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Search Publications by: Marc L. Salit (Assoc)

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Displaying 26 - 50 of 64

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

Using mixtures of biological samples as genome-scale process controls

September 17, 2015
Author(s)
Jerod R. Parsons, Patrick S. Pine, Marc L. Salit, Sarah A. Munro, Jennifer H. McDaniel
Background: Genome-scale “-omics” 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 as truth

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

The Use of Cause-and-Effect Analysis to Design a High Quality Nano-Cyto-Toxicology Assay

December 4, 2014
Author(s)
Matthias Rosslein, John T. Elliott, Marc L. Salit, Elijah 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 nanomaterials

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

Assessing technical performance in differential gene expression experiments with external spike- in RNA control ratio mixtures

September 25, 2014
Author(s)
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 metrics derived

Ontology Analysis if Global Gene Expression Differences of Human Bone Marrow Stromal Cells Cultured on 3D Scaffolds or 2D Films

July 31, 2014
Author(s)
Bryan A. Baker, Patrick S. Pine, Kaushik Chatterjee, Girish Kumar, Jennifer H. McDaniel, Marc L. Salit, Carl G. 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. Previous

Evaluation of the effect of donor variability on stem cell response to biomaterials

April 19, 2014
Author(s)
Stephen J. Florczyk, Bryan A. Baker, Sumona Sarkar, Jennifer H. McDaniel, Patrick S. Pine, Marc L. Salit, Carl G. 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 [1]. Biological

Morphological Changes Driven by Nanofibrous Scaffolds Induce Marrow Stromal Cell Osteogenesis

October 11, 2011
Author(s)
Carl G. Simon Jr., Kaushik Chatterjee, Christopher K. Tison, Girish Kumar, Patrick S. Pine, Marc L. Salit, Jennifer H. McDaniel, Marian F. Young
Cells are sensitive to tissue scaffold architecture and these cell-material interactions drive cell functions critical in tissue regeneration. Results presented here demonstrate that nanofiber scaffolds force primary human bone marrow stromal cells (hBMSCs

Synthetic spike-in standards for RNA-seq experiments

September 1, 2011
Author(s)
Marc L. Salit, Lichun Jiang, Felix Schlesinger, Brian Oliver, Carrie Davis, Yu Zhang, Renhua Li, Thomas R. Gingeras
High-throughput sequencing of cDNA (RNA-seq) is a widely deployed transcriptome profiling and annotation technique, but questions about the performance of different protocols and platforms remain. We used a newly developed pool of 96 synthetic RNAs with

Contributions of the EMERALD project to assessing and improving microarray data quality

January 1, 2011
Author(s)
Vidar Beisvag, Audrey Kauffmann, James Malone, Carole Foy, Marc L. Salit, Schimmel Heinz, Erik Bongcam-Rudloff, Ulf Landegren, Helen Parkinson, Wolfgang Huber, Alvis Brazma, Arne K. Sandvik, Martin Kuiper
While MIAME standards have helped to increase the value of microarray data deposited in public databases like ArrayExpress and GEO, limited means have been available to assess the quality of the data or to identify the procedures that were used to

Image-Based Feedback Control for Real-Time Sorting of Microspheres in a Microfluidic Device

January 1, 2010
Author(s)
Matt S. Munson, James Spotts, Antti Niemisto, Jyrki Selinummi, Jason G. Kralj, Marc L. Salit, Adrian Ozinsky
We have developed a fully automated control system to distribute user-defined numbers of antibody-functionalized fluorescent beads (scalable from tens to hundreds) to addressable assay chambers within a microfluidic PDMS device. We report an automated bead

Standards in Gene Expression Microarray Experiments

August 1, 2006
Author(s)
Marc L. Salit
The use of standards in gene expression measurements with DNA microarrays is ubiquitous—they just are not yet the kind of standards that have yielded microarray gene expression profiles that can be readily compared across different studies and different