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。Biochemical Properties and Roles of DprA Protein in Bacterial Natural Transformation, Virulence, and Pilin Variation
Dhirendra Kumar Sharma et al.
JOURNAL OF BACTERIOLOGY (2023)
Culture-based approaches to studying microbial dark matter
Xuesong He
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2023)
DPAM: A domain parser for AlphaFold models
Jing Zhang et al.
PROTEIN SCIENCE (2023)
Fast and accurate protein structure search with Foldseek
Michel van Kempen et al.
NATURE BIOTECHNOLOGY (2023)
Cultivation of a vampire: 'Candidatus Absconditicoccus praedator'
Michail M. Yakimov et al.
ENVIRONMENTAL MICROBIOLOGY (2022)
Acquisition of the arginine deiminase system benefits epiparasitic Saccharibacteria and their host bacteria in a mammalian niche environment
Jing Tian et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2022)
ComFC mediates transport and handling of single-stranded DNA during natural transformation
Prashant P. Damke et al.
NATURE COMMUNICATIONS (2022)
Strain-Level Variation and Diverse Host Bacterial Responses in Episymbiotic Saccharibacteria
Jie Nie et al.
MSYSTEMS (2022)
Type IV pili trigger episymbiotic association of Saccharibacteria with its bacterial host
Bingliang Xie et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2022)
Ancient origin and constrained evolution of the division and cell wall gene cluster in Bacteria
Daniela Megrian et al.
NATURE MICROBIOLOGY (2022)
Widespread but Poorly Understood Bacteria: Candidate Phyla Radiation
Yanhan Ji et al.
MICROORGANISMS (2022)
Proton Pumping ATPases: Rotational Catalysis, Physiological Roles in Oral Pathogenic Bacteria, and Inhibitors
Mizuki Sekiya
BIOLOGICAL & PHARMACEUTICAL BULLETIN (2022)
Omnipose: a high-precision morphology-independent solution for bacterial cell segmentation
Kevin J. Cutler et al.
NATURE METHODS (2022)
Symbiosis between Candidatus Patescibacteria and Archaea Discovered in Wastewater-Treating Bioreactors
Kyohei Kuroda et al.
MBIO (2022)
Mechanisms and clinical importance of bacteriophage resistance
Julia E. Egido et al.
FEMS MICROBIOLOGY REVIEWS (2022)
Episymbiotic Saccharibacteria suppresses gingival inflammation and bone loss in mice through host bacterial modulation
Otari Chipashvili et al.
CELL HOST & MICROBE (2021)
A rooted phylogeny resolves early bacterial evolution
Gareth A. Coleman et al.
SCIENCE (2021)
Reductive evolution and unique predatory mode in the CPR bacterium Vampirococcus lugosii
David Moreira et al.
NATURE COMMUNICATIONS (2021)
Cocultivation of an ultrasmall environmental parasitic bacterium with lytic ability against bacteria associated with wastewater foams
Steven Batinovic et al.
NATURE MICROBIOLOGY (2021)
Highly accurate protein structure prediction with AlphaFold
John Jumper et al.
NATURE (2021)
Protein tertiary structure prediction and refinement using deep learning and Rosetta in CASP14
Ivan Anishchenko et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2021)
Accurate prediction of protein structures and interactions using a three-track neural network
Minkyung Baek et al.
SCIENCE (2021)
Trycycler: consensus long-read assemblies for bacterial genomes
Ryan R. Wick et al.
GENOME BIOLOGY (2021)
The IMG/M data management and analysis system v.6.0: new tools and advanced capabilities
I-Min A. Chen et al.
NUCLEIC ACIDS RESEARCH (2021)
Pfam: The protein families database in 2021
Jaina Mistry et al.
NUCLEIC ACIDS RESEARCH (2021)
KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold
Takuya Aramaki et al.
BIOINFORMATICS (2020)
Insights Obtained by Culturing Saccharibacteria With Their Bacterial Hosts
B. Bor et al.
JOURNAL OF DENTAL RESEARCH (2020)
Ranking essential bacterial processes by speed of mutant death
Larry A. Gallagher et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)
Acquisition and Adaptation of Ultra-small Parasitic Reduced Genome Bacteria to Mammalian Hosts
Jeffrey S. McLean et al.
CELL REPORTS (2020)
Saccharibacteria (TM7) in the Human Oral Microbiome
B. Bor et al.
JOURNAL OF DENTAL RESEARCH (2019)
Protein-level assembly increases protein sequence recovery from metagenomic samples manyfold
Martin Steinegger et al.
NATURE METHODS (2019)
Mechanisms of DNA Uptake by Naturally Competent Bacteria
David Dubnau et al.
Annual Review of Genetics (2019)
Targeted isolation and cultivation of uncultivated bacteria by reverse genomics
Karissa L. Cross et al.
