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Bioreactor Scalability: Laboratory-Scale Bioreactor Design Influences Performance, Ecology, and Community Physiology in Expanded Granular Sludge Bed Bioreactors.
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- Frontiers in Microbiology, 2017, v. 8, p. 1, doi. 10.3389/fmicb.2017.00664
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- Article
Illumina error profiles: resolving fine-scale variation in metagenomic sequencing data.
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- BMC Bioinformatics, 2016, v. 17, p. 1, doi. 10.1186/s12859-016-0976-y
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- Article
Some Consequences of Demographic Stochasticity in Population Genetics.
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- Genetics, 2010, v. 185, n. 4, p. 1345, doi. 10.1534/genetics.110.115030
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- Article
Metagenetic analysis of patterns of distribution and diversity of marine meiobenthic eukaryotes.
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- Global Ecology & Biogeography, 2014, v. 23, n. 11, p. 1293, doi. 10.1111/geb.12223
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- Article
Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform.
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- Nucleic Acids Research, 2015, v. 43, n. 6, p. 1, doi. 10.1093/nar/gku1341
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- Article
Multivariate Cutoff Level Analysis (MultiCoLA) of large community data sets.
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- Nucleic Acids Research, 2010, v. 38, n. 15, p. e155, doi. 10.1093/nar/gkq545
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- Article
Strainberry: automated strain separation in low-complexity metagenomes using long reads.
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- Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-24515-9
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The effect of DNA extraction methodology on gut microbiota research applications.
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- BMC Research Notes, 2016, v. 9, p. 1, doi. 10.1186/s13104-016-2171-7
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Assessment of the influence of intrinsic environmental and geographical factors on the bacterial ecology of pit latrines.
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- Microbial Biotechnology, 2016, v. 9, n. 2, p. 209, doi. 10.1111/1751-7915.12334
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- Article
Corrigendum: Shotgun metagenomics, from sampling to analysis.
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- Nature Biotechnology, 2017, v. 35, n. 12, p. 1211, doi. 10.1038/nbt1217-1211b
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- Article
Shotgun metagenomics, from sampling to analysis.
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- Nature Biotechnology, 2017, v. 35, n. 9, p. 833, doi. 10.1038/nbt.3935
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- Article
Stable-isotope probing and metagenomics reveal predation by protozoa drives E. coli removal in slow sand filters.
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- ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2015, v. 9, n. 4, p. 797, doi. 10.1038/ismej.2014.175
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- Article
Diversity and dynamics of rare and of resident bacterial populations in coastal sands.
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- ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2012, v. 6, n. 3, p. 542, doi. 10.1038/ismej.2011.132
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- Article
The rational exploration of microbial diversity.
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- ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2008, v. 2, n. 10, p. 997, doi. 10.1038/ismej.2008.69
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- Article
Binning metagenomic contigs by coverage and composition.
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- Nature Methods, 2014, v. 11, n. 11, p. 1144, doi. 10.1038/nmeth.3103
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- Article
Accurate determination of microbial diversity from 454 pyrosequencing data.
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- Nature Methods, 2009, v. 6, n. 9, p. 639, doi. 10.1038/nmeth.1361
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- Article
Swarm v3: towards tera-scale amplicon clustering.
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- Bioinformatics, 2022, v. 38, n. 1, p. 267, doi. 10.1093/bioinformatics/btab493
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- Article
Benchmarking of viral haplotype reconstruction programmes: an overview of the capacities and limitations of currently available programmes.
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- Briefings in Bioinformatics, 2014, v. 15, n. 3, p. 431, doi. 10.1093/bib/bbs081
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- Article
Analysis of pit latrine microbiota reveals depth-related variation in composition, and key parameters and taxa associated with latrine fill-up rate.
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- Frontiers in Microbiology, 2022, v. 13, p. 1, doi. 10.3389/fmicb.2022.960747
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- Article
Metabarcoding and metabolome analyses of copepod grazing reveal feeding preference and linkage to metabolite classes in dynamic microbial plankton communities.
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- Molecular Ecology, 2016, v. 25, n. 21, p. 5585, doi. 10.1111/mec.13844
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- Article
STRONG: metagenomics strain resolution on assembly graphs.
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- Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02419-7
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- Article
Correction: Response of Archaeal and Bacterial Soil Communities to Changes Associated with Outdoor Cattle Overwintering.
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- PLoS ONE, 2015, v. 10, n. 9, p. 1, doi. 10.1371/journal.pone.0137815
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- Article
Response of Archaeal and Bacterial Soil Communities to Changes Associated with Outdoor Cattle Overwintering.
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- PLoS ONE, 2015, v. 10, n. 8, p. 1, doi. 10.1371/journal.pone.0135627
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- Article
Dynamics of Envelope Evolution in Clade C SHIV-Infected Pig-Tailed Macaques during Disease Progression Analyzed by Ultra-Deep Pyrosequencing.
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- PLoS ONE, 2012, v. 7, n. 3, p. 1, doi. 10.1371/journal.pone.0032827
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- Article
A Comparison of rpoB and 16S rRNA as Markers in Pyrosequencing Studies of Bacterial Diversity.
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- PLoS ONE, 2012, v. 7, n. 2, p. 1, doi. 10.1371/journal.pone.0030600
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- Article
Dirichlet Multinomial Mixtures: Generative Models for Microbial Metagenomics.
