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Publications

Search Publications by

Jennifer McDaniel (Fed)

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Displaying 1 - 11 of 11

The complete sequence of a human genome

March 31, 2022
Author(s)
Sergey Nurk, Sergey Koren, Arang Rhie, Mikko Rautiainen, Jennifer McDaniel, Nathanael David Olson, Justin Wagner, Justin Zook, Evan Eichler, Karen Miga, Adam Phillippy
Since its initial release in 2000, the human reference genome has covered only the euchromatic fraction of the genome, leaving important heterochromatic regions unfinished. Addressing the remaining 8% of the genome, the Telomere-to-Telomere (T2T)

An open resource for accurately benchmarking small variant and reference calls

April 1, 2019
Author(s)
Justin M. Zook, Jennifer H. McDaniel, Marc L. Salit, Nathanael D. Olson, Justin M. Wagner
Benchmark small variant calls are required for developing, optimizing and assessing the performance of sequencing and bioinformatics methods. Here, as part of the Genome in a Bottle (GIAB) Consortium, we apply a reproducible, cloud-based pipeline to

Genome-wide reconstruction of complex structural variants using read clouds

July 17, 2017
Author(s)
Noah Spies, Ziming Weng, Alex Bishara, Jennifer H. McDaniel, David N. Catoe, Justin M. Zook, Marc L. Salit, Robert B. West, Serafim Batzoglou, Arend Sidow
Recently developed methods that utilize partitioning of long genomic DNA fragments, and barcoding of shorter fragments derived from them, have succeeded in retaining long-range information in short sequencing reads. These so-called read cloud approaches

Roles of Nanofiber Scaffold Structure and Chemistry in Directing Human Bone Marrow Stromal Cell Response

August 22, 2016
Author(s)
Sumona Sarkar, Bryan A. Baker, Desu Chen, Patrick S. Pine, Jennifer H. McDaniel, Marc L. Salit, Wolfgang Losert, Carl G. Simon Jr., Joy P. Dunkers
Nanofiber technology has emerged as a promising tool to recapitulate the native extracellular matrix structure; however the properties of nanofibers governing cell-material interactions are still largely undetermined. In this study we have systematically

Extensive sequencing of seven human genomes to characterize benchmark reference materials

June 7, 2016
Author(s)
Justin M. Zook, Jennifer H. McDaniel, David N. Catoe, Lindsay Harris, Marc L. Salit
The Genome in a Bottle Consortium hosted by the National Institute of Standards and Technology, (NIST), is creating reference materials and data for human genome sequencing, as well as methods for genome comparison and benchmarking. Here, we describe a

DNA Extraction and DNA Damage Measurement in the Nematode Caenorhabditis elegans

November 1, 2015
Author(s)
Leona D. Scanlan, Pawel Jaruga, Sanem Hosbas Coskun, Jamie L. Almeida, David N. Catoe, Jennifer McDaniel, Miral M. Dizdar
Little is known about endogenous DNA damage in the nematode. In this work, we standardized the growth of the nematode in two different growth media (axenic CeHR supplemented with 20% milk and S-basal with E. coli), and developed a novel high-salt, phenol

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

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