Recent Publications

2018

author list
title
journal, location DOI:
T Barroso, F Conway, S Emel, D McMillan, D Young, H Karteszi, DR Gaya, K Gerasimidis
Patients with inflammatory bowel disease have higher abdominal adiposity and less skeletal mass than healthy controls
Annals of gastroenterology, 31(5): 566–571, 2018 DOI: 10.20524/aog.2018.0280
K Gerasimidis, S Milani, A Tester, O Purcell, C Woodley, M Tsiountsioura, A Koulieri, O Zerva, K Loizou, M Rafeey, M Kontogianni, C Wright
A multicentre development and evaluation of a dietetic referral score for nutritional risk in sick infants
Clinical Nutrition, In Press, 2018. DOI: 10.1016/j.clnu.2018.08.017
L De Ridder, A Assa, J Bronsky, C Romano, RK Russell, NA Afzal, C Hauer, D Knafelz, P Lionetti, C Strisciuglio, G Veres, H Winter, VM Wolters, M Sladek, AG Vulto, JA Dias
Use of Biosimilars in Paediatric Inflammatory Bowel Disease: An Updated Position Statement of the Paediatric IBD Porto Group of ESPGHAN
Journal of Pediatric Gastroenterology and Nutrition, In Press, 2018. DOI: 10.1097/MPG.0000000000002141
MA Altowati, S Shepherd, P McGrogan, RK Russell, SF Ahmed, SC Wong
Effects of Recombinant Human Growth Hormone in Children with Crohn’s Disease on the Muscle-Bone Unit: A Preliminary Study
Hormone research in paediatrics, 90 (2) pp: 1-4 2018. DOI: 10.1159/000492398
RD Eveleens, K Gerasimidis, M Chourdakis, K Huysentruyt, B Koletzko, JM Hulst, KFM Joosten
Current clinical trials in paediatrics: Report of the ESPEN special interest group in paediatrics
Clinical Nutrition ESPEN, 27 pp: 75-78, 2018. DOI: 10.1016/j.clnesp.2018.06.006
Y Zhou, E Millhouse, T Shaw, DF Lappin, R Rajendran, J Bagg, H Lin, G Ramage
Evaluating Streptococcus mutans Strain Dependent Characteristics in a Polymicrobial Biofilm Community
Frontiers in Microbiology, 9 pp: 1498, 2018. DOI: 10.3389/fmicb.2018.01498
E Neelis, B de Koning, E Rings, R Wijnen, B Nichols, J Hulst, K Gerasimidis
The Gut Microbiome in Patients with Intestinal Failure: Current Evidence and Implications for Clinical Practice
Journal of Parenteral and Enteral Nutrition, In Press, 2018. DOI: 10.1002/jpen.1423
O Koci, M Logan, V Svolos, RK Russell, K Gerasimidis, UZ Ijaz
An automated identification and analysis of ontological terms in gastrointestinal diseases and nutrition-related literature provides useful insights
PeerJ, 6 pp: e5047, 2018. DOI: 10.7717/peerj.5047
D Turner, FM Ruemmele, E Orlanski-Meyer, AM Griffiths, JM Carpi, J Bronsky, G Veres, M Aloi, C Strisciuglio, CP Braegger, A Assa, C Romano, S Hussey, M Stanton, M Pakarinen, L de Ridder, Lissy, KH Katsanos, NM Croft, VM Navas-Lopez, Victor Manuel, DC Wilson, S Lawrence, RK Russell
Management of Paediatric Ulcerative Colitis, Part 2: Acute Severe Colitis—An Evidence-based Consensus Guideline From the European Crohn's and Colitis Organization and the European Society of Paediatric Gastroenterology, Hepatology and Nutrition
Journal of Pediatric Gastroenterology and Nutrition, 67(2):292–310, 2018. DOI: 10.1097/MPG.0000000000002036
D Turner, FM Ruemmele, E Orlanski-Meyer, AM Griffiths, JM Carpi, J Bronsky, G Veres, M Aloi, C Strisciuglio, CP Braegger, A Assa, C Romano, S Hussey, M Stanton, M Pakarinen, L de Ridder, Lissy, KH Katsanos, NM Croft, VM Navas-Lopez, Victor Manuel, DC Wilson, S Lawrence, RK Russell
Management of Paediatric Ulcerative Colitis, Part 1: Ambulatory Care-An Evidence-based Guideline From European Crohn's and Colitis Organization and European Society of Paediatric Gastroenterology, Hepatology and Nutrition Ã
Journal of Pediatric Gastroenterology and Nutrition, 67(2):257–291, 2018. DOI: 10.1097/MPG.0000000000002035
R Kean, C Delaney, L Sherry, A Borman, EM Johnson, MD Richardson, R Rautemaa-Richardson, C Williams, G Ramage
Transcriptome Assembly and Profiling of Candida auris Reveals Novel Insights into Biofilm-Mediated Resistance
mSphere, 3(4): e00334-18, 2018. DOI: 10.1128/mSphere.00334-18
