Qualifications and Fellowship Awards

Academy of Medical Sciences, 2022: FMedSci
Royal Society of Edinburgh, 2022: FRSE
Faculty of Intensive Care Medicine, 2016: FFICM
Royal College of Physicians, 2016: FRCP(Ed)
University of Edinburgh, 2012: PhD “Statistical Genetics in Infectious Disease”
Royal College of Anaesthetists 2009: FRCA
Royal College of Physicians, 2005: MRCP(UK)
University of Edinburgh, 2002: MB,ChB
University of Edinburgh, 1999: BSc(Hons)(Med Sci) in Physiology

Selected prizes and awards

2023 Chancellor’s award for Research. An annual prize awarded by the Principal and Chancellor of the University of Edinburgh.
2022 Tenovus Scotland Lady Margaret McLellan Award. A biennial award for outstanding contributions to medical science in Scotland.
2021 Pride of Scotland “Special Recognition Award”. One of two public awards given each year to recognise oustanding public service in any field.
2021 RCPE Ballantyne Prize. The Royal College of Physicians of Edinburgh awards this prize, usually once every 10-15 years, for studies in the inheritance of disease.
2018 International Sepsis Forum Lowry-Fink Fellowship. The International Sepsis Forum selects one “rising star” in sepsis research worldwide each year to appoint to this position.
2014 Wellcome-Beit Prize Fellowship. Awarded to four intermediate fellowship candidates each year “to provide additional recognition for outstanding biomedical researchers.”
2013 Intensive Care Society Gold Medal. Awarded annually for research related to critical care medicine.
2013 ANZICS Global Rising Star Award. An annual award from the Australia and New Zealand Intensive Care Society.
2006 Nuffield Medal for the FRCA Primary. For obtaining the highest marks in the UK in this sitting.
2001 Sir William Darling Memorial Prize. Awarded by the Principal to the students “who have done most in any one year to advance the reputation of Edinburgh University”.

Current Employment

2022-present Co-Director, Pandemic Science Hub, University of Edinburgh
2021-present Professor of Experimental Medicine, University of Edinburgh
2021-present Wellcome Trust Senior Fellow, University of Edinburgh
2020-present Director of Research, UK Intensive Care Society
2019-present Visiting Professor, Peking University, Beijing, China
2014-present Honorary Consultant in Critical Care Medicine, Royal Infirmary of Edinburgh

Previous Employment

2014-21 Group Leader, Roslin Institute, University of Edinburgh
2014-20 Deputy Director of Research, UK Intensive Care Society
2014-20 Wellcome Trust Intermediate Clinical Fellow, University of Edinburgh
2014-15 Visiting Scientist, Broad Insitute of Harvard and MIT, Cambridge, MA
Nov 2014 Consultant to World Health Organisation on Ebola, WHO country HQ, Sierra Leone.
2013-14 Honorary Advanced Specialist Trainee, Critical Care, Royal Infirmary Edinburgh.
May 2013 Consultant to World Health Organisation on MERS/Influenza, WHO HQ, Geneva.
2008-14 Clinical Lecturer, University of Edinburgh & Honorary Specialist Trainee in Anaesthesia & Critical Care, South East Scotland School of Anaesthesia.
2007-08 Specialist Trainee, Anaesthesia & Critical Care, Royal Infirmary, Edinburgh.
2005-07 Senior House Officer, Anaesthesia & Critical Care, Royal Infirmary Edinburgh
2003-05 Senior House Officer, General Medicine, Western Infirmary, Glasgow.
2002-03 House Officer, Anaesthesia, Medicine & Surgery, Royal Infirmary, Edinburgh.

Research Grants

Funding Body & Title Start Amount Role
MRC: Edinburgh Molecular Mechanisms Cluster 01/03/24 (4y) £5,313,306 CI
EPSRC: Causality in Healthcare AI with Real Data 01/02/24 (5y) £6,000,000 Coapplicant
ISARIC CCP activation for acute hepatitis of unknown cause 01/10/22 (1y) £1,227,465 CI
Interim support for ISARIC4C CCP activation for acute severe hepatitis of unknown cause 01/06/22 (1y) £74,267 CI
Baillie Gifford Pandemic Science Hub 01/06/22 (5y) £14,700,000 Co-CI
CSO: Time critical precision medicine for acute critical illness (TRAITS) 01/04/22 (4y) £3,610,000 Coapplicant
Wellcome Senior Research Fellowship : Translational Genomics in Critical Care Medicine 01/11/21 (5y) £1,659,251 Applicant
UKRI: National Core Studies - Outbreak Data Analysis Platform 1/08/21 (1y) £958,915 CI
UKRI: UK Coronavirus Immunology consortium (UK-CIC) 25/08/20 (1y) £6,541,000 WP lead
UKRI: Post-hosCItalisation for COVID-19 follow-up (PHOSP) 21/07/20 (1y) £9,700,000 WP lead
DHSC: GenOMICC-Genomics England Partnership for whole genome sequencing 01/06/20 (1.5y) £28,000,000 CI
UKRI: ISARIC4C (Coronavirus Clinical Characterisation Consortium) 18/03/20 (1.5y) £5,958,870 CI
CSO: Coronavirus Clinical Characterisation (Scotland) 01/04/20 (1y) £296,773.90 Coapplicant
NIHR: Coronavirus Clinical Information Network (CO-CIN) 03/03/20 (2y) £8,900,000 Coapplicant
Technology Strategy Board: Establishing a Pipeline for African Swine Fever Virus Genetic Targets 01/10/19 (1.5y) £105,767 Coapplicant
Tropical Animal Genetics (UK) Ltd: Cell library for candidate genes involved in Newcastle Disease Virus infection in vitro 01/09/19 (3y) £100,000 Coapplicant
BBSRC: Host factors controlling foot-and-mouth disease virus (FMDV) replication: towards genetic control of FMD in pigs 01/08/19 (3y) £901,522 Coapplicant
Fiona Elizabeth Agnew Trust (FEAT): Genetics of Mortality in Critical Care (GenOMICC) 01/04/19 (3y) £120,000 CI
BBSRC 18ALERT Equipment Initiative: Large memory HPC infrastructure to underpin world-class biological research 01/04/19 (3y) £600,000 Coapplicant
Health Technology Accelerator Fund: Guiding Therapy in Septic Shock 08/01/19 (3y) £53,000 CI
Wellcome: Clinical PhD Fellowship for Dr Clark Russell 01/08/18 (3y) £650,000 Co-supervisor
BBSRC: Identification of interferon stimulated genes that restrict cross-species transmission of influenza A virus. 01/03/19 (3y) £756,000 Coapplicant
Wellcome: (Institution Strategic Support Fund) Generation of a constitutive Cas9 pig for gene-level pharmaceutical target validation. 01/06/18 (1y) £50,000 PI
Wellcome: Clinical PhD Fellowship for Dr Nick Parkinson 01/08/17 (3y) £650,000 CI
MRC: The SHIELD Consortium for Host Defence Therapeutics 01/11/16 (5y) £4,500,000 WP lead
Wellcome: Establishing causal relationships from phenotypic, genotypic, and proteomic data. 01/08/16 (3y) £650,000 Co-supervisor
BBSRC: Tools and resources: Generation of genome wide CRISPR libraries for pig and chicken 01/10/16 (1y) £88,000 Coapplicant
Wellcome Trust: A clinical trial of convalescent plasma for treatment of Ebolavirus disease 01/03/15 (1y) £120,000 Coapplicant
US Center for Disease Control: HostFlu observational study of influenza in Malawi 01/08/14 (5y) £160,000 Co-CI
Wellcome Intermediate Clinical Fellowship : Identification and characterisation of host factors underlying susceptibility to influenza 01/08/14 (4y) £1,011,082 Applicant
Wellcome Trust: (Institution Strategic Support Fund) The International Severe Influenza Genetics (ISIG) Programme 01/02/12 (1y) £47,531 CI
Wellcome: Mechanisms of Severe Acute Influenza Consortium (MOSAIC) 01/09/09 (5y) £3,645,239 WP lead
UK Embassy to United States of America UK/US Collaboration Development Award 01/08/10 (1mth) £1500 Applicant
Chief Scientist Office: (Project Grant) GenISIS: Genetics of Influenza Susceptibility in Scotland 01/11/09 (2y) £89,742 CI
Wellcome Trust: (Clinical Fellowship) Comparative genomics of the inflammatory response 01/08/09 (3y) £267,208 Applicant
British Heart Foundation: (Project Grant) Oxidative Stress, erythrocyte anion channel damage, and antioxidant function in healthy lowlanders at high altitude. 01/04/01 (1y) £10,525 CI
The Carnegie Trust for the Universities of Scotland: Apex Bolivia 2001 01/03/01 (1y) £2000 CI

Selected Publications (*joint authorship) (corresponding)

(h-index: 90 | citations: 62617 | ORCID:0000-0001-5258-793X )

Shankar-Hari M , Calandra T, Soares MP, Bauer M, Wiersinga WJ, Prescott HC, Knight JC, Baillie JK, Bos LDJ, Derde LPG, Finfer S, ..., van der Poll T. Reframing sepsis immunobiology for translation: towards informative subtyping and targeted immunomodulatory therapies. The Lancet. Respiratory Medicine (2024); doi:10.1016/S2213-2600(23)00468-X

Horby PW , Peto L, Staplin N, Campbell M, Pessoa-Amorim G, Mafham M, Emberson JR, Stewart R, Prudon B, Uriel A, ..., Baillie JK, Buch MH, Day J, Faust SN, Jaki T, Jeffery K, Juszczak E, Knight M, Lim WS, Montgomery A, Mumford A, Rowan K, Thwaites G, Haynes R, Landray MJ. Dimethyl fumarate in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial. Nature Communications (2024); 15: 924. PMC10831058

Devine K , Russell CD, Blanco GR, Walker BR, Homer NZM, Denham SG, Simpson JP, Leavy OC, Elneima O, McAuley HJC, ..., Kenneth Baillie J, Reynolds RM. Plasma steroid concentrations reflect acute disease severity and normalise during recovery in people hospitalised with COVID-19. Clinical Endocrinology (2024); 100: 317-327. doi:10.1111/cen.15012

Cho S , Premraj L, Battaglini D, Fanning JP, Suen J, Bassi GL, Fraser J, Robba C, Griffee M, Solomon T, ..., Baillie K, Sigfrid L, Scott JT, Citarella BW, Merson L, Arora RC, Whitman G, Thomson D, White N. Sex differences in post-acute neurological sequelae of SARS-CoV-2 and symptom resolution in adults after coronavirus disease 2019 hospitalization: an international multi-centre prospective observational study. Brain Communications (2024); 6: fcae036. PMC10914448

