Metagenomics coupled to next generation sequencing has transformed our understanding of the microbial world. It has allowed us to directly determine community structure and function in situ from the DNA of the organisms present. This is revolutionising microbial ecology. My research consists of the development of improved statistical and bioinformatics tools for interpreting this sequence data. These tools exploit advanced methods from machine learning and Bayesian statistics. I work on both 16S rRNA gene amplicon data, having developed the AmpliconNoise algorithm for error removal from 454 pyrosequenced amplicons (http://code.google.com/p/ampliconnoise/) and shotgun metagenomics for example the CONCOCT algorithm for automated genome extraction from shotgun metagenome reads (https://github.com/BinPro/CONCOCT). In addition, I also develop Bayesian statistical models for interpreting microbial community structure addressing questions such as are enterotypes real features of the human gut microbiome and are microbial communities neutrally assembled? In collaboration with numerous groups around the world I apply these methods to both environmental and host-associated microbial communities. For instance, with Dr Konstantinos Gerasimidis (Nutrition Group - University of Glasgow -- http://www.gla.ac.uk/schools/medicine/staff/konstantinosgerasimidis/) and Dr Nick Loman (University of Birmimgham - http://pathogenomics.bham.ac.uk/clinicogenomics/) I have resolved the changes in gut microbiota composition of children with Crohn's disease during treatment with exclusive enteral nutrition. This could potentially lead to improved therapeutic strategies. With Dr Gavin Collins (University of Galway - http://www.nuigalway.ie/microbiology/dr_gavin_collins.html) I study the structure of anaerobic digestion reactor communities. More efficient AD digesters will provide more effective biogas production from wastewater, reducing pollution and providing a renewable energy resource. I am currently employed as an MRC Principal Research Fellow as part of the Cloud Computing for Microbial Bioinformatics (CLIMB) consortium (http://www.climb.ac.uk/).
View Christopher's publications on Google Scholar.
- Quince, Christopher, Nurk, Sergey, Raguideau, Sébastien, James, Robert, Soyer, Orkun S., Summers, J. Kimberly, Limasset, Antoine, Eren, A. Murat, Chikhi, Rayan, Darling, Aaron E., 2021. STRONG : metagenomics strain resolution on assembly graphs. Genome Biology, 22 (1)
- Borsetto, Chiara, Raguideau, Sébastien, Travis, Emma Rachel, Kim, Dae-Wi, Lee, Do-Hoon, Bottrill, Andrew R., Stark, Richard Jan, Song, Lijiang, Cha, Chang-Jun, Pearson, Jonathan M., Quince, Christopher, Singer, Andrew C., Wellington, Elizabeth M. H., 2021. Impact of sulfamethoxazole on a riverine microbiome. Water Research, 201
- Lee, Kihyun, Kim, Dae-Wi, Lee, Do-Hoon, Kim, Yong-Seok, Bu, Ji-Hye, Cha, Ju-Hee, Thawng, Cung Nawl, Hwang, Eun-Mi, Seong, Hoon Je, Sul, Woo Jun, Wellington, Elizabeth M. H., Quince, Christopher, Cha, Chang-Jun, 2020. Mobile resistome of human gut and pathogen drives anthropogenic bloom of antibiotic resistance. Microbiome, 8 (1)
- Sagar, Nidhi M., Duboc, Henri, Kay, Gemma L., Alam, Mohammad T., Wicaksono, Alfian, Covington, James A., Quince, Christopher, Kokkorou, Margarita, Svolos, Vaios, Palmieri, Lola J., Gerasimidis, Konstantinos, Walters, Julian R. F., Arasaradnam, Ramesh P., 2020. The pathophysiology of bile acid diarrhoea : differences in the colonic microbiome, metabolome and bile acids. Scientific Reports, 10 (1)
- Sheridan, Paul O., Raguideau, Sébastien, Quince, Christopher, Holden, Jennifer, Thames Consortium,, Zhang, Lihong, Gubry-Rangin, Cécile, Williams, Tom A., 2020. Gene duplication drives genome expansion in a major lineage of Thaumarchaeota. Nature Communications, 11 (1)
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Svolos, Vaios, Hansen, Richard, Nichols, Ben, Quince, Christopher, Ijaz, Umer Z., Papadopoulou, Rodanthi T., Edwards, Christine A., Watson, David, Alghamdi, Adel, Brejnrod, Asker, Ansalone, Cecilia, Duncan, Hazel, Gervais, Lisa, Tayler, Rachel, Salmond, Jonathan, Bolognini, Daniele, Klopfleisch, Robert, Gaya, Daniel R., Milling, Simon, Russell, Richard K. et al (Select to open full list), 2019.
