Christopher Quince

Job Title

Associate Professor (Research Focussed)

Department

WMS - Biomedical Sciences

Phone

024 7652 2317

C.Quince@warwick.ac.uk

Research Interests

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/).

Biography

View Christopher's publications on Google Scholar.

Mahé, Frédéric, Czech, Lucas, Stamatakis, Alexandros, Quince, Christopher, de Vargas, Colomban, Dunthorn, Micah, Rognes, Torbjørn, 2022. Swarm v3 : towards tera-scale amplicon clustering. Bioinformatics, 38 (1), pp. 267-269
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
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)
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)
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
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.

All authors for Treatment of active Crohn's disease with an ordinary food-based diet that replicates exclusive enteral nutrition

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., Gerasimidis, Konstantinos

Treatment of active Crohn's disease with an ordinary food-based diet that replicates exclusive enteral nutrition. Gastroenterology, 156 (5), pp. 1354-1367.e6
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
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
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
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
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
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
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.

All authors for Critical assessment of metagenome interpretation - a benchmark of metagenomics software

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, Chikhi, Rayan, Nagarajan, Niranjan, Quince, Christopher, Meyer, Fernando, Balvociute, Monika, Hansen, Lars Hestbjerg, Sørensen, Søren J, Chia, Burton K H, Denis, Bertrand, Froula, Jeff L, Wang, Zhong, Egan, Robert, Don Kang, Dongwan, Cook, Jeffrey J, Deltel, Charles, Beckstette, Michael, Lemaitre, Claire, Peterlongo, Pierre, Rizk, Guillaume, Lavenier, Dominique, Wu, Yu-Wei, Singer, Steven W, Jain, Chirag, Strous, Marc, Klingenberg, Heiner, Meinicke, Peter, Barton, Michael D, Lingner, Thomas, Lin, Hsin-Hung, Liao, Yu-Chieh, Silva, Genivaldo Gueiros Z, Cuevas, Daniel A, Edwards, Robert A, Saha, Surya, Piro, Vitor C, Renard, Bernhard Y, Pop, Mihai, Klenk, Hans-Peter, Göker, Markus, Kyrpides, Nikos C, Woyke, Tanja, Vorholt, Julia A, Schulze-Lefert, Paul, Rubin, Edward M, Darling, Aaron E, Rattei, Thomas, McHardy, Alice C

Critical assessment of metagenome interpretation - a benchmark of metagenomics software. Nature Methods, 14 (11), pp. 1063-1071
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.

All authors for A communal catalogue reveals Earth's multiscale microbial diversity

