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Thomas AM

As seen in: PeerJ
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Articles by Thomas AM

Clinical strains isolated from early-stage colorectal cancer patients promote tumorigenesis

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By Thomas AM, Da Silva R, Douglas GM
| PeerJ
Daisuke Suzuki conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the article, and approved the final draft. Jiayue Yang performed the experiments, analyzed the data, authored or reviewed drafts of the article, and approved the final draft.
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From sequencing to intelligence: how AI is transforming metagenomics

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By Thomas AM, Da Silva R, Murray ER
| PeerJ
The Human Microbiome Project studies the various microbial communities that naturally inhabit healthy humans. This project provides a foundational overview of the human microbiome along with its role in health (Huttenhower et al., 2012). It investigates the healthy human microbiome across different body habitats, such as the gut, skin, and vagina. It has found that the composition of microbial communities varies across healthy individuals.
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Evidence from a broad-range PNA probe links several Prevotella species to bacterial vaginosis

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By Thomas AM, Mitchell CM, Taylor CM
| PeerJ
Evidence from a broad-range PNA probe links several Prevotella species to bacterial vaginosis 1Centre of Biological Engineering, University of Minho, Braga, Portugal 2INIAV—National Institute for Agrarian and Veterinary Research, Vila do Conde, Portugal 3Division of Infectious Diseases, University of Alabama—Birmingham, Birmingham, AL, United States of America 4LABBELS—Associate Laboratory, Braga, Portugal DOI 10.7717/peerj.20902 Academic Editor Rodolfo García-Contreras Subject Areas...
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RpNGS: an automated platform for pathogen identification and monitoring in clinical metagenomics data

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By Thomas AM, Connor TR, Juan Y-F, Juan YF
| PeerJ
RpNGS: an automated platform for pathogen identification and monitoring in clinical metagenomics data 1Department of Intensive Care Unit, The First Affiliated Hospital of Xi’an Medical University, Xi’an, Shaanxi, China 2Shaanxi Lifegen Co., Ltd, Xi’an, Shaanxi, China 3Guangdong Provincial Key Laboratory of Microbial Safety and Health, Institute of Microbiology, Guangzhou, China 4School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi’an, Shaanxi, China DOI...
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Distribution status and influencing factors of antibiotic resistance genes in the Chaohu Lake, China

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By Thomas AM, Blair JMA, EL M, Darby EM
| PeerJ
Distribution status and influencing factors of antibiotic resistance genes in the Chaohu Lake, China 1Key Laboratory of Environmental Hormones and Reproductive Development, Anhui Province, Fuyang Normal University, Fuyang, China 2School of Food and Biological Engineering, Hefei Normal University, Hefei, China 3School of Life Sciences, Anhui Medical University, Hefei, AnHui, China DOI 10.7717/peerj.19384 Academic Editor Simon Man Kit Cheung Subject Areas Microbiology, Freshwater Biology...
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RCE-IFE: recursive cluster elimination with intra-cluster feature elimination

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By Kim IF, Marshall KA, Thomas AM, Gabriel TR
| PeerJ
Recent advances in next generation sequencing and DNA microarray technologies allow scientists to easily access substantial amounts of gene expression data. The analysis of these data enables the discovery of coexpression patterns among genes and their connections to disease in order to achieve deeper insights into the molecular mechanisms of disease development, improve diagnosis, and develop more effective treatment plans (Rosati et al., 2024).
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Priority effects, nutrition and milk glycan-metabolic potential drive Bifidobacterium longum subspecies dynamics in the infant gut microbiome

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By Thomas AM, Giuseppe PO, Herbert RA, Lee MD
| PeerJ
Priority effects, nutrition and milk glycan-metabolic potential drive Bifidobacterium longum subspecies dynamics in the infant gut microbiome 1Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, Amsterdam, Netherlands 2Sarphati Amsterdam, Department of Public Health Service Amsterdam, Amsterdam, Netherlands 3Department of Sociology, University of Amsterdam, Amsterdam, Netherlands DOI 10.7717/peerj.18602 Academic Editor Aleksandra Galitsyna...
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Metagenome-wide characterization of shared antimicrobial resistance genes in sympatric people and lemurs in rural Madagascar

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By Leigh SR, Antimicrobial Resistance Collaborators, Thomas AM, Thomson NR
| PeerJ
Metagenome-wide characterization of shared antimicrobial resistance genes in sympatric people and lemurs in rural Madagascar 1Program in Population Biology, Ecology, and Evolution, Emory University, Atlanta, GA, United States of America 2Division of Infectious Diseases, School of Medicine, Emory University, Atlanta, GA, United States of America 3Department of Environmental Sciences, Emory University, Atlanta, GA, United States of America 4Centre ValBio, Ranomafana, Madagascar 5Department of...
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Glucagon-like Peptide-1 Receptor Agonists Use for Type 2 Diabetes Mellitus in End-Stage Renal Disease

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By Thomas AM, Ashley Thomas, Kristen Lamb, Olivia Howard
| ncbi.nlm.nih.gov
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MetaPhlAn 4 profiling of unknown species-level genome bins improves the characterization of diet-associated microbiome changes in mice

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By Thomas AM, Blanco-Míguez A, Huang KD, Lesker TR
| ncbi.nlm.nih.gov
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Dynamics of bacterial and archaeal communities during horse bedding and green waste composting

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By Dos Santos JB, Ali HRK, Thomas AM, Bernard KA
| PeerJ
Ammonification and Nitrification ESVs annotated as putative nitrogen cycle-associated species and differentially abundant between composting phases included 108 species associated with ammonification, one with ammonia oxidation, one with nitrate oxidation, 67 with nitrogen reduction, and six with nitrogen fixation (Fig. 5; File S2).
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Gut OncoMicrobiome Signatures (GOMS) as next-generation biomarkers for cancer immunotherapy

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By Thomas AM, Wargo JA
| ncbi.nlm.nih.gov
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