- Pasolli, Edoardo, Asnicar, Francesco, Manara, Serena, Zolfo, Moreno, Karcher, Nicolai, Armanini, Federica, Beghini, Francesco, Manghi, Paolo, Tett, Adrian, Ghensi, Paolo, Collado, Maria Carmen, Rice, Benjamin L., DuLong, Casey, Morgan, Xochitl C., Golden, Christopher D., Quince, Christopher, Huttenhower, Curtis, Segata, Nicola, 2019. Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle. CELL, 176 (3), pp. 649-662.e20
- Heidrich, E. S., Dolfing, J., Wade, M. J., Sloan, W. T., Quince, C., Curtis, T. P., 2018. Temperature, inocula and substrate : contrasting electroactive consortia, diversity and performance in microbial fuel cells. Bioelectrochemistry, 119, pp. 43-50
- Zhou, Zhemin, Lundstrøm, Inge, Tran-Dien, Alicia, Duchêne, Sebastián, Alikhan, Nabil-Fareed, Sergeant, Martin J., Langridge, Gemma, Fotakis, Anna K., Nair, Satheesh, Stenøien, Hans K., Hamre, Stian S., Casjens, Sherwood, Christophersen, Axel, Quince, Christopher, Thomson, Nicholas R., Weill, François-Xavier, Ho, Simon Y. W., Gilbert, M. Thomas P., Achtman, Mark, 2018. Pan-genome analysis of ancient and modern Salmonella enterica demonstrates genomic stability of the invasive Para C lineage for millennia. Current Biology, 28 (15), pp. 2420-2428
- Joyce, Aoife, Ijaz, Umer Z., Nzeteu, Corine, Vaughan, Aoife, Shirran, Sally L., Botting, Catherine H., Quince, Christopher, O'Flaherty, Vincent, Abram, Florence, 2018. Linking Microbial Community Structure and Function During the Acidified Anaerobic Digestion of Grass. Frontiers in Microbiology, 9
- Quince, Christopher, Delmont, Tom O., Raguideau, Sébastien, Alneberg, Johannes, Darling, Aaron E., Collins, Gavin, Eren, A. Murat, 2017. DESMAN : a new tool for de novo extraction of strains from metagenomes. Genome Biology, 18 (1)
- Fonseca, V. G., Sinniger, F., Gaspar, J. M., Quince, C., Creer, S., Power, Deborah M., Peck, Lloyd S., Clark, Melody S., 2017. Revealing higher than expected meiofaunal diversity in Antarctic sediments : a metabarcoding approach. Scientific Reports, 7 (1)
- Connelly, Stephanie, Shin, Seung G., Dillon, Robert J., Ijaz, Umer Z., Quince, Christopher, Sloan, William T., Collins, Gavin, 2017. Bioreactor scalability : laboratory-scale bioreactor design influences performance, ecology, and community physiology in expanded granular sludge bed bioreactors. Frontiers in Microbiology, 8
- Harris, Keith, Parsons, Todd L., Ijaz, Umer Z., Lahti, Leo, Holmes, Ian, Quince, Christopher, 2017. Linking statistical and ecological theory : Hubbell's unified neutral theory of biodiversity as a hierarchical Dirichlet process. Proceedings of the IEEE, 105 (3), pp. 516-529
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Sczyrba, Alexander, Hofmann, Peter, Belmann, Peter, Koslicki, David, Janssen, Stefan, Dröge, Johannes, Gregor, Ivan, Majda, Stephan, Fiedler, Jessika, Dahms, Eik, Bremges, Andreas, Fritz, Adrian, Garrido-Oter, Ruben, Jørgensen, Tue Sparholt, Shapiro, Nicole, Blood, Philip D, Gurevich, Alexey, Bai, Yang, Turaev, Dmitrij, DeMaere, Matthew Z et al (Select to open full list), 2017.
- Quince, Christopher, Walker, Alan W., Simpson, Jared T., Loman, Nicholas J., Segata, Nicola, 2017. Shotgun metagenomics, from sampling to analysis. Nature Biotechnology, 35 (9), pp. 833-844
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Thompson, Luke R., Sanders, Jon G., McDonald, Daniel, Amir, Amnon, Ladau, Joshua, Locey, Kenneth J., Prill, Robert J., Tripathi, Anupriya, Gibbons, Sean M., Ackermann, Gail, Navas-Molina, Jose A., Janssen, Stefan, Kopylova, Evguenia, Vázquez-Baeza, Yoshiki, González, Antonio, Morton, James T., Mirarab, Siavash, Zech Xu, Zhenjiang, Jiang, Lingjing, Haroon, Mohamed F. et al (Select to open full list), 2017.
