Characterizing the pre-clinical phase of inflammatory bowel disease.
Vestergaard MV, Allin KH, Poulsen GJ, Lee JC*, Jess T*. [* denotes joint senior authors]
Cell Rep Med. 4(11):101263 (2023)

  Resolving mechanisms of immune-mediated disease in primary CD4 T cells
Bourges C, Groff AF, Burren OS, Gerhardinger C, Mattioli K, Hutchinson A, Hu T, Anand T, Epping MW, Wallace C, Smith KGC, Rinn JL, Lee JC.
EMBO Mol Med 12:e12112 (2020)

  A blood-based prognostic biomarker in inflammatory bowel disease
Biasci D*, Lee JC* ^†, Noor NM, Pombal DR, Hou M, Lewis N, Ahmad T, Hart A, Parkes M, McKinney EF, Lyons PA, Smith KGC^†. [* denotes joint first authors, ^† denotes co-corresponding authors]
Gut. 68(8):1386-1395 (2019)

  Predicting outcomes for Crohn’s disease using a molecular biomarker (PROFILE): protocol for a multi-centre, randomised, biomarker-stratified trial.
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^†.  [^† denotes co-corresponding authors]
BMJ Open. 5;8(12):e026767 (2018)

  Genome-wide association study identifies distinct genetic contributions to prognosis and susceptibility in Crohn's disease.
Lee JC* ^†, Biasci D*, Roberts R, Gearry RB, Mansfield JC, Ahmad T, Prescott NJ, Satsangi J, Wilson DC, Jostins L, Anderson CA; UK IBD Genetics Consortium., Traherne JA, Lyons PA, Parkes M, Smith KGC^†. [* denotes joint first authors, ^† denotes co-corresponding authors]
Nat Genet. 49: 262-268 (2017)

  Genome-wide association study implicates immune activation of multiple integrin genes in inflammatory bowel disease.
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. [* denotes joint first authors]
Nat Genet. 49: 256-261 (2017)

  Association between genetic variation in FOXO3 and reductions in inflammation and disease activity in inflammatory polyarthritis.
Viatte S*, Lee JC*, Fu B, Espéli M, Lunt M, De Wolf JN, Wheeler L, Reynolds JA, Castelino M, Symmons DP, Lyons PA, Barton A, Smith KGC. [* denotes joint first authors]
Arthritis Rheumatol. 68(11):2629-2636. (2016)

  Human SNP links differential outcomes in inflammatory and infectious disease to a FOXO3-regulated pathway.
Lee JC, Espéli M, Anderson CA, Linterman MA, Pocock JM, Williams NJ, Roberts R, Viatte S, Fu B, Peshu N, Hien TT, Phu NH, Wesley E, Edwards C, Ahmad T, Mansfield JC, Gearry R, Dunstan S, Williams TN, Barton A, Vinuesa CG, UK IBD Genetics Consortium, Parkes M, Lyons PA, Smith KGC.
Cell 155(1):57-69 (2013)

  Gene-expression profiling of CD8 T-cells predicts prognosis in patients with Crohn disease and ulcerative colitis.
Lee JC, Lyons PA, McKinney EF, Sowerby JM, Carr EJ, Bredin F, Rickman HM, Ratlamwala H, Hatton A, Rayner TF, Parkes M, Smith KGC.
J Clin Invest. 121(10):4170-4179. (2011)

  Other publications

  miR-374a-5p regulates inflammatory genes and monocyte function in patients with inflammatory bowel disease.
Perez-Sanchez C, Barbera Betancourt A, Lyons PA, Zhang Z, Suo C, Lee JC, McKinney EF, Modis LK, Ellson C, Smith KGC.
J Exp Med. 219(5):e20211366. (2022)

  Antibody decay, T cell immunity and breakthrough infections following two SARS-CoV-2 vaccine doses in inflammatory bowel disease patients treated with infliximab and vedolizumab.
Lin S, Kennedy NA, Saifuddin A, Sandoval DM, Reynolds CJ, Seoane RC, Kottoor SH, Pieper FP, Lin KM, Butler DK, Chanchlani N, Nice R, Chee D, Bewshea C, Janjua M, McDonald TJ, Sebastian S, Alexander JL, Constable L, Lee JC, Murray CD, Hart AL, Irving PM, Jones GR, Kok KB, Lamb CA, Lees CW, Altmann DM, Boyton RJ, Goodhand JR, Powell N, Ahmad T; CLARITY IBD study.
Nat Commun. 13(1):1379. (2022)

  How Do We Predict a Patient's Disease Course and Whether They Will Respond to Specific Treatments? [REVIEW]
Verstockt B, Parkes M, Lee JC.
Gastroenterology. 162(5):1383-1395. (2022)

