Kenneth Baillie

Kenneth at the foot of Sajama, Bolivia; 2001

Kenneth Baillie founded Apex and led the group’s first expedition. He initiated the International HAPE Database project in 2004. He is a clinical lecturer in Critical Care Medicine at the Roslin Institute, University of Edinburgh. His main research interest is using our new understanding of the genome to better understand complex disease states, particularly infectious diseases and hypoxia.

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Recent publications:

1. Gateways to the FANTOM5 promoter level mammalian expression atlas.

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, Bertin N, Bono H, de Hoon M, ... ...Carninci P, Hayashizaki Y, Forrest AR, Kawaji H.
Genome Biol. 2015 Jan 5;16:22. PMID: 25723102

2. Gene regulation. Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells.

Arner E, Daub CO, Vitting-Seerup K, Andersson R, Lilje B, Drablos F, Lennartsson A, Ronnerblad M, Hrydziuszko O, Vitezic M, Freeman TC, Alhendi AM, Arner P, Axton R, Baillie JK, Beckhouse A, ... ...Forrest AR, Sandelin A, Carninci P, Hayashizaki Y.
Science. 2015 Feb 27;347(6225):1010-4. PMID: 25678556

3. Antiviral combinations for severe influenza.

Dunning J, Baillie JK, Cao B, Hayden FG.
Lancet Infect Dis. 2014 Dec;14(12):1259-70. PMID: 25213733

4. 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.

Mair-Jenkins J, Saavedra-Campos M, Baillie JK, Cleary P, Khaw FM, Lim WS, Makki S, Rooney KD, Beck CR.
J Infect Dis. 2015 Jan 1;211(1):80-90. PMID: 25030060

5. Translational genomics. Targeting the host immune response to fight infection.

Baillie JK.
Science. 2014 May 23;344(6186):807-8. PMID: 24855243

6. Stratified infection medicine: a call to arms.

Russell CD, Griffiths SJ, Baillie JK, Haas J.
Lancet Infect Dis. 2014 Jun;14(6):451. PMID: 24849724

7. A promoter-level mammalian expression atlas.

Forrest AR, Kawaji H, Rehli M, Baillie JK, de Hoon MJ, Haberle V, Lassmann T, Kulakovskiy IV, Lizio M, Itoh M, Andersson R, Mungall CJ, Meehan TF, Schmeier S, Bertin N, Jorgensen M, ... ...Sandelin A, Hume DA, Carninci P, Hayashizaki Y.
Nature. 2014 Mar 27;507(7493):462-70. PMID: 24670764

8. An atlas of active enhancers across human cell types and tissues.

Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T, Ntini E, Arner E, Valen E, Li K, Schwarzfischer L, Glatz D, ... ...Forrest AR, Carninci P, Rehli M, Sandelin A.
Nature. 2014 Mar 27;507(7493):455-61. PMID: 24670763

9. Open source clinical science for emerging infections.

Dunning JW, Merson L, Rohde GG, Gao Z, Semple MG, Tran D, Gordon A, Olliaro PL, Khoo SH, Bruzzone R, Horby P, Cobb JP, Longuere KS, Kellam P, Nichol A, Brett S, ... ...Openshaw PJ, Farrar J, Carson G, Baillie JK.
Lancet Infect Dis. 2014 Jan;14(1):8-9. PMID: 24355025

10. Transcriptional profiling of the human fibrillin/LTBP gene family, key regulators of mesenchymal cell functions.

Davis MR, Andersson R, Severin J, de Hoon M, Bertin N, Baillie JK, Kawaji H, Sandelin A, Forrest AR, Summers KM.
Mol Genet Metab. 2014 May;112(1):73-83. PMID: 24703491

11. Heteroresistance at the single-cell level: adapting to antibiotic stress through a population-based strategy and growth-controlled interphenotypic coordination.

