A5082851461- Chromosomal and Genetic Variations
- Genomics and Phylogenetic Studies
- Gene expression and cancer classification
- Nematode management and characterization studies
- Legume Nitrogen Fixing Symbiosis
- Evolution and Genetic Dynamics
- Genetic diversity and population structure
- Data Mining Algorithms and Applications
- Reproductive tract infections research
- Cancer Genomics and Diagnostics
- Genetic Mapping and Diversity in Plants and Animals
- Genetic Associations and Epidemiology
- Genomics and Rare Diseases
- Virus-based gene therapy research
- Microtubule and mitosis dynamics
- Reproductive Physiology in Livestock
- Epigenetics and DNA Methylation
- Ubiquitin and proteasome pathways
- Vector-borne infectious diseases
- Data Analysis with R
- Cancer Cells and Metastasis
- Plant Virus Research Studies
- Telomeres, Telomerase, and Senescence
- CRISPR and Genetic Engineering
Johns Hopkins University
2018-2024
Translational Genomics Research Institute
2024
University of Baltimore
2021
Abstract An important assessment prior to genome assembly and related analyses is profiling, where the k-mer frequencies within raw sequencing reads are analyzed estimate major characteristics such as size, heterozygosity, repetitiveness. Here we introduce GenomeScope 2.0 ( https://github.com/tbenavi1/genomescope2.0 ), which applies combinatorial theory establish a detailed mathematical model of how distributed in heterozygous polyploid genomes. We describe evaluate practical implementation...
Evolution without sex is predicted to impact genomes in numerous ways. Case studies of individual parthenogenetic animals have reported peculiar genomic features that were suggested be caused by their mode reproduction, including high heterozygosity, a abundance horizontally acquired genes, low transposable element load, or the presence palindromes. We systematically characterized these published 26 representing at least 18 independent transitions asexuality. Surprisingly, not single feature...
Abstract Human cell lines are fundamental tools in biomedical research and widely used disease modeling, drug development, many other domains. Here, we present chromosome-level, phased diploid genome assemblies of two popular human lines: the BJ foreskin fibroblast line IMR-90 fetal lung line. Our high-quality assemblies, generated using long-read Hi-C sequencing data, reveal substantial structural variation, including more than 50,000 insertions, deletions, duplications, inversions compared...
Abstract An important assessment prior to genome assembly and related analyses is profiling, where the k-mer frequencies within raw sequencing reads are analyzed estimate major characteristics such as size, heterozygosity, repetitiveness. Here we introduce GenomeScope 2.0 ( https://github.com/tbenavi1/genomescope2.0 ), which applies combinatorial theory establish a detailed mathematical model of how distributed in heterozygous polyploid genomes. We describe evaluate practical implementation...
Abstract Evolution without sex is predicted to impact genomes in numerous ways. Case studies of individual parthenogenetic animals have reported peculiar genomic features which were suggested be caused by their mode reproduction, including high heterozygosity, a abundance horizontally acquired genes, low transposable element load, or the presence palindromes. We systematically characterized these published 26 representing at least 18 independent transitions asexuality. Surprisingly, not...
Abstract Trichomonas vaginalis is the causative agent of venereal disease trichomoniasis which infects men and women globally associated with serious outcomes during pregnancy cancers human reproductive tract. Trichomonads parasitize a range hosts in addition to humans including birds, livestock, domesticated animals. Recent genetic analysis trichomonads recovered from columbid birds has provided evidence that these parasite species undergo frequent host-switching, current epoch spillover...
An increasingly important scenario in population genetics is when a large cohort has been genotyped using low-resolution approach (e.g., microarrays, exome capture, short-read WGS), from which few individuals are resequenced more comprehensive approach, especially long-read sequencing. The subset of selected should ensure that the captured genetic diversity fully representative and includes variants across all subpopulations. For example, human variation historically focused on with European...
Abstract An increasingly important scenario in population genetics is when a large cohort has been genotyped using low-resolution approach (e.g. microarrays, exome capture, short-read WGS), from which few individuals are selected for resequencing more comprehensive approach, especially long-read sequencing. The subset of should ensure that the captured genetic diversity fully representative and includes variants across all subpopulations. For example, human variation historically focused on...
Abstract Glioma is an aggressive cancer of the central nervous system that genetically characterized by aneuploidy and frequent structural variation (SV). We sought to investigate role telomere dysfunction (TD) in shaping SV landscape glioma. Normal human astrocytes (NHA) were engineered express viral E6E7 oncoproteins which are known spontaneously trigger TD suppressing p53/pRb. hypothesized NHA-E6E7 cells gradually accumulate SVs over time because progressive TD. therefore longitudinally...
Abstract Genomic studies of the malignant brain tumor glioma invariably rely on aligning sequencing reads to a reference genome such as HG38, even though no single can capture diversity an individual patient or cell line. To begin addressing these biases in genomics research, we sought construct chromosome-scale diploid-phased assembly normal human astrocyte (NHA) line that is frequently used basis for developing isogenic models. achieve this, generated 45x Pacific Biosciences HiFi data...