  A purine metabolic checkpoint that prevents autoimmunity and autoinflammation.
Saveljeva S, Sewell GW, Ramshorn K, Cader MZ, West JA, Clare S, Haag L, Pereira de
Almeida Rodrigues R, Unger LW, Belén Iglesias-Romero A, Holland LM, Bourges C, Md-Ibrahim MN, Jones JO, Blumberg RS, Lee JC, Kaneider NC, Lawley TD, Bradley A, Dougan G, Kaser A.
Cell Metabolism 4;34(1):106-124.e10. (2022)

  Impaired HA-specific T follicular helper cell and antibody responses to influenza vaccination are linked to inflammation in humans.
Hill DL, Whyte CE, Innocentin S, Lee JL, Dooley J, Wang J, James EA, Lee JC, Kwok WW, Zand MS, Liston A, Carr EJ, Linterman MA.
eLife. 2;10:e70554. (2021)

  Genetic feature engineering enables characterisation of shared risk factors in immune-mediated diseases.
Burren OS, Reales G, Wong L, Bowes J, Lee JC, Barton A, Lyons PA, Smith KGC, Thomson W, Kirk PDW, Wallace C.
Genome Med 25;12(1):106 (2021)

  Analytical Mistakes Confound Attempted Validation: A Response to "Transcription and DNA Methylation Patterns of Blood-Derived CD8+ T Cells Are Associated With Age and Inflammatory Bowel Disease But Do Not Predict Prognosis".
Lee JC, Lyons PA, McKinney EF.
Gastroenterology 160(6):2210-2211 (2021) 

  Identifying the immune interactions underlying HLA class I disease associations
Debebe B, Boelen L, Lee JC, IAVI Protocol C Investigators, Sanders EJ, Anzala O, Kamali A, Kaleebu P, Karita E, Kilembe W, Inambao M, Lakhi S, Allen S, Hunter E, Edward VA, Fast PE, Price MA, Gilmour J, Tang J, Thio CL, Astemborski J, Kirk G, Khakoo SI, Donfield SM, Goedert JJ, Asquith B.
eLife 2;9:e54558 (2020)

  FAMIN Is a Multifunctional Purine Enzyme Enabling the Purine Nucleotide Cycle.
Cader MZ, de Almeida Rodrigues RP, West JA, Sewell GW, Md-Ibrahim MN, Reikine S, Sirago G, Unger LW, Iglesias-Romero AB, Ramshorn K, Haag LM, Saveljeva S, Ebel JF, Rosenstiel P, Kaneider NC, Lee JC, Lawley TD, Bradley A, Dougan G, Modis Y, Griffin JL, Kaser A.
Cell 180(2):278-295 (2020)

  Analysis of the B cell receptor repertoire in six immune-mediated diseases
Bashford-Rogers RJM, Bergamaschi L, McKinney EF, Pombal DC, Mescia F, Lee JC, Thomas DC, Flint SM, Kellam P, Jayne DRW, Lyons PA, Smith KGC
Nature 574(7776):122-126 (2019)

  Personalised medicine in Crohn's disease.
Noor NM, Verstockt B, Parkes M, Lee JC.
Lancet Gastroenterol Hepatol. 5(1):80-92. (2020)

  The Firre locus produces a trans-acting RNA molecule that functions in hematopoiesis.
Lewandowski JP, Lee JC, Hwang T, Sunwoo H, Goldstein JM, Groff AF, Chang NP, Mallard W, Williams A, Henao-Meija J, Flavell RA, Lee JT, Gerhardinger C, Wagers AJ, Rinn JL.
Nat Commun. 10(1):5137 (2019)

  Adjustment for index event bias in genome-wide association studies of subsequent events.
Dudbridge F, Allen RJ, Sheehan NA, Schmidt AF, Lee JC, Jenkins RG, Wain LV, Hingorani AD, Patel RS.
Nat Commun. 5;10(1):1561. (2019)

  High-throughput functional analysis of lncRNA core promoters elucidates rules governing tissue specificity.
Mattioli K, Volders PJ, Gerhardinger C, Lee JC, Maass PG, Melé M, Rinn JL.
Genome Res. 29(3):344-355. (2019)

  EROS/CYBC1 mutations: Decreased NADPH oxidase function and chronic granulomatous disease.
Thomas DC, Charbonnier LM, Schejtman A, Aldhekri H, Coomber EL, Dufficy ER, Beenken AE, Lee JC, Clare S, Speak AO, Thrasher AJ, Santilli G, Al-Mousa H, Alkuraya FS, Chatila TA, Smith KGC.
J Allergy Clin Immunol. 143(2):782-785.e1 (2019)

  Genome-wide association studies in Crohn's disease: past, present and future [REVIEW]
Verstockt B, Smith KGC, Lee JC^†. [^† denotes corresponding author]
Clin Transl Immunology. 31;7(1):e1001. (2018)

