, J. E.
RESPIROLOGY 24(1):29-36, 2019
Re-engaging an inactive cohort of young adults: evaluating recruitment for the Kidskin Young Adult Myopia Study
Lingham, G.; Mackey, D. A.; Seed, N.; Ryan, L.; Milne, E.; Lucas, R. M.; Franchina, M.; Lee, S. S.; Yazar, S.
BMC Medical Research Methodology 20(1):127, 2020
SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes
Sungnak, W.; Huang, N.; Becavin, C.; Berg, M.; Queen, R.; Litvinukova, M.; Talavera-Lopez, C.; Maatz, H.; Reichart, D.; Sampaziotis, F.; Worlock, K. B.; Yoshida, M.; Barnes, J. L.; Network, H. C. A. Lung Biological Network
NATURE MEDICINE 26(5):681-687, 2020
Single-cell RNA-seq of human induced pluripotent stem cells reveals cellular heterogeneity and cell state transitions between subpopulations
Nguyen, Q. H.; Lukowski, S. W.; Chiu, H. S.; Senabouth, A.; Bruxner, T. J. C.; Christ, A. N.; Palpant, N. J.; Powell, J. E.
GENOME RESEARCH 28(7):1053-1066, 2018
Venomic, Transcriptomic, and Bioactivity Analyses of Pamphobeteus verdolaga Venom Reveal Complex Disulfide-Rich Peptides That Modulate Calcium Channels
Estrada-Gomez, S.; Cardoso, F. C.; Vargas-Munoz, L. J.; Quintana-Castillo, J. C.; Arenas Gomez, C. M.; Pineda, S. S.; Saldarriaga-Cordoba, M. M.
Toxins 11(9):496, 2019
Genotype-by-environment interactions inferred from genetic effects on phenotypic variability in the UK Biobank
Wang, H.; Zhang, F.; Zeng, J.; Wu, Y.; Kemper, K. E.; Xue, A.; Zhang, M.; Powell, J. E.; Goddard, M. E.; Wray, N. R.; Visscher, P. M.; McRae, A. F.; Yang, J.
Science Advances 5(8):eaaw3538, 2019
Optic Disc Measures in Obstructive Sleep Apnea: A Community-based Study of Middle-aged and Older Adults
Lee, S. S.; Sanfilippo, P. G.; Hunter, M.; Yazar, S.; James, A.; Mackey, D. A.
JOURNAL OF GLAUCOMA 29(5):337-343, 2020
Dynamics of human monocytes and airway macrophages during healthy aging and after transplant
Byrne, A. J.; Powell, J. E.; O'Sullivan, B. J.; Ogger, P. P.; Hoffland, A.; Cook, J.; Bonner, K. L.; Hewitt, R. J.; Wolf, S.; Ghai, P.; Walker, S. A.; Lukowski, S. W.; Molyneaux, P. L.; Saglani, S.; Chambers, D. C.; Maher, T. M.; Lloyd, C. M.
A model of impaired Langerhans cell maturation associated with HPV induced epithelial hyperplasia
Tuong, Z. K.; Lukowski, S. W.; Nguyen, Q. H.; Chandra, J.; Zhou, C.; Gillinder, K.; Bashaw, A. A.; Ferdinand, J. R.; Stewart, B. J.; Teoh, S. M.; Hanson, S. J.; Devitt, K.; Clatworthy, M. R.; Powell, J. E.; Frazer, I. H.
iScience 24(11):103326, 2021
ERICH3: vesicular association and antidepressant treatment response
Liu, D.; Zhuang, Y.; Zhang, L.; Gao, H.; Neavin, D.; Carrillo-Roa, T.; Wang, Y.; Yu, J.; Qin, S.; Kim, D. C.; Liu, E.; Nguyen, T. T. L.; Biernacka, J. M.; Kaddurah-Daouk, R.; Dunlop, B. W.; Craighead, W. E.; Mayberg, H. S.; Binder, E. B.; Frye, M. A.; Wang, L.; Weinshilboum, R. M.
MOLECULAR PSYCHIATRY 26(6):2415-2428, 2021
Single-cell transcriptional profiling of aortic endothelium identifies a hierarchy from endovascular progenitors to differentiated cells
Lukowski, S. W.; Patel, J.; Andersen, S. B.; Sim, S. L.; Wong, H. Y.; Tay, J.; Winkler, I.; Powell, J. E.; Khosrotehrani, K.
