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Bioinformatics

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Displaying 1 - 12 of 12

Inter-tool analysis of a NIST dataset for assessing baseline nucleic acid sequence screening

July 2, 2025
Author(s)
Tyler Laird, Samuel Forry, Kevin Flyangolts, Craig Bartling, Bryan Gemler, Jacob Beal, Tessa Alexanian, Nicole Wheeler, Krista Ternus, Todd Treangen, Gene D. Godbold, Michael Nute, Leonard Foner, Jens Berlips
Nucleic acid synthesis is a dual-use technology that can benefit fields such as biology, medicine, and information storage. However, synthetic nucleic acids could also potentially be used negligently and ultimately cause harm, or be used with malicious

Small variant benchmark from a complete assembly of X and Y chromosomes

January 8, 2025
Author(s)
Justin Wagner, Nathanael Olson, Jennifer McDaniel, Lindsay Harris, Chunlin Xiao, Fritz Sedlazeck, Kishwar Shafin, Andrew Carroll, Justin Zook
The sex chromosomes contain complex, important genes impacting medical phenotypes, but differ from the autosomes in their ploidy and large repetitive regions. To enable technology developers along with research and clinical laboratories to evaluate variant

Proteomic and Lipidomic Plasma Evaluations Reveal Biomarkers for Domoic Acid Toxicosis in California Sea Lions

November 24, 2024
Author(s)
Amie Solosky, Iliana Claudio, Kaylie Kirkwood, Jessie Chappel, Michael Janech, Alison Bland, Frances Gulland, Benjamin Neely, Erin Baker
Domoic acid is a neurotoxin secreted by the marine diatom genus Pseudo-nitzschia during toxic algal bloom events. California sea lions (Zalophus californianus) are exposed to domoic acid through the ingestion of fish that feed on toxic diatoms, resulting

The Platinum Pedigree: A long-read benchmark for genetic variants

October 3, 2024
Author(s)
Zev Kronenberg, Nathanael Olson, Justin Zook, Michael Eberle
Recent advances in genome sequencing have improved variant calling in complex regions of the human genome. However, it is difficult to quantify variant calling performance because existing standards often focus on specificity, neglecting completeness in

Jointly benchmarking small and structural variant calls with vcfdist

October 2, 2024
Author(s)
Tim Dunn, Justin Zook, James Holt, Satish Narayanasamy
In this work, we extend vcfdist to be the first variant call benchmarking tool to jointly evaluate phased single-nucleotide polymorphisms (SNPs), small insertions/deletions (INDELs), and structural variants (SVs) for the whole genome. First, we find that a

Quality Control in the Mass Spectrometry Proteomics Core: a Practical Primer

September 11, 2024
Author(s)
Ben Neely, Yasset Perez-Riverol, Magnus Palmblad
The past decade has seen widespread advances in quality control (QC) materials and software tools focused specifically on mass spectrometry–based proteomics, yet the rate of adoption is inconsistent. Despite the fundamental importance of QC, it typically

Genome-wide profiling of genetic variation at tandem repeat from long reads

July 4, 2024
Author(s)
Helyaneh Jam, Justin Zook, Sara Javadzadeh, Jonghun Park, Aarushi Sehgal, Melissa Gymrek
Tandem repeats are frequent across the human genome, and variation in repeat length has been linked to a variety of traits. Recent improvements in long read sequencing technologies have the potential to greatly improve TR analysis, especially for long or

A Draft Human Pangenome Reference

May 10, 2023
Author(s)
Wen-Wei Liao, Mobin Asri, Jana Ebler, Jennifer McDaniel, Nathanael David Olson, Justin Wagner, Justin Zook, Erik Garrison, Tobias Marschall, Ira Hall, Heng Li, Benedict Paten
Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals1. These assemblies cover more than 99% of the

Variant calling and benchmarking in an era of complete human genome sequences

April 14, 2023
Author(s)
Nathanael David Olson, Justin Wagner, Nathan Dwarshuis, Karen Miga, Marc L. Salit, Justin Zook
Genetic variant calling from DNA sequencing has enabled understanding of germline variation in hundreds of thousands of humans. Sequencing technologies and variant-calling methods have advanced rapidly, routinely providing reliable variant calls in most of
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