  Reduced monocyte and macrophage TNFSF15/TL1A expression is associated with susceptibility to inflammatory bowel disease.
Richard AC, Peters JE, Savinykh N, Lee JC, Hawley ET, Meylan F, Siegel RM, Lyons PA, Smith KGC.
PLoS Genet. 10;14(9):e1007458 (2018)

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

  Eros is a novel transmembrane protein that controls the phagocyte respiratory burst and is essential for innate immunity.
Thomas DC, Clare S, Sowerby JM, Pardo M, Juss JK, Goulding DA, van der Weyden L, Storisteanu D, Prakash A, Espéli M, Flint S, Lee JC, Hoenderdos K, Kane L, Harcourt K, Mukhopadhyay S, Umrania Y, Antrobus R, Nathan JA, Adams DJ, Bateman A, Choudhary JS, Lyons PA, Condliffe AM, Chilvers ER, Dougan G, Smith KG.
J Exp Med. 3;214(4):1111-1128 (2017)

  Beyond disease susceptibility - leveraging genome-wide association studies for new insights into complex disease biology. [REVIEW]
Lee JC
HLA. 90(6):329-334 (2017)

  Maintenance of macrophage transcriptional programs and intestinal homeostasis by epigenetic reader SP140
Mehta S, Cronkite DA, Basavappa M, Saunders TL, Adiliaghdam F, Amatullah H, Morrison SA, Pagan JD, Anthony RM, Tonnerre P, Lauer GM, Lee JC, Digumarthi S, Pantano L, Ho Sui SJ, Ji F, Sadreyev R, Zhou C, Mullen AC, Kumar V, Li Y, Wijmenga C, Xavier RJ, Means TK and Jeffrey KL.
Sci. Immunol. 2(9):eaag3160. (2017)

  Exploring the genetic architecture of inflammatory bowel disease by whole-genome sequencing identifies association at ADCY7.
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, Prescott NJ, Lees CW, Mathew CG, Parkes M, Barrett JC, Anderson CA.
Nat Genet. 49: 186-192 (2017)

  A protein-truncating R179X variant in RNF186 confers protection against ulcerative colitis.
Rivas MA, Graham D, Sulem P, Stevens C, Desch AN, Goyette P, Gudbjartsson D, Jonsdottir I, Thorsteinsdottir U, Degenhardt F, Mucha S, Kurki MI, Li D, D'Amato M, Annese V, Vermeire S, Weersma RK, Halfvarson J, Paavola-Sakki P, Lappalainen M, Lek M, Cummings B, Tukiainen T, Haritunians T, Halme L, Koskinen LL, Ananthakrishnan AN, Luo Y, Heap GA, Visschedijk MC; UK IBD Genetics Consortium.; NIDDK IBD Genetics Consortium., MacArthur DG, Neale BM, Ahmad T, Anderson CA, Brant SR, Duerr RH, Silverberg MS, Cho JH, Palotie A, Saavalainen P, Kontula K, Färkkilä M, McGovern DP, Franke A, Stefansson K, Rioux JD, Xavier RJ, Daly MJ, Barrett J, de Lange K, Edwards C, Hart A, Hawkey C, Jostins L, Kennedy N, Lamb C, Lee J, Lees C, Mansfield J, Mathew C, Mowatt C, Newman B, Nimmo E, Parkes M, Pollard M, Prescott N, Randall J, Rice D, Satsangi J, Simmons A, Tremelling M, Uhlig H, Wilson D, Abraham C, Achkar JP, Bitton A, Boucher G, Croitoru K, Fleshner P, Glas J, Kugathasan S, Limbergen JV, Milgrom R, Proctor D, Regueiro M, Schumm PL, Sharma Y, Stempak JM, Targan SR, Wang MH.
Nat Commun. 9;7:12342 (2016)

  A reference panel of 64,976 haplotypes for genotype imputation.
McCarthy S, Das S, Kretzschmar W, Delaneau O, Wood AR, Teumer A, Kang HM, Fuchsberger C, Danecek P, Sharp K, Luo Y, Sidore C, Kwong A, Timpson N, Koskinen S, Vrieze S, Scott LJ, Zhang H, Mahajan A, Veldink J, Peters U, Pato C, van Duijn CM, Gillies CE, Gandin I, Mezzavilla M, Gilly A, Cocca M, Traglia M, Angius A, Barrett JC, Boomsma D, Branham K, Breen G, Brummett CM, Busonero F, Campbell H, Chan A, Chen S, Chew E, Collins FS, Corbin LJ, Smith GD, Dedoussis G, Dorr M, Farmaki AE, Ferrucci L, Forer L, Fraser RM, Gabriel S, Levy S, Groop L, Harrison T, Hattersley A, Holmen OL, Hveem K, Kretzler M, Lee JC, McGue M, Meitinger T, Melzer D, Min JL, Mohlke KL, Vincent JB, Nauck M, Nickerson D, Palotie A, Pato M, Pirastu N, McInnis M, Richards JB, Sala C, Salomaa V, Schlessinger D, Schoenherr S, Slagboom PE, Small K, Spector T, Stambolian D, Tuke M, Tuomilehto J, Van den Berg LH, Van Rheenen W, Volker U, Wijmenga C, Toniolo D, Zeggini E, Gasparini P, Sampson MG, Wilson JF, Frayling T, de Bakker PI, Swertz MA, McCarroll S, Kooperberg C, Dekker A, Altshuler D, Willer C, Iacono W, Ripatti S, Soranzo N, Walter K, Swaroop A, Cucca F, Anderson CA, Myers RM, Boehnke M, McCarthy MI, Durbin R; Haplotype Reference Consortium.
Nat Genet. 48(10):1279-83. (2016)