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- PLoS ONE, 2012, v. 7, n. 2, p. 1, doi. 10.1371/journal.pone.0030126
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- Article
A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling.
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- BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-015-2194-9
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- Article
Functional responses of key marine bacteria to environmental change – toward genetic counselling for coastal waters.
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- Frontiers in Microbiology, 2022, v. 13, p. 1, doi. 10.3389/fmicb.2022.869093
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- Article
Removing Noise From Pyrosequenced Amplicons.
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- BMC Bioinformatics, 2011, v. 12, n. 1, p. 38, doi. 10.1186/1471-2105-12-38
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- Article
Macroevolutionary Dynamics in Micro-organisms: Generalists Give Rise to Specialists Across Biomes in the Ubiquitous Bacterial Phylum Myxococcota.
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- Molecular Biology & Evolution, 2024, v. 41, n. 5, p. 1, doi. 10.1093/molbev/msae088
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- Article
Ecosystem-wide metagenomic binning enables prediction of ecological niches from genomes.
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- Communications Biology, 2020, v. 3, n. 1, p. 1, doi. 10.1038/s42003-020-0856-x
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- Article
A note on the incidence of reverse complementary fungal ITS sequences in the public sequence databases and a software tool for their detection and reorientation.
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- Mycoscience (Springer Nature), 2011, v. 52, n. 4, p. 278, doi. 10.47371/s10267-010-0086-z
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- Article
Crop management shapes the diversity and activity of DNA and RNA viruses in the rhizosphere.
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- Microbiome, 2022, v. 10, n. 1, p. 1, doi. 10.1186/s40168-022-01371-3
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- Article
Rare but active taxa contribute to community dynamics of benthic biofilms in glacier-fed streams.
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- Environmental Microbiology, 2014, v. 16, n. 8, p. 2514, doi. 10.1111/1462-2920.12392
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- Article
Loss of microbial diversity in soils is coincident with reductions in some specialized functions.
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- Environmental Microbiology, 2014, v. 16, n. 8, p. 2408, doi. 10.1111/1462-2920.12353
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Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities.
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- Environmental Microbiology, 2013, v. 15, n. 6, p. 1882, doi. 10.1111/1462-2920.12086
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- Article
Metabolic independence drives gut microbial colonization and resilience in health and disease.
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- Genome Biology, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s13059-023-02924-x
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- Article
Deleting species from model food webs.
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- Oikos, 2005, v. 110, n. 2, p. 283, doi. 10.1111/j.0030-1299.2005.13493.x
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- Article
The pathophysiology of bile acid diarrhoea: differences in the colonic microbiome, metabolome and bile acids.
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- Scientific Reports, 2020, v. 10, n. 1, p. N.PAG, doi. 10.1038/s41598-020-77374-7
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- Article
Linking Microbial Community Structure and Function During the Acidified Anaerobic Digestion of Grass.
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- Frontiers in Microbiology, 2018, p. 1, doi. 10.3389/fmicb.2018.00540
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The distinct features of microbial ‘dysbiosis’ of Crohn’s disease do not occur to the same extent in their unaffected, genetically-linked kindred.
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- PLoS ONE, 2017, v. 12, n. 2, p. 1, doi. 10.1371/journal.pone.0172605
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- Article
High-quality metagenome assembly from long accurate reads with metaMDBG.
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- Nature Biotechnology, 2024, v. 42, n. 9, p. 1378, doi. 10.1038/s41587-023-01983-6
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- Article
Determining the optimal route of faecal microbiota transplant in patients with ulcerative colitis: the STOP-Colitis pilot RCT.
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- Efficacy & Mechanism Evaluation (EME), 2024, v. 11, n. 14, p. 1, doi. 10.3310/YCJD4579
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- Article
A Microbe Associated with Sleep Revealed by a Novel Systems Genetic Analysis of the Microbiome in Collaborative Cross Mice.
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- Genetics, 2020, v. 214, n. 3, p. 719, doi. 10.1534/genetics.119.303013
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- Article
Growth and Break-Up of Methanogenic Granules Suggests Mechanisms for Biofilm and Community Development.
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- Frontiers in Microbiology, 2020, v. 11, p. 1, doi. 10.3389/fmicb.2020.01126
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- Article
DESMAN: a new tool for de novo extraction of strains from metagenomes.
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- Genome Biology, 2017, v. 18, p. 1, doi. 10.1186/s13059-017-1309-9
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- Article
Towards standardization of the description and publication of next-generation sequencing datasets of fungal communities.
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- New Phytologist, 2011, v. 191, n. 2, p. 314, doi. 10.1111/j.1469-8137.2011.03755.x
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- Article
A Culture-Independent Sequence-Based Metagenomics Approach to the Investigation of an Outbreak of Shiga-Toxigenic Escherichia coli O104:H4.
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- JAMA: Journal of the American Medical Association, 2013, v. 309, n. 14, p. 1502, doi. 10.1001/jama.2013.3231
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- Article
Transient Suppression of Bacterial Populations Associated with Gut Health is Critical in Success of Exclusive Enteral Nutrition for Children with Crohn's Disease.
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- Journal of Crohn's & Colitis, 2023, v. 17, n. 7, p. 1103, doi. 10.1093/ecco-jcc/jjad031
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- Article
UCHIME improves sensitivity and speed of chimera detection.
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- Bioinformatics, 2011, v. 27, n. 16, p. 2194, doi. 10.1093/bioinformatics/btr381
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- Article