Wang X, Kang Y, Luo C, Zhao T, Liu L, Jiang X, Fu R, An S, Chen J, Jiang N, Ren L, Wang Q, Baillie JK, Gao Z, Yu J.
MBio. 2014 Feb 11;5(1):e00942-13. PMID: 24520060

12. Network analysis reveals distinct clinical syndromes underlying acute mountain sickness.

Hall DP, MacCormick IJ, Phythian-Adams AT, Rzechorzek NM, Hope-Jones D, Cosens S, Jackson S, Bates MG, Collier DJ, Hume DA, Freeman T, Thompson AA, Baillie JK.
PLoS One. 2014 Jan 22;9(1):e81229. PMID: 24465370

13. Deciding authorship order.

Brennan PM, Jubb A, Baillie JK, Partridge RW.
BMJ. 2013 Dec 16;347:f7182. PMID: 24342630

14. State of Knowledge and Data Gaps of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) in Humans.

Who Mers-Cov Research Group .
PLoS Curr. 2013 Nov 12;5. pii: ecurrents.outbreaks.0bf719e352e7478f8ad85fa30127ddb8. PMID: 24270606

15. An updated systematic review of the role of host genetics in susceptibility to influenza.

Horby P, Nguyen NY, Dunstan SJ, Baillie JK.
Influenza Other Respir Viruses. 2013 Sep;7 Suppl 2:37-41. PMID: 24034482

16. An expression atlas of human primary cells: inference of gene function from coexpression networks.

Mabbott NA, Baillie JK, Brown H, Freeman TC, Hume DA.
BMC Genomics. 2013 Sep 20;14:632. PMID: 24053356

17. Modelling mutational and selection pressures on dinucleotides in eukaryotic phyla--selection against CpG and UpA in cytoplasmically expressed RNA and in RNA viruses.

Simmonds P, Xia W, Baillie JK, McKinnon K.
BMC Genomics. 2013 Sep 10;14:610. PMID: 24020411

18. Influenza--time to target the host?

Baillie JK, Digard P.
N Engl J Med. 2013 Jul 11;369(2):191-3. PMID: 23841736

19. Endogenous retrotransposition activates oncogenic pathways in hepatocellular carcinoma.

Shukla R, Upton KR, Munoz-Lopez M, Gerhardt DJ, Fisher ME, Nguyen T, Brennan PM, Baillie JK, Collino A, Ghisletti S, Sinha S, Iannelli F, Radaelli E, Dos Santos A, Rapoud D, Guettier C, ... ...Ciccarelli FD, Garcia-Perez JL, Faivre J, Faulkner GJ.
Cell. 2013 Mar 28;153(1):101-11. PMID: 23540693

20. Wide variation and systematic bias in expert clinicians' perceptions of prognosis following brain injury.

Moore NA, Brennan PM, Baillie JK.
Br J Neurosurg. 2013 Jun;27(3):340-3. PMID: 23461749

21. A gene expression atlas of the domestic pig.

Freeman TC, Ivens A, Baillie JK, Beraldi D, Barnett MW, Dorward D, Downing A, Fairbairn L, Kapetanovic R, Raza S, Tomoiu A, Alberio R, Wu C, Su AI, Summers KM, Tuggle CK, Archibald AL, Hume DA.
BMC Biol. 2012 Nov 15;10:90. PMID: 23153189

22. Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages.

Schroder K, Irvine KM, Taylor MS, Bokil NJ, Le Cao KA, Masterman KA, Labzin LI, Semple CA, Kapetanovic R, Fairbairn L, Akalin A, Faulkner GJ, Baillie JK, Gongora M, Daub CO, Kawaji H, ... ...Hayashizaki Y, Lenhard B, Hume DA, Sweet MJ.
Proc Natl Acad Sci U S A. 2012 Apr 17;109(16):E944-53. PMID: 22451944

23. IFITM3 restricts the morbidity and mortality associated with influenza.

Everitt AR, Clare S, Pertel T, John SP, Wash RS, Smith SE, Chin CR, Feeley EM, Sims JS, Adams DJ, Wise HM, Kane L, Goulding D, Digard P, Anttila V, Baillie JK, ... ...Openshaw PJ, Dougan G, Brass AL, Kellam P.
Nature. 2012 Mar 25;484(7395):519-23. PMID: 22446628

24. The role of host genetics in susceptibility to influenza: a systematic review.

Horby P, Nguyen NY, Dunstan SJ, Baillie JK.
PLoS One. 2012;7(3):e33180. PMID: 22438897

25. Somatic retrotransposition alters the genetic landscape of the human brain.

Baillie JK, Barnett MW, Upton KR, Gerhardt DJ, Richmond TA, De Sapio F, Brennan PM, Rizzu P, Smith S, Fell M, Talbot RT, Gustincich S, Freeman TC, Mattick JS, Hume DA, Heutink P, Carninci P, Jeddeloh JA, Faulkner GJ.
Nature. 2011 Oct 30;479(7374):534-7. PMID: 22037309

26. Complete genome sequence of methicillin-sensitive Staphylococcus aureus containing a heterogeneic staphylococcal cassette chromosome element.

