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Number of items: 96.

2019

Svolos, Vaios, Hansen, Richard, Nichols, Ben, Quince, Christopher, Ijaz, Umer Z., Papadopoulou, Rodanthi T., Edwards, Christine A., Watson, David, Alghamdi, Adel, Brejnrod, Asker et al.

(2019) Treatment of active Crohn’s disease with an ordinary food-based diet that replicates exclusive enteral nutrition. Gastroenterology, 156 (5). 1354-1367.e6. doi:10.1053/j.gastro.2018.12.002

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 and Segata, Nicola (2019) Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle. CELL, 176 (3). 649-662.e20. doi:10.1016/j.cell.2019.01.001

2018

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. and 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. doi:10.1016/j.cub.2018.05.058

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. and 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. [Dataset]

Zhou, Zhemin, Luhmann, Nina, Alikhan, Nabil-Fareed, Quince, Christopher and Achtman, Mark (2018) Accurate reconstruction of microbial strains from metagenomic sequencing using representative reference genomes. In: RECOMB 2018 : International Conference on Research in Computational Molecular Biology, Paris, 21-24 Apr 2018. Published in: Lecture Notes in Computer Science, 10812 pp. 225-240. ISBN 9783319899299. ISSN 0302-9743. doi:10.1007/978-3-319-89929-9_15

Joyce, Aoife, Ijaz, Umer Z., Nzeteu, Corine, Vaughan, Aoife, Shirran, Sally L., Botting, Catherine H., Quince, Christopher, O’Flaherty, Vincent and Abram, Florence (2018) Linking Microbial Community Structure and Function During the Acidified Anaerobic Digestion of Grass. Frontiers in Microbiology, 9 . 540. doi:10.3389/fmicb.2018.00540

Heidrich, E. S., Dolfing, J., Wade, M. J., Sloan, W. T., Quince, C. and Curtis, T. P. (2018) Temperature, inocula and substrate : contrasting electroactive consortia, diversity and performance in microbial fuel cells. Bioelectrochemistry, 119 . pp. 43-50. doi:10.1016/j.bioelechem.2017.07.006

2017

Zhou, Zhemin, Luhmann, Nina, Alikhan, Nabil-Fareed, Quince, Christopher and Achtman, Mark (2017) Accurate reconstruction of microbial strains using representative reference genomes. Working Paper. BioRxiv: Cold Spring Harbour.

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 et al.

(2017) A communal catalogue reveals Earth’s multiscale microbial diversity. Nature . doi:10.1038/nature24621

Sczyrba, Alexander, Hofmann, Peter, Belmann, Peter, Koslicki, David, Janssen, Stefan, Dröge, Johannes, Gregor, Ivan, Majda, Stephan, Fiedler, Jessika, Dahms, Eik et al.

(2017) Critical assessment of metagenome interpretation - a benchmark of metagenomics software. Nature Methods, 14 (11). pp. 1063-1071. doi:10.1038/nmeth.4458

Quince, Christopher , Delmont, Tom O., Raguideau, Sébastien, Alneberg, Johannes, Darling, Aaron E., Collins, Gavin and Eren, A. Murat (2017) DESMAN : a new tool for de novo extraction of strains from metagenomes. Genome Biology, 18 (1). doi:10.1186/s13059-017-1309-9

Quince, Christopher, Walker, Alan W., Simpson, Jared T., Loman, Nicholas J. and Segata, Nicola (2017) Shotgun metagenomics, from sampling to analysis. Nature Biotechnology, 35 (9). pp. 833-844. doi:10.1038/nbt.3935

Fonseca, V. G., Sinniger, F., Gaspar, J. M., Quince, C., Creer, S., Power, Deborah M., Peck, Lloyd S. and Clark, Melody S. (2017) Revealing higher than expected meiofaunal diversity in Antarctic sediments : a metabarcoding approach. Scientific Reports, 7 (1). doi:10.1038/s41598-017-06687-x

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. and Gerasimidis, K. (2017) AODTH-007 Dietary manipulation of the healthy human and colitic rat gut microbiome by cd-treat diet and exclusive enteral nutrition; a proof of concept study. In: British Society of Gastroenterology, Annual General Meeting, 19–22 June 2017. Published in: Gut, 66 (Suppl 2). A202. ISBN 0017-5749.