- Ijaz, Umer Zeeshan, Quince, Christopher, Hanske, Laura, Loman, Nick, Calus, Szymon T., Bertz, Martin, Edwards, Christine A., Gaya, Daniel R., Hansen, Richard, McGrogan, Paraic, Russell, Richard K., Gerasimidis, Konstantinos, 2017. The distinct features of microbial 'dysbiosis' of Crohn's disease do not occur to the same extent in their unaffected, genetically-linked kindred.. PLoS One, 12 (2)
- D'Amore, Rosalinda, Ijaz, Umer Zeeshan, Schirmer, Melanie, Kenny, John G., Gregory, Richard, Darby, Alistair C., Shakya, Migun, Podar, Mircea, Quince, Christopher, Hall, Neil, 2016. A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling. BMC Genomics, 17 (1)
- Torondel, Belen, Ensink, Jeroen H.J., Gundogdu, Ozan, Ijaz, Umer Zeeshan, Parkhill, Julian, Abdelahi, Faraji, Nguyen, Viet-Anh, Sudgen, Steven, Gibson, Walter, Walker, Alan W., Quince, Christopher, 2016. Assessment of the influence of intrinsic environmental and geographical factors on the bacterial ecology of pit latrines. Microbial Biotechnology, 9 (2), pp. 209-223
- Haig, Sarah-Jane, Gauchotte-Lindsay, Caroline, Collins, Gavin, Quince, Christopher, 2016. Bioaugmentation mitigates the impact of estrogen on coliform-grazing protozoa in slow sand filters. Environmental Science & Technology, 50 (6), pp. 3101-3110
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Widder, Stefanie, Allen, Rosalind, Pfeiffer, Thomas, Curtis, Thomas P., Wiuf, Carsten, Sloan, William T., Cordero, Otto X., Brown, Sam P., Momeni, Babak, Shou, Wenying, Kettle, Helen, Flint, Harry J., Haas, Andreas F., Laroche, Beatrice, Kreft, Jan-Ulrich, Rainey, Paul B., Freilich, Shiri, Schuster, Stefan, Milferstedt, Kim, van der Meer, Jan R. et al (Select to open full list), 2016.
- Schirmer, Melanie, D'Amore, Rosalinda, Ijaz, Umer Z., Hall, Neil, Quince, Christopher, 2016. Illumina error profiles : resolving fine-scale variation in metagenomic sequencing data. BMC Bioinformatics, 17 (1), pp. 1-15
- Cho, Si-Kyung, Kim, Dong-Hoon, Quince, Christopher, Im, Wan-Taek, Oh, Sae-Eun, Shin, Seung Gu, 2016. Low-strength ultrasonication positively affects methanogenic granules toward higher AD performance : implications from microbial community shift. Ultrasonics Sonochemistry, 32, pp. 198-203
- Ray, Jessica L., Althammer, Julia, Skaar, Katrine S., Simonelli, Paolo, Larsen, Aud, Stoecker, Diane, Sazhin, Andrey, Ijaz, Umer Z., Quince, Christopher, Nejstgaard, Jens C., Frischer, Marc, Pohnert, Georg, Troedsson, Christofer, 2016. Metabarcoding and metabolome analyses of copepod grazing reveal feeding preference and linkage to metabolite classes in dynamic microbial plankton communities. Molecular Ecology, 25 (21), pp. 5585-5602
- Oton, Eduard Vico, Quince, Christopher, Nicol, Graeme W., Prosser, James I., Gubry-Rangin, Cécile, 2016. Phylogenetic congruence and ecological coherence in terrestrial Thaumarchaeota. The ISME Journal, 10 (1), pp. 85-96
- Gregor, Ivan, Dröge, Johannes, Schirmer, Melanie, Quince, Christopher, McHardy, Alice C., 2016. PhyloPythiaS+ : a self-training method for the rapid reconstruction of low-ranking taxonomic bins from metagenomes. PeerJ, 4
- Sinclair, Lucas, Ijaz, Umer Z., Jensen, Lars Juhl, Coolen, Marco J.L., Gubry-Rangin, Cecile, Chronáková, Alica, Oulas, Anastasis, Pavloudi, Christina, Schnetzer, Julia, Weimann, Aaron, Ijaz, Ali, Eiler, Alexander, Quince, Christopher, Pafilis, Evangelos, 2016. Seqenv : linking sequences to environments through text mining. PeerJ, 4
- Gerasimidis, Konstantinos, Bertz, Martin, Quince, Christopher, Brunner, Katja, Bruce, Alanna, Combet, Emilie, Calus, Szymon, Loman, Nick, Ijaz, Umer Zeeshan, 2016. The effect of DNA extraction methodology on gut microbiota research applications. BMC Research Notes, 9 (1)
- Rognes, Torbjørn, Flouri, Tomá?, Nichols, Ben, Quince, Christopher, Mahé, Frédéric, 2016. VSEARCH : a versatile open source tool for metagenomics. PeerJ, 4
- Haig, Sarah-Jane, Schirmer, Melanie, D'Amore, Rosalinda, Gibbs, Joseph, Davies, Robert L., Collins, Gavin, Quince, Christopher, 2015. Stable-isotope probing and metagenomics reveal predation by protozoa drives E. coli removal in slow sand filters. The ISME Journal, 9, pp. 797-808
