Latest Research

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
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Automated Infectious Disease Forecasting: Use-cases and Practical Considerations for Pipeline Implementation

Abstract: Real-time forecasting of disease outbreaks requires standardized outputs generated in a timely manner. Development of pipelines to automate infectious disease forecasts can ensure that parameterization and software dependencies are common to any execution of the forecasting code. Here we present our implementation of an automated cloud computing pipeline to... MORE
Image of a world map and virus cells.

FluFIVE: Publicly Hosted Flu Communication dashboard 

The Flu Forecasting Interpretation Visualization and Evaluation (FluFIVE) web application provides a user-friendly interface to explore probabilistic near-term forecasts of incident influenza hospitalizations in the United States. The source of forecasts is the CDC FluSight initiative, which since 2013 has served as a consortium to coordinate influenza forecasting efforts in the United States. FluFIVE provides forecast... MORE
SeqScreen logo. Text reads "Featured in GENOME BIOLOGY"

Signature Science Co-Authors Study Published in “BMC: Genome Biology”

Abstract The COVID-19 pandemic has emphasized the importance of accurate detection of known and emerging pathogens. However, robust characterization of pathogenic sequences remains an open challenge. To address this need we developed SeqScreen, which accurately characterizes short nucleotide sequences using taxonomic and functional labels and a customized set of curated... MORE
Digital illustrations of "bad bugs".

Minireview Published in ASM Infection and Immunity: Categorizing Sequences of Concern by Function To Better...

Abstract To identify sequences with a role in microbial pathogenesis, we assessed the adequacy of their annotation by existing controlled vocabularies and sequence databases. Our goal was to regularize descriptions of microbial pathogenesis for improved integration with bioinformatic applications. Here, we review the challenges of annotating sequences for pathogenic activity.... MORE
Close-up of skin with representation of protein

SigSci Scientists Co-author Study Published in “Journal of Proteomics”

Abstract We present an efficient protein extraction and in-solution enzymatic digestion protocol optimized for mass spectrometry-based proteomics studies of human skin samples. Human skin cells are a proteinaceous matrix that can enable forensic identification of individuals. We performed a systematic optimization of proteomic sample preparation for a protein-based human forensic identification... MORE
Image of a family tree and genetic data plot. Text reads "skater: This work was funded by the National Institute of Justice in collaboration with the University of North Texas Health Science Center"

skater: An R package for SNP-Based Kinship Analysis, Testing, and Evaluation

Abstract: Motivation: SNP-based kinship analysis with genome-wide relationship estimation and IBD segment analysis methods produces results that often require further downstream processing and manipulation. A dedicated software package that consistently and intuitively implements this analysis functionality is needed. Results: Here we present the skater R package for SNP-based kinship analysis, testing, and... MORE