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Bioscience

Biometrology

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Displaying 1 - 24 of 24

A mathematical framework to correct for compositionality in microbiome datasets

January 6, 2026
Author(s)
Samuel Forry, Stephanie Servetas, Jason Kralj, Monique Hunter, Jennifer Dootz
The increasing use of metagenomic sequencing (MGS) for microbiome analysis has significantly advanced our understanding of microbial communities and their roles in various biological processes, including human health, environmental cycling, and disease

AI and Flow Cytometry

November 10, 2025
Author(s)
Dawei Lin, Anupama Gururaj, Sheng Lin-Gibson, Lili Wang
Artificial intelligence (AI) and machine learning (ML) are transforming biotechnology and playing a key role in bioeconomy. One of the most important measurement capabilities at the forefront of biotechnology innovations is flow cytometry (FCM), a high

Report from the 2023 NIST-Hosted Workshop on Collaborative Efforts to Enable Adoption of Rapid Microbial Testing Methods for Advanced Therapy Products

September 26, 2025
Author(s)
Stephanie Servetas, Dawn Henke, Jason Kralj, Kirsten Parratt, Scott Jackson, Nancy Lin
On April 25, 2023, the National Institute of Standards and Technology (NIST) hosted a one-day hybrid workshop focused on bringing together organizations and working groups with the common goal of enabling validation and implementation of rapid microbial

Measurement quality metrics to improve absolute microbial cell counting

August 18, 2025
Author(s)
Kirsten Parratt, David Newton, Joy Dunkers, Jennifer Dootz, Monique Hunter, Alshae Logan, Laura Pierce, Sumona Sarkar, Stephanie Servetas, Nancy Lin
Total and viable microbial cell counts are increasingly important for applications including live biotherapeutic products, food safety, and probiotics. In microbiology, cells are quantified using methods such as colony forming unit (CFU), flow cytometry

Characterizing Cell-Free Transcription and Translation Dynamics with Nucleic Acid-Based Assays

August 10, 2025
Author(s)
Fernanda Piorino Macruz de Oliveira, Chad Alan Sundberg, Elizabeth Strychalski, Eugenia Romantseva
Characterization of cell-free expression (CFE) systems must expand beyond single spectrophotometric measurements of a green fluorescent protein to provide meaningful metrics of system performance over the course of a CFE reaction and enable the development

A Sensitivity Analysis of Methodological Variables Associated with Microbiome Measurements

January 14, 2025
Author(s)
Samuel Forry, Stephanie Servetas, Jennifer Dootz, Monique Hunter, Jason Kralj, James Filliben, Scott Jackson
The particular experimental methods employed during metagenomic sequencing analyses of microbiome samples can significantly impact the resulting data but typically vary substantially between laboratories. In this study, a full factorial experimental design

Jointly benchmarking small and structural variant calls with vcfdist

October 2, 2024
Author(s)
Tim Dunn, Justin Zook, James Holt, Satish Narayanasamy
In this work, we extend vcfdist to be the first variant call benchmarking tool to jointly evaluate phased single-nucleotide polymorphisms (SNPs), small insertions/deletions (INDELs), and structural variants (SVs) for the whole genome. First, we find that a

Optimizing Wastewater Surveillance: The Necessity of Standardized Reporting and Proficiency for Public Health

August 7, 2024
Author(s)
Ishi Keenum, Nancy Lin, Alshae Logan, Adam Gushgari, Nishita D'Souza4, Joshua Steele, Devrim Kaya, Lydia Gushgari
Wastewater-based surveillance (WBS) has emerged as a valuable tool for public health, allowing a greater understanding of disease prevalence in communities. With historical significance in monitoring polio transmission,1 WBS gained further prominence in

Towards Absolute Viability Measurements for Bacteria

September 12, 2021
Author(s)
Joy Dunkers, Hariharan Iyer, Brynna H. Jones, Charles Camp, Stephan J. Stranick, Nancy Lin
Quantifying viable, vegetative bacteria is a critical measurand in healthcare diagnostics, food safety, and antimicrobial development. Viability determination has traditionally relied on such techniques as plate counting, colorimetric or fluorescent

