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Dr Miles Parkes

Dr Miles Parkes

Miles Parkes is accepting applications for PhD students.

Miles Parkes is available for consultancy.

Research Interests

My interest is the molecular genetics of Crohn’s disease and ulcerative colitis. Our local IBD repository consists of >3000 DNA samples recruited from patients across Eastern England, intestinal biopsies from >400 IBD cases plus serum and stool samples. Current interests include fine mapping of the >160 confirmed IBD genetic susceptibility loci identified to date - using sequencing and array-based technologies together with expression and functional studies; functional interrogation of IBD-associated variants in primary human cells; investigation of differential methylation in colonoscopic biopsies and peripheral blood leukocyte subsets from IBD cases and controls; identification of microbial triggers of IBD, using metagenomic techniques; development of prognostic biomarkers in IBD; and participation in both investigator-led and commercial trials of new therapies in IBD.
We have close working relationships with colleagues at the Wellcome Trust Sanger Institute, with members of the UK IBD genetics research consortium (chaired by MP) and international IBD genetics research consortium (formerly chaired by MP), and with the Wellcome Trust Case Control Consortium.

Public and Patient Involvement/Engagement


In the UK, over 500,000 people live with Crohn’s disease (CD) or ulcerative colitis (UC), collectively known as inflammatory bowel disease or IBD. These conditions are characterised by debilitating abdominal symptoms, and, in their severe forms, have a major adverse impact on health and quality of life. To expedite research into CD and UC and help develop personalised therapies, the UK IBD Genetics Consortium and the National Institute for Health Research (NIHR) BioResource launched IBD BioResource in 2016. The IBD BioResource is a national platform designed to recruit over 25,000 recallable patients from hospitals UK-wide. For each enlisted participant, IBD BioResource holds DNA, health and lifestyle data and clinical data. All this information is made available to authorised investigators, of any background (i.e. university, industry or healthcare), who wish to undertake research studies and drive important IBD research. These may include taking fresh samples of blood, getting access to anonymised data or participating in clinical trials based on clinical and genetic characteristics. 


This year we have taken part in some PPI/E events/activities to raise awareness on IBD and highlight the importance of NIHR BioResource and IBD BioResource in facilitating important (IBD) research:


-20/05/19: World IBD day and International Clinical Trial day

IBD BioResource held a stand at the Main concourse of Addenbrookes Hospital to raise awareness on Crohn's and Colitis, and to engage with member of the public to describe IBD BioResource's aspirations and discuss how they can help us achieve our goals.


-07/09/19: ‘Patient Involvement in Research Day’ 

We took part in a ‘Patient Involvement in Research day’ organised by Crohn’s & Colitis UK.  Following a live–streamed presentation where we described the aims of IBD BioResource and its vision for the future of the Health Data Research Hub for IBD, patients were then invited to take part in a short online survey. The topics covered ‘access to medical and health records’, ‘long term storage and access to information/data’ and ‘genetic data, feedback and implication’. We have now obtained the feedback and views from more than 850 patients. ​


-10-13/10/19 New Scientist live Show

NIHR BioResource and IBD BioResource together held a stand at the New Scientist Live across the 4 days. Our hands-on activity and interactions with members of the NIHR and IBD BioResource provided a great opportunity for the public to understand what Research is, what the benefits are and what taking part involves. In particular, through the participation in a pretend ‘chocolate trial', over 1,000 people from all ages and background gained some insights into reading research information, give informed consent and be randomised to a 'trial chocolate’. 


-20/11/19 BRC open evening TBC

During this open evening, we are hoping to present the results of the 'Patient involvement in Research day' and introduce the aims and aspirations of the Health Data Research Hub for IBD.


genomics ; genetics ; biostatistics ; methylation ; mucosal immunology ; prognosis ; bioinformatics ; colitis


  • inflammatory bowel disease
  • Crohn's disease

Key Publications

Recent Scientific Publications

Parkes M; IBD BioResource Investigators​BD BioResource: an open-access platform of 25 000 patients to accelerate research in Crohn's and Colitis. Gut. 2019 Sep;68(9):1537-1540. doi: 10.1136/gutjnl-2019-318835. Epub 2019 Jul 3.​