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., Kanbar, Jad, Zhu, Qiyun, Jin Song, Se, Kosciolek, Tomasz, Bokulich, Nicholas A., Lefler, Joshua, Brislawn, Colin J., Humphrey, Gregory, Owens, Sarah M., Hampton-Marcell, Jarrad, Berg-Lyons, Donna, McKenzie, Valerie, Fierer, Noah, Fuhrman, Jed A., Clauset, Aaron, Stevens, Rick L., Shade, Ashley, Pollard, Katherine S., Goodwin, Kelly D., Jansson, Janet K., Gilbert, Jack A., Knight, Rob, Rivera, Jose L. Agosto, Al-Moosawi, Lisa, Alverdy, John, Amato, Katherine R., Andras, Jason, Angenent, Largus T., Antonopoulos, Dionysios A., Apprill, Amy, Armitage, David, Ballantine, Kate, Ba´rta, Jir?i´, Baum, Julia K., Berry, Allison, Bhatnagar, Ashish, Bhatnagar, Monica, Biddle, Jennifer F., Bittner, Lucie, Boldgiv, Bazartseren, Bottos, Eric, Boyer, Donal M., Braun, Josephine, Brazelton, William, Brearley, Francis Q., Campbell, Alexandra H., Caporaso, J. Gregory, Cardona, Cesar, Carroll, JoLynn, Cary, S. Craig, Casper, Brenda B., Charles, Trevor C., Chu, Haiyan, Claar, Danielle C., Clark, Robert G., Clayton, Jonathan B., Clemente, Jose C., Cochran, Alyssa, Coleman, Maureen L., Collins, Gavin, Colwell, Rita R., Contreras, Mo´nica, Crary, Benjamin B., Creer, Simon, Cristol, Daniel A., Crump, Byron C., Cui, Duoying, Daly, Sarah E., Davalos, Liliana, Dawson, Russell D., Defazio, Jennifer, Delsuc, Fre´de´ric, Dionisi, Hebe M., Dominguez-Bello, Maria Gloria, Dowell, Robin, Dubinsky, Eric A., Dunn, Peter O., Ercolini, Danilo, Espinoza, Robert E., Ezenwa, Vanessa, Fenner, Nathalie, Findlay, Helen S., Fleming, Irma D., Fogliano, Vincenzo, Forsman, Anna, Freeman, Chris, Friedman, Elliot S., Galindo, Giancarlo, Garcia, Liza, Garcia-Amado, Maria Alexandra, Garshelis, David, Gasser, Robin B., Gerdts, Gunnar, Gibson, Molly K., Gifford, Isaac, Gill, Ryan T., Giray, Tugrul, Gittel, Antje, Golyshin, Peter, Gong, Donglai, Grossart, Hans-Peter, Guyton, Kristina, Haig, Sarah-Jane, Hale, Vanessa, Hall, Ross Stephen, Hallam, Steven J., Handley, Kim M., Hasan, Nur A., Haydon, Shane R., Hickman, Jonathan E., Hidalgo, Glida, Hofmockel, Kirsten S., Hooker, Jeff, Hulth, Stefan, Hultman, Jenni, Hyde, Embriette, Iba´n~ez-A´lamo, Juan Diego, Jastrow, Julie D., Jex, Aaron R., Johnson, L. Scott, Johnston, Eric R., Joseph, Stephen, Jurburg, Stephanie D., Jurelevicius, Diogo, Karlsson, Anders, Karlsson, Roger, Kauppinen, Seth, Kellogg, Colleen T. E., Kennedy, Suzanne J., Kerkhof, Lee J., King, Gary M., Kling, George W., Koehler, Anson V., Krezalek, Monika, Kueneman, Jordan, Lamendella, Regina, Landon, Emily M., Lane-deGraaf, Kelly, LaRoche, Julie, Larsen, Peter, Laverock, Bonnie, Lax, Simon, Lentino, Miguel, Levin, Iris I., Liancourt, Pierre, Liang, Wenju, Linz, Alexandra M., Lipson, David A., Liu, Yongqin, Lladser, Manuel E., Lozada, Mariana, Spirito, Catherine M., MacCormack, Walter P., MacRae-Crerar, Aurora, Magris, Magda, Marti´n-Platero, Antonio M., Marti´n-Vivaldi, Manuel, Marti´nez, L. Margarita, Marti´nez-Bueno, Manuel, Marzinelli, Ezequiel M., Mason, Olivia U., Mayer, Gregory D., McDevitt-Irwin, Jamie M., McDonald, James E., McGuire, Krista L., McMahon, Katherine D., McMinds, Ryan, Medina, Mo´nica, Mendelson, Joseph R., Metcalf, Jessica L., Meyer, Folker, Michelangeli, Fabian, Miller, Kim, Mills, David A., Minich, Jeremiah, Mocali, Stefano, Moitinho-Silva, Lucas, Moore, Anni, Morgan-Kiss, Rachael M., Munroe, Paul, Myrold, David, Neufeld, Josh D., Ni, Yingying, Nicol, Graeme W., Nielsen, Shaun, Nissimov, Jozef I., Niu, Kefeng, Nolan, Matthew J., Noyce, Karen, O'Brien, Sarah L., Okamoto, Noriko, Orlando, Ludovic, Castellano, Yadira Ortiz, Osuolale, Olayinka, Oswald, Wyatt, Parnell, Jacob, Peralta-Sa´nchez, Juan M., Petraitis, Peter, Pfister, Catherine, Pilon-Smits, Elizabeth, Piombino, Paola, Pointing, Stephen B., Pollock, F. Joseph, Potter, Caitlin, Prithiviraj, Bharath, Quince, Christopher, Rani, Asha, Ranjan, Ravi, Rao, Subramanya, Rees, Andrew P., Richardson, Miles, Riebesell, Ulf, Robinson, Carol, Rockne, Karl J., Rodriguezl, Selena Marie, Rohwer, Forest, Roundstone, Wayne, Safran, Rebecca J., Sangwan, Naseer, Sanz, Virginia, Schrenk, Matthew, Schrenzel, Mark D., Scott, Nicole M., Seger, Rita L., Seguin-Orlando, Andaine, Seldin, Lucy, Seyler, Lauren M., Shakhsheer, Baddr, Sheets, Gabriela M., Shen, Congcong, Shi, Yu, Shin, Hakdong, Shogan, Benjamin D., Shutler, Dave, Siegel, Jeffrey, Simmons, Steve, Sjo¨ling, Sara, Smith, Daniel P., Soler, Juan J., Sperling, Martin, Steinberg, Peter D., Stephens, Brent, Stevens, Melita A., Taghavi, Safiyh, Tai, Vera, Tait, Karen, Tan, Chia L., Tas¸, Neslihan, Taylor, D. Lee, Thomas, Torsten, Timling, Ina, Turner, Benjamin L., Urich, Tim, Ursell, Luke K., van der Lelie, Daniel, Van Treuren, William, van Zwieten, Lukas, Vargas-Robles, Daniela, Thurber, Rebecca Vega, Vitaglione, Paola, Walker, Donald A., Walters, William A., Wang, Shi, Wang, Tao, Weaver, Tom, Webster, Nicole S., Wehrle, Beck, Weisenhorn, Pamela, Weiss, Sophie, Werner, Jeffrey J., West, Kristin, Whitehead, Andrew, Whitehead, Susan R., Whittingham, Linda A., Willerslev, Eske, Williams, Allison E., Wood, Stephen A., Woodhams, Douglas C., Yang, Yeqin, Zaneveld, Jesse, Zarraonaindia, Iratxe, Zhang, Qikun, Zhao, Hongxia

