☆ 4.7 Review

Illuminating the oral microbiome and its host interactions: recent advancements in omics and bioinformatics technologies in the context of oral microbiome research

FEMS MICROBIOLOGY REVIEWS (2023)

相关参考文献

注意：仅列出部分参考文献，下载原文获取全部文献信息。
Review Spectroscopy

Biological mass spectrometry enables spatiotemporal 'omics: From tissues to cells to organelles

Leena R. Pade et al.

Summary: Biological processes unfold across broad spatial and temporal dimensions, and measurement of the underlying molecular world is essential to their understanding. Mass spectrometry (MS) has advanced significantly, allowing for precise analysis of molecular architecture at various levels, with high detection sensitivity and scalability. This review highlights technology innovations that have improved sample collection and processing, chemical separation, ionization, and 'omics analyses, enabling deeper study of limited and dynamic specimens. The integration of orthogonal approaches from molecular and functional studies, combined with spatiotemporal MS, has become an exciting and powerful resource in the study of biological systems.

MASS SPECTROMETRY REVIEWS (2023)

添加到收藏夹
Article Biochemical Research Methods

Guiding the choice of informatics software and tools for lipidomics research applications

Zhixu Ni et al.

Summary: Progress in mass spectrometry lipidomics has led to a rapid increase in research in biology and biomedicine, generating large datasets that require sophisticated solutions for automated data processing. To address this issue, various software tools have been developed, but researchers often face difficulties in choosing the most suitable approach, resulting in inefficient and time-consuming ad hoc testing.

NATURE METHODS (2023)

添加到收藏夹
Article Biochemistry & Molecular Biology

De novo sequencing, diploid assembly, and annotation of the black carpenter ant, Camponotus pennsylvanicus, and its symbionts by one person for $1000, using nanopore sequencing

Christopher Faulk

Summary: In this study, the researcher successfully assembled the genome of the black carpenter ant using nanopore sequencing technology at a lower cost and time. The quality of the assembly was accurately assessed. The study also included the assembly of the mitochondrial genome and symbiotic bacteria genomes, as well as measurements of DNA methylation and hydroxymethylation. This method enables low-resource labs to obtain high-quality genome assemblies at a lower cost.

NUCLEIC ACIDS RESEARCH (2023)

添加到收藏夹
Article Dentistry, Oral Surgery & Medicine

Subgingival host-microbiome metatranscriptomic changes following scaling and root planing in grade II/III periodontitis

Ana E. Duran-Pinedo et al.

Summary: The study aimed to assess the effects of scaling and root planing (SRP) on the dynamics of gene expression by the host and the microbiome in subgingival plaque samples. The results showed that SRP resulted in significant rewiring of host and microbial activities in the progressing sites, while restructuring of the microbiome was minor in stable and fluctuating sites.

JOURNAL OF CLINICAL PERIODONTOLOGY (2023)

添加到收藏夹
Article Biochemistry & Molecular Biology

ChemFOnt: the chemical functional ontology resource

David S. Wishart et al.

Summary: ChemFOnt is an ontology that describes the functions and actions of biologically important chemicals, aiming to provide standardization and formal structure to the terms used in biochemistry, food chemistry, and environmental chemistry. Users can freely access the database or download the Web Ontology Language (OWL) file to analyze data, generate relationships, and assist in reasoning.

NUCLEIC ACIDS RESEARCH (2023)

添加到收藏夹
Article Biochemical Research Methods

Toward an Integrated Machine Learning Model of a Proteomics Experiment

Benjamin A. Neely et al.

Summary: In recent years, machine learning has made significant progress in modeling mass spectrometry data for proteomics analysis. A workshop was conducted to evaluate and explore machine learning applications in multidimensional mass spectrometry-based proteomics analysis. The workshop helped identify knowledge gaps, define needs, and discuss the possibilities, challenges, and future opportunities. The summary of the discussions conveys excitement about the potential of machine learning in proteomics and aims to inspire future research.

JOURNAL OF PROTEOME RESEARCH (2023)

添加到收藏夹
Article Biochemical Research Methods

An Introduction to Mass Spectrometry-Based Proteomics

Steven R. Shuken

Summary: Mass spectrometry is an extremely versatile tool for studying various aspects of the proteome. This tutorial aims to provide an accessible guide to the technical details of a simple quantitative proteomic experiment, explaining relevant concepts to those with limited knowledge of mass spectrometry and proteins. It covers experimental overview, data acquisition, processing and analysis, as well as briefly touching on advanced topics and future prospects of proteomics.

JOURNAL OF PROTEOME RESEARCH (2023)

添加到收藏夹
Letter Biotechnology & Applied Microbiology

Integrative analysis of multimodal mass spectrometry data in MZmine 3

Robin Schmid et al.

NATURE BIOTECHNOLOGY (2023)

添加到收藏夹
Article Multidisciplinary Sciences

MS2Query: reliable and scalable MS2 mass spectra-based analogue search

Niek F. de Jonge et al.

Summary: The authors have developed a machine learning approach, MS2Query, to facilitate chemical discovery in mass spectral libraries. This tool increases the annotation rate and aids in assessing novelty in metabolomics datasets. By integrating mass spectral embedding-based chemical similarity predictors and detected precursor masses, MS2Query offers a more reliable and efficient alternative for searching structurally related molecules in metabolomics studies.

NATURE COMMUNICATIONS (2023)

添加到收藏夹
Review Biochemistry & Molecular Biology

Simultaneous Quantitation and Discovery (SQUAD) Analysis: Combining the Best of Targeted and Untargeted Mass Spectrometry-Based Metabolomics

Bashar Amer et al.

Summary: Untargeted and targeted metabolomics workflows are traditionally used to understand the metabolome. However, these approaches require separate experiments and researchers have to compromise on either a low-accuracy overview or a detailed snapshot. This review presents a novel SQUAD metabolomics that combines targeted and untargeted workflows, allowing for both accurate quantification of targeted metabolites and identification of global metabolic changes. This approach provides a comprehensive understanding of biological systems in a single experiment.

METABOLITES (2023)

添加到收藏夹
Article Immunology

Gingival transcriptomic patterns of macrophage polarization during initiation, progression, and resolution of periodontitis

Octavio A. Gonzalez et al.

Summary: This study investigates the features of macrophage polarization in a nonhuman primate model of periodontitis, assessing gene expression profiles in gingival tissues during health, disease, and resolution. The results demonstrate age-related alterations in macrophage phenotypes and gene expression, highlighting the critical role of macrophage heterogeneity in immune responses. The findings provide valuable insights into the disease mechanisms involved in periodontal lesion formation.

CLINICAL AND EXPERIMENTAL IMMUNOLOGY (2023)

添加到收藏夹
Article Biochemical Research Methods

SemiBin2: self-supervised contrastive learning leads to better MAGs for short- and long-read sequencing

Shaojun Pan et al.

Summary: This study proposes a new semi-supervised binning method, SemiBin2, which utilizes self-supervised learning to learn feature embeddings from contigs. The results show that self-supervised learning achieves better performance than semi-supervised learning used in SemiBin1, and SemiBin2 outperforms other state-of-the-art binners. The proposed method also shows improved performance in handling long-read data.

BIOINFORMATICS (2023)

添加到收藏夹
Review Cell Biology

Metabolite discovery: Biochemistry's scientific driver

Martin Giera et al.

Summary: Metabolite identification is a significant challenge and opportunity in biochemistry. The characterization and quantification of metabolites in living organisms has resulted in a valuable biochemical knowledgebase and serves as the foundation for metabolism research in the 21st century. However, the characterization of newly discovered metabolites has remained a persistent obstacle. Crystallography, NMR spectroscopy, and mass spectrometry are important techniques in this field, with the latter being particularly useful when coupled with high-performance separation technologies and database solutions. Furthermore, the development of artificial intelligence technologies is rapidly advancing to help overcome the challenges in metabolite identification.

CELL METABOLISM (2022)

添加到收藏夹
Article Biochemical Research Methods

Current state-of-the-art of separation methods used in LC-MS based metabolomics and lipidomics

Eva-Maria Harrieder et al.

Summary: Metabolomics and lipidomics involve the large-scale analysis of metabolites, requiring advanced analytical methods. Liquid Chromatography-Mass Spectrometry (LC-MS) is a commonly used technique that provides different selectivities in separation and high sensitivity in detection. Due to the huge chemical diversity, there is no single analysis method that can cover the entire range of metabolites or lipids, leading to the use of different separation methods. This review explores the current use of LC-MS in metabolomics and lipidomics using data from public databases, and highlights potential future trends and improvements needed.

JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES (2022)

添加到收藏夹
Article Chemistry, Multidisciplinary

Native mass spectrometry-based metabolomics identifies metal-binding compounds

Allegra T. Aron et al.

