Publications by authors named "Chienchi Lo"

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Standardized and accessible multi-omics bioinformatics workflows through the NMDC EDGE resource.
Julia M Kelliher, Yan Xu, Mark C Flynn, Michal Babinski, Shane Canon, Yuri E Corilo, Chien-Chi Lo, Emiley A Eloe-Fadrosh

Comput Struct Biotechnol J· December 2024

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Recommendations for Uniform Variant Calling of SARS-CoV-2 Genome Sequence across Bioinformatic Workflows.
Ryan Connor, Migun Shakya, David A Yarmosh, Wolfgang Maier, Ross Martin, Chien-Chi Lo

Viruses· March 2024

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Bridging Place-Based Astrobiology Education with Genomics, Including Descriptions of Three Novel Bacterial Species Isolated from Mars Analog Sites of Cultural Relevance.
Rebecca D Prescott, Yvonne L Chan, Eric J Tong, Fiona Bunn, Chiyoko T Onouye, Chien-Chi Lo

Astrobiology· December 2023

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Genomic and Phenotypic Characterization of Shiga Toxin-Producing Strains Isolated from Wild Birds in a Major Agricultural Region in California.
Michelle Qiu Carter, Beatriz Quiñones, Xiaohua He, Antares Pham, Diana Carychao, Chien-Chi Lo

Microorganisms· November 2023

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Benchmark datasets for SARS-CoV-2 surveillance bioinformatics.
Lingzi Xiaoli, Jill V Hagey, Daniel J Park, Christopher A Gulvik, Erin L Young, Chien-Chi Lo

PeerJ· January 2023

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Towards increased accuracy and reproducibility in SARS-CoV-2 next generation sequence analysis for public health surveillance.
Ryan Connor, David A Yarmosh, Wolfgang Maier, Migun Shakya, Ross Martin, Chien-Chi Lo

bioRxiv· November 2022

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Precise Genomic Riboregulator Control of Metabolic Flux in Microbial Systems.
Naresh Pandey, Steffi A Davison, Malathy Krishnamurthy, Daniel S Trettel, Chien-Chi Lo

ACS Synth Biol· October 2022

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EDGE COVID-19: a web platform to generate submission-ready genomes from SARS-CoV-2 sequencing efforts.
Chien-Chi Lo, Migun Shakya, Ryan Connor, Karen Davenport, Mark Flynn

Bioinformatics· May 2022

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Comparative Genomics Applied to Systematically Assess Pathogenicity Potential in Shiga Toxin-Producing O145:H28.
Michelle Qiu Carter, Nicole Laniohan, Chien-Chi Lo, Patrick S G Chain

Microorganisms· April 2022

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Challenges in Bioinformatics Workflows for Processing Microbiome Omics Data at Scale.
Bin Hu, Shane Canon, Emiley A Eloe-Fadrosh, Anubhav, Michal Babinski, Yuri Corilo, Chien-Chi Lo

Front Bioinform· January 2022

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Discovery of an Antarctic Ascidian-Associated Uncultivated with Antimelanoma Palmerolide Biosynthetic Potential.
Alison E Murray, Chien-Chi Lo, Hajnalka E Daligault, Nicole E Avalon, Robert W Read

mSphere· December 2021

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Bioinformatic and Mechanistic Analysis of the Palmerolide PKS-NRPS Biosynthetic Pathway From the Microbiome of an Antarctic Ascidian.
Nicole E Avalon, Alison E Murray, Hajnalka E Daligault, Chien-Chi Lo, Karen W Davenport

Front Chem· December 2021

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A public website for the automated assessment and validation of SARS-CoV-2 diagnostic PCR assays.
Po-E Li, Adán Myers Y Gutiérrez, Karen Davenport, Mark Flynn, Bin Hu, Chien-Chi Lo

Bioinformatics· May 2021

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The Gut Microbiome and Alcoholic Liver Disease: Ethanol Consumption Drives Consistent and Reproducible Alteration in Gut Microbiota in Mice.
Erick S LeBrun, Meghali Nighot, Viszwapriya Dharmaprakash, Anand Kumar, Chien-Chi Lo

Life (Basel)· December 2020

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The National Microbiome Data Collaborative: enabling microbiome science.
Elisha M Wood-Charlson, Anubhav, Deanna Auberry, Hannah Blanco, Mark I Borkum, Yuri E Corilo, Chien-Chi Lo, Emiley A Eloe-Fadrosh

Nat Rev Microbiol· June 2020

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Uncovering the Core Microbiome and Distribution of Palmerolide in Across the Anvers Island Archipelago Antarctica.
Alison E Murray, Nicole E Avalon, Lucas Bishop, Karen W Davenport, Erwan Delage, Chien-Chi Lo

Mar Drugs· June 2020

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Standardized phylogenetic and molecular evolutionary analysis applied to species across the microbial tree of life.
Migun Shakya, Sanaa A Ahmed, Karen W Davenport, Mark C Flynn, Chien-Chi Lo

Sci Rep· February 2020

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Advances and Challenges in Metatranscriptomic Analysis.
Migun Shakya, Chien-Chi Lo, Patrick S G Chain

Front Genet· September 2019

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Investigating intestinal permeability and gut microbiota roles in acute coronary syndrome patients.
Tarik Alhmoud, Anand Kumar, Chien-Chi Lo, Rana Al-Sadi, Stacey Clegg, Ihab Alomari, Momchilo Vuyisich

Hum Microb J· August 2019

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Diagnostic targETEd seQuencing adjudicaTion (DETEQT): Algorithms for Adjudicating Targeted Infectious Disease Next-Generation Sequencing Panels.
Turner A Conrad, Chien-Chi Lo, Jeffrey W Koehler, Amanda S Graham, Christopher P Stefan

J Mol Diagn· January 2019

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"Candidatus Nitrosotenuis aquarius," an Ammonia-Oxidizing Archaeon from a Freshwater Aquarium Biofilter.
Laura A Sauder, Katja Engel, Chien-Chi Lo, Patrick Chain, Josh D Neufeld

Appl Environ Microbiol· October 2018

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Correction for Johnson et al., "Complete Genome Sequences for 35 Biothreat Assay-Relevant Species".
Shannon L Johnson, Hajnalka E Daligault, Karen W Davenport, James Jaissle, Kenneth G Frey, Chien-Chi Lo

Genome Announc· January 2018

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Brief Protocol for EDGE Bioinformatics: Analyzing Microbial and Metagenomic NGS Data.
Casandra Philipson, Karen Davenport, Logan Voegtly, Chien-Chi Lo, Po-E Li

Bio Protoc· December 2017

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Major changes in microbial diversity and community composition across gut sections of a juvenile Panchlora cockroach.
Erin A Gontang, Frank O Aylward, Camila Carlos, Tijana Glavina Del Rio, Mansi Chovatia, Chien-Chi Lo

PLoS One· September 2017

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High-Quality Draft Genome Sequences of Four Lignocellulose-Degrading Bacteria Isolated from Puerto Rican Forest Soil: sp., sp., sp., and sp.
Hannah L Woo, Kristen M DeAngelis, Hazuki Teshima, Karen Davenport, Hajnalka Daligault, Chien-Chi Lo

Genome Announc· May 2017

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