  In vivo characterization of Linc-p21 reveals functional cis-regulatory DNA elements.
Groff AF, Sanchez-Gomez DB, Soruco MML, Gerhardinger C, Barutcu AR, Li E, Elcavage L, Plana O, Sanchez LV, Lee JC, Sauvageau M, Rinn JL.
Cell Reports 23;16(8):2178-86. (2016)

  Targeted genomic analysis reveals widespread autoimmune disease association with variants that regulate gene expression in the TNF superfamily cytokine signalling network.
Richard AC, Peters JE, Lee JC, Vahedi G, Schäffer AA, Siegel RM, Lyons PA, Smith KGC.
Genome Med. 19;8(1):76. (2016)

  Predicting Outcomes to Optimize Disease Management in Inflammatory Bowel Diseases.
Torres J, Caprioli F, Katsanos KH, Lobatón T, Micic D, Zerôncio M, Van Assche G, Lee JC, Lindsay JO, Rubin DT, Panaccione R, Colombel JF.
J Crohns Colitis. 10(12):1385-1394 (2016)

  Insight into Genotype-Phenotype Associations through eQTL Mapping in Multiple Cell Types in Health and Immune-Mediated Disease.
Peters JE, Lyons PA, Lee JC, Richard AC, Fortune MD, Newcombe PJ, Richardson S, Smith KGC.
PLoS Genet. 25;12(3):e1005908. (2016)

  The cellular composition of the human immune system is shaped by age and cohabitation.
Carr EJ, Dooley J, Garcia-Perez JE, Lagou V, Lee JC, Wouters C, Meyts I, Goris A, Boeckxstaens G, Linterman MA, Liston A.
Nat Immunol. 17(4):461-8. (2016)

  Inherited determinants of Crohn's disease and ulcerative colitis phenotypes: a genetic association study.
Cleynen I, Boucher G, Jostins L, Schumm LP, Zeissig S, Ahmad T, Andersen V, Andrews JM, Annese V, Brand S, Brant SR, Cho JH, Daly MJ, Dubinsky M, Duerr RH, Ferguson LR, Franke A, Gearry RB, Goyette P, Hakonarson H, Halfvarson J, Hov JR, Huang H, Kennedy NA, Kupcinskas L, Lawrance IC, Lee JC, Satsangi J, Schreiber S, Théâtre E, van der Meulen-de Jong AE, Weersma RK, Wilson DC; 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.
Lancet. 9;387(10014):156-67. (2016)

  MT-HESS: An efficient Bayesian approach for simultaneous association detection in OMICS datasets, with application to eQTL mapping in multiple tissues
Lewin A, Saadi H, Peters JE, Moreno-Moral A, Lee JC, Smith KG, Petretto E, Bottolo L, Richardson S
Bioinformatics 15;32(4):523-32. (2016)

  Low Serum Levels of MicroRNA-19 Are Associated with a Stricturing Crohn's Disease Phenotype.
Lewis A, Mehta S, Hanna LN, Rogalski LA, Jeffery R, Nijhuis A, Kumagai T, Biancheri P, Bundy JG, Bishop CL, Feakins R, Di Sabatino A, Lee JC, Lindsay JO, Silver A.
Inflamm Bowel Dis. 21(8):1926-34. (2015)

  Leucocyte subset-specific type 1 interferon signatures in SLE and other immune-mediated diseases.
Flint SM, Jovanovic V, Teo BW, Mak A, Thumboo J, McKinney EF, Lee JC, MacAry P, Kemeny DM, Jayne DR, Fong KY, Lyons PA, Smith KGC.
RMD Open. 16;2(1):e000183. doi: 10.1136/rmdopen-2015-000183. eCollection (2016).

