A5059839433- Cancer Genomics and Diagnostics
- Gene expression and cancer classification
- Bioinformatics and Genomic Networks
- Molecular Biology Techniques and Applications
- RNA modifications and cancer
- Genomics and Phylogenetic Studies
- Epigenetics and DNA Methylation
- Ferroptosis and cancer prognosis
- Lung Cancer Treatments and Mutations
- Genomics and Chromatin Dynamics
- Genetic factors in colorectal cancer
- Genetics, Bioinformatics, and Biomedical Research
- Neuroblastoma Research and Treatments
- Cancer-related molecular mechanisms research
- Genomics and Rare Diseases
- Chromosomal and Genetic Variations
- Uterine Myomas and Treatments
- Glioma Diagnosis and Treatment
- RNA and protein synthesis mechanisms
- Pancreatic and Hepatic Oncology Research
- Evolution and Genetic Dynamics
- Scientific Computing and Data Management
- Cancer Cells and Metastasis
- Advanced Breast Cancer Therapies
- Genetic Associations and Epidemiology
University of California, Santa Cruz
2015-2025
Shenzhen Pingle Orthopedic Hospital
2025
Guangzhou University of Chinese Medicine
2025
Santa Cruz County Office of Education
2016-2019
Howard Hughes Medical Institute
2010-2018
Center for Innovation
2016
University of Washington
2016
National Institutes of Health
2015
University of California System
2015
Harvard University Press
2011
Plasmodium falciparum is the causative agent of most burdensome form human malaria, affecting 200–300 million individuals per year worldwide. The recently sequenced genome P. revealed over 5,400 genes, which 60% encode proteins unknown function. Insights into biochemical function and regulation these genes will provide foundation for future drug vaccine development efforts toward eradication this disease. By analyzing complete asexual intraerythrocytic developmental cycle (IDC) transcriptome...
Abstract Motivation: High-throughput data is providing a comprehensive view of the molecular changes in cancer tissues. New technologies allow for simultaneous genome-wide assay state genome copy number variation, gene expression, DNA methylation and epigenetics tumor samples cell lines. Analyses current sets find that genetic alterations between patients can differ but often involve common pathways. It therefore critical to identify relevant pathways involved progression detect how they are...
Abstract UCSC Xena is a visual exploration resource for both public and private omics data, supported through the web-based Browser multiple turn-key Hubs. This unique archecture allows researchers to view their own data securely, using Hubs, simultaneously visualizing large cancer genomics datasets, including TCGA GDC. Data integration occurs only within Browser, keeping private. supports virtually any functional SNVs, INDELs, structural variants, CNV, expression, DNA methylation, ATAC-seq...
The UCSC Cancer Genomics Browser (https://genome-cancer.ucsc.edu/) is a web-based application that integrates relevant data, analysis and visualization, allowing users to easily discover share their research observations. Users can explore the relationship between genomic alterations phenotypes by visualizing various -omic data alongside clinical phenotypic features, such as age, subtype classifications biomarkers. currently hosts 575 public datasets from genome-wide analyses of over 227 000...
The UCSC Cancer Genomics Browser (https://genome-cancer.ucsc.edu) offers interactive visualization and exploration of TCGA genomic, phenotypic, clinical data, as produced by the Genome Atlas Research Network. Researchers can explore impact genomic alterations on phenotypes visualizing gene protein expression, copy number, DNA methylation, somatic mutation pathway inference data alongside features, Pan-Cancer subtype classifications biomarkers. Integrated Kaplan-Meier survival analysis helps...
Many DNA-hypermethylated cancer genes are occupied by the Polycomb (PcG) repressor complex in embryonic stem cells (ESCs). Their prevalence full spectrum of cancers, exact context chromatin involved, and their status adult cell renewal systems unknown. Using a genome-wide analysis, we demonstrate that ∼75% hypermethylated marked PcG bivalent both ESCs stem/progenitor cells. A large number these key developmental regulators, subset, which call “DNA hypermethylation module,” comprises portion...
The worldwide persistence of drug-resistant Plasmodium falciparum, the most lethal variety human malaria, is a global health concern. P. falciparum sequencing project has brought new opportunities for identifying molecular targets antimalarial drug and vaccine development. We developed software package, ArrayOligoSelector, to design an open reading frame (ORF)-specific DNA microarray using publicly available genome sequence. Each gene was represented by one or more long 70 mer...
The UCSC Cancer Genomics Browser (https://genome-cancer.ucsc.edu/) is a set of web-based tools to display, investigate and analyse cancer genomics data its associated clinical information. browser provides whole-genome base-pair level views several different types data, including some next-generation sequencing platforms. ability view multiple datasets together allows users make comparisons across types. Biological pathways, collections genes, genomic or information can be used sort,...
Reverse phase protein array (RPPA) technology introduced a miniaturized "antigen-down" or "dot-blot" immunoassay suitable for quantifying the relative, semi-quantitative quantitative (if well-accepted reference standard exists) abundance of total levels and post-translational modifications across variety biological samples including cultured cells, tissues, body fluids. The recent evolution RPPA combined with more sophisticated sample handling, optical detection, quality control, better...
