A5020821330- Chromosomal and Genetic Variations
- Genomics and Phylogenetic Studies
- Genetic diversity and population structure
- Cancer Immunotherapy and Biomarkers
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Animal Behavior and Reproduction
- Animal Genetics and Reproduction
- Genomics and Chromatin Dynamics
- RNA modifications and cancer
- Epigenetics and DNA Methylation
- Systemic Lupus Erythematosus Research
- Congenital heart defects research
- Cancer Diagnosis and Treatment
- Acute Myeloid Leukemia Research
- Gestational Trophoblastic Disease Studies
- Ethics and Legal Issues in Pediatric Healthcare
- Neurogenetic and Muscular Disorders Research
- Prion Diseases and Protein Misfolding
- T-cell and B-cell Immunology
- Retinoids in leukemia and cellular processes
- Multiple and Secondary Primary Cancers
- Cystic Fibrosis Research Advances
- Prenatal Screening and Diagnostics
- Turfgrass Adaptation and Management
- Plant Reproductive Biology
University of Kentucky
2015-2023
University Hospitals of Cleveland
2022-2023
University Hospitals Seidman Cancer Center
2023
Case Western Reserve University
2022-2023
Center for Human Genetics
2021-2023
University School
2023
Carnegie Institution for Science
2018-2022
Department of Embryology
2018-2022
The sea lamprey (Petromyzon marinus) serves as a comparative model for reconstructing vertebrate evolution. To enable more informed analyses, we developed new assembly of the germline genome that integrates several complementary data sets. Analysis this highly contiguous (chromosome-scale) shows both chromosomal and whole-genome duplications have played significant roles in evolution ancestral genomes, including chromosomes carry six HOX clusters. also contains hundred genes are reproducibly...
Abstract Methylation of cytosines is a prototypic epigenetic modification the DNA. It has been implicated in various regulatory mechanisms across animal kingdom and particularly vertebrates. We mapped DNA methylation 580 species (535 vertebrates, 45 invertebrates), resulting 2443 genome-scale profiles multiple organs. Bioinformatic analysis this large dataset quantified association with underlying genomic sequence throughout vertebrate evolution. observed broadly conserved link two major...
It is generally accepted that many genes present in vertebrate genomes owe their origin to two whole-genome duplications occurred deep the ancestry of lineage. However, details regarding timing and outcome these are not well resolved. We high-density meiotic comparative genomic maps for sea lamprey ( Petromyzon marinus ), a representative an ancient lineage diverged from all other vertebrates ∼550 million years ago. Linkage analyses yielded total 95 linkage groups, similar estimated number...
The axolotl ( Ambystoma mexicanum ) provides critical models for studying regeneration, evolution, and development. However, its large genome (∼32 Gb) presents a formidable barrier to genetic analyses. Recent efforts have yielded assemblies consisting of thousands unordered scaffolds that resolve gene structures, but do not yet permit large-scale analyses structure function. We adapted an established mapping approach leverage dense SNP typing information the first time assemble into 14...
Abstract Vertebrates exhibit substantial diversity in genome size and some of the largest genomes exist species that uniquely inform diverse areas basic biomedical research. For example, salamander Ambystoma mexicanum (the Mexican axolotl) is a model organism for studies regeneration, development evolution, yet its ~10× larger than human genome. As part hierarchical approach toward improving resources species, we generated 600 Gb shotgun sequence data developed methods sequencing individual...
Vertebrates harbor recognizably orthologous gene complements but vary 100-fold in genome size. How chromosomal organization scales with expansion is unclear, and how acute changes regulation, as during axolotl limb regeneration, occur the context of a vast has remained riddle. Here, we describe chromosome-scale assembly giant, 32 Gb genome. Hi-C contact data revealed scaling properties interphase mitotic chromosome organization. Analysis yielded understanding evolution large, syntenic...
The sea lamprey (Petromyzon marinus) represents one of the few vertebrate species known to undergo large-scale programmatic elimination genomic DNA over course its normal development. Programmed genome rearrangements (PGRs) result in reproducible loss ~20% from somatic cell lineages during early embryogenesis. Studies PGR hold potential provide novel insights related maintenance stability cycle and coordination between mechanisms responsible for accurate distribution chromosomes into...
Abstract In the Mexican axolotl ( Ambystoma mexicanum ), sex is determined by a single Mendelian factor, yet its chromosomes do not exhibit morphological differentiation typical of many vertebrate taxa that possess sex-determining locus. As are theorized to differentiate rapidly, species with undifferentiated provide opportunity reconstruct early events in chromosome evolution. Whole genome sequencing 48 salamanders, targeted and situ hybridization were used identify homomorphic carries an A...
Patients with certain autoimmune conditions are at a reduced risk of developing breast cancer compared to the general population. Despite this, little is known about outcomes in patients who have concurrent diagnosis.This study differences between women had or did not an diagnosis. The SEER-Medicare databases (2007-2014) were used identify and diagnosis codes those disorder.The studied diseases prevalence 27% among 137,324 cancer. Autoimmune disease was associated significantly longer...
Abstract Methylation of cytosines is the prototypic epigenetic modification DNA. It has been implicated in various regulatory mechanisms throughout animal kingdom and particularly vertebrates. We mapped DNA methylation 580 species (535 vertebrates, 45 invertebrates), resulting 2443 genome-scale, base-resolution profiles primary tissue samples from organs. Reference-genome independent analysis this comprehensive dataset quantified association with underlying genomic sequence vertebrate...
The lampbrush chromosomes (LBCs) in oocytes of the Mexican axolotl (Ambystoma mexicanum) were identified some time ago by their relative lengths and predicted centromeres, but they have never been associated completely with mitotic karyotype, linkage maps or genome assembly. We 9 LBCs using RNAseq to identify actively transcribed genes 13 BAC (bacterial artificial clone) probes containing pieces active genes. Using read coverage analysis find candidate centromere sequences, we developed a...
ABSTRACT The axolotl ( Ambystoma mexicanum ) provides critical models for studying regeneration, evolution and development. However, its large genome (~32 gigabases) presents a formidable barrier to genetic analyses. Recent efforts have yielded assemblies consisting of thousands unordered scaffolds that resolve gene structures, but do not yet permit scale analyses structure function. We adapted an established mapping approach leverage dense SNP typing information the first time assemble into...
ABSTRACT In the Mexican axolotl ( Ambystoma mexicanum ) sex is known to be determined by a single Mendelian factor, yet chromosomes of this model salamander do not exhibit morphological differentiation that typical many vertebrate taxa possess sex-determining locus. Differentiated are thought evolve rapidly in context gene and, therefore, undifferentiated provide an exceptional opportunity reconstruct early events chromosome evolution. Whole sequencing, whole genome resequencing (48...
1020 Background: Patients with autoimmune disease, specifically systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), and Sjogren syndrome, are at reduced risk of developing breast cancer compared to those without a prior history disease. Despite this, little is known about the survival patients concurrent disease cancer. This study outcomes in Methods: was retrospective analysis from SEER-Medicare databases 2007-2014 were identified using ICD-9 codes. The effects on overall (OS)...
A 38-year-old male patient presented with clinical symptoms of shortness breath, chest pain and scattered bruising. Initial workup showed elevated D-dimer (14 137 ng/mL) LDH (388 U/L). CT angiography the bilateral pulmonary embolisms left pleural effusion that was negative for malignant cells on cytological examination. Full blood count demonstrated leukocytes (10.5 × 109/L), hemoglobin (88 g/L), platelets (115 109/L). Coagulation screening abnormal a prolonged prothrombin time (PT),...