- Quince, Christopher, Ijaz, Umer Zeeshan, Loman, Nick, Eren, A. Murat, Saulnier, Delphine, Russell, Julie, Haig, Sarah J., Calus, Szymon T., Quick, Joshua, Barclay, Andrew, Bertz, Martin, Blaut, Michael, Hansen, Richard, McGrogan, Paraic, Russell, Richard K., Edwards, Christine A., Gerasimidis, Konstantinos, 2015. Extensive modulation of the fecal metagenome in children with Crohn's Disease during exclusive enteral nutrition. The American Journal of Gastroenterology, 110 (12), pp. 1718-1729
- Chronáková, Alica, Schloter-Hai, Brigitte, Radl, Viviane, Endesfelder, David, Quince, Christopher, Elhottová, Dana, ?imek, Miloslav, Schloter, Michael, 2015. Correction : Response of archaeal and bacterial soil communities to changes associated with outdoor cattle overwintering. PLoS One, 10 (9)
- Moreno-Hagelsieb, Gabriel, Chronáková, Alica, Schloter-Hai, Brigitte, Radl, Viviane, Endesfelder, David, Quince, Christopher, Elhottová, Dana, ?imek, Miloslav, Schloter, Michael, 2015. Response of archaeal and bacterial soil communities to changes associated with outdoor cattle overwintering. PLoS One, 10 (8)
- Haig, Sarah-Jane, Quince, Christopher, Davies, Robert L., Dorea, Caetano C., Collins, Gavin, 2015. The relationship between microbial community evenness and function in slow sand filters. mBio, 6 (5), pp. e00729-15
- Mahé, Frédéric, Rognes, Torbjørn, Quince, Christopher, de Vargas, Colomban, Dunthorn, Micah, 2015. Swarm v2 : highly-scalable and high-resolution amplicon clustering. PeerJ, 3
- Eren, A. Murat, Esen, Özcan C., Quince, Christopher, Vineis, Joseph H., Morrison, Hilary G., Sogin, Mitchell L., Delmont, Tom O., 2015. Anvi'o: an advanced analysis and visualization platform for ?omics data. PeerJ, 3
- Schirmer, Melanie, Ijaz, Umer Z., D'Amore, Rosalinda, Hall, Neil, Sloan, William T., Quince, Christopher, 2015. Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform. Nucleic Acids Research, 43 (6), pp. e37-e37
- Fonseca, Vera G., Carvalho, Gary R., Nichols, Ben, Quince, Christopher, Johnson, Harriet F., Neill, Simon P., Lambshead, John D., Thomas, W. Kelley, Power, Deborah M., Creer, Simon, 2014. Metagenetic analysis of patterns of distribution and diversity of marine meiobenthic eukaryotes. Global Ecology and Biogeography, 23 (11), pp. 1293-1302
- Haig, Sarah-Jane, Quince, Christopher, Davies, Robert L., Dorea, Caetano C., Collins, Gavin, 2014. Replicating the microbial community and water quality performance of full-scale slow sand filters in laboratory-scale filters. Water Research, 61, pp. 141-151
- Widder, S., Besemer, K., Singer, G. A., Ceola, S., Bertuzzo, E., Quince, Christopher, Sloan, W. T., Rinaldo, A., Battin, T. J., 2014. Fluvial network organization imprints on microbial co-occurrence networks. Proceedings of the National Academy of Sciences of the United States of America, 111 (35), pp. 12799-12804
- Schirmer, M., Sloan, W. T., Quince, Christopher, 2014. Benchmarking of viral haplotype reconstruction programmes: an overview of the capacities and limitations of currently available programmes. Briefings in Bioinformatics, 15 (3), pp. 431-442
- Mahé, Frédéric, Rognes, Torbjørn, Quince, Christopher, de Vargas, Colomban, Dunthorn, Micah, 2014. Swarm : robust and fast clustering method for amplicon-based studies. PeerJ, 2
- Wilhelm, Linda, Besemer, Katharina, Fasching, Christina, Urich, Tim, Singer, Gabriel A., Quince, Christopher, Battin, Tom J., 2014. Rare but active taxa contribute to community dynamics of benthic biofilms in glacier-fed streams. Environmental Microbiology, 16 (8), pp. 2514-2524
- Gerasimidis, Konstantinos, Russell, Richard, Hansen, Richard, Quince, Christopher, Loman, Nick, Bertz, Martin, Hanske, Laura, Blaut, Michael, McGrogan, Paraic, Edwards, Christine A., 2014. Role of faecalibacterium prausnitzii in Crohn's Disease. Inflammatory Bowel Diseases, 20 (7), pp. E18-E19
- Singh, Brajesh K., Quince, Christopher, Macdonald, Catriona A., Khachane, Amit, Thomas, Nadine, Al-Soud, Waleed Abu, Sørensen, Søren J., He, Zhili, White, Duncan, Sinclair, Alex, Crooks, Bill, Zhou, Jizhong, Campbell, Colin D., 2014. Loss of microbial diversity in soils is coincident with reductions in some specialized functions. Environmental Microbiology, 16 (8), pp. 2408-2420