Castro-Dopico T, Dennison TW, Ferdinand JR, Mathews RJ, Fleming A, Clift D, Stewart BJ, Jing C, Strongili K, Labzin LI, Monk E, Saeb-Parsy K, Bryant CE, Clare S, Parkes M and Clatworthy M. Anti-commensal IgG drives intestinal inflammation and type 17 immunity. Immunity. 2019 Apr 16;50(4):1099-1114

Rengarajan S, Vivio EE, Parkes M, Peterson DA, Roberson EDO, Newberry RD, Ciorba MA, Hsieh CS. Dynamic immunoglobulin responses to gut bacteria during inflammatory bowel disease. Gut Microbes. 2019 Jun 16:1-16. doi: 10.1080/19490976.2019.1626683.

Snowden JA, Hawkey C, Hind D, Swaby L, Mellor K, Emsley R, Mandefield L, Lee E, Badoglio M, Polge E, Labopin M, Gribben J, Pockley AG, Foulds GA, Lobo A, Travis S, Parkes M, Satsangi J, Papaioannou D, Lindsay JO. Autologous stem cell transplantation in refractory Crohn's disease - low intensity therapy evaluation (ASTIClite): study protocols for a multicentre, randomised controlled trial and observational follow up study. BMC Gastroenterol. 2019 May 31;19(1):82. doi: 10.1186/s12876-019-0992-2.

Biasci D, Lee JC, Noor NM, Pombal DR, Hou M, Lewis N, Ahmad T, Hart A, Parkes M, McKinney EF, Lyons PA, Smith KGC. A blood-based prognostic biomarker in IBD. Gut. 2019 Aug;68(8):1386-1395. doi: 10.1136/gutjnl-2019-318343. Epub 2019 Apr 27.

Kennedy NA, Heap GA, Green HD, Hamilton B, Bewshea C, Walker GJ, Thomas A, Nice R, Perry MH, Bouri S, Chanchlani N, Heerasing NM, Hendy P, Lin S, Gaya DR, Cummings JRF, Selinger CP, Lees CW, Hart AL, Parkes M, Sebastian S, Mansfield JC, Irving PM, Lindsay J, Russell RK, McDonald TJ, McGovern D, Goodhand JR, Ahmad T; UK Inflammatory Bowel Disease Pharmacogenetics Study Group. Predictors of anti-TNF treatment failure in anti-TNF-naive patients with active luminal Crohn's disease: a prospective, multicentre, cohort study. Lancet Gastroenterol Hepatol. 2019 May;4(5):341-353. doi: 10.1016/S2468-1253(19)30012-3. Epub 2019 Feb 27.

Walker GJ, Harrison JW, Heap GA, Voskuil MD, Andersen V, Anderson CA, Ananthakrishnan AN, Barrett JC, Beaugerie L, Bewshea CM, Cole AT, Cummings FR, Daly MJ, Ellul P, Fedorak RN, Festen EAM, Florin TH, Gaya DR, Halfvarson J, Hart AL, Heerasing NM, Hendy P, Irving PM, Jones SE, Koskela J, Lindsay JO, Mansfield JC, McGovern D, Parkes M, Pollok RCG, Ramakrishnan S, Rampton DS, Rivas MA, Russell RK, Schultz M, Sebastian S, Seksik P, Singh A, So K, Sokol H, Subramaniam K, Todd A, Annese V, Weersma RK, Xavier R, Ward R, Weedon MN, Goodhand JR, Kennedy NA, Ahmad T; IBD Pharmacogenetics Study Group. Association of Genetic Variants in NUDT15 With Thiopurine-Induced Myelosuppression in Patients With Inflammatory Bowel Disease. JAMA. 2019 Feb 26;321(8):773-785. doi: 10.1001/jama.2019.0709.

Kennedy NA, Lamb CA, Berry SH, Walker AW, Mansfield J, Parkes M, Simpkins R, Tremelling M, Nutland S; UK IBD Genetics Consortium, Parkhill J, Probert C, Hold GL, Lees CW. The Impact of NOD2 Variants on Fecal Microbiota in Crohn's Disease and Controls Without Gastrointestinal Disease. Inflamm Bowel Dis. 2018 Feb 15;24(3):583-592. doi: 10.1093/ibd/izx061.

