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Items: 1 to 50 of 77

1.

Author Correction: Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes.

Delmont TO, Quince C, Shaiber A, Esen ÖC, Lee ST, Rappé MS, McLellan SL, Lücker S, Eren AM.

Nat Microbiol. 2018 Aug;3(8):963. doi: 10.1038/s41564-018-0209-4.

PMID:
30042441
2.

Pan-genome Analysis of Ancient and Modern Salmonella enterica Demonstrates Genomic Stability of the Invasive Para C Lineage for Millennia.

Zhou Z, Lundstrøm I, Tran-Dien A, Duchêne S, Alikhan NF, Sergeant MJ, Langridge G, Fotakis AK, Nair S, Stenøien HK, Hamre SS, Casjens S, Christophersen A, Quince C, Thomson NR, Weill FX, Ho SYW, Gilbert MTP, Achtman M.

Curr Biol. 2018 Aug 6;28(15):2420-2428.e10. doi: 10.1016/j.cub.2018.05.058. Epub 2018 Jul 19.

3.

Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes.

Delmont TO, Quince C, Shaiber A, Esen ÖC, Lee ST, Rappé MS, McLellan SL, Lücker S, Eren AM.

Nat Microbiol. 2018 Jul;3(7):804-813. doi: 10.1038/s41564-018-0176-9. Epub 2018 Jun 11. Erratum in: Nat Microbiol. 2018 Aug;3(8):963.

PMID:
29891866
4.

Linking Microbial Community Structure and Function During the Acidified Anaerobic Digestion of Grass.

Joyce A, Ijaz UZ, Nzeteu C, Vaughan A, Shirran SL, Botting CH, Quince C, O'Flaherty V, Abram F.

Front Microbiol. 2018 Mar 21;9:540. doi: 10.3389/fmicb.2018.00540. eCollection 2018.

5.

Publisher Correction: Enterotypes in the landscape of gut microbial community composition.

Costea PI, Hildebrand F, Arumugam M, Bäckhed F, Blaser MJ, Bushman FD, de Vos WM, Ehrlich SD, Fraser CM, Hattori M, Huttenhower C, Jeffery IB, Knights D, Lewis JD, Ley RE, Ochman H, O'Toole PW, Quince C, Relman DA, Shanahan F, Sunagawa S, Wang J, Weinstock GM, Wu GD, Zeller G, Zhao L, Raes J, Knight R, Bork P.

Nat Microbiol. 2018 Mar;3(3):388. doi: 10.1038/s41564-018-0114-x.

PMID:
29440750
6.

Enterotypes in the landscape of gut microbial community composition.

Costea PI, Hildebrand F, Arumugam M, Bäckhed F, Blaser MJ, Bushman FD, de Vos WM, Ehrlich SD, Fraser CM, Hattori M, Huttenhower C, Jeffery IB, Knights D, Lewis JD, Ley RE, Ochman H, O'Toole PW, Quince C, Relman DA, Shanahan F, Sunagawa S, Wang J, Weinstock GM, Wu GD, Zeller G, Zhao L, Raes J, Knight R, Bork P.

Nat Microbiol. 2018 Jan;3(1):8-16. doi: 10.1038/s41564-017-0072-8. Epub 2017 Dec 18. Review. Erratum in: Nat Microbiol. 2018 Feb 13;:.

7.

Corrigendum: Shotgun metagenomics, from sampling to analysis.

Quince C, Walker AW, Simpson JT, Loman NJ, Segata N.

Nat Biotechnol. 2017 Dec 8;35(12):1211. doi: 10.1038/nbt1217-1211b.

PMID:
29220029
8.

Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software.

