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Identification of diversity-generating retroelements in human microbiomes

International journal of molecular sciences, 2014-08, Vol.15 (8), p.14234-14246

Ye, Yuzhen

2014

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FragGeneScan: predicting genes in short and error-prone reads

Nucleic acids research, 2010-11, Vol.38 (20), p.e191-e191

2010

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Protein embedding based alignment

BMC bioinformatics, 2024-02, Vol.25 (1), p.85-85, Article 85

2024

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RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data

Bioinformatics, 2012-01, Vol.28 (1), p.125-126

2012

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Accurate de novo peptide sequencing using fully convolutional neural networks

Nature communications, 2023-12, Vol.14 (1), p.7974-7974, Article 7974

2023

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Metaproteomics as a tool for studying the protein landscape of human-gut bacterial species

PLoS computational biology, 2022-03, Vol.18 (3), p.e1009397-e1009397

2022

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Meta-analysis of microbiome association networks reveal patterns of dysbiosis in diseased microbiomes

Scientific reports, 2022-10, Vol.12 (1), p.17482-13, Article 17482

2022

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Incorporating metabolic activity, taxonomy and community structure to improve microbiome-based predictive models for host phenotype prediction

Gut microbes, 2024, Vol.16 (1), p.2302076

2024

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A core human microbiome as viewed through 16S rRNA sequence clusters

PloS one, 2012-06, Vol.7 (6), p.e34242-e34242

2012

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RAPSearch: a fast protein similarity search tool for short reads

BMC bioinformatics, 2011-05, Vol.12 (1), p.159-159, Article 159

2011

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A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes

PLoS computational biology, 2009-08, Vol.5 (8), p.e1000465-e1000465

2009

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A Graph-Centric Approach for Metagenome-Guided Peptide and Protein Identification in Metaproteomics

PLoS computational biology, 2016-12, Vol.12 (12), p.e1005224-e1005224

2016

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Comparison of CRISPR–Cas Immune Systems in Healthcare-Related Pathogens

Frontiers in microbiology, 2021-10, Vol.12, p.758782-758782

2021

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Diversity and dynamics of the CRISPR-Cas systems associated with Bacteroides fragilis in human population

BMC genomics, 2022-08, Vol.23 (1), p.1-573, Article 573

2022

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Long reads reveal the diversification and dynamics of CRISPR reservoir in microbiomes

BMC genomics, 2019-07, Vol.20 (1), p.567-12, Article 567

2019

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In situ confinement growth of peasecod-like N-doped carbon nanotubes encapsulate bimetallic FeCu alloy as a bifunctional oxygen reaction cathode electrocatalyst for sustainable energy batteries

Journal of alloys and compounds, 2020-06, Vol.826, p.154152, Article 154152

2020

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Using high-abundance proteins as guides for fast and effective peptide/protein identification from human gut metaproteomic data

Microbiome, 2021-04, Vol.9 (1), p.80-80, Article 80

2021

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Revealing bacteria-phage interactions in human microbiome through the CRISPR-Cas immune systems

Frontiers in cellular and infection microbiology, 2022-09, Vol.12, p.933516

2022

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Diverse CRISPRs evolving in human microbiomes

PLoS genetics, 2012-06, Vol.8 (6), p.e1002441-e1002441

2012

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Not all predicted CRISPR-Cas systems are equal: isolated cas genes and classes of CRISPR like elements

BMC bioinformatics, 2017-02, Vol.18 (1), p.92-92, Article 92

2017

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Model-based and phylogenetically adjusted quantification of metabolic interaction between microbial species

PLoS computational biology, 2020-10, Vol.16 (10), p.e1007951-e1007951

2020

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Strain level microbial detection and quantification with applications to single cell metagenomics

Nature communications, 2022-10, Vol.13 (1), p.6430-19, Article 6430

2022

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Metagenomics： Facts and Artifacts, and Computational Challenges

Journal of computer science and technology, 2010-01, Vol.25 (1), p.71-81

2010

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Msi2‐mediated MiR7a‐1 processing repression promotes myogenesis

Journal of cachexia, sarcopenia and muscle, 2022-02, Vol.13 (1), p.728-742

2022

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Identification and classification of reverse transcriptases in bacterial genomes and metagenomes

Nucleic acids research, 2022-03, Vol.50 (5), p.e29-e29

2022

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Identification of diversity-generating retroelements in human microbiomes

FragGeneScan: predicting genes in short and error-prone reads

Protein embedding based alignment

RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data

Accurate de novo peptide sequencing using fully convolutional neural networks

Metaproteomics as a tool for studying the protein landscape of human-gut bacterial species

Meta-analysis of microbiome association networks reveal patterns of dysbiosis in diseased microbiomes

Incorporating metabolic activity, taxonomy and community structure to improve microbiome-based predictive models for host phenotype prediction

A core human microbiome as viewed through 16S rRNA sequence clusters

RAPSearch: a fast protein similarity search tool for short reads

A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes

A Graph-Centric Approach for Metagenome-Guided Peptide and Protein Identification in Metaproteomics

Comparison of CRISPR–Cas Immune Systems in Healthcare-Related Pathogens

Diversity and dynamics of the CRISPR-Cas systems associated with Bacteroides fragilis in human population

Long reads reveal the diversification and dynamics of CRISPR reservoir in microbiomes

In situ confinement growth of peasecod-like N-doped carbon nanotubes encapsulate bimetallic FeCu alloy as a bifunctional oxygen reaction cathode electrocatalyst for sustainable energy batteries

Using high-abundance proteins as guides for fast and effective peptide/protein identification from human gut metaproteomic data

Revealing bacteria-phage interactions in human microbiome through the CRISPR-Cas immune systems

Diverse CRISPRs evolving in human microbiomes

Not all predicted CRISPR-Cas systems are equal: isolated cas genes and classes of CRISPR like elements

Model-based and phylogenetically adjusted quantification of metabolic interaction between microbial species

Strain level microbial detection and quantification with applications to single cell metagenomics

Metagenomics： Facts and Artifacts, and Computational Challenges

Msi2‐mediated MiR7a‐1 processing repression promotes myogenesis

Identification and classification of reverse transcriptases in bacterial genomes and metagenomes

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