A5049099147- Parasites and Host Interactions
- SARS-CoV-2 and COVID-19 Research
- Immune Cell Function and Interaction
- vaccines and immunoinformatics approaches
- T-cell and B-cell Immunology
- Zoonotic diseases and public health
- Renal Diseases and Glomerulopathies
- Blood groups and transfusion
- Monoclonal and Polyclonal Antibodies Research
- Multiple Sclerosis Research Studies
- Complement system in diseases
- Genomics and Phylogenetic Studies
- Plant Virus Research Studies
- Atherosclerosis and Cardiovascular Diseases
- Health and Medical Research Impacts
- Immunotherapy and Immune Responses
- Animal Virus Infections Studies
- Palliative Care and End-of-Life Issues
- Genome Rearrangement Algorithms
- Microtubule and mitosis dynamics
- Innovative Microfluidic and Catalytic Techniques Innovation
- Cellular transport and secretion
- Family and Patient Care in Intensive Care Units
- Cardiac Health and Mental Health
- Global Maternal and Child Health
University of California, San Francisco
2023-2025
University of Colorado Denver
2019-2022
University of Colorado Anschutz Medical Campus
2019-2021
American Heart Association
2013
University of Kentucky
2013
University of South Florida
2013
Mayo Clinic
2013
Background: The complement system has been suspected to play a role in multiple sclerosis (MS) due presence of activation products MS lesions. Objective: We sought understand whether variation the component 4 (C4) gene is associated with MS. Methods: Here we used next-generation sequencing and our novel bioinformatics tool, C4Investigator , interrogate C4 copy number Results: found higher overall controls ( p < 10 −16 odds ratio (OR) = 0.43, 95% confidence interval (CI): 0.37–0.49)...
Abstract Due to the scope and impact of COVID-19 pandemic there exists a strong desire understand where SARS-CoV-2 virus came from how it jumped species boundaries humans. Molecular evolutionary analyses can trace viral origins by establishing relatedness divergence times viruses identifying past selective pressures. However, we must uphold rigorous standards inference interpretation on this topic because ramifications being wrong. Here, dispute conclusions Xia (2020. Extreme genomic CpG...
Abstract Although B cells are implicated in multiple sclerosis (MS) pathophysiology, a predictive or diagnostic autoantibody remains elusive. Here, the Department of Defense Serum Repository (DoDSR), cohort over 10 million individuals, was used to generate whole-proteome profiles hundreds patients with MS (PwMS) years before and subsequently after onset. This analysis defines unique cluster PwMS that share an signature against common motif has similarity many human pathogens. These exhibit...
Abstract The extremely high levels of genetic polymorphism within the human major histocompatibility complex (MHC) limit usefulness reference-based alignment methods for sequence assembly. We incorporate a short read de novo assembly algorithm into workflow novel application to MHC. MHConstructor is containerized pipeline designed high-throughput, haplotype-informed, reproducible both whole genome sequencing and target-capture data in large, population cohorts. To-date, no other...
McCabe, Pamela J. PhD, RN, ACNS-BC; Wade, Kristen MPH; Morgan, Louise MSN; Biddle, Martha APRN, CCNS; Beckie, Theresa M. RN Author Information
Abstract The complement component 4 gene locus, composed of the C4A and C4B genes located on chromosome 6, encodes for C4 protein, a key intermediate in classical lectin pathways system. system is an important modulator immune activity also involved clearance complexes cellular debris. locus exhibits copy number variation, with each composite varying between 0-5 copies per haplotype, vary size depending presence HERV retrovirus intron 9, denoted by C4(L) long-form C4(S) short-form, which...
The complement component 4 gene loci, composed of the C4A and C4B genes located on chromosome 6, encodes for (C4) proteins, a key intermediate in classical lectin pathways system. system is an important modulator immune activity also involved clearance complexes cellular debris. loci exhibit copy number variation, with each composite varying between 0 5 copies per haplotype. vary size depending presence human endogenous retrovirus (HERV) intron 9, denoted by C4(L) long‐form C4(S) short‐form,...
The extremely high levels of genetic polymorphism within the human major histocompatibility complex (MHC) limit usefulness reference-based alignment methods for sequence assembly. We incorporate a short-read, de novo assembly algorithm into workflow novel application to MHC. MHConstructor is containerized pipeline designed high-throughput, haplotype-informed, reproducible both whole genome sequencing and target capture short-read data in large, population cohorts. To-date, no other...
Abstract The increasingly widespread availability of genomic data has created a growing need for fast, sensitive and scalable comparative analysis methods. A key aspect is the study synteny, co-localized gene clusters shared among genomes due to descent from common ancestors. Synteny can provide unique insight into origin, function, evolution genome architectures, but methods identify syntenic patterns in datasets are often inflexible slow, use diverse definitions what counts as likely...
Expression quantitative trait loci (eQTL) analyses detect genetic variants (SNPs) associated with RNA expression levels of genes. The conventional eQTL analysis is to perform individual tests for each gene-SNP pair using simple linear regression and the test on tissue separately ignoring extensive information known about in other tissue(s). Although Bayesian models have been recently developed improve prediction multiple tissues, they are often based uninformative priors or treat all tissues...
The global community has adopted ambitious goals to eliminate schistosomiasis as a public health problem, and new tools are needed achieve them. Mass drug administration programs, for example, have reduced the burden of schistosomiasis, but identification hotspots persistent reemergent transmission threaten progress towards elimination underscore need couple treatment with interventions that reduce transmission. Recent advances in DNA sequencing technologies make whole genome valuable...
Schistosomiasis is a neglected tropical disease caused by multiple parasitic Schistosoma species, and which impacts over 200 million people globally, mainly in low- middle-income countries. Genomic surveillance to detect evidence for natural selection schistosome populations represents an emerging promising approach identify interpret responses ongoing control efforts or other environmental factors. Here we review how genomic variation used selection, these approaches have been applied...
Since the initial reported discovery of SARS-CoV-2 in late 2019, genomic surveillance has been an important tool to understand its transmission and evolution. Here, we sought describe underlying regional phylodynamics before during a rapid spreading event that was documented by protocols United States Air Force Academy (USAFA) October-November 2020. We used replicate long-read sequencing on Colorado genomes collected July through November 2020 at University Anschutz Medical campus Aurora...
ABSTRACT Since the initial reported discovery of SARS-CoV-2 in late 2019, genomic surveillance has been an important tool to understand its transmission and evolution. Here, we describe a case study sequencing Colorado samples collected August through November 2020 at University Anschutz Medical campus Aurora United States Air Force Academy Springs. We obtained nearly complete sequences for 44 genomes, inferred ancestral shared among these local samples, used NextStrain variant clade...