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List of works by Chien-Chi Lo

A Public Website for the Automated Assessment and Validation of SARS-CoV-2 Diagnostic PCR Assays

scientific article published on 10 August 2020

A programmable droplet-based microfluidic device applied to multiparameter analysis of single microbes and microbial communities

scientific article

ADEPT, a dynamic next generation sequencing data error-detection program with trimming

scientific article

Adaptation genomics of a small-colony variant in a Pseudomonas chlororaphis 30-84 biofilm.

scientific article

Advances and Challenges in Metatranscriptomic Analysis

scientific article published on 25 September 2019

Artificial polyploidy improves bacterial single cell genome recovery

scientific article

Benchmark datasets for SARS-CoV-2 surveillance bioinformatics

scientific article published in 2022

Biostimulation and microbial community profiling reveal insights on RDX transformation in groundwater

scientific article

CRP-Mediated Carbon Catabolite Regulation of Yersinia pestis Biofilm Formation Is Enhanced by the Carbon Storage Regulator Protein, CsrA.

scientific article published on 25 August 2015

Capturing single cell genomes of active polysaccharide degraders: an unexpected contribution of Verrucomicrobia.

scientific article

Cohesion group approach for evolutionary analysis of aspartokinase, an enzyme that feeds a branched network of many biochemical pathways.

scientific article published on December 2009

Community and gene composition of a human dental plaque microbiota obtained by metagenomic sequencing.

scientific article

Comparative Genomics Applied to Systematically Assess Pathogenicity Potential in Shiga Toxin-Producing <i>Escherichia coli</i> O145:H28

scientific article published on 21 April 2022

Complete Genome Assembly of a Quality Control Reference Isolate, Moraxella catarrhalis Strain ATCC 25240.

scientific article

Complete Genome Sequence of Type Strain Pasteurella multocida subsp. multocida ATCC 43137.

scientific article

Complete genome sequences for 35 biothreat assay-relevant bacillus species

scientific article

Correction for Johnson et al., "Complete Genome Sequences for 35 Biothreat Assay-Relevant Bacillus Species".

scientific article published on 18 January 2018

Diagnostic targETEd seQuencing adjudicaTion (DETEQT): Algorithms for Adjudicating Targeted Infectious Disease Next-Generation Sequencing Panels

scientific article published on 28 September 2018

Draft Genome Assembly of Bordetella bronchiseptica ATCC 10580, a Historical Canine Clinical Isolate.

scientific article

Draft Genome Assembly of Klebsiella pneumoniae Type Strain ATCC 13883

scientific article

Draft Genome Assembly of Ralstonia pickettii Type Strain K-288 (ATCC 27853).

scientific article

Draft Genome Sequence of Methylomicrobium buryatense Strain 5G, a Haloalkaline-Tolerant Methanotrophic Bacterium

scientific article published on 27 June 2013

Draft Genome Sequence of Thauera sp. Strain SWB20, Isolated from a Singapore Wastewater Treatment Facility Using Gel Microdroplets

scientific article

Draft Genomes for Eight Burkholderia mallei Isolates from Turkey.

scientific article

EDGE COVID-19: a web platform to generate submission-ready genomes from SARS-CoV-2 sequencing efforts

scientific article published in 2022

Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform

scientific article

First Complete Genome Sequence of Felis catus Gammaherpesvirus 1.

scientific article

Genome Assembly of Methicillin-Resistant Quality Control Strain Staphylococcus aureus CDC73-57501 (ATCC 29247).

scientific article

Genome Assembly of Shigella flexneri ATCC 12022, a Quality Control Reference Strain

scientific article

Genome Sequence of Aeribacillus pallidus Strain GS3372, an Endospore-Forming Bacterium Isolated in a Deep Geothermal Reservoir.

scientific article

Genome Sequence of Anoxybacillus geothermalis Strain GSsed3, a Novel Thermophilic Endospore-Forming Species

scientific article published on 11 June 2015

Genome Sequence of Bacillus alveayuensis Strain 24KAM51, a Halotolerant Thermophile Isolated from a Hydrothermal Vent

scientific article

Genome Sequences of Two Klebsiella pneumoniae Isolates from Different Geographical Regions, Argentina (Strain JHCK1) and the United States (Strain VA360)

scientific article published on March 2013

Genome sequence of Kingella kingae septic arthritis isolate PYKK081.

scientific article

Genomic characterization reveals significant divergence within Chlorella sorokiniana (Chlorellales, Trebouxiophyceae)

scientific article published in 2018

Genomic comparison of Escherichia coli O104:H4 isolates from 2009 and 2011 reveals plasmid, and prophage heterogeneity, including shiga toxin encoding phage stx2

scientific article

Genomics for key players in the N cycle from guinea pigs to the next frontier

scientific article published on January 2011

High-Quality Draft Genome Sequences of Four Lignocellulose-Degrading Bacteria Isolated from Puerto Rican Forest Soil: Gordonia sp., Paenibacillus sp., Variovorax sp., and Vogesella sp.

scientific article

Identification of Lineage Associated Virulence Genes in Shiga Toxin-Producing Escherichia Coli by Pangenome Analysis

scientific article published in 2021

Improved assemblies using a source-agnostic pipeline for MetaGenomic Assembly by Merging (MeGAMerge) of contigs.

scientific article

Major changes in microbial diversity and community composition across gut sections of a juvenile Panchlora cockroach

scientific article

Nearly finished genomes produced using gel microdroplet culturing reveal substantial intraspecies genomic diversity within the human microbiome

scientific article

Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis.

scientific article

Pathogen comparative genomics in the next-generation sequencing era: genome alignments, pangenomics and metagenomics.

scientific article

Rapid evaluation and quality control of next generation sequencing data with FaQCs.

scientific article

Recruiting human microbiome shotgun data to site-specific reference genomes

scientific article

Saliva microbiomes distinguish caries-active from healthy human populations ⬇️

scientific article published on June 30, 2011

Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage

scientific article published on January 2013

Standardized phylogenetic and molecular evolutionary analysis applied to species across the microbial tree of life

scientific article published on 03 February 2020

The Gut Microbiome and Alcoholic Liver Disease: Ethanol Consumption Drives Consistent and Reproducible Alteration in Gut Microbiota in Mice

scientific article published on 24 December 2020

The National Microbiome Data Collaborative: enabling microbiome science

scientific article published on 29 April 2020

The alternative translational profile that underlies the immune-evasive state of persistence in Chlamydiaceae exploits differential tryptophan contents of the protein repertoire

scientific article

Thirty-Two Complete Genome Assemblies of Nine Yersinia Species, Including Y. pestis, Y. pseudotuberculosis, and Y. enterocolitica

scientific article published on 30 April 2015

Transmission of single HIV-1 genomes and dynamics of early immune escape revealed by ultra-deep sequencing

scientific article

Twenty Whole-Genome Bacillus sp. Assemblies

scientific article

Uncovering the Core Microbiome and Distribution of Palmerolide in Synoicum adareanum Across the Anvers Island Archipelago, Antarctica

scientific article published on 02 June 2020

Under-detection of endospore-forming Firmicutes in metagenomic data

scientific article

Whole-Genome Yersinia sp. Assemblies from 10 Diverse Strains

scientific article

Whole-genome assemblies of 56 burkholderia species

scientific article

Whole-genome sequences of 24 Brucella strains.

scientific article

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