Cell Reports 27(9):2748-2758.e3, 2019
Comprehensive Multiple eQTL Detection and Its Application to GWAS Interpretation
Zeng, B.; Lloyd-Jones, L. R.; Montgomery, G. W.; Metspalu, A.; Esko, T.; Franke, L.; Vosa, U.; Claringbould, A.; Brigham, K. L.; Quyyumi, A. A.; Idaghdour, Y.; Yang, J.; Visscher, P. M.; Powell, J. E.; Gibson, G.
GENETICS 212(3):905-918, 2019
Single-cell transcriptomics of alloreactive CD4+ T cells over time reveals divergent fates during gut graft-versus-host disease
Engel, J. A.; Lee, H. J.; Williams, C. G.; Kuns, R.; Olver, S.; Lansink, L. I.; Soon, M. S.; Andersen, S. B.; Powell, J. E.; Svensson, V.; Teichmann, S. A.; Hill, G. R.; Varelias, A.; Koyama, M.; Haque, A.
Journal of Clinical Investigation Insight 5(13):e137990, 2020
Role of PDGF-A/B Ligands in Cardiac Repair After Myocardial Infarction
Kalra, K.; Eberhard, J.; Farbehi, N.; Chong, J. J.; Xaymardan, M.
Frontiers in Cell and Developmental Biology 9:669188, 2021
A single-cell tumor immune atlas for precision oncology
Nieto, P.; Elosua-Bayes, M.; Trincado, J. L.; Marchese, D.; Massoni-Badosa, R.; Salvany, M.; Henriques, A.; Nieto, J.; Aguilar-Fernandez, S.; Mereu, E.; Moutinho, C.; Ruiz, S.; Lorden, P.; Chin, V. T.; Kaczorowski, D.; Chan, C. L.; Gallagher, R.; Chou, A.; Planas-Rigol, E.; Rubio-Perez, C.; Gut, I.; Piulats, J. M.; Seoane, J.; Powell, J. E.; Batlle, E.; Heyn, H.
GENOME RESEARCH 31(10):1913-1926, 2021
The single-cell eQTLGen consortium
van der Wijst, M.; de Vries, D. H.; Groot, H. E.; Trynka, G.; Hon, C. C.; Bonder, M. J.; Stegle, O.; Nawijn, M. C.; Idaghdour, Y.; van der Harst, P.; Ye, C. J.; Powell, J.; Theis, F. J.; Mahfouz, A.; Heinig, M.; Franke, L.
eLife 9:e52155, 2021
Single-cell RNA counting at allele and isoform resolution using Smart-seq3
Hagemann-Jensen, M.; Ziegenhain, C.; Chen, P.; Ramskold, D.; Hendriks, G. J.; Larsson, A. J. M.; Faridani, O. R.; Sandberg, R.
NATURE BIOTECHNOLOGY 38(6):708-714, 2020
Physical Activity and Cardiovascular Fitness During Childhood and Adolescence: Association With Retinal Nerve Fibre Layer Thickness in Young Adulthood
Lee, S. S.; McVeigh, J.; Straker, L.; Howie, E. K.; Yazar, S.; Haynes, A.; Green, D. J.; Hewitt, A. W.; Mackey, D. A.
JOURNAL OF GLAUCOMA 30(9):813-819, 2021
The autotaxin-lysophosphatidic acid pathway mediates mesenchymal cell recruitment and fibrotic contraction in lung transplant fibrosis
Sinclair, K. A.; Yerkovich, S. T.; Hopkins, P. M.; Fieuw, A. M.; Ford, P.; Powell, J. E.; O'Sullivan, B.; Chambers, D. C.
ascend: R package for analysis of single-cell RNA-seq data
Senabouth, A.; Lukowski, S. W.; Hernandez, J. A.; Andersen, S. B.; Mei, X.; Nguyen, Q. H.; Powell, J. E.
GigaScience 8(8):pii: giz087, 2019
Do Levels of Stress Markers Influence the Retinal Nerve Fiber Layer Thickness in Young Adults?
Lee, S. S.; Sanfilippo, P. G.; Yazar, S.; Pennell, C. E.; Hewitt, A. W.; Wang, C. A.; Martin, W. N.; Mackey, D. A.