Summary: This two-step native electrospray ionization-mass spectrometry method, combining post-column pH adjustment and metal infusion, enables the identification of metal-binding compounds in complex samples based on defined mass (m/z) offsets, making it a potential essential strategy for elucidating metal-binding molecules in biology.

NATURE CHEMISTRY (2022)

添加到收藏夹
Article Biochemistry & Molecular Biology

Nanopore sequencing of RNA and cDNA molecules in Escherichia coli

Felix Gruenberger et al.

Summary: This study presents an experimental and bioinformatic workflow for ONT RNA-seq in the bacterial model organism Escherichia coli, highlighting critical steps of library preparation and computational analysis. The study compares the applicability and advantages of different ONT-based RNA sequencing protocols and finds that PCR-cDNA-seq offers improved yield and accuracy compared to direct RNA sequencing. The study demonstrates the potential of nanopore RNA-seq as a valuable alternative method for RNA analysis in prokaryotes.

RNA (2022)

添加到收藏夹
Article Biochemical Research Methods

Polypolish: Short-read polishing of long-read bacterial genome assemblies

Ryan R. Wick et al.

Summary: Polypolish is a new short-read polisher that uses all-per-read alignments to fix errors in repeat sequences that other polishers cannot. It performed well in benchmarking tests and introduced minimal errors during the polishing process.

PLOS COMPUTATIONAL BIOLOGY (2022)

添加到收藏夹
Review Biochemical Research Methods

An overview of technologies for MS-based proteomics-centric multi-omics

Andrew T. Rajczewski et al.

Summary: Proteomics, using mass spectrometry, is a valuable tool in biomedical and basic biological research to identify proteins in a system of interest. When integrated with other 'omics' data, such as transcriptomics, genomics, and metabolomics, it provides a more comprehensive understanding of biological systems and their responses to stimuli. This integration, known as multi-omics, requires complete and accurate proteomics data and can be challenging for inexperienced researchers.

EXPERT REVIEW OF PROTEOMICS (2022)

添加到收藏夹
Article Ecology

Metagenomic methylation patterns resolve bacterial genomes of unusual size and structural complexity

Elizabeth G. Wilbanks et al.

Summary: The plasticity of bacterial and archaeal genomes makes it challenging to recover complete genomes from metagenomes. In this study, the researchers used strain-specific patterns of DNA methylation to successfully resolve complex bacterial genomes from metagenomic data. They recovered the largest and most complex circularized bacterial genome ever recovered from a metagenome and identified instances of horizontal gene transfer, phage infection, and strain-level structural variation.

ISME JOURNAL (2022)

添加到收藏夹
Article Microbiology

mucG, mucH, and mucl Modulate Production of Mutanocyclin and Reutericyclins in Streptococcus mutans B04Sm5

Jonathon L. Baker et al.

Summary: This study revealed the evolution of an ancestral S. mutans muc into different lineages and the horizontal transfer of muc to other S. mutans clades. The mucH gene was found to be a transcriptional activator of muc, while mucG and mud played important roles in the production of reutericyclins and mutanocyclin and the inhibition of neighboring commensal streptococci. Further research is needed to fully understand the regulatory mechanisms involved.

JOURNAL OF BACTERIOLOGY (2022)

添加到收藏夹
Review Microbiology

Mass spectrometry-based metabolomics in microbiome investigations

Anelize Bauermeister et al.

Summary: Mass spectrometry-based metabolomics is a key technology for detecting and identifying small molecules produced by the human microbiota and understanding their functional role. Microbiotas play a malleable part in ecosystems, affecting not only their specific niche but also distant environments. Data analysis, especially in the context of microbiome analysis, remains a challenge, with emphasis placed on integrative approaches and the integration of microbiome sequencing data.

NATURE REVIEWS MICROBIOLOGY (2022)

添加到收藏夹
Review Biotechnology & Applied Microbiology

Single-cell mass spectrometry

Mohammad Tajik et al.

Summary: Recent advances in mass spectrometry (MS) have allowed for the measurement of multiple molecules in single cells. This is crucial for understanding the molecular heterogeneity and function of individual cells. In this review, we discuss different methods of single-cell MS, including high-throughput, targeted, mass cytometry-based approaches, and antibody-free methods, for detailed profiling of the proteome and metabolome of single cells. We also explore the advantages and disadvantages of these methods and the challenges and opportunities for further improvements in single-cell MS. These methods have found applications in biomedical research, such as revealing tumor heterogeneity and conducting high-content drug screening.

TRENDS IN BIOTECHNOLOGY (2022)

添加到收藏夹
Article Genetics & Heredity

Over 50,000 Metagenomically Assembled Draft Genomes for the Human Oral Microbiome Reveal New Taxa

Jie Zhu et al.

Summary: By analyzing a large number of oral metagenomic samples, researchers obtained a comprehensive collection of oral microbial genomes. These genomes provide valuable insights into the potential drug metabolism and disease diagnosis capabilities of oral microbes.

GENOMICS PROTEOMICS & BIOINFORMATICS (2022)

添加到收藏夹
Article Immunology

Multi-Omics Analysis Reveals the Systematic Relationship Between Oral Homeostasis and Chronic Sleep Deprivation in Rats

Pan Chen et al.

Summary: Sleep deprivation can lead to oral inflammation and subtle changes in the oral microbiota. Multi-omics analysis reveals the relationship between sleep deficiency and oral health, helping to further understand the role of oral homeostasis in the impact of sleep deprivation on human health and disease.

FRONTIERS IN IMMUNOLOGY (2022)

添加到收藏夹
Article Microbiology

Global transcriptional response of oral squamous cell carcinoma cell lines to health-associated oral bacteria-an in vitro study

Divyashri Baraniya et al.

Summary: This study explores the role of health-associated oral bacteria in oral squamous cell carcinoma (OSCC) cell lines. The results show that different species of bacteria have varying effects on the cell lines, including inhibition of cancer-associated pathways, activation of acute phase response, and pro-inflammatory pathways. These findings provide a new understanding of oral cancer.

JOURNAL OF ORAL MICROBIOLOGY (2022)

添加到收藏夹
Article Microbiology

MetaDecoder: a novel method for clustering metagenomic contigs

Cong-Cong Liu et al.

Summary: In this study, a novel clustering algorithm called MetaDecoder was introduced, which can classify metagenomic contigs based on the frequencies of k-mers and coverages. Benchmark tests on simulated and real-world datasets demonstrated that MetaDecoder can effectively cluster metagenomic contigs and has the potential to be a promising approach.

MICROBIOME (2022)

添加到收藏夹
Article Microbiology

Analysis of the Streptococcus mutans Proteome during Acid and Oxidative Stress Reveals Modules of Protein Coexpression and an Expanded Role for the TreR Transcriptional Regulator

Elizabeth L. Tinder et al.

Summary: This study examines the proteome of Streptococcus mutans during growth in acidic and oxidative stresses, as well as in deletion mutants, and identifies differentially expressed proteins and coexpressed protein modules responsive to stress conditions. The presence of the TreR protein is linked to mutacin production and oxidative stress. This dataset provides valuable insights for understanding S. mutans pathogenesis and developing improved strategies for dental caries prevention and treatment.

MSYSTEMS (2022)

添加到收藏夹
Article Biochemistry & Molecular Biology

Analyzing rare mutations in metagenomes assembled using long and accurate reads

Marcus W. Fedarko et al.

Summary: The emergence of long and accurate HiFi sequencing technology has greatly enhanced our ability to study complete metagenomes by facilitating the identification and phasing of rare mutations in metagenome-assembled genomes (MAGs). However, the challenges of identifying rare mutations, estimating false-discovery rate (FDR), and phasing mutations in the context of HiFi data are still open problems. In this study, we introduce a pipeline called strainFlye for the FDR-controlled identification and analysis of rare mutations in MAGs assembled using HiFi reads. Our results demonstrate the potential of deep HiFi sequencing to reveal and phase thousands of rare mutations in a single MAG, identify mutational hotspots and coldspots, and provide insights into MAGs' growth dynamics.

GENOME RESEARCH (2022)

添加到收藏夹
Article Biochemical Research Methods

Binning long reads in metagenomics datasets using composition and coverage information

Anuradha Wickramarachchi et al.

Summary: This study presents a new reference-free binning approach, LRBinner, for the metagenomic binning of long reads. The experimental results show that LRBinner achieves the best binning accuracy in most cases and handles complete datasets without any sampling. Binning reads using LRBinner reduces computational resources required for assembly and attains satisfactory assembly qualities.

ALGORITHMS FOR MOLECULAR BIOLOGY (2022)

添加到收藏夹
Article Multidisciplinary Sciences

AlphaPeptDeep: a modular deep learning framework to predict peptide properties for proteomics

Wen-Feng Zeng et al.

