4.7 Article

Genomic analysis of 61 Chlamydia psittaci strains reveals extensive divergence associated with host preference

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。
Article Biochemistry & Molecular Biology

AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models

Mihaly Varadi et al.

Summary: AlphaFold DB is an openly accessible database with high-accuracy protein-structure predictions, powered by DeepMind's AlphaFold v2.0. It provides programmatic access to a vast number of predicted structures and is expanding to cover more sequences.

NUCLEIC ACIDS RESEARCH (2022)

Article Biochemical Research Methods

ColabFold: making protein folding accessible to all

Milot Mirdita et al.

Summary: ColabFold combines fast homology search and optimized model utilization to offer accelerated prediction of protein structures and complexes, with a processing speed that is 40-60 times faster. It serves as a free and accessible platform for protein folding, capable of predicting close to 1,000 structures per day.

NATURE METHODS (2022)

Article Immunology

Genomic Analysis of MSM Rectal Chiamydia trachomatis Isolates Identifies Predicted Tissue-Tropic Lineages Generated by Intraspecies Lateral Gene Transfer-Mediated Evolution

Robert J. Suchland et al.

Summary: Chlamydia trachomatis is an obligate intracellular bacterium that causes serious diseases in humans. This study focuses on the rectal infection and disease caused by this pathogen, which is an important but understudied aspect of C. trachomatis natural history. Through genome sequence analysis and a genome-wide association study, possible tropism-predictive loci for male rectal C. trachomatis infections were identified, as well as predicted surface-exposed variable regions of Pmp proteins that may play a role in differences between rectal and cervical tropism.

INFECTION AND IMMUNITY (2022)

Article Biochemistry & Molecular Biology

UCSF ChimeraX: Structure visualization for researchers, educators, and developers

Eric F. Pettersen et al.

Summary: UCSF ChimeraX is a powerful visualization program with enhanced performance and graphics, offering new tools and analysis features, support for various areas like virtual reality, and improved ease of use, along with an app store for researchers to contribute new tools.

PROTEIN SCIENCE (2021)

Article Biochemical Research Methods

New strategies to improve minimap2 alignment accuracy

Heng Li

Summary: The latest version of minimap2 v2.22 has made improvements in accurately mapping long reads to highly repetitive regions and in allowing alignments through insertions or deletions up to 100 kb by default, addressing major weaknesses in earlier versions.

BIOINFORMATICS (2021)

Article Biology

Twelve years of SAMtools and BCFtools

Petr Danecek et al.

Summary: SAMtools and BCFtools are widely used tools for processing high-throughput sequencing data, with a history of 12 years of continuous development and improvement. These packages have been utilized in various software projects and genomic pipelines and are freely available on GitHub.

GIGASCIENCE (2021)

Article Microbiology

Pmp Repertoires Influence the Different Infectious Potential of Avian and Mammalian Chlamydia psittaci Strains

Alison Favaroni et al.

Summary: Chlamydia psittaci, the etiological agent of chlamydiosis in birds, can also infect humans, causing severe systemic disease. Variation in Pmps, especially the G group, may contribute to the host tropism of avian and mammalian C. psittaci strains. Adhesins like Pmp22D, Pmp8G, and OmcB play essential roles in infection, while Pmp17G may be a key player in host adaptation to avian cells.

FRONTIERS IN MICROBIOLOGY (2021)

Article Microbiology

A New SNP-Based Genotyping Method for C. psittaci: Application to Field Samples for Quick Identification

Fabien Vorimore et al.

Summary: C. psittaci is the causative agent of avian chlamydiosis and human psittacosis. A PCR-HRM assay was developed to screen for phylogenetically informative SNPs related to the identified C. psittaci lineages, allowing quick identification of the source of infection. The method was validated with reference strains and field isolates, and was consistent with previous genotyping data.

MICROORGANISMS (2021)

Article Multidisciplinary Sciences

Highly accurate protein structure prediction with AlphaFold

John Jumper et al.

Summary: Proteins are essential for life, and accurate prediction of their structures is a crucial research problem. Current experimental methods are time-consuming, highlighting the need for accurate computational approaches to address the gap in structural coverage. Despite recent progress, existing methods fall short of atomic accuracy in protein structure prediction.