- Alneberg, Johannes, Bjarnason, Brynjar Smári, de Bruijn, Ino, Schirmer, Melanie, Quick, Joshua, Ijaz, Umer Z., Lahti, Leo, Loman, Nicholas J., Andersson, Anders F., Quince, Christopher, 2014. Binning metagenomic contigs by coverage and composition. Nature Methods, 11, pp. 1144-1146
- Loman, Nicholas J., Constantinidou, Chrystala, Christner, Martin, Rohde, Holger, Chan, Jacqueline, Quick, Joshua, Weir, Jacqueline C., Quince, Christopher, Smith, Geoffrey, Betley, Jason R., Aepfelbacher, Martin, Pallen, Mark J., 2013. A culture-independent sequence-based metagenomics approach to the investigation of an outbreak of Shiga-Toxigenic Escherichia coli O104:H4. JAMA: The Journal of the American Medical Association, 309 (14), pp. 1502-1510
- Jakobsson, Hedvig E., Abrahamsson, Thomas R., Jenmalm, Maria C., Harris, Keith, Quince, Christopher, Jernberg, Cecilia, Björkstén, Bengt, Engstrand, Lars, Andersson, Anders F., 2013. Decreased gut microbiota diversity, delayed Bacteroidetes colonisation and reduced Th1 responses in infants delivered by Caesarean section. Gut, 63 (4), pp. 559-566
- Quince, Christopher, Lundin, E. E., Andreasson, A. N., Greco, D., Rafter, J., Talley, N. J., Agreus, L., Andersson, A. F., Engstrand, L., D'Amato, M., 2013. The impact of Crohn's disease genes on healthy human gut microbiota : a pilot study. Gut, 62 (6), pp. 952-954
- Holmes, Ian, Harris, Keith, Quince, Christopher, 2012. Dirichlet multinomial mixtures : generative models for microbial metagenomics. PLoS One, 7 (2)
- Quince, Christopher, Lanzen, Anders, Davenport, Russell J., Turnbaugh, Peter J., 2011. Removing noise from pyrosequenced amplicons. BMC Bioinformatics, 12 (1)
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Gilbert, Jack A., Meyer, Folker, Antonopoulos, Dion, Balaji, Pavan, Brown, C. Titus, Brown, Christopher T., Desai, Narayan, Eisen, Jonathan A., Evers, Dirk, Field, Dawn, Feng, Wu, Huson, Daniel, Jansson, Janet, Knight, Rob, Knight, James, Kolker, Eugene, Konstantindis, Kostas, Kostka, Joel, Kyrpides, Nikos, Mackelprang, Rachel et al (Select to open full list), 2010.
- Jones, Oliver A. H., Lear, Gavin, Welji, Aalim M., Collins, Gavin, Quince, Christopher, 2016. Community metabolomics in environmental microbiology. In Beale, D.; Kouremenos, K.; Palombo, E. (eds.), Microbial Metabolomics, Cham, Springer, pp. 199-224
- Zhou, Zhemin, Luhmann, Nina, Alikhan, Nabil-Fareed, Quince, Christopher, Achtman, Mark, 2018. Accurate reconstruction of microbial strains from metagenomic sequencing using representative reference genomes. RECOMB 2018 : International Conference on Research in Computational Molecular Biology, Paris, 21-24 Apr 2018, Published in Lecture Notes in Computer Science, pp. 225-240
- Castelino, M., Tutino, M., Moat, J., Ijaz, U. Z., Parslew, R., Al-Sharqi, A., Warren, R. B., Quince, Christopher, Ho, P., Upton, M., Eyre, S., Barton, A., 2017. AB0115C Comparison of the bacterial stool microbiota in established psoriatic arthritis (PSA) and psoriasis (PSC) - exploratory analysis of pilot data. Annual European Congress of Rheumatology, 14?17 June 2017, Published in Annals of the Rheumatic Diseases, pp. 1087-1087
- Svolos, V., Hansen, R., Ijaz, U. Z., Quince, Christopher, Watson, D., Alghamdi, A., Brejnrod, A., Ansalone, C., Milling, S., Gaya, D., Russell, R., Gerasimidis, K., 2017. Dietary manipulation of the healthy human and colitic murine gut microbiome by CD-TREAT diet and exclusive enteral nutrition; a proof of concept study. 12th Congress of ECCO, Barcelona, Spain, 15-18 Feb 2017, Published in Journal of Crohn's and Colitis, pp. S29-S30
- Svolos, V., Hansen, R., Ijaz, U. Z., Quince, Christopher, Watson, D., Alghamdi, A., Brejnrod, A., Ansalone, C., Klopfleisch, R., Milling, S., Gaya, D. R., Russell, R. K., Gerasimidis, K., 2017. Dietary manipulation of the healthy human and colitic rat gut microbiome by cd-treat diet and exclusive enteral nutrition; a proof of concept study. British Society of Gastroenterology, Annual General Meeting, 19?22 June 2017, Published in Gut