JOURNAL OF GLAUCOMA 29(7):587-592, 2020
Detection of HPV E7 Transcription at Single-Cell Resolution in Epidermis
Lukowski, S. W.; Tuong, Z. K.; Noske, K.; Senabouth, A.; Nguyen, Q. H.; Andersen, S. B.; Soyer, H. P.; Frazer, I. H.; Powell, J. E.
Large-scale cis- and trans-eQTL analyses identify thousands of genetic loci and polygenic scores that regulate blood gene expression
Vosa, U.; Claringbould, A.; Westra, H. J.; Bonder, M. J.; Deelen, P.; Zeng, B.; Kirsten, H.; Saha, A.; Kreuzhuber, R.; Yazar, S.; Brugge, H.; Oelen, R.; de Vries, D. H.; van der Wijst, M. G. P.; Kasela, S.; Pervjakova, N.; Alves, I.; Fave, M. J.; Agbessi, M.; Christiansen, M. W.; Jansen, R.; Seppala, I.; Tong, L.; Teumer, A.; Schramm, K.; Hemani, G.; Verlouw, J.; Yaghootkar, H.; Sonmez Flitman, R.; Brown, A.; Kukushkina, V.; Kalnapenkis, A.; Rueger, S.; Porcu, E.; Kronberg, J.; Kettunen, J.; Lee, B.; Zhang, F.; Qi, T.; Hernandez, J. A.; Arindrarto, W.; Beutner, F.; Consortium, Bios; i, Q. T. L. Consortium; Dmitrieva, J.; Elansary, M.; Fairfax, B. P.; Georges, M.; Heijmans, B. T.; Hewitt, A. W.; Kahonen, M.; Kim, Y.; Knight, J. C.; Kovacs, P.; Krohn, K.; Li, S.; Loeffler, M.; Marigorta, U. M.; Mei, H.; Momozawa, Y.; Muller-Nurasyid, M.; Nauck, M.; Nivard, M. G.; Penninx, Bwjh; Pritchard, J. K.; Raitakari, O. T.; Rotzschke, O.; Slagboom, E. P.; Stehouwer, C. D. A.; Stumvoll, M.; Sullivan, P.; t Hoen, P. A. C.; Thiery, J.; Tonjes, A.; van Dongen, J.; van Iterson, M.; Veldink, J. H.; Volker, U.; Warmerdam, R.; Wijmenga, C.; Swertz, M.; Andiappan, A.; Montgomery, G. W.; Ripatti, S.; Perola, M.; Kutalik, Z.; Dermitzakis, E.; Bergmann, S.; Frayling, T.; van Meurs, J.; Prokisch, H.; Ahsan, H.; Pierce, B. L.; Lehtimaki, T.; Boomsma, D. I.; Psaty, B. M.; Gharib, S. A.; Awadalla, P.; Milani, L.; Ouwehand, W. H.; Downes, K.; Stegle, O.; Battle, A.; Visscher, P. M.; Yang, J.; Scholz, M.; Powell, J.; Gibson, G.; Esko, T.; Franke, L.
NATURE GENETICS 53(9):1300-1310, 2021
Analytical Guidelines for co-fractionation Mass Spectrometry Obtained through Global Profiling of Gold Standard Saccharomyces cerevisiae Protein Complexes
Pang, C. N. I.; Ballouz, S.; Weissberger, D.; Thibaut, L. M.; Hamey, J. J.; Gillis, J.; Wilkins, M. R.; Hart-Smith, G.
MOLECULAR & CELLULAR PROTEOMICS 19(11):1876-1895, 2020
Metastatic pancreatic ductal adenocarcinoma: diagnosis and treatment with a view to the future
Pokorny, A. M. J.; Chin, V. T.; Nagrial, A. M.; Yip, D.; Chantrill, L. A.
Rationale and protocol for the 7- and 8-year longitudinal assessments of eye health in a cohort of young adults in the Raine Study
Lee, S. S.; Lingham, G.; Yazar, S.; Sanfilippo, P. G.; Charng, J.; Chen, F. K.; Hewitt, A. W.; Ng, F.; Hammond, C.; Straker, L. M.; Eastwood, P. R.; MacGregor, S.; Rose, K. A.; Lucas, R. M.; Guggenheim, J. A.; Saw, S. M.; Coroneo, M. T.; He, M.; Mackey, D. A.
