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Toward Accurate and Quantitative Comparative Metagenomics

Cell, 2016-08, Vol.166 (5), p.1103-1116

2016

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Evolutionary dynamics of bacteria in the gut microbiome within and across hosts

PLoS biology, 2019-01, Vol.17 (1), p.e3000102-e3000102

2019

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New insights from uncultivated genomes of the global human gut microbiome

Nature (London), 2019-04, Vol.568 (7753), p.505-510

2019

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An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography

Genome research, 2016-11, Vol.26 (11), p.1612-1625

2016

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Enhancer–promoter interactions are encoded by complex genomic signatures on looping chromatin

Nature genetics, 2016-05, Vol.48 (5), p.488-496

2016

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A unified catalog of 204,938 reference genomes from the human gut microbiome

Nature biotechnology, 2021-01, Vol.39 (1), p.105-114

2021

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Exploring the roles of RNAs in chromatin architecture using deep learning

Nature communications, 2024-07, Vol.15 (1), p.6373-14, Article 6373

2024

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Proteobacteria explain significant functional variability in the human gut microbiome

Microbiome, 2017-03, Vol.5 (1), p.36-36, Article 36

2017

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Broad host range of SARS-CoV-2 predicted by comparative and structural analysis of ACE2 in vertebrates

Proceedings of the National Academy of Sciences - PNAS, 2020-09, Vol.117 (36), p.22311-22322

2020

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Human Disease Modeling Reveals Integrated Transcriptional and Epigenetic Mechanisms of NOTCH1 Haploinsufficiency

Cell, 2015-03, Vol.160 (6), p.1072-1086

2015

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Detection of nonneutral substitution rates on mammalian phylogenies

Genome research, 2010-01, Vol.20 (1), p.110-121

2010

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Human gut bacterial metabolism drives Th17 activation and colitis

Cell host & microbe, 2022-01, Vol.30 (1), p.17-30.e9

2022

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Continental-scale distributions of dust-associated bacteria and fungi

Proceedings of the National Academy of Sciences - PNAS, 2015-05, Vol.112 (18), p.5756-5761

2015

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Principles of meiotic chromosome assembly revealed in S. cerevisiae

Nature communications, 2019-10, Vol.10 (1), p.4795-12, Article 4795

2019

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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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Modulation of a Circulating Uremic Solute via Rational Genetic Manipulation of the Gut Microbiota

Cell host & microbe, 2016-12, Vol.20 (6), p.709-715

2016

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Reconstructing the Microbial Diversity and Function of Pre-Agricultural Tallgrass Prairie Soils in the United States

Science (American Association for the Advancement of Science), 2013-11, Vol.342 (6158), p.621-624

2013

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Marked seasonal variation in the wild mouse gut microbiota

The ISME Journal, 2015-11, Vol.9 (11), p.2423-2434

2015

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A taxonomic signature of obesity in the microbiome? Getting to the guts of the matter

PloS one, 2014-01, Vol.9 (1), p.e84689-e84689

2014

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CellWalker integrates single-cell and bulk data to resolve regulatory elements across cell types in complex tissues

Genome Biology, 2021-02, Vol.22 (1), p.61-61, Article 61

2021

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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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A transcriptional switch governs fibroblast activation in heart disease

Nature (London), 2021-07, Vol.595 (7867), p.438-443

2021

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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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Molecular basis of CTCF binding polarity in genome folding

Nature communications, 2020-11, Vol.11 (1), p.5612-5612, Article 5612

2020

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Toward Accurate and Quantitative Comparative Metagenomics

Evolutionary dynamics of bacteria in the gut microbiome within and across hosts

New insights from uncultivated genomes of the global human gut microbiome

An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography

Enhancer–promoter interactions are encoded by complex genomic signatures on looping chromatin

A unified catalog of 204,938 reference genomes from the human gut microbiome

Exploring the roles of RNAs in chromatin architecture using deep learning

Proteobacteria explain significant functional variability in the human gut microbiome

Broad host range of SARS-CoV-2 predicted by comparative and structural analysis of ACE2 in vertebrates

Human Disease Modeling Reveals Integrated Transcriptional and Epigenetic Mechanisms of NOTCH1 Haploinsufficiency

Detection of nonneutral substitution rates on mammalian phylogenies

Human gut bacterial metabolism drives Th17 activation and colitis

Continental-scale distributions of dust-associated bacteria and fungi

Principles of meiotic chromosome assembly revealed in S. cerevisiae

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

Modulation of a Circulating Uremic Solute via Rational Genetic Manipulation of the Gut Microbiota

Reconstructing the Microbial Diversity and Function of Pre-Agricultural Tallgrass Prairie Soils in the United States

Marked seasonal variation in the wild mouse gut microbiota

A taxonomic signature of obesity in the microbiome? Getting to the guts of the matter

CellWalker integrates single-cell and bulk data to resolve regulatory elements across cell types in complex tissues

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

A transcriptional switch governs fibroblast activation in heart disease

Maast: genotyping thousands of microbial strains efficiently

Molecular basis of CTCF binding polarity in genome folding

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