Sczyrba A, Hofmann P, Belmann P, Koslicki D, Janssen S, Dröge J, Gregor I, Majda S, Fiedler J, Dahms E, Bremges A, Fritz A, Garrido-Oter R, Jørgensen TS, Shapiro N, Blood PD, Gurevich A, Bai Y, Turaev D, DeMaere MZ, Chikhi R, Nagarajan N, Quince C, Meyer F, Balvočiūtė M, Hansen LH, Sørensen SJ, Chia BKH, Denis B, Froula JL, Wang Z, Egan R, Don Kang D, Cook JJ, Deltel C, Beckstette M, Lemaitre C, Peterlongo P, Rizk G, Lavenier D, Wu YW, Singer SW, Jain C, Strous M, Klingenberg H, Meinicke P, Barton MD, Lingner T, Lin HH, Liao YC, Silva GGZ, Cuevas DA, Edwards RA, Saha S, Piro VC, Renard BY, Pop M, Klenk HP, Göker M, Kyrpides NC, Woyke T, Vorholt JA, Schulze-Lefert P, Rubin EM, Darling AE, Rattei T, McHardy AC.

Nat Methods. 2017 Nov;14(11):1063-1071. doi: 10.1038/nmeth.4458. Epub 2017 Oct 2.

9.

DESMAN: a new tool for de novo extraction of strains from metagenomes.

Quince C, Delmont TO, Raguideau S, Alneberg J, Darling AE, Collins G, Eren AM.

Genome Biol. 2017 Sep 21;18(1):181. doi: 10.1186/s13059-017-1309-9.

10.

Temperature, inocula and substrate: Contrasting electroactive consortia, diversity and performance in microbial fuel cells.

Heidrich ES, Dolfing J, Wade MJ, Sloan WT, Quince C, Curtis TP.

Bioelectrochemistry. 2018 Feb;119:43-50. doi: 10.1016/j.bioelechem.2017.07.006. Epub 2017 Jul 22.

11.

Shotgun metagenomics, from sampling to analysis.

Quince C, Walker AW, Simpson JT, Loman NJ, Segata N.

Nat Biotechnol. 2017 Sep 12;35(9):833-844. doi: 10.1038/nbt.3935. Review. Erratum in: Nat Biotechnol. 2017 Dec 8;35(12 ):1211.

PMID:
28898207
12.

Revealing higher than expected meiofaunal diversity in Antarctic sediments: a metabarcoding approach.

Fonseca VG, Sinniger F, Gaspar JM, Quince C, Creer S, Power DM, Peck LS, Clark MS.

Sci Rep. 2017 Jul 21;7(1):6094. doi: 10.1038/s41598-017-06687-x.

13.

Bioreactor Scalability: Laboratory-Scale Bioreactor Design Influences Performance, Ecology, and Community Physiology in Expanded Granular Sludge Bed Bioreactors.

Connelly S, Shin SG, Dillon RJ, Ijaz UZ, Quince C, Sloan WT, Collins G.

Front Microbiol. 2017 May 1;8:664. doi: 10.3389/fmicb.2017.00664. eCollection 2017.

14.

The distinct features of microbial 'dysbiosis' of Crohn's disease do not occur to the same extent in their unaffected, genetically-linked kindred.

Ijaz UZ, Quince C, Hanske L, Loman N, Calus ST, Bertz M, Edwards CA, Gaya DR, Hansen R, McGrogan P, Russell RK, Gerasimidis K.

PLoS One. 2017 Feb 21;12(2):e0172605. doi: 10.1371/journal.pone.0172605. eCollection 2017.

15.

Seqenv: linking sequences to environments through text mining.

Sinclair L, Ijaz UZ, Jensen LJ, Coolen MJL, Gubry-Rangin C, Chroňáková A, Oulas A, Pavloudi C, Schnetzer J, Weimann A, Ijaz A, Eiler A, Quince C, Pafilis E.

PeerJ. 2016 Dec 20;4:e2690. doi: 10.7717/peerj.2690. eCollection 2016.

16.

Metabarcoding and metabolome analyses of copepod grazing reveal feeding preference and linkage to metabolite classes in dynamic microbial plankton communities.

Ray JL, Althammer J, Skaar KS, Simonelli P, Larsen A, Stoecker D, Sazhin A, Ijaz UZ, Quince C, Nejstgaard JC, Frischer M, Pohnert G, Troedsson C.

Mol Ecol. 2016 Nov;25(21):5585-5602. doi: 10.1111/mec.13844. Epub 2016 Oct 20.

PMID:
27662431
17.

VSEARCH: a versatile open source tool for metagenomics.

Rognes T, Flouri T, Nichols B, Quince C, Mahé F.