Taking advantage of the complete genome sequences several mammals, we developed a novel method to detect losses well-established genes in human through syntenic mapping gene structures between human, mouse, and dog genomes. Unlike most previous genomic methods for pseudogene identification, this analysis is able differentiate from pseudogenes formed shortly after segmental duplication or generated via retrotransposition. Therefore, it enables us find that were inactivated long their birth,...
The detection of somatic single nucleotide variants is a crucial component to the characterization cancer genome. Mutation calling algorithms thus far have focused on comparing normal and tumor genomes from same individual. In recent years, it has become routine for projects like Cancer Genome Atlas (TCGA) also sequence RNA. Here we present RADIA (RNA DNA Integrated Analysis), novel computational method combining patient-matched with RNA detect mutations. inclusion increases power mutations,...
The UCSC Cancer Genomics Browser (https://genome-cancer.ucsc.edu) comprises a suite of web-based tools to integrate, visualize and analyze cancer genomics clinical data. browser displays whole-genome views genome-wide experimental measurements for multiple samples alongside their associated information. Multiple data sets can be viewed simultaneously as coordinated 'heatmap tracks' compare across studies or different modalities. Users order, filter, aggregate, classify display interactively...
Abstract The UCSC Xena platform (http://xena.ucsc.edu/) allows biologists and bioinformaticians to securely analyze visualize their private functional genomics data in the context of public genomic clinical sets. consists a set federated hubs browser, which integrates across hubs, providing one location all data. Our expanding Data Hubs currently hosts 1400+ sets from more than 35 cancer types, as well Pan-Cancer serve seminal scientific community, including latest TCGA, TARGET, ICGC, GTEx...
<h3>Importance</h3> Pediatric cancers are epigenetic diseases; therefore, considering tumor gene expression information is necessary for a complete understanding of the tumorigenic processes. <h3>Objective</h3> To evaluate feasibility and utility incorporating comparative into precision medicine framework difficult-to-treat pediatric young adult patients with cancer. <h3>Design, Setting, Participants</h3> This cohort study was conducted as consortium between University California, Santa Cruz...
Abstract The Pan-Cancer Analysis of Whole Genomes (PCAWG) project generated a vast amount whole-genome cancer sequencing resource data. Here, as part the ICGC/TCGA Consortium, which aggregated whole genome data from 2658 cancers across 38 tumor types, we provide user’s guide to five publicly available online exploration and visualization tools introduced in PCAWG marker paper. These are ICGC Data Portal, UCSC Xena, Chromothripsis Explorer, Expression Atlas, PCAWG-Scout. We detail use cases...
Osteoporosis (OP), marked by reduced bone density and structural decay, poses a heightened risk of fractures. Our study formulates predictive diagnostic model for OP analyzing differential gene expression, thereby improving early diagnosis therapeutic approaches. Using GSE62402, GSE56815, GSE35958 datasets from the Gene Expression Omnibus (GEO) database, we identified differentially expressed genes (DEGs) via R packages, evaluated underlying molecular mechanisms network analysis. Immune...
Abstract UCSC Xena (https://xena.ucsc.edu) is a popular web-based visual integration and exploration tool for multiomic data associated clinical phenotypic annotations. users want to be able run Gene Set Enrichment Analysis (GSEA) compare gene expression between their two dynamically created sample subgroups determine which programs are upregulated or downregulated. However, the traditional GSEA implementation was not performant enough support Xena’s interactive visualizations. To overcome...
RTK/RAS/RAF pathway alterations (RPAs) are a hallmark of lung adenocarcinoma (LUAD). In this study, we use whole-genome sequencing (WGS) 85 cases found to be RPA(-) by previous studies from The Cancer Genome Atlas (TCGA) characterize the minority LUADs lacking apparent in pathway. We show that WGS analysis uncovers RPA(+) 28 (33%) samples. Among remaining 57 cases, observe focal deletions targeting promoter or transcription start site STK11 (n = 7) KEAP1 3), and mutations associated with...
The best known property of plant proteinase inhibitor II (PIN2) genes is their wound-inducible expression in leaves and constitutive flowers. Here we show by promoter analysis transgenic plants situ reverse transcription-PCR (RT-PCR) that SaPIN2b, a member the PIN2 gene family nightshade (Solanum americanum), also constitutively expressed glandular trichomes. SaPIN2b its deletions were cloned fused upstream beta-glucuronidase (GUS) to transform tobacco (Nicotiana tabacum) plants....
ABSTRACT Toil is portable, open-source workflow software that supports contemporary definition languages and can be used to securely reproducibly run scientific workflows efficiently at large-scale. To demonstrate Toil, we processed over 20,000 RNA-seq samples create a consistent meta-analysis of five datasets free computational batch effects make freely available. Nearly all the were analysed in under four days using commercial cloud cluster 32,000 preemptable cores.