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
2015-present Deputy Director of Research, UK Intensive Care Society

Previous Employment

2014-2020 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 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 (inc. suppl. award £1m) 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 86 | h-index 37 | 11001 citations | ORCID:0000-0001-5258-793X

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

Peng Y , Mentzer AJ, Liu G, Yao X, Yin Z, Dong D, Dejnirattisai W, Rostron T, Supasa P, Liu C, ..., Baillie JK, Moore S, Openshaw PJ, Ansari A, Dunachie S, Barnes E, Frater J, Kerr G, Goulder P, Lockett T, Levin R, Cornall RJ, Conlon C, Klenerman P, McMichael A, Screaton G, Mongkolsapaya J, Knight JC, Ogg G, Dong T. Broad and strong memory CD4 bioRxiv : The Preprint Server for Biology: 2020; PMC7302222

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

Bretherick AD , Canela-Xandri O, Joshi PK, Clark DW, Rawlik K, Boutin TS, Zeng Y, Amador C, Navarro P, Rudan I, ..., Ponting*, Chris P., Baillie*, J Kenneth, Haley*, Chris. Proteome-by-Phenome Mendelian Randomisation Detects 38 Proteins with Causal Roles in Human Diseases and Traits bioRxiv: 2019; 631747. doi:10/gf2zwm

Clohisey S , Parkinson N, Wang B, Bertin N, Wise H, Tomoiu A, Consortium F, Summers KM, Carninci P, Forrest AA, ..., Baillie JK. Comprehensive Characterisation of Molecular Host-Pathogen Interactions in Influenza A Virus-Infected Human Macrophages bioRxiv: 2019; 670919. doi:10/gf5dvf

Neyton L , Zheng X, Skouras C, Wilson AB, Gutmann MU, Yau C, Uings IJ, Rao FV, Nicolas A, Marshall C, ..., Baillie*, J Kenneth, Mole*, Damian James. Multiomic Definition of Generalizable Endotypes in Human Acute Pancreatitis. bioRxiv: 2019; 539569. doi:10/gf2zwn

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


“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.