Search filters

List of works by Christopher Quince

A comparison of rpoB and 16S rRNA as markers in pyrosequencing studies of bacterial diversity

scientific article

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

scientific article published on 14 January 2016

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

scientific article

Absorption and fixation times for neutral and quasi-neutral populations with density dependence

scientific article published on 18 September 2008

Accurate determination of microbial diversity from 454 pyrosequencing data

scientific article

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

scientific article

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

scientific article published on 15 February 2016

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

scientific article published on 19 December 2012

Binning metagenomic contigs by coverage and composition

scientific article

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

scientific article published on 19 February 2016

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

scientific article

Biphasic growth in fish I: theoretical foundations

scientific article published on 7 July 2008

Biphasic growth in fish II: empirical assessment

scientific article

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

scientific article published on 29 March 2016

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

scientific article

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

scientific article published on 2 October 2017

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

scientific article published on 21 September 2017

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

scientific article

Dirichlet multinomial mixtures: generative models for microbial metagenomics

scientific article (publication date: 2012)

Diversity and dynamics of rare and of resident bacterial populations in coastal sands

scientific article

Dynamics of envelope evolution in clade C SHIV-infected pig-tailed macaques during disease progression analyzed by ultra-deep pyrosequencing

scientific article

Enterotypes in the landscape of gut microbial community composition.

scientific article published on 18 December 2017

Environmental microbiology through the lens of high-throughput DNA sequencing: synopsis of current platforms and bioinformatics approaches

scientific article published on 28 July 2012

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

scientific article (publication date: 21 May 2013)

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

scientific article published on 3 November 2015

Extinction times and moment closure in the stochastic logistic process

scientific article published on 01 March 2004

Fixation in haploid populations exhibiting density dependence I: The non-neutral case

scientific article published on 15 December 2006

Fixation in haploid populations exhibiting density dependence II: the quasi-neutral case

scientific article published on 27 April 2007

Fluvial network organization imprints on microbial co-occurrence networks

scientific article

Headwaters are critical reservoirs of microbial diversity for fluvial networks.

scientific article published on 2 October 2013

Hepatitis C virus transmission bottlenecks analyzed by deep sequencing.

scientific article

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

scientific article

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

scientific article published on 13 January 2015

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

scientific article published on 21 March 2018

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

scientific article published on 15 January 2014

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

scientific article published on 9 March 2016

Machine learning based prediction of functional capabilities in metagenomically assembled microbial genomes

scholarly article published 25 April 2018

Meeting report: the terabase metagenomics workshop and the vision of an Earth microbiome project

scientific article

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

scientific article published on 23 September 2016

Multivariate Cutoff Level Analysis (MultiCoLA) of large community data sets

scientific article

Niche specialization of terrestrial archaeal ammonia oxidizers

scientific article published on 8 December 2011

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

scientific article published on 11 June 2018

Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins

scientific article

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

scientific article published on 19 July 2018

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

scientific article

Phylogenetic congruence and ecological coherence in terrestrial Thaumarchaeota

scientific article published on 3 July 2015

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

scientific article published on 18 February 2014

Removing noise from pyrosequenced amplicons

scientific article

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

scientific article

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

scientific article

Response to Kaakoush et al.

scientific article published in July 2016

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

scientific article

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

scientific article

Sample richness and genetic diversity as drivers of chimera formation in nSSU metagenetic analyses

scientific article

Seqenv: linking sequences to environments through text mining

scientific article

Seqenv: linking sequences to environments through text mining

Shotgun metagenomics, from sampling to analysis

scientific article published on September 2017

Some consequences of demographic stochasticity in population genetics

scientific article published on 10 May 2010

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

scientific article published on 17 March 2015

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

scientific article

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

scientific article published on 25 September 2014

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

scientific article

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

scientific article

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

scientific article

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

scientific article published on 7 January 2013

The impact of mortality on predator population size and stability in systems with stage-structured prey

scientific article published on 22 July 2005

The impact of nonlinear functional responses on the long-term evolution of food web structure

scientific article published in August 2004

The rational exploration of microbial diversity

scientific article

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

scientific article published on 13 October 2015

Towards standardization of the description and publication of next-generation sequencing datasets of fungal communities

scientific article published in 2011

Treatment of Active Crohn’s Disease With an Ordinary Food-based Diet That Replicates Exclusive Enteral Nutrition

scientific article published on 11 December 2018

UCHIME improves sensitivity and speed of chimera detection ⬇️

scientific article (publication date: 15 August 2011)

V-REVCOMP: automated high-throughput detection of reverse complementary 16S rRNA gene sequences in large environmental and taxonomic datasets

scientific article published on 27 April 2011

VSEARCH: a versatile open source tool for metagenomics

scientific article

Paulina is supported by:

About Paulina

Help