NATURE BIOTECHNOLOGY (2019)
The distinction of CPR bacteria from other bacteria based on protein family content
Raphael Meheust et al.
NATURE COMMUNICATIONS (2019)
Fermentation Revisited: How Do Microorganisms Survive Under Energy-Limited Conditions?
Armen Trchounian et al.
TRENDS IN BIOCHEMICAL SCIENCES (2019)
KBase: The United States Department of Energy Systems Biology Knowledgebase
Adam P. Arkin et al.
NATURE BIOTECHNOLOGY (2018)
Retraction of DNA-bound type IV competence pili initiates DNA uptake during natural transformation in Vibrio cholerae
Courtney K. Ellison et al.
NATURE MICROBIOLOGY (2018)
A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life
Donovan H. Parks et al.
NATURE BIOTECHNOLOGY (2018)
Biosynthetic capacity, metabolic variety and unusual biology in the CPR and DPANN radiations
Cindy J. Castelle et al.
NATURE REVIEWS MICROBIOLOGY (2018)
Rapid evolution of decreased host susceptibility drives a stable relationship between ultrasmall parasite TM7x and its bacterial host
Batbileg Bor et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)
Hybrid assembly of the large and highly repetitive genome of Aegilops tauschii, a progenitor of bread wheat, with the MaSuRCA mega-reads algorithm
Aleksey V. Zimin et al.
GENOME RESEARCH (2017)
Culture-independent discovery of natural products from soil metagenomes
Micah Katz et al.
JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY (2016)
The adaptive evolution of virulence: a review of theoretical predictions and empirical tests
Clayton E. Cressler et al.
PARASITOLOGY (2016)
Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences
Heng Li
BIOINFORMATICS (2016)
W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis
Jana Trifinopoulos et al.
NUCLEIC ACIDS RESEARCH (2016)
Kinetics of DNA uptake during transformation provide evidence for a translocation ratchet mechanism
Christof Hepp et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)
Unusual biology across a group comprising more than 15% of domain Bacteria
Christopher T. Brown et al.
NATURE (2015)
TRANSIT - A Software Tool for Himar1 TnSeq Analysis
Michael A. DeJesus et al.
PLOS COMPUTATIONAL BIOLOGY (2015)
Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle
Xuesong He et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)
Prokka: rapid prokaryotic genome annotation
Torsten Seemann
BIOINFORMATICS (2014)
Bacterial transformation: distribution, shared mechanisms and divergent control
Calum Johnston et al.
NATURE REVIEWS MICROBIOLOGY (2014)
ECOD: An Evolutionary Classification of Protein Domains
Hua Cheng et al.
PLOS COMPUTATIONAL BIOLOGY (2014)
Insights into the phylogeny and coding potential of microbial dark matter
Christian Rinke et al.
NATURE (2013)
Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes
Mads Albertsen et al.
NATURE BIOTECHNOLOGY (2013)
Sequencing ancient calcified dental plaque shows changes in oral microbiota with dietary shifts of the Neolithic and Industrial revolutions
Christina J. Adler et al.
NATURE GENETICS (2013)
Engineered Luciferase Reporter from a Deep Sea Shrimp Utilizing a Novel Imidazopyrazinone Substrate
Mary P. Hall et al.
ACS CHEMICAL BIOLOGY (2012)
HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment
Michael Remmert et al.
NATURE METHODS (2012)
Accelerated Profile HMM Searches
Sean R. Eddy
PLOS COMPUTATIONAL BIOLOGY (2011)
BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments
Alexis Criscuolo et al.
BMC EVOLUTIONARY BIOLOGY (2010)
The Human Oral Microbiome
Floyd E. Dewhirst et al.
JOURNAL OF BACTERIOLOGY (2010)
Dissecting biological dark matter with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth
Yann Marcy et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)
UniRef: comprehensive and non-redundant UniProt reference clusters
Baris E. Suzek et al.
BIOINFORMATICS (2007)
Targeted access to the genomes of low-abundance organisms in complex microbial communities
Mircea Podar et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2007)
Single-cell enumeration of an uncultivated TM7 subgroup in the human subgingival crevice
CC Ouverney et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2003)
Prevalence of bacteria of division TM7 in human subgingival plaque and their association with disease
MM Brinig et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2003)
Evolution of arginine deiminase (ADI) pathway genes
M Zúniga et al.
MOLECULAR PHYLOGENETICS AND EVOLUTION (2002)
Bacterial diversity in human subgingival plaque
BJ Paster et al.
JOURNAL OF BACTERIOLOGY (2001)
Characterization of Actinomyces isolates from samples from the human urogenital tract:: description of Actinomyces urogenitalis sp nov.
N Nikolaitchouk et al.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY (2000)
KEGG: Kyoto Encyclopedia of Genes and Genomes
M Kanehisa et al.
NUCLEIC ACIDS RESEARCH (2000)