- Svolos, V., Hansen, R., Hughes, K., Ijaz, U. Z., Quince, Christopher, Gaya, D., Russell, R., Gersimidis, K., 2016. OP018. 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, pp. S14.2-S15
- Ocejo, M., Oporto, B., Lanzen, A., Quince, Christopher, Hurtado, A., 2016. 16S rRNA gene-based characterization of the chicken caecal microbiome across age. 4th World Congress on Targeting Microbiota 2016 (International Society of Microbiota), Paris, 17-19 Oct 2016, Published in Journal of International Society of Microbiota
- Sagar, Nidhi M., Kay, Gemma L., O'Connell, N., Nwokolo, Chuka U., Bardhan, Karna Dev, Quince, Christopher, Pallen, Mark J., Arasaradnam, Ramesh P., 2016. PWE-061 Dysbiosis in patients with bile acid diarrhoea (BAD) demonstrated using 16S RNA gene sequencing. British Society of Gastroenterology, Annual General Meeting, 20?23 Jun 2016, Published in Gut, pp. A168-A168
- Zhou, Zhemin, Lundstrøm, Inge, Dien, Alicia Tran, Duchêne, Sebastián, Alikhan, Nabil-Fareed, Sergeant, Martin J., Langridge, Gemma, Fotakis, Anna K., Nair, Satheesh, Stenøien, Hans K., Hamre, Stian S., Casjens, Sherwood, Quince, Christopher, Christophersen, Axel, Thomson, Nicholas R., Weill, François-Xavier, Ho, Simon, Gilbert, M. Thomas P., Achtman, Mark, 2018. Data for Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica. Archive package of additional figures, tables and data. Warwick Medical School, University of Warwick
- Zhou, Zhemin, Lundstrøm, Inge, Dien, Alicia Tran, Duchêne, Sebastián, Alikhan, Nabil-Fareed, Sergeant, Martin J., Langridge, Gemma, Fotakis, Anna K., Nair, Satheesh, Stenøien, Hans K., Hamre, Stian S., Casjens, Sherwood, Quince, Christopher, Christophersen, Axel, Thomson, Nicholas R., Weill, François-Xavier, Ho, Simon, Gilbert, M. Thomas P., Achtman, Mark, 2018. Data for Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica: ancestral reconstruction 1. Warwick Medical School, University of Warwick
- Zhou, Zhemin, Lundstrøm, Inge, Dien, Alicia Tran, Duchêne, Sebastián, Alikhan, Nabil-Fareed, Sergeant, Martin J., Langridge, Gemma, Fotakis, Anna K., Nair, Satheesh, Stenøien, Hans K., Hamre, Stian S., Casjens, Sherwood, Quince, Christopher, Christophersen, Axel, Thomson, Nicholas R., Weill, François-Xavier, Ho, Simon, Gilbert, M. Thomas P., Achtman, Mark, 2018. Data for Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica: ancestral reconstruction 2. Warwick Medical School, University of Warwick
- Zhou, Zhemin, Lundstrøm, Inge, Dien, Alicia Tran, Duchêne, Sebastián, Alikhan, Nabil-Fareed, Sergeant, Martin J., Langridge, Gemma, Fotakis, Anna K., Nair, Satheesh, Stenøien, Hans K., Hamre, Stian S., Casjens, Sherwood, Quince, Christopher, Christophersen, Axel, Thomson, Nicholas R., Weill, François-Xavier, Ho, Simon, Gilbert, M. Thomas P., Achtman, Mark, 2018. Data for Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica: Concoct 1. Warwick Medical School, University of Warwick
- Zhou, Zhemin, Lundstrøm, Inge, Dien, Alicia Tran, Duchêne, Sebastián, Alikhan, Nabil-Fareed, Sergeant, Martin J., Langridge, Gemma, Fotakis, Anna K., Nair, Satheesh, Stenøien, Hans K., Hamre, Stian S., Casjens, Sherwood, Quince, Christopher, Christophersen, Axel, Thomson, Nicholas R., Weill, François-Xavier, Ho, Simon, Gilbert, M. Thomas P., Achtman, Mark, 2018. Data for Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica: Concoct 2. Warwick Medical School, University of Warwick
- Zhou, Zhemin, Lundstrøm, Inge, Dien, Alicia Tran, Duchêne, Sebastián, Alikhan, Nabil-Fareed, Sergeant, Martin J., Langridge, Gemma, Fotakis, Anna K., Nair, Satheesh, Stenøien, Hans K., Hamre, Stian S., Casjens, Sherwood, Quince, Christopher, Christophersen, Axel, Thomson, Nicholas R., Weill, François-Xavier, Ho, Simon, Gilbert, M. Thomas P., Achtman, Mark, 2018. Data for Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica: Concoct 3. Warwick Medical School, University of Warwick
- Zhou, Zhemin, Lundstrøm, Inge, Dien, Alicia Tran, Duchêne, Sebastián, Alikhan, Nabil-Fareed, Sergeant, Martin J., Langridge, Gemma, Fotakis, Anna K., Nair, Satheesh, Stenøien, Hans K., Hamre, Stian S., Casjens, Sherwood, Quince, Christopher, Christophersen, Axel, Thomson, Nicholas R., Weill, François-Xavier, Ho, Simon, Gilbert, M. Thomas P., Achtman, Mark, 2018. Data for Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica: Concoct 4. Warwick Medical School, University of Warwick
