Gustavo Arango-Argoty
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View article: An artificial intelligence-based model for prediction of clonal hematopoiesis variants in cell-free DNA samples
An artificial intelligence-based model for prediction of clonal hematopoiesis variants in cell-free DNA samples Open
Circulating tumor DNA is a critical biomarker in cancer diagnostics, but its accurate interpretation requires careful consideration of clonal hematopoiesis (CH), which can contribute to variants in cell-free DNA and potentially obscure tru…
View article: Pretrained transformers applied to clinical studies improve predictions of treatment efficacy and associated biomarkers
Pretrained transformers applied to clinical studies improve predictions of treatment efficacy and associated biomarkers Open
View article: An artificial intelligence-based model for prediction of Clonal Hematopoiesis mutants in cell-free DNA samples
An artificial intelligence-based model for prediction of Clonal Hematopoiesis mutants in cell-free DNA samples Open
Circulating tumor DNA is a critical biomarker in cancer diagnostics, but its accurate interpretation requires careful consideration of clonal hematopoiesis (CH), which can contribute to variants in cell-free DNA and potentially obscure tru…
View article: Machine learning modeling of patient health signals informs long-term survival on immune checkpoint inhibitor therapy
Machine learning modeling of patient health signals informs long-term survival on immune checkpoint inhibitor therapy Open
System-level patient health signals, as captured by treatment-emergent adverse events (TEAEs), might contain correlates of immune checkpoint inhibitor (ICI) therapy response. Using all TEAEs and a novel machine learning modeling approach, …
View article: AI-based predictive biomarker discovery via contrastive learning retrospectively improves clinical trial outcome
AI-based predictive biomarker discovery via contrastive learning retrospectively improves clinical trial outcome Open
Modern clinical trials can capture tens of thousands of clinicogenomic measurements per individual. Employing manual approaches to discover predictive biomarkers, as differentiated from prognostic markers, is a challenging task. To address…
View article: AI-Driven Predictive Biomarker Discovery with Contrastive Learning to Improve Clinical Trial Outcomes
AI-Driven Predictive Biomarker Discovery with Contrastive Learning to Improve Clinical Trial Outcomes Open
Modern clinical trials can capture tens of thousands of clinicogenomic measurements per individual. Discovering predictive biomarkers, as opposed to prognostic markers, is challenging when using manual approaches. To address this, we prese…
View article: Pretrained transformers applied to clinical studies improve predictions of treatment efficacy and associated biomarkers
Pretrained transformers applied to clinical studies improve predictions of treatment efficacy and associated biomarkers Open
Cancer treatment has made significant advancements in recent decades, leading to improved outcomes and quality of life for many patients. Despite the array of available therapies, including targeted, hormone, and checkpoint blockade immuno…
View article: Enhanced GII.4 human norovirus infection in gnotobiotic pigs transplanted with a human gut microbiota
Enhanced GII.4 human norovirus infection in gnotobiotic pigs transplanted with a human gut microbiota Open
The role of commensal microbiota in enteric viral infections has been explored extensively, but the interaction between human gut microbiota (HGM) and human norovirus (HuNoV) is poorly understood. In this study, we established an HGM-Trans…
View article: Demonstrating a Comprehensive Wastewater-Based Surveillance Approach That Differentiates Globally Sourced Resistomes
Demonstrating a Comprehensive Wastewater-Based Surveillance Approach That Differentiates Globally Sourced Resistomes Open
Wastewater-based surveillance (WBS) for disease monitoring is highly promising but requires consistent methodologies that incorporate predetermined objectives, targets, and metrics. Herein, we describe a comprehensive metagenomics-based ap…
View article: Wastewater Based Epidemiology Enabled Surveillance of Antibiotic Resistance
Wastewater Based Epidemiology Enabled Surveillance of Antibiotic Resistance Open
Wastewater-based epidemiology (WBE) for disease monitoring is highly promising, but requires consistent methodologies that incorporate predetermined objectives, targets, and metrics. We demonstrate a comprehensive metagenomics-based approa…