Swets MC , Kerr S, Scott-Brown J, Brown AB, Gupta R, Millar JE, Spata E, McCurrach F, Bretherick AD, Docherty A, ..., Baillie JK. Evaluation of pragmatic oxygenation measurement as a proxy for Covid-19 severity. Nature Communications (2023); 14: 7374. PMC10651917

Sidhu JK , Siggins MK, Liew F, Russell CD, Uruchurtu ASS, Davis C, Turtle L, Moore SC, Hardwick HE, Oosthuyzen W, ..., Baillie JK, Openshaw PJM, Thwaites RS. Delayed mucosal anti-viral responses despite robust peripheral inflammation in fatal COVID-19. The Journal of Infectious Diseases (2023); doi:10.1093/infdis/jiad590

Michael BD , Dunai C, Needham EJ, Tharmaratnam K, Williams R, Huang Y, Boardman SA, Clark JJ, Sharma P, Subramaniam K, ..., Baillie JK, Openshaw PJ, Semple MG, Taams LS, Menon DK. Para-infectious brain injury in COVID-19 persists at follow-up despite attenuated cytokine and autoantibody responses. Nature Communications (2023); 14: 8487. PMC10746705

Costigan D , Fenn J, Yen S, Ilott N, Bullers S, Hale J, Greenhalf W, Conibear E, Koycheva A, Madon K, ..., Baillie JK, Semple MG, Openshaw PJM, Pearson C, Johnson J, Lalvani A, Thornton EE. A pro-inflammatory gut mucosal cytokine response is associated with mild COVID-19 disease and superior induction of serum antibodies. Mucosal Immunology (2023); doi:10.1016/j.mucimm.2023.11.005

Burke J , Pugh D, Farrah T, Hamid C, Godden E, MacGillivray TJ, Dhaun N, Baillie JK, King S, MacCormick IJC. Evaluation of an Automated Choroid Segmentation Algorithm in a Longitudinal Kidney Donor and Recipient Cohort. Translational Vision Science and Technology (2023); 12: 19. PMC10668611

Zhu Y , Almeida FJ, Baillie JK, Bowen AC, Britton PN, Brizuela ME, Buonsenso D, Burgner D, Chew KY, Chokephaibulkit K, Cohen C, ..., Short KR. International Pediatric COVID-19 Severity Over the Course of the Pandemic. JAMA Pediatrics (2023); PMC10442787

Pannhorst K , Carlson J, Hölper JE, Grey F, Baillie JK, Höper D, Wöhnke E, Franzke K, Karger A, Fuchs W, Mettenleiter TC. The non-classical major histocompatibility complex II protein SLA-DM is crucial for African swine fever virus replication. Scientific Reports (2023); 13: 10342. PMC10442341

Hayes AJ , Zheng X, O’Kelly J, Neyton LPA, Bochkina NA, Uings I, Liddle J, Baillie JK, Just G, Binnie M, Homer NZM, ..., Mole DJ. Kynurenine monooxygenase regulates inflammation during critical illness and recovery in experimental acute pancreatitis. Cell Reports (2023); 42: 112763. doi:10.1016/j.celrep.2023.112763

Pairo-Castineira E , Rawlik K, Bretherick AD, Qi T, Wu Y, Nassiri I, McConkey GA, Zechner M, Klaric L, Griffiths F, ..., Baillie JK. Author Correction: GWAS and meta-analysis identifies 49 genetic variants underlying critical COVID-19. Nature (2023); doi:10.1038/s41586-023-06383-z

Yang H , Sun H, Brackenridge S, Zhuang X, Wing PAC, Quastel M, Walters L, Garner L, Wang B, Yao X, ..., Baillie JK, Mentzer AJ, Klenerman P, Borrow P, Dong T, McKeating JA, Gillespie GM, McMichael AJ. HLA-E-restricted SARS-CoV-2-specific T cells from convalescent COVID-19 patients suppress virus replication despite HLA class Ia down-regulation. Science Immunology (2023); 8: eabl8881. doi:10.1126/sciimmunol.abl8881

Docherty AB , Farrell J, Thorpe M, Egan C, Dunn S, Norman L, Shaw CA, Law A, Leeming G, Norris L, ..., Baillie JK, Pius R, Seth S, Harrison EM, Lone NI. Patient emergency health-care use before hospital admission for COVID-19 and long-term outcomes in Scotland: a national cohort study. The Lancet. Digital Health (2023); 5: e446-e457. doi:10.1016/S2589-7500(23)00051-1

Pauley E , Drake TM, Griffith DM, Sigfrid L, Lone NI, Harrison EM, Baillie JK, Scott JT, Walsh TS, Semple MG, Docherty AB. Recovery from Covid-19 critical illness: A secondary analysis of the ISARIC4C CCP-UK cohort study and the RECOVER trial. Journal of The Intensive Care Society (2023); 24: 162-169. PMC10225805

Gillan JL , Chokshi M, Hardisty GR, Clohisey Hendry S, Prasca-Chamorro D, Robinson NJ, Lasota B, Clark R, Murphy L, Whyte MKB, Baillie JK, Davidson DJ, Bao G, Gray RD. CAGE sequencing reveals CFTR-dependent dysregulation of type I IFN signaling in activated cystic fibrosis macrophages. Science Advances (2023); 9: eadg5128. doi:10.1126/sciadv.adg5128

Pairo-Castineira E , Rawlik K, Bretherick AD, Qi T, Wu Y, Nassiri I, McConkey GA, Zechner M, Klaric L, Griffiths F, ..., Baillie JK. GWAS and meta-analysis identifies 49 genetic variants underlying critical COVID-19. Nature (2023); doi:10.1038/s41586-023-06034-3

Morris KM , Mishra A, Raut AA, Gaunt ER, Borowska D, Kuo RI, Wang B, Vijayakumar P, Chingtham S, Dutta R, Baillie K, Digard P, Vervelde L, Burt DW, Smith J. Corrigendum: The molecular basis of differential host responses to avian influenza viruses in avian species with differing susceptibility. Frontiers In Cellular and Infection Microbiology (2023); 13: 1194878. PMC10112380

Parker E , Thomas J, Roper KJ, Ijaz S, Edwards T, Marchesin F, Katsanovskaja K, Lett L, Jones C, Hardwick HE, ..., Baillie JK, Openshaw PJM, Turtle L, Ho A, Semple MG, Paxton WA, Tedder RS, Pollakis G. SARS-CoV-2 antibody responses associate with sex, age and disease severity in previously uninfected people admitted to hospital with COVID-19: An ISARIC4C prospective study. Frontiers In Immunology (2023); 14: 1146702. PMC10087108

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

Morris KM , Mishra A, Raut AA, Gaunt ER, Borowska D, Kuo RI, Wang B, Vijayakumar P, Chingtham S, Dutta R, Baillie K, Digard P, Vervelde L, Burt DW, Smith J. The molecular basis of differential host responses to avian influenza viruses in avian species with differing susceptibility. Frontiers In Cellular and Infection Microbiology (2023); 13: 1067993. PMC10011077

Goldswain H , Dong X, Penrice-Randal R, Alruwaili M, Shawli GT, Prince T, Williamson MK, Raghwani J, Randle N, Jones B, ..., Baillie JK, Emmett SR, Digard P, Matthews DA, Turtle L, Darby AC, Davidson AD, Carroll MW, Hiscox JA. The P323L substitution in the SARS-CoV-2 polymerase (NSP12) confers a selective advantage during infection. Genome Biology (2023); 24: 47. PMC10009825

Hamilton F , Mentzer AJ, Parks T, Baillie JK, Smith GD, Ghazal P, Timpson NJ. Variation in ERAP2 has opposing effects on severe respiratory infection and autoimmune disease. American Journal of Human Genetics (2023); doi:10.1016/j.ajhg.2023.02.008

Kartsonaki C , Baillie JK, Barrio NG, Baruch J, Beane A, Blumberg L, Bozza F, Broadley T, Burrell A, Carson G, Citarella BW, ..., Olliaro PL. Characteristics and outcomes of an international cohort of 600 000 hospitalized patients with COVID-19. International Journal of Epidemiology (2023); doi:10.1093/ije/dyad012

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

Turtle L , Thorpe M, Drake TM, Swets M, Palmieri C, Russell CD, Ho A, Aston S, Wootton DG, Richter A, ..., Baillie JK, Semple MG, Docherty AB. Outcome of COVID-19 in hospitalised immunocompromised patients: An analysis of the WHO ISARIC CCP-UK prospective cohort study. PLoS Medicine (2023); 20: e1004086. PMC9928075

Ryan EM , Sadiku P, Coelho P, Watts ER, Zhang A, Howden AJM, Sanchez-Garcia MA, Bewley M, Cole J, McHugh BJ, ..., Baillie K, Cantrell DA, McCafferty J, Choudhury G, Singh D, Dockrell DH, Whyte MKB, Walmsley SR. NRF2 Activation Reprogrammes Defects in Oxidative Metabolism to Restore Macrophage Function in COPD. American Journal of Respiratory and Critical Care Medicine (2023); doi:10.1164/rccm.202203-0482OC

Liew F , Talwar S, Cross A, Willett BJ, Scott S, Logan N, Siggins MK, Swieboda D, Sidhu JK, Efstathiou C, ..., Baillie JK, Semple MG, Brightling C, Thwaites RS, Turtle L, Openshaw PJM. SARS-CoV-2-specific nasal IgA wanes 9 months after hospitalisation with COVID-19 and is not induced by subsequent vaccination. Ebiomedicine (2023); 87: 104402. PMC9762734

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

Vink E , Davis C, MacLean A, Pascall D, McDonald SE, Gunson R, Hardwick HE, Oosthuyzen W, Openshaw PJM, Baillie JK, Semple MG, Ho A. Viral Coinfections in Hospitalized Coronavirus Disease 2019 Patients Recruited to the International Severe Acute Respiratory and Emerging Infections Consortium WHO Clinical Characterisation Protocol UK Study. Open Forum Infectious Diseases (2022); 9: ofac531. PMC9619746