  T-cell exhaustion, co-stimulation and clinical outcome in autoimmunity and infection.
McKinney EF, Lee JC, Jayne DR, Lyons PA, Smith KGC.
Nature 523(7562):612-6. (2015)

  Association analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations.
Liu JZ, van Sommeren S, Huang H, Ng SC, Alberts R, Takahashi A, Ripke S, Lee JC, Jostins L, Shah T, Abedian S, Cheon JH, Cho J, Daryani NE, Franke L, Fuyuno Y, Hart A, Juyal RC, Juyal G, Kim WH, Morris AP, Poustchi H, Newman WG, Midha V, Orchard TR, Vahedi H, Sood A, Sung JJ, Malekzadeh R, Westra HJ, Yamazaki K, Yang SK; International Multiple Sclerosis Genetics Consortium; International IBD Genetics Consortium, Barrett JC, Franke A, Alizadeh BZ, Parkes M, B K T, Daly MJ, Kubo M, Anderson CA, Weersma RK.
Nat Genet. 47(9):979-86. (2015)

  Pooled sequencing of 531 genes in inflammatory bowel disease identifies an associated rare variant in BTNL2 and implicates other immune related genes.
Prescott NJ, Lehne B, Stone K, Lee JC, Taylor K, Knight J, Papouli E, Mirza MM, Simpson MA, Spain SL, Lu G, Fraternali F, Bumpstead SJ, Gray E, Amar A, Bye H, Green P, Chung-Faye G, Hayee B, Pollok R, Satsangi J, Parkes M, Barrett JC, Mansfield JC, Sanderson J, Lewis CM, Weale ME, Schlitt T, Mathew CG; UK IBD Genetics Consortium.
PLoS Genet. 11;11(2):e1004955. (2015)

  HLA-DQA1-HLA-DRB1 variants confer susceptibility to pancreatitis induced by thiopurine immunosuppressants.
Heap GA, Weedon MN, Bewshea CM, Singh A, Chen M, Satchwell JB, Vivian JP, So K, Dubois PC, Andrews JM, Annese V, Bampton P, Barnardo M, Bell S, Cole A, Connor SJ, Creed T, Cummings FR, D'Amato M, Daneshmend TK, Fedorak RN, Florin TH, Gaya DR, Greig E, Halfvarson J, Hart A, Irving PM, Jones G, Karban A, Lawrance IC, Lee JC, Lees C, Lev-Tzion R, Lindsay JO, Mansfield J, Mawdsley J, Mazhar Z, Parkes M, Parnell K, Orchard TR, Radford-Smith G, Russell RK, Reffitt D, Satsangi J, Silverberg MS, Sturniolo GC, Tremelling M, Tsianos EV, van Heel DA, Walsh A, Watermeyer G, Weersma RK, Zeissig S, Rossjohn J, Holden AL; International Serious Adverse Events Consortium; IBD Pharmacogenetics Study Group, Ahmad T.
Nat Genet. 46(10):1131-4. (2014)

  Prognosis in autoimmune and infectious disease: new insights from genetics. [REVIEW]
Lee JC^†, Smith KGC. [^† denotes corresponding author]
Clin Transl Immunology. 16;3(5):e15. (2014)

  Comparison of gene expression microarray data with count-based RNA measurements informs microarray interpretation.
Richard AC, Lyons PA, Peters JE, Biasci D, Flint SM, Lee JC, McKinney EF, Siegel RM, Smith KGC.v BMC Genomics. 4;15:649. (2014)

  Novel developments in Crohn's disease (Issue 28)
Edited by: Van der Woude CJ, Lee JC
Best Pract Res Clin Gastroenterol. 28(3) (2014)

  Safety of the colonoscope magnetic imaging device (ScopeGuide) in patients with implantable cardiac devices.
Corbett GD, Lim YC, Lee JC, Chernolesskiy A, Pugh PJ, Cameron EA.
Endoscopy. 46(2):135-8 (2014)

  Negligible impact of rare autoimmune-locus coding-region variants on missing heritability.
Hunt KA, Mistry V, Bockett NA, Ahmad T, Ban M, Barker JN, Barrett JC, Blackburn H, Brand O, Burren O, Capon F, Compston A, Gough SC, Jostins L, Kong Y, Lee JC, Lek M, MacArthur DG, Mansfield JC, Mathew CG, Mein CA, Mirza M, Nutland S, Onengut-Gumuscu S, Papouli E, Parkes M, Rich SS, Sawcer S, Satsangi J, Simmonds MJ, Trembath RC, Walker NM, Wozniak E, Todd JA, Simpson MA, Plagnol V, van Heel DA.
Nature 498(7453):232-5. (2013)