Summary: Machine learning and deep learning are becoming increasingly important in MS-based proteomics. AlphaPeptDeep is a modular Python framework built on PyTorch that can learn and predict peptide properties. It features a model shop that allows non-specialists to create models easily. AlphaPeptDeep can also predict sequence-based properties and performs well in predicting retention time, collisional cross sections, and fragment intensities.

NATURE COMMUNICATIONS (2022)

添加到收藏夹
Article Microbiology

Nanopore long-read-only metagenomics enables complete and high-quality genome reconstruction from mock and complex metagenomes

Lei Liu et al.

Summary: NanoPhase is an open-source tool that enables the reconstruction of reference-quality genomes from complex metagenomes using only Nanopore long reads. It improves the quality and contiguity of MAGs, allowing for a more comprehensive investigation of target microbiomes.

MICROBIOME (2022)

添加到收藏夹
Article Dentistry, Oral Surgery & Medicine

Oral microbiome diversity: The curious case of Corynebacterium sp. isolation

Puthayalai Treerat et al.

Summary: This study isolated different species of Corynebacterium and studied the specific mechanism of C. durum in its interactions with Streptococcus sanguinis. Genome sequencing of the newly isolated strains placed them closer to Actinomyces. Several comprehensive strategies should be considered when taxonomically identifying closely related microorganisms.

MOLECULAR ORAL MICROBIOLOGY (2022)

添加到收藏夹
Article Biotechnology & Applied Microbiology

Enhancing untargeted metabolomics using metadata-based source annotation

Julia M. Gauglitz et al.

Summary: This study introduces a reference-data-driven analysis approach to increase the usage of metabolomics MS/MS data and enable empirical evaluation of dietary patterns from untargeted data.

NATURE BIOTECHNOLOGY (2022)

添加到收藏夹
Article Biochemical Research Methods

Oxford Nanopore R10.4 long-read sequencing enables the generation of near-finished bacterial genomes from pure cultures and metagenomes without short-read or reference polishing

Mantas Sereika et al.

Summary: This study demonstrates that near-finished microbial genomes can be generated using only Oxford Nanopore R10.4 data, without the need for short-read or reference polishing. This finding simplifies the microbial genome sequencing process and improves the accuracy and continuity of sequencing results.

NATURE METHODS (2022)

添加到收藏夹
Article Biochemical Research Methods

Using MetaboAnalyst 5.0 for LC-HRMS spectra processing, multi-omics integration and covariate adjustment of global metabolomics data

Zhiqiang Pang et al.

Summary: Liquid chromatography coupled with high-resolution mass spectrometry (LC-HRMS) is widely used in global metabolomics studies, but there are still challenges in data processing, statistical analysis, and functional interpretation. To overcome these barriers, the MetaboAnalyst platform has been updated to provide step-by-step instructions.

NATURE PROTOCOLS (2022)

添加到收藏夹
Article Multidisciplinary Sciences

A streamlined platform for analyzing tera-scale DDA and DIA mass spectrometry data enables highly sensitive immunopeptidomics

Lei Xin et al.

Summary: In this study, the authors present a computational platform that integrates data-dependent and data-independent acquisition mass spectrometry approaches for deeper immunopeptidome analysis. The platform utilizes deep learning-based solutions to enhance sensitivity and accuracy of peptide identification, leading to the discovery of more peptide precursors compared to other systems. Additionally, the platform identifies potential T-cell epitopes for COVID-19 vaccine development in the SARS-CoV-2 immunopeptidome.

NATURE COMMUNICATIONS (2022)

添加到收藏夹
Review Immunology

Current State and Challenges of the Global Outcomes of Dental Caries Research in the Meta-Omics Era

Dina G. Moussa et al.

Summary: Dental caries is a metabolic disorder caused by multiple factors, involving microbiome composition, functionality, and host genetic variation. The latest omics studies have provided us with a deeper understanding and helped explore future research questions and designs.

FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY (2022)

添加到收藏夹
Review Microbiology

Introduction to the principles and methods underlying the recovery of metagenome-assembled genomes from metagenomic data

Gleb Goussarov et al.

Summary: The rise of metagenomics is crucial for understanding the genetic diversity of microorganisms in complex environments. However, it is a relatively new discipline that requires complex bioinformatics techniques. In this article, the authors provide a review of the underlying principles and methods in metagenomics to guide microbiologists in entering this field. The article focuses on a workflow for reconstructing individual genomes, known as metagenome-assembled genomes.

MICROBIOLOGYOPEN (2022)

添加到收藏夹
Article Biochemical Research Methods

VEBA: a modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes

Josh L. Espinoza et al.

Summary: VEBA is an end-to-end metagenomics software suite that allows for the recovery, quality assessment, and classification of microbial genomes from all domains of life. It utilizes cutting-edge algorithms to recover more genomes than existing methods through novel iterative binning and clustering-based dereplication strategies. In addition, VEBA automates the detection of candidate phyla radiation bacteria and provides flexibility for specific analytical tasks.

BMC BIOINFORMATICS (2022)

添加到收藏夹
Article Biochemical Research Methods

binny: an automated binning algorithm to recover high-quality genomes from complex metagenomic datasets

Oskar Hickl et al.

Summary: binny is a binning tool that can generate high-quality metagenome-assembled genomes (MAG) from both contiguous and highly fragmented genomes. It outperforms other methods and can find unique genomes that other methods cannot detect.

BRIEFINGS IN BIOINFORMATICS (2022)

添加到收藏夹
Article Microbiology

Transcriptome of Epibiont Saccharibacteria Nanosynbacter lyticus Strain TM7x During the Establishment of Symbiosis

Erik L. Hendrickson et al.

Summary: The research reveals that Saccharibacteria Nanosynbacter lyticus establishes a stable epibiotic relationship with its host bacterium, showing dynamic shifts in gene expression and functions during stable symbiosis. These results imply that TM7x and its host bacteria keep a delicate balance to sustain an episymbiotic lifestyle.

JOURNAL OF BACTERIOLOGY (2022)

添加到收藏夹
Article Dentistry, Oral Surgery & Medicine

Expression of periodontitis susceptibility genes in human gingiva using single-cell RNA sequencing

Ana J. Caetano et al.

Summary: This study used single-cell transcriptomics to investigate the cell-type specificity of periodontitis susceptibility genes. The results suggest that macrophages express a higher number of disease-associated genes, indicating their potential role in disease pathogenesis.

JOURNAL OF PERIODONTAL RESEARCH (2022)

添加到收藏夹
Review Biotechnology & Applied Microbiology

Prediction of peptide mass spectral libraries with machine learning

Juergen Cox

Summary: Proteomics is undergoing a transformation with the use of deep learning methods to predict peptide fragmentation spectra. These methods have superseded traditional approaches and shown improved sensitivity and specificity in peptide identification. Machine learning has significant applications in immunopeptidomics and proteogenomics, although challenges remain in predicting spectra for modified peptides and cross-linked peptide pairs.

NATURE BIOTECHNOLOGY (2022)

添加到收藏夹
Article Biochemical Research Methods

Metagenome analysis using the Kraken software suite

Jennifer Lu et al.

Summary: This article introduces a step-by-step protocol for the computational analysis of high-throughput DNA sequencing data using the Kraken suite. The protocol includes classification, quantification, and visualization, and can be used for quantifying species in a microbial community and identifying pathogens in clinical samples.

NATURE PROTOCOLS (2022)

添加到收藏夹
Article Immunology

Multi-omics analysis reveals the effects of microbiota on oral homeostasis

Huiqing Long et al.

Summary: Microbiota and chronic stress have significant effects on the morphological structures and molecular function of oral homeostasis. Microbiota reshapes the structure of the oral epithelial barrier and changes the function of molecular biology through the immune response and mitochondrial metabolic process, thus maintaining oral homeostasis. Chronic stress enhances the regulatory effects of microbiota on oral homeostasis.

FRONTIERS IN IMMUNOLOGY (2022)

添加到收藏夹
Review Genetics & Heredity

Modification mapping by nanopore sequencing

Laura K. White et al.

Summary: This review provides an introduction to nanopore sequencing and its use in direct detection of nucleic acid modifications. Nanopore sequencing, as a third generation sequencing technology, offers advantages in high throughput and direct detection of nucleic acid modifications. Numerous endogenous and synthetic nucleic acid modifications have been studied using nanopore sequencing. Advances in sequencing chemistry and analysis methods are expected to improve the identification and quantification of these epigenetic marks.

