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Search Publications by: Justin Zook (Fed)

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Displaying 51 - 72 of 72

Clinical Implications of Technical Performance in Medical Genome Sequencing

March 2, 2016
Author(s)
Justin M. Zook, James Priest, Rachel Goldfeder, Megan Grove, Daryl Waggott, Matthew Wheeler, Euan Ashley, Marc L. Salit
As next-generation sequencing is becoming routinely applied to clinical care, the predictive characteristics and limitations of whole exome and whole genome sequencing need to be well-understood. The Genome in a Bottle Consortium has recently published a

SVClassify: a method to use multiple datasets to classify candidate structural variants into true positives and false positives

January 16, 2016
Author(s)
Justin M. Zook, Hemang M. Parikh, Desu Chen, Hariharan K. Iyer, Marc L. Salit, Wolfgang Losert
The human genome contains variants ranging in size from small single nucleotide polymorphisms (SNPs) to large structural variants (SVs). While high-quality benchmark small variant calls have recently been developed by the Genome in a Bottle Consortium, no

Benchmarks for genome sequencing

September 23, 2015
Author(s)
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 sequencing

svviz: a read viewer for validating structural variants

August 18, 2015
Author(s)
Noah Spies, Justin M. Zook, Marc L. Salit, Arend Sidow
We present svviz, a sequencing read visualizer for structural variants (SVs) that sorts and displays only reads relevant to a candidate SV. This is accomplished by searching input bam(s) for potentially relevant reads, realigning them against the inferred

Quantifying and Improving Clinical-grade Coverage and Accuracy using Augmented Exome Sequencing

July 16, 2015
Author(s)
Justin M. Zook, Anil Patwardhan, Marc L. Salit, Carlos Bustamante, Euan Ashley, Michael Snyder, John West, Richard Chen
Exome sequencing is increasingly used for the clinical evaluation of genetic disease, yet accuracy and coverage in medically interpretable parts of the genome remains under-characterized. We evaluate recently developed exome sequencing platforms in the

Best Practices for Evaluating Single Nucleotide Variant Calling Methods for Microbial Genomics

July 7, 2015
Author(s)
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 sequencing

International Interlaboratory Study Comparing Single Organism 16S rRNA Sequencing Data: Going Beyond Consensus Sequence Comparisons

March 5, 2015
Author(s)
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 assurance for

An analytical framework for optimizing variant discovery from personal genomes

February 25, 2015
Author(s)
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

Genomic Reference Materials for Clinical Application

November 21, 2014
Author(s)
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

Disentangling the effects of polymer coatings on silver nanoparticle agglomeration, dissolution, and toxicity to determine mechanisms of nanotoxicity

September 1, 2012
Author(s)
Justin M. Zook, Melissa D. 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)

Measuring agglomerate size distribution and dependence of localized surface plasmon resonance absorbance on gold nanoparticle agglomerate size using analytical ultracentrifugation

September 3, 2011
Author(s)
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

Nanomaterial Toxicity: Emerging Standards and Efforts to Support Standards Development

February 1, 2011
Author(s)
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 developing

Magnetic connectors for microfluidic applications

January 1, 2010
Author(s)
Francisco J. 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 needles and
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