Barrett E, Ross RP, O’Toole PW, Fitzgerald GF, Stanton C. γ-Aminobutyric acid production by cuyturable bacteria from the human intestine. J Appl Microbiol. 2012 May 21. doi: 10.1111/j.1365-2672.2012.05344.x.

Cotter PD, Stanton C, Ross RP, Hill C. The impact of antibiotics on the gut microbiota as revealed by high throughput DNA sequencing. Discov Med. 2012 Mar;13(70):193-9.

Wall R, Marques TM, O’Sullivan O, Ross RP, Shanahan F, Quigley EM, Dinan TG, Kiely B, Fitzgerald GF, Cotter PD, Fouhy F, Stanton C. Contrasting effects of Bifidobacterium breve NCIMB 702258 and Bifidobacterium breve DPC 6330 on the composition of murine brain fatty acid and gut microbiota. Am J Clin Nutr. 2012 May;95(5):1278-87.

 Brint, E. K., MacSharry, J., Fanning, A., Shanahan, F., & Quigley, E. M. (2011). Differential expression of toll-like receptors in patients with irritable bowel syndrome. Am J Gastroenterol, 106(2), 329-336. doi: ajg2010438

Craig O, O’Neill S, O’Neill F, McLaughlin P, McGarrigle A, McWilliams S, O’Connor O, Desmond A, Walsh EK, Ryan M, Maher M, Shanahan F. Diagnotstic Accuracy of Computed Tomography Using Lower Doses of Radiation for Patients With Crohn’s Disease. Clin Gastroenterol Hepatol. 2012 Mar 31. [Epub ahead of print]

Craig, O. F., Hyland, N. P., & Quigley, E. M. (2011). Functional dyspepsia: eosinophils, macrophages, and the postinfectious state. Gastroenterology, 140(3), 1092-1094; discussion 1094-1095. doi: S0016-5085(11)00064-3

Dal-Paz, K., Moraes-Filho, J. P., Navarro-Rodriguez, T., Eisig, J. N., Barbuti, R., & Quigley, E. M. (2011). Low levels of adherence with proton pump inhibitor therapy contribute to therapeutic failure in gastroesophageal reflux disease. Dis Esophagus. doi: 10.1111/j.1442-2050.2011.01227.x

Hill, C.  2011. Microbes and food, partners in sickness and in health. Microbial. Biotech.  4:117-118.

Konieczna P, Groeger D, Ziegler M, Frei R, Ferstl R, Shanahan F, Quigley EM, Kiely B, Akdis CA, O’Mahony L. Bifidobacterium infantis 35624 administration induces Foxp3 T regulatory cells in human peripheral blood: potential role for myeloid and plasmacytoid dendritic cells.  Gut. 2011 Nov 3. [Epub ahead of print] PMID: 2205206.

McKernan, D. P., Gaszner, G., Quigley, E. M., Cryan, J. F., & Dinan, T. G. (2011). Altered peripheral toll-like receptor responses in the irritable bowel syndrome. Aliment Pharmacol Ther, 33(9), 1045-1052. doi: 10.1111/j.1365-2036.2011.04624.x

Murphy, E. E., Cotter, P. D., Hogan, A., O’Sullivan, O., Joyce, A., Fouhy, F., Shanahan, F. (2011). The Gut Microbiota – A Realistic Therapeutic Target in Obesity and Metabolic Dysregulation. Gastroenterology, 140(5), S103-S104.

Quigley EMM. Is digestive comfort a relevant health care issue? Ann Gastroenterol Hepatol March 2011 Vol 2 Issue 1.

Quigley EMM. Antibiotics in irritable bowel syndrome: a novel approach to a challenging disorder. Clin Invest 2011;1:479-82.

