Related references
Note: Only part of the references are listed.Current challenges and best-practice protocols for microbiome analysis
Richa Bharti et al.
BRIEFINGS IN BIOINFORMATICS (2021)
Optimization of 16S rRNA gene analysis for use in the diagnostic clinical microbiology service
Dan Sune et al.
JOURNAL OF MICROBIOLOGICAL METHODS (2020)
Comparing bioinformatic pipelines for microbial 16S rRNA amplicon sequencing
Andrei Prodan et al.
PLOS ONE (2020)
A Multiplex Fluidic Chip for Rapid Phenotypic Antibiotic Susceptibility Testing
Pikkei Wistrand-Yuen et al.
MBIO (2020)
Toward Standards in Clinical Microbiota Studies: Comparison of Three DNA Extraction Methods and Two Bioinformatic Pipelines
Q. R. Ducarmon et al.
MSYSTEMS (2020)
A preliminary study on the potential of Nanopore MinION and Illumina MiSeq 16S rRNA gene sequencing to characterize building-dust microbiomes
Anders B. Nygaard et al.
SCIENTIFIC REPORTS (2020)
Library preparation for next generation sequencing: A review of automation strategies
J. F. Hess et al.
BIOTECHNOLOGY ADVANCES (2020)
Testing the advantages and disadvantages of short- and long- read eukaryotic metagenomics using simulated reads
William S. Pearman et al.
BMC BIOINFORMATICS (2020)
Automation of Amplicon-Based Library Preparation for Next-Generation Sequencing by Centrifugal Microfluidics
Jacob Friedrich Hess et al.
ANALYTICAL CHEMISTRY (2020)
Performance and Application of 16S rRNA Gene Cycle Sequencing for Routine Identification of Bacteria in the Clinical Microbiology Laboratory
Deirdre L. Church et al.
CLINICAL MICROBIOLOGY REVIEWS (2020)
Improving Diagnostic and Laboratory Capacity Helps in Control of Infection: an Indian Perspective
Sanjay Bhattacharya
CURRENT TREATMENT OPTIONS IN INFECTIOUS DISEASES (2020)
Impact of antibiotic administration on blood culture positivity at the beginning of sepsis: a prospective clinical cohort study
C. S. Scheer et al.
CLINICAL MICROBIOLOGY AND INFECTION (2019)
Next-Generation Sequencing of Infectious Pathogens
Marta Gwinn et al.
JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION (2019)
Clinical metagenomics
Charles Y. Chiu et al.
NATURE REVIEWS GENETICS (2019)
The effect of 16S rRNA region choice on bacterial community metabarcoding results
Yu. S. Bukin et al.
SCIENTIFIC DATA (2019)
Ultrafast Parallelized Microfluidic Platform for Antimicrobial Susceptibility Testing of Gram Positive and Negative Bacteria
Wenjing Kang et al.
ANALYTICAL CHEMISTRY (2019)
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
Evan Bolyen et al.
NATURE BIOTECHNOLOGY (2019)
Improved Species-Level Clinical Identification of Enterobacteriaceae through Broad-Range dnaJ PCR and Sequencing
Kathryn McLean et al.
JOURNAL OF CLINICAL MICROBIOLOGY (2019)
Electronic Health Record Use in Public Health Infectious Disease Surveillance, USA, 2018-2019
Sarah J. Willis et al.
CURRENT INFECTIOUS DISEASE REPORTS (2019)
Insights into microbial community structure and diversity in oil palm waste compost
Nurshafika Abd Khalid et al.
3 BIOTECH (2019)
Diversity of endocervical microbiota associated with genital Chlamydia trachomatis infection and infertility among women visiting obstetrics and gynecology clinics in Malaysia
Heng Choon Cheong et al.
PLOS ONE (2019)
Strategies for Genomic Medicine Education in Low- and Middle-Income Countries
Nirmala D. Sirisena et al.
