Author details

Full Name

Todd J Treangen

Affiliation

ORCID

Career Start Year

2006

Papers

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
36993481	Ultra-high throughput mapping of genetic design space.		2023
37603771	Minmers are a generalization of minimizers that enable unbiased local Jaccard estimation.	Bioinformatics	2023
37986916	Crykey: Rapid Identification of SARS-CoV-2 Cryptic Mutations in Wastewater.		2023
37800925	Evolutionary and spatiotemporal analyses reveal multiple introductions and cryptic transmission of SARS-CoV-2 VOC/VOI in Malta.		2023
37626231	The long game of tenure.		2023
37962956	The pan-microbiome profiling system Taxa4Meta identifies clinical dysbiotic features and classifies diarrheal disease.		2023
36824759	Olivar: automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens.		2023
37325780	Minmers are a generalization of minimizers that enable unbiased local Jaccard estimation.	bioRxiv	2023
37198181	Enabling accurate and early detection of recently emerged SARS-CoV-2 variants of concern in wastewater.		2023
37387148	Bakdrive: identifying a minimum set of bacterial species driving interactions across multiple microbial communities.		2023
37180048	Improved understanding of biorisk for research involving microbial modification using annotated sequences of concern.		2023
35051130	Notes from the Field: Early Evidence of the SARS-CoV-2 B.1.1.529 (Omicron) Variant in Community Wastewater - United States, November-December 2021.	Morbidity and Mortality Weekly Report	2022
35773532	Emu: species-level microbial community profiling of full-length 16S rRNA Oxford Nanopore sequencing data.	Nature Methods	2022
35395314	Direct comparison of RT-ddPCR and targeted amplicon sequencing for SARS-CoV-2 mutation monitoring in wastewater.	Science of the Total Environment	2022
36038949	Multiple genome alignment in the telomere-to-telomere assembly era.	Genome Biol	2022
36357382	De novo identification of microbial contaminants in low microbial biomass microbiomes with Squeegee.	Nature Communications	2022
36036505	Systematic Analysis of Mobile Genetic Elements Mediating Î²-Lactamase Gene Amplification in Noncarbapenemase-Producing Carbapenem-Resistant <i>Enterobacterales</i> Bloodstream Infections.	mSystems	2022
35898338	QuaID: Enabling Earlier Detection of Recently Emerged SARS-CoV-2 Variants of Concern in Wastewater.		2022
35832621	KOMB: K-core based de novo characterization of copy number variation in microbiomes.	Computational and Structural Biotechnology Journal	2022
35562867	Fecal Microbiota Transplantation Derived from Alzheimer's Disease Mice Worsens Brain Trauma Outcomes in Wild-Type Controls.	International Journal of Molecular Sciences	2022
35365602	Current progress and open challenges for applying deep learning across the biosciences.	Nat Commun	2022
36262335	The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms.	F1000Res	2022
35725628	SeqScreen: accurate and sensitive functional screening of pathogenic sequences via ensemble learning.		2022
36476670	Analysis of bronchoalveolar lavage fluid metatranscriptomes among patients with COVID-19 disease.		2022
34519774	Infectious Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in Exhaled Aerosols and Efficacy of Masks During Early Mild Infection.	Clin Infect Dis	2022
35288552	Rescuing low frequency variants within intra-host viral populations directly from Oxford Nanopore sequencing data.	Nat Commun	2022
34780277	Categorizing Sequences of Concern by Function To Better Assess Mechanisms of Microbial Pathogenesis.	Infection and Immunity	2022
35284846	Alterations to the gut microbiome after sport-related concussion in a collegiate football players cohort: A pilot study.	Brain, Behavior, and Immunity - Health	2022
35242361	Limited genomic reconstruction of SARS-CoV-2 transmission history within local epidemiological clusters.	Virus Evolution	2022
34779841	It takes guts to learn: machine learning techniques for disease detection from the gut microbiome.	Emerging topics in life sciences	2021
33972927	Accelerating SARS-CoV-2 low frequency variant calling on ultra deep sequencing datasets.		2021
33910614	Natural tannin extracts supplementation for COVID-19 patients (TanCOVID): a structured summary of a study protocol for a randomized controlled trial.	Trials	2021
33637701	PlasmidHawk improves lab of origin prediction of engineered plasmids using sequence alignment.	Nature Communications	2021
33948587	The Great Deceiver: miR-2392's Hidden Role in Driving SARS-CoV-2 Infection.	bioRxiv	2021
33602693	SARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission.	Genome Res	2021
34518837	Rescuing Low Frequency Variants within Intra-Host Viral Populations directly from Oxford Nanopore sequencing data.	bioRxiv	2021
34624208	Role of miR-2392 in driving SARS-CoV-2 infection.	Cell Rep	2021
34561697	Vulcan: Improved long-read mapping and structural variant calling via dual-mode alignment.	Gigascience	2021
32637955	Hidden genomic diversity of SARS-CoV-2: implications for qRT-PCR diagnostics and transmission.	bioRxiv	2020
31726395	Comparative metagenomic analysis of microbial taxonomic and functional variations in untreated surface and reclaimed waters used in irrigation applications.	Water Research	2020
32338745	To Petabytes and beyond: recent advances in probabilistic and signal processing algorithms and their application to metagenomics.	Nucleic Acids Research	2020
32760120	Synthetic DNA and biosecurity: Nuances of predicting pathogenicity and the impetus for novel computational approaches for screening oligonucleotides.	PLoS Pathog	2020
33242417	Comprehensive Multi-omics Analysis Reveals Mitochondrial Stress as a Central Biological Hub for Spaceflight Impact.	Cell	2020
31451112	MetaCarvel: linking assembly graph motifs to biological variants.		2019
28968737	Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes.	Brief Bioinform	2019
30467235	You can't always sequence your way out of a tight spot: Next-generation sequencing holds great promise for pathogen detection, but the devil is in the details.	EMBO Reports	2018
30546361	Traumatic Brain Injury in Mice Induces Acute Bacterial Dysbiosis Within the Fecal Microbiome.	Frontiers in Immunology	2018
30396371	Current progress and future opportunities in applications of bioinformatics for biodefense and pathogen detection: report from the Winter Mid-Atlantic Microbiome Meet-up, College Park, MD, January 10, 2018.	Microbiome	2018
30373669	RefSeq database growth influences the accuracy of k-mer-based lowest common ancestor species identification.	Genome Biol	2018
28798168	Draft Genome Sequences from a Novel Clade of <i>Bacillus cereusÂ Sensu Lato</i> Strains, Isolated from the International Space Station.	Genome Announc	2017