A5065776736- Genomics and Phylogenetic Studies
- X-ray Diffraction in Crystallography
- Crystallization and Solubility Studies
- Health and Wellbeing Research
- Ecology and Conservation Studies
- CRISPR and Genetic Engineering
- Epigenetics and DNA Methylation
- Genomics and Rare Diseases
- Genetic factors in colorectal cancer
- Genomics and Chromatin Dynamics
- Chromosomal and Genetic Variations
- Cancer Genomics and Diagnostics
- Gene expression and cancer classification
- Education and Learning Interventions
- Plant tissue culture and regeneration
- Seed Germination and Physiology
- Single-cell and spatial transcriptomics
- Agriculture, Soil, Plant Science
- RNA modifications and cancer
- Education, Safety, and Science Studies
- Molecular Biology Techniques and Applications
- Nutrition, Health and Food Behavior
- Adipokines, Inflammation, and Metabolic Diseases
- Plant and animal studies
- Cancer-related gene regulation
Fox Chase Cancer Center
2022-2025
Stanford Medicine
2017-2025
Stanford University
2018-2024
Johns Hopkins University
2024
Korea Forest Service
2015-2024
Palo Alto University
2023
Chungbuk National University
2022
Korea Institute of Brain Science
2022
Stratford University
2022
Cold Spring Harbor Laboratory
2012-2019
Ray Ming, Robert Paull, Qingyi Yu and colleagues report the genome sequences of two cultivated pineapple varieties one wild relative. Their analysis supports use as a reference for monocot comparative genomics provides insight into evolution crassulacean acid metabolism photosynthesis. Pineapple (Ananas comosus (L.) Merr.) is most economically valuable crop possessing (CAM), photosynthetic carbon assimilation pathway with high water-use efficiency, second important tropical fruit. We...
Transformative technologies are enabling the construction of three dimensional (3D) maps tissues with unprecedented spatial and molecular resolution. Over next seven years, NIH Common Fund Human Biomolecular Atlas Program (HuBMAP) intends to develop a widely accessible framework for comprehensively mapping human body at single-cell resolution by supporting technology development, data acquisition, detailed mapping. HuBMAP will integrate its efforts other funding agencies, programs,...
Abstract Background The use of high throughput genome-sequencing technologies has uncovered a large extent structural variation in eukaryotic genomes that makes important contributions to genomic diversity and phenotypic variation. When the different strains given organism are compared, whole genome resequencing data typically aligned an established reference sequence. However, when differs significant ways from individuals under study, analysis is often incomplete or inaccurate. Results...
ABSTRACT Background Sugarcane cultivars are polyploid interspecific hybrids of giant genomes, typically with 10–13 sets chromosomes from 2 Saccharum species. The ploidy, hybridity, and size the genome, estimated to have >10 Gb, pose a challenge for sequencing. Results Here we present gene space assembly SP80-3280, including 373,869 putative genes their potential regulatory regions. alignment single-copy in diploid grasses indicates that could resolve 2–6 (up 15) homo(eo)logs 99.1%...
Abstract Third-generation long-range DNA sequencing and mapping technologies are creating a renaissance in high-quality genome sequencing. Unlike second-generation sequencing, which produces short reads few hundred base-pairs long, third-generation single-molecule generate over 10,000 bp or map 100,000 molecules. We analyze how increased read lengths can be used to address longstanding problems de novo assembly, structural variation analysis haplotype phasing.
Genome resequencing and short read mapping are two of the primary tools genomics used for many important applications. The current state-of-the-art in uses quality values scores to evaluate reliability mapping. These attributes, however, assigned individual reads do not directly measure problematic repeats across genome. Here, we present Mappability Score (GMS) as a novel complexity GMS is weighted probability that any could be unambiguously mapped given position thus measures overall...
Abstract Third generation single molecule sequencing technology is poised to revolutionize genomics by enabling the of long, individual molecules DNA and RNA. These technologies now routinely produce reads exceeding 5,000 basepairs, can achieve as long 50,000 basepairs. Here we evaluate limits assessing impact read in assembly human genome 25 other important genomes across tree life. From this, develop a new data-driven model using support vector regression that accurately predict...
Abstract Motivation: Genomics is expanding from a single reference per species paradigm into more comprehensive pan-genome approach that analyzes multiple individuals together. A compressed de Bruijn graph sophisticated data structure for representing the genomes of entire populations. It robustly encodes shared segments, simple single-nucleotide polymorphisms and complex structural variations far beyond what can be represented in collection linear sequences alone. Results: We explore deep...