FRONTIERS IN GENETICS (2019)
Rapid bacterial identification by direct PCR amplification of 16S rRNA genes using the MinION nanopore sequencer
Shinichi Kai et al.
FEBS OPEN BIO (2019)
Essential Diagnostics for the Use of World Health Organization Essential Medicines
Lee F. Schroeder et al.
CLINICAL CHEMISTRY (2018)
Next-generation sequencing technologies and their application to the study and control of bacterial infections
J. Besser et al.
CLINICAL MICROBIOLOGY AND INFECTION (2018)
Development and evaluation of a culture-free microbiota profiling platform (MYcrobiota) for clinical diagnostics
Stefan A. Boers et al.
EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES (2018)
Laboratory medicine in low-income and middle-income countries: progress and challenges
John N. Nkengasong et al.
LANCET (2018)
Pathology and laboratory medicine in low-income and middle-income countries 2: Improving pathology and laboratory medicine in low-income and middle-income countries: roadmap to solutions
Shahin Sayed et al.
LANCET (2018)
Pathology and laboratory medicine in low-income and middle-income countries 1: Access to pathology and laboratory medicine services: a crucial gap
Michael L. Wilson et al.
LANCET (2018)
Pathology and laboratory medicine in low-income and middle-income countries 3: Delivering modern, high-quality, affordable pathology and laboratory medicine to low-income and middle-income countries: a call to action
Susan Horton et al.
LANCET (2018)
Germline and somatic variant identification using BGISEQ-500 and HiSeq X Ten whole genome sequencing
Ann-Marie Patch et al.
PLOS ONE (2018)
Investigating the impact of poverty on colonization and infection with drug-resistant organisms in humans: a systematic review
Vivian Alividza et al.
INFECTIOUS DISEASES OF POVERTY (2018)
A 16S rRNA gene sequencing and analysis protocol for the Illumina MiniSeq platform
Monica Pichler et al.
MICROBIOLOGYOPEN (2018)
Blood Culture Turnaround Time in US Acute Care Hospitals and Implications for Laboratory Process Optimization
Ying P. Tabak et al.
JOURNAL OF CLINICAL MICROBIOLOGY (2018)
Comparative performance of the BGISEQ-500 and Illumina HiSeq4000 sequencing platforms for transcriptome analysis in plants
Fu-Yuan Zhu et al.
PLANT METHODS (2018)
Detection of pathogenic bacteria in the blood from sepsis patients using 16S rRNA gene amplicon sequencing analysis
Nobuo Watanabe et al.
PLOS ONE (2018)
Denoising the Denoisers: an independent evaluation of microbiome sequence error-correction approaches
Jacob T. Nearing et al.
PEERJ (2018)
Clinical Metagenomic Next-Generation Sequencing for Pathogen Detection
Wei Gu et al.
Annual Review of Pathology-Mechanisms of Disease (2018)
Impact of DNA extraction method and targeted 16S-rRNA hypervariable region on oral microbiota profiling
Fei Teng et al.
SCIENTIFIC REPORTS (2018)
Understanding the Promises and Hurdles of Metagenomic Next-Generation Sequencing as a Diagnostic Tool for Infectious Diseases
Patricia J. Simner et al.
CLINICAL INFECTIOUS DISEASES (2018)
A Next-Generation Sequencing PrimerHow Does It Work and What Can It Do?
Yuriy O. Alekseyev et al.
ACADEMIC PATHOLOGY (2018)
An Essential Pathology Package for Low- and Middle-Income Countries
Kenneth A. Fleming et al.
AMERICAN JOURNAL OF CLINICAL PATHOLOGY (2017)
What's in a Name? New Bacterial Species and Changes to Taxonomic Status from 2012 through 2015
Erik Munson et al.
JOURNAL OF CLINICAL MICROBIOLOGY (2017)
The 17th International Congress on Infectious Diseases workshop on developing infection prevention and control resources for low- and middle-income countries
Sangeeta Sastry et al.
INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES (2017)
16S rRNA gene sequencing on a benchtop sequencer: accuracy for identification of clinically important bacteria
G. S. Watts et al.
JOURNAL OF APPLIED MICROBIOLOGY (2017)
Application of next generation sequencing in clinical microbiology and infection prevention
Ruud H. Deurenberg et al.
JOURNAL OF BIOTECHNOLOGY (2017)
25 years of serving the community with ribosomal RNA gene reference databases and tools
Frank Oliver Gloeckner et al.
JOURNAL OF BIOTECHNOLOGY (2017)
Targeted next-generation sequencing of the 16S-23S rRNA region for culture-independent bacterial identification - increased discrimination of closely related species
Artur J. Sabat et al.
SCIENTIFIC REPORTS (2017)
Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing
Sarah Siu Tze Mak et al.
GIGASCIENCE (2017)
Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns
Amnon Amir et al.
MSYSTEMS (2017)
BBMerge - Accurate paired shotgun read merging via overlap
Brian Bushnell et al.
PLOS ONE (2017)
Validation of Metagenomic Next-Generation Sequencing Tests for Universal Pathogen Detection
Robert Schlaberg et al.
ARCHIVES OF PATHOLOGY & LABORATORY MEDICINE (2017)
SILVA, RDP, Greengenes, NCBI and OTT - how do these taxonomies compare?
Monika Balvociute et al.
BMC GENOMICS (2017)
A Model Study of In Silico Proficiency Testing for Clinical Next-Generation Sequencing
Eric J. Duncavage et al.
ARCHIVES OF PATHOLOGY & LABORATORY MEDICINE (2016)
Sensitivity and correlation of hypervariable regions in 16S rRNA genes in phylogenetic analysis
Bo Yang et al.
BMC BIOINFORMATICS (2016)
16S rRNA gene sequencing of mock microbial populations- impact of DNA extraction method, primer choice and sequencing platform
Fiona Fouhy et al.
BMC MICROBIOLOGY (2016)
Clinical Next Generation Sequencing Outperforms Standard Microbiological Culture for Characterizing Polymicrobial Samples
Lisa A. Cummings et al.
CLINICAL CHEMISTRY (2016)
High Throughput Sequencing: An Overview of Sequencing Chemistry
Sheetal Ambardar et al.
INDIAN JOURNAL OF MICROBIOLOGY (2016)
DADA2: High-resolution sample inference from Illumina amplicon data
Benjamin J. Callahan et al.
NATURE METHODS (2016)
Characterization of the Gut Microbiome Using 16S or Shotgun Metagenomics
Juan Jovel et al.
FRONTIERS IN MICROBIOLOGY (2016)
Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system
Patrick D. Schloss et al.
PEERJ (2016)
A perspective on 16S rRNA operational taxonomic unit clustering using sequence similarity
Nam-Phuong Nguyen et al.
NPJ BIOFILMS AND MICROBIOMES (2016)
Helicobacter pylori Eradication Causes Perturbation of the Human Gut Microbiome in Young Adults
Theresa Wan-Chen Yap et al.
PLOS ONE (2016)
Key success factors behind electronic medical record adoption in Thailand
Kanida Narattharaksa et al.
JOURNAL OF HEALTH ORGANIZATION AND MANAGEMENT (2016)
Electronic Medical Records in low to middle income countries: The case of Khayelitsha Hospital, South Africa
Emmanuel C. Ohuabunwa et al.
AFRICAN JOURNAL OF EMERGENCY MEDICINE (2016)
PEAT: an intelligent and efficient paired-end sequencing adapter trimming algorithm
Yun-Lung Li et al.
BMC BIOINFORMATICS (2015)
Current and Past Strategies for Bacterial Culture in Clinical Microbiology
Jean-Christophe Lagier et al.
CLINICAL MICROBIOLOGY REVIEWS (2015)
The Rebirth of Culture in Microbiology through the Example of Culturomics To Study Human Gut Microbiota
Jean-Christophe Lagier et al.
