A5083421459- Genetic Associations and Epidemiology
- Genomics and Phylogenetic Studies
- Genomics and Chromatin Dynamics
- RNA and protein synthesis mechanisms
- Genomic variations and chromosomal abnormalities
- RNA Research and Splicing
- Cancer Genomics and Diagnostics
- Genomics and Rare Diseases
- CRISPR and Genetic Engineering
- Genetic Mapping and Diversity in Plants and Animals
- RNA modifications and cancer
- RNA regulation and disease
- Pluripotent Stem Cells Research
- Epigenetics and DNA Methylation
- Pancreatic function and diabetes
- Retinal Development and Disorders
- Chronic Lymphocytic Leukemia Research
- Single-cell and spatial transcriptomics
- Molecular Biology Techniques and Applications
- Congenital heart defects research
- Chromosomal and Genetic Variations
- Blood Coagulation and Thrombosis Mechanisms
- Chronic Myeloid Leukemia Treatments
- Bioinformatics and Genomic Networks
- Venous Thromboembolism Diagnosis and Management
University of California, San Diego
2016-2025
UC San Diego Health System
2022-2024
University College Dublin
2024
La Jolla Alcohol Research
2011-2023
Rady Children's Hospital-San Diego
2013-2022
UiT The Arctic University of Norway
2016-2019
Cancer Genetics (United States)
2019
Cancer Research Center
2019
Moores Cancer Center
2010-2017
Boston Children's Hospital
2015
Comparison of DNA sequences from different species is a fundamental method for identifying functional elements in genomes. Here, we describe the VISTA family tools created to assist biologists carrying out this task. Our first server at http://www-gsd.lbl.gov/vista/ was launched summer 2000 and designed align long genomic visualize these alignments with associated annotations. Currently site includes multiple comparative genomics provides users rich capabilities browse pre-computed...
PipMaker ( http://bio.cse.psu.edu ) is a World-Wide Web site for comparing two long DNA sequences to identify conserved segments and producing informative, high-resolution displays of the resulting alignments. One display percent identity plot (pip), which shows both position in one sequence degree similarity each aligning segment between compact easily understandable form. Positions along horizontal axis can be labeled with features such as exons genes repetitive elements, colors used...
Global patterns of human DNA sequence variation (haplotypes) defined by common single nucleotide polymorphisms (SNPs) have important implications for identifying disease associations and traits. We used high-density oligonucleotide arrays, in combination with somatic cell genetics, to identify a large fraction all chromosome 21 SNPs directly observe the haplotype structure these SNPs. This reveals blocks limited diversity which more than 80% global sample can typically be characterized only...
Individual differences in DNA sequence are the genetic basis of human variability. We have characterized whole-genome patterns common variation by genotyping 1,586,383 single-nucleotide polymorphisms (SNPs) 71 Americans European, African, and Asian ancestry. Our results indicate that these SNPs capture most as a result linkage disequilibrium, correlation among SNP alleles. observe strong between extended regions disequilibrium functional genomic elements. data provide tool for exploring many...
Abstract Summary: VISTA is a program for visualizing global DNA sequence alignments of arbitrary length. It has clean output, allowing easy identification similarity, and easily configurable, enabling the visualization various lengths at different levels resolution. currently available on web, thus access by all researchers. Availability: server web http://www-gsd.lbl.gov/vista. The source code upon request. Contact: vista@lbl.gov To whom correspondence should be addressed.
Long-range regulatory elements are difficult to discover experimentally; however, they tend be conserved among mammals, suggesting that cross-species sequence comparisons should identify them. To search for sequences, we examined about 1 megabase of orthologous human and mouse sequences noncoding with greater than or equal 70% identity over at least 100 base pairs. Ninety meeting these criteria were discovered, the analysis 15 found across mammals. Characterization largest element in yeast...
The genomes of individuals from the same species vary in sequence as a result different evolutionary processes. To examine patterns of, and forces shaping, variation Arabidopsis thaliana , we performed high-density array resequencing 20 diverse strains (accessions). More than 1 million nonredundant single-nucleotide polymorphisms (SNPs) were identified at moderate false discovery rates (FDRs), ∼4% genome was being highly dissimilar or deleted relative to reference sequence. Patterns...
Rice, the primary source of dietary calories for half humanity, is first crop plant which a high-quality reference genome sequence from single variety was produced. We used resequencing microarrays to interrogate 100 Mb unique fraction 20 diverse varieties and landraces that capture impressive genotypic phenotypic diversity domesticated rice. Here, we report distribution 160,000 nonredundant SNPs. Introgression patterns shared SNPs revealed breeding history relationships among varieties;...
Abstract Background Next generation sequencing (NGS) platforms are currently being utilized for targeted of candidate genes or genomic intervals to perform sequence-based association studies. To evaluate these this application, we analyzed human sequence generated by the Roche 454, Illumina GA, and ABI SOLiD technologies same 260 kb in four individuals. Results Local characteristics contribute systematic variability coverage (>100-fold difference per-base coverage), resulting patterns...
Mutations in the splicing factor SF3B1 are found several cancer types and have been associated with various defects. Using transcriptome sequencing data from chronic lymphocytic leukemia, breast uveal melanoma tumor samples, we show that hundreds of cryptic 3' splice sites (3'SSs) used cancers mutations. We define necessary sequence context for observed SSs propose 3'SS selection is a result mutations causing shift sterically protected region downstream branch point. While most 3'SSs present...