Casey S. Greene
A5050692257- Bioinformatics and Genomic Networks
- Gene expression and cancer classification
- Ovarian cancer diagnosis and treatment
- Cancer Genomics and Diagnostics
- Single-cell and spatial transcriptomics
- Cancer-related molecular mechanisms research
- Systemic Sclerosis and Related Diseases
- Connective Tissue Growth Factor Research
- Biomedical Text Mining and Ontologies
- Scientific Computing and Data Management
- Cell Image Analysis Techniques
- Molecular Biology Techniques and Applications
- Pancreatic and Hepatic Oncology Research
- Genetics, Bioinformatics, and Biomedical Research
- Genomics and Phylogenetic Studies
- Genetic Associations and Epidemiology
- Evolutionary Algorithms and Applications
- Peptidase Inhibition and Analysis
- Research Data Management Practices
- Gene Regulatory Network Analysis
- SARS-CoV-2 and COVID-19 Research
- Machine Learning in Healthcare
- Evolution and Genetic Dynamics
- Bacterial biofilms and quorum sensing
- RNA Research and Splicing
University of Colorado Denver
2020-2025
University of Colorado Anschutz Medical Campus
2021-2025
Colorado School of Public Health
2022-2025
Translational Therapeutics (United States)
2015-2024
University of Pennsylvania
2015-2024
Alex's Lemonade Stand Foundation
2017-2023
Gordon and Betty Moore Foundation
2020-2023
National Cancer Institute
2023
National Human Genome Research Institute
2022-2023
University of Colorado System
2022
Highlights•Alteration map of 10 signaling pathways across 9,125 samples from 33 cancer types•Reusable, curated pathway templates that include a catalogue driver genes•57% tumors have at least one potentially actionable alteration in these pathways•Co-occurrence alterations suggests combination therapy opportunitiesSummaryGenetic control cell-cycle progression, apoptosis, and cell growth are common hallmarks cancer, but the extent, mechanisms, co-occurrence differ between individual tumor...
<h2>Summary</h2> DNA damage repair (DDR) pathways modulate cancer risk, progression, and therapeutic response. We systematically analyzed somatic alterations to provide a comprehensive view of DDR deficiency across 33 types. Mutations with accompanying loss heterozygosity were observed in over 1/3 genes, including <i>TP53</i> <i>BRCA1/2</i>. Other prevalent included epigenetic silencing the direct genes <i>EXO5</i>, <i>MGMT</i>, <i>ALKBH3</i> ∼20% samples. Homologous recombination (HRD) was...
Background: Data sharing accelerates scientific progress but individual-level data while preserving patient privacy presents a barrier. Methods and Results: Using pairs of deep neural networks, we generated simulated, synthetic participants that closely resemble the SPRINT trial (Systolic Blood Pressure Trial). We showed such paired networks can be trained with differential privacy, formal framework limits likelihood queries participants’ could identify real participant in trial. Machine...
Replication has become the gold standard for assessing statistical results from genome-wide association studies. Unfortunately this replication requirement may cause real genetic effects to be missed. A result can fail replicate numerous reasons including inadequate sample size or variability in phenotype definitions across independent samples. In studies allele frequencies of polymorphisms differ due sampling error population differences. We hypothesize that some statistically significant...
Cell-lineage-specific transcripts are essential for differentiated tissue function, implicated in hereditary organ failure, and mediate acquired chronic diseases. However, experimental identification of cell-lineage-specific genes a genome-scale manner is infeasible most solid human tissues. We developed the first method to identify with expression, even lineages not separable by microdissection. Our machine-learning-based approach leverages high-throughput data from homogenates novel...
Recent work has highlighted the tumor microenvironment as a central player in cancer. In particular, interactions between and immune cells may help drive development of brain tumors such glioblastoma multiforme (GBM). Despite significant research into molecular classification glioblastoma, few studies have characterized comprehensive manner infiltrate situ within different GBM subtypes.In this study, we use an unbiased, automated immunohistochemistry-based approach to determine phenotype...
Precision medicine initiatives across the globe have led to a revolution of repositories linking large-scale genomic data with electronic health records, enabling analyses entire phenome. Many these focus solely on research insights, leading limited direct benefit patients. We describe biobank at Colorado Center for Personalized Medicine (CCPM Biobank) that was jointly developed by University Anschutz Medical Campus and UCHealth serve as unique, dual-purpose clinical resource accelerating...
The factors shaping human microbiome variation are a major focus of biomedical research. While other fields have used large sequencing compendia to extract insights requiring otherwise impractical sample sizes, the field has lacked comparably sized resource for 16S rRNA gene amplicon commonly quantify composition. To address this gap, we processed 168,464 publicly available gut samples with uniform pipeline. We use compendium evaluate geographic and technical effects on variation. find that...
While single-cell experiments provide deep cellular resolution within a single sample, some are inherently more challenging than bulk due to dissociation difficulties, cost, or limited tissue availability. This creates situation where we have profiles of one sample condition, and across multiple samples conditions. To bridge this gap, propose BuDDI (BUlk Deconvolution with Domain Invariance). utilizes domain adaptation techniques effectively integrate available corpora case-control reference...
Patient interactions with health care providers result in entries to electronic records (EHRs). EHRs were built for clinical and billing purposes but contain many data points about an individual. Mining these provides opportunities extract phenotypes, which can be paired genetic identify genes underlying common human diseases. This task remains challenging: high quality phenotyping is costly requires physician review; fields the are sparsely filled; our definitions of diseases continuing...
The website Sci-Hub enables users to download PDF versions of scholarly articles, including many articles that are paywalled at their journal’s site. has grown rapidly since its creation in 2011, but the extent coverage been unclear. Here we report that, as March 2017, Sci-Hub’s database contains 68.9% 81.6 million registered with Crossref and 85.1% published toll access journals. We find varies by discipline publisher, preferentially covers popular, content. For provides greater than...
Precision oncology uses genomic evidence to match patients with treatment but often fails identify all who may respond. The transcriptome of these "hidden responders" reveal responsive molecular states. We describe and evaluate a machine-learning approach classify aberrant pathway activity in tumors, which aid hidden responder identification. algorithm integrates RNA-seq, copy number, mutations from 33 different cancer types across Cancer Genome Atlas (TCGA) PanCanAtlas project predict...