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Search Publications by: Samuel P. Forry (Fed)

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Displaying 1 - 25 of 28

Beyond Sequence Similarity: The Case for Function-Based Screening of Nucleic Acid Synthesis

May 13, 2026
Author(s)
Gary Able, Tessa Alexanian, Jacob Beal, James Diggans, Kevin Flyangolts, Gene D. Godbold, Eric Horvitz, Bin Hu, Caitlin Jagla, Rassin Lababidi, Brittany Rife Magalis, Sebastian Rivera, Bruce Wittmann, Samuel Forry, David Ross, Sheng Lin-Gibson, Samuel Curtis
Synthetic nucleic acids are a key input to modern biotechnology, yet they represent dual-use materials that require robust screening to mitigate biosecurity risks. The prevailing screening paradigm identifies sequences of concern (SoCs) through sequence

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

Inter-tool analysis of a NIST dataset for assessing baseline nucleic acid sequence screening

July 10, 2025
Author(s)
Tyler Laird, Kevin Flyangolts, Craig Bartling, Bryan Gemler, Jacob Beal, Tom Mitchell, Steven T. Murphy, Jens Berlips, Leonard Foner, Ryan Doughty, Felix Qunitana, Michael Nute, Todd J. Treangen, Gene D. Godbold, Krista Ternus, Tessa Alexanian, Nicole Wheeler, Samuel Forry
Nucleic acid synthesis is a dual-use technology that can benefit fields such as biology, medicine, and information storage. However, synthetic nucleic acids could also potentially be used negligently and ultimately cause harm, or be used with malicious

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

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

Revealing thermodynamics of DNA origami folding via affine transformations

June 4, 2020
Author(s)
Jacob M. Majikes, Paul N. Patrone, Daniel R. Schiffels, Michael P. Zwolak, Anthony J. Kearsley, Samuel P. Forry, James A. Liddle
Structural DNA nanotechnology, as exemplified by DNA origami, has enabled the design and construction of molecularly precise objects for a myriad of applications. However, limitations in imaging, and other characterization approaches, make a quantitative

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

Automation of Antimicrobial Activity Screening

March 12, 2016
Author(s)
Samuel P. Forry, Meggan C. Madonna, Daneli Lopez-Perez, Nancy J. Lin, Madeleine D. Pasco
ABSTRACT: Manual and automated methods were compared for routine screening of compounds for antimicrobial activity. Automation generally accelerated assays and required less user intervention while producing comparable results. Automated protocols were

Theoretical Analysis of a Magnetophoresis-Diffusion T-Sensor Immunoassay

August 6, 2013
Author(s)
Thomas P. Forbes, Matt S. Munson, Samuel P. Forry
Microfluidic immunoassays have demonstrated broad application to the detection and quantification of analytes ranging from small drug molecules to large proteins and biomolecules. These systems exhibit short length scales, reduced sample volumes, and

Capturing Rare Cells From Blood Using a Packed Bed of Custom-Synthesized Chitosan Microparticles

July 1, 2013
Author(s)
Chandamany Arya, Jason Kralj, Kunqiang Jiang, Matt S. Munson, Thomas Forbes, Don L. DeVoe, Srinivasa R. Raghavan, Samuel Forry
Uniform multifunctional chitosan microparticles were produced in large numbers using a simple and inexpensive microtubing arrangement. The particles were functionalized through both physical encapsulation of carbon black, to attenuate autofluorescence, and

Simple device for rare cell capture from whole blood

September 26, 2012
Author(s)
Jason G. Kralj, Samuel P. Forry, Matt S. Munson, Thomas P. Forbes, Chandamany Arya, Lynn Sorbara, Alessandro Tona, Sudhir Srivastava
We have developed a system to isolate rare cells from whole blood using commercially available components and simple microfluidics that can provide biologists with the capabilities of the monolithic devices. We characterized the capture of MCF-7 cells

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

On-chip CO2 control for microfluidic cell culture

January 1, 2011
Author(s)
Samuel P. Forry, Laurie E. Locascio
Carbon dioxide partial pressure (PCO2) was controlled on-chip by flowing pre-equilibrated aqueous solutions through control channels across the device. Elevated PCO2 (e.g. 0.05 atm) was modulated in neighboring stagnant channels via equilibration through

Quantum Dot FRET Sensor for Enzymatic Activity in Microfluidic Device

June 22, 2010
Author(s)
Georgeta Crivat, Sandra M. Da Silva, Darwin Reyes-Hernandez, Samuel Forry, Laurie E. Locascio, Michael Gaitan, Nitsa Rosenzweig, Zeev Rosenzweig
This paper describes the development of new fluorescence resonance energy transfer (FRET)-based quantum dot probes for proteolytic activity. The CdSe/ZnS quantum dots are incorporated into a thin polymeric film, which is prepared by layer-by-layer

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

T7-Based Linear Amplification of Low Concentration mRNA Samples using Beads and Microfluidics for Global Gene Expression Measurements

April 7, 2009
Author(s)
Jason G. Kralj, Audrey Player, Hope Sedrick, Matt S. Munson, David Petersen, Samuel P. Forry, Paul Meltzer, Ernest Kawasaki, Laurie E. Locascio
We show single-cell level linear amplification of gene expression libraries immobilized on a microfluidic packed bed. This is a critical step in the Eberwine process, which is used to amplify messenger RNA (mRNA) for gene expression profiling. Microarray
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