CLINICAL MICROBIOLOGY REVIEWS (2015)
Whole genome sequencing in clinical and public health microbiology
J. C. Kwong et al.
PATHOLOGY (2015)
Use of 16S rRNA Gene for Identification of a Broad Range of Clinically Relevant Bacterial Pathogens
Ramya Srinivasan et al.
PLOS ONE (2015)
The Road to Metagenomics: From Microbiology to DNA Sequencing Technologies and Bioinformatics
Alejandra Escobar-Zepeda et al.
FRONTIERS IN GENETICS (2015)
Next generation sequencing technology: Advances and applications
H. P. J. Buermans et al.
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE (2014)
Trimmomatic: a flexible trimmer for Illumina sequence data
Anthony M. Bolger et al.
BIOINFORMATICS (2014)
Reagent and laboratory contamination can critically impact sequence-based microbiome analyses
Susannah J. Salter et al.
BMC BIOLOGY (2014)
Improving the work efficiency of healthcare-associated infection surveillance using electronic medical records
Yu-Sheng Lo et al.
COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE (2014)
Ribosomal Database Project: data and tools for high throughput rRNA analysis
James R. Cole et al.
NUCLEIC ACIDS RESEARCH (2014)
Dramatic reduction of culture time of Mycobacterium tuberculosis
Ramzi Ghodbane et al.
SCIENTIFIC REPORTS (2014)
Clinical detection and characterization of bacterial pathogens in the genomics era
Pierre-Edouard Fournier et al.
GENOME MEDICINE (2014)
A commentary on the role of molecular technology and automation in clinical diagnostics
Ciara O'Connor et al.
BIOENGINEERED (2014)
The armadillo: a model for the neuropathy of leprosy and potentially other neurodegenerative diseases
Rahul Sharma et al.
DISEASE MODELS & MECHANISMS (2013)
Outbreak Investigation Using High-Throughput Genome Sequencing within a Diagnostic Microbiology Laboratory
Norelle L. Sherry et al.
JOURNAL OF CLINICAL MICROBIOLOGY (2013)
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
Christian Quast et al.
NUCLEIC ACIDS RESEARCH (2013)
Rapid 16S rRNA Next-Generation Sequencing of Polymicrobial Clinical Samples for Diagnosis of Complex Bacterial Infections
Stephen J. Salipante et al.
PLOS ONE (2013)
A Microfluidic DNA Library Preparation Platform for Next-Generation Sequencing
Hanyoup Kim et al.
PLOS ONE (2013)
The Diagnostic Performance of a Single GeneXpert MTB/RIF Assay in an Intensified Tuberculosis Case Finding Survey among HIV-Infected Prisoners in Malaysia
Haider Abdulrazzaq Abed Al-Darraji et al.
PLOS ONE (2013)
A Microfluidic Device for Preparing Next Generation DNA Sequencing Libraries and for Automating Other Laboratory Protocols That Require One or More Column Chromatography Steps
Swee Jin Tan et al.
PLOS ONE (2013)
Characteristics and outcomes of culture-negative versus culture-positive severe sepsis
Jason Phua et al.
CRITICAL CARE (2013)
Palindromic sequence impedes sequencing-by-ligation mechanism
Yu-Feng Huang et al.
BMC SYSTEMS BIOLOGY (2012)
Does This Adult Patient With Suspected Bacteremia Require Blood Cultures?
Bryan Coburn et al.
JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION (2012)
The NCBI Taxonomy database
Scott Federhen
NUCLEIC ACIDS RESEARCH (2012)
Experience of quality management system in a clinical laboratory in Nigeria
Rosemary A. Audu et al.
AFRICAN JOURNAL OF LABORATORY MEDICINE (2012)
Generation of Multimillion-Sequence 16S rRNA Gene Libraries from Complex Microbial Communities by Assembling Paired-End Illumina Reads
Andrea K. Bartram et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2011)
Microbial Dysbiosis in Colorectal Cancer (CRC) Patients
Iradj Sobhani et al.
