Latest Research

Abstract: Operational infectious disease modeling efforts are important to public health response before, during, and after outbreak events. Recent collaborative initiatives have demonstrated the success of hubs, which openly solicit modeling output from contributors. Automation techniques can help improve timeliness of submissions to hubs. Furthermore, we suggest that containerization approaches... MORE

Abstract: Unbiased long read sequencing holds enormous potential for the detection of pathogen sequences in clinical samples. However, the untargeted nature of these methods precludes conventional PCR approaches, and the metagenomic content of each sample increases the challenge of bioinformatic analysis. Here, we evaluate a previously described novel workflow for... MORE

Abstract: Unbiased long read sequencing approaches for clinical metagenomic sample analysis holds enormous potential for pathogen detection, including improved detection of unknown, novel or emerging viruses. However, the rapid rate of development in nanopore sequencing and library preparation methods complicates the process of selecting a standardized method for unbiased RNA... MORE

Abstract: Introduction: Recent regulations from United States Government agencies reshape the screening of synthetic nucleic acids. These take a step away from categorizing hazard on the basis of “bad” taxa and invoke the function of the sequence in pathogenesis or intoxication. Ascertaining functions related to pathogenesis and distinguishing these from other... MORE

Abstract Biomanufacturing practitioners and researchers describe the norms that should govern the growing, global field, to include safety, security, sustainability, and social responsibility. These ‘4S Principles’ should be broadly adopted so that the future of the field may provide the greatest benefits to society. The Promise of the Bioeconomy: Bioindustrial manufacturing... MORE

Abstract The COVID-19 pandemic forever underscored the need for bio-surveillance platforms capable of rapidly detecting emerging 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 reads remains... MORE

Abstract Regulation of research on microbes that cause disease in humans has historically been focused on taxonomic lists of ‘bad bugs’. However, given our increased knowledge of these pathogens through inexpensive genome sequencing, 5 decades of research in microbial pathogenesis, and the burgeoning capacity of synthetic biologists, the limitations of this... MORE

Abstract R packages are the fundamental units of reproducible code in R, providing a mechanism for distributing user-developed code, documentation, and data. Docker is a virtualization technology that allows applications and their dependencies to be distributed and run reproducibly across platforms. The pracpac package provides an interface to create Docker... MORE

Abstract Microarray processing, which interrogates hundreds of thousands of single nucleotide polymorphisms (SNPs) across the human genome, has recently gained traction in forensics due to its use in forensic genetic genealogy, which is based on analysis using SNPs to compare distant relatives in publicly curated databases for the purposes of... MORE

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