BMJ Open 10(3):e033440, 2020
Time spent outdoors through childhood and adolescence - assessed by 25-hydroxyvitamin D concentration - and risk of myopia at 20 years
Lingham, G.; Mackey, D. A.; Zhu, K.; Lucas, R. M.; Black, L. J.; Oddy, W. H.; Holt, P.; Walsh, J. P.; Sanfilippo, P. G.; Chan She Ping-Delfos, W.; Yazar, S.
ACTA OPHTHALMOLOGICA 99(6):679-687, 2021
Genome-wide association study of intraocular pressure uncovers new pathways to glaucoma
MacGregor, S.; Ong, J. S.; An, J.; Han, X.; Zhou, T.; Siggs, O. M.; Law, M. H.; Souzeau, E.; Sharma, S.; Lynn, D. J.; Beesley, J.; Sheldrick, B.; Mills, R. A.; Landers, J.; Ruddle, J. B.; Graham, S. L.; Healey, P. R.; White, A. J. R.; Casson, R. J.; Best, S.; Grigg, J. R.; Goldberg, I.; Powell, J. E.; Whiteman, D. C.; Radford-Smith, G. L.; Martin, N. G.; Montgomery, G. W.; Burdon, K. P.; Mackey, D. A.; Gharahkhani, P.; Craig, J. E.; Hewitt, A. W.
NATURE GENETICS 50(8):1067-1071, 2018
Is Dietary Vitamin A Associated with Myopia from Adolescence to Young Adulthood?
Ng, F. J.; Mackey, D. A.; O'Sullivan, T. A.; Oddy, W. H.; Yazar, S.
Translational Vision Science & Technology 9(6):29, 2020
Genetic and epigenetic factors associated with increased severity of Covid-19
Yildirim, Z.; Sahin, O. S.; Yazar, S.; Bozok Cetintas, V.
CELL BIOLOGY INTERNATIONAL 45(6):1158-1174, 2021
A single-cell transcriptome atlas of the adult human retina
Lukowski, S. W.; Lo, C. Y.; Sharov, A. A.; Nguyen, Q.; Fang, L.; Hung, S. S.; Zhu, L.; Zhang, T.; Grunert, U.; Nguyen, T.; Senabouth, A.; Jabbari, J. S.; Welby, E.; Sowden, J. C.; Waugh, H. S.; Mackey, A.; Pollock, G.; Lamb, T. D.; Wang, P. Y.; Hewitt, A. W.; Gillies, M. C.; Powell, J. E.; Wong, R. C.
EMBO JOURNAL 38(18):e100811, 2019
Transcriptomic Profiling of Human Pluripotent Stem Cell-derived Retinal Pigment Epithelium over Time
Lidgerwood, G. E.; Senabouth, A.; Smith-Anttila, C. J. A.; Gnanasambandapillai, V.; Kaczorowski, D. C.; Amann-Zalcenstein, D.; Fletcher, E. L.; Naik, S. H.; Hewitt, A. W.; Powell, J. E.; Pebay, A.
Septic Shock: A Genomewide Association Study and Polygenic Risk Score Analysis
D'Urso, S.; Rajbhandari, D.; Peach, E.; de Guzman, E.; Li, Q.; Medland, S. E.; Gordon, S. D.; Martin, N. G.; Group, Charge Inflammation Working; Ligthart, S.; Brown, M. A.; Powell, J.; McArthur, C.; Rhodes, A.; Meyer, J.; Finfer, S.; Myburgh, J.; Blumenthal, A.; Cohen, J.; Venkatesh, B.; Cuellar-Partida, G.; Evans, D. M.
Twin Research and Human Genetics 23(4):204-213, 2020
The effect of antibiotics on clinical outcomes in immune-checkpoint blockade: a systematic review and meta-analysis of observational studies
Wilson, B. E.; Routy, B.; Nagrial, A.; Chin, V. T.
Benchmarking of cell type deconvolution pipelines for transcriptomics data
Cobos, F. A.; Alquicira-Hernandez, J.; Powell, J. E.; Mestdagh, P.; De Preter, K.
