Baillie lab, Roslin Institute,
University of Edinburgh


Publications

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

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

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

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

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

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

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

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

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

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

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 (2021); 591: 92-98. doi:10.1038/s41586-020-03065-y

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

Klaric L , Gisby JS, Papadaki A, Muckian MD, Macdonald-Dunlop E, Zhao JH, Tokolyi A, Persyn E, Pairo-Castineira E, Morris AP, ..., Baillie JK, Paul DS, Joshi PK, Butterworth AS, Mälarstig A, Pirastu N, Wilson JF, Peters JE. Mendelian randomisation identifies alternative splicing of the FAS death receptor as a mediator of severe COVID-19. Medrxiv : The Preprint Server For Health Sciences (2021); PMC8043484

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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, ..., Summers C. 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

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

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

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

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

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

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

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

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

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

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

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

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. PMC7158987

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

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

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

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

. 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. doi:10.1136/bmj.f7182

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

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. doi:10.1136/jramc-157-01-12

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

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

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