A5046737885- Advanced Proteomics Techniques and Applications
- Prostate Cancer Treatment and Research
- Radiomics and Machine Learning in Medical Imaging
- Cancer, Lipids, and Metabolism
- Molecular Biology Techniques and Applications
- Health Systems, Economic Evaluations, Quality of Life
- Prostate Cancer Diagnosis and Treatment
- Genomics and Phylogenetic Studies
- RNA and protein synthesis mechanisms
- Cancer Genomics and Diagnostics
- Gender and Technology in Education
- CRISPR and Genetic Engineering
- Gene expression and cancer classification
- Image Processing and 3D Reconstruction
- Educational Assessment and Pedagogy
- Higher Education and Teaching Methods
- Diverse Educational Innovations Studies
- Metabolomics and Mass Spectrometry Studies
- Intelligent Tutoring Systems and Adaptive Learning
- Brain Metastases and Treatment
- Scientific Computing and Data Management
- Lung Cancer Research Studies
- Digestive system and related health
- Evolution and Genetic Dynamics
- Machine Learning in Bioinformatics
University of California, Los Angeles
2023-2024
Precision Research (United States)
2024
APLA Health
2023
Purdue University Northwest
2021
University of Virginia
2013-2014
Scottish Power (United Kingdom)
2009
Abstract This paper describes a set of anomaly‐detection techniques and their applicability to wind turbine fault identification. It explains how the have been adapted analyse supervisory control data acquisition acquired from farm, automating simplifying operators' analysis task by interpreting volume available. The are brought together into one system collate output provide single decision support environment for an operator. framework used is novel multi‐agent architecture that offers...
Abstract Motivation The ongoing expansion in the volume of biomedical data has contributed to a growing complexity tools and technologies used research with an increased reliance on complex workflows written orchestration languages such as Nextflow integrate algorithms into processing pipelines. use involving various led scrutiny software development practices avoid errors individual connections between them. Results To facilitate test-driven pipelines, we created NFTest, framework for...
Abstract Motivation The volume of biomedical data generated each year is growing exponentially as high-throughput molecular, imaging and mHealth technologies expand. This rise in has contributed to an increasing reliance on demand for computational methods, consequently increased attention software quality integrity. Results To simplify verification diverse data-processing pipelines, we created PipeVal, a light-weight, easy-to-use, extensible tool file validation. It open-source, easy...
Abstract Gene expression is a multi-step transformation of biological information from its storage form (DNA) into functional forms (protein and some RNAs). Regulatory activities at each step this multiply single gene myriad proteoforms. Proteogenomics the study how genomic transcriptomic variation creates proteoform diversity, limited by challenges modeling complexities gene-expression. We therefore created moPepGen, graph-based algorithm that comprehensively enumerates proteoforms in...
DNA sequencing continues to get cheaper and faster. In parallel, algorithmic innovations have allowed inference of a wide range nuclear, mitochondrial, somatic evolutionary from data. To make automated, high-quality more readily available, we created an extensible Nextflow meta-pipeline called metapipeline-DNA. Metapipeline-DNA supports processing raw reads through alignment, variant detection, quality control subclonal reconstruction. Each step quality-control, data-visualization multiple...
Abstract Background: Localized prostate tumors show significant spatial heterogeneity, with regions of high-grade disease adjacent to lower grade disease. Consequently, cancer biopsies are prone sampling bias, potentially leading underestimation tumor grade. To study the clinical, epidemiologic, and molecular hallmarks this phenomenon, we conducted a prospective upgrading: differences in detected between biopsy surgery. Methods: We established prospective, multi-institutional cohort men...
Prostate cancer is frequently treated with radiotherapy. Unfortunately, aggressive radioresistant relapses can arise, and the molecular underpinnings of radioresistance are unknown. Modern clinical radiotherapy evolving to deliver higher doses radiation in fewer fractions (hypofractionation). We therefore analyzed genomic, transcriptomic, proteomic data characterize prostate cells both conventionally fractionated hypofractionated Independent fractionation schedule, resistance involved...
Abstract Reference genomes are foundational to modern genomics. Our growing understanding of genome structure leads continual improvements in reference and new “builds” with incompatible coordinate systems. We quantified the impact build on germline somatic variant calling by analyzing tumour-normal whole-genome pairs against two most widely used human builds. The average individual had a build-discordance 3.8% for SNPs, 8.6% SVs, 25.9% SNVs 49.6% SVs. Build-discordant variants not simply...
Somatic mosaicism is an important cause of disease, but mosaic and somatic variants are often challenging to detect because they exist in only a fraction cells. To address the need for benchmarking subclonal normal cell populations, we developed benchmark containing Genome Bottle Consortium (GIAB) HG002 reference material DNA from large batch lymphoblastoid line. First, used variant caller with high coverage (300x) Illumina whole genome sequencing data Ashkenazi Jewish trio not detected at...
Intra-tumoural heterogeneity complicates cancer prognosis and impairs treatment success. One of the ways subclonal reconstruction (SRC) quantifies intra-tumoural is by estimating number subclones present in bulk DNA sequencing data. SRC algorithms are probabilistic need to be initialized a random seed. However, seeds used bioinformatics rarely reported literature. Thus, impact initializing seed on solutions has not been studied. To address this gap, we generated set ten systematically...
e13108 Background: Breast cancer is the leading cause of cancer-related deaths among women in Brazil and type with highest incidence. When diagnosed at early stages, it has an overall five-year survival rate up to 90%. However, advanced reduced about 24%, 90% stage IV die metastatic complications. Brain one most common sites breast patients, even though a site poor prognosis, mutational profile brain tumors poorly described literature. Therefore, we understand that identification this may...
Multifocal prostate cancer is a prevalent phenomenon, with most cases remaining uncharacterized from genomic perspective. A patient presented bilateral cancer. On systematic biopsy, two indistinguishable clinicopathologic lesions were detected. Whole-genome sequencing displayed somatically unrelated tumours distinct driver CNA regions, suggesting independent origins of the tumors. We demonstrated that similar multifocal tumours, which might be interpreted as clonal disease, can in fact...
<p>Supporting data for differential RNA abundance analysis</p>
<p>Prostate cancer cohort characteristics</p>
<p>Prostate cancer cohort characteristics</p>