A communal catalogue reveals Earth's multiscale microbial diversity. Nature
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)
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)
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
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)
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
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
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
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
Rognes, Torbjørn, Flouri, Tomá?, Nichols, Ben, Quince, Christopher, Mahé, Frédéric, 2016. VSEARCH : a versatile open source tool for metagenomics. PeerJ, 4
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
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)
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
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
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.

All authors for Challenges in microbial ecology : building predictive understanding of community function and dynamics

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., Großkopf, Tobias, Huisman, Jef, Free, Andrew, Picioreanu, Cristian, Quince, Christopher, Klapper, Isaac, Labarthe, Simon, Smets, Barth F., Wang, Harris, Soyer, Orkun S., Allison, Steven D., Chong, James, Cosentino-Lagomarsino, Marco, Croze, Ottavio A., Hamelin, Jérôme, Harmand, Jérôme, Hoyle, Rebecca, Hwa, Terence T., Jin, Qusheng, Johnson, David R., de Lorenzo, Víctor, Mobilia, Mauro, Murphy, Barry, Peaudecerf, François, Prosser, James I., Quinn, Robert A., Ralser, Markus, Smith, Alison G., Steyer, Jean-Philippe, Swainston, Neil, Tarnita, Corina E., Trably, Eric, Warren, Patrick B., Wilmes, Paul

Challenges in microbial ecology : building predictive understanding of community function and dynamics. The ISME Journal, 2016 (10), pp. 2557-2568
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)
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
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
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
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, 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
Mahé, Frédéric, Rognes, Torbjørn, Quince, Christopher, de Vargas, Colomban, Dunthorn, Micah, 2015. Swarm v2 : highly-scalable and high-resolution amplicon clustering. PeerJ, 3
Mahé, Frédéric, Rognes, Torbjørn, Quince, Christopher, de Vargas, Colomban, Dunthorn, Micah, 2014. Swarm : robust and fast clustering method for amplicon-based studies. PeerJ, 2
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
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
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
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
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
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
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
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
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
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
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)
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.

All authors for Meeting Report: The Terabase Metagenomics Workshop and the Vision of an Earth Microbiome Project

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, McHardy, Alice, Quince, Christopher, Raes, Jeroen, Sczyrba, Alexander, Shade, Ashley, Stevens, Rick

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

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., 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., 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
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
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
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

'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. University of Warwick, Warwick Medical School
'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. University of Warwick, Warwick Medical School
'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 1. University of Warwick, Warwick Medical School
'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 6. University of Warwick, Warwick Medical School
'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. University of Warwick, Warwick Medical School
'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. University of Warwick, Warwick Medical School
'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 3. University of Warwick, Warwick Medical School
'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 4. University of Warwick, Warwick Medical School
'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. University of Warwick, Warwick Medical School
'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. University of Warwick, Warwick Medical School
'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. University of Warwick, Warwick Medical School
'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 4. University of Warwick, Warwick Medical School
'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: Salmonella supertree 2. University of Warwick, Warwick Medical School
'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: Salmonella supertree 1. University of Warwick, Warwick Medical School
'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: Salmonella supertree 3. University of Warwick, Warwick Medical School
'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: workflow. University of Warwick, Warwick Medical School
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. University of Warwick, Warwick Medical School
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 4. University of Warwick, Warwick Medical School
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 3. University of Warwick, Warwick Medical School
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. University of Warwick, Warwick Medical School
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. University of Warwick, Warwick Medical School
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. University of Warwick, Warwick Medical School
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 1. University of Warwick, Warwick Medical School
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 2. University of Warwick, Warwick Medical School
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. University of Warwick, Warwick Medical School
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. University of Warwick, Warwick Medical School
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. University of Warwick, Warwick Medical School
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. University of Warwick, Warwick Medical School
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. University of Warwick, Warwick Medical School
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. University of Warwick, Warwick Medical School
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. University of Warwick, Warwick Medical School
Ijaz, Ali Z., Jeffries, Thomas, Quince, Christopher, Hamonts, Kelly, Singh, Brajesh, 2017. TaxaSE : exploiting evolutionary conservation within 16S rDNA sequences for enhanced taxonomic annotation. PeerJ Preprints, PeerJ Preprints
Zhou, Zhemin, Luhmann, Nina, Alikhan, Nabil-Fareed, Quince, Christopher, Achtman, Mark, 2017. Accurate reconstruction of microbial strains using representative reference genomes. biorxiv, Cold Spring Harbour
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, 2017. Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica. biorxiv, Cold Spring Harbour
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, Green, Monica H., Christophersen, Axel, Quince, Christopher, Thomson, Nicholas R., Weill, François-Xavier, Ho, Simon, Thomas, M., Gilbert, P. et al (Select to open full list), 2017.

