A5053736401- Genomics and Phylogenetic Studies
- Genetic Mapping and Diversity in Plants and Animals
- Genetic diversity and population structure
- Chromosomal and Genetic Variations
- Cancer Genomics and Diagnostics
- Gut microbiota and health
- RNA modifications and cancer
- Molecular Biology Techniques and Applications
- Insect symbiosis and bacterial influences
- Liver Disease Diagnosis and Treatment
- Monoclonal and Polyclonal Antibodies Research
- Bacteriophages and microbial interactions
- Escherichia coli research studies
- RNA and protein synthesis mechanisms
- Genetic and phenotypic traits in livestock
- CAR-T cell therapy research
- Plant Disease Resistance and Genetics
- Microbial Community Ecology and Physiology
- Acute Lymphoblastic Leukemia research
- Evolution and Genetic Dynamics
- Semiconductor materials and interfaces
- Probiotics and Fermented Foods
- Genomics and Chromatin Dynamics
- Bacterial Genetics and Biotechnology
- Cancer-related molecular mechanisms research
University of North Carolina at Chapel Hill
2016-2025
University of Pennsylvania
2010-2025
St. Jude Children's Research Hospital
2024
Johns Hopkins Medicine
2023
Johns Hopkins University
2023
Texas Tech University
2023
St. Augustine College
2023
Health Information Management
2023
Westmead Hospital
2022
University of North Carolina System
2022
The Collaborative Cross (CC) is a mouse recombinant inbred strain panel that being developed as resource for mammalian systems genetics. Here we describe an experiment uses partially CC lines to evaluate the genetic properties and utility of this emerging resource. Genome-wide analysis incipient strains reveals high diversity, balanced allele frequencies, dense, evenly distributed recombination sites—all ideal qualities genetics We map discrete, complex, biomolecular traits contrast two...
Genetic variation contributes to host responses and outcomes following infection by influenza A virus or other viral infections. Yet narrow windows of disease symptoms confounding environmental factors have made it difficult identify polymorphic genes that contribute differential in human populations. Therefore, control for these variables a system models the levels genetic diversity found outbred populations such as humans, we used incipient lines highly genetically diverse Collaborative...
Significance Despite fascinating scientists for over 200 years, little at the molecular level is known about tardigrades, microscopic animals resistant to extreme stresses. We present genome of a tardigrade. Approximately one-sixth genes in tardigrade were found have been acquired through horizontal transfer, proportion nearly double previous cases gene transfer (HGT) animals. Foreign impacted composition genome: supplementing, expanding, and replacing endogenous families, including those...
Over 100 years of studies in Drosophila melanogaster and related species the genus have facilitated key discoveries genetics, genomics, evolution. While high-quality genome assemblies exist for several this group, they only encompass a small fraction genus. Recent advances long-read sequencing allow tens or even hundreds to be efficiently generated. Here, we utilize Oxford Nanopore build an open community resource 101 lines 93 drosophilid encompassing 14 groups 35 sub-groups. The genomes are...
The Collaborative Cross (CC) is a panel of recombinant inbred lines derived from eight genetically diverse laboratory strains. Recently, the genetic architecture CC population was reported based on genotype single male per line, and other publications incompletely mice that have been used to map variety traits. three breeding sites, in US, Israel, Australia, are actively collaborating accelerate inbreeding process through marker-assisted expedite community access deemed reached defined...
Long read sequencing is changing the landscape of genomic research, especially de novo assembly. Despite high error rate inherent to long technologies, increased lengths dramatically improve continuity and accuracy genome assemblies. However, cost throughput these technologies limits their application complex genomes. One solution decrease time assemble novel genomes by leveraging "hybrid" assemblies that use reads for scaffolding short accuracy. We describe a method multi-string...
Objective Conflicting microbiota data exist for primary sclerosing cholangitis (PSC) and experimental models. Goal: define the function of complex resident microbes their association relevant to PSC patients by studying germ-free (GF) antibiotic-treated specific pathogen-free (SPF) multidrug-resistant 2 deficient ( mdr2 −/− ) mice microbial profiles in patient cohorts. Design We measured weights, liver enzymes, RNA expression, histological, immunohistochemical fibrotic biochemical...