Li D, Chu Y, Ren L, Li X, Yuan L, Kang Y, Zhang W, Yang Y, Wang X, Baillie JK, Yu J, Gao Z.
Sci China Life Sci. 2013 Mar;56(3):268-74. PMID: 23526394

27. Retinal vessel tortuosity in response to hypobaric hypoxia.

MacCormick IJ, Somner J, Morris DS, MacGillivray TJ, Bourne RR, Huang SS, MacCormick A, Aspinall PA, Baillie JK, Thompson AA, Dhillon B.
High Alt Med Biol. 2012 Dec;13(4):263-8. PMID: 23270443

28. 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.

Kobayashi A, Donaldson DS, Kanaya T, Fukuda S, Baillie JK, Freeman TC, Ohno H, Williams IR, Mabbott NA.
DNA Res. 2012 Oct;19(5):407-22. PMID: 22991451

29. Is somatic retrotransposition a parasitic or symbiotic phenomenon?

Upton KR, Baillie JK, Faulkner GJ.
Mob Genet Elements. 2011 Nov 1;1(4):279-282. PMID: 22545239

30. High altitude adaptation in Daghestani populations from the Caucasus.

Pagani L, Ayub Q, MacArthur DG, Xue Y, Baillie JK, Chen Y, Kozarewa I, Turner DJ, Tofanelli S, Bulayeva K, Kidd K, Paoli G, Tyler-Smith C.
Hum Genet. 2012 Mar;131(3):423-33. PMID: 21904933

31. Sildenafil citrate for the prevention of high altitude hypoxic pulmonary hypertension: double blind, randomized, placebo-controlled trial.

Bates MG, Thompson AA, Baillie JK, Sutherland AI, Irving JB, Hirani N, Webb DJ.
High Alt Med Biol. 2011 Fall;12(3):207-14. PMID: 21962063

32. Expression of mesenchyme-specific gene signatures by follicular dendritic cells: insights from the meta-analysis of microarray data from multiple mouse cell populations.

Mabbott NA, Kenneth Baillie J, Kobayashi A, Donaldson DS, Ohmori H, Yoon SO, Freedman AS, Freeman TC, Summers KM.
Immunology. 2011 Aug;133(4):482-98. PMID: 21635249

33. High altitude pulmonary oedema.

Hall DP, Duncan K, Baillie JK.
J R Army Med Corps. 2011 Mar;157(1):68-72. PMID: 21465914

34. Incidence and predictors of acute mountain sickness among trekkers on Mount Kilimanjaro.

Jackson SJ, Varley J, Sellers C, Josephs K, Codrington L, Duke G, Njelekela MA, Drummond G, Sutherland AI, Thompson AA, Baillie JK.
High Alt Med Biol. 2010 Fall;11(3):217-22. PMID: 20919888

35. Meta-analysis of lineage-specific gene expression signatures in mouse leukocyte populations.

Mabbott NA, Kenneth Baillie J, Hume DA, Freeman TC.
Immunobiology. 2010 Sep-Oct;215(9-10):724-36. PMID: 20580463

36. Medicine at high altitudes: danger and opportunity.

Baillie JK.
Journal of the Royal College of Physicians of Edinburgh 2009; 39:162-5.

37. Passage of pathogenic microorganisms through breathing system filters used in anaesthesia and intensive care.

Scott DH, Fraser S, Willson P, Drummond GB, Baillie JK.
Anaesthesia. 2010 Jul;65(7):670-3. PMID: 20374232

38. Functional clustering and lineage markers: insights into cellular differentiation and gene function from large-scale microarray studies of purified primary cell populations.

