Latest Research

Bronchial pathways and covid molecule illustration with a lightning bolt dividing the two lungs.

Analysis of Bronchoalveolar Lavage Fluid Metatranscriptomes Among Patients with COVID-19 Disease

Abstract To better understand the potential relationship between COVID-19 disease and hologenome microbial community dynamics and functional profiles, we conducted a multivariate taxonomic and functional microbiome comparison of publicly available human bronchoalveolar lavage fluid (BALF) metatranscriptome samples amongst COVID-19 (n = 32), community acquired pneumonia (CAP) (n = 25), and uninfected samples (n = 29). We... MORE
Stylized flow chart. Text reads "K2V"

k2v: A Containerized Workflow for Creating VCF Files from Kintelligence Targeted Sequencing Data

Abstract The ForenSeq Kintelligence kit developed by Verogen is a targeted Illumina sequencing assay that genotypes 10,230 single nucleotide polymorphisms designed for forensic genetic genealogy, forensic DNA phenotyping, and ancestry inference. We developed k2v, a containerized workflow for creating standard specification-compliant variant call format (VCF) files from the custom output... MORE
Data plot and a virus cell

Forecasting Influenza-Like Illness (ILI) during the COVID-19 Pandemic

Abstract Near-term probabilistic forecasts for infectious diseases such as COVID-19 and influenza play an important role in public health communication and policymaking. From 2013-2019, the FluSight challenge run by the Centers for Disease Control and Prevention invited researchers to develop and submit forecasts using influenza-like illness (ILI) as a measure... MORE
Stylized DNA helix in front of GATCs with checkmark. Text reads "Internal Validation of Enhanced Laboratory Methods for ForenSeq® Kintelligence Kit"

Internal Validation of the ForenSeq Kintelligence Kit for Application to Forensic Genetic Genealogy

Abstract Forensic Genetic Genealogy (FGG) requires high density single nucleotide polymorphism (SNP) profiles to infer distant relationships. The ForenSeq Kintelligence kit is a recently developed method targeting approximately 10,000 SNPs that were selected to be compatible with genetic genealogy databases, while avoiding medically relevant SNPs. The targeted PCR method is... MORE
Image of algae on surface of water. Text reads "Sequencing and classifying harmful algal bloom samples"

Paper Published in “Data in Brief”: Environmental DNA sequencing dataset from Lake Erie algal blooms...

Abstract Here we describe a publicly available environmental DNA (eDNA) sequence dataset, consisting of samples collected from a National Oceanic and Atmospheric Administration (NOAA) Great Lakes Environmental Research Laboratory (GLERL) on Lake Erie. We sequenced samples drawn from before, during, and after a 2019 Microcystis harmful algal bloom (HAB) using 3rd generation... MORE
Image of an x-ray style scan of a backpack

Paper Published in “SPIE. Digital Library”: Development of a High-Energy X-ray Diffractometer for Quality Control...

Abstract The Transportation Security Laboratory of the Department of Homeland Security Science and Technology Directorate is tasked with establishing quality control metrics for assessing the performance of x-ray imaging technologies used by airport security. In conformity with that mission, a high-energy x-ray diffraction apparatus was constructed to characterize the xray... MORE
Diagram of a ball-and-stick model. Text reads "Relationship Inference Paper Published; Featured in Forensic Genomics".

Paper Published in “Forensic Genomics”: Relationship Inference with Low-Coverage Whole Genome Sequencing on Forensic Samples

Abstract Background: Single nucleotide polymorphism (SNP)-based kinship analysis is now a cornerstone of modern forensic genomics. Imputation can be used to augment genome-wide SNP data from low-coverage whole-genome sequencing (LCWGS). The impact of imputation after LCWGS on genotyping error and its subsequent impact on kinship analysis are unknown. Methods: We assessed the... MORE
Thumbnail of the front and back of the CEAT - Covid-19 Exposure Assessment Tool. Text reads "CEAT Tool Paper Published"

Paper Published in “Science Advances”: COVID-19 Exposure Assessment Tool (CEAT): Exposure quantification based on ventilation,...

Abstract The coronavirus disease 2019 (COVID-19) Exposure Assessment Tool (CEAT) allows users to compare respiratory relative risk to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) for various scenarios, providing understanding of how combinations of protective measures affect risk. CEAT incorporates mechanistic, stochastic, and epidemiological factors including the (i) emission rate... MORE
Illustration of connected people icons in front of a cityscape. Text reads "Kinship Analysis"

SigSci Scientists Co-Author Study Published in “Frontiers in Genetics”

Abstract Technological advances in sequencing and single nucleotide polymorphism (SNP) genotyping microarray technology have facilitated advances in forensic analysis beyond short tandem repeat (STR) profiling, enabling the identification of unknown DNA samples and distant relationships. Forensic genetic genealogy (FGG) has facilitated the identification of distant relatives of both unidentified remains... MORE