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Search Publications by: Nathanael David Olson (Fed)

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Displaying 26 - 50 of 66

A robust benchmark for detection of germline large deletions and insertions

June 15, 2020
Author(s)
Justin Zook, Nathanael David Olson, Marc Salit, Fritz Sedlazeck
New technologies and analysis methods are enabling genomic structural variants (SVs) to be detected with ever-increasing accuracy, resolution and comprehensiveness. To help translate these methods to routine research and clinical practice, we developed a

Assembly and annotation of an Ashkenazi human reference genome

June 2, 2020
Author(s)
Justin M. Zook, Justin M. Wagner, Nathanael D. Olson, Steven L. Salzberg, Alaina Shumate, Aleksey V. Zimin, Daniela Puiu, Mihaela Pertea, Marc Salit
Thousands of experiments and studies use the human reference genome as a resource each year. This single reference genome, GRCh38, is a mosaic created from a small number of individuals, representing a very small sample of the human population. There is a

A framework for assessing 16S rRNA marker-gene survey data analysis methods using mixtures.

March 13, 2020
Author(s)
Nathanael David Olson, Senthil Kumar, Stephanie Hao, Winston Timp, Marc L. Salit, O Colin Stine, Hector Corrada Bravo
Background: There are a variety of bioinformatic pipelines and downstream analysis methods for analyzing 16S rRNA marker-gene surveys. However, appropriate assessment datasets and metrics are needed as there is limited guidance to decide between available

High-coverage, long-read sequencing of Chinese trio reference samples

June 14, 2019
Author(s)
Justin M. Zook, Nathanael D. Olson, Marc L. Salit, Aaron Wenger, Chunlin Xiao, Robert Sebra
Genome In a Bottle (GIAB) is a consortium hosted by the National Institute of Standards and Technology whose primary objective is the development and characterization of human genomic reference materials. The consortium includes representatives from

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

Impact of conventional wastewater treatment and reuse site practices on the bacterial community structure of reclaimed water

October 15, 2018
Author(s)
Prachi Kulkarni, Nathanael David Olson, Joseph N. Paulson, Mihai Pop, Cynthia Maddox, Emma Claye, Rachel E. Rosenberg Goldstein, Manan Sharma, Amy R. Sapkota
Reclaimed water use continues to expand across the United States, from areas that have access to advanced, potable-level treated reclaimed water, to areas that only have access to reclaimed water treated at conventional municipal wastewater treatment

Using metagenomic methods to detect organismal contaminants in microbial materials.

September 12, 2017
Author(s)
Nathanael D. Olson, Justin M. Zook, Jayne B. Morrow, Nancy J. Lin
High sensitivity methods as next generation sequencing and PCR are adversely impacted by organismal and DNA contaminants. Current methods for detecting contaminants in microbial materials (genomic DNA and cultures) are not sensitive enough and require

Metagenomic assembly through the lens of validation: a review of recent advances in assessing and improving the quality of genes and genomes assembled from metagenomes.

August 6, 2017
Author(s)
Nathanael Olson, Chris M. Hill, Vistoria Cepeda-Espinoza, Jay Ghurye, Sergey Koren, Todd J. Treangen, Mihai Pop
Metagenomic samples are snapshots of complex ecosystems at work. These samples often involve hundreds of bacteria from known and unknown species, contain multiple strain variants, and vary greatly both within and across environments. Many microbes found in

Occurrence of Antibiotic Residues in Differentially Treated Wastewater and in Reclaimed Water Utilized in Spray Irrigation

June 21, 2017
Author(s)
Prachi Kulkarni, Nathanael David Olson, Greg Raspanti, Rachel F. Rosenberg Goldstein, Shawn G. Gibbs, Amir Sapkota, Amy Sapkota
The objective of this study was to evaluate concentrations of antibiotics in differentially treated wastewater and reclaimed water. Wastewater (from several treatment processes), final effluent and reclaimed water samples (n=72) from four U.S. wastewater

Performing Skin Microbiome Research: A Method to the Madness

March 1, 2017
Author(s)
Heidi H. Kong, Bjorn Andersson, Thomas Clavel, John E. Common, Scott Jackson, Nathanael David Olson, Julia Segre, Claudia Traidl-Hoffman
Growing interest in microbial contributions to human health and disease has increasingly led investigators to examine the microbiome in both healthy skin and cutaneous disorders, including acne, psoriasis, and atopic dermatitis. The need for common

PEPR: Pipeline for Evaluating Prokaryotic References

April 1, 2016
Author(s)
Nathanael D. Olson, Justin M. Zook, Daniel V. Samarov, Scott A. Jackson, Marc L. Salit
The rapid adoption of microbial whole genome sequencing in public health, clinical testing, and forensic labo-ratories requires the use of validated and well characterized measurement processes. Reference materials thatare well characterized and