List of works - Chien-Chi Lo

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

scientific article

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

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

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

scientific article

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

scientific article

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

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

scientific article

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

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

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

scientific article

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

scientific article

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

scientific article published on 27 June 2013

Complete genome sequences for 35 biothreat assay-relevant bacillus species

scientific article

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

scientific article

Under-detection of endospore-forming Firmicutes in metagenomic data

scientific article

Artificial polyploidy improves bacterial single cell genome recovery

scientific article

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

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

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

scientific article

Genome sequence of Kingella kingae septic arthritis isolate PYKK081.

scientific article

Whole-genome assemblies of 56 burkholderia species

scientific article

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

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

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

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

Advances and Challenges in Metatranscriptomic Analysis

scientific article published on 25 September 2019

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

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

scientific article

Whole-genome sequences of 24 Brucella strains.

scientific article

Whole-Genome Yersinia sp. Assemblies from 10 Diverse Strains

scientific article

Recruiting human microbiome shotgun data to site-specific reference genomes

scientific article

First Complete Genome Sequence of Felis catus Gammaherpesvirus 1.

scientific article

Twenty Whole-Genome Bacillus sp. Assemblies

scientific article

Draft Genome Assembly of Klebsiella pneumoniae Type Strain ATCC 13883

scientific article

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

scientific article

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

scientific article published on January 2011

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

scientific article

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

scientific article

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

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

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

scientific article

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

scientific article

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

scientific article published on 03 February 2020

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

scientific article published on 28 September 2018

Draft Genomes for Eight Burkholderia mallei Isolates from Turkey.

scientific article

The National Microbiome Data Collaborative: enabling microbiome science

scientific article published on 29 April 2020

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

scientific article published in 2018

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

scientific article published on 10 August 2020

List of works by Chien-Chi Lo

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

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

Saliva microbiomes distinguish caries-active from healthy human populations

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

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

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

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

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

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

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

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

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

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

Complete genome sequences for 35 biothreat assay-relevant bacillus species

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

Under-detection of endospore-forming Firmicutes in metagenomic data

Artificial polyploidy improves bacterial single cell genome recovery

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

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

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

Genome sequence of Kingella kingae septic arthritis isolate PYKK081.

Whole-genome assemblies of 56 burkholderia species

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

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

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

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

Advances and Challenges in Metatranscriptomic Analysis

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.

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

Whole-genome sequences of 24 Brucella strains.

Whole-Genome Yersinia sp. Assemblies from 10 Diverse Strains

Recruiting human microbiome shotgun data to site-specific reference genomes

First Complete Genome Sequence of Felis catus Gammaherpesvirus 1.

Twenty Whole-Genome Bacillus sp. Assemblies

Draft Genome Assembly of Klebsiella pneumoniae Type Strain ATCC 13883

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

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

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

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

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

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

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

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

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

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

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

Draft Genomes for Eight Burkholderia mallei Isolates from Turkey.

The National Microbiome Data Collaborative: enabling microbiome science

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

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