FRONTIERS IN GENETICS (2022)

添加到收藏夹
Article Microbiology

Using Nanopore Sequencing to Obtain Complete Bacterial Genomes from Saliva Samples

Jonathon L. Baker

Summary: Recent advances in nanopore sequencing technology and genome assembly methods have made it possible to obtain complete bacterial genomes from human saliva samples. This study presents methods using Oxford Nanopore (ONT) and IIlumina sequencing to obtain 11 complete bacterial genomes from human saliva samples, enabling accurate pangenome analysis and providing insights into the lifestyle and ecological role of these bacteria within the human oral microbiota.

MSYSTEMS (2022)

添加到收藏夹
Review Endocrinology & Metabolism

Good practices and recommendations for using and benchmarking computational metabolomics metabolite annotation tools

Niek F. de Jonge et al.

Summary: This article introduces the recent advances in computational metabolite annotation workflows, with a special focus on the evaluation and comparison of these tools. While the progress is significant and promising, inconsistencies in benchmarking different tools hinder users from selecting the most appropriate method. The article summarizes the benchmarking strategies of different tools and provides recommendations.

METABOLOMICS (2022)

添加到收藏夹
Article Genetics & Heredity

Investigating CRISPR spacer targets and their impact on genomic diversification of Streptococcus mutans

Alejandro R. R. Walker et al.

Summary: CRISPR-Cas is a bacterial immune system that provides immunity against foreign DNA. The study found that S. mutans strains primarily target phage DNA with their CRISPR spacers, and they have also developed immunity against plasmids and integrative and conjugative elements. While there may also be considerable immunity against bacterial DNA, further investigation is needed. However, at a species-level, CRISPR-Cas has minimal impact on horizontal gene transfer constraints.

FRONTIERS IN GENETICS (2022)

添加到收藏夹
Article Endocrinology & Metabolism

PeakForest: a multi-platform digital infrastructure for interoperable metabolite spectral data and metadata management

Nils Paulhe et al.

Summary: A comprehensive resource, PeakForest addresses the technical bottleneck in annotating large-scale spectral data and identifying metabolites in metabolomics laboratories. It provides a structured database with tools for data curation and browsing, facilitating the sharing and integration of spectral data across laboratories.

METABOLOMICS (2022)

添加到收藏夹
Article Biochemistry & Molecular Biology

Nanopore sequencing of RNA and cDNA molecules in Escherichia coli

Felix Gruenberger et al.

Summary: High-throughput sequencing has revolutionized our understanding of transcriptome architectures. The introduction of ONT single-molecule sequencing platform has allowed for sequencing full-length transcripts of eukaryotic and viral RNAs, but applications in prokaryotes remain limited. A comprehensive study on ONT RNA-seq in Escherichia coli demonstrates that (PCR)-cDNA-seq offers improved yield and accuracy compared to direct RNA sequencing, making it a valuable tool for quantitative measurements and precise transcript analysis.

RNA (2022)

添加到收藏夹
Article Biochemistry & Molecular Biology

Deep metagenomics examines the oral microbiome during dental caries, revealing novel taxa and co-occurrences with host molecules

Jonathon L. Baker et al.

Summary: This study analyzed the oral microbiome and host cytokines in children with dental caries and healthy dentition, uncovering novel bacterial species and differences in microbial composition and host immune markers between the two groups. The findings expand knowledge on the etiology of dental caries and provide potential therapeutic targets for future research.

GENOME RESEARCH (2021)

添加到收藏夹
Article Biochemistry & Molecular Biology

Chemically informed analyses of metabolomics mass spectrometry data with Qemistree

Anupriya Tripathi et al.

Summary: Qemistree is a data exploration strategy based on the hierarchical organization of molecular fingerprints predicted from fragmentation spectra, allowing mass spectrometry data to be represented in the context of sample metadata and chemical ontologies. The software pipeline is freely available to the microbiome and metabolomics communities as a QIIME2 plugin and a global natural products social molecular networking workflow, providing tools to compare metabolomics samples across different experimental conditions and to visualize chemical diversity in a collection of samples.

NATURE CHEMICAL BIOLOGY (2021)

添加到收藏夹
Review Dentistry, Oral Surgery & Medicine

Metatranscriptomic analyses of the oral microbiome

Ana E. Duran-Pinedo

Summary: The oral microbiome composition and gene-expression profiles play crucial roles in disease development, especially in periodontal disease and caries. The functional activities of different species within the subgingival microbiota are interconnected, and efforts are being made to identify changes associated with transitions between health and disease.

PERIODONTOLOGY 2000 (2021)

添加到收藏夹
Review Dentistry, Oral Surgery & Medicine

Metaproteome and metabolome of oral microbial communities

Nagihan Bostanci et al.

Summary: This article focuses on metaproteomic and metabolomic approaches for oral biologic samples, revealing the functionality and underlying regulatory processes within various oral microbial communities. Knowledge of the proteomic interplay and metabolic interactions of microorganisms within oral biofilm and salivary microbiome communities is presented and discussed from clinical and basic research perspectives.

PERIODONTOLOGY 2000 (2021)

添加到收藏夹
Review Dentistry, Oral Surgery & Medicine

Probing periodontal microbial dark matter using metataxonomics and metagenomics

Purnima S. Kumar et al.

Summary: The study of the periodontal microbial community has been influenced by a long history of cultivation-based and microscopic investigations, leading to the recognition of a discrepancy between culturable and uncultured bacteria. The development of DNA sequencing as a tool to study microbial dark matter has revolutionized the field, enabling the discovery of new species and functions and challenging traditional views on the role of the oral microbiome in health and disease.

PERIODONTOLOGY 2000 (2021)

添加到收藏夹
Article Multidisciplinary Sciences

Long-read metagenomics using PromethION uncovers oral bacteriophages and their interaction with host bacteria

Koji Yahara et al.

Summary: This study utilizes PromethION for long-read metagenomic analysis, identifying hundreds of viral contigs in human saliva and shedding light on the interactions between bacteriophages and host bacteria.

NATURE COMMUNICATIONS (2021)

添加到收藏夹
Editorial Material Microbiology

Community-led, integrated, reproducible multi-omics with anvi'o

A. Murat Eren et al.

Summary: In microbiology, there is an abundance of big data, but the workflows designed to interpret the data may constrain the biological questions that can be asked. Anvi'o, a community-led multi-omics platform, is maturing into an open software ecosystem that reduces constraints in 'omics data analyses.

NATURE MICROBIOLOGY (2021)

添加到收藏夹
Review Biotechnology & Applied Microbiology

Nanopore sequencing technology, bioinformatics and applications

Yunhao Wang et al.

Summary: Advancements in nanopore technologies for sequencing long DNA and RNA molecules have greatly improved accuracy, read length, and throughput. The field of nanopore sequencing continues to offer opportunities for enhancing data quality and analytical approaches through the development of new technologies tailored to specific applications.

NATURE BIOTECHNOLOGY (2021)

添加到收藏夹
Article Cell Biology

Full-length transcript sequencing of human and mouse cerebral cortex identifies widespread isoform diversity and alternative splicing

Szi Kay Leung et al.

Summary: Using long-read isoform sequencing, this study generated full-length transcript sequences in the human and mouse cortex, identifying new transcripts and similar global patterns of transcript diversity. Species-specific differences in certain genes were observed, as well as developmental changes in alternative splicing in the cortex.

CELL REPORTS (2021)

添加到收藏夹
Article Biotechnology & Applied Microbiology

Long-read metagenomics retrieves complete single-contig bacterial genomes from canine feces

Anna Cusco et al.

Summary: Long-read sequencing in metagenomics allows for the assembly of complete genomes from complex microbial communities, providing important biological information that is often missed by short-read sequencing. In this study, long-read metagenomics with Nanopore sequencing successfully retrieved eight high-quality metagenome-assembled genomes (HQ MAGs) from a dog fecal sample, including crucial ribosomal genes and tRNAs. Additionally, high-molecular-weight DNA extraction improved assembly contiguity and recovery of rRNA operons, demonstrating the significance of long reads in metagenomics research.

BMC GENOMICS (2021)

添加到收藏夹
Article Biochemistry & Molecular Biology

iNetModels 2.0: an interactive visualization and database of multi-omics data

Muhammad Arif et al.

Summary: iNetModels is an interactive database and visualization platform that showcases the associations between various omics data, allowing users to explore human wellness and disease research with ease.

NUCLEIC ACIDS RESEARCH (2021)

添加到收藏夹
Article Biology

Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3

Francesco Beghini et al.

Summary: Culture-independent analyses of microbial communities have advanced significantly in the past decade, particularly due to the emergence of Shotgun Metagenomics. bioBakery 3, a newly developed toolset, enhances the accuracy and scope of taxonomic, functional, and phylogenetic profiling in microbial community studies by providing an expanding set of reference sequences.

