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Author: Justin Zook
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1. Why human genome sequencing platforms differ: Integrating sequencing datasets to understand biases and form consensus variant calls
Justin M Zook, Brad Chapman, Winston Hide, Marc L Salit
Hundreds of thousands of differences exist between human whole genome variant calls from different sequencing platforms and variant calling pipelines, but the reasons for these differences are poorly understood. Well-characterized whole genome Refer ...
2. Next-generation Sequencing: Guidance for the Translation from Research to Clinical Applications
Justin M Zook, Amy Gargis, Lisa Kalman, Ira Lubin
We would like to draw your readers‰ attention to the Next-generation Sequencing: Standardization of Clinical Testing (Nex-StoCT)
guidelines, which represent an initial step toward ensuring that the results derived from next-generation sequencing (N ...
3. Disentangling the effects of polymer coatings on silver nanoparticle agglomeration, dissolution, and toxicity to determine mechanisms of nanotoxicity
Justin M Zook, Melissa Danielle Halter, Danielle Cleveland, Stephen E Long
Silver nanoparticles (AgNPs) are frequently coated by a variety of polymers, which may affect various intertwined mechanisms of toxicity, including agglomeration and dissolution rate. Here, we measure how citrate, dextran, poly(ethylene glycol) (PEG ...
4. Synthetic spike-in standards improve run-specific systematic error analysis for DNA and RNA sequencing
Justin M Zook, Daniel Victor Samarov, Jennifer H McDaniel, Shurjo Sen, Marc L Salit
While the importance of random sequencing errors decreases at higher DNA or RNA sequencing depths, systematic sequencing
errors (SSEs) dominate at high sequencing depths and can be difficult to distinguish from biological variants. These SSEs can ...
5. Stable nanoparticle aggregates/agglomerates of different sizes and the effect of their size on hemolytic cytotoxicity
Justin M Zook, Robert I. MacCuspie, Laurie E Locascio, Michael W Halter, John T Elliott
Methods to disperse nanoparticles reproducibly in aqueous solutions compatible with cell-based assays are critical for studying cytotoxicity. Here, we disperse gold and silver nanoparticles in cell culture media, letting them agglomerate to a variet ...
6. Measuring agglomerate size distribution and dependence of localized surface plasmon resonance
absorbance on gold nanoparticle agglomerate size using analytical ultracentrifugation
Justin M Zook, Vinayak Rastogi, Robert I. MacCuspie, Athena M Keene, Jeffrey A Fagan
Nanoparticles frequently agglomerate when dispersed into relevant biological and environmental
media, with the resulting change to the effective size distribution dramatically affecting the
potential nanotoxicity and the absorbance for biosensor ...
7. Measuring silver nanoparticle dissolution in complex biological and environmental matrices using UV-Visible absorbance
Justin M Zook, Stephen E Long, Danielle Cleveland, Carly Lay Geronimo, Robert I. MacCuspie
Distinguishing the toxic effects of nanoparticles (NPs) themselves from the well-studied toxic effects of their ions is a critical but challenging measurement for nanotoxicity studies and regulation. This measurement is especially difficult for silv ...
8. Nanomaterial Toxicity: Emerging Standards and Efforts to Support Standards Development
Laurie E Locascio, Vytautas Reipa, Justin M Zook, Richard C. Pleus
For the first time in the history of industrialization, nanotechnology offers the unique opportunity to consider material safety ahead of its full implementation. Many scientists around the world have been motivated by this and are working on develo ...
9. Effects of temperature, acyl chain length, and flow-rate ratio on liposome formation and size in a microfluidic hydrodyanmic focusing device
Justin M Zook, Wyatt N Vreeland
Microfluidic hydrodynamic focusing of an alcohol/lipid mixture into a narrow fluid stream by two oblique buffer streams provides a controlled and reproducible method of forming phospholipid bilayer vesicles (i.e., liposomes) with relatively monodispe ...
10. Magnetic connectors for microfluidic applications
Francisco Javier Atencia, Gregory A Cooksey, Andreas Jahn, Justin M Zook, Wyatt N Vreeland, Laurie E Locascio
We present a new type of connector based on a simple idea: using a ring magnet on one side of the microfluidic chip and a disc magnet on the other side to provide the interfacial force necessary to provide a sealed connection between tubing or needle ...