Quigley, E. M. (2011). Antibiotics for irritable bowel syndrome: hitting the target, but what is it? Gastroenterology, 141(1), 391-393. doi: S0016-5085(11)00636-6 [pii]

Quigley, E. M. (2011). Bifidobacterium bifidum MIMBb75 in irritable bowel syndrome. Aliment Pharmacol Ther, 34(1), 100-101; author reply 101. doi: 10.1111/j.1365-2036.2011.04671.x

Quigley, E. M. (2011). Commensal bacteria: the link between IBS and IBD? Curr Opin Clin Nutr Metab Care, 14(5), 497-503. doi: 10.1097/MCO.0b013e328348c033

Quigley, E. M. (2011). Microflora modulation of motility. J Neurogastroenterol Motil, 17(2), 140-147. doi: 10.5056/jnm.2010.17.2.140

Quigley, E. M. (2011). Probiotics in functional bowel disorders getting it right. J Clin Gastroenterol, 45(6), 481-482. doi: 10.1097/MCG.0b013e3182175d7f

Quigley, E. M. (2011). The enteric microbiota in the pathogenesis and management of constipation. Best Pract Res Clin Gastroenterol, 25(1), 119-126. doi: S1521-6918(11)00004-7 [pii]

Quigley EM, Sperber AD, Drossman DA. WGO – Rome Foundation Joint Symposium Summary: IBS-The Global Perspective. J Clin Gastroenterol. 2011;45:i-ii.

Quigley, E. M. (2011). Therapies aimed at the gut microbiota and inflammation: antibiotics, prebiotics, probiotics, synbiotics, anti-inflammatory therapies. Gastroenterol Clin North Am, 40(1), 207-222. doi: S0889-8553(10)00133-0 [pii]

Shanahan, F. (2011). Molecular mechanisms of probiotic action: it’s all in the strains! Gut, 60(8), 1026-1027. doi: gut.2011.241026 [pii]

Shanahan, F. (2011). The colonic microflora and probiotic therapy in health and disease. Curr Opin Gastroenterol, 27(1), 61-65. doi: 10.1097/MOG.0b013e328340076f

Shanahan, F., & Murphy, E. (2011). The hybrid science of diet, microbes, and metabolic health. Am J Clin Nutr, 94(1), 1-2. doi: ajcn.111.018473 [pii]

Clarke G, Fitzgerald P, Hennessey AA, Cassidy EM, Quigley EM, Ross P, Stanton C, Cryan JF, Dinan TG. Marked elevations in pro-inflammatory polyunsaturated fatty acid metabolites in females with irritable bowel syndrome. J Lipid Res. 2010 May;51(5):1186-92

Codling C, O’Mahony L, Shanahan F, Quigley EM, Marchesi JR. A molecular analysis of fecal and mucosal bacterial communities in irritable bowel syndrome. Dig Dis Sci 2010; Feb;55(2):392-7

Keohane J, O’Mahony C, O’Mahony L, O’Mahony S, Quigley EMM, Shanahan F. Irritable bowel syndrome-type symptoms in patients with inflammatory bowel disease: a real association or reflection of occult inflammation? Am J Gastroenterology 2010 Apr 13. [Epub ahead of print] PMID: 20389294

Mueller-Lissner S, Quigley EM, Helfrich I, Schaefer E. Drug treatment of chronic-intermittent abdominal cramping and pain: a multi-national survey on usage and attitudes. Aliment Pharmacol Ther 2010; 31: epub ahead of print.

Quigley EM, Abu-Shanab A. Small intestinal bacterial overgrowth. Infect Dis Clin North Am. 2010 Dec;24(4):943-59, viii-ix.

Sibartie S, Scully P, Keohane J, O’Neill S, O’Mahony J, O’Hanlon D, Kirwan WO, O’Mahony L, Shanahan F. Mycobacterium avium subsp. Paratuberculosis (MAP) as a modifying factor in Crohn’s disease. Inflamm Bowel Dis. 2010 Feb;16(2):296-304 

Clarke G, Fitzgerald P, Cryan JF, Cassidy EM, Quigley EM, Dinan TG.  Tryptophan degradation in irritable bowel syndrome: evidence of indoleamine 2,3-dioxygenase activation in a male cohort. BMC Gastroenterology. 2009 20;9:6

Clayton, E.M., Rea, M.C., Shanahan, F., Quigley, E.M., Kiely, B.E., Hill, C., Ross, R.P.  (2009). The vexed relationship between Clostridium difficile and Inflammatory Bowel Disease: an assessment of carriage in an outpatient setting among patients in remission.  American Journal of Gastroenterology May;104(5):1162-9.