Sczyrba, Alexander, Hofmann, Peter, Belmann, Peter, Koslicki, David, Janssen, Stefan, Droege, Johannes, Gregor, Ivan, Majda, Stephan, Fiedler, Jessika, Dahms, Eik et al.

(2017) Critical assessment of metagenome interpretation − a benchmark of computational metagenomics software. Working Paper. bioRxiv: Cold Spring Harbour Laboratory. (Unpublished)

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. and Barton, A. (2017) AB0115C Comparison of the bacterial stool microbiota in established psoriatic arthritis (PSA) and psoriasis (PSC) - exploratory analysis of pilot data. In: Annual European Congress of Rheumatology, 14–17 June 2017. Published in: Annals of the Rheumatic Diseases, 76 (Suppl 2). p. 1087. ISSN 0003-4967.

Connelly, Stephanie, Shin, Seung G., Dillon, Robert J., Ijaz, Umer Z., Quince, Christopher, Sloan, William T. and 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 . 664. doi:10.3389/fmicb.2017.00664

Ijaz, Ali Z., Jeffries, Thomas, Quince, Christopher, Hamonts, Kelly and Singh, Brajesh (2017) TaxaSE : exploiting evolutionary conservation within 16S rDNA sequences for enhanced taxonomic annotation. Working Paper. PeerJ Preprints.

Harris, Keith, Parsons, Todd L., Ijaz, Umer Z., Lahti, Leo, Holmes, Ian and 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. doi:10.1109/JPROC.2015.2428213

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. and 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). e0172605. doi:10.1371/journal.pone.0172605

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. and Achtman, Mark (2017) Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica. Working Paper. BioRxiv: Cold Spring Harbour.

Svolos, V., Hansen, R., Ijaz, U. Z., Quince, Christopher, Watson, D., Alghamdi, A., Brejnrod, A., Ansalone, C., Milling, S., Gaya, D., Russell, R. and Gerasimidis, K. (2017) DOP008 Dietary manipulation of the healthy human and colitic murine gut microbiome by CD-TREAT diet and exclusive enteral nutrition; a proof of concept study. In: 12th Congress of ECCO, Barcelona, Spain, 15-18 Feb 2017. Published in: Journal of Crohn's and Colitis, 11 (Suppl_1). S29-S30. ISSN 1873-9946. doi:10.1093/ecco-jcc/jjx002.045

2016

Sinclair, Lucas, Ijaz, Umer Z., Jensen, Lars Juhl, Coolen, Marco J.L., Gubry-Rangin, Cecile, Chroňáková, Alica, Oulas, Anastasis, Pavloudi, Christina, Schnetzer, Julia, Weimann, Aaron, Ijaz, Ali, Eiler, Alexander, Quince, Christopher and Pafilis, Evangelos (2016) Seqenv : linking sequences to environments through text mining. PeerJ, 4 . e2690. doi:10.7717/peerj.2690

Widder, Stefanie, Allen, Rosalind, Pfeiffer, Thomas, Curtis, Thomas P., Wiuf, Carsten, Sloan, William T., Cordero, Otto X., Brown, Sam P., Momeni, Babak, Shou, Wenying et al.