Swann OV , Lone NI, Harrison EM, Tomlinson LA, Walker AJ, Seaborne MJ, Pollock L, Farrell J, Hall PS, Seth S, ..., Baillie JK, Katikireddi SV, Akbari A, Lyons R, Simpson CR, Semple MG, Goldacre B, Brophy S, Sheikh A, Docherty AB. Studying the Long-term Impact of COVID-19 in Kids (SLICK). Healthcare use and costs in children and young people following community-acquired SARS-CoV-2 infection: protocol for an observational study using linked primary and secondary routinely collected healthcare data from England, Scotland and Wales. BMJ Open (2022); 12: e063271. PMC9659708

Stewart I , Jacob J, George PM, Molyneaux PL, Porter JC, Allen RJ, Aslani S, Baillie JK, Barratt SL, Beirne P, Bianchi SM, ..., Jenkins RG. Residual Lung Abnormalities Following COVID-19 Hospitalization: Interim Analysis of the UKILD Post-COVID Study. American Journal of Respiratory and Critical Care Medicine (2022); doi:10.1164/rccm.202203-0564OC

Jefferson E , Cole C, Mumtaz S, Cox S, Giles T, Adejumo S, Urwin E, Lea D, McDonald C, Best J, ..., Baillie JK, Tang M, Leeming G, Power L, Breeze T, Gilson N, Murray DJ, Orton C, Pierce I, Hall I, Ladhani S, Whitaker M, Shallcross L, Seymour D, Varma S, Reilly G, Morris A, Hopkins S, Sheikh A, Quinlan P. CO-CONNECT: A hybrid architecture to facilitate rapid discovery and access to UK wide data in the response to the COVID-19 pandemic. Journal of Medical Internet Research (2022); doi:10.2196/40035

Grundmann A , Wu C, Hardwick M, Baillie JK, Openshaw PJM, Semple MG, Böhning D, Pett S, Michael BD, Thomas RH, Galea I. Fewer COVID-19 Neurological Complications with Dexamethasone and Remdesivir. Annals of Neurology (2022); doi:10.1002/ana.26536

Gonçalves BP , Hall M, Jassat W, Balan V, Murthy S, Kartsonaki C, Semple MG, Rojek A, Baruch J, Reyes LF, Dasgupta A, Dunning J, Citarella BW, Pritchard M, Martín-Quiros A, Sili U, Baillie JK, ..., Olliaro PL. An international observational study to assess the impact of the Omicron variant emergence on the clinical epidemiology of COVID-19 in hospitalised patients. Elife (2022); 11: PMC9534549

Butler-Laporte G , Povysil G, Kosmicki JA, Cirulli ET, Drivas T, Furini S, Saad C, Schmidt A, Olszewski P, Korotko U, Quinodoz M, Çelik E, Kundu K, Walter K, Jung J, Stockwell AD, Sloofman LG, Jordan DM, Thompson RC, Del Valle D, Simons N, Cheng E, Sebra R, Schadt EE, Kim-Schulze S, Gnjatic S, Merad M, Buxbaum JD, Beckmann ND, Charney AW, Przychodzen B, Chang T, Pottinger TD, Shang N, Brand F, Fava F, Mari F, Chwialkowska K, Niemira M, Pula S, Baillie JK, ..., Richards JB. Exome-wide association study to identify rare variants influencing COVID-19 outcomes: Results from the Host Genetics Initiative. PLoS Genetics (2022); 18: e1010367. PMC9632827

Siggins MK , Davies K, Fellows R, Thwaites RS, Baillie JK, Semple MG, Openshaw PJM, Zelek WM, Harris CL, Morgan BP. Alternative pathway dysregulation in tissues drives sustained complement activation and predicts outcome across the disease course in COVID-19. Immunology (2022); doi:10.1111/imm.13585

The RECOVERY Collaborative Group. . Casirivimab and imdevimab in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial. Lancet (London, England) (2022); 399: 665-676. PMC8830904

The RECOVERY Collaborative Group. . Baricitinib in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial and updated meta-analysis. Lancet (London, England) (2022); 400: 359-368. PMC9333998

The RECOVERY Collaborative Group. . Aspirin in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial. Lancet (London, England) (2022); 399: 143-151. PMC8598213

Lawler PR , Goligher EC, Berger JS, Neal MD, McVerry BJ, Nicolau JC, Gong MN, Carrier M, Rosenson RS, Reynolds HR, ..., Zarychanski R. Therapeutic Anticoagulation with Heparin in Noncritically Ill Patients with Covid-19. The New England Journal of Medicine (2021); 385: 790-802. PMC8362594

The RECOVERY Collaborative Group. . Convalescent plasma in patients admitted to hospital with COVID-19 (RECOVERY): a randomised controlled, open-label, platform trial. Lancet (London, England) (2021); 397: 2049-2059. PMC8121538

The RECOVERY Collaborative Group. . Azithromycin in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial. Lancet (London, England) (2021); 397: 605-612. PMC7884931

Horby PW , Mafham M, Bell JL, Linsell L, Staplin N, Emberson J, Palfreeman A, Raw J, Elmahi E, Prudon B, ..., Baillie JK, Chappell LC, Faust SN, Jaki T, Jefferey K, Lim WS, Montgomery A, Rowan K, Juszczak E, Haynes R, Landray MJ. Lopinavir-ritonavir in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial. Lancet (London, England) (2020); 396: 1345-1352. PMC7535623

Wang B , Law A, Regan T, Parkinson N, Cole J, Russell CD, Dockrell DH, Gutmann MU, Baillie JK. Systematic comparison of ranking aggregation methods for gene lists in experimental results. Bioinformatics (Oxford, England) (2022); doi:10.1093/bioinformatics/btac621

Kleeman SO , Cordioli M, Timmers PRHJ, Khan A, Tober-Lau P, Kurth F, Demichev V, Meyer HV, Wilson JF, Ralser M, ..., Baillie K, Janowitz T. Cystatin C is associated with adverse COVID-19 outcomes in diverse populations. Iscience (2022); 105040. PMC9428108

Zhou Y , Shalhoub RN, Rogers SN, Yu S, Gu M, Fabre MA, Quiros PM, Diangson A, Deng W, Anand S, ..., Baillie K, Dunbar CE, Vassiliou GS. Clonal Hematopoiesis Is Not Significantly Associated with Covid-19 Disease Severity. Blood (2022); PMC9293387

Mirchandani AS , Jenkins SJ, Bain CC, Sanchez-Garcia MA, Lawson H, Coelho P, Murphy F, Griffith DM, Zhang A, Morrison T, ..., Baillie JK, Clohisey S, Pridans C, Campana L, Lewis PS, Simpson AJ, Dockrell DH, Schwarze J, Hirani N, Ratcliffe PJ, Pugh CW, Kranc K, Forbes SJ, Whyte MKB, Walmsley SR. Author Correction: Hypoxia shapes the immune landscape in lung injury and promotes the persistence of inflammation. Nature Immunology (2022); PMC9295113

McNaughton AL , Paton RS, Edmans M, Youngs J, Wellens J, Phalora P, Fyfe A, Belij-Rammerstorfer S, Bolton JS, Ball J, ..., Baillie JK, Semple MG, Openshaw PJ, Obolski U, Turner M, Carroll M, Mongkolsapaya J, Screaton G, Kennedy SH, Jarvis L, Barnes E, Dunachie S, Lourenço J, Matthews PC, Bicanic T, Klenerman P, Gupta S, Thompson CP. Fatal COVID-19 outcomes are associated with an antibody response targeting epitopes shared with endemic coronaviruses. JCI Insight (2022); 7: PMC9310533

Zhang S , Cooper-Knock J, Weimer AK, Shi M, Kozhaya L, Unutmaz D, Harvey C, Julian TH, Furini S, Frullanti E, ..., Baillie JK, Davis MM, Tsao PS, Snyder MP. Multiomic analysis reveals cell-type-specific molecular determinants of COVID-19 severity. Cell Systems (2022); doi:10.1016/j.cels.2022.05.007

Stewart A , Sinclair E, Ng JC, O’Hare JS, Page A, Serangeli I, Margreitter C, Orsenigo F, Longman K, Frampas C, ..., Baillie JK, Scott JT, Semple MG, Bailey MJ, Fraternali F, Dunn-Walters DK. Pandemic, Epidemic, Endemic: B Cell Repertoire Analysis Reveals Unique Anti-Viral Responses to SARS-CoV-2, Ebola and Respiratory Syncytial Virus. Frontiers In Immunology (2022); 13: 807104. PMC9111746

Relph KA , Russell CD, Fairfield CJ, Turtle L, de Silva TI, Siggins MK, Drake TM, Thwaites RS, Abrams S, Moore SC, ..., Baillie JK, Semple MG, Ho A. Procalcitonin Is Not a Reliable Biomarker of Bacterial Coinfection in People With Coronavirus Disease 2019 Undergoing Microbiological Investigation at the Time of Hospital Admission. Open Forum Infectious Diseases (2022); 9: ofac179. PMC9070482

Mirchandani AS , Jenkins SJ, Bain CC, Sanchez-Garcia MA, Lawson H, Coelho P, Murphy F, Griffith DM, Zhang A, Morrison T, ..., Baillie JK, Clohisey S, Pridans C, Campana L, Lewis PS, Simpson AJ, Dockrell DH, Schwarze J, Hirani N, Ratcliffe PJ, Pugh CW, Kranc K, Forbes SJ, Whyte MKB, Walmsley SR. Hypoxia shapes the immune landscape in lung injury and promotes the persistence of inflammation. Nature Immunology (2022); 23: 927-939. doi:10.1038/s41590-022-01216-z

Maslove DM , Tang B, Shankar-Hari M, Lawler PR, Angus DC, Baillie JK, Baron RM, Bauer M, Buchman TG, Calfee CS, Dos Santos CC, ..., Marshall JC. Redefining critical illness. Nature Medicine (2022); 28: 1141-1148. doi:10.1038/s41591-022-01843-x

Ijaz S , Dicks S, Jegatheesan K, Parker E, Katsanovskaja K, Vink E, McClure MO, Shute J, Hope J, Cook N, ..., Baillie JK, Semple MG, Tedder RS. Mapping of SARS-CoV-2 IgM and IgG in gingival crevicular fluid: Antibody dynamics and linkage to severity of COVID-19 in hospital inpatients. The Journal of Infection (2022); doi:10.1016/j.jinf.2022.05.033

Dong X , Penrice-Randal R, Goldswain H, Prince T, Randle N, Donovan-Banfield I, Salguero FJ, Tree J, Vamos E, Nelson C, ..., Baillie JK, Openshaw PJM, Turtle L, Matthews DA, Carroll MW, Darby AC, Hiscox JA. Analysis of SARS-CoV-2 known and novel subgenomic mRNAs in cell culture, animal model, and clinical samples using LeTRS, a bioinformatic tool to identify unique sequence identifiers. Gigascience (2022); 11: doi:10.1093/gigascience/giac045