Morcos A, Dinan T, Quigley EM (2009) Irritable bowel syndrome: Role of food in pathogenesis and management J Dig Dis. 10(4):237-46.

O’Mahony D, Murphy KB, MacSharry J, Boileau T, Sunvold G, Reinhart G, Kiely B, Shanahan F, O’Mahony L. Portrait of a canine probiotic Bifidobacterium–from gut to gut. Vet Microbiol. 2009 Oct 20;139(1-2):106-12.

Quigley EM, Vandeplassche L, Kerstens R, Ausma J. Clinical trial: the efficacy, impact on quality of life, and safety and tolerability of prucalopride in serere chronic constipation - a 12-week, randomized, double-blinded, placebo-controlled study. Aliment Pharmacol Ther. 2009 Feb 1;29(3):315-28. Epub 2008 Nov 8

Desmond AN, O’Regan K, Curran C, McWilliams S, Fitzgerald T, Maher MM, Shanahan F. Crohn’s disease: factors associatedwith exposure to high levels of diagnostic radiation. Gut. 2008 Nov;57(11):1524-9. Epub 2008 Apr 28. PubMedPMID: 18443021.

Dinan TG, Clarke G, Quigley EM, Scott LV, Shanahan F, Cryan J, Cooney J, Keeling PW. Enhanced cholinergic-mediated increase in the pro-inflammatory cytokine IL-6 in irritable bowel syndrome: role of muscarinic receptors. Am J Gastroenterol. 2008;103:2570-6

Feighery LM, Smith P, O’Mahony L, Fallon PG, Brayden DJ. Effect of Lactobacillus salivarius 433118 on intestinal inflammation, immunity status and in vitro colon function in two mouse models of inflammatroy bowel disease. Dig Dis Sci. 2008 Sep;53(9):2495-506. Epub 2007 Dec 20.

Fitzgerald P, Cassidy EM, Clarke G, Scully P, Barry S, Quigley EMM, Shanahan F, Cryan JF, Dinan TG. Tryptophan catabolism in females with irritable bowel syndrome: relationship to interferon-gamma, severity of symptoms and psychiatric co-morbidity. Neurogastroenterol Motil. 2008 20(12):1291-7.

Macsharry J, O’Mahony L, Fannning A, Bairead E, Sherlock G, Tiesman J, Fulmer A, Kiely B, Dinan TG, Shanahan F, Quigley EM. Mucosal cytokine imbalance in irritable bowel syndrome. Scand J Gastroenterol. 2008 43(12):1467-76

Ryan KA, Jayaraman T, Daly P, Canchaya C, Curran S, Fang F, Quigley EM, O’Toole PW. Isolation of lactobacilli with probiotic properties from the human stomach. Lett Appl Microbiol. 2008 Oct;47(4):269-74.

Scanlan PD, Shanahan F, Marchesi JR. Culture-independent analysis of desulfovibrios in the human distal colon of healthy, colorectal cancer and polypectomized individuals. FEMS Microbiol Ecol. 69(2): 213-21.]

O’Mahony L, O’Callaghan L, McCarthy J, Shilling D, Scully P, Sibartie S, Kavanagh E, Kirwin WO, Redmond HP, Collins JK, Shanahan F. Differential cytokine response from dendritic cells to commensal and pathogenic bacteria in different lymphoid compartments in humans. Am J Physiol Gastrointest Liver Physiol. 2006 Apr;290(4):G839-45

Scanlan PD, Shanahan F, O’Mahony C, Marchesi JR. (2006). Culture-Independent Analyses of Temporal Variation of the Dominant Fecal Microbiota and Targeted Bacterial Subgroups in Crohn’s Disease. Clin Microbiol. 2006 November; 44(11): 3980–3988.

Whorwell PJ, Altringer L, Morel J, Bond Y, Charbonneau D, O’Mahony L, Kiely B, Shanahan F, Quigley EM. Efficacy of an encapsulated probiotic Bifidobacterium infantis 35624 in women with irritable bowel syndrome. Am J Gastroenterol. 2006 Jul;101(7):1581-90.