(2016) Challenges in microbial ecology : building predictive understanding of community function and dynamics. The ISME Journal, 2016 (10). pp. 2557-2568. doi:10.1038/ismej.2016.45

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 and 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. doi:10.1111/mec.13844

Rognes, Torbjørn, Flouri, Tomáš, Nichols, Ben, Quince, Christopher and Mahé, Frédéric (2016) VSEARCH : a versatile open source tool for metagenomics. PeerJ, 4 . e2584. doi:10.7717/peerj.2584

Cho, Si-Kyung, Kim, Dong-Hoon, Quince, Christopher, Im, Wan-Taek, Oh, Sae-Eun and 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. doi:10.1016/j.ultsonch.2016.03.010

Quince, Christopher, Connelly, Stephanie, Raguideau, Sebastien, Alneberg, Johannes, Shin, Seung Gu, Collins, Gavin and Eren, A. Murat (2016) De novo extraction of microbial strains from metagenomes reveals intra-species niche partitioning. Working Paper. bioRxiv: Cold Spring Harbour Laboratory. (Unpublished)

Nichols, Ben and Quince, Christopher (2016) Simera : modelling the PCR process to simulate realistic chimera formation. Working Paper. bioRxiv: Cold Spring Harbour Laboratory. (Unpublished)

Sagar, Nidhi M., Kay, Gemma L., O’Connell, N., Nwokolo, Chuka U., Bardhan, Karna Dev, Quince, Christopher, Pallen, Mark J. and Arasaradnam, Ramesh P. (2016) PWE-061 Dysbiosis in patients with bile acid diarrhoea (BAD) demonstrated using 16S RNA gene sequencing. In: British Society of Gastroenterology, Annual General Meeting, 20–23 Jun 2016. Published in: Gut, 65 (Supplement 1). A168-A168. ISSN 0017-5749. doi:10.1136/gutjnl-2016-312388.307

Gregor, Ivan, Dröge, Johannes, Schirmer, Melanie, Quince, Christopher and McHardy, Alice C. (2016) PhyloPythiaS+ : a self-training method for the rapid reconstruction of low-ranking taxonomic bins from metagenomes. PeerJ, 4 . e1603. doi:10.7717/peerj.1603

Gerasimidis, Konstantinos, Bertz, Martin, Quince, Christopher, Brunner, Katja, Bruce, Alanna, Combet, Emilie, Calus, Szymon, Loman, Nick and Ijaz, Umer Zeeshan (2016) The effect of DNA extraction methodology on gut microbiota research applications. BMC Research Notes, 9 (1). 365. doi:10.1186/s13104-016-2171-7

Gerasimidis, Konstantinos, Ijaz, Umer Z., Edwards, Christine, Russell, Richard K., Quince, Christopher and Hansen, Richard (2016) Response to Kaakoush et al. The American Journal of Gastroenterology, 111 (7). pp. 1033-1034. doi:10.1038/ajg.2016.169

Schirmer, Melanie, D’Amore, Rosalinda, Ijaz, Umer Z., Hall, Neil and Quince, Christopher (2016) Illumina error profiles : resolving fine-scale variation in metagenomic sequencing data. BMC Bioinformatics, 17 (1). pp. 1-15. 125. doi:10.1186/s12859-016-0976-y

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. and 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. doi:10.1111/1751-7915.12334

Haig, Sarah-Jane, Gauchotte-Lindsay, Caroline, Collins, Gavin and 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. doi:10.1021/acs.est.5b05027

Svolos, V., Hansen, R., Hughes, K., Ijaz, U. Z., Quince, Christopher, Gaya, D., Russell, R. and 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. In: UNSPECIFIED. Published in: Journal of Crohn's and Colitis, 10 (supplement 1). S14.2-S15. ISSN 1873-9946. doi:10.1093/ecco-jcc/jjw019.017

D’Amore, Rosalinda, Ijaz, Umer Zeeshan, Schirmer, Melanie, Kenny, John G., Gregory, Richard, Darby, Alistair C., Shakya, Migun, Podar, Mircea, Quince, Christopher and Hall, Neil (2016) A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling. BMC Genomics, 17 (1). doi:10.1186/s12864-015-2194-9

Ocejo, M., Oporto, B., Lanzen, A., Quince, Christopher and Hurtado, A. (2016) 16S rRNA gene-based characterization of the chicken caecal microbiome across age. In: 4th World Congress on Targeting Microbiota 2016 (International Society of Microbiota), , Paris, 17-19 Oct 2016. Published in: Journal of International Society of Microbiota , 3 (1).