- Zhou, Zhemin, Lundstrøm, Inge, Dien, Alicia Tran, Duchêne, Sebastián, Alikhan, Nabil-Fareed, Sergeant, Martin J., Langridge, Gemma, Fotakis, Anna K., Nair, Satheesh, Stenøien, Hans K., Hamre, Stian S., Casjens, Sherwood, Quince, Christopher, Christophersen, Axel, Thomson, Nicholas R., Weill, François-Xavier, Ho, Simon, Gilbert, M. Thomas P., Achtman, Mark, 2018. Data for Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica: Concoct 5. Warwick Medical School, University of Warwick
- Zhou, Zhemin, Lundstrøm, Inge, Dien, Alicia Tran, Duchêne, Sebastián, Alikhan, Nabil-Fareed, Sergeant, Martin J., Langridge, Gemma, Fotakis, Anna K., Nair, Satheesh, Stenøien, Hans K., Hamre, Stian S., Casjens, Sherwood, Quince, Christopher, Christophersen, Axel, Thomson, Nicholas R., Weill, François-Xavier, Ho, Simon, Gilbert, M. Thomas P., Achtman, Mark, 2018. Data for Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica: Concoct 6. Warwick Medical School, University of Warwick
- Zhou, Zhemin, Lundstrøm, Inge, Dien, Alicia Tran, Duchêne, Sebastián, Alikhan, Nabil-Fareed, Sergeant, Martin J., Langridge, Gemma, Fotakis, Anna K., Nair, Satheesh, Stenøien, Hans K., Hamre, Stian S., Casjens, Sherwood, Quince, Christopher, Christophersen, Axel, Thomson, Nicholas R., Weill, François-Xavier, Ho, Simon, Gilbert, M. Thomas P., Achtman, Mark, 2018. Data for Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica: Concoct 7. Warwick Medical School, University of Warwick
- Zhou, Zhemin, Lundstrøm, Inge, Dien, Alicia Tran, Duchêne, Sebastián, Alikhan, Nabil-Fareed, Sergeant, Martin J., Langridge, Gemma, Fotakis, Anna K., Nair, Satheesh, Stenøien, Hans K., Hamre, Stian S., Casjens, Sherwood, Quince, Christopher, Christophersen, Axel, Thomson, Nicholas R., Weill, François-Xavier, Ho, Simon, Gilbert, M. Thomas P., Achtman, Mark, 2018. Data for Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica: Concoct 8. Warwick Medical School, University of Warwick
- Zhou, Zhemin, Lundstrøm, Inge, Dien, Alicia Tran, Duchêne, Sebastián, Alikhan, Nabil-Fareed, Sergeant, Martin J., Langridge, Gemma, Fotakis, Anna K., Nair, Satheesh, Stenøien, Hans K., Hamre, Stian S., Casjens, Sherwood, Quince, Christopher, Christophersen, Axel, Thomson, Nicholas R., Weill, François-Xavier, Ho, Simon, Gilbert, M. Thomas P., Achtman, Mark, 2018. Data for Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica: date estimation 1. Warwick Medical School, University of Warwick
- Zhou, Zhemin, Lundstrøm, Inge, Dien, Alicia Tran, Duchêne, Sebastián, Alikhan, Nabil-Fareed, Sergeant, Martin J., Langridge, Gemma, Fotakis, Anna K., Nair, Satheesh, Stenøien, Hans K., Hamre, Stian S., Casjens, Sherwood, Quince, Christopher, Christophersen, Axel, Thomson, Nicholas R., Weill, François-Xavier, Ho, Simon, Gilbert, M. Thomas P., Achtman, Mark, 2018. Data for Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica: date estimation 2. Warwick Medical School, University of Warwick
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- Zhou, Zhemin, Lundstrøm, Inge, Dien, Alicia Tran, Duchêne, Sebastián, Alikhan, Nabil-Fareed, Sergeant, Martin J., Langridge, Gemma, Fotakis, Anna K., Nair, Satheesh, Stenøien, Hans K., Hamre, Stian S., Casjens, Sherwood, Quince, Christopher, Christophersen, Axel, Thomson, Nicholas R., Weill, François-Xavier, Ho, Simon, Gilbert, M. Thomas P., Achtman, Mark, 2018. Data for Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica: ParaC Pan-genome 5. Warwick Medical School, University of Warwick
- Zhou, Zhemin, Lundstrøm, Inge, Dien, Alicia Tran, Duchêne, Sebastián, Alikhan, Nabil-Fareed, Sergeant, Martin J., Langridge, Gemma, Fotakis, Anna K., Nair, Satheesh, Stenøien, Hans K., Hamre, Stian S., Casjens, Sherwood, Quince, Christopher, Christophersen, Axel, Thomson, Nicholas R., Weill, François-Xavier, Ho, Simon, Gilbert, M. Thomas P., Achtman, Mark, 2018. Data for Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica: ParaC Pan-genome 7. Warwick Medical School, University of Warwick
