fiphde was originally created to operationally forecast influenza hospitalizations during the 2021-22 and 2022-23 seasons of the FluSight challenge. The package includes functions for data retrieval, modeling, near-term forecasting, and forecast summarization. Functionality from fiphde has been implemented for other infectious disease forecasting, including the 2022-23 DoD COVID-like illness forecasting... MORE

Abstract The COVID-19 pandemic forever underscored the need for biosurveillance platforms capable of rapid detection of previously unseen pathogens. Oxford Nanopore Technology (ONT) couples long-read sequencing with in-field capability, opening the door to real-time, in-field biosurveillance. Though a promising technology, streaming assignment of accurate functional and taxonomic labels with nanopore... MORE

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 10,230 SNPs that were selected to be compatible with genetic genealogy databases, whereas avoiding medically relevant SNPs. The targeted polymerase chain reaction method is... MORE

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

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

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

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