A5025119065- Genomics and Phylogenetic Studies
- Epigenetics and DNA Methylation
- RNA modifications and cancer
- Molecular Biology Techniques and Applications
- Microbial Community Ecology and Physiology
- Cancer Genomics and Diagnostics
- Bacteriophages and microbial interactions
- Gut microbiota and health
- Single-cell and spatial transcriptomics
- Genetic Associations and Epidemiology
- Genetic Syndromes and Imprinting
- Protist diversity and phylogeny
- RNA Research and Splicing
- Acute Myeloid Leukemia Research
- Plant and Fungal Interactions Research
- SARS-CoV-2 detection and testing
- Endoplasmic Reticulum Stress and Disease
- Cancer-related molecular mechanisms research
- Prenatal Screening and Diagnostics
- Biosensors and Analytical Detection
- Cancer-related gene regulation
- Peroxisome Proliferator-Activated Receptors
- RNA and protein synthesis mechanisms
- Methane Hydrates and Related Phenomena
- Genetic Mapping and Diversity in Plants and Animals
Oxford Nanopore Technologies (United Kingdom)
2021-2024
Icahn School of Medicine at Mount Sinai
2013-2018
Rosetta Stone (United States)
2010-2011
Genome-wide association studies (GWAS) have demonstrated the ability to identify strongest causal common variants in complex human diseases. However, date, massive data generated from GWAS not been maximally explored true associations that fail meet stringent level of required achieve genome-wide significance. Genetics gene expression (GGE) shown promise towards identifying DNA variations associated with disease and providing a path functionally characterize findings GWAS. Here, we present...
To map the genetics of gene expression in metabolically relevant tissues and investigate diversity SNPs (eSNPs) multiple from same individual, we collected four approximately 1000 patients undergoing Roux-en-Y gastric bypass (RYGB) clinical traits associated with their weight loss co-morbidities. We then performed high-throughput genotyping profiling carried out a genome-wide association analyses for more than 100,000 representing tissues: liver, omental adipose, subcutaneous stomach....
ABSTRACT Prior to the epidemic that emerged in Haiti October of 2010, cholera had not been documented this country. After its introduction, a strain Vibrio cholerae O1 spread rapidly throughout Haiti, where it caused over 600,000 cases disease and >7,500 deaths first two years epidemic. We applied whole-genome sequencing temporal series V. isolates from gain insight into mode tempo evolution isolated population O1. Phylogenetic Bayesian analyses supported hypothesis all sample set...
Viruses are the most abundant biological entities on Earth and play key roles in host ecology, evolution, horizontal gene transfer. Despite recent progress viral metagenomics, inherent genetic complexity of virus populations still poses technical difficulties for recovering complete genomes from natural assemblages. To address these challenges, we developed an assembly-free, single-molecule nanopore sequencing approach, enabling direct recovery genome sequences environmental samples. Our...
N6-Methyladenine (m 6 dA) has been discovered as a novel form of DNA methylation prevalent in eukaryotes; however, methods for high-resolution mapping m dA events are still lacking. Single-molecule real-time (SMRT) sequencing enabled the detection at single-nucleotide resolution prokaryotic genomes, but its application to detecting eukaryotic genomes not rigorously examined. Herein, we identified unique characteristics methylomes that fundamentally differ from those prokaryotes. Based on...
ABSTRACT Metagenomics has enabled the rapid, unbiased detection of microbes across diverse sample types, leading to exciting discoveries in infectious disease, microbiome, and viral research. However, analysis metagenomic data is often complex computationally resource-intensive. CZ ID a free, cloud-based genomic platform that enables researchers detect using data, identify antimicrobial resistance genes, generate consensus genomes. With ID, can upload raw sequencing find matches NCBI...
Abstract Beyond its role in host defense, bacterial DNA methylation also plays important roles the regulation of gene expression, virulence and antibiotic resistance. Bacterial cells a clonal population can generate epigenetic heterogeneity to increase population-level phenotypic plasticity. Single molecule, real-time (SMRT) sequencing enables detection N6-methyladenine N4-methylcytosine, two major types modifications comprising methylome. However, existing SMRT sequencing-based methods for...
Abstract LamPORE™ is a rapid way of testing/screening large numbers samples for the presence or absence SARS-CoV-2, virus causing COVID-19. It combines barcoded multi-target amplification, 15-minute library preparation and real-time nanopore sequencing. Starting with extracted RNA, results can be obtained from 12 in approximately an hour 96 under 2 hours. High scalability achieved by combinatorial barcoding. Performance characteristics are currently being established regulatory clearance to...
The assignment of variants across haplotypes, phasing, is crucial for predicting the consequences, interaction, and inheritance mutations a key step in improving our understanding phenotype disease. However, phasing limited by read length stretches homozygosity along genome. To overcome this limitation, we designed MethPhaser, method that utilizes methylation signals from Oxford Nanopore Technologies to extend Single Nucleotide Variation (SNV)-based phasing. We demonstrate haplotype-specific...
