A5071945201- Chromosomal and Genetic Variations
- Genomic variations and chromosomal abnormalities
- Gene expression and cancer classification
- Cancer Genomics and Diagnostics
- Genomics and Phylogenetic Studies
- Molecular Biology Techniques and Applications
- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- Advanced biosensing and bioanalysis techniques
- Genomics and Chromatin Dynamics
- Epigenetics and DNA Methylation
- Biofuel production and bioconversion
- Plant Molecular Biology Research
- CRISPR and Genetic Engineering
- Polysaccharides and Plant Cell Walls
- RNA Research and Splicing
- Genomics and Rare Diseases
- Wheat and Barley Genetics and Pathology
- Plant nutrient uptake and metabolism
- Genetic Mapping and Diversity in Plants and Animals
- Plant Disease Resistance and Genetics
- Machine Learning in Bioinformatics
- Lung Cancer Treatments and Mutations
- Genetic factors in colorectal cancer
- Plant Reproductive Biology
Roche (United States)
2020-2022
La Roche College
2010-2021
Roche (Sweden)
2021
Madison Group (United States)
2018
Roche (Switzerland)
2005-2015
Michigan State University
2015
United States Department of Agriculture
2010
Agricultural Research Service
2010
University of Minnesota
2010
Creative Technologies (United States)
2009
Disease resistance is associated with a plant defense response that involves an integrated set of signal transduction pathways. Changes in the expression patterns 2,375 selected genes were examined simultaneously by cDNA microarray analysis Arabidopsis thaliana after inoculation incompatible fungal pathogen Alternaria brassicicola or treatment defense-related signaling molecules salicylic acid (SA), methyl jasmonate (MJ), ethylene. Substantial changes (up- and down-regulation) steady-state...
Physical interactions between genetic elements located throughout the genome play important roles in gene regulation and can be identified with Chromosome Conformation Capture (3C) methodology. 3C converts physical chromatin into specific ligation products, which are quantified individually by PCR. Here we present a high-throughput approach, 3C-Carbon Copy (5C), that employs microarrays or quantitative DNA sequencing using 454-technology as detection methods. We applied 5C to analyze 400-kb...
Clear-cell renal cell carcinoma (ccRCC) exhibits a broad range of metastatic phenotypes that have not been systematically studied to date. Here, we analyzed 575 primary and 335 biopsies across 100 patients with ccRCC, including two cases sampledat post-mortem. Metastatic competence was afforded by chromosome complexity, identify 9p loss as highly selected event driving metastasis ccRCC-related mortality (p = 0.0014). Distinct patterns dissemination were observed, rapid progression multiple...
Following the domestication of maize over past approximately 10,000 years, breeders have exploited extensive genetic diversity this species to mold its phenotype meet human needs. The extent structural variation, including copy number variation (CNV) and presence/absence (PAV), which are thought contribute extraordinary phenotypic plasticity important crop, not been elucidated. Whole-genome, array-based, comparative genomic hybridization (CGH) revealed a level between inbred lines B73 Mo17...
In many higher plants, cellulose synthesis is inhibited by isoxaben and thiazolidinone herbicides such as 5-tert-butyl-carbamoyloxy-3-(3-trifluromethyl) phenyl-4-thiazolidinone. Semidominant mutations at the IXR1 IXR2 loci of Arabidopsis confer resistance. Isolation gene map-based cloning revealed that it encodes AtCESA3 isoform synthase. The two known mutant alleles contain point replace glycine 998 with aspartic acid, threonine 942 isoleucine, respectively. occur in a highly conserved...
The distribution of cytosine methylation in 6.2 Mb the mouse genome was tested using cohybridization genomic representations from a methylation-sensitive restriction enzyme and its methylation-insensitive isoschizomer. This assay, termed HELP ( H paII tiny fragment E nrichment by L igation-mediated P CR), allows both intragenomic profiling intergenomic comparisons methylation. profile shows most to be contiguous methylated sequence with occasional clusters hypomethylated loci, usually but...