NATURE (2021)

Article Biochemistry & Molecular Biology

pLannotate: engineered plasmid annotation

Matthew J. McGuffie et al.

Summary: Engineered plasmids are widely used in biological sciences. However, their functional elements are often incompletely annotated, leading to potential unintended consequences or failed experiments. The open source pLannotate web server provides a comprehensive annotation tool for plasmid features, powered by large genetic parts and protein databases.

NUCLEIC ACIDS RESEARCH (2021)

Article Microbiology

The Nature and Extent of Plasmid Variation in Chlamydia trachomatis

Charlotte A. Jones et al.

MICROORGANISMS (2020)

Article Multidisciplinary Sciences

Diversity in Chlamydial plasmids

Kolos V. Szabo et al.

PLOS ONE (2020)

Article Biotechnology & Applied Microbiology

Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction

Olga M. Sigalova et al.

BMC GENOMICS (2019)

Article Biotechnology & Applied Microbiology

Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery

Robert D. Stewart et al.

NATURE BIOTECHNOLOGY (2019)

Article Parasitology

Whole-genome sequencing of ocular Chlamydia trachomatis isolates from Gadarif State, Sudan

Abdulazeem Abdulsalam Ibrahim Alkhidir et al.

PARASITES & VECTORS (2019)

Article Biochemical Research Methods

fastp: an ultra-fast all-in-one FASTQ preprocessor

Shifu Chen et al.

BIOINFORMATICS (2018)

Article Biotechnology & Applied Microbiology

Virulence-related comparative transcriptomics of infectious and non-infectious chlamydial particles

Thomas Beder et al.

BMC GENOMICS (2018)

Article Biochemistry & Molecular Biology

Pushing the limits of de novo genome assembly for complex prokaryotic genomes harboring very long, near identical repeats

Michael Schmid et al.

NUCLEIC ACIDS RESEARCH (2018)

Article Biochemical Research Methods

Phandango: an interactive viewer for bacterial population genomics

James Hadfield et al.

BIOINFORMATICS (2018)

Article Public, Environmental & Occupational Health

Intersectoral action for health: preventing psittacosis spread after one reported case

V. L. Ferreira et al.

EPIDEMIOLOGY AND INFECTION (2017)

Letter Biotechnology & Applied Microbiology

MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets

Martin Steinegger et al.

NATURE BIOTECHNOLOGY (2017)

Letter Respiratory System

Atypical Chlamydia Psittad Pneumonia. Four Related Cases

Nuria Arenas-Valls et al.

ARCHIVOS DE BRONCONEUMOLOGIA (2017)

Article Infectious Diseases

Psittacosis outbreak in Tayside, Scotland, December 2011 to February 2012

C C McGuigan et al.

Eurosurveillance (2017)

Article Microbiology

SEROPREVALENCE OF CHLAMYDOPHILA PSITTACI AMONG EMPLOYEES OF TWO GERMAN DUCK FARMS

Raimond Lugert et al.

EUROPEAN JOURNAL OF MICROBIOLOGY AND IMMUNOLOGY (2017)

Article Biochemical Research Methods

Icarus: visualizer for de novo assembly evaluation

Alla Mikheenko et al.

BIOINFORMATICS (2016)

Article Biochemical Research Methods

Bandage: interactive visualization ofde novogenome assemblies: Fig. 1.

Ryan R. Wick et al.

BIOINFORMATICS (2015)

Article Biochemical Research Methods

Roary: rapid large-scale prokaryote pan genome analysis

Andrew J. Page et al.

BIOINFORMATICS (2015)

Article Biochemistry & Molecular Biology

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

Nicholas J. Croucher et al.

NUCLEIC ACIDS RESEARCH (2015)

Article Immunology

Chlamydia psittaci in ducks: a hidden health risk for poultry workers

Fabien Vorimore et al.

PATHOGENS AND DISEASE (2015)

Article Microbiology

Avian Chlamydiosis

Konrad Sachse et al.

CURRENT CLINICAL MICROBIOLOGY REPORTS (2015)

Article Biochemical Research Methods

Prokka: rapid prokaryotic genome annotation

Torsten Seemann

BIOINFORMATICS (2014)

Article Biochemical Research Methods

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

Alexandros Stamatakis

BIOINFORMATICS (2014)

Review Infectious Diseases

Evolution, phylogeny, and molecular epidemiology of Chlamydia

Alexandra Nunes et al.

