Adam C. English
A5089632191- Genomics and Phylogenetic Studies
- Genomics and Rare Diseases
- Chromosomal and Genetic Variations
- Genomic variations and chromosomal abnormalities
- Plant tissue culture and regeneration
- Biblical Studies and Interpretation
- Plant Reproductive Biology
- RNA and protein synthesis mechanisms
- Religion, Society, and Development
- Gene expression and cancer classification
- Bioinformatics and Genomic Networks
- Reformation and Early Modern Christianity
- Cancer Genomics and Diagnostics
- Religion and Society Interactions
- Insect symbiosis and bacterial influences
- Genetic Associations and Epidemiology
- Phytoplasmas and Hemiptera pathogens
- CRISPR and Genetic Engineering
- Genomics and Chromatin Dynamics
- American Constitutional Law and Politics
- Genetic Neurodegenerative Diseases
- Christian Theology and Mission
- Medieval Philosophy and Theology
- Karl Barth and Christian Theology
- Molecular Biology Techniques and Applications
Baylor College of Medicine
2012-2024
Baylor Genetics
2012-2024
Campbell University
2004-2020
Spiral Foundation
2018-2020
Illumina (United States)
2017-2019
Los Alamos National Laboratory
2017-2019
University of Washington
2018
NewYork–Presbyterian Hospital
2018
University of Pennsylvania
2018
Boston University
2018
Many genomes have been sequenced to high-quality draft status using Sanger capillary electrophoresis and/or newer short-read sequence data and whole genome assembly techniques. However, even the best contain gaps other imperfections due limitations in input techniques used build assemblies. Sequencing biases, repetitive genomic features, polymorphism, complicating factors all come together make some regions difficult or impossible assemble. Traditionally, were upgraded "phase 3 finished"...
Massively parallel DNA sequencing generates staggering amounts of data. Decreasing cost, increasing throughput, and improved annotation have expanded the diversity genomics applications in research clinical practice. This expanding scale creates analytical challenges: accommodating peak compute demand, coordinating secure access for multiple analysts, sharing validated tools results. To address these challenges, we developed Mercury analysis pipeline deployed it local hardware Amazon Web...
Abstract Hundreds of thousands human whole genome sequencing (WGS) datasets will be generated over the next few years. These data are more valuable in aggregate: joint analysis genomes from many sources increases sample size and statistical power. A central challenge for is that different WGS processing pipelines cause substantial differences variant calling combined datasets, necessitating computationally expensive reprocessing. This approach no longer tenable given scale current studies...
The fundamental challenge of multi-sample structural variant (SV) analysis such as merging and benchmarking is identifying when two SVs are the same. Common approaches for comparing were developed alongside technologies which produce ill-defined boundaries. As SV detection becomes more exact, algorithms to preserve this refined signal needed. Here, we present Truvari-an comparison, annotation, toolkit-and demonstrate effect comparison choices by building population-level VCFs from 36...
Research and medical genomics require comprehensive scalable solutions to drive the discovery of novel disease targets, evolutionary drivers, genetic markers with clinical significance. This necessitates a framework identify all types variants independent their size (e.g., SNV/SV) or location repeats). Here we present DRAGEN that utilizes methods based on multigenomes, hardware acceleration, machine learning variant detection provide insights into individual genomes ~30min computation time...
Journal Article Against War: Views from the Underside of Modernity Get access Modernity. By Nelson Maldonado-Torres. Durham: Duke University Press, 2008. 360 pp. $84.95 cloth, $23.95 paper. Adam C. English Campbell UniversityBuies Creek, North Carolina englisha@campbell.edu Search for other works by this author on: Oxford Academic Google Scholar Church and State, Volume 51, Issue 1, Winter 2009, Pages 152–153, https://doi.org/10.1093/jcs/csp021 Published: 27 August 2009
Characterizing large genomic variants is essential to expanding the research and clinical applications of genome sequencing. While multiple data types methods are available detect these structural (SVs), they remain less characterized than smaller because SV diversity, complexity, size. These challenges exacerbated by experimental computational demands analysis. Here, we characterize content a personal with Parliament, publicly consensus SV-calling infrastructure that merges detection...
As resequencing projects become more prevalent across a larger number of species, accurate variant identification will further elucidate the nature genetic diversity and increasingly relevant in genomic studies. However, variants via DNA sequencing is limited by both incomplete information provided reads genome itself. Long-read technologies provide high-resolution access to structural often inaccessible shorter reads. We present PBHoney, software that considers intra-read discordance...
