You searched on: Author: Marc Salit
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1. Using mixtures of biological samples as genome-scale process controls
Jerod R Parsons, Patrick S Pine, Marc L Salit, Sarah A Munro, Jennifer H McDaniel
Genome-scale ,-omicsŠ measurements are challenging to benchmark, due to the enormous number of individual measurands.
Mixtures of previously-characterized samples can be used to benchmark repeat performance using mixture proportions ...
2. Quantifying and Improving Clinical-grade Coverage and Accuracy using Augmented Exome Sequencing
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 t ...
3. Optimization of Next-Generation Sequencing Informatics Pipelines for Clinical Laboratory Practice
Justin M Zook, Amy Gargis, Lisa Kalman, Ira Lubin, Marc L Salit
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 ...
4. 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 ...
5. The Use of Cause-and-Effect Analysis to Design a High Quality Nano-Cyto-Toxicology Assay
Matthias Rosslein, John T Elliott, Marc L Salit, Elijah J Petersen, Cordula Hirsch, Harald Krug, Peter Wick
An important consideration in developing standards and regulations that govern the production and
use of commercial nanoscale materials is the development of robust and reliable measurements to
assess potential biological effects of these nanomat ...
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. Assessing technical performance in differential gene expression experiments with external spike-
in RNA control ratio mixtures
Sarah A Munro, Steven P Lund, Patrick S Pine, Hans Binder, Djork-Arne Clevert, Ana Conesa, Joaquin Dopazo, Mario Fasold, Sepp Hochreiter, Huixao Hong, Nederah Jafari, David P Kreil, Pawel P Labaj, Yang Liao, Simon Lin, Christopher E Mason, Javier Santoyo, Steven J Schrodi, Leming Shi, Wei Shi, Gordon K Smyth, Nancy Stralis-Pavese, Zhenqiang Su, Charles Wang, Jian Wang, Joshua Xu, Zhan Ye, Yong Yang, Ying Yu, Paul Zumbo, Marc L Salit
There is a critical need for standard approaches to assess, report and compare the technical
performance of genome-scale differential gene expression experiments. Here we assess technical
performance with a proposed standard ,dashboard‰ of metric ...
8. Ontology Analysis if Global Gene Expression Differences of Human Bone Marrow Stromal Cells Cultured on 3D Scaffolds or 2D Films
Bryan A. Baker, Patrick S Pine, Kaushik Chatterjee, Girish Kumar, Jennifer H McDaniel, Marc L Salit, Carl George Simon Jr.
Differences in gene expression of human bone marrow stromal cells (hBMSCs) during culture in three-dimensional (3D) nanofiber scaffolds or on two-dimensional (2D) films were investigated via pathway analysis of microarray mRNA expression profiles. P ...
9. Evaluation of the effect of donor variability on stem cell response to biomaterials
Stephen J Florczyk, Bryan A. Baker, Sumona Sarkar, Jennifer H McDaniel, Patrick S Pine, Marc L Salit, Carl George Simon Jr.
Previous research from our group indicated that nanofiber scaffolds promoted osteogenic
differentiation of human bone marrow stromal cells (hBMSC) and similar gene expression to osteogenic
supplement (OS) induced osteogenic differentiation . ...
10. 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 ...