A5030786757- CAR-T cell therapy research
- Bioinformatics and Genomic Networks
- Computational Drug Discovery Methods
- Cancer Immunotherapy and Biomarkers
- Gene expression and cancer classification
- Immune cells in cancer
- Genetic Associations and Epidemiology
- Cellular Mechanics and Interactions
- Lymphoma Diagnosis and Treatment
- Signaling Pathways in Disease
- Melanoma and MAPK Pathways
- Protein Degradation and Inhibitors
- Medical Imaging Techniques and Applications
- 3D Printing in Biomedical Research
- Cancer Genomics and Diagnostics
- Advancements in Semiconductor Devices and Circuit Design
- Neuroinflammation and Neurodegeneration Mechanisms
- Immune Cell Function and Interaction
- Single-cell and spatial transcriptomics
- Radiomics and Machine Learning in Medical Imaging
- Genomics and Chromatin Dynamics
- Integrated Circuits and Semiconductor Failure Analysis
- Chemical Synthesis and Analysis
- Nanofabrication and Lithography Techniques
- Neuroscience and Neural Engineering
National Cancer Institute
2018-2025
National Institutes of Health
2018-2025
Center for Cancer Research
2021-2024
University of Maryland, College Park
2016-2023
Abstract Motivation Mutual exclusivity is a widely recognized property of many cancer drivers. Knowledge about these relationships can provide important insights into drivers, cancer-driving pathways and subtypes. It also be used to predict new functional interactions between driving genes uncover novel Currently, most mutual analyses are preformed focusing on limited set in part due the computational cost required rigorously compute P-values. Results To reduce computing perform less...
The analysis of the mutational landscape cancer, including mutual exclusivity and co-occurrence mutations, has been instrumental in studying disease. We hypothesized that exploring interplay between co-occurrence, exclusivity, functional interactions genes will further improve our understanding disease help to uncover new relations cancer driving pathways. To this end, we designed a general framework, BeWith, for identifying modules with different combinations mutation interaction patterns....
Abstract Background: AI is transforming precision oncology, especially with pretrained deep learning (DL) models (foundation models; FM) extracting tumor-related genomic and transcriptomic patterns from digitized whole-slide histopathology images (WSIs). However, while proteomics closer to cell function phenotypes, few studies focus on deriving protein-level insights WSIs, partly due limited matched cohorts. To address this, we offer Path2Prots, a weakly-supervised DL method estimate...
// Michal Alon 1 , Rand Arafeh Joo Sang Lee 2, 3 Sanna Madan Shelly Kalaora Adi Nagler Tereza Abgarian Polina Greenberg Eytan Ruppin and Yardena Samuels Molecular Cell Biology Department, Weizmann Institute of Science, Rehovot, Israel 2 Center for Bioinformatics Computational Biology, The University Maryland, College Park, USA Cancer Data Science Lab, National Institute, Health, Bethesda, Correspondence to: Samuels, email: Yardena.samuels@weizmann.ac.il Keywords: melanoma; NF1; CAPN1;...
Chimeric antigen receptor (CAR) T cell therapies have yielded transformative clinical successes for patients with blood tumors, but their full potential remains to be unleashed against solid tumors. One challenge is finding selective targets, which we define intuitively surface proteins that are expressed widely by cancer cells minimally healthy in the tumor microenvironment and other normal tissues. Analyzing patient single-cell transcriptomics data, first defined quantified selectivity...
The tremendous success of chimeric antigen receptor (CAR) T cells in children and young adults (CAYAs) with relapsed/refractory B-cell acute lymphoblastic leukemia is tempered by toxicities such as cytokine release syndrome (CRS). Despite expansive information about CRS, profiling specific end-organ secondary to CAR T-cell therapy CAYAs limited. This retrospective, single-center study sought characterize adverse events (AEs) experienced during the first 30 days after infusion. AEs graded...
Abstract The U.S. Food and Drug Administration (FDA) recently approved the treatment with pembrolizumab, an immune checkpoint inhibitor (ICI) targeting PD1 (anti-PD1), for patients advanced solid tumors a high tumor mutational burden (TMB) (defined as TMB ≥10 mutations/Mb). However, following recent studies suggest that levels response to ICI may differ between male female melanoma patients, we investigated whether using this high-TMB threshold selecting anti-PD1 induce sex-dependent bias....
Abstract The advancement of chimeric antigen receptor (CAR) T-cell therapy has been groundbreaking in the treatment hematological malignancies. However, its application solid tumors is constrained by variability and unintended off-tumor, on-target toxicities. Addressing these issues, we introduce a genetic algorithm to analyze single-cell transcriptomics data from patient tumors. This method pinpoints sets surface antigens exclusive cancer cells, utilizing logical operators "AND," "OR,"...
Abstract The aging of the immune system substantially impacts individual responses, yet accurately quantifying age remains a complex challenge. Here we developed IMMClock , novel clock that uses gene expression data to predict biological CD8⁺ T cells, CD4⁺ and NK cells. accuracy is first validated across multiple independent datasets, demonstrating its robustness. Second, utilizing IMMClock, find intrinsic cellular processes are more strongly altered during than differentiation processes....
Mutual exclusivity is a widely recognized property of many cancer drivers. Knowledge about these relationships can provide important insights into drivers, cancer-driving pathways, and subtypes. It also be used to predict new functional interactions between driving genes uncover novel Currently, most mutual analyses are preformed focusing on limited set in part due the computational cost required rigorously compute p-values. To reduce computing perform less restricted analysis, we developed...
Abstract BACKGROUND: Chimeric antigen receptor (CAR) T cell therapies have yielded transformative clinical success for patients with blood tumors, but their full potential remains to be unleashed against solid tumors. One challenge is finding selective targets: surface proteins that are expressed widely by cancer cells and minimally healthy in the tumor microenvironment other normal tissues. METHODS: Analyzing pan-cancer patient single transcriptomics data, we first define quantify...
Mutual exclusivity is a frequently observed property of mutations in cancer. Uncovering these relationships can provide insights into cancer driving mutations, cancer-related pathways and subtypes In addition, it potentially be used to predict novel functional interactions between genes. Most previous mutual analyses are preformed on small number genes partly due the computational cost required rigorously estimate significance exclusivity. With WeSME, we efficiently compute p-values while...