THE GUT MICROBIOME AND XENOBIOTICS: IDENTIFYING KNOWLEDGE GAPS

July 1, 2020
Author(s)
Vicki L. Sutherland, Charlene A. McQueen, donna Mendrick, donna gulezian, Carl Cerniglia, Steven Foley, Samuel Forry, Sangeeta Khare, Xue Liang, Jose E. Manautou, Donald Tweedie, howard young, Alexander Aleksenkyo, frank burns, Rod Dietert, Katherine Karberg, alan wilson, connie chen
There is an increasing awareness that the gut microbiome plays a critical role in human health and disease, but mechanistic insights are often lacking. In June 2018, the Health and Environmental Sciences Institute (HESI) held a workshop, "The Gut

EcoFAB: Advancing microbiome science through standardized fabricated ecosystems

June 21, 2019
Author(s)
Karsten Zengler, Kirsten Hofmockel, Scott Behie, Hans Bernstein, James Brown, Jos? Dinneny, Sheri Floge, Samuel Forry, Matthias Hess, Scott Jackson, Stephen Lindemann, Jennifer Pett-Ridge, Elizabeth Shank, Ophelia Venturelli, Matthew Wallenstein, Nitin Baliga, Christer Jansson, Trent Northen
Microbiome science is arguably the fastest-advancing research field in biology today. However, current efforts are largely focused on disparate and often irreproducible experimental systems. Here we present the results of a one-and-a-half-day workshop that

Report from the Winter Mid-Atlantic Microbiome Meet-up on Biodefense and Pathogen Detection, College Park, MD January 10th, 2018

November 5, 2018
Author(s)
Jacquelyn S. Meisel, Daniel Nasko, Brian Brubach, Victoria Cepeda Espinoza, Jessica Chopyk, Hector Corrada Bravo, Marcus Fedarko, Jay Ghurye, Kiran Javkar, Nathan D. Olson, Nidhi Shah, Sarah M. Allard, Adam L. Bazinet, Nichloas H. Bergman, Alexis Brown, Greg Caporaso, Sean Conlan, Jocelyn DiRuggiero, Samuel Forry, Nur A. Hasan, John Julias, Paul M. Luethy, Donald K. Milton, Brian Ondov, Sarah Preheim, Tara O'Toole, Stephanie Rogers, M.J. Rosovitz, Eric G. Sakowski, Nils O. Schliebs, Daniel D. Sommer, Krista Ternus, German Uritskiy, Sean X. Zhang, Mihai Pop, Todd Treangen
The Mid-Atlantic Microbiome Meet-up (M3) organization held its fourth meeting on January 10, 2018 in College Park, Maryland. M3 brings together academic, government, and industry groups in the broadly-defined mid-Atlantic region to share ideas and develop

Regulation of Oxygen Level and Pervaporation in Microfluidic Devices

October 13, 2011
Author(s)
Peter C. Thomas, Srinivasa R. Raghavan, Samuel Forry
Oxygen level plays a critical role in maintaining cell homeostasis. Misregulation of oxygen levels in cell culture have been shown to impact cell growth, death and differentiation. As such, proper management of oxygen level is required in cell based assays

ON-CHIP PERVAPORATION-FREE CONTROL OF GAS PARTIAL PRESSURES

October 2, 2011
Author(s)
Peter C. Thomas, Laurie E. Locascio, Srinivasa R. Raghavan, Samuel Forry
Pre-equilibrated aqueous solutions were used on-chip to simultaneously mitigate pervaporation and modulate the partial pressures of oxygen (PO2) and carbon dioxide (PCO2) in stagnant culture chambers. This approach enabled long-term (>1 week), stopped-flow

Monitoring and Controlling Oxygen Levels in Microfluidic Devices

April 30, 2010
Author(s)
Samuel Forry, Peter C. Thomas, Srinivasa R. Raghavan
Mammalian cell culture has been traditionally performed in a static oxygen concentration of 20 mol %. However, oxygen level in vivo is significantly more hypoxic with an average oxygen concentration of 3 mol % to 5 mol %. In addition, many cells within the
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