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Accurate and sensitive detection of microbial eukaryotes from whole metagenome shotgun sequencing

Microbiome, 2021-03, Vol.9 (1), p.58-18, Article 58

2021

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Single cell genome sequencing of laboratory mouse microbiota improves taxonomic and functional resolution of this model microbial community

PloS one, 2022-04, Vol.17 (4), p.e0261795-e0261795

2022

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Profile hidden Markov models for the detection of viruses within metagenomic sequence data

PloS one, 2014-08, Vol.9 (8), p.e105067-e105067

2014

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Maast: genotyping thousands of microbial strains efficiently

Genome Biology, 2023-08, Vol.24 (1), p.186-186, Article 186

2023

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Phylogeny-corrected identification of microbial gene families relevant to human gut colonization

PLoS computational biology, 2018-08, Vol.14 (8), p.e1006242

2018

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A Metagenomic Meta-analysis Reveals Functional Signatures of Health and Disease in the Human Gut Microbiome

mSystems, 2019-07, Vol.4 (4)

2019

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Dynamic and Coordinated Epigenetic Regulation of Developmental Transitions in the Cardiac Lineage

Cell, 2012-09, Vol.151 (1), p.206-220

2012

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Culturing of a complex gut microbial community in mucin-hydrogel carriers reveals strain- and gene-associated spatial organization

Nature communications, 2023-06, Vol.14 (1), p.3510-3510, Article 3510

2023

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An atlas of lamina-associated chromatin across twelve human cell types reveals an intermediate chromatin subtype

Genome Biology, 2023-01, Vol.24 (1), p.16-35, Article 16

2023

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A most wanted list of conserved microbial protein families with no known domains

PloS one, 2018-10, Vol.13 (10), p.e0205749-e0205749

2018

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Hotspots of biased nucleotide substitutions in human genes

PLoS biology, 2009-01, Vol.7 (1), p.e26-e26

2009

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Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome

Genome Biology, 2015-03, Vol.16 (1), p.51-51, Article 51

2015

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SIMMER employs similarity algorithms to accurately identify human gut microbiome species and enzymes capable of known chemical transformations

eLife, 2023-06, Vol.12

2023

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Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes

PLoS computational biology, 2015-11, Vol.11 (11), p.e1004573-e1004573

2015

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Forces shaping the fastest evolving regions in the human genome

PLoS genetics, 2006-10, Vol.2 (10), p.e168-e168

2006

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The phylogenetic diversity of metagenomes

PloS one, 2011-08, Vol.6 (8), p.e23214-e23214

2011

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Genes expressed in specific areas of the human fetal cerebral cortex display distinct patterns of evolution

PloS one, 2011-03, Vol.6 (3), p.e17753-e17753

2011

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Analysis of human accelerated DNA regions using archaic hominin genomes

PloS one, 2012-03, Vol.7 (3), p.e32877-e32877

2012

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Caloric restriction disrupts the microbiota and colonization resistance

Nature (London), 2021-07, Vol.595 (7866), p.272-277

2021

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Evolution of lysine acetylation in the RNA polymerase II C-terminal domain

BMC evolutionary biology, 2015-03, Vol.15 (1), p.35, Article 35

2015

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From Genes to Milk: Genomic Organization and Epigenetic Regulation of the Mammary Transcriptome

PloS one, 2013-09, Vol.8 (9), p.e75030-e75030

2013

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MetaQuery: a web server for rapid annotation and quantitative analysis of specific genes in the human gut microbiome

Bioinformatics, 2015-10, Vol.31 (20), p.3368-3370

2015

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Global ecotypes in the ubiquitous marine clade SAR86

The ISME Journal, 2020-01, Vol.14 (1), p.178-188

2020

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Novel genes exhibit distinct patterns of function acquisition and network integration

Genome biology, 2010-12, Vol.11 (12), p.R127-R127

2010

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The Role of GC-Biased Gene Conversion in Shaping the Fastest Evolving Regions of the Human Genome

Molecular biology and evolution, 2012-03, Vol.29 (3), p.1047-1057

2012

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Accurate and sensitive detection of microbial eukaryotes from whole metagenome shotgun sequencing

Single cell genome sequencing of laboratory mouse microbiota improves taxonomic and functional resolution of this model microbial community

Profile hidden Markov models for the detection of viruses within metagenomic sequence data

Maast: genotyping thousands of microbial strains efficiently

Phylogeny-corrected identification of microbial gene families relevant to human gut colonization

A Metagenomic Meta-analysis Reveals Functional Signatures of Health and Disease in the Human Gut Microbiome

Dynamic and Coordinated Epigenetic Regulation of Developmental Transitions in the Cardiac Lineage

Culturing of a complex gut microbial community in mucin-hydrogel carriers reveals strain- and gene-associated spatial organization

An atlas of lamina-associated chromatin across twelve human cell types reveals an intermediate chromatin subtype

A most wanted list of conserved microbial protein families with no known domains

Hotspots of biased nucleotide substitutions in human genes

Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome

SIMMER employs similarity algorithms to accurately identify human gut microbiome species and enzymes capable of known chemical transformations

Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes

Forces shaping the fastest evolving regions in the human genome

The phylogenetic diversity of metagenomes

Genes expressed in specific areas of the human fetal cerebral cortex display distinct patterns of evolution

Analysis of human accelerated DNA regions using archaic hominin genomes

Caloric restriction disrupts the microbiota and colonization resistance

Evolution of lysine acetylation in the RNA polymerase II C-terminal domain

From Genes to Milk: Genomic Organization and Epigenetic Regulation of the Mammary Transcriptome

MetaQuery: a web server for rapid annotation and quantitative analysis of specific genes in the human gut microbiome

Global ecotypes in the ubiquitous marine clade SAR86

Novel genes exhibit distinct patterns of function acquisition and network integration

The Role of GC-Biased Gene Conversion in Shaping the Fastest Evolving Regions of the Human Genome

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