Selected Publications (*joint authorship) (^†corresponding)

Morfopoulou S , Buddle S, Montaguth OET, Atkinson L, Guerra-Assunção JA, Marjaneh MM, Chiozzi RZ, Storey N, Campos L, Hutchinson JC, ..., Baillie K, Semple MG, Martin J, Ushiro-Lumb I, Noursadeghi M, Deheragoda M, Hadzic N, Grammatikopoulos T, Brown R, Kelgeri C, Thalassinos K, Waddington SN, Jacques TS, Thomson E, Levin M, Brown JR, Breuer J. Genomic investigations of unexplained acute hepatitis in children. Nature (2023); doi:10.1038/s41586-023-06003-w

Ho A , Orton R, Tayler R, Asamaphan P, Herder V, Davis C, Tong L, Smollett K, Manali M, Allan J, ..., Baillie JK, Thomson EC. Adeno-associated virus 2 infection in children with non-A-E hepatitis. Nature (2023); doi:10.1038/s41586-023-05948-2

Russell CD , Lone NI, Baillie JK. Comorbidities, multimorbidity and COVID-19. Nature Medicine (2023); 29: 334-343. doi:10.1038/s41591-022-02156-9

Hamilton FW , Thomas M, Arnold D, Palmer T, Moran E, Mentzer AJ, Maskell N, Baillie JK, Summers C, Hingorani A, MacGowan A, ..., Timpson NJ. Therapeutic potential of IL6R blockade for the treatment of sepsis and sepsis-related death: A Mendelian randomisation study. PLoS Medicine (2023); 20: e1004174. PMC9925069

Swets MC , Russell CD, Harrison EM, Docherty AB, Lone N, Girvan M, Hardwick HE, Visser LG, Openshaw PJM, Groeneveld GH, ..., Baillie JK. SARS-CoV-2 co-infection with influenza viruses, respiratory syncytial virus, or adenoviruses. Lancet (London, England) (2022); doi:10.1016/S0140-6736(22)00383-X

Kousathanas A , Pairo-Castineira E, Rawlik K, Stuckey A, Odhams CA, Walker S, Russell CD, Malinauskas T, Wu Y, Millar J, ..., Baillie JK. Whole genome sequencing reveals host factors underlying critical Covid-19. Nature (2022); doi:10.1038/s41586-022-04576-6

RECOVERY Collaborative Group . Tocilizumab in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial. Lancet (London, England) (2021); 397: 1637-1645. PMC8084355

HGI C . Mapping the human genetic architecture of COVID-19. Nature (2021); doi:10.1038/s41586-021-03767-x

Horby P , Lim WS, Emberson JR, Mafham M, Bell JL, Linsell L, Staplin N, Brightling C, Ustianowski A, Elmahi E, ..., Baillie JK, Haynes R, Landray MJ. Dexamethasone in Hospitalized Patients with Covid-19. The New England Journal of Medicine (2021); 384: 693-704. PMC7383595

Gupta RK , Harrison EM, Ho A, Docherty AB, Knight SR, van Smeden M, Abubakar I, Lipman M, Quartagno M, Pius R, ..., Baillie JK, Semple MG, Noursadeghi M. Development and validation of the ISARIC 4C Deterioration model for adults hospitalised with COVID-19: a prospective cohort study. The Lancet. Respiratory Medicine (2021); 9: 349-359. PMC7832571

Read JM , Green CA, Harrison EM, Docherty AB, Funk S, Harrison J, Girvan M, Hardwick HE, Turtle L, Dunning J, ..., Baillie JK, Semple MG. Hospital-acquired SARS-CoV-2 infection in the UK’s first COVID-19 pandemic wave. Lancet (London, England) (2021); doi:10.1016/S0140-6736(21)01786-4

Thomson EC , Rosen LE, Shepherd JG, Spreafico R, da Silva Filipe A, Wojcechowskyj JA, Davis C, Piccoli L, Pascall DJ, Dillen J, ..., Baillie JK, Chodera JD, Rihn SJ, Lycett SJ, Virgin HW, Telenti A, Corti D, Robertson DL, Snell G. Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Cell (2021); 184: 1171-1187.e20. PMC7843029