All authors for Data for Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica

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, Green, Monica H., Christophersen, Axel, Quince, Christopher, Thomson, Nicholas R., Weill, François-Xavier, Ho, Simon, Thomas, M., Gilbert, P., Achtman, Mark

Data for Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica. Warwick Medical School, University of Warwick
Sczyrba, Alexander, Hofmann, Peter, Belmann, Peter, Koslicki, David, Janssen, Stefan, Droege, Johannes, Gregor, Ivan, Majda, Stephan, Fiedler, Jessika, Dahms, Eik, Bremges, Andreas, Fritz, Adrian, Garrido-Oter, Ruben, Sparholt Jorgensen, Tue, Shapiro, Nicole, Blood, Philip D., Gurevich, Alexey, Bai, Yang, Turaev, Dmitrij, DeMaere, Matthew Z. et al (Select to open full list), 2017.

All authors for Critical assessment of metagenome interpretation - a benchmark of computational metagenomics software

Sczyrba, Alexander, Hofmann, Peter, Belmann, Peter, Koslicki, David, Janssen, Stefan, Droege, Johannes, Gregor, Ivan, Majda, Stephan, Fiedler, Jessika, Dahms, Eik, Bremges, Andreas, Fritz, Adrian, Garrido-Oter, Ruben, Sparholt Jorgensen, Tue, Shapiro, Nicole, Blood, Philip D., Gurevich, Alexey, Bai, Yang, Turaev, Dmitrij, DeMaere, Matthew Z., Chikhi, Rayan, Nagarajan, Niranjan, Quince, Christopher, Meyer, Fernando, Balvociute, Monika, Hestbjerg Hansen, Lars, Sorensen, Soren J., Chia, Burton K. H., Denis, Bertrand, Froula, Jeff L., Wang, Zhong, Egan, Robert, Kang, Dongwan Don, Cook, Jeffrey J., Deltel, Charles, Beckstette, Michael, Lemaitre, Claire, Peterlongo, Pierre, Rizk, Guillaume, Lavenier, Dominique, Wu, Yu-Wei, Singer, Steven W., Jain, Chirag, Strous, Marc, Klingenberg, Heiner, Meinicke, Peter, Barton, Michael, Lingner, Thomas, Lin, Hsin-Hung, Liao, Yu-Chieh, Gueiros Z Silva, Genivaldo, Cuevas, Daniel A., Edwards, Robert A., Saha, Surya, Piro, Vitor C., Renard, Bernhard Y., Pop, Mihai, Klenk, Hans-Peter, Goeker, Markus, Kyrpides, Nikos C., Woyke, Tanja, Vorholt, Julia A., Schulze-Lefert, Paul, Rubin, Edward M., Darling, Aaron E., Rattei, Thomas, McHardy, Alice C.

Critical assessment of metagenome interpretation - a benchmark of computational metagenomics software. Cold Spring Harbour Laboratory
Gerasimidis, Konstantinos, Ijaz, Umer Z., Edwards, Christine, Russell, Richard K., Quince, Christopher, Hansen, Richard, 2016. Response to Kaakoush et al.. The American Journal of Gastroenterology, Nature Publishing Group, pp. 1033-1034
Bowen, Emma J., Parsons, Todd L., Curtis, Thomas P., Plotkin, Joshua B., Quince, Christopher, 2016. Integrating theory and experiment to explain the breakdown of population synchrony in a complex microbial community. University of Warwick, Warwick Medical School
Quince, Christopher, Connelly, Stephanie, Raguideau, Sebastien, Alneberg, Johannes, Shin, Seung Gu, Collins, Gavin, Eren, A. Murat, 2016. De novo extraction of microbial strains from metagenomes reveals intra-species niche partitioning. Cold Spring Harbour Laboratory
Nichols, Ben, Quince, Christopher, 2016. Simera : modelling the PCR process to simulate realistic chimera formation. Cold Spring Harbour Laboratory
Quince, Christopher, Lanzén, Anders, Curtis, Thomas P., Davenport, Russell J., Hall, Neil, Head, Ian M., Read, L Fiona, Sloan, William T., 2009. Accurate determination of microbial diversity from 454 pyrosequencing data. Nature Methods, pp. 639-641

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 Dec 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