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Natural Killer cells demonstrate distinct eQTL and transcriptome-wide disease associations, highlighting their role in autoimmunity.
Gilchrist JJ, Makino S, Naranbhai V, Sharma PK, Koturan S, Tong O, Taylor CA, Watson RA, de Los Aires AV, Cooper R, Lau E, Danielli S, Hameiri-Bowen D, Lee W, Ng E, Whalley J, Knight JC, Fairfax BP. Gilchrist JJ, et al. Among authors: whalley j. Nat Commun. 2022 Jul 14;13(1):4073. doi: 10.1038/s41467-022-31626-4. Nat Commun. 2022. PMID: 35835762 Free PMC article.
Analyses of non-coding somatic drivers in 2,658 cancer whole genomes.
Rheinbay E, Nielsen MM, Abascal F, Wala JA, Shapira O, Tiao G, Hornshøj H, Hess JM, Juul RI, Lin Z, Feuerbach L, Sabarinathan R, Madsen T, Kim J, Mularoni L, Shuai S, Lanzós A, Herrmann C, Maruvka YE, Shen C, Amin SB, Bandopadhayay P, Bertl J, Boroevich KA, Busanovich J, Carlevaro-Fita J, Chakravarty D, Chan CWY, Craft D, Dhingra P, Diamanti K, Fonseca NA, Gonzalez-Perez A, Guo Q, Hamilton MP, Haradhvala NJ, Hong C, Isaev K, Johnson TA, Juul M, Kahles A, Kahraman A, Kim Y, Komorowski J, Kumar K, Kumar S, Lee D, Lehmann KV, Li Y, Liu EM, Lochovsky L, Park K, Pich O, Roberts ND, Saksena G, Schumacher SE, Sidiropoulos N, Sieverling L, Sinnott-Armstrong N, Stewart C, Tamborero D, Tubio JMC, Umer HM, Uusküla-Reimand L, Wadelius C, Wadi L, Yao X, Zhang CZ, Zhang J, Haber JE, Hobolth A, Imielinski M, Kellis M, Lawrence MS, von Mering C, Nakagawa H, Raphael BJ, Rubin MA, Sander C, Stein LD, Stuart JM, Tsunoda T, Wheeler DA, Johnson R, Reimand J, Gerstein M, Khurana E, Campbell PJ, López-Bigas N; PCAWG Drivers and Functional Interpretation Working Group; PCAWG Structural Variation Working Group; Weischenfeldt J, Beroukhim R, Martincorena I, Pedersen JS, Getz G; PCAWG Consortium. Rheinbay E, et al. Nature. 2020 Feb;578(7793):102-111. doi: 10.1038/s41586-020-1965-x. Epub 2020 Feb 5. Nature. 2020. PMID: 32025015 Free PMC article.
Using de novo assembly to identify structural variation of eight complex immune system gene regions.
Zhang JY, Roberts H, Flores DSC, Cutler AJ, Brown AC, Whalley JP, Mielczarek O, Buck D, Lockstone H, Xella B, Oliver K, Corton C, Betteridge E, Bashford-Rogers R, Knight JC, Todd JA, Band G. Zhang JY, et al. Among authors: whalley jp. PLoS Comput Biol. 2021 Aug 3;17(8):e1009254. doi: 10.1371/journal.pcbi.1009254. eCollection 2021 Aug. PLoS Comput Biol. 2021. PMID: 34343164 Free PMC article.
Constructing custom-made radiotranscriptomic signatures of vascular inflammation from routine CT angiograms: a prospective outcomes validation study in COVID-19.
Kotanidis CP, Xie C, Alexander D, Rodrigues JCL, Burnham K, Mentzer A, O'Connor D, Knight J, Siddique M, Lockstone H, Thomas S, Kotronias R, Oikonomou EK, Badi I, Lyasheva M, Shirodaria C, Lumley SF, Constantinides B, Sanderson N, Rodger G, Chau KK, Lodge A, Tsakok M, Gleeson F, Adlam D, Rao P, Indrajeet D, Deshpande A, Bajaj A, Hudson BJ, Srivastava V, Farid S, Krasopoulos G, Sayeed R, Ho LP, Neubauer S, Newby DE, Channon KM, Deanfield J, Antoniades C; COMBAT Consortium; ORFAN investigators. Kotanidis CP, et al. Lancet Digit Health. 2022 Oct;4(10):e705-e716. doi: 10.1016/S2589-7500(22)00132-7. Epub 2022 Aug 26. Lancet Digit Health. 2022. PMID: 36038496 Free PMC article.
Single cell spatial analysis reveals inflammatory foci of immature neutrophil and CD8 T cells in COVID-19 lungs.
Weeratunga P, Denney L, Bull JA, Repapi E, Sergeant M, Etherington R, Vuppussetty C, Turner GDH, Clelland C, Woo J, Cross A, Issa F, de Andrea CE, Melero Bermejo I, Sims D, McGowan S, Zurke YX, Ahern DJ, Gamez EC, Whalley J, Richards D, Klenerman P, Monaco C, Udalova IA, Dong T, Antanaviciute A, Ogg G, Knight JC, Byrne HM, Taylor S, Ho LP. Weeratunga P, et al. Among authors: whalley j. Nat Commun. 2023 Nov 8;14(1):7216. doi: 10.1038/s41467-023-42421-0. Nat Commun. 2023. PMID: 37940670 Free PMC article.
Integrative pathway enrichment analysis of multivariate omics data.
Paczkowska M, Barenboim J, Sintupisut N, Fox NS, Zhu H, Abd-Rabbo D, Mee MW, Boutros PC; PCAWG Drivers and Functional Interpretation Working Group; Reimand J; PCAWG Consortium. Paczkowska M, et al. Nat Commun. 2020 Feb 5;11(1):735. doi: 10.1038/s41467-019-13983-9. Nat Commun. 2020. PMID: 32024846 Free PMC article.
164 results