Jones, Oliver A. H., Lear, Gavin, Welji, Aalim M., Collins, Gavin and Quince, Christopher (2016) Community metabolomics in environmental microbiology. In: Beale, D. and Kouremenos, K. and Palombo, E., (eds.) Microbial Metabolomics. Cham: Springer, pp. 199-224. ISBN 9783319463247

Bowen, Emma J., Parsons, Todd L., Curtis, Thomas P., Plotkin, Joshua B. and Quince, Christopher (2016) Integrating theory and experiment to explain the breakdown of population synchrony in a complex microbial community. Working Paper. Coventry, UK : University of Warwick, Warwick Medical School. (Unpublished)

Oton, Eduard Vico, Quince, Christopher, Nicol, Graeme W., Prosser, James I. and Gubry-Rangin, Cécile (2016) Phylogenetic congruence and ecological coherence in terrestrial Thaumarchaeota. The ISME Journal, 10 (1). pp. 85-96. doi:10.1038/ismej.2015.101

2015

Mahé, Frédéric, Rognes, Torbjørn, Quince, Christopher, de Vargas, Colomban and Dunthorn, Micah (2015) Swarm v2 : highly-scalable and high-resolution amplicon clustering. PeerJ, 3 . e1420. doi:10.7717/peerj.1420

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. and 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. doi:10.1038/ajg.2015.357

Haig, Sarah-Jane, Quince, Christopher, Davies, Robert L., Dorea, Caetano C. and Collins, Gavin (2015) The relationship between microbial community evenness and function in slow sand filters. mBio, 6 (5). e00729-15. doi:10.1128/mBio.00729-15

Eren, A. Murat, Esen, Özcan C., Quince, Christopher, Vineis, Joseph H., Morrison, Hilary G., Sogin, Mitchell L. and Delmont, Tom O. (2015) Anvi’o: an advanced analysis and visualization platform for ‘omics data. PeerJ, 3 . e1319. doi:10.7717/peerj.1319

Chroňáková, Alica, Schloter-Hai, Brigitte, Radl, Viviane, Endesfelder, David, Quince, Christopher, Elhottová, Dana, Šimek, Miloslav and Schloter, Michael (2015) Correction : Response of archaeal and bacterial soil communities to changes associated with outdoor cattle overwintering. PLoS One, 10 (9). e0137815. doi:10.1371/journal.pone.0137815

Moreno-Hagelsieb, Gabriel, Chroňáková, Alica, Schloter-Hai, Brigitte, Radl, Viviane, Endesfelder, David, Quince, Christopher, Elhottová, Dana, Šimek, Miloslav and Schloter, Michael (2015) Response of archaeal and bacterial soil communities to changes associated with outdoor cattle overwintering. PLoS One, 10 (8). e0135627. doi:10.1371/journal.pone.0135627

Schirmer, Melanie, Ijaz, Umer Z., D'Amore, Rosalinda, Hall, Neil, Sloan, William T. and Quince, Christopher (2015) Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform. Nucleic Acids Research, 43 (6). e37-e37. doi:10.1093/nar/gku1341

Haig, Sarah-Jane, Schirmer, Melanie, D'Amore, Rosalinda, Gibbs, Joseph, Davies, Robert L., Collins, Gavin and 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. doi:10.1038/ismej.2014.175

2014

Schirmer, M., Sloan, W. T. and 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. doi:10.1093/bib/bbs081

Mahé, Frédéric, Rognes, Torbjørn, Quince, Christopher, de Vargas, Colomban and Dunthorn, Micah (2014) Swarm : robust and fast clustering method for amplicon-based studies. PeerJ, 2 . e593. doi:10.7717/peerj.593