Prince T , Dong X, Penrice-Randal R, Randle N, Hartley C, Goldswain H, Jones B, Semple MG, Baillie JK, Openshaw PJM, Turtle L, ..., Hiscox JA. Analysis of SARS-CoV-2 in Nasopharyngeal Samples from Patients with COVID-19 Illustrates Population Variation and Diverse Phenotypes, Placing the Growth Properties of Variants of Concern in Context with Other Lineages. Msphere (2022); e0091321. doi:10.1128/msphere.00913-21

Millar JE , Neyton L, Seth S, Dunning J, Merson L, Murthy S, Russell CD, Keating S, Swets M, Sudre CH, ..., Baillie JK. Distinct clinical symptom patterns in patients hospitalised with COVID-19 in an analysis of 59,011 patients in the ISARIC-4C study. Scientific Reports (2022); 12: 6843. doi:10.1038/s41598-022-08032-3

Swann OV , Pollock L, Holden KA, Munro APS, Bennett A, Williams TC, Turtle L, Fairfield CJ, Drake TM, Faust SN, ..., Baillie JK, Harrison EM, Docherty AB, Semple MG. Comparison of UK paediatric SARS-CoV-2 admissions across the first and second pandemic waves. Pediatric Research (2022); doi:10.1038/s41390-022-02052-5

Yang Z , MacDonald-Dunlop E, Chen J, Zhai R, Li T, Richmond A, Klaric L, Pirastu N, Ning Z, Zheng C, ..., Baillie JK, Mälarstig A, Reiner AP, Wilson JF, Shen X. Genetic Landscape of the ACE2 Coronavirus Receptor. Circulation (2022); doi:10.1161/CIRCULATIONAHA.121.057888

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

Närhi F , Moonesinghe SR, Shenkin SD, Drake TM, Mulholland RH, Donegan C, Dunning J, Fairfield CJ, Girvan M, Hardwick HE, ..., Baillie JK, Harrison EM, Semple MG, Docherty AB. Implementation of corticosteroids in treatment of COVID-19 in the ISARIC WHO Clinical Characterisation Protocol UK: prospective, cohort study. The Lancet. Digital Health (2022); 4: e220-e234. PMC8940185

Norris T , Razieh C, Yates T, Zaccardi F, Gillies CL, Chudasama YV, Rowlands A, Davies MJ, McCann GP, Banerjee A, ..., Baillie JK, Semple MG, Lawson CA, Khunti K. Admission Blood Glucose Level and Its Association With Cardiovascular and Renal Complications in Patients Hospitalized With COVID-19. Diabetes Care (2022); doi:10.2337/dc21-1709

Timimi L , Figueras-Novoa C, Marcassa E, Florey O, Baillie JK, Beale R, Ulferts R. The V-ATPase complex regulates non-canonical Atg8-family protein lipidation through ATG16L1 recruitment. Autophagy (2022); 1-2. doi:10.1080/15548627.2022.2029233

Turton HA , Pickworth J, Paterson GG, Lawrie A, Baillie JK, Thompson AAR. Soluble P-Selectin and von Willebrand Factor Rise in Healthy Volunteers Following Non-exertional Ascent to High Altitude. Frontiers In Physiology (2022); 13: 825819. PMC8889065

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

David A , Parkinson N, Peacock TP, Pairo-Castineira E, Khanna T, Cobat A, Tenesa A, Sancho-Shimizu V, Casanova J, Abel L, ..., Baillie JK, Sternberg MJ. A common TMPRSS2 variant has a protective effect against severe COVID-19. Current Research In Translational Medicine (2022); 70: 103333. doi:10.1016/j.retram.2022.103333

Rosadas C , Khan M, Parker E, Marchesin F, Katsanovskaja K, Sureda-Vives M, Fernandez N, Randell P, Harvey R, Lilley A, ..., Baillie JK, Openshaw PJ, G Semple M, Cherepanov P, O McClure M, S Tedder R. Detection and Quantification of Antibody to SARS CoV 2 Receptor Binding Domain provides enhanced Sensitivity, Specificity and Utility. Journal of Virological Methods (2022); 114475. PMC8782753

Perkins GD , Ji C, Connolly BA, Couper K, Lall R, Baillie JK, Bradley JM, Dark P, Dave C, De Soyza A, Dennis AV, ..., McAuley DF. Effect of Noninvasive Respiratory Strategies on Intubation or Mortality Among Patients With Acute Hypoxemic Respiratory Failure and COVID-19: The RECOVERY-RS Randomized Clinical Trial. JAMA (2022); doi:10.1001/jama.2022.0028

Dejnirattisai W , Huo J, Zhou D, Zahradník J, Supasa P, Liu C, Duyvesteyn HME, Ginn HM, Mentzer AJ, Tuekprakhon A, ..., Baillie V, Serafin N, Kwatra G, Da Silva K, Madhi SA, Nunes MC, Malik T, Openshaw PJM, Baillie JK, Semple MG, Townsend AR, Huang KA, Tan TK, Carroll MW, Klenerman P, Barnes E, Dunachie SJ, Constantinides B, Webster H, Crook D, Pollard AJ, Lambe T, Paterson NG, Williams MA, Hall DR, Fry EE, Mongkolsapaya J, Ren J, Schreiber G, Stuart DI, Screaton GR. SARS-CoV-2 Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses. Cell (2022); PMC8723827

Hall MD , Baruch J, Carson G, Citarella BW, Dagens A, Dankwa EA, Donnelly CA, Dunning J, Escher M, Kartsonaki C, ..., Olliaro PL. Ten months of temporal variation in the clinical journey of hospitalised patients with COVID-19: An observational cohort. Elife (2021); 10: PMC8791638

Huffman JE , Butler-Laporte G, Khan A, Pairo-Castineira E, Drivas TG, Peloso GM, Nakanishi T, Ganna A, Verma A, Baillie JK, Kiryluk K, Richards JB, Zeberg H. Multi-ancestry fine mapping implicates OAS1 splicing in risk of severe COVID-19. Nature Genetics (2022); doi:10.1038/s41588-021-00996-8

Dejnirattisai W , Huo J, Zhou D, Zahradník J, Supasa P, Liu C, Duyvesteyn HME, Ginn HM, Mentzer AJ, Tuekprakhon A, ..., Baillie V, Serafin N, Ditse Z, Silva KD, Madhi S, Nunes MC, Malik T, Openshaw PJ, Baillie JK, Semple MG, Townsend AR, Huang KA, Tan TK, Carroll MW, Klenerman P, Barnes E, Dunachie SJ, Constantinides B, Webster H, Crook D, Pollard AJ, Lambe T, Paterson NG, Williams MA, Hall DR, Fry EE, Mongkolsapaya J, Ren J, Schreiber G, Stuart DI, Screaton GR. Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses. Biorxiv : The Preprint Server For Biology (2021); PMC8722586

Norris T , Razieh C, Zaccardi F, Yates T, Islam N, Gillies CL, Chudasama YV, Rowlands AV, Davies MJ, McCann GP, ..., Baillie JK, Semple MG, Lawson CA, Khunti K. Impact of cardiometabolic multimorbidity and ethnicity on cardiovascular/renal complications in patients with COVID-19. Heart (British Cardiac Society) (2021); doi:10.1136/heartjnl-2021-320047

Fallerini C , Picchiotti N, Baldassarri M, Zguro K, Daga S, Fava F, Benetti E, Amitrano S, Bruttini M, Palmieri M, ..., Baillie JK, Schmidt A, Frithiof R, Mari F, Renieri A, Furini S. Common, low-frequency, rare, and ultra-rare coding variants contribute to COVID-19 severity. Human Genetics (2021); doi:10.1007/s00439-021-02397-7

Cushnan D , Berka R, Bertolli O, Williams P, Schofield D, Joshi I, Favaro A, Halling-Brown M, Imreh G, Jefferson E, ..., Baillie K, Openshaw PJ, Semple MG, Rubin C, Howlett A, Rockall AG, Bhayat A, Fascia D, Sudlow C, Jacob J. Towards nationally curated data archives for clinical radiology image analysis at scale: Learnings from national data collection in response to a pandemic. Digital Health (2021); 7: 20552076211048654. PMC8637703

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

Bloom CI , Drake TM, Docherty AB, Lipworth BJ, Johnston SL, Nguyen-Van-Tam JS, Carson G, Dunning J, Harrison EM, Baillie JK, Semple MG, Cullinan P, Openshaw PJM. Risk of adverse outcomes in patients with underlying respiratory conditions admitted to hospital with COVID-19: a national, multicentre prospective cohort study using the ISARIC WHO Clinical Characterisation Protocol UK. The Lancet. Respiratory Medicine (2021); doi:10.1016/S2213-2600(21)00013-8

Adaken C , Scott JT, Sharma R, Gopal R, Dicks S, Niazi S, Ijaz S, Edwards T, Smith CC, Cole CP, ..., Baillie JK, Shindo N, Pfeifer D, Hoover DL, Fischer II WA, Wohl DA, Thielman NM, Smith PG, Dimelow RJ, Tedder RS, Semple MG, Paxton WA, Pollakis G. Ebola virus antibody decay-stimulation in a high proportion of survivors. Nature (2021); 590: 468-472. PMC7839293

Docherty AB , Mulholland RH, Lone NI, Cheyne CP, De Angelis D, Diaz-Ordaz K, Donegan C, Drake TM, Dunning J, Funk S, ..., Baillie JK, Harrison EM, Semple MG. Changes in in-hospital mortality in the first wave of COVID-19: a multicentre prospective observational cohort study using the WHO Clinical Characterisation Protocol UK. The Lancet. Respiratory Medicine (2021); PMC8121531

DeMerle KM , Angus DC, Baillie JK, Brant E, Calfee CS, Carcillo J, Chang CH, Dickson R, Evans I, Gordon AC, Kennedy J, ..., Seymour CW. Sepsis Subclasses: A Framework for Development and Interpretation. Critical Care Medicine (2021); 49: 748-759. doi:10.1097/CCM.0000000000004842

Dorward DA , Russell CD, Um IH, Elshani M, Armstrong SD, Penrice-Randal R, Millar T, Lerpiniere CEB, Tagliavini G, Hartley CS, ..., Baillie JK, Dhaliwal K, Wallace WA, Bellamy COC, Prost S, Smith C, Hiscox JA, Harrison DJ, Lucas CD. Tissue-Specific Immunopathology in Fatal COVID-19. American Journal of Respiratory and Critical Care Medicine (2021); 203: 192-201. PMC7874430

