A5064746876- Genomics and Phylogenetic Studies
- RNA modifications and cancer
- Advanced biosensing and bioanalysis techniques
- Plant Molecular Biology Research
- Chromosomal and Genetic Variations
- Zebrafish Biomedical Research Applications
- RNA Research and Splicing
- Bacteriophages and microbial interactions
- RNA and protein synthesis mechanisms
- Plant tissue culture and regeneration
- Pluripotent Stem Cells Research
- Cell Adhesion Molecules Research
- Phagocytosis and Immune Regulation
- Genomics and Chromatin Dynamics
- Mitochondrial Function and Pathology
- Cocoa and Sweet Potato Agronomy
- CRISPR and Genetic Engineering
- Cancer Genomics and Diagnostics
- Plant Reproductive Biology
- Genetics and Neurodevelopmental Disorders
- Extracellular vesicles in disease
- Genetic Neurodegenerative Diseases
- Genomic variations and chromosomal abnormalities
- Postharvest Quality and Shelf Life Management
- Advances in Cucurbitaceae Research
University of Michigan
2019-2024
Michigan State University
2012-2014
Genome-wide association studies have revealed that 88% of disease-associated single-nucleotide polymorphisms (SNPs) reside in noncoding regions. However, SNPs remain understudied, partly because they are challenging to prioritize for experimental validation. To address this deficiency, we developed the SNP effect matrix pipeline (SEMpl).SEMpl estimates transcription factor-binding affinity by observing differences chromatin immunoprecipitation followed deep sequencing signal intensity within...
Mobile element insertions (MEIs) are repetitive genomic sequences that contribute to genetic variation and can lead disorders. Targeted whole-genome approaches using short-read sequencing have been developed identify reference non-reference MEIs; however, the read length hampers detection of these elements in complex regions. Here, we pair Cas9-targeted nanopore with computational methodologies capture active MEIs human genomes. We demonstrate parallel enrichment for distinct classes MEIs,...
Recombinant plasmid vectors are versatile tools that have facilitated discoveries in molecular biology, genetics, proteomics, and many other fields. As the enzymatic bacterial processes used to create recombinant DNA can introduce errors, sequence validation is an essential step assembly. Sanger sequencing current standard for validation; however, this method limited by inability through complex secondary structure lacks scalability when applied full-plasmid of multiple plasmids owing...
Intronic GGGGCC hexanucleotide repeat expansions in C9orf72 are the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Despite its intronic location, this avidly supports synthesis pathogenic dipeptide (DPR) proteins via repeat-associated non AUG (RAN) translation. However, template RNA species that undergoes RAN translation endogenously remains unclear. Using long-read based 5 prime ligase mediated rapid amplification cDNA ends (Repeat RLM...
Abstract Tandem repeat sequences comprise approximately 8% of the human genome and are linked to more than 50 neurodegenerative disorders. Accurate characterization disease-associated loci remains resource intensive often lacks high resolution genotype calls. We introduce a multiplexed, targeted nanopore sequencing panel HMMSTR, sequence-based tandem copy number caller. HMMSTR outperforms current signal- callers relative two assemblies we show it performs with accuracy in heterozygous...
Abstract Recombinant plasmid vectors are versatile tools which have facilitated discoveries in molecular biology, genetics, proteomics, and many other fields. As the enzymatic bacterial processes used to create recombinant DNA can introduce errors, sequence validation is an essential step assembly. Sanger sequencing current standard for validation, however this method limited by inability through complex secondary structure lacks scalability when applied full-plasmid of multiple plasmids due...
This is the Boyle lab's protocol for using Cas9 to target transposable elements within genomic DNA Oxford Nanopore Technologies (ONT) R10 flow cells.
Tandem repeat sequences comprise approximately 8% of the human genome and are linked to more than 50 neurodegenerative disorders. Accurate characterization disease-associated loci remains resource intensive often lacks high resolution genotype calls. We introduce a multiplexed, targeted nanopore sequencing panel HMMSTR, sequence-based tandem copy number caller which outperforms current signal- callers relative two assemblies we show it performs with accuracy in heterozygous regions at low...
Somatic mutations in individual cells lead to genomic mosaicism, contributing the intricate regulatory landscape of genetic disorders and cancers. To evaluate refine detection somatic mosaicism across different technologies with personalized donor-specific assembly (DSA), we obtained tissue from dorsolateral prefrontal cortex (DLPFC) a post-mortem neurotypical 31-year-old individual. We sequenced bulk DLPFC using Oxford Nanopore Technologies (~60X), NovaSeq (~30X), linked-read sequencing...
Abstract Mobile element insertions (MEIs) are highly repetitive genomic sequences that contribute to inter- and intra-individual genetic variation can lead disorders. Targeted whole-genome approaches using short-read sequencing have been developed identify reference non-reference MEIs; however, the read length hampers detection of these elements in complex regions. Here, we pair Cas9 targeted nanopore with computational methodologies capture active MEIs human genomes. We demonstrate parallel...
Abstract Background Zebrafish are a foundational model organism for studying the spatio-temporal activity of genes and their regulatory sequences. A variety approaches currently available editing modifying gene expression in zebrafish, including RNAi, Cre/lox, CRISPR-Cas9. However, lac operator-repressor system, component E. coli operon which has been adapted use many other species is valuable, flexible tool inducible modulation expression, not previously tested zebrafish. Results Here we...
Zebrafish are a foundational model organism for studying the spatio-temporal activity of genes and their regulatory sequences. A variety approaches currently available editing modifying gene expression in zebrafish, including RNAi, Cre/lox, CRISPR-Cas9. However, lac operator-repressor system, an E. coli operon component which has been adapted use many other species is valuable, flexible tool inducible modulation studies, not previously tested zebrafish. Here we demonstrate that system...