Qualifications and Fellowship Awards
| University of Edinburgh, 1999: | BSc(Hons)(Med Sci) in Physiology |
| University of Edinburgh, 2002: | MB,ChB |
| Royal College of Physicians, 2005: | MRCP(UK) |
| Royal College of Anaesthetists 2009: | FRCA |
| University of Edinburgh, 2012: | PhD “Statistical Genetics in Infectious Disease” |
| Royal College of Physicians, 2016: | FRCP(Ed) |
| Faculty of Intensive Care Medicine, 2016: | FFICM |
Selected prizes and awards
| 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
| 2014-present | Group Leader, Roslin Institute, University of Edinburgh |
| 2014-present | Honorary Consultant in Critical Care Medicine, Royal Infirmary of Edinburgh |
| 2019-present | Visiting Professor, Peking University, Beijing, China |
| 2020-present | Director of Research, UK Intensive Care Society |
Previous Employment
| 2014-2020 | Wellcome Trust Intermediate Clinical Fellow, University of Edinburgh |
| 2012-present | Deputy Director of Research, UK Intensive Care Society |
| 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 and 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 |
| UKRI: UK Coronavirus Immunology consortium (UK-CIC) | 25/08/20 (1 yr) | £6,541,000 | WP lead |
| UKRI: Post-hospitalisation for COVID-19 follow-up study (PHOSP-COVID) | 21/07/20 (1 yr) | £9,700,000 | WP lead |
| DHSC: GenOMICC-Genomics England Partnership for whole genome sequencing | 01/06/20 (1.5 yrs) | £28,000,000 | PI |
| UKRI: ISARIC - Coronavirus Clinical Characterisation Consortium (ISARIC-4C) | 18/03/20 (1.5 yrs) | £5,958,870 | PI |
| CSO: Coronavirus Clinical Characterisation (Scotland) | 01/04/20 (1 yrs) | £296,773.90 | Co-applicant |
| Coronavirus Clinical Information Network (CO-CIN) Study | 03/03/20 (1 yrs) | £553,862 | Co-applicant |
| Technology Strategy Board: Establishing a Pipeline for African Swine Fever Virus Genetic Targets | 01/10/19 (1.5 yrs) | £105,767 | Co-applicant |
| Tropical Animal Genetics (UK) Ltd: Cell library for candidate genes involved in Newcastle Disease Virus infection in vitro | 01/09/19 (3 yrs) | £100,000 | Co-applicant |
| BBSRC: Host factors controlling foot-and-mouth disease virus (FMDV) replication: towards genetic control of FMD in pigs | 01/08/19 (3 yrs) | £901,522 | Co-applicant |
| Fiona Elizabeth Agnew Trust (FEAT): Genetics of Mortality in Critical Care (GenOMICC) Study | 01/04/19 (3 yrs) | £120,000 | PI |
| BBSRC 18ALERT Equipment Initiative: Large memory HPC infrastructure to underpin world-class biological research | 01/04/19 (3 yrs) | £600,000 | Co-applicant |
| Health Technology Accelerator Fund: Guiding Therapy in Septic Shock | 08/01/19 (3 yrs) | £53,000 | PI |
| Wellcome Trust: Clinical PhD Fellowship for Dr Clark Russell | 01/08/18 (3 yrs) | £650,000 | Co-supervisor |
| BBSRC: Identification of interferon stimulated genes that restrict cross-species transmission of influenza A virus. | 01/03/19 (3yrs) | £756,000 | Co-applicant |
| Wellcome Trust: (Institution Strategic Support Fund) Generation of a constitutive Cas9 pig for gene-level pharmaceutical target validation. | 01/06/18 (1 yr) | £50,000 | PI |
| Wellcome Trust: Clinical PhD Fellowship for Dr Nick Parkinson | 01/08/17 (3 yrs) | £650,000 | PI |
| MRC: The SHIELD Consortium for Host Defence Therapeutics | 01/11/16 (5yrs) | £4,500,000 | WP lead |
| Wellcome Trust: Establishing causal relationships from phenotypic, genotypic, and proteomic data. | 01/08/16 (3 yrs) | £650,000 | Co-supervisor |
| BBSRC: Tools and resources: Generation of genome wide CRISPR libraries for pig and chicken | 01/10/16 (1yr) | £88,000 | Co-applicant |
| Wellcome Trust: A clinical trial of convalescent plasma for treatment of Ebolavirus disease | 01/03/15 (1yr) | £120,000 | Co-applicant |
| US Center for Disease Control: HostFlu observational study of influenza in Malawi | 01/08/14 (5yrs) | £160,000 | Co-PI (host genomics) |
| Wellcome Trust: (Intermediate Clinical Fellowship) Identification and characterisation of host factors underlying susceptibility to influenza | 01/08/14 (4yrs) | £1,011,082 | Applicant |
| Wellcome Trust: (Institution Strategic Support Fund) The International Severe Influenza Genetics (ISIG) Programme | 01/02/12 (1yr) | £47,531 | Co-applicant |
| Wellcome Trust: (Programme Grant) Mechanisms of Severe Acute Influenza Consortium (MOSAIC). | 01/09/09 (5yrs) | £3,645,239 | WP lead (host genomics) |
| 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 (2yrs) | £89,742 | PI |
| Wellcome Trust: (Clinical Fellowship) Comparative genomics of the inflammatory response | 01/08/09 (3yrs) | £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 (1yr) | £10,525 | PI |
| The Carnegie Trust for the Universities of Scotland: Apex Bolivia 2001 | 01/03/01 (1yr) | £2000 | PI |
Selected Publications
Metrics: Total 94 | h-index 41 | 13537 citations | ORCID:0000-0001-5258-793X
Dorward DA , Russell CD, Um IH, Elshani M, Armstrong SD, Penrice-Randal R, Millar T, Lerpiniere CE, Tagliavini G, Hartley CS, ..., Baillie JK, Dhaliwal K, Wallace WA, Bellamy CO, 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: 2020; doi:10.1164/rccm.202008-3265OC