Drake TM , Riad AM, Fairfield CJ, Egan C, Knight SR, Pius R, Hardwick HE, Norman L, Shaw CA, McLean KA, ..., Baillie JK, Harrison EM, Semple MG. Characterisation of in-hospital complications associated with COVID-19 using the ISARIC WHO Clinical Characterisation Protocol UK: a prospective, multicentre cohort study. Lancet (London, England) (2021); 398: 223-237. doi:10.1016/S0140-6736(21)00799-6

Dolby HW , Potey P, Wilder-Smith AB, Clohisey S, Millar JE, Baillie JK, Dorward DA, Lucas CD, Russell CD. Histological Evidence of Pulmonary Microthrombosis and Vasculitis in Life-Threatening Respiratory Virus Diseases. Open Forum Infectious Diseases (2021); 8: ofaa640. PMC7798721

Drake TM , Fairfield CJ, Pius R, Knight SR, Norman L, Girvan M, Hardwick HE, Docherty AB, Thwaites RS, Openshaw PJM, Baillie JK, Harrison EM, Semple MG. Non-steroidal anti-inflammatory drug use and outcomes of COVID-19 in the ISARIC Clinical Characterisation Protocol UK cohort: a matched, prospective cohort study. The Lancet. Rheumatology (2021); PMC8104907

Evans RA , McAuley H, Harrison EM, Shikotra A, Singapuri A, Sereno M, Elneima O, Docherty AB, Lone NI, Leavy OC, Daines L, Baillie JK, ..., Brightling CE. Physical, cognitive, and mental health impacts of COVID-19 after hospitalisation (PHOSP-COVID): a UK multicentre, prospective cohort study. The Lancet. Respiratory Medicine (2021); doi:10.1016/S2213-2600(21)00383-0

Fadista J , Kraven LM, Karjalainen J, Andrews SJ, Geller F, Baillie JK, Wain LV, Jenkins RG, Feenstra B. Shared genetic etiology between idiopathic pulmonary fibrosis and COVID-19 severity. Ebiomedicine (2021); 65: 103277. PMC7946355

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

Hölper JE , Grey F, Baillie JK, Regan T, Parkinson NJ, Höper D, Thamamongood T, Schwemmle M, Pannhorst K, Wendt L, Mettenleiter TC, Klupp BG. A Genome-Wide CRISPR/Cas9 Screen Reveals the Requirement of Host Sphingomyelin Synthase 1 for Infection with Pseudorabies Virus Mutant gD Viruses (2021); 13: doi:10.3390/v13081574

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

Hurst EA , Mellanby RJ, Handel I, Griffith DM, Rossi AG, Walsh TS, Shankar-Hari M, Dunning J, Homer NZ, Denham SG, ..., Baillie JK, Russell CD. Vitamin D insufficiency in COVID-19 and influenza A, and critical illness survivors: a cross-sectional study. BMJ Open (2021); 11: e055435. doi:10.1136/bmjopen-2021-055435

Knight SR , Gupta RK, Ho A, Pius R, Buchan I, Carson G, Drake TM, Dunning J, Fairfield CJ, Gamble C, ..., Baillie JK, Docherty A, Semple MG, Noursadeghi M, Harrison EM. Prospective validation of the 4C prognostic models for adults hospitalised with COVID-19 using the ISARIC WHO Clinical Characterisation Protocol. Thorax (2021); doi:10.1136/thoraxjnl-2021-217629

Kosmicki JA , Horowitz JE, Banerjee N, Lanche R, Marcketta A, Maxwell E, Bai X, Sun D, Backman JD, Sharma D, ..., Baillie JK, Butler-Laporte G, Nakanishi T, Lathrop M, Richards JB, Jones M, Balasubramanian S, Salerno W, Shuldiner AR, Marchini J, Overton JD, Habegger L, Cantor MN, Reid JG, Baras A, Abecasis GR, Ferreira MAR. Pan-ancestry exome-wide association analyses of COVID-19 outcomes in 586,157 individuals. American Journal of Human Genetics (2021); doi:10.1016/j.ajhg.2021.05.017

Marciniak SJ , Farrell J, Rostron A, Smith I, Openshaw PJM, Baillie JK, Docherty A, Semple MG. COVID-19 Pneumothorax in the United Kingdom: a prospective observational study using the ISARIC WHO clinical characterisation protocol. The European Respiratory Journal (2021); doi:10.1183/13993003.00929-2021

Fanning JP , Murthy S, Obonyo NG, Baillie JK, Webb S, Dalton HJ, Fraser JF. Global infectious disease research collaborations in crises: building capacity and inclusivity through cooperation. Globalization and Health (2021); 17: 84. doi:10.1186/s12992-021-00731-2

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

Maslove DM , Baillie JK. Two Key Takeaways From a Year of Pandemic Research. Critical Care Medicine (2021); doi:10.1097/CCM.0000000000005078

Millar JE , Wildi K, Bartnikowski N, Bouquet M, Hyslop K, Passmore MR, Ki KK, See Hoe LE, Obonyo NG, Neyton L, ..., Baillie JK, Li Bassi G, Suen JY, McAuley DF, Fraser JF. Characterizing preclinical sub-phenotypic models of acute respiratory distress syndrome: An experimental ovine study. Physiological Reports (2021); 9: e15048. doi:10.14814/phy2.15048

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

Russell CD , Fairfield CJ, Drake TM, Turtle L, Seaton RA, Wootton DG, Sigfrid L, Harrison EM, Docherty AB, de Silva TI, ..., Baillie JK, Semple MG, Ho A. Co-infections, secondary infections, and antimicrobial use in patients hospitalised with COVID-19 during the first pandemic wave from the ISARIC WHO CCP-UK study: a multicentre, prospective cohort study. The Lancet. Microbe (2021); PMC8172149

Russell CD , Valanciute A, Gachanja NN, Stephen J, Penrice-Randal R, Armstrong SD, Clohisey S, Wang B, Al Qsous W, Wallace WA, ..., Baillie JK, Akram AR, Dorward DA, Lucas CD. Tissue Proteomic Analysis Identifies Mechanisms and Stages of Immunopathology in Fatal COVID-19. American Journal of Respiratory Cell and Molecular Biology (2021); doi:10.1165/rcmb.2021-0358OC

Sadiku P , Willson JA, Ryan EM, Sammut D, Coelho P, Watts ER, Grecian R, Young JM, Bewley M, Arienti S, ..., Baillie K, Thompson AAR, Morgan J, Acosta-Sanchez A, Dardé VM, Duran J, Guinovart JJ, Rodriguez-Blanco G, Von Kriegsheim A, Meehan RR, Mazzone M, Dockrell DH, Ghesquiere B, Carmeliet P, Whyte MKB, Walmsley SR. Neutrophils Fuel Effective Immune Responses through Gluconeogenesis and Glycogenesis. Cell Metabolism (2021); 33: 411-423.e4. PMC7863914

Sadiku P , Willson JA, Ryan EM, Sammut D, Coelho P, Watts ER, Grecian R, Young JM, Bewley M, Arienti S, ..., Baillie K, Thompson AAR, Morgan J, Acosta-Sanchez A, Dardé VM, Duran J, Guinovart JJ, Rodriguez-Blanco G, Von Kriegsheim A, Meehan RR, Mazzone M, Dockrell DH, Ghesquiere B, Carmeliet P, Whyte MKB, Walmsley SR. Neutrophils fuel effective immune responses through gluconeogenesis and glycogenesis. Cell Metabolism (2021); 33: 1062-1064. PMC8102058

Shaw RJ , Abrams ST, Austin J, Taylor JM, Lane S, Dutt T, Downey C, Du M, Turtle L, Baillie JK, Openshaw PJM, Wang G, Semple MG, Toh C. Circulating histones play a central role in COVID-19-associated coagulopathy and mortality. Haematologica (2021); doi:10.3324/haematol.2021.278492

Sigfrid L , Drake TM, Pauley E, Jesudason EC, Olliaro P, Lim WS, Gillesen A, Berry C, Lowe DJ, McPeake J, ..., Baillie JK, Openshaw P, Harrison EM, Docherty AB, Semple MG, Scott JT. Long Covid in adults discharged from UK hospitals after Covid-19: A prospective, multicentre cohort study using the ISARIC WHO Clinical Characterisation Protocol. The Lancet Regional Health. Europe (2021); 100186. PMC8343377

Soveg FW , Schwerk J, Gokhale NS, Cerosaletti K, Smith JR, Pairo-Castineira E, Kell AM, Forero A, Zaver SA, Esser-Nobis K, ..., Baillie JK, Buckner JH, Gale M, Savan R. Endomembrane targeting of human OAS1 p46 augments antiviral activity. Elife (2021); 10: doi:10.7554/eLife.71047

Sullivan MK , Lees JS, Drake TM, Docherty AB, Oates G, Hardwick HE, Russell CD, Merson L, Dunning J, Nguyen-Van-Tam JS, ..., Baillie JK. Acute kidney injury in patients hospitalised with COVID-19 from the ISARIC WHO CCP-UK Study: a prospective, multicentre cohort study. Nephrology, Dialysis, Transplantation : Official Publication of The European Dialysis and Transplant Association - European Renal Association (2021); doi:10.1093/ndt/gfab303

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

Townsend A , Rijal P, Xiao J, Tan TK, Huang KA, Schimanski L, Huo J, Gupta N, Rahikainen R, Matthews PC, ..., Baillie JK, Moore SC, Openshaw PJM, Semple MG, Turtle LCW, Ainsworth M, Allcock A, Beer S, Bibi S, Skelly D, Stafford L, Jeffrey K, O’Donnell D, Clutterbuck E, Espinosa A, Mendoza M, Georgiou D, Lockett T, Martinez J, Perez E, Gallardo Sanchez V, Scozzafava G, Sobrinodiaz A, Thraves H, Joly E. A haemagglutination test for rapid detection of antibodies to SARS-CoV-2. Nature Communications (2021); 12: 1951. PMC8007702

Ulferts R , Marcassa E, Timimi L, Lee LC, Daley A, Montaner B, Turner SD, Florey O, Baillie JK, Beale R. Subtractive CRISPR screen identifies the ATG16L1/vacuolar ATPase axis as required for non-canonical LC3 lipidation. Cell Reports (2021); 37: 109899. doi:10.1016/j.celrep.2021.109899

