Garvan Institute of Medical Research

TNFAIP3 Reduction-of-Function Drives Female Infertility and CNS Inflammation

Zammit, N. W.; McDowell, J.; Warren, J.; Muskovic, W.; Gamble, J.; Shi, Y. C.; Kaczorowski, D.; Chan, C. L.; Powell, J.; Ormandy, C.; Brown, D.; Oakes, S. R.; Grey, S. T.

Frontiers in Immunology 13 :811525, 2022 10.3389/fimmu.2022.811525

DevKidCC allows for robust classification and direct comparisons of kidney organoid datasets

Wilson, S. B.; Howden, S. E.; Vanslambrouck, J. M.; Dorison, A.; Alquicira-Hernandez, J.; Powell, J. E.; Little, M. H.

Genome Medicine 14 (1) :19, 2022 10.1186/s13073-022-01023-z

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 10.1186/s13059-021-02547-0

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 10.1016/j.molmed.2021.09.006

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 10.1101/gr.273300.120

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 10.1016/j.isci.2021.103326

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 10.1007/s00134-021-06464-5

A single-cell and spatially resolved atlas of human breast cancers

Wu, S. Z.; Al-Eryani, G.; Roden, D. L.; Junankar, S.; Harvey, K.; Andersson, A.; Thennavan, A.; Wang, C.; Torpy, J. R.; Bartonicek, N.; Wang, T.; Larsson, L.; Kaczorowski, D.; Weisenfeld, N. I.; Uytingco, C. R.; Chew, J. G.; Bent, Z. W.; Chan, C. L.; Gnanasambandapillai, V.; Dutertre, C. A.; Gluch, L.; Hui, M. N.; Beith, J.; Parker, A.; Robbins, E.; Segara, D.; Cooper, C.; Mak, C.; Chan, B.; Warrier, S.; Ginhoux, F.; Millar, E.; Powell, J. E.; Williams, S. R.; Liu, X. S.; O'Toole, S.; Lim, E.; Lundeberg, J.; Perou, C. M.; Swarbrick, A.

NATURE GENETICS 53 (9) :1334-1347, 2021 10.1038/s41588-021-00911-1

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 10.1038/s41588-021-00913-z

DNA methylation is required to maintain both DNA replication timing precision and 3D genome organization integrity

Du, Q.; Smith, G. C.; Luu, P. L.; Ferguson, J. M.; Armstrong, N. J.; Caldon, C. E.; Campbell, E. M.; Nair, S. S.; Zotenko, E.; Gould, C. M.; Buckley, M.; Chia, K. M.; Portman, N.; Lim, E.; Kaczorowski, D.; Chan, C. L.; Barton, K.; Deveson, I. W.; Smith, M. A.; Powell, J. E.; Skvortsova, K.; Stirzaker, C.; Achinger-Kawecka, J.; Clark, S. J.

Cell Reports 36 (12) :109722, 2021 10.1016/j.celrep.2021.109722

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 10.1038/s41586-021-03765-z

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 10.3389/fgene.2021.666771

No evidence that plasmablasts transdifferentiate into developing neutrophils in severe COVID-19 disease

Alquicira-Hernandez, J.; Powell, J. E.; Phan, T. G.

Clinical & Translational Immunology 10 (7) :e1308, 2021 10.1002/cti2.1308

Genetic variation affects morphological retinal phenotypes extracted from UK Biobank optical coherence tomography images

Currant, H.; Hysi, P.; Fitzgerald, T. W.; Gharahkhani, P.; Bonnemaijer, P. W. M.; Senabouth, A.; Hewitt, A. W.; Eye, U. K. Biobank; Vision, Consortium; International Glaucoma Genetics, Consortium; Atan, D.; Aung, T.; Charng, J.; Choquet, H.; Craig, J.; Khaw, P. T.; Klaver, C. C. W.; Kubo, M.; Ong, J. S.; Pasquale, L. R.; Reisman, C. A.; Daniszewski, M.; Powell, J. E.; Pebay, A.; Simcoe, M. J.; Thiadens, Aahj; van Duijn, C. M.; Yazar, S.; Jorgenson, E.; MacGregor, S.; Hammond, C. J.; Mackey, D. A.; Wiggs, J. L.; Foster, P. J.; Patel, P. J.; Birney, E.; Khawaja, A. P.

PLoS Genetics 17 (5) :e1009497, 2021 10.1371/journal.pgen.1009497

Antigen-driven EGR2 expression is required for exhausted CD8(+) T cell stability and maintenance

Wagle, M. V.; Vervoort, S. J.; Kelly, M. J.; Van Der Byl, W.; Peters, T. J.; Martin, B. P.; Martelotto, L. G.; Nussing, S.; Ramsbottom, K. M.; Torpy, J. R.; Knight, D.; Reading, S.; Thia, K.; Miosge, L. A.; Howard, D. R.; Gloury, R.; Gabriel, S. S.; Utzschneider, D. T.; Oliaro, J.; Powell, J. D.; Luciani, F.; Trapani, J. A.; Johnstone, R. W.; Kallies, A.; Goodnow, C. C.; Parish, I. A.

Nature Communications 12 (1) :2782, 2021 10.1038/s41467-021-23044-9

Cryopreservation of human cancers conserves tumour heterogeneity for single-cell multi-omics analysis

Wu, S. Z.; Roden, D. L.; Al-Eryani, G.; Bartonicek, N.; Harvey, K.; Cazet, A. S.; Chan, C. L.; Junankar, S.; Hui, M. N.; Millar, E. A.; Beretov, J.; Horvath, L.; Joshua, A. M.; Stricker, P.; Wilmott, J. S.; Quek, C.; Long, G. V.; Scolyer, R. A.; Yeung, B. Z.; Segara, D.; Mak, C.; Warrier, S.; Powell, J. E.; O'Toole, S.; Lim, E.; Swarbrick, A.

Genome Medicine 13 (1) :81, 2021 10.1186/s13073-021-00885-z