PLOS ONE (2011)
Resources and Costs for Microbial Sequence Analysis Evaluated Using Virtual Machines and Cloud Computing
Samuel V. Angiuoli et al.
PLOS ONE (2011)
The Role of Standards and Training in Preparing for Accreditation
Sheila Woodcock et al.
AMERICAN JOURNAL OF CLINICAL PATHOLOGY (2010)
Genome sequencing on nanoballs
Gregory J. Porreca
NATURE BIOTECHNOLOGY (2010)
QIIME allows analysis of high-throughput community sequencing data
J. Gregory Caporaso et al.
NATURE METHODS (2010)
DNA, RNA, and Protein Extraction: The Past and The Present
Siun Chee Tan et al.
JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY (2009)
Detection of Mycobacterium tuberculosis complex organisms in the stools of patients with pulmonary tuberculosis
Amel El Khechine et al.
MICROBIOLOGY-SGM (2009)
Real-Time DNA Sequencing from Single Polymerase Molecules
John Eid et al.
SCIENCE (2009)
Comparison of 3 swab transport systems for direct release and recovery of aerobic and anaerobic bacteria
Kenneth G. Van Horn et al.
DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE (2008)
A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning
Anton Valouev et al.
GENOME RESEARCH (2008)
A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria
Soumitesh Chakravorty et al.
JOURNAL OF MICROBIOLOGICAL METHODS (2007)
Environmental shotgun sequencing: Its potential and challenges for studying the hidden world of microbes
Jonathan A. Eisen
PLOS BIOLOGY (2007)
Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB
T. Z. DeSantis et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2006)
The role of 16S rRNA gene sequencing in identification of microorganisms misidentified by conventional methods
CA Petti et al.
JOURNAL OF CLINICAL MICROBIOLOGY (2005)
Prolonged incubation and extensive subculturing do not increase recovery of clinically significant microorganisms from standard automated blood cultures
EJ Baron et al.
CLINICAL INFECTIOUS DISEASES (2005)
Use of shell-vial cell culture assay for isolation of bacteria from clinical specimens: 13 Years of experience
F Gouriet et al.
JOURNAL OF CLINICAL MICROBIOLOGY (2005)
Bioinformatics for whole-genome shotgun sequencing of microbial communities
K Chen et al.
PLOS COMPUTATIONAL BIOLOGY (2005)
Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases
JE Clarridge
CLINICAL MICROBIOLOGY REVIEWS (2004)
Gene sequence-based criteria for identification of new Rickettsia isolates and description of Rickettsia heilongjiangensis sp nov
PE Fournier et al.
JOURNAL OF CLINICAL MICROBIOLOGY (2003)
Impact of genotypic studies on mycobacterial taxonomy: the new mycobacteria of the 1990s
E Tortoli
CLINICAL MICROBIOLOGY REVIEWS (2003)
Cultivating the uncultured
K Zengler et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)
Genetic classification and differentiation of Bartonella species based on comparison of partial ftsZ gene sequences
Z Zeaiter et al.
JOURNAL OF CLINICAL MICROBIOLOGY (2002)
Unculturable bacteria - the uncharacterized organisms that cause oral infections
W Wade
JOURNAL OF THE ROYAL SOCIETY OF MEDICINE (2002)
A flea-associated rickettsia pathogenic for humans
D Raoult et al.
EMERGING INFECTIOUS DISEASES (2001)
Detection and identification of mycobacteria by amplification of the internal transcribed spacer regions with genus- and species-specific PCR primers
HY Park et al.
JOURNAL OF CLINICAL MICROBIOLOGY (2000)
DNA-based diagnostic approaches for identification of Burkholderia cepacia complex, Burkholderia vietnamiensis, Burkholderia multivorans, Burkholderia stabilis, and Burkholderia cepacia genomovars I and III
E Mahenthiralingam et al.
JOURNAL OF CLINICAL MICROBIOLOGY (2000)