Wickenhagen A , Sugrue E, Lytras S, Kuchi S, Noerenberg M, Turnbull ML, Loney C, Herder V, Allan J, Jarmson I, Cameron-Ruiz N, Varjak M, Pinto RM, Lee JY, Iselin L, Palmalux N, Stewart DG, Swingler S, Greenwood EJD, Crozier TWM, Gu Q, Davies EL, Clohisey S, Wang B, Trindade Maranhão Costa F, Freire Santana M, de Lima Ferreira LC, Murphy L, Fawkes A, Meynert A, Grimes G, Da Silva Filho JL, Marti M, Hughes J, Stanton RJ, Wang ECY, Ho A, Davis I, Jarrett RF, Castello A, Robertson DL, Semple MG, Openshaw PJM, Palmarini M, Lehner PJ, Baillie JK, Rihn SJ, Wilson SJ, Baillie JK, ..., Young P. A prenylated dsRNA sensor protects against severe COVID-19. Science (New York, N.Y.) (2021); eabj3624. doi:10.1126/science.abj3624

Wild JM , Porter JC, Molyneaux PL, George PM, Stewart I, Allen RJ, Aul R, Baillie JK, Barratt SL, Beirne P, Bianchi SM, ..., Jenkins RG. Understanding the burden of interstitial lung disease post-COVID-19: the UK Interstitial Lung Disease-Long COVID Study (UKILD-Long COVID). BMJ Open Respiratory Research (2021); 8: doi:10.1136/bmjresp-2021-001049

Winslow RL , Zhou J, Windle EF, Nur I, Lall R, Ji C, Millar JE, Dark PM, Naisbitt J, Simonds A, ..., Baillie JK, Perkins GD, Semple MG, McAuley DF, Green CA. SARS-CoV-2 environmental contamination from hospitalised patients with COVID-19 receiving aerosol-generating procedures. Thorax (2021); doi:10.1136/thoraxjnl-2021-218035

Wright J , Achana F, Diwakar L, Semple MG, Carroll WD, Baillie K, Thompson C, Alcock A, Kemp TS. Cycle threshold values are inversely associated with poorer outcomes in hospitalised patients with Covid-19: a prospective, observational cohort study conducted at a UK tertiary hospital. International Journal of Infectious Diseases : IJID : Official Publication of The International Society For Infectious Diseases (2021); doi:10.1016/j.ijid.2021.08.022

Yates T , Zaccardi F, Islam N, Razieh C, Gillies CL, Lawson CA, Chudasama Y, Rowlands A, Davies MJ, Docherty AB, ..., Baillie JK, Semple MG, Khunti K. Obesity, chronic disease, age, and in-hospital mortality in patients with covid-19: analysis of ISARIC clinical characterisation protocol UK cohort. BMC Infectious Diseases (2021); 21: 717. doi:10.1186/s12879-021-06466-0

Yates T , Zaccardi F, Islam N, Razieh C, Gillies CL, Lawson CA, Chudasama Y, Rowlands A, Davies MJ, Docherty AB, ..., Baillie JK, Semple MG, Khunti K. Obesity, Ethnicity, and Risk of Critical Care, Mechanical Ventilation, and Mortality in Patients Admitted to Hospital with COVID-19: Analysis of the ISARIC CCP-UK Cohort. Obesity (Silver Spring, Md.) (2021); doi:10.1002/oby.23178

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

Adams ER , Ainsworth M, Anand R, Andersson MI, Auckland K, Baillie JK, Barnes E, Beer S, Bell JI, Berry T, Bibi S, ..., Whitehouse J. Antibody testing for COVID-19: A report from the National COVID Scientific Advisory Panel. Wellcome Open Research (2020); 5: 139. PMC7941096

Andersson MI , Arancibia-Carcamo CV, Auckland K, Baillie JK, Barnes E, Beneke T, Bibi S, Brooks T, Carroll M, Crook D, Dingle K, ..., Zambon M. SARS-CoV-2 RNA detected in blood products from patients with COVID-19 is not associated with infectious virus. Wellcome Open Research (2020); 5: 181. PMC7689603

REMAP-CAP Investigators. . Effect of Hydrocortisone on Mortality and Organ Support in Patients With Severe COVID-19: The REMAP-CAP COVID-19 Corticosteroid Domain Randomized Clinical Trial. JAMA (2020); 324: 1317-1329. PMC7489418

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

Drake TM , Docherty AB, Harrison EM, Quint JK, Adamali H, Agnew S, Babu S, Barber CM, Barratt S, Bendstrup E, ..., Baillie JK, Openshaw PJM, Semple MG, Stewart I, Jenkins RG. Outcome of Hospitalization for COVID-19 in Patients with Interstitial Lung Disease. An International Multicenter Study. American Journal of Respiratory and Critical Care Medicine (2020); 202: 1656-1665. PMC7737581

Geretti AM , Stockdale AJ, Kelly SH, Cevik M, Collins S, Waters L, Villa G, Docherty A, Harrison EM, Turtle L, ..., Baillie JK, Sabin CA, Semple MG. Outcomes of COVID-19 related hospitalization among people with HIV in the ISARIC WHO Clinical Characterization Protocol (UK): a prospective observational study. Clinical Infectious Diseases : An Official Publication of The Infectious Diseases Society of America (2020); PMC7665382

Harris C , Carson G, Baillie JK, Horby P, Nair H. An evidence-based framework for priority clinical research questions for COVID-19. Journal of Global Health (2020); 10: 011001. PMC7125419

Ho JSY , Angel M, Ma Y, Sloan E, Wang G, Martinez-Romero C, Alenquer M, Roudko V, Chung L, Zheng S, ..., Baillie JK, Miraldi ER, Benner C, Brierley I, Digard P, Łuksza M, Firth AE, Krogan N, Greenbaum BD, MacLeod MK, van Bakel H, Garcìa-Sastre A, Yewdell JW, Hutchinson E, Marazzi I. Hybrid Gene Origination Creates Human-Virus Chimeric Proteins during Infection. Cell (2020); 181: 1502-1517.e23. PMC7323901

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

Jacob J , Alexander D, Baillie JK, Berka R, Bertolli O, Blackwood J, Buchan I, Bloomfield C, Cushnan D, Docherty A, Edey A, ..., Joshi I. Using imaging to combat a pandemic: rationale for developing the UK National COVID-19 Chest Imaging Database. The European Respiratory Journal (2020); 56: PMC7331656

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

Millar JE , Bartnikowski N, Passmore MR, Obonyo NG, Malfertheiner MV, von Bahr V, Redd MA, See Hoe L, Ki KK, Pedersen S, ..., Baillie JK, Shekar K, Palpant N, Suen JY, Matthay MA, McAuley DF, Fraser JF. Combined Mesenchymal Stromal Cell Therapy and Extracorporeal Membrane Oxygenation in Acute Respiratory Distress Syndrome. A Randomized Controlled Trial in Sheep. American Journal of Respiratory and Critical Care Medicine (2020); 202: 383-392. PMC7397785

Moore SC , Penrice-Randal R, Alruwaili M, Randle N, Armstrong S, Hartley C, Haldenby S, Dong X, Alrezaihi A, Almsaud M, ..., Baillie JK, Carroll MW, Stewart J, Darby A, Semple M, Turtle L, Hiscox JA. Amplicon-Based Detection and Sequencing of SARS-CoV-2 in Nasopharyngeal Swabs from Patients With COVID-19 and Identification of Deletions in the Viral Genome That Encode Proteins Involved in Interferon Antagonism. Viruses (2020); 12: PMC7602519

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

Palmieri C , Palmer D, Openshaw PJM, Baillie JK, Semple MG, Turtle L. Cancer datasets and the SARS-CoV-2 pandemic: establishing principles for collaboration. ESMO Open (2020); 5: e000825. PMC7252983

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

Paterson GG , Young JM, Willson JA, Graham CJ, Dru RC, Lee EW, Torpey GS, Walmsley SR, Chan MV, Warner TD, Baillie JK, Thompson AAR. Hypoxia Modulates Platelet Purinergic Signalling Pathways. Thrombosis and Haemostasis (2020); 120: 253-261. PMC7286126

Peng Y , Mentzer AJ, Liu G, Yao X, Yin Z, Dong D, Dejnirattisai W, Rostron T, Supasa P, Liu C, ..., Baillie JK, Moore SC, Openshaw PJM, Ansari MA, Dunachie S, Barnes E, Frater J, Kerr G, Goulder P, Lockett T, Levin R, Zhang Y, Jing R, Ho L, Cornall RJ, Conlon CP, Klenerman P, Screaton GR, Mongkolsapaya J, McMichael A, Knight JC, Ogg G, Dong T. Broad and strong memory CD4 Nature Immunology (2020); 21: 1336-1345. doi:10.1038/s41590-020-0782-6

Perkins GD , Couper K, Connolly B, Baillie JK, Bradley JM, Dark P, De Soyza A, Gorman E, Gray A, Hamilton L, Hart N, ..., McAuley DF. RECOVERY- Respiratory Support: Respiratory Strategies for patients with suspected or proven COVID-19 respiratory failure; Continuous Positive Airway Pressure, High-flow Nasal Oxygen, and standard care: A structured summary of a study protocol for a randomised controlled trial. Trials (2020); 21: 687. PMC7388424

Ramilowski JA , Yip CW, Agrawal S, Chang J, Ciani Y, Kulakovskiy IV, Mendez M, Ooi JLC, Ouyang JF, Parkinson N, ..., Baillie JK, Forrest ARR, Guigó R, Hoffman MM, Hon CC, Kasukawa T, Kauppinen S, Kere J, Lenhard B, Schneider C, Suzuki H, Yagi K, de Hoon MJL, Shin JW, Carninci P. Functional annotation of human long noncoding RNAs via molecular phenotyping. Genome Research (2020); 30: 1060-1072. PMC7397864

Russell CD , Millar JE, Baillie JK. Clinical evidence does not support corticosteroid treatment for 2019-nCoV lung injury. Lancet (London, England) (2020); 395: 473-475. PMC7134694

Swann OV , Holden KA, Turtle L, Pollock L, Fairfield CJ, Drake TM, Seth S, Egan C, Hardwick HE, Halpin S, ..., Baillie JK, Harrison EM, Docherty AB, Semple MG. Clinical characteristics of children and young people admitted to hospital with covid-19 in United Kingdom: prospective multicentre observational cohort study. BMJ (Clinical Research Ed.) (2020); 370: m3249. PMC7488201