Parkes M, Noor NM, Dowling F, Leung H, Bond S, Whitehead L, Upponi S, Kinnon P, Sandham AP, Lyons PA, McKinney EF, Smith KGC, Lee JC. PRedicting Outcomes For Crohn's dIsease using a moLecular biomarkEr (PROFILE): protocol for a multicentre, randomised, biomarker-stratified trial. BMJ Open. 2018 Dec 5;8(12):e026767

Kiely CJ, Clark A, Bhattacharyya J, Moran GW, Lee JC, Parkes M. Acetarsol Suppositories: Effective Treatment for Refractory Proctitis in a Cohort of Patients with Inflammatory Bowel Disease. Dig Dis Sci. 2018 Apr;63(4):1011-1015.

Tschurtschenthaler M, Adolph TE, Ashcroft JW, Niederreiter L, Bharti R, Saveljeva S, Bhattacharyya J, Flak MB, Shih DQ, Fuhler GM, Parkes M, Kohno K, Iwawaki T, Janneke van der Woude C, Harding HP, Smith AM, Peppelenbosch MP, Targan SR, Ron D, Rosenstiel P, Blumberg RS, Kaser A. Defective ATG16L1-mediated removal of IRE1α drives Crohn's disease-like ileitis. J Exp Med. 2017 Feb;214(2):401-422

Huang H, Fang M, Jostins L, Umićević Mirkov M, Boucher G, Anderson CA, Andersen V, Cleynen I, Cortes A, Crins F, D'Amato M, Deffontaine V, Dmitrieva J, Docampo E, Elansary M, Farh KK, Franke A, Gori AS, Goyette P, Halfvarson J, Haritunians T, Knight J, Lawrance IC, Lees CW, Louis E, Mariman R, Meuwissen T, Mni M, Momozawa Y, Parkes M, Spain SL, Théâtre E, Trynka G, Satsangi J, van Sommeren S, Vermeire S, Xavier RJ; International IBD Genetics Consortium, Weersma RK, Duerr RH, Mathew CG, Rioux JD, McGovern DPB, Cho JH, Georges M, Daly MJ, Barrett JC. Fine-mapping inflammatory bowel disease loci to single-variant resolution. Nature. 2017 Jul 13;547(7662):173-178

Lee JC, Biasci D, Roberts R, Gearry RB, Mansfield JC, Ahmad T, Prescott NJ, Satsangi J, Wilson DC, Jostins L, Anderson CA, the UK IBD Genetics Consortium, Traherne JA,. Lyons PA, Parkes M, Smith KGC. Genome-wide association study reveals distinct genetic contributions to prognosis and susceptibility in Crohn's disease. Nature Genetics.  2017 Feb;49(2):262-268

Luo Y, de Lange KM, Jostins L, Moutsianas L, Randall J, Kennedy NA, Lamb CA, McCarthy S, Ahmad T, Edwards C, Serra EG, Hart A, Hawkey C, Mansfield JC, Mowat C, Newman WG, Nichols S, Pollard M, Satsangi J, Simmons A, Tremelling M, Uhlig H, Wilson DC, Lee JC, Lees CW, Mathew CG, Parkes M, Barrett JC, Anderson CA. Exploring the genetic architecture of inflammatory bowel disease by whole-genome sequencing identifies association at ADCY7. Nature Genetics. 2017 Feb;49(2):186-192

de Lange KM, Moutsianas L, Lee JC, Lamb CA, Luo Y, Kennedy NA, Jostins L, Rice DL, Gutierrez-Achury J, Ji SG, Heap G, Nimmo ER, Edwards C, Henderson P, Mowat C, Sanderson J, Satsangi J, Simmons A, Wilson DC, Tremelling M, Hart A, Mathew CG, Newman WG, Parkes M, Lees CW, Uhlig H, Hawkey C, Prescott NJ, Ahmad T, Mansfield JC, Anderson CA, Barrett JC. Genome-wide association study implicates immune activation of multiple integrin genes in inflammatory bowel disease. Nature Genetics. 2017 Feb;49(2):256-261.

Cesarini M, Collins GS, Rönnblom A, Santos A, Wang LM, Sjöberg D, Parkes M, Keshav S, Travis SP. Predicting the Individual Risk of Acute Severe Colitis at Diagnosis. J Crohns Colitis. 2016 Sep.