Abstract Lifelong regular physical activity is associated with reduced risk of type 2 diabetes (T2D), maintenance muscle mass and increased metabolic capacity. However, little known about epigenetic mechanisms that might contribute to these beneficial effects in aged individuals. We investigated the effect lifelong on global DNA methylation patterns skeletal healthy men, who had either performed exercise or remained sedentary their entire lives (average age 62 years). was significantly lower...
Abstract Epigenetic landscapes can shape physiologic and disease phenotypes. We used integrative, high resolution multi-omics methods to delineate the methylome landscape characterize oncogenic drivers of esophageal squamous cell carcinoma (ESCC). found 98% CpGs are hypomethylated across ESCC genome. Hypo-methylated regions enriched in areas with heterochromatin binding markers (H3K9me3, H3K27me3), while hyper-methylated polycomb repressive complex (EZH2/SUZ12) recognizing regions. Altered...
Gut microbial communities can respond to antibiotic perturbations by rapidly altering their taxonomic and functional composition. However, little is known about the strain-level processes that drive this collective response. Here, we characterize gut microbiome of a single individual at high temporal genetic resolution through period health, disease, treatment, recovery. We used deep, linked-read metagenomic sequencing track longitudinal trajectories thousands nucleotide variants within 36...
Abstract Although three-dimensional (3D) genome architecture is crucial for gene regulation, its role in disease remains elusive. We traced the evolution and malignant transformation of colorectal cancer (CRC) by generating high-resolution chromatin conformation maps 33 colon samples spanning different stages early neoplastic growth persons with familial adenomatous polyposis (FAP). Our analysis revealed a substantial progressive loss genome-wide cis-regulatory connectivity at malignancy...
Abstract Detection of somatic variation using sequence from disease-control matched data sets is a critical first step. In many cases including cancer, however, it hard to isolate pure disease tissue, and the impurity hinders accurate mutation analysis by disrupting overall allele frequencies. Here, we propose new method, Virmid, that explicitly determines level in sample, uses for improved detection variation. Extensive tests on simulated real sequencing breast cancer hemimegalencephaly...
Long-read and short-read sequencing technologies offer competing advantages for eukaryotic genome projects. Combinations of both may be appropriate surveys within-species genomic variation. We developed a hybrid assembly pipeline called "Alpaca" that can operate on 20X long-read coverage plus about 50X short-insert long-insert coverage. To preclude collapse tandem repeats, Alpaca relies base-call-corrected long reads contig formation. Compared to two other protocols, demonstrated the most...
Azo-coupled macrocyclic chromoionophores incorporating benzene (L(1)) and pyridine (L(2)) subunits were synthesized, respectively. In a cation-induced color change experiment, both receptors showed Hg(2+) selectivity. However, L(1) gave larger hypsochromic shift than L(2), suggesting that the presence of unit in L(2) may inhibit Hg...N-azo interaction. The observed Hg(2+)-selective changes for found to be controlled by anion-coordination ability. NMR titration proposed receptor ligand with...
New sulfur-containing mixed-donor macrocycles L(1)-L(4) with different donor sets and/or ring sizes (L(1), 20-membered O(3)S(2); L(2), NO(2)S(2); L(3), O(2)S(3); and L(4), 23-membered O(4)S(2)) were synthesized structurally characterized by X-ray analysis. A comparative investigation of the coordination behavior these macrocyclic ligands silver(I) salts copper(I) iodide is reported. The structures seven complexes (1-7) have been determined, a range structural types modes, including mono- to...
We report the first high-quality genome-wide assembly for Arctica islandica, longest-lived non-colonial species, with a reported maximum life span of 507 years. The genome was assembled using short- and long-read DNA sequencing RNA four tissues. All assessment approaches indicated that is complete, contiguous, accurate. size estimated at 1781.15 million base pairs (Mbps) coverage 247.8×. heterozygous rate 1.15% repeat content 67.66%. Genome completeness evaluated by complete BUSCOs 92.7%....
Abstract Background: In the USA it is estimated that more than half-million cancer cases are associated with obesity. Colorectal Cancer (CRC) one of most common types cancer, and rising death rates underscores need for a feasible tailored algorithm to aid in disease management such as blood-based test, i.e., liquid biopsy. Here, we investigate multimodal assessment markers, cell-free DNA (cfDNA) methylation signatures, levels Aspartate Aminotransferase (AST), Alanine (ALT), Carcinoembryonic...
The objectives of the present study were to determine effect sun exposure and aerobic exercise on quality sleep investigate sleep-related hormonal responses in college-aged males.In this study, cross-over design was utilized. subjects (N = 10) without any physical problems or disorders participated experimental performed 4 protocols only (for 30 minutes, EG1) protocol, (walking jogging for EG2) with (EG3) control (no no exposure, EG4) protocol. Each protocol 5 times per week one-week break...