Advanced resources for genome-assisted research in barley (Hordeum vulgare) including a whole-genome shotgun assembly and an integrated physical map have recently become available. These made possible studies that aim to assess genetic diversity or isolate single genes by resequencing silico variant detection. However such approach remains expensive given the 5 Gb size of genome. Targeted sequencing mRNA-coding exome reduces genomic complexity more than 50-fold, thus dramatically reducing...
Microarrays containing 195,000 in situ synthesized oligonucleotide features have been created using a benchtop, maskless photolithographic instrument. This instrument, the Maskless Array Synthesizer (MAS), uses digital light processor (DLP) developed by Texas Instruments. The DLP creates patterns of UV used light-directed synthesis oligonucleotides. mask eliminates need for expensive and time-consuming chromium masks. In this report, we describe experiments which tested technology DNA on...
Abstract Understanding the genes and genetic pathways targeted by recurrent chromosomal imbalances in malignancy, along with molecular mechanisms that generate imbalances, are important problems cancer biology. In this report, we demonstrate oligonucleotide array CGH (oaCGH) analysis can routinely map imbalance breakpoints at exon‐level resolution, including single copy number genomic alterations. Different tiling‐path designs were used study: a whole‐genome 6‐kb median probe spacing...
Cytogenetic analysis of acute myeloid leukemia (AML) cells has accelerated the identification genes important for AML pathogenesis. To complement cytogenetic studies and to identify altered in genomes, we performed genome-wide copy number with paired normal tumor DNA obtained from 86 adult patients de novo using 1.85 million feature SNP arrays. Acquired alterations (CNAs) were confirmed an ultra-dense array comparative genomic hybridization platform. A total 201 somatic CNAs found genomes...
Submicroscopic (less than 2 Mb) segmental DNA copy number changes are a recently recognized source of genetic variability between individuals. The biological consequences variants (CNVs) largely undefined. In some cases, CNVs that cause gene dosage effects have been implicated in phenotypic variation. detected diverse species, including mice and humans. Published studies limited by resolution strain selection. We chose to study 21 well-characterized inbred mouse strains the focus an...
Intramolecular electron transfers within the mixed valence states of ligand bridged hexaruthenium clusters Ru3(μ3-O)(μ-CH3CO2)6(CO)(L)(μ-L')Ru3(μ3-O)(μ-CH3CO2)6(CO)(L) (L' = 1,4-pyrazine; L 4-dimethylaminopyridine (1), pyridine (2), 4-cyanopyridine (3), or L' 4,4'-bipyridine; (4), (5), (6)) were examined. Two discrete and reversible single reductions are evident by cyclic voltammetry in redox chemistry 1−5, intercluster charge-transfer complexes well-defined. The splitting reduction waves,...
Lung cancer is the leading cause of cancer-related death, with non-small cell lung (NSCLC) being predominant form disease. Most caused by accumulation genomic alterations due to tobacco exposure. To uncover its mutational landscape, we performed whole-exome sequencing in 31 NSCLCs and their matched normal tissue samples. We identified both common unique mutation spectra pathway activation adenocarcinomas squamous carcinomas, two major histologies NSCLC. In addition identifying previously...
DNA methylation can play important roles in the regulation of transposable elements and genes. A collection mutant alleles for 11 maize (Zea mays) genes predicted to controlling were isolated through forward- or reverse-genetic approaches. Low-coverage whole-genome bisulfite sequencing high-coverage sequence-capture applied lines determine context- locus-specific effects these mutations on profiles. Plants containing components RNA-directed pathway exhibit loss CHH at many loci as well CG...
Abstract We have developed a solution-based method for targeted DNA capture-sequencing that is directed to the complete human exome. Using this approach allows discovery of greater than 95% all expected heterozygous singe base variants, requires as little 3 Gbp raw sequence data and constitutes an effective tool identifying rare coding alleles in large scale genomic studies.
Soybean (Glycine max) is a self-pollinating species that has relatively low nucleotide polymorphism rates compared with other crop species. Despite the rate of polymorphisms, wide range heritable phenotypic variation exists. There even evidence for among individuals within some cultivars. Williams 82, soybean cultivar used to produce reference genome sequence, was derived from backcrossing Phytophthora root rot resistance locus donor parent Kingwa into recurrent Williams. To explore genetic...