Haig, Sarah-Jane, Quince, Christopher, Davies, Robert L., Dorea, Caetano C. and 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. doi:10.1016/j.watres.2014.05.008

Widder, S., Besemer, K., Singer, G. A., Ceola, S., Bertuzzo, E., Quince, Christopher, Sloan, W. T., Rinaldo, A. and 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. doi:10.1073/pnas.1411723111

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 and 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. doi:10.1111/1462-2920.12353

Wilhelm, Linda, Besemer, Katharina, Fasching, Christina, Urich, Tim, Singer, Gabriel A., Quince, Christopher and 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. doi:10.1111/1462-2920.12392

Alneberg, Johannes, Bjarnason, Brynjar Smári, de Bruijn, Ino, Schirmer, Melanie, Quick, Joshua, Ijaz, Umer Z., Lahti, Leo, Loman, Nicholas J., Andersson, Anders F. and Quince, Christopher (2014) Binning metagenomic contigs by coverage and composition. Nature Methods, Volume 11 . pp. 1144-1146. doi:10.1038/nmeth.3103

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. and Creer, Simon (2014) Metagenetic analysis of patterns of distribution and diversity of marine meiobenthic eukaryotes. Global Ecology and Biogeography, 23 (11). pp. 1293-1302. doi:10.1111/geb.12223

Gerasimidis, Konstantinos, Russell, Richard, Hansen, Richard, Quince, Christopher, Loman, Nick, Bertz, Martin, Hanske, Laura, Blaut, Michael, McGrogan, Paraic and Edwards, Christine A. (2014) Role of faecalibacterium prausnitzii in Crohnʼs Disease. Inflammatory Bowel Diseases, 20 (7). E18-E19. doi:10.1097/MIB.0000000000000079

2013

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 and 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, Volume 309 (Number 14). pp. 1502-1510. doi:10.1001/jama.2013.3231

Jakobsson, Hedvig E., Abrahamsson, Thomas R., Jenmalm, Maria C., Harris, Keith, Quince, Christopher , Jernberg, Cecilia, Björkstén, Bengt, Engstrand, Lars and 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. doi:10.1136/gutjnl-2012-303249

Quince, Christopher , Lundin, E. E., Andreasson, A. N., Greco, D., Rafter, J., Talley, N. J., Agreus, L., Andersson, A. F., Engstrand, L. and D'Amato, M. (2013) The impact of Crohn's disease genes on healthy human gut microbiota : a pilot study. Gut, Volume 62 (Number 6). pp. 952-954. doi:10.1136/gutjnl-2012-304214

2012

Holmes, Ian, Harris, Keith and Quince, Christopher (2012) Dirichlet multinomial mixtures : generative models for microbial metagenomics. PLoS One, Volume 7 (Number 2). Article number e30126. doi:10.1371/journal.pone.0030126

2011

Quince, Christopher, Lanzen, Anders, Davenport, Russell J. and Turnbaugh, Peter J. (2011) Removing noise from pyrosequenced amplicons. BMC Bioinformatics, Volume 12 (Number 1). Article number 38. doi:10.1186/1471-2105-12-38

2010

Gilbert, Jack A., Meyer, Folker, Antonopoulos, Dion, Balaji, Pavan, Brown, C. Titus, Brown, Christopher T., Desai, Narayan, Eisen, Jonathan A., Evers, Dirk, Field, Dawn et al.

(2010) Meeting Report: The Terabase Metagenomics Workshop and the Vision of an Earth Microbiome Project. Standards in Genomic Sciences, 3 (3). pp. 243-248. doi:10.4056/sigs.1433550

2009

Quince, Christopher, Lanzén, Anders, Curtis, Thomas P., Davenport, Russell J., Hall, Neil, Head, Ian M., Read, L Fiona and Sloan, William T. (2009) Accurate determination of microbial diversity from 454 pyrosequencing data. Nature Methods, 6 (9). pp. 639-641. doi:10.1038/nmeth.1361

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