Ellinghaus D, Jostins L, Spain SL, Cortes A…. Karlsen TH, Barrett JC, Parkes M, Brown MA, Franke A. Analysis of five chronic inflammatory diseases identifies 27 new associations and highlights disease-specific patterns at shared loci. Nature Genetics. 2016 May;48(5):510-8

Cleynen I, Boucher G, Jostins L, Schumm LP, Zeissig S, Ahmad T, … International Inflammatory Bowel Disease Genetics Consortium, Parkes M, Vermeire S, Rioux JD, Mansfield J, Silverberg MS, Radford-Smith G, McGovern DP, Barrett JC, Lees CW. Inherited determinants of Crohn's disease and ulcerative colitis phenotypes: a genetic association study. Lancet. 2016 9;387(10014):156-67.

Liu JZ, van Sommeren S, Huang H, Ng SC, Alberts R, Takahashi A… International IBD Genetics Consortium, Barrett JC, Franke A, Alizadeh BZ, Parkes M, B K T, Daly MJ, Kubo M, Anderson CA, Weersma RK. Association analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations. Nature Genetics. 2015 Sep;47(9):979-86.

Jason M. Norman, Scott A. Handley, Megan T. Baldridge, Lindsay Droit, Catherine Y. Liu, Brian C. Keller, Amal Kambal, Cynthia L. Monaco, Guoyan Zhao, Phillip Fleshner, Thaddeus S. Stappenbeck, Dermot P.B. McGovern, Ali Keshavarzian, Ece A. Mutlu, Jenny Sauk, Dirk Gevers, Ramnik J. Xavier, David Wang, Miles Parkes, and Herbert W. Virgin. Alterations in the Enteric Virome in Inflammatory Bowel Disease. Cell 2015 Jan 29;160(3):447-60

Raine T, Liu JZ, Anderson CA, Parkes M*, Kaser A* (* denotes shared senior author). Generation of primary human intestinal T cell transcriptomes reveals differential expression at genetic risk loci for immune-mediated disease. Gut. 2014 May 5. doi: 10.1136/gutjnl-2013-306657.

Lee JC, Espéli M, Anderson CA, Linterman MA, Pocock JM, Williams NJ, Roberts R, Viatte S, Fu B, Peshu N, Ahmad T, Mansfield JC, Gearry R, Dunstan S, Williams TN, Barton A, Vinuesa CG; UK IBD Genetics Consortium, Parkes M, Lyons PA, Smith KG.    Human SNP Links Differential Outcomes in Inflammatory and Infectious Disease to a FOXO3-Regulated Pathway. Cell. 2013 Sep 26;155(1):57-69.

Parkes M, Cortes A, van Heel D, Brown M. Analysis Article: Genetic insights into common pathways and complex relationships among immune mediated diseases. Nature Reviews Genetics 2013. Sep;14(9):661-73.


Other recent publications

  • Parkes M and IBD BioResource Investigators. IBD BioResource: an open-access platform of 25 000 patients to accelerate research in Crohn's and Colitis. Gut. 2019 Jul 3. pii: gutjnl-2019-318835. doi: 10.1136/gutjnl-2019-318835.


  •  Weersma RK, Parkes M. Diverticular disease: picking pockets and population biobanks. Gut. 2019 May;68(5):769-770. doi: 10.1136/gutjnl-2019-318231. Epub 2019 Mar 2.


  • Parkes M. On the threshold of personalized medicine in inflammatory bowel disease: Next generation genetic predictors. J Gastroenterol Hepatol. 2018 Sep;33 Suppl 3:5-6. doi: 10.1111/jgh.14416.


  • Parkes M, Noor NM, Dowling F, Leung H, Bond S, Whitehead L, Upponi S, Kinnon P, Sandham AP, Lyons PA, McKinney EF, Smith KGC, Lee JC. PRedicting Outcomes For Crohn's dIsease using a moLecular biomarkEr (PROFILE): protocol for a multicentre, randomised, biomarker-stratified trial. BMJ Open. 2018 Dec 5;8(12):e026767. doi: 10.1136/bmjopen-2018-026767.


  • Patel R, Coulter LL, Rimmer J, Parkes M, Chinnery PF, Swift O. Mitochondrial neurogastrointestinal encephalopathy: a clinicopathological mimic of Crohn's disease. BMC Gastroenterol. 2019 Jan 15;19(1):11. doi: 10.1186/s12876-018-0925-5.