To investigate the origins and stages of vertebrate adaptive radiation, we reconstructed spatial temporal histories alleles underlying major phenotypic axes diversification from genomes 202 Caribbean pupfishes. On a single Bahamian island, ancient standing variation disjunct geographic sources was reassembled into new combinations under strong directional selection for adaptation to novel trophic niches scale-eating molluscivory. We found evidence two longstanding hypotheses radiation:...
Although plastid genome (plastome) structure is highly conserved across most seed plants, investigations during the past two decades have revealed several disparately related lineages that experienced substantial rearrangements. Most plastomes contain a large inverted repeat and single-copy regions, few dispersed repeats; however, of some taxa harbour long sequences (>300 bp). These repeats make it challenging to assemble complete using short-read data, leading misassemblies consensus with...
Abstract As the accuracy and throughput of nanopore sequencing improve, it is increasingly common to perform long-read first de novo genome assemblies followed by polishing with accurate short reads. We briefly introduce FMLRC2, successor original FM-index Long Read Corrector (FMLRC), illustrate its performance as a fast assembly polisher for both bacterial eukaryotic genomes.
Abstract Several studies have documented the significant impact of methodological choices in microbiome analyses. The myriad options available complicate replication results and generally limit comparability findings between independent that use differing techniques measurement pipelines. Here we describe Mosaic Standards Challenge (MSC), an international interlaboratory study designed to assess variables on results. MSC did not prescribe methods but rather asked participating labs analyze 7...
Although cure rates for childhood acute lymphoblastic leukemia (ALL) exceed 90%, ALL remains a leading cause of cancer death in children. Half relapses arise children initially classified with standard-risk (SR) disease.
Abstract A distinct population of white matter progenitor cells (WMPCs), competent but not committed to generate oligodendrocytes, remains ubiquitous in the adult human subcortical matter. These are present both sexes and into senescence may constitute as much 4% capsular Transduction dissociates with plasmids bearing early oligodendrocytic promoters driving fluorescent reporters permits separation these at high yield purity, does based on their expression A2B5 immunoreactivity. Isolates...
The severe acute respiratory syndrome coronavirus 2 pandemic is characterized by the emergence of novel variants concern (VOCs) that replace ancestral strains. Here, we dissect complex selective pressures evaluating variant fitness and adaptation in human tissues. We evaluate viral properties host responses to reconstruct forces behind D614G through Omicron (BA.1) emergence. observe differential replication airway epithelia, differences cellular tropism, virus-induced cytotoxicity....
Antinuclear antibodies (ANAs) reactive with a limited spectrum of nuclear antigens are characteristic systemic lupus erythematosus (SLE) and other collagen vascular diseases, also associated certain viral infections. The factors that initiate ANA production determine specificity not well understood. In this study, high titer ANAs specific for the p53 tumor suppressor protein were induced in mice immunized purified complexes murine Simian virus 40 large T antigen (SVT), but either separately....
Genome browsers are a common tool used by biologists to visualize genomic features including genes, polymorphisms, and many others. However, existing genome visualization tools not well-suited perform meaningful comparative analysis among large number of genomes. With the increasing quantity availability data, there is an increased burden provide useful for comparison multiple collinear genomes such as panels model organisms which basis much current genetic research. We have developed novel...
CD8 T cells protect the host from disease caused by intracellular pathogens, such as Toxoplasma gondii (T. gondii) protozoan parasite. Despite complexity of T. proteome, cell responses are restricted to only a small number peptide epitopes derived limited set antigenic precursors. This phenomenon is known immunodominance and key effective vaccine design. However, mechanisms that determine immunogenicity hierarchy parasite antigens not well understood. Here, using genetically modified...
Val-->Ala mutations within the effective transmembrane segment of a model single-spanning membrane protein, 50-residue major coat (gene VIII) protein bacteriophage M13, are shown to have sequence-dependent impacts on stabilization membrane-embedded helical dimeric structures. Randomized mutagenesis performed hydrophobic 21-39 (YIGYAWAMV-VVIVGATIGI) produced library viable mutants which included those in each four valine residues was replaced by an alanine residue. Significant variations...
X chromosome inactivation (XCI) is the mammalian mechanism of dosage compensation that balances X-linked gene expression between sexes. Early during female development, each cell embryo proper independently inactivates one its two parental X-chromosomes. In mice, choice which inactivated affected by genotype a cis-acting locus, X-chromosome controlling element (Xce). Xce has been localized to 1.9 Mb interval within X-inactivation center (Xic), yet molecular identity and action remain...