Thwaites RS , Sanchez Sevilla Uruchurtu A, Siggins MK, Liew F, Russell CD, Moore SC, Fairfield C, Carter E, Abrams S, Short C, ..., Baillie JK, Openshaw PJ. Inflammatory profiles across the spectrum of disease reveal a distinct role for GM-CSF in severe COVID-19. Science Immunology (2021); 6: PMC8128298

Pairo-Castineira E , Clohisey S, Klaric L, Bretherick AD, Rawlik K, Pasko D, Walker S, Parkinson N, Fourman MH, Russell CD, ..., Baillie JK. Genetic mechanisms of critical illness in COVID-19. Nature (2020); 591: 92-98. doi:10.1038/s41586-020-03065-y

Bretherick AD , Canela-Xandri O, Joshi PK, Clark DW, Rawlik K, Boutin TS, Zeng Y, Amador C, Navarro P, Rudan I, ..., Baillie JK, Haley C. Linking protein to phenotype with Mendelian Randomization detects 38 proteins with causal roles in human diseases and traits. PLoS Genetics (2020); 16: e1008785. PMC7337286

Clohisey S , Parkinson N, Wang B, Bertin N, Wise H, Tomoiu A, Summers KM, Hendry RW, Carninci P, Forrest ARR, ..., Baillie JK. Comprehensive Characterization of Transcriptional Activity during Influenza A Virus Infection Reveals Biases in Cap-Snatching of Host RNA Sequences. Journal of Virology (2020); 94: PMC7199409

Docherty AB , Harrison EM, Green CA, Hardwick HE, Pius R, Norman L, Holden KA, Read JM, Dondelinger F, Carson G, ..., Baillie JK, Semple MG. Features of 20133 UK patients in hospital with covid-19 using the ISARIC WHO Clinical Characterisation Protocol: prospective observational cohort study. BMJ (Clinical Research Ed.) (2020); 369: m1985. PMC7243036

Horby P , Mafham M, Linsell L, Bell JL, Staplin N, Emberson JR, Wiselka M, Ustianowski A, Elmahi E, Prudon B, ..., Baillie JK, Chappell LC, Faust SN, Jaki T, Jeffery K, Lim WS, Montgomery A, Rowan K, Tarning J, Watson JA, White NJ, Juszczak E, Haynes R, Landray MJ. Effect of Hydroxychloroquine in Hospitalized Patients with Covid-19. The New England Journal of Medicine (2020); 383: 2030-2040. PMC7556338

Knight SR , Ho A, Pius R, Buchan I, Carson G, Drake TM, Dunning J, Fairfield CJ, Gamble C, Green CA, ..., Baillie JK, Semple MG, Docherty AB, Harrison EM. Risk stratification of patients admitted to hospital with covid-19 using the ISARIC WHO Clinical Characterisation Protocol: development and validation of the 4C Mortality Score. BMJ (Clinical Research Ed.) (2020); 370: m3339. PMC7116472

Li B , Clohisey SM, Chia BS, Wang B, Cui A, Eisenhaure T, Schweitzer LD, Hoover P, Parkinson NJ, Nachshon A, ..., Baillie JK, Hacohen N. Genome-wide CRISPR screen identifies host dependency factors for influenza A virus infection. Nature Communications (2020); 11: 164. PMC6952391

Neyton LPA , Zheng X, Skouras C, Doeschl-Wilson A, Gutmann MU, Uings I, Rao FV, Nicolas A, Marshall C, Wilson L, Baillie JK, Mole DJ. Molecular Patterns in Acute Pancreatitis Reflect Generalizable Endotypes of the Host Response to Systemic Injury in Humans. Annals of Surgery (2020); doi:10.1097/SLA.0000000000003974

