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1. SVClassify: a method to use multiple datasets to classify candidate structural variants into true positives and false positives
Published: 1/16/2016
Authors: Justin M Zook, Hemang M. Parikh, Desu Chen, Hariharan K Iyer, Marc L Salit, Wolfgang Losert
Abstract: 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 Consorti ...
http://www.nist.gov/manuscript-publication-search.cfm?pub_id=918034

2. Benchmarks for genome sequencing
Published: 9/23/2015
Authors: Justin M Zook, Marc L Salit
Abstract: 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 ...
http://www.nist.gov/manuscript-publication-search.cfm?pub_id=919330

3. svviz: a read viewer for validating structural variants
Published: 8/18/2015
Authors: Noah Spies, Justin M Zook, Marc L Salit, Arend Sidow
Abstract: 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 i ...
http://www.nist.gov/manuscript-publication-search.cfm?pub_id=918148

4. Quantifying and Improving Clinical-grade Coverage and Accuracy using Augmented Exome Sequencing
Published: 7/16/2015
Authors: Justin M Zook, Anil Patwardhan, Marc L Salit, Carlos Bustamante, Euan Ashley, Michael Snyder, John West, Richard Chen
Abstract: 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 t ...
http://www.nist.gov/manuscript-publication-search.cfm?pub_id=917740

5. Optimization of Next-Generation Sequencing Informatics Pipelines for Clinical Laboratory Practice
Published: 7/8/2015
Authors: Justin M Zook, Amy Gargis, Lisa Kalman, Ira Lubin, Marc L Salit
Abstract: We direct your readers' attention to the principles and guidelines (see Supplementary Guidelines) developed by the Next-generation Sequencing: Standardization of Clinical Testing II (Nex-StoCT II) informatics workgroup, which was convened by the Cent ...
http://www.nist.gov/manuscript-publication-search.cfm?pub_id=916037

6. Best Practices for Evaluating Single Nucleotide Variant Calling Methods for Microbial Genomics
Published: 7/7/2015
Authors: 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
Abstract: 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 ...
http://www.nist.gov/manuscript-publication-search.cfm?pub_id=918229

7. Measuring silver nanoparticle dissolution in complex biological and environmental matrices using UV/visible absorbance measurements
Series: Special Publication (NIST SP)
Report Number: 1200-13
Published: 6/3/2015
Authors: Justin M Zook, Robert MacCuspie, Stephen E Long, Elijah J Petersen
Abstract: 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 ...
http://www.nist.gov/manuscript-publication-search.cfm?pub_id=917792

8. Reliable preparation of nanoparticle agglomerates of different sizes in cell culture media
Series: Special Publication (NIST SP)
Report Number: 1200-14
Published: 6/3/2015
Authors: Justin M Zook, Robert MacCuspie, John T Elliott, Elijah J Petersen
Abstract: 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 ...
http://www.nist.gov/manuscript-publication-search.cfm?pub_id=917800

9. International Interlaboratory Study Comparing Single Organism 16S rRNA Sequencing Data: Going Beyond Consensus Sequence Comparisons
Published: 3/5/2015
Authors: Nathanael D Olson, Justin M Zook, Steven P Lund, Fabiola Rojas-Cornejo, Jim Huggett, Jayne B Morrow
Abstract: 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 ...
http://www.nist.gov/manuscript-publication-search.cfm?pub_id=915125

10. An analytical framework for optimizing variant discovery from personal genomes
Published: 2/25/2015
Authors: Justin M Zook, Gareth Highnam, Jason Wang, Dean Kusler, Vinaya Vijayan, Nir Leibovich, David Mittelman
Abstract: 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 ...
http://www.nist.gov/manuscript-publication-search.cfm?pub_id=916355



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