ELIFE (2021)

添加到收藏夹
Article Biotechnology & Applied Microbiology

Pangenome analysis and virulence profiling of Streptococcus intermedius

Dhiraj Sinha et al.

Summary: By analyzing the genomes of 27 S. intermedius strains causing different infections, specific virulence genes were found to be associated with strains causing brain abscess or broncho-pulmonary infection compared to those causing liver and abdominal abscess. This study provides insight into the pathogenesis of S. intermedius and highlights potential diagnostic targets.

BMC GENOMICS (2021)

添加到收藏夹
Article Biochemistry & Molecular Biology

Human oral mucosa cell atlas reveals a stromal-neutrophil axis regulating tissue immunity

Drake Winslow Williams et al.

Summary: The oral mucosa is an understudied barrier tissue rich in antigens and commensals, susceptible to periodontitis. By compiling a single-cell transcriptome atlas, researchers identified inflammatory epithelial and stromal cell populations promoting antimicrobial defenses and neutrophil recruitment. Exaggerated stromal cell responsiveness was found to enhance neutrophil and leukocyte infiltration in periodontitis, highlighting the role of tissue stroma in regulating mucosal tissue homeostasis and disease pathogenesis.

CELL (2021)

添加到收藏夹
Article Dentistry, Oral Surgery & Medicine

The Human Salivary Proteome Wiki: A Community-Driven Research Platform

W. W. Lau et al.

Summary: Saliva is now being used for on-site, remote, and real-time monitoring of oral and systemic health. The Human Salivary Proteome (HSP) Wiki is a public platform that integrates data from various sources to help researchers explore the protein composition of saliva.

JOURNAL OF DENTAL RESEARCH (2021)

添加到收藏夹
Editorial Material Multidisciplinary Sciences

PROTEOMICS AT THE SINGLE-CELL LEVEL

Jeffrey M. Perkel

NATURE (2021)

添加到收藏夹
Article Biochemical Research Methods

Mass spectrometry-based metabolomics: a guide for annotation, quantification and best reporting practices

Saleh Alseekh et al.

Summary: Compound identification and reliable quantification in metabolomics are complicated by the chemical complexity and dynamic range of the metabolome, while quantification in complex mixtures can be further complicated by ion suppression and the presence of isomers.

NATURE METHODS (2021)

添加到收藏夹
Article Multidisciplinary Sciences

Ion identity molecular networking for mass spectrometry-based metabolomics in the GNPS environment

Robin Schmid et al.

Summary: The authors develop a new Ion Identity Molecular Networking (IIMN) approach that integrates chromatographic peak shape correlation analysis to connect and collapse different ion species of the same molecule, improving network connectivity for structurally related molecules.

NATURE COMMUNICATIONS (2021)

添加到收藏夹
Letter Multidisciplinary Sciences

Re-evaluating the evidence for a universal genetic boundary among microbial species

Connor S. Murray et al.

NATURE COMMUNICATIONS (2021)

添加到收藏夹
Article Microbiology

Single-Cell RNA Sequencing Elucidates the Structure and Organization of Microbial Communities

Melanie A. Brennan et al.

Summary: Clonal bacterial populations exhibit various forms of heterogeneity, which impact productivity and disease virulence. Single-cell RNA sequencing (scRNA-seq) is considered a valuable approach to examine this heterogeneity, but current methods face challenges when applied to bacteria.

FRONTIERS IN MICROBIOLOGY (2021)

添加到收藏夹
Article Microbiology

Ultra-accurate microbial amplicon sequencing with synthetic long reads

Benjamin J. Callahan et al.

Summary: LoopSeq is a commercially available synthetic long-read (SLR) sequencing technology that generates highly accurate long reads from standard short reads, enabling direct identification of microbial genes and species in complex samples. Compared to standard Illumina amplicon sequencing, LoopSeq offers an order-of-magnitude improvement in length and accuracy, allowing accurate identification of species and strains from complex to low-biomass microbiome samples.

MICROBIOME (2021)

添加到收藏夹
Article Microbiology

Complete Genomes of Clade G6 Saccharibacteria Suggest a Divergent Ecological Niche and Lifestyle

Jonathon L. Baker

Summary: The study identified highly novel Saccharibacteria G6 branch, with highly divergent genomes compared to G1 branch, having 50% of core genes with unknown functions. The G6 branch may have a distinct lifestyle and ecological niche, possibly related to alternative hosts and/or host dependencies.

MSPHERE (2021)

添加到收藏夹
Article Microbiology

Genomic Stability and Genetic Defense Systems in Dolosigranulum pigrum, a Candidate Beneficial Bacterium from the Human Microbiome

Stephany Flores Ramos et al.

Summary: Dolosigranulum pigrum is positively associated with indicators of health in multiple epidemiological studies of human nasal microbiota. Comparative genome analysis of 28 strains collected over 20 years revealed highly conserved chromosomal synteny and identified defense mechanisms against mobile genetic elements. This suggests a potential role for D. pigrum as a therapeutic bacterium.

MSYSTEMS (2021)

添加到收藏夹
Article Microbiology

Comparative Pan-Genome Analysis of Oral Veillonella Species

Izumi Mashima et al.

Summary: The genus Veillonella in the oral microbiome includes eight species with important metabolic pathways utilizing lactate as an energy source. Through a comparative pan-genome analysis, it was found that these species have conserved pathways using carbohydrates other than lactate as an energy source, helping to understand the metabolic network in oral microbiomes.

MICROORGANISMS (2021)

添加到收藏夹
Article Biotechnology & Applied Microbiology

Trycycler: consensus long-read assemblies for bacterial genomes

Ryan R. Wick et al.

Summary: Trycycler is a tool that produces a consensus assembly from multiple input assemblies to reduce errors in long-read sequencing. Post-assembly polishing further improves accuracy. Multiple users converge on similar assemblies that are more accurate than those produced by automated assembly tools.

GENOME BIOLOGY (2021)

添加到收藏夹
Article Biotechnology & Applied Microbiology

STAT: a fast, scalable, MinHash-based k-mer tool to assess Sequence Read Archive next-generation sequence submissions

Kenneth S. Katz et al.

Summary: The study introduces a new tool, STAT, for fast taxonomic diversity assessment of submissions to NCBI, independent of metadata. The tool is accurate, reliable, and scalable, providing a reliable criteria for data selection by the scientific community, while also enhancing the submission metadata with taxonomic terms.

GENOME BIOLOGY (2021)

添加到收藏夹
Article Dentistry, Oral Surgery & Medicine

Oral Microbiome and Gingival Gene Expression of Inflammatory Biomolecules With Aging and Periodontitis

Jeffrey L. Ebersole et al.

Summary: This study observed age-related differences in inflammatory response characteristics, including chemokine receptor gene and cytokine expression levels. Specific chemokine and chemokine receptor genes were affected by the disease process, with predominant changes during disease initiation.

FRONTIERS IN ORAL HEALTH (2021)

添加到收藏夹
Review Biochemistry & Molecular Biology

The oralome and its dysbiosis: New insights into oral microbiome-host interactions

Allan Radaic et al.

Summary: The oralome is a summary of the interactions between oral microorganisms and the host, which can impact the health and disease status of the host. Current research focuses on changes in the oral microbiome in the oral environment and discusses techniques for modulating the dysbiotic oral microbiome to prevent and treat diseases.

COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL (2021)

添加到收藏夹
Article Multidisciplinary Sciences

Microbial single-cell RNA sequencing by split-pool barcoding

Anna Kuchina et al.

Summary: microSPLiT is a high-throughput single-cell RNA sequencing method that can resolve heterogeneous transcriptional states in Gram-negative and Gram-positive bacteria. Researchers used microSPLiT to process Bacillus subtilis cells and obtained detailed information on changes in metabolism and lifestyle, as well as identified new gene expression states in the bacterial population.

SCIENCE (2021)

添加到收藏夹
Review Immunology

Local and systemic mechanisms linking periodontal disease and inflammatory comorbidities

George Hajishengallis et al.

Summary: Periodontitis is causally linked to the development of other chronic inflammatory diseases outside the oral mucosa, and intervention studies have shown that local treatment of periodontitis can ameliorate surrogate markers of comorbid conditions. Experimental animal studies have further strengthened the potential causal link by establishing biologically plausible and clinically consistent mechanisms. Understanding the impact of disseminated periodontal pathogens and systemic inflammation associated with periodontitis on extra-oral pathologies may lead to new therapeutic options to reduce the risk of periodontitis-associated comorbidities.

NATURE REVIEWS IMMUNOLOGY (2021)

添加到收藏夹
Article Biotechnology & Applied Microbiology

Auto-deconvolution and molecular networking of gas chromatography-mass spectrometry data

Alexander A. Aksenov et al.

