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1. An analytical framework for optimizing variant discovery from personal genomes
Justin M Zook, Gareth Highnam, Jason Wang, Dean Kusler, Vinaya Vijayan, Nir Leibovich, David Mittelman
The standardization and performance testing of analysis tools is a prerequisite to widespread adoption of high-throughput sequencing, particularly in the clinic. However, performance testing is currently complicated by the paucity of standards and co ...
2. Benchmarks for genome sequencing
Justin M Zook, Marc L Salit
In this issue, Griffith et al. present one of the most comprehensive genome-sequence data sets to date from a patient with myeloid leukemia, including sequencing of normal tissue, primary cancer, and a relapse. Their raw data from a variety of sequen ...
3. Best Practices for Evaluating Single Nucleotide Variant Calling Methods for Microbial Genomics
Nathanael D Olson, Steven P Lund, Rebecca Colman, Jeffery T. Foster, Jason W. Sahl, James M. Schupp, Paul Keim, Jayne B Morrow, Marc L Salit, Justin M Zook
Innovations in sequencing technologies have allowed biologists to make incredible advances in understanding
biological systems. As experience grows, researchers increasingly recognize that analyzing the wealth of data
provided by these new sequen ...
4. 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 ...
5. 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 ...
6. Genomic Reference Materials for Clinical Application
Justin M Zook, Marc L Salit
Reference Materials are well-characterized, homogeneous, and stable samples that can be used to understand measurement performance. The Genome in a Bottle Consortium is developing whole human genome DNA Reference Materials from large batches of DNA ...
7. International Interlaboratory Study Comparing Single Organism 16S rRNA Sequencing Data: Going Beyond
Consensus Sequence Comparisons
Nathanael D Olson, Justin M Zook, Steven P Lund, Fabiola Rojas-Cornejo, Jim Huggett, Jayne B Morrow
The Consultative Committee for Amount of Substance established a working group to advance the
metrology of microbial identification and quantification. This study represents the initial step
towards international comparability and measurement as ...
8. 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 ...
9. 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 ...
10. Measuring silver nanoparticle dissolution in complex biological and environmental matrices using
UV/visible absorbance measurements
Special Publication (NIST SP)
Justin M Zook, Robert MacCuspie, Stephen E Long, Elijah J Petersen
This special publication is one in a series stemming from the National Nanotechnology Initiative
(NNI) Nano-EHS Research Strategy which identified Nanomaterial Measurement Infrastructure as one of
the essential areas of research needed in order t ...