Nature Communications 11(1):6291, 2020
Chemotherapy and radiotherapy for advanced pancreatic cancer
Chin, V.; Nagrial, A.; Sjoquist, K.; O'Connor, C. A.; Chantrill, L.; Biankin, A. V.; Scholten, R. J.; Yip, D.
Cochrane Database of Systematic Reviews 3:CD011044, 2018
DropletQC: improved identification of empty droplets and damaged cells in single-cell RNA-seq data
Muskovic, W.; Powell, J. E.
GENOME BIOLOGY 22(1):329, 2021
Age-dependent regional retinal nerve fibre changes in SIX1/SIX6 polymorphism
Charng, J.; Simcoe, M.; Sanfilippo, P. G.; Allingham, R. R.; Hewitt, A. W.; Hammond, C. J.; Mackey, D. A.; Yazar, S.
Scientific Reports 10(1):12485, 2020
Single-cell expression profiling reveals dynamic flux of cardiac stromal, vascular and immune cells in health and injury
Farbehi, N.; Patrick, R.; Dorison, A.; Xaymardan, M.; Janbandhu, V.; Wystub-Lis, K.; Ho, J. W.; Nordon, R. E.; Harvey, R. P.
eLife 8:pii: 43882, 2019
Itaconate controls the severity of pulmonary fibrosis
Ogger, P. P.; Albers, G. J.; Hewitt, R. J.; O'Sullivan, B. J.; Powell, J. E.; Calamita, E.; Ghai, P.; Walker, S. A.; McErlean, P.; Saunders, P.; Kingston, S.; Molyneaux, P. L.; Halket, J. M.; Gray, R.; Chambers, D. C.; Maher, T. M.; Lloyd, C. M.; Byrne, A. J.
Science Immunology 5(52):eabc1884, 2020
Programmatic access to bacterial regulatory networks with regutools
Chavez, J.; Barberena-Jonas, C.; Sotelo-Fonseca, J. E.; Alquicira-Hernandez, J.; Salgado, H.; Collado-Torres, L.; Reyes, A.
Bioinformatics 36(16):4532-4534, 2020
Single-Cell Profiling Identifies Key Pathways Expressed by iPSCs Cultured in Different Commercial Media
Daniszewski, M.; Nguyen, Q.; Chy, H. S.; Singh, V.; Crombie, D. E.; Kulkarni, T.; Liang, H. H.; Sivakumaran, P.; Lidgerwood, G. E.; Hernandez, D.; Conquest, A.; Rooney, L. A.; Chevalier, S.; Andersen, S. B.; Senabouth, A.; Vickers, J. C.; Mackey, D. A.; Craig, J. E.; Laslett, A. L.; Hewitt, A. W.; Powell, J. E.; Pebay, A.
iScience 7:30-39, 2018
Integrating single-cell genomics pipelines to discover mechanisms of stem cell differentiation
Shen, S.; Sun, Y.; Matsumoto, M.; Shim, W. J.; Sinniah, E.; Wilson, S. B.; Werner, T.; Wu, Z.; Bradford, S. T.; Hudson, J.; Little, M. H.; Powell, J.; Nguyen, Q.; Palpant, N. J.
TRENDS IN MOLECULAR MEDICINE 27(12):1135-1158, 2021
How many young drivers do not meet the driver licencing vision requirements?
Tu, M. Y.; Yazar, S.; Mackey, D. A.; Lee, S. S. Y.
Change in the prevalence of myopia in Australian middle-aged adults across 20 years
Mackey, D. A.; Lingham, G.; Lee, S. S.; Hunter, M.; Wood, D.; Hewitt, A. W.; Mitchell, P.; Taylor, H. R.; Hammond, C. J.; Yazar, S.
Clincal & experimental opthalmology 49(9):1039-1047, 2021
Hepatic expression profiling identifies steatosis-independent and steatosis-driven advanced fibrosis genes
Ramnath, D.; Irvine, K. M.; Lukowski, S. W.; Horsfall, L. U.; Loh, Z.; Clouston, A. D.; Patel, P. J.; Fagan, K. J.; Iyer, A.; Lampe, G.; Stow, J. L.; Schroder, K.; Fairlie, D. P.; Powell, J. E.; Powell, E. E.; Sweet, M. J.
Journal of Clinical Investigation Insight 3(14):e120274, 2018