  Association Between Variants of PRDM1 and NDP52 and Crohn's Disease, Based on Exome Sequencing and Functional Studies.
Ellinghaus D*, Zhang H*, Zeissig S*, Lipinski S, Till A, Jiang T, Stade B, Bromberg Y, Ellinghaus E, Keller A, Rivas MA, Skieceviciene J, Doncheva NT, Liu X, Liu Q, Jiang F, Forster M, Mayr G, Albrecht M, Häsler R, Boehm BO, Goodall J, Berzuini CR, Lee J, Andersen V, Vogel U, Kupcinskas L, Kayser M, Krawczak M, Nikolaus S, Weersma RK, Ponsioen CY, Sans M, Wijmenga C, Strachan DP, McArdle WL, Vermeire S, Rutgeerts P, Sanderson JD, Mathew CG, Vatn MH, Wang J, Nöthen MM, Duerr RH, Büning C, Brand S, Glas J, Winkelmann J, Illig T, Latiano A, Annese V, Halfvarson J, D'Amato M, Daly MJ, Nothnagel M, Karlsen TH, Subramani S, Rosenstiel P, Schreiber S, Parkes M, Franke A.
Gastroenterology. 145(2):339-47. (2013)

  Comparison of Pentax HiLine and Olympus Lucera systems at screening colonoscopy.
Chernolesskiy A, Swain D, Lee JC, Corbett GD, Cameron EA.
World J Gastrointest Endosc. 16;5(2):62-6. (2013)

  Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
Jostins L*, Ripke S*, Weersma RK, Duerr RH, McGovern DP, Hui KY, Lee JC, Schumm LP, Sharma Y, Anderson CA, Essers J, Mitjovic M, Ning K, Cleynen I, Theatre E, Spain SL, Raychaudhuri S, Goyette P, Wei Z, Abraham C, Achkar JP, Ahmad T, Amininejad L, Ananthakrishnan A, Andersen V, Andrews JM, Baidoo L, Balschun T, Bampton PA, Bitton A, Boucher G, Brand S, Büning C, Cohain A, Cichon S, D’Amato M, De Jong D, Devaney KL, Dubinsky M, Edwards C, Ellinghaus D, Ferguson LR, Franchimont D, Fransen K, Gearry R, Gieger C, Glas J, Haritunians T, Hart A, Hawkey C, Hedl M, Hu X, Karlsen TK, Kupcinskas L, Kugathasan S, Latiano A, Laukens D, Lawrance IC, Lees CW, Louis E, Mahy G, Mansfield J, Morgan AR, Mowat C, Newman W, Palmieri O, Ponsioen CY, Potocnik U, Prescott NJ, Regueiro M, Rotter JI, Russell RK, Sanderson JD, Sans M, Satsangi J, Schreiber S, Simms L, Sventoraityte J, Targan SR, Taylor KD, Tremelling M, Verspaget HW, De Vos M, Wijmenga C, Wilson DC, Winkelmann J, Xavier RJ, Zeissig S, Zhang CK, Zhao H, The International IBD Genetics Consortium, Silverberg MS, Annese V, Hakonarson H, Brant SR, Radford-Smith G, Mathew CG, Rioux JD, Schadt EE, Daly MJ, Franke A, Parkes M, Vermeire S, Barrett JC*, Cho JH*.
Nature 491(7422):119-24. (2012)

  Predicting the course of IBD: light at the end of the tunnel? [REVIEW]
Lee JC.
Dig Dis. 2012;30 Suppl 1:95-9

  Rare and functional SIAE variants are not associated with autoimmune disease risk in up to 66,924 individuals of European ancestry.
Hunt KA, Smyth DJ, Balschun T, Ban M, Mistry V, Ahmad T, Anand V, Barrett JC, Bhaw-Rosun L, Bockett NA, Brand OJ, Brouwer E, Concannon P, Cooper JD, Dias KR, van Diemen CC, Dubois PC, Edkins S, Fölster-Holst R, Fransen K, Glass DN, Heap GA, Hofmann S, Huizinga TW, Hunt S, Langford C, Lee J, Mansfield J, Marrosu MG, Mathew CG, Mein CA, Müller-Quernheim J, Nutland S, Onengut-Gumuscu S, Ouwehand W, Pearce K, Prescott NJ, Posthumus MD, Potter S, Rosati G, Sambrook J, Satsangi J, Schreiber S, Shtir C, Simmonds MJ, Sudman M, Thompson SD, Toes R, Trynka G, Vyse TJ, Walker NM, Weidinger S, Zhernakova A, Zoledziewska M; Type  Diabetes Genetics Consortium; UK Inflammatory Bowel Disease (IBD) Genetics Consortium; Wellcome Trust Case Control Consortium, Weersma RK, Gough SC, Sawcer S, Wijmenga C, Parkes M, Cucca F, Franke A, Deloukas P, Rich SS,Todd JA, van Heel DA.
Nat Genet. 44:3-5. (2011)

  Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47.
Anderson CA, Boucher G, Lees CW, Franke A, D'Amato M, Taylor KD, Lee JC, Goyette P, Imielinski M, Latiano A, Lagacé C, Scott R, Amininejad L, Bumpstead S, Baidoo L, Baldassano RN, Barclay M, Bayless TM, Brand S, Büning C, Colombel JF, Denson LA, De Vos M, Dubinsky M, Edwards C, Ellinghaus D, Fehrmann RS, Floyd JA, Florin T, Franchimont D, Franke L, Georges M, Glas J, Glazer NL, Guthery SL, Haritunians T, Hayward NK, Hugot JP, Jobin G, Laukens D, Lawrance I, Lémann M, Levine A, Libioulle C, Louis E, McGovern DP, Milla M, Montgomery GW, Morley KI, Mowat C, Ng A, Newman W, Ophoff RA, Papi L, Palmieri O, Peyrin-Biroulet L, Panés J, Phillips A, Prescott NJ, Proctor DD, Roberts R, Russell R, Rutgeerts P, Sanderson J, Sans M, Schumm P, Seibold F, Sharma Y, Simms LA, Seielstad M, Steinhart AH, Targan SR, van den Berg LH, Vatn M, Verspaget H, Walters T, Wijmenga C, Wilson DC, Westra HJ, Xavier RJ, Zhao ZZ, Ponsioen CY, Andersen V, Torkvist L, Gazouli M, Anagnou NP, Karlsen TH, Kupcinskas L, Sventoraityte J, Mansfield JC, Kugathasan S, Silverberg MS, Halfvarson J, Rotter JI, Mathew CG, Griffiths AM, Gearry R, Ahmad T, Brant SR, Chamaillard M, Satsangi J, Cho JH, Schreiber S, Daly MJ, Barrett JC, Parkes M, Annese V, Hakonarson H, Radford-Smith G, Duerr RH, Vermeire S, Weersma RK, Rioux JD.
Nat Genet. 43(3):246-52. (2011)

  Genetic association between NLRP3 variants and Crohn's disease does not replicate in a large UK panel.
Lewis GJ, Massey DC, Zhang H, Bredin F, Tremelling M, Lee JC, Berzuini C, Parkes M.
Inflamm Bowel Dis. 17(6):1387-91. (2011)

  100 genes for IBD….. whatever next? [REVIEW]
Lee JC, Parkes M.
IBD Monitor 11(3):103-111. (2011)

  Genome-wide association studies and Crohn's disease. [REVIEW]
Lee JC, Parkes M
Brief Funct Genomics. 10(2):71-6. (2011)

  Genome-wide meta-analysis increases to 71 the number of confirmed Crohn’s disease susceptibility loci.
Franke A, McGovern DP, Barrett JC, Wang K, Radford-Smith GL, Ahmad T, Lees CW, Balschun T, Lee J, Roberts R, Anderson CA, Bis JC, Bumpstead S, Ellinghaus D, Festen EM, Georges M, Green T, Haritunians T, Jostins L, Latiano A, Mathew CG, Montgomery GW, Prescott NJ, Raychaudhuri S, Rotter JI, Schumm P, Sharma Y, Simms LA, Taylor KD, Whiteman D, Wijmenga C, Baldassano RN, Barclay M, Bayless TM, Brand S, Büning C, Cohen A, Colombel JF, Cottone M, Stronati L, Denson T, De Vos M, D'Inca R, Dubinsky M, Edwards C, Florin T, Franchimont D, Gearry R, Glas J, Van Gossum A, Guthery SL, Halfvarson J, Verspaget HW, Hugot JP, Karban A, Laukens D, Lawrance I, Lemann M, Levine A, Libioulle C, Louis E, Mowat C, Newman W, Panés J, Phillips A, Proctor DD, Regueiro M, Russell R, Rutgeerts P, Sanderson J, Sans M, Seibold F, Steinhart AH, Stokkers PC, Torkvist L, Kullak-Ublick G, Wilson D, Walters T, Targan SR, Brant SR, Rioux JD, D'Amato M, Weersma RK, Kugathasan S, Griffiths AM, Mansfield JC, Vermeire S, Duerr RH, Silverberg MS, Satsangi J, Schreiber S, Cho JH, Annese V, Hakonarson H, Daly MJ, Parkes M.
Nat Genet. 42:1118-25. (2010)

  Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls.
Craddock N, Hurles ME, Cardin N, Pearson RD, Plagnol V, Robson S, Vukcevic D, Barnes C, Conrad DF, Giannoulatou E, Holmes C, Marchini JL, Stirrups K, Tobin MD, Wain LV, Yau C, Aerts J, Ahmad T, Andrews TD, Arbury H, Attwood A, Auton A, Ball SG, Balmforth AJ, Barrett JC, Barroso I, Barton A, Bennett AJ, Bhaskar S, Blaszczyk K, Bowes J, Brand OJ, Braund PS, Bredin F, Breen G, Brown MJ, Bruce IN, Bull J, Burren OS, Burton J, Byrnes J, Caesar S, Clee CM, Coffey AJ, Connell JM, Cooper JD, Dominiczak AF, Downes K, Drummond HE, Dudakia D, Dunham A, Ebbs B, Eccles D, Edkins S, Edwards C, Elliot A, Emery P, Evans DM, Evans G, Eyre S, Farmer A, Ferrier IN, Feuk L, Fitzgerald T, Flynn E, Forbes A, Forty L, Franklyn JA, Freathy RM, Gibbs P, Gilbert P, Gokumen O, Gordon-Smith K, Gray E, Green E, Groves CJ, Grozeva D, Gwilliam R, Hall A, Hammond N, Hardy M, Harrison P, Hassanali N, Hebaishi H, Hines S, Hinks A, Hitman GA, Hocking L, Howard E, Howard P, Howson JM, Hughes D, Hunt S, Isaacs JD, Jain M, Jewell DP, Johnson T, Jolley JD, Jones IR, Jones LA, Kirov G, Langford CF, Lango-Allen H, Lathrop GM, Lee J, Lee KL, Lees C, Lewis K, Lindgren CM, Maisuria-Armer M, Maller J, Mansfield J, Martin P, Massey DC, McArdle WL, McGuffin P, McLay KE, Mentzer A, Mimmack ML, Morgan AE, Morris AP, Mowat C, Myers S, Newman W, Nimmo ER, O'Donovan MC, Onipinla A, Onyiah I, Ovington NR, Owen MJ, Palin K, Parnell K, Pernet D, Perry JR, Phillips A, Pinto D, Prescott NJ, Prokopenko I, Quail MA, Rafelt S, Rayner NW, Redon R, Reid DM, Renwick, Ring SM, Robertson N, Russell E, St Clair D, Sambrook JG, Sanderson JD, Schuilenburg H, Scott CE, Scott R, Seal S, Shaw-Hawkins S, Shields BM, Simmonds MJ, Smyth DJ, Somaskantharajah E, Spanova K, Steer S, Stephens J, Stevens HE, Stone MA, Su Z, Symmons DP, Thompson JR, Thomson W, Travers ME, Turnbull C, Valsesia A, Walker M, Walker NM, Wallace C, Warren-Perry M, Watkins NA, Webster J, Weedon MN, Wilson AG, Woodburn M, Wordsworth BP, Young AH, Zeggini E, Carter NP, Frayling TM, Lee C, McVean G, Munroe PB, Palotie A, Sawcer SJ, Scherer SW, Strachan DP, Tyler-Smith C, Brown MA, Burton PR, Caulfield MJ, Compston A, Farrall M, Gough SC, Hall AS, Hattersley AT, Hill AV, Mathew CG, Pembrey M, Satsangi J, Stratton MR, Worthington J, Deloukas P, Duncanson A, Kwiatkowski DP, McCarthy MI, Ouwehand W, Parkes M, Rahman N, Todd JA, Samani NJ, Donnelly P.
Nature. 464(7289):713-20. (2010)

  Genome-wide association study of ulcerative colitis identifies three new susceptibility loci, including the HNF4A region.
Barrett JC, Lee JC, Lees CW, Prescott NJ, Anderson CA, Phillips A, Wesley E, Parnell K, Zhang H, Drummond H, Nimmo ER, Massey D, Blaszczyk K, Elliott T, Cotterill L, Dallal H, Lobo AJ, Mowat C, Sanderson JD, Jewell DP, Newman WG, Edwards C, Ahmad T, Mansfield JC, Satsangi J, Parkes M, Mathew CG; Wellcome Trust Case Control Consortium 2, Donnelly P, Peltonen L, Blackwell JM, Bramon E, Brown MA, Casas JP, Corvin A, Craddock N, Deloukas P, Duncanson A, Jankowski J, Markus HS, Mathew CG, McCarthy MI, Palmer CN, Plomin R, Rautanen A, Sawcer SJ, Samani N, Trembath RC, Viswanathan AC, Wood N, Spencer CC, Barrett JC, Bellenguez C, Davison D, Freeman C, Strange A, Donnelly P, Langford C, Hunt SE, Edkins S, Gwilliam R, Blackburn H, Bumpstead SJ, Dronov S, Gillman M, Gray E, Hammond N, Jayakumar A, McCann OT, Liddle J, Perez ML, Potter SC, Ravindrarajah R, Ricketts M, Waller M, Weston P, Widaa S, Whittaker P, Deloukas P, Peltonen L, Mathew CG, Blackwell JM, Brown MA, Corvin A, McCarthy MI, Spencer CC, Attwood AP, Stephens J, Sambrook J, Ouwehand WH, McArdle WL, Ring SM, Strachan DP.
Nat Genet. 41(12):1330-4. (2009)

  Pneumocystis jiroveci pneumonia and pneumomediastinum in an anti-TNFα naive patient with ulcerative colitis.
Lee JC, Bell DC, Guinness RM, Ahmad T.
World J Gastroenterol. 21;15(15):1897-900. (2009)