PeerJ. 2016 Oct 18;4:e2584. eCollection 2016.

18.

Challenges in microbial ecology: building predictive understanding of community function and dynamics.

Widder S, Allen RJ, Pfeiffer T, Curtis TP, Wiuf C, Sloan WT, Cordero OX, Brown SP, Momeni B, Shou W, Kettle H, Flint HJ, Haas AF, Laroche B, Kreft JU, Rainey PB, Freilich S, Schuster S, Milferstedt K, van der Meer JR, Groβkopf T, Huisman J, Free A, Picioreanu C, Quince C, Klapper I, Labarthe S, Smets BF, Wang H; Isaac Newton Institute Fellows, Soyer OS.

ISME J. 2016 Nov;10(11):2557-2568. doi: 10.1038/ismej.2016.45. Epub 2016 Mar 29. Review.

19.

The effect of DNA extraction methodology on gut microbiota research applications.

Gerasimidis K, Bertz M, Quince C, Brunner K, Bruce A, Combet E, Calus S, Loman N, Ijaz UZ.

BMC Res Notes. 2016 Jul 26;9:365. doi: 10.1186/s13104-016-2171-7.

20.

Response to Kaakoush et al.

Gerasimidis K, Ijaz UZ, Edwards C, Russell RK, Quince C, Hansen R.

Am J Gastroenterol. 2016 Jul;111(7):1033-4. doi: 10.1038/ajg.2016.169. No abstract available.

PMID:
27356826
21.

Low-strength ultrasonication positively affects methanogenic granules toward higher AD performance: Implications from microbial community shift.

Cho SK, Kim DH, Quince C, Im WT, Oh SE, Shin SG.

Ultrason Sonochem. 2016 Sep;32:198-203. doi: 10.1016/j.ultsonch.2016.03.010. Epub 2016 Mar 9.

PMID:
27150761
22.

Illumina error profiles: resolving fine-scale variation in metagenomic sequencing data.

Schirmer M, D'Amore R, Ijaz UZ, Hall N, Quince C.

BMC Bioinformatics. 2016 Mar 11;17:125. doi: 10.1186/s12859-016-0976-y.

23.

Bioaugmentation Mitigates the Impact of Estrogen on Coliform-Grazing Protozoa in Slow Sand Filters.

Haig SJ, Gauchotte-Lindsay C, Collins G, Quince C.

Environ Sci Technol. 2016 Mar 15;50(6):3101-10. doi: 10.1021/acs.est.5b05027. Epub 2016 Mar 3.

24.

Assessment of the influence of intrinsic environmental and geographical factors on the bacterial ecology of pit latrines.

Torondel B, Ensink JH, Gundogdu O, Ijaz UZ, Parkhill J, Abdelahi F, Nguyen VA, Sudgen S, Gibson W, Walker AW, Quince C.

Microb Biotechnol. 2016 Mar;9(2):209-23. doi: 10.1111/1751-7915.12334. Epub 2016 Feb 15.

25.

PhyloPythiaS+: a self-training method for the rapid reconstruction of low-ranking taxonomic bins from metagenomes.

Gregor I, Dröge J, Schirmer M, Quince C, McHardy AC.

PeerJ. 2016 Feb 8;4:e1603. doi: 10.7717/peerj.1603. eCollection 2016.

26.

A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling.

D'Amore R, Ijaz UZ, Schirmer M, Kenny JG, Gregory R, Darby AC, Shakya M, Podar M, Quince C, Hall N.

BMC Genomics. 2016 Jan 14;17:55. doi: 10.1186/s12864-015-2194-9.

27.

Swarm v2: highly-scalable and high-resolution amplicon clustering.

Mahé F, Rognes T, Quince C, de Vargas C, Dunthorn M.

PeerJ. 2015 Dec 10;3:e1420. doi: 10.7717/peerj.1420. eCollection 2015.

28.

Extensive Modulation of the Fecal Metagenome in Children With Crohn's Disease During Exclusive Enteral Nutrition.

Quince C, Ijaz UZ, Loman N, Eren AM, Saulnier D, Russell J, Haig SJ, Calus ST, Quick J, Barclay A, Bertz M, Blaut M, Hansen R, McGrogan P, Russell RK, Edwards CA, Gerasimidis K.