View article: Triclosan has a robust, yet reversible impact on human gut microbial composition in vitro
Triclosan has a robust, yet reversible impact on human gut microbial composition in vitro Open
The recent ban of the antimicrobial compound triclosan from use in consumer soaps followed research that showcased the risk it poses to the environment and to human health. Triclosan has been found in human plasma, urine and milk, demonstr…
View article: ARGminer: a web platform for the crowdsourcing-based curation of antibiotic resistance genes
ARGminer: a web platform for the crowdsourcing-based curation of antibiotic resistance genes Open
Curation of antibiotic resistance gene (ARG) databases is a labor-intensive process that requires expert knowledge to manually collect, correct, and/or annotate individual genes. Correspondingly, updates to existing databases tend to be in…
View article: A Pilot Study of Chicago Waterways as Reservoirs of Multidrug-Resistant <i>Enterobacteriaceae</i> (MDR-Ent) in a High-Risk Region for Community-Acquired MDR-Ent Infection in Children
A Pilot Study of Chicago Waterways as Reservoirs of Multidrug-Resistant <i>Enterobacteriaceae</i> (MDR-Ent) in a High-Risk Region for Community-Acquired MDR-Ent Infection in Children Open
Community-acquired multidrug resistant Enterobacteriaceae (MDR-Ent) infections continue to increase in the United States. In prior studies, we identified neighboring regions in Chicago, Illinois, where children have 5 to 6 times greater od…
View article: Enhanced GII.4 human norovirus infection in gnotobiotic pigs transplanted with a human gut microbiota
Enhanced GII.4 human norovirus infection in gnotobiotic pigs transplanted with a human gut microbiota Open
The role of commensal microbiota in enteric viral infections has been explored extensively, but the interaction between human gut microbiota (HGM) and human norovirus (HuNoV) is poorly understood. In this study, we established an HGM-Trans…
View article: Comparison of Whole-Genome Sequences of<i>Legionella pneumophila</i>in Tap Water and in Clinical Strains, Flint, Michigan, USA, 2016
Comparison of Whole-Genome Sequences of<i>Legionella pneumophila</i>in Tap Water and in Clinical Strains, Flint, Michigan, USA, 2016 Open
During the water crisis in Flint, Michigan, USA (2014-2015), 2 outbreaks of Legionnaires' disease occurred in Genesee County, Michigan. We compared whole-genome sequences of 10 clinical Legionella pneumophila isolates submitted to a labora…
View article: Identification of discriminatory antibiotic resistance genes among environmental resistomes using extremely randomized tree algorithm
Identification of discriminatory antibiotic resistance genes among environmental resistomes using extremely randomized tree algorithm Open
Here a new methodology was formulated to characterize and compare variances in ARG profiles between metagenomic data sets derived from similar/dissimilar environments. Specifically, identification of discriminatory ARGs among samples repre…
View article: NanoARG: a web service for detecting and contextualizing antimicrobial resistance genes from nanopore-derived metagenomes
NanoARG: a web service for detecting and contextualizing antimicrobial resistance genes from nanopore-derived metagenomes Open
View article: Effects of Dairy Manure-Based Amendments and Soil Texture on Lettuce- and Radish-Associated Microbiota and Resistomes
Effects of Dairy Manure-Based Amendments and Soil Texture on Lettuce- and Radish-Associated Microbiota and Resistomes Open
A controlled, integrated, and replicated greenhouse study, along with comprehensive metagenomic analysis, revealed that multiple preharvest factors, including antibiotic use during manure collection, composting, biological soil amendment, …
View article: MetaMLP: A fast word embedding based classifier to profile target gene databases in metagenomic samples
MetaMLP: A fast word embedding based classifier to profile target gene databases in metagenomic samples Open
The functional profile of metagenomic samples allows the understanding of the role of the microbes in their environment. Such analysis consists of assigning short sequencing reads to a particular functional category. Normally, manually cur…
View article: Additional file 1: of NanoARG: a web service for detecting and contextualizing antimicrobial resistance genes from nanopore-derived metagenomes