C Varsos, T Patkos, A Oulas, C Pavloudi, A Gougousis, UZ Ijaz, I Filiopoulou, N Pattakos, EV Berghe, A Fernandez-Guerra, S Faulwetter, E Chatzinikolaou, E Pafilis, C Beikiari, M Doerr, and C Arvantidis
Optimized R functions for analysis of ecological community data using the R virtual laboratory (RvLab)
Biodiversity Data Journal, 4:e8357, 2016. DOI:10.3897/BDJ.4.e8357
Accompanying Software: RvLab
C Pedersen, P Hinton, E Gallagher, F Horton, R Ellis, UZ Ijaz, H Wu, E Jaiyeola, O Diribe, GR Gibson, T Duparc, PD Cani, J Wright, D Russell-Jones, RL Ragione, and MD Robertson
Galacto-Oligosaccharide has no Effect on Glucose Tolerance, inflammatory Markers or Intestinal Permeability in well-controlled Type 2 Diabetes
Proceedings of the Nutrition Society, 75(OCE3), 2016. DOI:10.1017/S0029665116001191
C Pedersen, E Gallagher, F Horton, RJ Ellis, UZ Ijaz, H Wu, E Jaiyeola, O Diribe, T Duparc, PD Cani, GR Gibson, P Hinton, J Wright, D Russell-Jones, R La Ragione, and MD Robertson
Host-microbiome interactions in human type 2 diabetes following prebiotic dietary fibre (galacto-oligosaccharide) intake
British Journal of Nutrition, 116(11):1869-1877, 2016. DOI:10.1017/S0007114516004086
K Gerasimidis, M Bertz, C Quince, K Brunner, A Bruce, E Combet, ST Calus, N Loman, and UZ Ijaz
The effect of DNA extraction methodology on gut microbiota research applications
BMC Research Notes, 9:365, 2016. DOI:10.1186/s13104-016-2171-7
V Svolos*, R Hansen, K Hughes, UZ Ijaz, C Quince, D Gaya, R Russell, and K Gerasimidis
The impact of 'Crohn's Disease-TReatment-with-EATing' diet (CD-TREAT diet) and exclusive enteral nutrition on healthy gut bacteria metabolism
Journal of Crohn's and Colitis, 10(suppl 1):S14-S15, 2016. DOI:10.1093/ecco-jcc/jjw019.017
*Winner of Best investigator-initiated study (IIS) Award at the 11th Congress of ECCO
K Gerasimidis, UZ Ijaz, C Edwards, RK Russell, C Quince, and R Hansen
Response to Kaakoush et al.
American Journal of Gastroenterology, 111(7):1033-1034, 2016.
M Schirmer, R D'Amore, UZ Ijaz, N Hall, and C Quince
Illumina error profiles: Resolving fine-scale variation in metagenomic sequencing
BMC Bioinformatics, 17:125, 2016. DOI:10.1186/s12859-016-0976-y
Code
R D'Amore, UZ Ijaz, M Schirmer, J Kenny, R Gregory, AC Darby, M Shakya, M Podar, C Quince, and N Hall
A comprehensive benchmarking study of next-generation sequencing platforms for 16S rRNA community profiling
BMC Genomics, 17:55, 2016. DOI:10.1186/s12864-015-2194-9
Code
C Quince, UZ Ijaz, N Loman, AM Eren, D Saulnier, J Russell, SJ Haig, ST Calus, J Quick, A Barclay, M Bertz, M Blaut, R Hansen, P McGrogan, RK Russell, C Edwards, and K Gerasimidis
Extensive modulation of the fecal metagenome in children with Crohn's disease during exclusive enteral nutrition
American Journal of Gastroenterology, 110:1718-1729, 2015. DOI:10.1038/ajg.2015.357
MJ Khan, C Quince, V S, UZ Ijaz, N Loman, ST Calus, J Quick, SJ Haig, MG Shaikh, CA Edwards, and K Gerasimidis
A detailed analysis of the gut microbial diversity and metabolic activity in children with obesity of different aetiology and lean controls
Proceedings of the Nutrition Society, 74(OCE1):E75, 2015.
K Harris, TL Parsons, UZ Ijaz, L Lahti, I Holmes, and C Quince
Linking statistical and ecological theory: Hubbell's unified neutral theory of biodiversity as a hierarchical Dirichlet process
Proceedings of the IEEE, pp. 1-14 (Early Online Publication)
Accompanying Software: NMGS
J Alneberg, BS Bjarnason, I de Bruijn, M Schirmer, J Quick, UZ Ijaz, L Lahti, NJ Loman, AF Andersson, and C Quince
Binning metagenomic contigs by coverage and composition.
Nature Methods, 2014.
Accompanying Software: CONCOCT, TAXAassign
K Gerasimidis, N Loman, J Quick, ST Calus, UZ Ijaz, P McGrogan, CA Edwards, C Quince, and R. K. Russell
O-05: Metagenomic analysis of the gut microbiome during a course of Exclusive Enteral Nutrition (EEN) provides novel insights on mechanism of EEN action
Journal of Crohn's and Colitis, 8(Supplement 2):S393-S394, 2014.