Parkinson N , Rodgers N, Head Fourman M, Wang B, Zechner M, Swets MC, Millar JE, Law A, Russell CD, Baillie JK, Clohisey S. Dynamic data-driven meta-analysis for prioritisation of host genes implicated in COVID-19. Scientific Reports (2020); 10: 22303. PMC7749145

Clohisey S , Baillie JK. Host susceptibility to severe influenza A virus infection. Critical Care (London, England) (2019); 23: 303. PMC6729070

Baillie JK , Bretherick A, Haley CS, Clohisey S, Gray A, Neyton LPA, Barrett J, Stahl EA, Tenesa A, Andersson R, Brown JB, ..., Hume DA. Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease. PLoS Computational Biology (2018); 14: e1005934. PMC5849332

Roach RC , Hackett PH, Oelz O, Bärtsch P, Luks AM, MacInnis MJ, Baillie JK. The 2018 Lake Louise Acute Mountain Sickness Score. High Altitude Medicine and Biology (2018); 19: 4-6. PMC6191821

Arabi YM , Balkhy HH, Hayden FG, Bouchama A, Luke T, Baillie JK, Al-Omari A, Hajeer AH, Senga M, Denison MR, Nguyen-Van-Tam JS, ..., Fowler RA. Middle East Respiratory Syndrome. The New England Journal of Medicine (2017); 376: 584-594. PMC5362064

Baillie JK , Arner E, Daub C, De Hoon M, Itoh M, Kawaji H, Lassmann T, Carninci P, Forrest ARR, Hayashizaki Y, Faulkner GJ, ..., Hume DA. Analysis of the human monocyte-derived macrophage transcriptome and response to lipopolysaccharide provides new insights into genetic aetiology of inflammatory bowel disease. PLoS Genetics (2017); 13: e1006641. PMC5358891

Baillie JK . Translational genomics. Targeting the host immune response to fight infection. Science (New York, N.Y.) (2014); 344: 807-8. doi:10.1126/science.1255074

Dunning JW , Merson L, Rohde GGU, Gao Z, Semple MG, Tran D, Gordon A, Olliaro PL, Khoo SH, Bruzzone R, ..., Baillie JK. Open source clinical science for emerging infections. The Lancet. Infectious Diseases (2014); 14: 8-9. PMC7158987

Forrest ARR*, Kawaji H*, Rehli M*, Baillie JK*, , de Hoon MJL, Haberle V, Lassmann T, Kulakovskiy IV, Lizio M, Itoh M, Andersson R, Mungall CJ, Meehan TF, Schmeier S, ..., Hayashizaki Y. A promoter-level mammalian expression atlas. Nature (2014); 507: 462-70. PMC4529748

Hall DP , MacCormick IJC, Phythian-Adams AT, Rzechorzek NM, Hope-Jones D, Cosens S, Jackson S, Bates MGD, Collier DJ, Hume DA, ..., Baillie JK. Network analysis reveals distinct clinical syndromes underlying acute mountain sickness. Plos One (2014); 9: e81229. PMC3898916

Baillie JK , Digard P. Influenza–time to target the host? The New England Journal of Medicine (2013); 369: 191-3. doi:10.1056/NEJMcibr1304414

Everitt AR , Clare S, Pertel T, John SP, Wash RS, Smith SE, Chin CR, Feeley EM, Sims JS, Adams DJ, ..., Baillie JK, Walsh TS, Hume DA, Palotie A, Xue Y, Colonna V, Tyler-Smith C, Dunning J, Gordon SB, Smyth RL, Openshaw PJ, Dougan G, Brass AL, Kellam P. IFITM3 restricts the morbidity and mortality associated with influenza. Nature (2012); 484: 519-23. PMC3648786

Baillie JK , Barnett MW, Upton KR, Gerhardt DJ, Richmond TA, De Sapio F, Brennan PM, Rizzu P, Smith S, Fell M, Talbot RT, ..., Faulkner GJ. Somatic retrotransposition alters the genetic landscape of the human brain. Nature (2011); 479: 534-7. PMC3224101