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Outputs

Papers

 

2016

Lucas Sinclair, Umer Z Ijaz, Lars Juhl Jensen, Marco JL Coolen, Cecile Gubry-Rangin, Alica Chroňáková, Anastasis Oulas, Christina Pavloudi, Julia Schnetzer, Aaron Weimann, Ali Ijaz, Alexander Eiler, Christopher Quince, Evangelos Pafilis 2016. Seqenv: linking sequences to environments through text mining. PeerJ 4: e2690.

Pascoe B, Meric G, Yahara K, Wimaralathna H, Murray S, Hitchings MD, Sproston EL, Carrillo CD, Taboada EN, Cooper KK, Huynh S, Cody AJ, Jolley KA, Maiden MC, McCarthy ND, Didelot X, Parker C, Sheppard SK. (2016) Local genes for local bacteria: evidence of allopatry in the genomes of transatlantic Campylobacter populations. PeerJ Preprints 4:e2638v1

Esson D, Mather AE, Scanlan E, Gupta S, de Vries SPW, Bailey D, Harris SR, McKinley TJ, Méric G, Berry SK, Mastroeni P, Sheppard SK, Christie G, Thomson NR, Parkhill J, Maskell D, Grant AJ. (2016) Genomic variations leading to alterations in cell morphology of Campylobacter spp. Scientific Reports 6:38303. 

Woodcock DJ, Krusche P, Strachan NJC, Forbes KJ, Cohan FM, Méric G, Sheppard SK. (2016) Genomic plasticity and rapid host switching promote the evolution of generalism in the zoonotic pathogen Campylobacter. bioRxiv 080077; doi:10.1101/

Monteil CL, Yahara K, Studholme DJ, Mageiros L, Méric G, Swingle B, Morris CE, Vinatzer BA, Sheppard SK. (2016) Population-genomic insights into emergence, crop-adaptation, and dissemination of Pseudomonas syringae pathogens. Microbial Genomics 2(10): doi:10.1099/mgen.0.000089

McNally A, Oren Y, Kelly D, Pascoe B, Dunn S, Sreecharan T, Vehkala M, Välimäki N, Prentice MB, Ashour A, Avram O, Pupko T, Dobrindt U, Literak I, Guenther S, Schaufler K, Wieler LH, Zhiyong Z, Sheppard SK, McInerney JO, Corander J. (2016) Combined Analysis of Variation in Core, Accessory and Regulatory Genome Regions Provides a Super-Resolution View into the Evolution of Bacterial Populations. PLoS Genetics 12(9): e1006280. doi: 10.1371/journal.pgen.1006280

Yana X, Li Z, Chlebowiczc MA, Tao X, Ni M, Hu Y, Li Z, Grundmann H, Murray S, Pascoe B, Sheppard SK, Bo X, Maarten van Dijl J, Du P, Zhang M, You Y, Yu X, Meng F, Wang S, Zhang J. (2016) Genetic features of livestock-associated Staphylococcus aureus ST9 isolates from Chinese pigs that carry the lsa(E) gene for quinupristin/dalfopristin resistance. International Journal of Medical Microbiology 306(8):722–729

Thorell K, Yahara K, Berthenet E, Lawson DJ, Kato I, Tenorio Mendez A, Canzian F, Mercedes Bravo M, Suzuki R, Yamaoka Y, Torres J, Sheppard SK, Falush D. (2016) Rapid evolution of distinct Helicobacter pylori subpopulations in the Americas.

Culebro A, Revez J, Pascoe B, Friedmann Y, Hitchings MD, Stupak J, Sheppard SK, Li J, Rossi M. (2016) Large sequence diversity within biosynthesis locus and common biochemical features of Campylobacter coli lipooligosaccharides. Journal of Bacteriology 198(20):2829-40

Sankar A, Malone B, Bayliss SC, Pascoe B, Méric G, Hitchings MD, Sheppard SK, Feil EJ, Corander J, Honkela A. (2016) Bayesian identification of bacterial strains from sequencing data. Microbial Genomics 2(8): doi:10.1099/mgen.0.000075

Gilbert MJ, Miller WG, Yee E, Zomer AL, van der Graaf-van Bloois L, Fitzgerald C, Forbes KJ, Méric G, Sheppard SK, Wagenaar JA, Duim B. (2016) Comparative Genomics of Campylobacter fetus from Reptiles and Mammals Reveals Divergent Evolution in Host-Associated Lineages. Genome Biology and Evolution. 2;8(6):2006-19.

Mainda G, Lupolova N, Sikakwa L, Bessell PR, Muma JB, Hoyle DV, McAteer SP, Gibbs K, Williams NJ, Sheppard SK, La Ragione RM, Cordoni G, Argyle SA, Wagner S, Chase-Topping ME, Dallman TJ, Stevens MP, Bronsvoort BM, Gally DL. Phylogenomic approaches to determine the zoonotic potential of Shiga toxin-producing Escherichia coli (STEC) isolated from Zambian dairy cattle. Scientific Reports. 25(6):26589.

Jessica L Ray, Julia Althammer, Katrine S Skaar, Paolo Simonelli, Aud Larsen, Diane Stoecker, Andrey Sazhin, Umer Z Ijaz, Christopher Quince, Jens C Nejstgaard, Marc Frischer, Georg Pohnert, Christofer Troedsson. Metabarcoding and metabolome analyses of copepod grazing reveal feeding preference and linkage to metabolite classes in dynamic microbial plankton communities 2016. Molecular ecology 25 (21): 5585-5602.