Thompson CP , Grayson NE, Paton RS, Bolton JS, Lourenço J, Penman BS, Lee LN, Odon V, Mongkolsapaya J, Chinnakannan S, ..., Baillie K, Harvala H, Screaton GR, Temperton N, Klenerman P, Jarvis LM, Gupta S, Simmonds P. Detection of neutralising antibodies to SARS-CoV-2 to determine population exposure in Scottish blood donors between March and May 2020. Euro Surveillance : Bulletin Europeen Sur Les Maladies Transmissibles = European Communicable Disease Bulletin (2020); 25: PMC7651873

Watson K , Russell CD, Baillie JK, Dhaliwal K, Fitzgerald JR, Mitchell TJ, Simpson AJ, Renshaw SA, Dockrell DH. Developing Novel Host-Based Therapies Targeting Microbicidal Responses in Macrophages and Neutrophils to Combat Bacterial Antimicrobial Resistance. Frontiers In Immunology (2020); 11: 786. PMC7289984

Chang EM , Bretherick A, Drummond GB, Baillie JK. Predictive validity of a novel non-invasive estimation of effective shunt fraction in critically ill patients. Intensive Care Medicine Experimental (2019); 7: 49. PMC6701711

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

Flanders CA , Rocke AS, Edwardson SA, Baillie JK, Walsh TS. The effect of dexmedetomidine and clonidine on the inflammatory response in critical illness: a systematic review of animal and human studies. Critical Care (London, England) (2019); 23: 402. PMC6907244

Russell CD , Parajuli A, Gale HJ, Bulteel NS, Schuetz P, de Jager CPC, Loonen AJM, Merekoulias GI, Baillie JK. The utility of peripheral blood leucocyte ratios as biomarkers in infectious diseases: A systematic review and meta-analysis. The Journal of Infection (2019); 78: 339-348. PMC7173077

Scicluna BP , Baillie JK. The Search for Efficacious New Therapies in Sepsis Needs to Embrace Heterogeneity. American Journal of Respiratory and Critical Care Medicine (2019); 199: 936-938. PMC6467300

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

Rocke AS , Paterson GG, Barber MT, Jackson AIR, Main SE, Stannett C, Schnopp MF, MacInnis M, Baillie JK, Horn EH, Moores C, Harrison P, Nimmo AF, Thompson AAR. Thromboelastometry and Platelet Function during Acclimatization to High Altitude. Thrombosis and Haemostasis (2018); 118: 63-71. PMC6260116

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

Noguchi S , Arakawa T, Fukuda S, Furuno M, Hasegawa A, Hori F, Ishikawa-Kato S, Kaida K, Kaiho A, Kanamori-Katayama M, Kawashima T, Kojima M, Kubosaki A, Manabe R, Murata M, Nagao-Sato S, Nakazato K, Ninomiya N, Nishiyori-Sueki H, Noma S, Saijyo E, Saka A, Sakai M, Simon C, Suzuki N, Tagami M, Watanabe S, Yoshida S, Arner P, Axton RA, Babina M, Baillie JK, ..., Hayashizaki Y. FANTOM5 CAGE profiles of human and mouse samples. Scientific Data (2017); 4: 170112. PMC5574368

Russell CD , Baillie JK. Treatable traits and therapeutic targets: Goals for systems biology in infectious disease. Current Opinion In Systems Biology (2017); 2: 140-146. PMC7185428

Grabert K , Michoel T, Karavolos MH, Clohisey S, Baillie JK, Stevens MP, Freeman TC, Summers KM, McColl BW. Microglial brain region-dependent diversity and selective regional sensitivities to aging. Nature Neuroscience (2016); 19: 504-16. PMC4768346

Arner E , Daub CO, Vitting-Seerup K, Andersson R, Lilje B, Drabløs F, Lennartsson A, Rönnerblad M, Hrydziuszko O, Vitezic M, Freeman TC, Alhendi AMN, Arner P, Axton R, Baillie JK, ..., Hayashizaki Y. Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells. Science (New York, N.Y.) (2015); 347: 1010-4. PMC4681433

Lizio M , Harshbarger J, Shimoji H, Severin J, Kasukawa T, Sahin S, Abugessaisa I, Fukuda S, Hori F, Ishikawa-Kato S, Mungall CJ, Arner E, Baillie JK, ..., Kawaji H. Gateways to the FANTOM5 promoter level mammalian expression atlas. Genome Biology (2015); 16: 22. PMC4310165

Mair-Jenkins J , Saavedra-Campos M, Baillie JK, Cleary P, Khaw F, Lim WS, Makki S, Rooney KD, Nguyen-Van-Tam JS, Beck CR. The effectiveness of convalescent plasma and hyperimmune immunoglobulin for the treatment of severe acute respiratory infections of viral etiology: a systematic review and exploratory meta-analysis. The Journal of Infectious Diseases (2015); 211: 80-90. PMC4264590

Patarčić I , Gelemanović A, Kirin M, Kolčić I, Theodoratou E, Baillie JK, de Jong MD, Rudan I, Campbell H, Polašek O. The role of host genetic factors in respiratory tract infectious diseases: systematic review, meta-analyses and field synopsis. Scientific Reports (2015); 5: 16119. PMC4630784

Andersson R , Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T, ..., Baillie JK, Ishizu Y, Shimizu Y, Furuhata E, Maeda S, Negishi Y, Mungall CJ, Meehan TF, Lassmann T, Itoh M, Kawaji H, Kondo N, Kawai J, Lennartsson A, Daub CO, Heutink P, Hume DA, Jensen TH, Suzuki H, Hayashizaki Y, Müller F, Forrest ARR, Carninci P, Rehli M, Sandelin A. An atlas of active enhancers across human cell types and tissues. Nature (2014); 507: 455-461. PMC5215096

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

Davis MR , Andersson R, Severin J, de Hoon M, Bertin N, Baillie JK, Kawaji H, Sandelin A, Forrest ARR, Summers KM. Transcriptional profiling of the human fibrillin/LTBP gene family, key regulators of mesenchymal cell functions. Molecular Genetics and Metabolism (2014); 112: 73-83. PMC4019825

Dunning J , Baillie JK, Cao B, Hayden FG. Antiviral combinations for severe influenza. The Lancet. Infectious Diseases (2014); 14: 1259-70. PMC7164787

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

Russell CD , Griffiths SJ, Baillie JK, Haas J. Stratified infection medicine: a call to arms. The Lancet. Infectious Diseases (2014); 14: 451. doi:10.1016/S1473-3099(14)70774-1

Wang X , Kang Y, Luo C, Zhao T, Liu L, Jiang X, Fu R, An S, Chen J, Jiang N, ..., Baillie JK, Gao Z, Yu J. Heteroresistance at the single-cell level: adapting to antibiotic stress through a population-based strategy and growth-controlled interphenotypic coordination. Mbio (2014); 5: e00942-13. PMC3950525

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

Brennan PM , Jubb A, Baillie JK, Partridge RW. Deciding authorship order. BMJ (Clinical Research Ed.) (2013); 347: f7182. doi:10.1136/bmj.f7182

Horby P , Nguyen NY, Dunstan SJ, Baillie JK. An updated systematic review of the role of host genetics in susceptibility to influenza. Influenza and Other Respiratory Viruses (2013); 7 Suppl 2: 37-41. PMC5909389

Li D , Chu Y, Ren L, Li X, Yuan L, Kang Y, Zhang W, Yang Y, Wang X, Baillie JK, Yu J, Gao Z. Complete genome sequence of methicillin-sensitive Staphylococcus aureus containing a heterogeneic staphylococcal cassette chromosome element. Science China. Life Sciences (2013); 56: 268-74. doi:10.1007/s11427-013-4453-9

Mabbott NA , Baillie JK, Brown H, Freeman TC, Hume DA. An expression atlas of human primary cells: inference of gene function from coexpression networks. BMC Genomics (2013); 14: 632. PMC3849585

Moore NA , Brennan PM, Baillie JK. Wide variation and systematic bias in expert clinicians’ perceptions of prognosis following brain injury. British Journal of Neurosurgery (2013); 27: 340-3. doi:10.3109/02688697.2012.754402

Shukla R , Upton KR, Muñoz-Lopez M, Gerhardt DJ, Fisher ME, Nguyen T, Brennan PM, Baillie JK, Collino A, Ghisletti S, Sinha S, ..., Faulkner GJ. Endogenous retrotransposition activates oncogenic pathways in hepatocellular carcinoma. Cell (2013); 153: 101-11. PMC3898742

Simmonds P , Xia W, Baillie JK, McKinnon K. Modelling mutational and selection pressures on dinucleotides in eukaryotic phyla–selection against CpG and UpA in cytoplasmically expressed RNA and in RNA viruses. BMC Genomics (2013); 14: 610. PMC3829696

. State of Knowledge and Data Gaps of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) in Humans. PLoS Currents (2013); 5: PMC3828229

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

Freeman TC , Ivens A, Baillie JK, Beraldi D, Barnett MW, Dorward D, Downing A, Fairbairn L, Kapetanovic R, Raza S, Tomoiu A, ..., Hume DA. A gene expression atlas of the domestic pig. BMC Biology (2012); 10: 90. PMC3814290

Horby P , Nguyen NY, Dunstan SJ, Baillie JK. The role of host genetics in susceptibility to influenza: a systematic review. Plos One (2012); 7: e33180. PMC3305291

Kobayashi A , Donaldson DS, Kanaya T, Fukuda S, Baillie JK, Freeman TC, Ohno H, Williams IR, Mabbott NA. Identification of novel genes selectively expressed in the follicle-associated epithelium from the meta-analysis of transcriptomics data from multiple mouse cell and tissue populations. DNA Research : An International Journal For Rapid Publication of Reports On Genes and Genomes (2012); 19: 407-22. PMC3473373

MacCormick IJC , Somner J, Morris DS, MacGillivray TJ, Bourne RRA, Huang SS, MacCormick A, Aspinall PA, Baillie JK, Thompson AAR, Dhillon B. Retinal vessel tortuosity in response to hypobaric hypoxia. High Altitude Medicine and Biology (2012); 13: 263-8. doi:10.1089/ham.2011.1097

Pagani L , Ayub Q, MacArthur DG, Xue Y, Baillie JK, Chen Y, Kozarewa I, Turner DJ, Tofanelli S, Bulayeva K, Kidd K, ..., Tyler-Smith C. High altitude adaptation in Daghestani populations from the Caucasus. Human Genetics (2012); 131: 423-33. PMC3312735

