A5006902919- DNA Repair Mechanisms
- Epigenetics and DNA Methylation
- RNA modifications and cancer
- Cancer Genomics and Diagnostics
- Cancer-related molecular mechanisms research
- Molecular Biology Techniques and Applications
- Bioinformatics and Genomic Networks
- Machine Learning in Bioinformatics
- Genetics and Neurodevelopmental Disorders
- Cholangiocarcinoma and Gallbladder Cancer Studies
- Computational Drug Discovery Methods
- Cervical Cancer and HPV Research
- Genetic factors in colorectal cancer
- Gene expression and cancer classification
- Lung Cancer Research Studies
- Advanced Breast Cancer Therapies
- Bacteriophages and microbial interactions
- Biosensors and Analytical Detection
- Lung Cancer Treatments and Mutations
- Advanced biosensing and bioanalysis techniques
- Amino Acid Enzymes and Metabolism
University of California, San Diego
2024
National Academy of Agricultural Science
2015
Harvard University
2005
Abstract Cyclin-dependent kinase 4 and 6 inhibitors (CDK4/6is) have revolutionized breast cancer therapy. However, <50% of patients an objective response, nearly all develop resistance during To elucidate the underlying mechanisms, we constructed interpretable deep learning model response to palbociclib, a CDK4/6i, based on reference map multiprotein assemblies in cancer. The identifies eight core that integrate rare common alterations across 90 genes stratify palbociclib-sensitive versus...
Rapid proliferation is a hallmark of cancer associated with sensitivity to therapeutics that cause DNA replication stress (RS). Many tumors exhibit drug resistance, however, via molecular pathways are incompletely understood. Here, we develop an ensemble predictive models elucidate how mutations impact the response common RS-inducing (RSi) agents. The implement recent advances in deep learning facilitate multidrug prediction and mechanistic interpretation. Initial studies tumor cells...
Whole-cell Systemic Evolution of Ligands by Exponential enrichment (SELEX) is the process which aptamers specific to target cells are developed. Aptamers selected whole-cell SELEX have high affinity and specificity for bacterial surface molecules live targets. To identify DNA Staphylococcus aureus, we applied our rapid method a single-stranded ssDNA library. improve selectivity aptamers, designed, selected, developed two categories that were kinds SELEX, mixing combining FACS analysis...
Abstract Genome-wide association studies have linked millions of genetic variants to biomedical phenotypes, but their utility has been limited by a lack mechanistic understanding and widespread epistatic interactions. Recently, Transformer models emerged as powerful general-purpose architecture in machine learning, with potential address these other challenges. Accordingly, here we introduce the Genotype-to-Phenotype (G2PT), framework for modeling hierarchical information flow among...
<p>Supplementary Figure S1. Aspects of replication stress addressed by cancer therapeutics. Supplementary S2. Nested systems in tumors (NeST). S3. VNN schematic. S4. Performance and interpretation the multi-drug VNN. S5. Evaluation assemblies systematic drug sensitivity screens. S6. Survival analysis cisplatin-treated TCGA cohorts.</p>
<p>Supplementary Figure S1. Aspects of replication stress addressed by cancer therapeutics. Supplementary S2. Nested systems in tumors (NeST). S3. VNN schematic. S4. Performance and interpretation the multi-drug VNN. S5. Evaluation assemblies systematic drug sensitivity screens. S6. Survival analysis cisplatin-treated TCGA cohorts.</p>
<div>Abstract<p>Rapid proliferation is a hallmark of cancer associated with sensitivity to therapeutics that cause DNA replication stress (RS). Many tumors exhibit drug resistance, however, via molecular pathways are incompletely understood. Here, we develop an ensemble predictive models elucidate how mutations impact the response common RS-inducing (RSi) agents. The implement recent advances in deep learning facilitate multidrug prediction and mechanistic interpretation. Initial...
<div>Abstract<p>Rapid proliferation is a hallmark of cancer associated with sensitivity to therapeutics that cause DNA replication stress (RS). Many tumors exhibit drug resistance, however, via molecular pathways are incompletely understood. Here, we develop an ensemble predictive models elucidate how mutations impact the response common RS-inducing (RSi) agents. The implement recent advances in deep learning facilitate multidrug prediction and mechanistic interpretation. Initial...
Abstract Motivation: Many machine learning models have been proposed that use genotypes to predict various phenotypes. Recently, these focused not only on an accurate prediction but mechanistic interpretation, in they attempt describe the hierarchy of biological systems underlying predicted phenotype. Such still face major challenges, however, including how robustly quantify importance mediating phenotypic outcomes and represent bidirectional flow information among genes, systems,...
<p>Supplementary Figure S1. Aspects of replication stress addressed by cancer therapeutics. Supplementary S2. Nested systems in tumors (NeST). S3. VNN schematic. S4. Performance and interpretation the multi-drug VNN. S5. Evaluation assemblies systematic drug sensitivity screens. S6. Survival analysis cisplatin-treated TCGA cohorts.</p>