Summary: This study developed a machine learning approach that enables auto-deconvolution of gas chromatography-mass spectrometry data for the analysis and comparison of chemical compounds.

NATURE BIOTECHNOLOGY (2021)

添加到收藏夹
Article Biochemical Research Methods

Proteomics, Lipidomics, Metabolomics, and 16S DNA Sequencing of Dental Plaque From Patients With Diabetes and Periodontal Disease

Katherine A. Overmyer et al.

Summary: The study investigated the complex microbial interactions of the oral microbiome with human health through multiple analyses, revealing distinctive features related to prediabetes, type 2 diabetes, and periodontal diseases, such as increased abundance of specific microorganisms and significant changes in specific lipids and proteins in different groups. The findings also highlighted a novel microbial metabolic pathway and significant associations of host-derived proteins with periodontal diseases.

MOLECULAR & CELLULAR PROTEOMICS (2021)

添加到收藏夹
Review Dentistry, Oral Surgery & Medicine

Single-Cell Genomics and the Oral Microbiome

M. Balachandran et al.

JOURNAL OF DENTAL RESEARCH (2020)

添加到收藏夹
Article Biotechnology & Applied Microbiology

Complete, closed bacterial genomes from microbiomes using nanopore sequencing

Eli L. Moss et al.

NATURE BIOTECHNOLOGY (2020)

添加到收藏夹
Letter Biotechnology & Applied Microbiology

Mass spectrometry searches using MASST

Mingxun Wang et al.

NATURE BIOTECHNOLOGY (2020)

添加到收藏夹
Review Dentistry, Oral Surgery & Medicine

Host-microbe interactions: Profiles in the transcriptome, the proteome, and the metabolome

Trang Nguyen et al.

PERIODONTOLOGY 2000 (2020)

添加到收藏夹
Article Multidisciplinary Sciences

Similar genomic patterns of clinical infective endocarditis and oral isolates of Streptococcus sanguinis and Streptococcus gordonii

Katrine Hojholt Iversen et al.

SCIENTIFIC REPORTS (2020)

添加到收藏夹
Review Biochemistry & Molecular Biology

Accurate and complete genomes from metagenomes

Lin-Xing Chen et al.

GENOME RESEARCH (2020)

添加到收藏夹
Review Biochemistry & Molecular Biology

Bioinformatics Methods for Mass Spectrometry-Based Proteomics Data Analysis

Chen Chen et al.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2020)

添加到收藏夹
Review Biochemistry & Molecular Biology

Special Issue about Head and Neck Cancers: HPV Positive Cancers

Panagiota Economopoulou et al.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2020)

添加到收藏夹
Article Biology

Evaluating the genome and resistome of extensively drug-resistant Klebsiella pneumoniae using native DNA and RNA Nanopore sequencing

Miranda E. Pitt et al.

GIGASCIENCE (2020)

添加到收藏夹
Article Microbiology

A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae

Jinshui Zheng et al.

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY (2020)

添加到收藏夹
Article Multidisciplinary Sciences

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0

Francesco Asnicar et al.

NATURE COMMUNICATIONS (2020)

添加到收藏夹
Article Microbiology

Prokaryotic single-cell RNA sequencing by in situ combinatorial indexing

Sydney B. Blattman et al.

NATURE MICROBIOLOGY (2020)

添加到收藏夹
Letter Biotechnology & Applied Microbiology

PICRUSt2 for prediction of metagenome functions

Gavin M. Douglas et al.

NATURE BIOTECHNOLOGY (2020)

添加到收藏夹
Article Microbiology

Tannerella serpentiformis sp. nov., isolated from the human mouth

Katherine Ansbro et al.

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY (2020)

添加到收藏夹
Article Biotechnology & Applied Microbiology

A lipidome atlas in MS-DIAL 4

Hiroshi Tsugawa et al.

NATURE BIOTECHNOLOGY (2020)

添加到收藏夹
Article Cell Biology

Acquisition and Adaptation of Ultra-small Parasitic Reduced Genome Bacteria to Mammalian Hosts

Jeffrey S. McLean et al.

CELL REPORTS (2020)

添加到收藏夹
Article Biochemical Research Methods

Feature-based molecular networking in the GNPS analysis environment

Louis-Felix Nothias et al.

NATURE METHODS (2020)

添加到收藏夹
Article Biochemical Research Methods

metaFlye: scalable long-read metagenome assembly using repeat graphs

Mikhail Kolmogorov et al.

NATURE METHODS (2020)

添加到收藏夹
Article Biology

Metagenomics of the modern and historical human oral microbiome with phylogenetic studies on Streptococcus mutans and Streptococcus sobrinus

Mark Achtman et al.

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2020)

添加到收藏夹
Article Immunology

Proteome and Microbiome Mapping of Human Gingival Tissue in Health and Disease

Kai Bao et al.

FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY (2020)

添加到收藏夹
Article Microbiology

Single-cell RNA-sequencing reports growth-condition-specific global transcriptomes of individual bacteria

Fabian Imdahl et al.

NATURE MICROBIOLOGY (2020)

添加到收藏夹
Article Biotechnology & Applied Microbiology

Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome

Alon Shaiber et al.

GENOME BIOLOGY (2020)

添加到收藏夹
Article Biotechnology & Applied Microbiology

Metapangenomics of the oral microbiome provides insights into habitat adaptation and cultivar diversity

Daniel R. Utter et al.

GENOME BIOLOGY (2020)

添加到收藏夹
Review Biotechnology & Applied Microbiology

Opportunities and challenges in long-read sequencing data analysis

Shanika L. Amarasinghe et al.

GENOME BIOLOGY (2020)

添加到收藏夹
Article Ecology

Discovery of a Novel Periodontal Disease-Associated Bacterium

Pedro J. Torres et al.

MICROBIAL ECOLOGY (2019)

添加到收藏夹
Article Biochemical Research Methods

MaxQuant. Live Enables Global Targeting of More Than 25,000 Peptides

Christoph Wichmann et al.

MOLECULAR & CELLULAR PROTEOMICS (2019)

添加到收藏夹
Article Biochemical Research Methods

SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information

Kai Duhrkop et al.

NATURE METHODS (2019)

添加到收藏夹
Article Biochemistry & Molecular Biology

Efficient and unique cobarcoding of second-generation sequencing reads from long DNA molecules enabling cost-effective and accurate sequencing, haplotyping, and de novo assembly

Ou Wang et al.

GENOME RESEARCH (2019)

添加到收藏夹
Article Biotechnology & Applied Microbiology

Assembly of long, error-prone reads using repeat graphs

Mikhail Kolmogorov et al.

NATURE BIOTECHNOLOGY (2019)

添加到收藏夹
Letter Biotechnology & Applied Microbiology

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

Evan Bolyen et al.

NATURE BIOTECHNOLOGY (2019)

添加到收藏夹
Article Biochemical Research Methods

Best practices and benchmarks for intact protein analysis for top-down mass spectrometry

Daniel P. Donnelly et al.

NATURE METHODS (2019)

添加到收藏夹
Article Multidisciplinary Sciences

Establishing microbial composition measurement standards with reference frames

James T. Morton et al.

NATURE COMMUNICATIONS (2019)

添加到收藏夹
Article Multidisciplinary Sciences

MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies

Dongwan D. Kang et al.

PEERJ (2019)

添加到收藏夹
Article Biotechnology & Applied Microbiology

Targeted isolation and cultivation of uncultivated bacteria by reverse genomics

Karissa L. Cross et al.

NATURE BIOTECHNOLOGY (2019)

添加到收藏夹
Article Biotechnology & Applied Microbiology

Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome

Aaron M. Wenger et al.

NATURE BIOTECHNOLOGY (2019)

添加到收藏夹
Article Biology

rnaSPAdes: a de novo transcriptome assembler and its application to RNA-Seq data

Elena Bushmanova et al.

GIGASCIENCE (2019)

添加到收藏夹
Article Biochemical Research Methods

Learning representations of microbe-metabolite interactions

James T. Morton et al.

NATURE METHODS (2019)

添加到收藏夹
Article Biochemistry & Molecular Biology

Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle

Edoardo Pasolli et al.

CELL (2019)

添加到收藏夹
Article Dentistry, Oral Surgery & Medicine

Role of Saliva and Salivary Diagnostics in the Advancement of Oral Health

C. Dawes et al.

JOURNAL OF DENTAL RESEARCH (2019)

添加到收藏夹
Letter Biotechnology & Applied Microbiology

Errors in long-read assemblies can critically affect protein prediction

Mick Watson et al.

NATURE BIOTECHNOLOGY (2019)

添加到收藏夹
Article Microbiology

Metagenome sequencing-based strain-level and functional characterization of supragingival microbiome associated with dental caries in children

Nezar Noor Al-Hebshi et al.