Hume DA, Summers KM, Raza S, Baillie JK, Freeman TC.
Genomics. 2010 Jun;95(6):328-38. PMID: 20211243

39. Measurement errors caused by incompatibility of apparatus.

Paul A, Baillie JK, Drummond GB.
Eur J Anaesthesiol. 2009 Nov;26(11):977-80. PMID: 19707147

40. The citric acid cough threshold and the ventilatory response to carbon dioxide on ascent to high altitude.

Thompson AA, Baillie JK, Bates MG, Schnopp MF, Simpson A, Partridge RW, Drummond GB, Mason NP.
Respir Med. 2009 Aug;103(8):1182-8. PMID: 19303278

41. Oral antioxidant supplementation does not prevent acute mountain sickness: double blind, randomized placebo-controlled trial.

Baillie JK, Thompson AA, Irving JB, Bates MG, Sutherland AI, Macnee W, Maxwell SR, Webb DJ.
QJM. 2009 May;102(5):341-8. PMID: 19273551

42. NT-proBNP does not rise on acute ascent to high altitude.

Toshner MR, Thompson AA, Irving JB, Baillie JK, Morton JJ, Peacock AJ.
High Alt Med Biol. 2008 Winter;9(4):307-10. PMID: 19115915

43. Simple, easily memorised "rules of thumb" for the rapid assessment of physiological compensation for respiratory acid-base disorders.

Baillie JK.
Thorax. 2008 Mar;63(3):289-90. PMID: 18308967

44. Contamination of anaesthetic machines with pathogenic organisms.

Baillie JK, Sultan P, Graveling E, Forrest C, Lafong C.
Anaesthesia. 2007 Dec;62(12):1257-61. PMID: 17991263

45. Activated protein C: controversy and hope in the treatment of sepsis.

Baillie JK.
Curr Opin Investig Drugs. 2007 Nov;8(11):933-8. PMID: 17979027

46. Endogenous urate production augments plasma antioxidant capacity in healthy lowland subjects exposed to high altitude.

Baillie JK, Bates MG, Thompson AA, Waring WS, Partridge RW, Schnopp MF, Simpson A, Gulliver-Sloan F, Maxwell SR, Webb DJ.
Chest. 2007 May;131(5):1473-8. PMID: 17494796

47. Phosphodiesterase type 5 inhibitors in the treatment and prevention of high altitude pulmonary edema.

Bates MG, Thompson AA, Baillie JK.
Curr Opin Investig Drugs. 2007 Mar;8(3):226-31. PMID: 17408118

48. Endothelial nitric oxide synthase polymorphisms do not influence pulmonary artery systolic pressure at altitude.

Smith EM, Baillie JK, Thompson AA, Irving JB, Porteous D, Webb DJ.
High Alt Med Biol. 2006 Fall;7(3):221-7. PMID: 16978134

49. Change in plasma vascular endothelial growth factor during onset and recovery from acute mountain sickness.

Dorward DA, Thompson AA, Baillie JK, MacDougall M, Hirani N.
Respir Med. 2007 Mar;101(3):587-94. PMID: 16890420

50. Pericardial effusions in healthy lowlanders after acute ascent to high altitude.

Thompson AA, Baillie JK, Toshner M, Maxwell SR, Webb DJ, Irving JB.
Heart. 2006 Apr;92(4):539-40. PMID: 16537774

51. The mechanism of action of gabapentin in neuropathic pain.

Baillie JK, Power I.
Curr Opin Investig Drugs. 2006 Jan;7(1):33-9. PMID: 16425669

52. Drotrecogin alfa (activated) in severe sepsis.

Baillie JK, Murray G.
N Engl J Med. 2006 Jan 5;354(1):94-6. PMID: 16395834

53. The Chacaltaya High Altitude Laboratory.

Baillie JK, Thompson AAR, Bates MGD, Schnopp MS, Simpson A, Partridge R.
Journal of the Royal College of Physicians of Edinburgh 34: 130-133.

54. Morphine, gabapentin, or their combination for neuropathic pain.

Baillie JK, Power I.
N Engl J Med. 2005 Jun 23;352(25):2650-1. PMID: 15972877