Torbjørn Rognes, Tomáš Flouri, Ben Nichols, Christopher Quince, Frédéric Mahé. VSEARCH: a versatile open source tool for metagenomics 2016. PeerJ 4: e2584.

Konstantinos Gerasimidis, Martin Bertz, Christopher Quince, Katja Brunner, Alanna Bruce, Emilie Combet, Szymon Calus, Nick Loman, Umer Zeeshan Ijaz 2016. The effect of DNA extraction methodology on gut microbiota research applications. BMC Research Notes 9 (1): 365.

Stefanie Widder, Rosalind J Allen, Thomas Pfeiffer, Thomas P Curtis, Carsten Wiuf, William T Sloan, Otto X Cordero, Sam P Brown, Babak Momeni, Wenying Shou, Helen Kettle, Harry J Flint, Andreas F Haas, Béatrice Laroche, Jan-Ulrich Kreft, Paul B Rainey, Shiri Freilich, Stefan Schuster, Kim Milferstedt, Jan R van der Meer, Tobias Groβkopf, Jef Huisman, Andrew Free, Cristian Picioreanu, Christopher Quince, Isaac Klapper, Simon Labarthe, Barth F Smets, Harris Wang, Orkun S Soyer 2016. Challenges in microbial ecology: building predictive understanding of community function and dynamics. The ISME journal 10(11):2557-2568.

Melanie Schirmer, Rosalinda D’Amore, Umer Z Ijaz, Neil Hall, Christopher Quince 2016. Illumina error profiles: resolving fine-scale variation in metagenomic sequencing data. BMC bioinformatics 17 (1): 1

Sarah-Jane Haig, Caroline Gauchotte-Lindsay, Gavin Collins, Christopher Quince 2016. Bioaugmentation Mitigates the Impact of Estrogen on Coliform-Grazing Protozoa in Slow Sand Filters. Environmental science & technology 50 (6): 3101-3110

Belen Torondel, Jeroen HJ Ensink, Ozan Gundogdu, Umer Zeeshan Ijaz, Julian Parkhill, Faraji Abdelahi, Viet‐Anh Nguyen, Steven Sudgen, Walter Gibson, Alan W Walker, Christopher Quince 2016. Assessment of the influence of intrinsic environmental and geographical factors on the bacterial ecology of pit latrines. Microbial biotechnology 9 (2): 209-223.

Eduard Vico Oton, Christopher Quince, Graeme W Nicol, James I Prosser, Cécile Gubry-Rangin 2016. Phylogenetic congruence and ecological coherence in terrestrial Thaumarchaeota 2016. The ISME journal 10(1): 85-96.

Connor, T.R et al. CLIMB (the Cloud Infrastructure for Microbial Bioinformatics): an online resource for the medical microbiology community. Microbial Genomics. Aug 2016 doi: 10.1099/mgen.0.000086

Quick J, Loman NJ et al. Real-time, portable genome sequencing for Ebola surveillance. Nature. 2016 Feb 11;530(7589):228-32. doi: 10.1038/nature16996. Epub 2016 Feb 3.

 

2015

Connor, T.R et al. Species-wide whole genome sequencing reveals historical global spread and recent local persistence in Shigella flexneri. eLife 2015;4:e07335

Gesing S, Connor TR and Ian Taylor.  Genomics and Biological Big Data: Facing Current and Future Challenges around Data and Software Sharing and Reproducibility. 2015 Nov. arXiv:1511.02689

D’Amore, R., U. Z. Ijaz, M. Schirmer, J. Kenny, R. Gregory, A. C. Darby, M. Shakya, M. Podar, C. Quince, and N. Hall 2015. A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling. Accepted BMC Genomics.

Quince, C., U. Z. Ijaz, N. Loman, A. M. Eren, D. Saulnier, J. Russell, S. J. Haig, S. T. Calus, J. Quick, A. Barclay, M. Bertz, M. Blaut, R. Hansen, P. McGrogan, R. K. Russell, C. A. Edwards, and K. Gerasimidis 2015. Extensive modulation of the fecal metagenome in children with Crohn’s disease during exclusive enteral nutrition. American Journal of Gastroenterolgy doi: 10.1038/ajg.2015.357.

Haig, S. J., C. Quince, R.L. Davies, C.C. Dorea, and G. Collins, 2015. The relationship between microbial community evenness and function in slow sand filters. mBio 6, e00729-15.

Oton, E.V., C. Quince, G. W. Nicol, J. I. Prosser, and C. Gubry-Rangin 2015. Phylogenetic congruence and ecological coherence in terrestrial Thaumarchaeota. The ISME Journal doi:10.1038/ismej.2015.101.

Harris, K., T.L. Parsons, U.Z. Ijaz, L. Lahti, I. Holmes, and C. Quince, 2015. Linking statistical and ecological theory: Hubbell’s unified neutral theory of biodiversity as a hierarchical Dirichlet process. Proceedings of the IEEE: doi: 10.1109/JPROC.2015.2428213.

 

Talks

Microbiomes and metagenomes: window on the past, promises for the future   Midlands Molecular Microbiology meeting     Nottingham    September 2015

Genomics and metagenomics in medical microbiology: opportunities and challenges  BMFZ meeting   Düsseldorf     November 2015

Implementing a nationwide cyber infrastructure for microbiology: CLIMB    UCISA Infrastructure Group Meeting  Oxford October 2015

Bioinformatics showcase  Applied Bioinformatics and Public Health Microbiology Cambridge  May 2015

CLIMB  Balti and Bioinformatics     Birmingham  May   2014

 

 

Training

For a list of past training events please follow see our training page