INFECTION GENETICS AND EVOLUTION (2014)

Letter Immunology

Rapid Metagenomic Diagnostics for Suspected Outbreak of Severe Pneumonia

Nicole Fischer et al.

EMERGING INFECTIOUS DISEASES (2014)

Article Biochemical Research Methods

QUAST: quality assessment tool for genome assemblies

Alexey Gurevich et al.

BIOINFORMATICS (2013)

Article Biochemistry & Molecular Biology

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

Kazutaka Katoh et al.

MOLECULAR BIOLOGY AND EVOLUTION (2013)

Article Biochemical Research Methods

ART: a next-generation sequencing read simulator

Weichun Huang et al.

BIOINFORMATICS (2012)

Article Biochemistry & Molecular Biology

Evolution and Conservation of Predicted Inclusion Membrane Proteins in Chlamydiae

Erika I. Lutter et al.

COMPARATIVE AND FUNCTIONAL GENOMICS (2012)

Article Biotechnology & Applied Microbiology

The limitations of draft assemblies for understanding prokaryotic adaptation and evolution

N. Ricker et al.

GENOMICS (2012)

Article Biochemical Research Methods

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

Anton Bankevich et al.

JOURNAL OF COMPUTATIONAL BIOLOGY (2012)

Article Multidisciplinary Sciences

The Chlamydia psittaci Genome: A Comparative Analysis of Intracellular Pathogens

Anja Voigt et al.

PLOS ONE (2012)

Review Cell Biology

Bacterial subversion of host actin dynamics at the plasma membrane

Rey Carabeo

CELLULAR MICROBIOLOGY (2011)

Article Biochemistry & Molecular Biology

Unity in Variety-The Pan-Genome of the Chlamydiae

Astrid Collingro et al.

MOLECULAR BIOLOGY AND EVOLUTION (2011)

Article Multidisciplinary Sciences

Chlamydia Species-Dependent Differences in the Growth Requirement for Lysosomes

Scot P. Ouellette et al.

PLOS ONE (2011)

Article Biochemical Research Methods

The Newick utilities: high-throughput phylogenetic tree processing in the Unix shell

Thomas Junier et al.

BIOINFORMATICS (2010)

Review Microbiology

Acquisition of nutrients by Chlamydiae: unique challenges of living in an intracellular compartment

Hector Alex Saka et al.

CURRENT OPINION IN MICROBIOLOGY (2010)

Article Biotechnology & Applied Microbiology

Co-evolution of genomes and plasmids within Chlamydia trachomatis and the emergence in Sweden of a new variant strain

Helena M. B. Seth-Smith et al.

BMC GENOMICS (2009)

Review Infectious Diseases

Zoonotic Chlamydophila psittaci infections from a clinical perspective

D. S. A. Beeckman et al.

CLINICAL MICROBIOLOGY AND INFECTION (2009)

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)

Article Microbiology

Chlamydial infections in duck farms associated with human cases of psittacosis in France

Karine Laroucau et al.

VETERINARY MICROBIOLOGY (2009)

Article Microbiology

Simultaneous zoonotic transmission of Chlamydophila psittaci genotypes D, F and E/B to a veterinary scientist

Caroline Van Droogenbroeck et al.

VETERINARY MICROBIOLOGY (2009)

Article Public, Environmental & Occupational Health

Chlamydophila psittaci infections in humans during an outbreak of psittacosis from poultry in Germany

W. Gaede et al.

ZOONOSES AND PUBLIC HEALTH (2008)

Article Biochemistry & Molecular Biology

Structural basis for the function of Clostridium difficile toxin B

DJ Reinert et al.

JOURNAL OF MOLECULAR BIOLOGY (2005)

Article Medicine, General & Internal

Familial cases of psittacosis: Possible person-to-person transmission

I Ito et al.

INTERNAL MEDICINE (2002)

Article Multidisciplinary Sciences

Chlamydia trachomatis cytotoxicity associated with complete and partial cytotoxin genes

RJ Belland et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2001)