Melissa Meredith
A5013925822- Genomics and Phylogenetic Studies
- RNA modifications and cancer
- Chromosomal and Genetic Variations
- Genomics and Rare Diseases
- Epigenetics and DNA Methylation
- Algorithms and Data Compression
- Telomeres, Telomerase, and Senescence
- DNA Repair Mechanisms
- Cancer Genomics and Diagnostics
- CRISPR and Genetic Engineering
- Bioinformatics and Genomic Networks
- RNA and protein synthesis mechanisms
- Genomics and Chromatin Dynamics
- Molecular Biology Techniques and Applications
- Advanced Neural Network Applications
University of California, Santa Cruz
2021-2025
Genomics (United Kingdom)
2024
Compared to its predecessors, the Telomere-to-Telomere CHM13 genome adds nearly 200 million base pairs of sequence, corrects thousands structural errors, and unlocks most complex regions human for clinical functional study. We show how this reference universally improves read mapping variant calling 3202 17 globally diverse samples sequenced with short long reads, respectively. identify hundreds variants per sample in previously unresolved regions, showcasing promise T2T-CHM13 evolutionary...
Reference-free genome phasing is vital for understanding allele inheritance and the impact of single-molecule DNA variation on phenotypes. To achieve thorough across homozygous or repetitive regions genome, long-read sequencing technologies are often used to perform phased de novo assembly. As a step toward reducing cost complexity this type analysis, we describe new methods accurately Oxford Nanopore Technologies (ONT) sequence data with Shasta assembler modular tool extending chromosome...
DNA methylation most commonly occurs as 5-methylcytosine (5mC) in the human genome and has been associated with diseases. Recent developments single-molecule sequencing technologies (Oxford Nanopore Technologies (ONT) Pacific Biosciences) have enabled readouts of long, native molecules, including cytosine methylation. ONT recently upgraded their chemistry kits from R9 to R10 version, which yielded increased accuracy throughput. However effects on detection not yet documented. Here, we...
Abstract Compared to its predecessors, the Telomere-to-Telomere CHM13 genome adds nearly 200 Mbp of sequence, corrects thousands structural errors, and unlocks most complex regions human clinical functional study. Here we demonstrate how new reference universally improves read mapping variant calling for 3,202 17 globally diverse samples sequenced with short long reads, respectively. We identify hundreds novel variants per sample—a frontier evolutionary biomedical discovery. Simultaneously,...
Long-read sequencing technologies substantially overcome the limitations of short-reads but to date have not been considered as feasible replacement at scale due a combination being too expensive, scalable enough, or error-prone. Here, we develop an efficient and wet lab computational protocol for Oxford Nanopore Technologies (ONT) long-read that seeks provide genuine alternative large-scale genomics projects. We applied our cell lines brain tissue samples part pilot project NIH Center...
Abstract DNA methylation most commonly occurs as 5-methylcytosine (5-mC) in the human genome and has been associated with diseases. Recent developments single-molecule sequencing technologies (Oxford Nanopore Technologies (ONT) Pacific Biosciences) have enabled readouts of long, native molecules, including cytosine methylation. ONT recently upgraded their chemistry kits from R9 to R10 version, which yielded increased accuracy throughput. However effects on detection not yet documented. Here...
Abstract As a step towards simplifying and reducing the cost of haplotype resolved de novo assembly, we describe new methods for accurately phasing nanopore data with Shasta genome assembler modular tool extending to chromosome scale called GFAse. We test using variants Oxford Nanopore Technologies’ (ONT) PromethION sequencing, including those proximity ligation show that newer, higher accuracy ONT reads substantially improve assembly quality.
Structural variants (SVs) drive gene expression in the human brain and are causative of many neurological conditions. However, most existing genetic studies have been based on short-read sequencing methods, which capture fewer than half SVs present any one individual. Long-read (LRS) enhances our ability to detect disease-associated functionally relevant structural (SVs); however, its application large-scale genomic has limited by challenges sample preparation high costs. Here, we leverage a...
ABSTRACT The chromosome 5p15.33 region, which encodes telomerase reverse transcriptase (TERT), harbors multiple germline variants identified by genome-wide association studies (GWAS) as risk for some cancers but protective others. We characterized a variable number tandem repeat within TERT intron 6 (VNTR6-1, 38-bp unit) and observed strong between VNTR6-1 alleles (Short: 24-27 repeats, Long: 40.5-66.5 repeats) GWAS signals 4. Specifically, fully explained the rs2242652 partially rs10069690....