Angus DC , Derde L, Al-Beidh F, Annane D, Arabi Y, Beane A, van Bentum-Puijk W, Berry L, Bhimani Z, Bonten M, Bradbury C, Brunkhorst F, Buxton M, Buzgau A, Cheng AC, de Jong M, Detry M, Estcourt L, Fitzgerald M, Goossens H, Green C, Haniffa R, Higgins AM, Horvat C, Hullegie SJ, Kruger P, Lamontagne F, Lawler PR, Linstrum K, Litton E, Lorenzi E, Marshall J, McAuley D, McGlothin A, McGuinness S, McVerry B, Montgomery S, Mouncey P, Murthy S, Nichol A, Parke R, Parker J, Rowan K, Sanil A, Santos M, Saunders C, Seymour C, Turner A, van de Veerdonk F, Venkatesh B, Zarychanski R, Berry S, Lewis RJ, McArthur C, Webb SA, Gordon AC, Al-Beidh F, Angus D, Annane D, Arabi Y, van Bentum-Puijk W, Berry S, Beane A, Bhimani Z, Bonten M, Bradbury C, Brunkhorst F, Buxton M, Cheng A, De Jong M, Derde L, Estcourt L, Goossens H, Gordon A, Green C, Haniffa R, Lamontagne F, Lawler P, Litton E, Marshall J, McArthur C, McAuley D, McGuinness S, McVerry B, Montgomery S, Mouncey P, Murthy S, Nichol A, Parke R, Rowan K, Seymour C, Turner A, van de Veerdonk F, Webb S, Zarychanski R, Campbell L, Forbes A, Gattas D, Heritier S, Higgins L, Kruger P, Peake S, Presneill J, Seppelt I, Trapani T, Young P, Bagshaw S, Daneman N, Ferguson N, Misak C, Santos M, Hullegie S, Pletz M, Rohde G, Rowan K, Alexander B, Basile K, Girard T, Horvat C, Huang D, Linstrum K, Vates J, Beasley R, Fowler R, McGloughlin S, Morpeth S, Paterson D, Venkatesh B, Uyeki T, Baillie K, ..., Carr-Knott L. 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
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: doi:10.2807/1560-7917.ES.2020.25.42.2000685
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; doi:10.1093/cid/ciaa1605
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: doi:10.3390/v12101164
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; doi:10.1056/NEJMoa2022926
Pairo-Castineira E , Clohisey S, Klaric L, Bretherick A, Rawlik K, Parkinson N, Pasko D, Walker S, Richmond A, Fourman MH, ..., Baillie JK. Genetic Mechanisms of Critical Illness in Covid-19 medRxiv: 2020; 2020.09.24.20200048. doi:10.1101/2020.09.24.20200048
Millar JE , Neyton L, Seth S, Dunning J, Merson L, Murthy S, Russell CD, Keating S, Swets M, Sudre CH, ..., Baillie JK. Robust, Reproducible Clinical Patterns in Hospitalised Patients with COVID-19 medRxiv: 2020; 2020.08.14.20168088. doi:10.1101/2020.08.14.20168088
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; doi:10.1164/rccm.202007-2794OC
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. doi:10.1136/bmj.m3249
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; doi:10.1038/s41590-020-0782-6
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. doi:10.1136/bmj.m3339
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. doi:10.1186/s13063-020-04617-3
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; doi:10.1101/gr.254219.119
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 - Preliminary Report. The New England Journal of Medicine: 2020; doi:10.1056/NEJMoa2021436
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. doi:10.1371/journal.pgen.1008785
Akhvlediani T , Ali SM, Angus DC, Arabi YM, Ashraf S, Baillie JK, Bakamutumaho B, Beane A, Bozza F, Brett SJ, Bruzzone R, ..., Webb S. Global Outbreak Research: Harmony Not Hegemony The Lancet Infectious Diseases: 2020; 0: doi:10/ggx55b
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; doi:10.1183/13993003.01809-2020
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
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; doi:10.1016/j.cell.2020.05.035
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
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 20 133 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. doi:10.1136/bmj.m1985
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
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 ECMO in ARDS: A Controlled Experimental Study in Sheep. American Journal of Respiratory and Critical Care Medicine: 2020; doi:10.1164/rccm.201911-2143OC
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
Clohisey S , Parkinson N, Wang B, Bertin N, Wise H, Tomoiu A, Summers KM, Hendry RW, Carninci P, Forrest ARR, ..., Baillie JK. Comprehensive characterisation of transcriptional activity during influenza A virus infection reveals biases in cap-snatching of host RNA sequences. Journal of Virology: 2020; doi:10.1128/JVI.01720-19
Russell CD , Millar JE, Baillie JK. Clinical evidence does not support corticosteroid treatment for 2019-nCoV lung injury. Lancet (London, England): 2020; doi:10.1016/S0140-6736(20)30317-2
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. doi:10.1038/s41467-019-13965-x
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: 2019; doi:10.1055/s-0039-3400305
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. doi:10.1186/s13054-019-2690-4