Additional file 1: of NanoARG: a web service for detecting and contextualizing antimicrobial resistance genes from nanopore-derived metagenomes Open
Table S1. Pseudomonas aeruginosa-like identified nanopore reads. (XLSX 4 kb)
View article: Additional file 2: of NanoARG: a web service for detecting and contextualizing antimicrobial resistance genes from nanopore-derived metagenomes
Additional file 2: of NanoARG: a web service for detecting and contextualizing antimicrobial resistance genes from nanopore-derived metagenomes Open
Table S2. Acinetobacter baumannii-like identified nanopore reads. (XLSX 4 kb)
View article: Additional file 2: of Identification of discriminatory antibiotic resistance genes among environmental resistomes using extremely randomized tree algorithm
Additional file 2: of Identification of discriminatory antibiotic resistance genes among environmental resistomes using extremely randomized tree algorithm Open
SI simulated data. (XLSX 32 kb)
View article: NanoARG: A web service for identification of antimicrobial resistance elements from nanopore-derived environmental metagenomes
NanoARG: A web service for identification of antimicrobial resistance elements from nanopore-derived environmental metagenomes Open
Direct selection pressures imposed by antibiotics, indirect pressures by co-selective agents, and horizontal gene transfer are fundamental drivers of the evolution and spread of antibiotic resistance. Therefore, effective environmental mon…
View article: ARGminer: A web platform for crowdsourcing-based curation of antibiotic resistance genes
ARGminer: A web platform for crowdsourcing-based curation of antibiotic resistance genes Open
Curation of antibiotic resistance gene (ARG) databases is labor intensive and requires expert knowledge to manually collect, correct, and/or annotate individual genes. Consequently, most existing ARG databases contain only a small number o…
View article: DeepARG: a deep learning approach for predicting antibiotic resistance genes from metagenomic data
DeepARG: a deep learning approach for predicting antibiotic resistance genes from metagenomic data Open
The deep learning models developed here offer more accurate antimicrobial resistance annotation relative to current bioinformatics practice. DeepARG does not require strict cutoffs, which enables identification of a much broader diversity …
View article: Apigenin Impacts the Growth of the Gut Microbiota and Alters the Gene Expression of Enterococcus
Apigenin Impacts the Growth of the Gut Microbiota and Alters the Gene Expression of Enterococcus Open
Apigenin is a major dietary flavonoid with many bioactivities, widely distributed in plants. Apigenin reaches the colon region intact and interacts there with the human gut microbiota, however there is little research on how apigenin affec…
View article: DeepARG: A deep learning approach for predicting antibiotic resistance genes from metagenomic data
DeepARG: A deep learning approach for predicting antibiotic resistance genes from metagenomic data Open
Growing concerns regarding increasing rates of antibiotic resistance call for global monitoring efforts. Monitoring of environmental media (e.g., wastewater, agricultural waste, food, and water) is of particular interest as these media can…
View article: MetaStorm: A Public Resource for Customizable Metagenomics Annotation
MetaStorm: A Public Resource for Customizable Metagenomics Annotation Open
Metagenomics is a trending research area, calling for the need to analyze large quantities of data generated from next generation DNA sequencing technologies. The need to store, retrieve, analyze, share, and visualize such data challenges …
View article: Noncoding RNAs that associate with YB-1 alter proliferation in prostate cancer cells
Noncoding RNAs that associate with YB-1 alter proliferation in prostate cancer cells Open
The highly conserved, multifunctional YB-1 is a powerful breast cancer prognostic indicator. We report on a pervasive role for YB-1 in which it associates with thousands of nonpolyadenylated short RNAs (shyRNAs) that are further processed …
View article: Genome-Wide Transcript Profiling Reveals Novel Breast Cancer-Associated Intronic Sense RNAs
Genome-Wide Transcript Profiling Reveals Novel Breast Cancer-Associated Intronic Sense RNAs Open
Non-coding RNAs (ncRNAs) play major roles in development and cancer progression. To identify novel ncRNAs that may identify key pathways in breast cancer development, we performed high-throughput transcript profiling of tumor and normal ma…