Whole-genome sequencing and comparative genomic analysis of immune-related genes Cercocebus atys Macaca mulatta identify candidate genes, such as ICAM2 TLR4, that may explain the AIDS resistance C. atys. Sooty mangabeys are a primate model for non-pathogenic simian immunodeficiency virus (SIV) infection. Guido Silvestri colleagues sequenced genome captive sooty mangabey from Yerkes National Primate Research Center in Atlanta, Georgia. They compared this with sequences other primates suggest...
Research and medical genomics require comprehensive, scalable methods for the discovery of novel disease targets, evolutionary drivers genetic markers with clinical significance. This necessitates a framework to identify all types variants independent their size or location. Here we present DRAGEN, which uses multigenome mapping pangenome references, hardware acceleration machine learning-based variant detection provide insights into individual genomes, ~30 min computation time from raw...
https://citrusgreening.org/.
Generation of long (>5 Kb) DNA sequencing reads provides an approach for interrogation complex regions in the human genome. Currently, large-insert whole genome (WGS) technologies from Pacific Biosciences (PacBio) enable analysis chromosomal structural variations (SVs), but cost to achieve required sequence coverage across entire is high.We developed a method (termed PacBio-LITS) that combines oligonucleotide-based target-capture enrichment with PacBio library preparation facilitate SV...
Abstract New technologies and analysis methods are enabling genomic structural variants (SVs) to be detected with ever-increasing accuracy, resolution, comprehensiveness. Translating these routine research clinical practice requires robust benchmark sets. We developed the first set for identification of both false negative positive germline SVs, which complements recent efforts emphasizing increasingly comprehensive characterization SVs. To create this a broadly consented son in Personal...
Abstract Background The growing volume and heterogeneity of next-generation sequencing (NGS) data complicate the further optimization identifying DNA variation, especially considering that curated high-confidence variant call sets frequently used to validate these methods are generally developed from analysis comparatively small homogeneous sample sets. Findings We have xAtlas, a single-sample caller for single-nucleotide variants (SNVs) insertions deletions (indels) in NGS data. xAtlas...
Abstract For multi-sample structural variant analyses like merging, benchmarking, and annotation, the fundamental operation is to identify when two SVs are same. Commonly applied approaches for comparing were developed alongside technologies which produce ill-defined boundaries. As SV detection becomes more exact, algorithms preserve this refined signal needed. Here we present Truvari - a comparison, annotation analysis toolkit demonstrate effect of comparison choices by building...
Abstract Tandem repeat (TR) variation is associated with gene expression changes and over 50 rare monogenic diseases. Recent advances in sequencing have enabled accurate, long reads that can characterize the full-length sequence methylation profile of TRs. However, despite these technology, computational methods to fully tandem repeats across genome do not exist. To address this gap, we introduce tools for genotyping (TRGT), visualization an accompanying TR database. TRGT accurately resolves...
Tandem repeats (TRs) are highly polymorphic in the human genome, have thousands of associated molecular traits, and linked to over 60 disease phenotypes. However, their complexity often excludes them from at-scale studies due challenges with variant calling, representation, lack a genome-wide standard. To promote TR methods development, we create comprehensive catalog regions explore its properties across 86 samples. We then curate variants GIAB HG002 individual tandem repeat benchmark. also...
The heterogeneity of the whole-exome sequencing (WES) data generation methods present a challenge to joint analysis. Here we bioinformatics strategy for joint-calling 20,504 WES samples collected across nine studies and sequenced using ten capture kits in fourteen centers Alzheimer's Disease Sequencing Project. joint-genotype called variant-called format (VCF) file contains only positions within union kits. VCF was then processed specifically account batch effects arising from use different...
Ever larger Structural Variant (SV) catalogs highlighting the diversity within and between populations help researchers better understand links SVs disease. The identification of from DNA sequence data is non-trivial requires a balance comprehensiveness precision. Here we present catalog 355,667 (59.34% novel) across autosomes X chromosome (50bp+) 138,134 individuals in diverse TOPMed consortium. We describe our methodologies for SV inference resulting high variant quality >90% allele...
Abstract Background Around 14% of protein-coding genes Arabidopsis thaliana from the TAIR9 genome release are annotated as producing multiple transcript variants through alternative splicing. However, for most alternatively spliced in , relative expression level individual splicing is unknown. Results We investigated prevalence (AS) events using ESTs. found that AS with ample EST coverage, majority overlapping ESTs strongly supported one major choice, less than 10% supporting minor form....