Abstract Borgs are huge extrachromosomal elements (ECE) of anaerobic methane-consuming “ Candidatus Methanoperedens” archaea. Here, we used nanopore sequencing to validate published complete genomes curated from short reads and reconstruct new genomes. 13 four near-complete linear share 40 genes that define a largely syntenous genome backbone. We use these conserved identify peatland soil delineate Borg phylogeny, revealing two major clades. Remarkably, encoding nanowire-like...
Immunoglobulin (IGH, IGK, IGL) loci in the human genome are highly polymorphic regions that encode building blocks of light and heavy chain IG proteins dimerize to form antibodies. The processes V(D)J recombination somatic hypermutation B cells responsible for creating an enormous reservoir specific antibodies capable binding a vast array possible antigens. However, antibody repertoire is fundamentally limited by set variable (V), diversity (D), joining (J) alleles present germline loci. To...
Atherosclerosis represents the most significant risk factor for coronary artery disease (CAD), leading cause of death in developed countries. To better understand pathogenesis atherosclerosis, we applied a likeli-hood-based model selection method to infer gene-disease causality relationships aortic lesion trait segregating mouse population demonstrating spectrum susceptibility developing atherosclerotic lesions. We identified 292 genes that tested causal lesions from liver and adipose...
Immunoglobulin (IGH, IGK, IGL) loci in the human genome are highly polymorphic regions that encode building blocks of light and heavy chain IG proteins dimerize to form antibodies. The processes V(D)J recombination somatic hypermutation B cells responsible for creating an enormous reservoir specific antibodies capable binding a vast array possible antigens. However, antibody repertoire is fundamentally limited by set variable (V), diversity (D), joining (J) alleles present germline loci. To...
Intrachromosomal triplications (TRP) can contribute to disease etiology via gene dosage effects, disruption, position or fusion formation. Recently, post-zygotic de novo adjacent copy-number neutral genomic intervals with runs of homozygosity (ROH) have been shown result in uniparental isodisomy (UPD). The structure these complex rearrangements (CGRs) shows a consistent pattern an inverted triplication flanked by duplications (DUP-TRP/INV-DUP) formed iterative DNA replisome...
Horizontal gene transfer accelerates microbial evolution, promoting diversification and adaptation. The globally abundant marine cyanobacterium Prochlorococcus has a highly streamlined genome with frequent exchange reflected in its extensive pangenome. source of genomic variability, however, remains elusive since most cells lack the common mechanisms that enable horizontal transfer, including conjugation, transformation, plasmids prophages. Examining 623 genomes, we reveal diverse system...
Abstract The assignment of variants across haplotypes, phasing, is crucial for predicting the consequences, interaction, and inheritance mutations a key step in improving our understanding phenotype disease. However, phasing limited by read length stretches homozygosity along genome. To overcome this limitation, we designed MethPhaser, first method that utilizes methylation signals from Oxford Nanopore Technologies to extend SNV-based phasing. Across control samples, phase N50 almost 3-fold...
ABSTRACT RNA splicing factors are recurrently affected by alteration-of-function mutations in clonal blood disorders, highlighting the importance of regulation hematopoiesis. However, our understanding impact dysregulated has been hampered inability to distinguish mutant and wildtype cells primary patient samples, cell-type complexity hematopoietic system, sparse biased coverage splice junctions short-read sequencing typically used single-cell sequencing. To overcome these limitations, we...
Abstract Viruses are the most abundant biological entities on Earth, and play key roles in host ecology, evolution, horizontal gene transfer. Despite recent progress viral metagenomics, inherent genetic complexity of virus populations still poses technical difficulties for recovering complete genomes from natural assemblages. To address these challenges, we developed an assembly-free, single-molecule nanopore sequencing approach enabling direct recovery high-quality genome sequences...
Abstract Comprehensive genome-wide analyses of bacterial DNA methylation have not been possible until the recent advent single molecule, real-time (SMRT) sequencing. This technology enables direct detection N6-methyladenine (6mA) and 4-methylcytosine (4mC) at nucleotide resolution on a scale. The distributions these two major types methylation, along with 5-methylcytosine (5mC), comprise methylome, some rare exceptions notwithstanding. SMRT sequencing has already revealed marked diversity in...
Abstract Osteosarcoma (OS) is an aggressive bone malignancy affecting children and young adults. Implementation optimization of neoadjuvant chemotherapy led to significant improvements in outcome, but patients with recurrence or metastases at diagnosis continue have poor prognosis. Whole genome sequencing (WGS) revealed that a hallmark OS highly rearranged complex copy number aberrations rather than point mutations. A better understanding the key genomic epigenetic factors driving clonal...