JOURNAL OF ORAL MICROBIOLOGY (2019)

添加到收藏夹
Review Chemistry, Analytical

New mass spectrometry technologies contributing towards comprehensive and high throughput omics analyses of single cells

Sneha P. Couvillion et al.

ANALYST (2019)

添加到收藏夹
Article Biotechnology & Applied Microbiology

Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation

John Beaulaurier et al.

NATURE BIOTECHNOLOGY (2018)

添加到收藏夹
Article Biochemical Research Methods

3D molecular cartography using LC-MS facilitated by Optimus and 'ili software

Ivan Protsyuk et al.

NATURE PROTOCOLS (2018)

添加到收藏夹
Article Biochemical Research Methods

Parallelization of MAFFT for large-scale multiple sequence alignments

Tsukasa Nakamura et al.

BIOINFORMATICS (2018)

添加到收藏夹
Article Biochemical Research Methods

Minimap2: pairwise alignment for nucleotide sequences

Heng Li

BIOINFORMATICS (2018)

添加到收藏夹
Review Microbiology

Rapid and robust MALDI-TOF MS techniques for microbial identification: a brief overview of their diverse applications

Kyoung-Soon Jang et al.

JOURNAL OF MICROBIOLOGY (2018)

添加到收藏夹
Article Biochemical Research Methods

Highly parallel direct RNA sequencing on an array of nanopores

Daniel R. Garalde et al.

NATURE METHODS (2018)

添加到收藏夹
Article Biochemical Research Methods

Data processing, multi-omic pathway mapping, and metabolite activity analysis using XCMS Online

Erica M. Forsberg et al.

NATURE PROTOCOLS (2018)

添加到收藏夹
Review Microbiology

Best practices for analysing microbiomes

Rob Knight et al.

NATURE REVIEWS MICROBIOLOGY (2018)

添加到收藏夹
Review Biochemistry & Molecular Biology

Oral Biofilms: Pathogens, Matrix, and Polymicrobial Interactions in Microenvironments

William H. Bowen et al.

TRENDS IN MICROBIOLOGY (2018)

添加到收藏夹
Article Microbiology

Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy

Christian M. K. Sieber et al.

NATURE MICROBIOLOGY (2018)

添加到收藏夹
Article Microbiology

Genome-Based Taxonomic Classification of the Phylum Actinobacteria

Imen Nouioui et al.

FRONTIERS IN MICROBIOLOGY (2018)

添加到收藏夹
Software Review Microbiology

MetaWRAP-a flexible pipeline for genome-resolved metagenomic data analysis

Gherman V. Uritskiy et al.

MICROBIOME (2018)

添加到收藏夹
Review Microbiology

The oral microbiota: dynamic communities and host interactions

Richard J. Lamont et al.

NATURE REVIEWS MICROBIOLOGY (2018)

添加到收藏夹
Article Multidisciplinary Sciences

High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries

Chirag Jain et al.

NATURE COMMUNICATIONS (2018)

添加到收藏夹
Article Microbiology

Uncovering complex microbiome activities via metatranscriptomics during 24hours of oral biofilm assembly and maturation

Anna Edlund et al.

MICROBIOME (2018)

添加到收藏夹
Article Microbiology

Species Designations Belie Phenotypic and Genotypic Heterogeneity in Oral Streptococci

Irina M. Velsko et al.

MSYSTEMS (2018)

添加到收藏夹
Article Microbiology

New Insights into Human Nostril Microbiome from the Expanded Human Oral Microbiome Database (eHOMD): a Resource for the Microbiome of the Human Aerodigestive Tract

Isabel F. Escapa et al.

MSYSTEMS (2018)

添加到收藏夹
Article Biochemical Research Methods

FDR-controlled metabolite annotation for high-resolution imaging mass spectrometry

Andrew Palmer et al.

NATURE METHODS (2017)

添加到收藏夹
Article Biochemistry & Molecular Biology

metaSPAdes: a new versatile metagenomic assembler

Sergey Nurk et al.

GENOME RESEARCH (2017)

添加到收藏夹
Article Biochemistry & Molecular Biology

Fast and accurate de novo genome assembly from long uncorrected reads

Robert Vaser et al.

GENOME RESEARCH (2017)

添加到收藏夹
Article Biochemistry & Molecular Biology

Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation

Sergey Koren et al.

GENOME RESEARCH (2017)

添加到收藏夹
Review Biology

Epstein-Barr virus infection and nasopharyngeal carcinoma

Sai Wah Tsao et al.

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2017)

添加到收藏夹
Article Multidisciplinary Sciences

De novo peptide sequencing by deep learning

Ngoc Hieu Tran et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)

添加到收藏夹
Review Biochemistry & Molecular Biology

Ecology of the Oral Microbiome: Beyond Bacteria

Jonathon L. Baker et al.

TRENDS IN MICROBIOLOGY (2017)

添加到收藏夹
Article Biochemical Research Methods

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

Ryan R. Wick et al.

PLOS COMPUTATIONAL BIOLOGY (2017)

添加到收藏夹
Article Microbiology

Microbiome Datasets Are Compositional: And This Is Not Optional

Gregory B. Gloor et al.

FRONTIERS IN MICROBIOLOGY (2017)

添加到收藏夹
Article Microbiology

Balance Trees Reveal Microbial Niche Differentiation

James T. Morton et al.

MSYSTEMS (2017)

添加到收藏夹
Article Biotechnology & Applied Microbiology

Metagenomic and metatranscriptomic analysis of saliva reveals disease-associated microbiota in patients with periodontitis and dental caries

Daniel Belstrom et al.

NPJ BIOFILMS AND MICROBIOMES (2017)

添加到收藏夹
Article Biotechnology & Applied Microbiology

Assembling metagenomes, one community at a time

Andries Johannes van der Walt et al.

BMC GENOMICS (2017)

添加到收藏夹
Article Biochemical Research Methods

MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets

Yu-Wei Wu et al.

BIOINFORMATICS (2016)

添加到收藏夹
Article Biochemical Research Methods

HYBRIDSPADES: an algorithm for hybrid assembly of short and long reads

Dmitry Antipov et al.

BIOINFORMATICS (2016)

添加到收藏夹
Article Biochemical Research Methods

Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences

Heng Li

BIOINFORMATICS (2016)

添加到收藏夹
Article Biotechnology & Applied Microbiology

Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking

Mingxun Wang et al.

NATURE BIOTECHNOLOGY (2016)

添加到收藏夹
Article Biochemical Research Methods

OpenMS: a flexible open-source software platform for mass spectrometry data analysis

Hannes L. Roest et al.

NATURE METHODS (2016)

添加到收藏夹
Article Biochemical Research Methods

DADA2: High-resolution sample inference from Illumina amplicon data

Benjamin J. Callahan et al.

NATURE METHODS (2016)

添加到收藏夹
Article Biochemical Research Methods

The MaxQuant computational platform for mass spectrometry-based shotgun proteomics

Stefka Tyanova et al.

NATURE PROTOCOLS (2016)

添加到收藏夹
Article Multidisciplinary Sciences

FAMSA: Fast and accurate multiple sequence alignment of huge protein families

Sebastian Deorowicz et al.

SCIENTIFIC REPORTS (2016)

添加到收藏夹
Article Biotechnology & Applied Microbiology

The real cost of sequencing: scaling computation to keep pace with data generation

Paul Muir et al.

GENOME BIOLOGY (2016)

添加到收藏夹
Article Biochemical Research Methods

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

Dinghua Li et al.

BIOINFORMATICS (2015)

添加到收藏夹
Article Biochemical Research Methods

Roary: rapid large-scale prokaryote pan genome analysis

Andrew J. Page et al.

BIOINFORMATICS (2015)

添加到收藏夹
Article Ecology

Meta-omics uncover temporal regulation of pathways across oral microbiome genera during in vitro sugar metabolism

Anna Edlund et al.

ISME JOURNAL (2015)

添加到收藏夹
Editorial Material Biochemical Research Methods

Focus on the 20-Year Anniversary of SEQUEST

Jennifer S. Brodbelt et al.

JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY (2015)

添加到收藏夹
Article Biochemical Research Methods

A complete bacterial genome assembled de novo using only nanopore sequencing data

Nicholas J. Loman et al.

NATURE METHODS (2015)

添加到收藏夹
Article Biochemical Research Methods

Improved data analysis for the MinION nanopore sequencer

Miten Jain et al.

NATURE METHODS (2015)

添加到收藏夹
Article Biochemical Research Methods

The human oral metaproteome reveals potential biomarkers for caries disease

Pedro Belda-Ferre et al.

