Publications by authors named "Justin Shaffer"

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Culture-independent meta-pangenomics enabled by long-read metagenomics reveals associations with pediatric undernutrition.
Jeremiah J Minich, Nicholas Allsing, M Omar Din, Michael J Tisza, Kenneth Maleta, Justin Shaffer

Cell· November 2025

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Streamlined extraction of nucleic acids and metabolites from low- and high-biomass samples using isopropanol and matrix tubes.
Caitriona Brennan, Justin P Shaffer, Pedro Belda-Ferre, Ipsita Mohanty, Yuhan Weng

Microbiol Spectr· November 2025

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Community assembly modeling of microbial evolution within Barrett's esophagus and esophageal adenocarcinoma.
Caitlin Guccione, Igor Sfiligoi, Antonio Gonzalez, Justin P Shaffer, Mariya Kazachkova

bioRxiv· January 2025

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Correction for Zhu et al., "Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy".
Qiyun Zhu, Shi Huang, Antonio Gonzalez, Imran McGrath, Daniel McDonald, Justin P Shaffer

mSystems· November 2024

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Peripheral neuronal activation shapes the microbiome and alters gut physiology.
Jessica A Griffiths, Bryan B Yoo, Peter Thuy-Boun, Victor J Cantu, Kelly C Weldon, Justin P Shaffer

Cell Rep· April 2024

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Author Correction: Enhancing untargeted metabolomics using metadata-based source annotation.
Julia M Gauglitz, Kiana A West, Wout Bittremieux, Candace L Williams, Kelly C Weldon, Justin P Shaffer

Nat Biotechnol· November 2023

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Developing Science Literacy in Students and Society: Theory, Research, and Practice.
Nicole C Kelp, Melissa McCartney, Mark A Sarvary, Justin F Shaffer, Michael J Wolyniak

J Microbiol Biol Educ· August 2023

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Comprehensive evaluation of shotgun metagenomics, amplicon sequencing, and harmonization of these platforms for epidemiological studies.
Mykhaylo Usyk, Brandilyn A Peters, Smruthi Karthikeyan, Daniel McDonald, Christopher C Sollecito, Justin P Shaffer

Cell Rep Methods· January 2023

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Enhancing untargeted metabolomics using metadata-based source annotation.
Julia M Gauglitz, Kiana A West, Wout Bittremieux, Candace L Williams, Kelly C Weldon, Justin P Shaffer

Nat Biotechnol· December 2022

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Standardized multi-omics of Earth's microbiomes reveals microbial and metabolite diversity.
Justin P Shaffer, Louis-Félix Nothias, Luke R Thompson, Jon G Sanders, Rodolfo A Salido

Nat Microbiol· December 2022

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Postnatal exposure to ambient air pollutants is associated with the composition of the infant gut microbiota at 6-months of age.
Maximilian J Bailey, Elizabeth A Holzhausen, Zachariah E M Morgan, Noopur Naik, Justin P Shaffer

Gut Microbes· August 2022

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Compositionally Aware Phylogenetic Beta-Diversity Measures Better Resolve Microbiomes Associated with Phenotype.
Cameron Martino, Daniel McDonald, Kalen Cantrell, Amanda Hazel Dilmore, Yoshiki Vázquez-Baeza, Justin P Shaffer

mSystems· June 2022

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A comparison of six DNA extraction protocols for 16S, ITS and shotgun metagenomic sequencing of microbial communities.
Justin P Shaffer, Carolina S Carpenter, Cameron Martino, Rodolfo A Salido, Jeremiah J Minich

Biotechniques· June 2022

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Transcriptional Profiles of a Foliar Fungal Endophyte (, Ascomycota) and Its Bacterial Symbiont (, ) Reveal Sulfur Exchange and Growth Regulation during Early Phases of Symbiotic Interaction.
Justin P Shaffer, Morgan E Carter, Joseph E Spraker, Meara Clark, Brian A Smith

mSystems· April 2022

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Swapping Metagenomics Preprocessing Pipeline Components Offers Speed and Sensitivity Increases.
George Armstrong, Cameron Martino, Justin Morris, Behnam Khaleghi, Jaeyoung Kang, Justin P Shaffer

mSystems· April 2022

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Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy.
Qiyun Zhu, Shi Huang, Antonio Gonzalez, Imran McGrath, Daniel McDonald, Justin P Shaffer

mSystems· April 2022

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SALSA, a genetically encoded biosensor for spatiotemporal quantification of Notch signal transduction in vivo.
Justin M Shaffer, Iva Greenwald

Dev Cell· April 2022

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Early life gut microbiota is associated with rapid infant growth in Hispanics from Southern California.
Tanya L Alderete, Roshonda B Jones, Justin P Shaffer, Elizabeth A Holzhausen, William B Patterson

Gut Microbes· January 2022

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Floxed exon (Flexon): A flexibly positioned stop cassette for recombinase-mediated conditional gene expression.
Justin M Shaffer, Iva Greenwald

Proc Natl Acad Sci U S A· January 2022

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The motivational system of task values and anticipated emotions in daily academic behavior.
Osman Umarji, Peter McPartlan, Julia Moeller, Qiujie Li, Justin Shaffer

Motiv Emot· July 2021

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A Tale of Two Institutions: Analyzing the Impact of Gamified Student Response Systems on Student Anxiety in Two Different Introductory Biology Courses.
Sarah J Adkins-Jablonsky, Justin F Shaffer, J Jeffrey Morris, Ben England, Samiksha Raut

CBE Life Sci Educ· June 2021

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SARS-CoV-2 detection status associates with bacterial community composition in patients and the hospital environment.
Clarisse Marotz, Pedro Belda-Ferre, Farhana Ali, Promi Das, Shi Huang, Justin P Shaffer

Microbiome· June 2021

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Erratum: Ultralow-input single-tube linked-read library method enables short-read second-generation sequencing systems to routinely generate highly accurate and economical long-range sequencing information.
Zhoutao Chen, Long Pham, Tsai-Chin Wu, Guoya Mo, Yu Xia, Justin Shaffer

Genome Res· May 2021

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Correction for Vangay et al., "Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative's Workshop and Follow-On Activities".
Pajau Vangay, Josephine Burgin, Anjanette Johnston, Kristen L Beck, Daniel C Berrios, Justin P Shaffer

mSystems· May 2021

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