Schroder K , Irvine KM, Taylor MS, Bokil NJ, Le Cao K, Masterman K, Labzin LI, Semple CA, Kapetanovic R, Fairbairn L, Akalin A, Faulkner GJ, Baillie JK, ..., Sweet MJ. Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages. Proceedings of The National Academy of Sciences of The United States of America (2012); 109: E944-53. PMC3341041

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

Bates MGD , Thompson AAR, Baillie JK, Sutherland AI, Irving JB, Hirani N, Webb DJ. Sildenafil citrate for the prevention of high altitude hypoxic pulmonary hypertension: double blind, randomized, placebo-controlled trial. High Altitude Medicine and Biology (2011); 12: 207-14. doi:10.1089/ham.2011.0007

Hall DP , Duncan K, Baillie JK. High altitude pulmonary oedema. Journal of The Royal Army Medical Corps (2011); 157: 68-72. doi:10.1136/jramc-157-01-12

Mabbott NA , Baillie JK, Kobayashi A, Donaldson DS, Ohmori H, Yoon S, Freedman AS, Freeman TC, Summers KM. Expression of mesenchyme-specific gene signatures by follicular dendritic cells: insights from the meta-analysis of microarray data from multiple mouse cell populations. Immunology (2011); 133: 482-98. PMC3143359

Upton KR , Baillie JK, Faulkner GJ. Is somatic retrotransposition a parasitic or symbiotic phenomenon? Mobile Genetic Elements (2011); 1: 279-282. PMC3337137

Hume DA , Summers KM, Raza S, Baillie JK, Freeman TC. Functional clustering and lineage markers: insights into cellular differentiation and gene function from large-scale microarray studies of purified primary cell populations. Genomics (2010); 95: 328-38. doi:10.1016/j.ygeno.2010.03.002

Jackson SJ , Varley J, Sellers C, Josephs K, Codrington L, Duke G, Njelekela MA, Drummond G, Sutherland AI, Thompson AAR, Baillie JK. Incidence and predictors of acute mountain sickness among trekkers on Mount Kilimanjaro. High Altitude Medicine and Biology (2010); 11: 217-22. doi:10.1089/ham.2010.1003

Mabbott NA , Baillie JK, Hume DA, Freeman TC. Meta-analysis of lineage-specific gene expression signatures in mouse leukocyte populations. Immunobiology (2010); 215: 724-36. doi:10.1016/j.imbio.2010.05.012

Scott DHT , Fraser S, Willson P, Drummond GB, Baillie JK. Passage of pathogenic microorganisms through breathing system filters used in anaesthesia and intensive care. Anaesthesia (2010); 65: 670-3. doi:10.1111/j.1365-2044.2010.06327.x

Baillie JK , Thompson AAR, Irving JB, Bates MGD, Sutherland AI, Macnee W, Maxwell SRJ, Webb DJ. Oral antioxidant supplementation does not prevent acute mountain sickness: double blind, randomized placebo-controlled trial. QJM : Monthly Journal of The Association of Physicians (2009); 102: 341-8. doi:10.1093/qjmed/hcp026

Paul A , Baillie JK, Drummond GB. Measurement errors caused by incompatibility of apparatus. European Journal of Anaesthesiology (2009); 26: 977-80. doi:10.1097/EJA.0b013e3283313ff3

Thompson AAR , Baillie JK, Bates MGD, Schnopp MF, Simpson A, Partridge RW, Drummond GB, Mason NP. The citric acid cough threshold and the ventilatory response to carbon dioxide on ascent to high altitude. Respiratory Medicine (2009); 103: 1182-8. doi:10.1016/j.rmed.2009.02.007

Baillie JK . Simple, easily memorised "rules of thumb" for the rapid assessment of physiological compensation for respiratory acid-base disorders. Thorax (2008); 63: 289-90. doi:10.1136/thx.2007.091223

Toshner MR , Thompson AAR, Irving JB, Baillie JK, Morton JJ, Peacock AJ. NT-proBNP does not rise on acute ascent to high altitude. High Altitude Medicine and Biology (2008); 9: 307-10. doi:10.1089/ham.2008.1054

Baillie JK . Activated protein C: controversy and hope in the treatment of sepsis. Current Opinion In Investigational Drugs (London, England : 2000) (2007); 8: 933-8. PMID:17979027

Baillie JK , Sultan P, Graveling E, Forrest C, Lafong C. Contamination of anaesthetic machines with pathogenic organisms. Anaesthesia (2007); 62: 1257-61. doi:10.1111/j.1365-2044.2007.05261.x

Baillie JK , Bates MGD, Thompson AAR, Waring WS, Partridge RW, Schnopp MF, Simpson A, Gulliver-Sloan F, Maxwell SRJ, Webb DJ. Endogenous urate production augments plasma antioxidant capacity in healthy lowland subjects exposed to high altitude. Chest (2007); 131: 1473-8. doi:10.1378/chest.06-2235

Bates MGD , Thompson AAR, Baillie JK. Phosphodiesterase type 5 inhibitors in the treatment and prevention of high altitude pulmonary edema. Current Opinion In Investigational Drugs (London, England : 2000) (2007); 8: 226-31. PMID:17408118

Dorward DA , Thompson AAR, Baillie JK, MacDougall M, Hirani N. Change in plasma vascular endothelial growth factor during onset and recovery from acute mountain sickness. Respiratory Medicine (2007); 101: 587-94. doi:10.1016/j.rmed.2006.06.014

Baillie JK , Murray G. Drotrecogin alfa (activated) in severe sepsis. The New England Journal of Medicine (2006); 354: 94-6; author reply 94-6. PMID:16395834

Baillie JK , Power I. The mechanism of action of gabapentin in neuropathic pain. Current Opinion In Investigational Drugs (London, England : 2000) (2006); 7: 33-9. PMID:16425669

Smith EMD , Baillie JK, Thompson AAR, Irving JB, Porteous D, Webb DJ. Endothelial nitric oxide synthase polymorphisms do not influence pulmonary artery systolic pressure at altitude. High Altitude Medicine and Biology (2006); 7: 221-7. doi:10.1089/ham.2006.7.221

Thompson AAR , Baillie JK, Toshner M, Maxwell SRJ, Webb DJ, Irving JB. Pericardial effusions in healthy lowlanders after acute ascent to high altitude. Heart (British Cardiac Society) (2006); 92: 539-40. PMC1860857

Baillie JK , Power I. Morphine, gabapentin, or their combination for neuropathic pain. The New England Journal of Medicine (2005); 352: 2650-1; author reply 2650-1. doi:10.1056/NEJM200506233522520

Selected Invited Lectures

“RECOVERY: Dexamethasone is an effective treatment for Covid-19” Opening plenary, European Society for Intensive Care Medicine Annual Meeting, November 2020

“Optimisation and meta-analysis of genome-scale signals” CRISPR and beyond: perturbations at scale to understand genomes, Wellcome Trust Genome Campus, Hinxton, UK, September 2020

“Genetic effects on outcomes in sepsis: What mechanisms are amenable to treatment” World Congress of Intensive Care, Melbourne, October 2019

“EBOLA / MERS / influenza pandemics” World Congress of Intensive Care, Melbourne, October 2019

“Distinguishing adaptive from maladaptive processes in sepsis.” Sepsis 2019, Rio de Janiero, May 2019

“Extremes of human physiology - sorting out adaptive and maladaptive processes” Futuristic Medicine, Royal College of Physicians of Edinburgh, Feb 2019

“Transcriptomic biomarkers of critical illness” British Pharmacology Society Annual Meeting, London, December 2018

“Genomic stratification in critical illness” Intensive Care Society State of the Art Meeting, London, December 2018

“Genome editing studies of severe influenza” British Thoracic Society Annual Meeting, London, December 2018

“Gene-level target validation in large animals” One Health Symposium, University of Edinburgh, October 2018

“Understanding disease pathogenesis through functional genomics” RIKEN institute seminar, Yokohama, October 2018

“Biological endotypes in sepsis” Sepsis 2018, Bangkok, October 2018

“Sepsis: a syndrome simultaneously too broad and too narrow” Sepsis update meeting, Glasgow, September 2018

“Preparedness and management of global pandemics.” European Society of Intensive Care Medicine NEXT Webinar, September 2018

“Viral host genomic interactions.” Cambridge Centre for Cardiovascular and Respiratory Research Seminar, Cambridge, September 2018

“Applications of functional genomics and genome editing in post-GWAS analyses” BRIC institute seminar, Copenhagen, May 2018

“Precision medicine through genome-scale technologies” China-UK Life Sciences Summit, Beijing, September 2017

“Data-driven identification of syndromes at high altitude” 10th Kno2wledge meeting, London, May 2017

Public lecture: “Starved of Oxygen” Pint of Science, Edinburgh, May 2017

“Sepsis - what underlies individual susceptibility?” Singapore-ANZICS Research Meeting, Singapore, March 2015

“International collaboration in research during outbreaks” Singapore-ANZICS Research Meeting, Singapore, March 2015

“Host genetic susceptibility to influenza - moving towards therapeutic targets” Broad Institute Seminar Series on Infectious Diseases, Cambridge (MA), January 2015

“Why do some people get sepsis while others don’t?” Intensive Care Society State of the Art Meeting, London, December 2014.

“Host genetics of influenza susceptibility” Keystone Symposium on Pathogenesis of Respiratory Viruses, Keystone, Colorado, January 2014.

“Redefining Acute Mountain Sickness” Session chair and speaker, World Congress on Mountain Medicine, Bolzano 2014.

“Virus:host interactions: time to focus on the host?” ANZICS Global Rising Star Fellowship Session, Hobart, Tasmania, October 2013

“Genomics in Anaesthesia and Critical Care” Royal College of Anaesthetists Jubilee Meeting, “Rising star” Session. October 2013

“Large scale biological research in critical care” World Federation of Intensive and Critical Care Societies 11th Congress, Durban, South Africa, August 2013

“Using coexpression to maximise statistical power in genome-wide studies” Computational Genomics Analysis and Training Programme, Oxford, Feb 2012

“Challenges in Severe Acute Respiratory Illness” European Society of Clinical Microbiology and Infectious Diseases, Barcelona, Jan 2012

Co-chair, Biological Studies group. InFACT/Li Ka Shing Knowledge Institute/ISARIC colloquium on SARI research, Toronto, June 2011.

“Host genetic studies” NIH Flu002/Flu003 Analysis planning meeting, Boston, Oct 2011.