Am J Gastroenterol. 2015 Dec;110(12):1718-29; quiz 1730. doi: 10.1038/ajg.2015.357. Epub 2015 Nov 3.

29.

Anvi'o: an advanced analysis and visualization platform for 'omics data.

Eren AM, Esen ÖC, Quince C, Vineis JH, Morrison HG, Sogin ML, Delmont TO.

PeerJ. 2015 Oct 8;3:e1319. doi: 10.7717/peerj.1319. eCollection 2015.

30.

The relationship between microbial community evenness and function in slow sand filters.

Haig SJ, Quince C, Davies RL, Dorea CC, Collins G.

MBio. 2015 Oct 13;6(5):e00729-15. doi: 10.1128/mBio.00729-15.

31.

Correction: Response of Archaeal and Bacterial Soil Communities to Changes Associated with Outdoor Cattle Overwintering.

Chroňáková A, Schloter-Hai B, Radl V, Endesfelder D, Quince C, Elhottová D, Šimek M, Schloter M.

PLoS One. 2015 Sep 8;10(9):e0137815. doi: 10.1371/journal.pone.0137815. eCollection 2015. No abstract available.

32.

The skin microbiome in psoriatic arthritis: methodology development and pilot data.

Castelino M, Eyre S, Moat J, Fox G, Martin P, Ijaz U, Quince C, Ho P, Upton M, Barton A.

Lancet. 2015 Feb 26;385 Suppl 1:S27. doi: 10.1016/S0140-6736(15)60342-7.

PMID:
26312849
33.

Response of Archaeal and Bacterial Soil Communities to Changes Associated with Outdoor Cattle Overwintering.

Chroňáková A, Schloter-Hai B, Radl V, Endesfelder D, Quince C, Elhottová D, Šimek M, Schloter M.

PLoS One. 2015 Aug 14;10(8):e0135627. doi: 10.1371/journal.pone.0135627. eCollection 2015. Erratum in: PLoS One. 2015;10(9):e0137815.

34.

Phylogenetic congruence and ecological coherence in terrestrial Thaumarchaeota.

Oton EV, Quince C, Nicol GW, Prosser JI, Gubry-Rangin C.

ISME J. 2016 Jan;10(1):85-96. doi: 10.1038/ismej.2015.101. Epub 2015 Jul 3.

35.

Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform.

Schirmer M, Ijaz UZ, D'Amore R, Hall N, Sloan WT, Quince C.

Nucleic Acids Res. 2015 Mar 31;43(6):e37. doi: 10.1093/nar/gku1341. Epub 2015 Jan 13.

36.

Stable-isotope probing and metagenomics reveal predation by protozoa drives E. coli removal in slow sand filters.

Haig SJ, Schirmer M, D'Amore R, Gibbs J, Davies RL, Collins G, Quince C.

ISME J. 2015 Mar 17;9(4):797-808. doi: 10.1038/ismej.2014.175.

37.

Swarm: robust and fast clustering method for amplicon-based studies.

Mahé F, Rognes T, Quince C, de Vargas C, Dunthorn M.

PeerJ. 2014 Sep 25;2:e593. doi: 10.7717/peerj.593. eCollection 2014.

38.

Binning metagenomic contigs by coverage and composition.

Alneberg J, Bjarnason BS, de Bruijn I, Schirmer M, Quick J, Ijaz UZ, Lahti L, Loman NJ, Andersson AF, Quince C.

Nat Methods. 2014 Nov;11(11):1144-6. doi: 10.1038/nmeth.3103. Epub 2014 Sep 14.

PMID:
25218180
39.

Fluvial network organization imprints on microbial co-occurrence networks.

Widder S, Besemer K, Singer GA, Ceola S, Bertuzzo E, Quince C, Sloan WT, Rinaldo A, Battin TJ.

Proc Natl Acad Sci U S A. 2014 Sep 2;111(35):12799-804. doi: 10.1073/pnas.1411723111. Epub 2014 Aug 18.

40.

Replicating the microbial community and water quality performance of full-scale slow sand filters in laboratory-scale filters.