PROTEOMICS (2015)

添加到收藏夹
Article Microbiology

Dynamic Changes in the Subgingival Microbiome and Their Potential for Diagnosis and Prognosis of Periodontitis

Baochen Shi et al.

MBIO (2015)

添加到收藏夹
Article Genetics & Heredity

Functional signatures of oral dysbiosis during periodontitis progression revealed by microbial metatranscriptome analysis

Susan Yost et al.

GENOME MEDICINE (2015)

添加到收藏夹
Article Immunology

Transcriptomic analysis of three Veillonella spp. present in carious dentine and in the saliva of caries-free individuals

Thuy Do et al.

FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY (2015)

添加到收藏夹
Article Biotechnology & Applied Microbiology

De novo assembly of bacterial transcriptomes from RNA-seq data

Brian Tjaden

GENOME BIOLOGY (2015)

添加到收藏夹
Article Biochemistry & Molecular Biology

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

Lam-Tung Nguyen et al.

MOLECULAR BIOLOGY AND EVOLUTION (2015)

添加到收藏夹
Article Biochemical Research Methods

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

Yang Liao et al.

BIOINFORMATICS (2014)

添加到收藏夹
Review Biochemical Research Methods

Toward better understanding of artifacts in variant calling from high-coverage samples

Heng Li

BIOINFORMATICS (2014)

添加到收藏夹
Article Biochemical Research Methods

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

Alexandros Stamatakis

BIOINFORMATICS (2014)

添加到收藏夹
Article Microbiology

Diversity and genomic insights into the uncultured Chloroflexi from the human microbiota

Alisha G. Campbell et al.

ENVIRONMENTAL MICROBIOLOGY (2014)

添加到收藏夹
Article Microbiology

Streptococcus dentisani sp nov., a novel member of the mitis group

Anny Camelo-Castillo et al.

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY (2014)

添加到收藏夹
Article Ecology

The social structure of microbial community involved in colonization resistance

Xuesong He et al.

ISME JOURNAL (2014)

添加到收藏夹
Article Ecology

Community-wide transcriptome of the oral microbiome in subjects with and without periodontitis

Ana E. Duran-Pinedo et al.

ISME JOURNAL (2014)

添加到收藏夹
Article Biochemical Research Methods

Binning metagenomic contigs by coverage and composition

Johannes Alneberg et al.

NATURE METHODS (2014)

添加到收藏夹
Article Multidisciplinary Sciences

Single Cell Genomics of Uncultured, Health-Associated Tannerella BU063 (Oral Taxon 286) and Comparison to the Closely Related Pathogen Tannerella forsythia

Clifford J. Beall et al.

PLOS ONE (2014)

添加到收藏夹
Article Multidisciplinary Sciences

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

Bruce J. Walker et al.

PLOS ONE (2014)

添加到收藏夹
Article Microbiology

Metatranscriptomics of the Human Oral Microbiome during Health and Disease

Peter Jorth et al.

MBIO (2014)

添加到收藏夹
Article Immunology

Functional expression of dental plaque microbiota

Scott N. Peterson et al.

FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY (2014)

添加到收藏夹
Article Multidisciplinary Sciences

PhyloSift: phylogenetic analysis of genomes and metagenomes

Aaron E. Darling et al.

PEERJ (2014)

添加到收藏夹
Article Microbiology

Unifying the analysis of high-throughput sequencing datasets: characterizing RNA-seq, 16S rRNA gene sequencing and selective growth experiments by compositional data analysis

Andrew D. Fernandes et al.

MICROBIOME (2014)

添加到收藏夹
Article Biochemical Research Methods

UniNovo: a universal tool for de novo peptide sequencing

Kyowon Jeong et al.

BIOINFORMATICS (2013)

添加到收藏夹
Article Biochemistry & Molecular Biology

Genome of the pathogen Porphyromonas gingivalis recovered from a biofilm in a hospital sink using a high-throughput single-cell genomics platform

Jeffrey S. McLean et al.

GENOME RESEARCH (2013)

添加到收藏夹
Article Biochemistry & Molecular Biology

Evolutionary and Population Genomics of the Cavity Causing Bacteria Streptococcus mutans

Omar E. Cornejo et al.

MOLECULAR BIOLOGY AND EVOLUTION (2013)

添加到收藏夹
Article Biochemical Research Methods

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

Chen-Shan Chin et al.

NATURE METHODS (2013)

添加到收藏夹
Article Multidisciplinary Sciences

Multiple Single-Cell Genomes Provide Insight into Functions of Uncultured Deltaproteobacteria in the Human Oral Cavity

Alisha G. Campbell et al.

PLOS ONE (2013)

添加到收藏夹
Article Multidisciplinary Sciences

Phenotypic Heterogeneity of Genomically-Diverse Isolates of Streptococcus mutans

Sara R. Palmer et al.

PLOS ONE (2013)

添加到收藏夹
Article Ecology

The oral metagenome in health and disease

Pedro Belda-Ferre et al.

ISME JOURNAL (2012)

添加到收藏夹
Article Multidisciplinary Sciences

Structure, function and diversity of the healthy human microbiome

Curtis Huttenhower et al.

NATURE (2012)

添加到收藏夹
Article Biotechnology & Applied Microbiology

Hybrid error correction and de novo assembly of single-molecule sequencing reads

Sergey Koren et al.

NATURE BIOTECHNOLOGY (2012)

添加到收藏夹
Article Biochemical Research Methods

Fast gapped-read alignment with Bowtie 2

Ben Langmead et al.

NATURE METHODS (2012)

添加到收藏夹
Article Biochemistry & Molecular Biology

PanOCT: automated clustering of orthologs using conserved gene neighborhood for pan-genomic analysis of bacterial strains and closely related species

Derrick E. Fouts et al.

NUCLEIC ACIDS RESEARCH (2012)

添加到收藏夹
Review Microbiology

Applications of MALDI-TOF mass spectrometry in clinical diagnostic microbiology

Antony Croxatto et al.

FEMS MICROBIOLOGY REVIEWS (2012)

添加到收藏夹
Article Biotechnology & Applied Microbiology

Full-length transcriptome assembly from RNA-Seq data without a reference genome

Manfred G. Grabherr et al.

NATURE BIOTECHNOLOGY (2011)

添加到收藏夹
Article Mathematical & Computational Biology

The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information

Tsute Chen et al.

DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION (2010)

添加到收藏夹
Article Biochemistry & Molecular Biology

Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding

Kevin Judd McKernan et al.

GENOME RESEARCH (2009)

添加到收藏夹
Article Biochemistry & Molecular Biology

ABySS: A parallel assembler for short read sequence data

Jared T. Simpson et al.

GENOME RESEARCH (2009)

添加到收藏夹
Article Biochemistry & Molecular Biology

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

Morgan N. Price et al.

MOLECULAR BIOLOGY AND EVOLUTION (2009)

添加到收藏夹
Article Biochemistry & Molecular Biology

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

Daniel R. Zerbino et al.

GENOME RESEARCH (2008)

添加到收藏夹
Article Multidisciplinary Sciences

Accurate whole human genome sequencing using reversible terminator chemistry

David R. Bentley et al.

NATURE (2008)

添加到收藏夹
Article Multidisciplinary Sciences

Metagenomic analysis of the human distal gut microbiome

Steven R. Gill et al.

SCIENCE (2006)

添加到收藏夹
Article Multidisciplinary Sciences

Genome sequencing in microfabricated high-density picolitre reactors

M Margulies et al.

NATURE (2005)

添加到收藏夹
Article Multidisciplinary Sciences

Obesity alters gut microbial ecology

RE Ley et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)

添加到收藏夹
Article Microbiology

Proteome analysis of Streptococcus mutans metabolic phenotype during acid tolerance

MCL Len et al.

MICROBIOLOGY-SGM (2004)

添加到收藏夹
Article Multidisciplinary Sciences

Environmental genome shotgun sequencing of the Sargasso Sea

JC Venter et al.

SCIENCE (2004)

添加到收藏夹
Article Biotechnology & Applied Microbiology

Shifts in the membrane fatty acid profile of Streptococcus mutans enhance survival in acidic environments

EA Fozo et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2004)

添加到收藏夹
Article Biochemical Research Methods

MUSCLE: a multiple sequence alignment method with reduced time and space complexity

RC Edgar

BMC BIOINFORMATICS (2004)

添加到收藏夹
Article Pharmacology & Pharmacy

Solexa Ltd

S Bennett

PHARMACOGENOMICS (2004)

添加到收藏夹
研讨会 海报 问题 讨论圈 基金 期刊 论文 科研社交 资讯集成 审稿人 关于我们 常见问题 移动App 隐私条款 使用条款
© Peeref 2019-2024. All rights reserved.