- Zhou, Zhemin, Lundstrøm, Inge, Dien, Alicia Tran, Duchêne, Sebastián, Alikhan, Nabil-Fareed, Sergeant, Martin J., Langridge, Gemma, Fotakis, Anna K., Nair, Satheesh, Stenøien, Hans K., Hamre, Stian S., Casjens, Sherwood, Quince, Christopher, Christophersen, Axel, Thomson, Nicholas R., Weill, François-Xavier, Ho, Simon, Gilbert, M. Thomas P., Achtman, Mark, 2018. Data for Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica: ParaC Pan-genome 8. Warwick Medical School, University of Warwick
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- Zhou, Zhemin, Lundstrøm, Inge, Dien, Alicia Tran, Duchêne, Sebastián, Alikhan, Nabil-Fareed, Sergeant, Martin J., Langridge, Gemma, Fotakis, Anna K., Nair, Satheesh, Stenøien, Hans K., Hamre, Stian S., Casjens, Sherwood, Quince, Christopher, Christophersen, Axel, Thomson, Nicholas R., Weill, François-Xavier, Ho, Simon, Gilbert, M. Thomas P., Achtman, Mark, 2018. Data for Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica: ParaC genome SNPs 2. Warwick Medical School, University of Warwick
- Zhou, Zhemin, Lundstrøm, Inge, Dien, Alicia Tran, Duchêne, Sebastián, Alikhan, Nabil-Fareed, Sergeant, Martin J., Langridge, Gemma, Fotakis, Anna K., Nair, Satheesh, Stenøien, Hans K., Hamre, Stian S., Casjens, Sherwood, Quince, Christopher, Christophersen, Axel, Thomson, Nicholas R., Weill, François-Xavier, Ho, Simon, Gilbert, M. Thomas P., Achtman, Mark, 2018. Data for Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica: ParaC genome SNPs 3. Warwick Medical School, University of Warwick
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Title | Funder | Award start | Award end |
---|---|---|---|
CLIMB 2 | MRC | 01 Apr 2020 | 31 Mar 2025 |
NIHR HPRU in Gastrointestinal Infections | National Institute for Health Research (DoH) | 01 Apr 2020 | 31 Mar 2025 |
HPRU in Genomics and Enabling at University of Warwick | National Institute for Health Research (DoH) | 01 Apr 2020 | 31 Mar 2025 |
Resolving the fate and studying the impact of pharmaceutical wastes on the environment and local community of a pharmaceutical manufacturing hub | NERC | 01 Oct 2020 | 01 Apr 2024 |
Unravelling the diversity and function of the fine root endophyte | NERC | 02 Sep 2019 | 31 Aug 2023 |
Health Data Research UK | Health Data Research UK | 02 Apr 2018 | 01 Apr 2023 |
BBSRC BBR - EBI Metagenomics - enabling the reconstruction of microbial populations (Warwick Component) | BBSRC | 03 Sep 2018 | 02 Sep 2021 |
LinkPI: Linking Phenotype function with Identity: a novel integrated single-cell technology and metagenomics approach - Nerc Global Partnership seedcorn fund | NERC | 01 Nov 2018 | 31 Aug 2021 |
Wellcome Trust Investigator Award - Deep evolutionary history of bacterial pathogens | Wellcome Trust | 01 Sep 2016 | 31 Aug 2021 |
The clinical effectiveness of CD-TREAT and its microbial mechanisms of action in patients with active Crohns disease | Leona M. and Harry B. Helmsley Charitable Trust | 15 Mar 2019 | 14 May 2021 |
Strain resolved metagenomics for medical microbiology | MRC | 01 Oct 2019 | 15 Apr 2021 |
New approaches to resolving community metaproteomes: ComProt | NERC | 01 Jan 2019 | 31 Dec 2019 |
MRC-KHIDI UK-KOREA PARTNERING AWARDS -Exploring the relationship between antibiotic persistence and antibiotic resistance in exposed bacteria in environmental locations | MRC | 31 May 2018 | 30 Apr 2019 |
Programme Integration Group (PIG) - Using next generation sequencing to reveal human impact on aquatic reservoirs of antibiotic resistant bacteria at the catchment scale | NERC | 01 Jul 2017 | 31 Dec 2018 |
MRC AMR Development Grant application - AMREPAK: Novel inter-disciplinary approaches for identifying and tackling the spread of AntiMicrobial Resistance through Environmental pathways in PAKistan | MRC | 01 Oct 2017 | 31 Mar 2018 |
Predictive Temporal Analysis of Functional Microbiomes in UK's Anerobic Digestion Reactors | BBSRC | 01 Jul 2016 | 07 Mar 2018 |
Newton fund via FIOCRUZ, Brazil: Leishmaniasis in the Brazilian Amazon: the role of accessory microbiota in disease progression, pathobiology and immunity | RCUK | 01 Jan 2015 | 31 Mar 2017 |