Haig SJ, Quince C, Davies RL, Dorea CC, Collins G.

Water Res. 2014 Sep 15;61:141-51. doi: 10.1016/j.watres.2014.05.008. Epub 2014 May 22.

PMID:
24908577
41.

Role of Faecalibacterium prausnitzii in Crohn's Disease: friend, foe, or does not really matter?

Gerasimidis K, Russell R, Hansen R, Quince C, Loman N, Bertz M, Hanske L, Blaut M, McGrogan P, Edwards CA.

Inflamm Bowel Dis. 2014 Jul;20(7):E18-9. doi: 10.1097/MIB.0000000000000079. No abstract available.

PMID:
24859302
42.

Rare but active taxa contribute to community dynamics of benthic biofilms in glacier-fed streams.

Wilhelm L, Besemer K, Fasching C, Urich T, Singer GA, Quince C, Battin TJ.

Environ Microbiol. 2014 Aug;16(8):2514-24. doi: 10.1111/1462-2920.12392. Epub 2014 Feb 18.

PMID:
24428193
43.

Loss of microbial diversity in soils is coincident with reductions in some specialized functions.

Singh BK, Quince C, Macdonald CA, Khachane A, Thomas N, Al-Soud WA, Sørensen SJ, He Z, White D, Sinclair A, Crooks B, Zhou J, Campbell CD.

Environ Microbiol. 2014 Aug;16(8):2408-20. doi: 10.1111/1462-2920.12353. Epub 2014 Jan 15.

PMID:
24422656
44.

Headwaters are critical reservoirs of microbial diversity for fluvial networks.

Besemer K, Singer G, Quince C, Bertuzzo E, Sloan W, Battin TJ.

Proc Biol Sci. 2013 Oct 2;280(1771):20131760. doi: 10.1098/rspb.2013.1760. Print 2013 Nov 22.

45.

Decreased gut microbiota diversity, delayed Bacteroidetes colonisation and reduced Th1 responses in infants delivered by caesarean section.

Jakobsson HE, Abrahamsson TR, Jenmalm MC, Harris K, Quince C, Jernberg C, Björkstén B, Engstrand L, Andersson AF.

Gut. 2014 Apr;63(4):559-66. doi: 10.1136/gutjnl-2012-303249. Epub 2013 Aug 7.

46.

Evolution of the plankton paleome in the Black Sea from the Deglacial to Anthropocene.

Coolen MJ, Orsi WD, Balkema C, Quince C, Harris K, Sylva SP, Filipova-Marinova M, Giosan L.

Proc Natl Acad Sci U S A. 2013 May 21;110(21):8609-14. doi: 10.1073/pnas.1219283110. Epub 2013 May 6.

47.

A culture-independent sequence-based metagenomics approach to the investigation of an outbreak of Shiga-toxigenic Escherichia coli O104:H4.

Loman NJ, Constantinidou C, Christner M, Rohde H, Chan JZ, Quick J, Weir JC, Quince C, Smith GP, Betley JR, Aepfelbacher M, Pallen MJ.

JAMA. 2013 Apr 10;309(14):1502-10. doi: 10.1001/jama.2013.3231.

PMID:
23571589
48.

Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities.

Shakya M, Quince C, Campbell JH, Yang ZK, Schadt CW, Podar M.

Environ Microbiol. 2013 Jun;15(6):1882-99. doi: 10.1111/1462-2920.12086. Epub 2013 Feb 6.

49.

The impact of Crohn's disease genes on healthy human gut microbiota: a pilot study.

Quince C, Lundin EE, Andreasson AN, Greco D, Rafter J, Talley NJ, Agreus L, Andersson AF, Engstrand L, D'Amato M.

Gut. 2013 Jun;62(6):952-4. doi: 10.1136/gutjnl-2012-304214. Epub 2013 Jan 7. No abstract available.

PMID:
23297005
50.

Benchmarking of viral haplotype reconstruction programmes: an overview of the capacities and limitations of currently available programmes.

Schirmer M, Sloan WT, Quince C.

Brief Bioinform. 2014 May;15(3):431-42. doi: 10.1093/bib/bbs081. Epub 2012 Dec 19. Review.

PMID:
23257116

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