Clohisey S , Baillie JK. Host susceptibility to severe influenza A virus infection. Critical Care (London, England): 2019; 23: 303. doi:10.1186/s13054-019-2566-7
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. doi:10.1186/s40635-019-0262-1
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; doi:10.1016/j.jinf.2019.02.006
Scicluna BP , Baillie JK. The Search for Efficacious New Therapies in Sepsis Needs to Embrace Heterogeneity. American Journal of Respiratory and Critical Care Medicine: 2018; doi:10.1164/rccm.201811-2148ED
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
Rocke AS , Paterson GG, Barber MT, Jackson AIR, Main S, Stannett C, Schnopp MF, Baillie JK, Horne 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. doi:10.1160/TH17-02-0138
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
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
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
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
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
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
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
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
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
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
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
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
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
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. doi:10.1016/S1473-3099(13)70327-X
Dunning J , Baillie JK, Cao B, Hayden FG. Antiviral combinations for severe influenza. The Lancet. Infectious Diseases: 2014; 14: 1259-70. doi:10.1016/S1473-3099(14)70821-7
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
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
WHO consensus review committee . State of Knowledge and Data Gaps of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) in Humans. PLoS Currents: 2013; 5: PMC3828229
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
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
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
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
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
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
Brennan PM , Jubb A, Baillie JK, Partridge RW. Deciding authorship order. BMJ (Clinical Research Ed.): 2013; 347: f7182. PMID:24342630
Baillie JK , Digard P. Influenza–time to target the host? The New England Journal of Medicine: 2013; 369: 191-3. doi:10.1056/NEJMcibr1304414
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
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
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
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
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
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
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
Upton KR , Baillie JK, Faulkner GJ. Is somatic retrotransposition a parasitic or symbiotic phenomenon? Mobile Genetic Elements: 2011; 1: 279-282. PMC3337137
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
Hall DP , Duncan K, Baillie JK. High altitude pulmonary oedema. Journal of the Royal Army Medical Corps: 2011; 157: 68-72. PMID:21465914
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
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
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
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
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
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
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
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
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 . 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
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
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
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
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 . 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
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
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
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
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. 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
Planned
“RECOVERY: Dexamethasone is an effective treatment for Covid-19” Opening plenary, European Society for Intensive Care Medicine Annual Meeting, November 2020
Completed
“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
“Integrating genome-wide data to identify therapeutic targets in critical illness.” Nepean Society for Critical Care, Sydney, October 2019
“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
“Lungs 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
“Should we give less oxygen?” Sepsis 2018, Bangkok, 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.