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View article: Epigenetic profiling reveals key super-enhancer networks driving oncogenesis in HPV-positive HNSCC
Epigenetic profiling reveals key super-enhancer networks driving oncogenesis in HPV-positive HNSCC Open
Human papillomavirus-positive (HPV+) head and neck squamous cell carcinoma (HNSCC) is a growing subset of cancer cases distinct from HPV-negative by fewer genetic mutations and prevalent epigenetic dysregulation. We mapped H3K27ac-marked s…
View article: Development and validation of the Immune Profile Score (IPS), a novel multiomic algorithmic assay for stratifying outcomes in a real-world cohort of patients with advanced solid cancer treated with immune checkpoint inhibitors
Development and validation of the Immune Profile Score (IPS), a novel multiomic algorithmic assay for stratifying outcomes in a real-world cohort of patients with advanced solid cancer treated with immune checkpoint inhibitors Open
Background Immune checkpoint inhibitors (ICIs) have transformed the oncology treatment landscape. Despite substantial improvements for some patients, the majority do not benefit from ICIs, indicating a need for predictive biomarkers to bet…
View article: Development and validation of the Immune Profile Score (IPS), a novel multi-omic algorithmic assay for stratifying outcomes in a real-world cohort of advanced solid cancer patients treated with immune checkpoint inhibitors
Development and validation of the Immune Profile Score (IPS), a novel multi-omic algorithmic assay for stratifying outcomes in a real-world cohort of advanced solid cancer patients treated with immune checkpoint inhibitors Open
Background Immune checkpoint inhibitors (ICIs) have transformed the oncology treatment landscape. Despite substantial improvements for some patients, the majority do not benefit from ICIs, indicating a need for predictive biomarkers to bet…
View article: Antibody dependent cell-mediated cytotoxicity selection pressure induces diverse mechanisms of resistance
Antibody dependent cell-mediated cytotoxicity selection pressure induces diverse mechanisms of resistance Open
Targeted monoclonal antibody therapy has emerged as a powerful therapeutic strategy for cancer. However, only a minority of patients have durable responses and the development of resistance remains a major clinical obstacle. Antibody-depen…
View article: Transcriptomic forecasting with neural ordinary differential equations
Transcriptomic forecasting with neural ordinary differential equations Open
Single-cell transcriptomics technologies can uncover changes in the molecular states that underlie cellular phenotypes. However, understanding the dynamic cellular processes requires extending from inferring trajectories from snapshots of …
View article: Data from Interrogation of T Cell–enriched Tumors Reveals Prognostic and Immunotherapeutic Implications of Polyamine Metabolism
Data from Interrogation of T Cell–enriched Tumors Reveals Prognostic and Immunotherapeutic Implications of Polyamine Metabolism Open
Metabolic features of the tumor microenvironment (TME) antagonize antitumor immunity. We hypothesized that T cell–infiltrated (Thi) tumors with a known antigen should exhibit superior clinical outcomes, though some fare worse given unfavor…
View article: Supplemental Figures S1-S10 from Interrogation of T Cell–enriched Tumors Reveals Prognostic and Immunotherapeutic Implications of Polyamine Metabolism
Supplemental Figures S1-S10 from Interrogation of T Cell–enriched Tumors Reveals Prognostic and Immunotherapeutic Implications of Polyamine Metabolism Open
Supplemental Figures S1-10
View article: Supplemental Figures S1-S10 from Interrogation of T Cell–enriched Tumors Reveals Prognostic and Immunotherapeutic Implications of Polyamine Metabolism
Supplemental Figures S1-S10 from Interrogation of T Cell–enriched Tumors Reveals Prognostic and Immunotherapeutic Implications of Polyamine Metabolism Open
Supplemental Figures S1-10
View article: Data from Interrogation of T Cell–enriched Tumors Reveals Prognostic and Immunotherapeutic Implications of Polyamine Metabolism
Data from Interrogation of T Cell–enriched Tumors Reveals Prognostic and Immunotherapeutic Implications of Polyamine Metabolism Open
Metabolic features of the tumor microenvironment (TME) antagonize antitumor immunity. We hypothesized that T cell–infiltrated (Thi) tumors with a known antigen should exhibit superior clinical outcomes, though some fare worse given unfavor…
View article: Supplementary Tables S1-S17 from Interrogation of T Cell–enriched Tumors Reveals Prognostic and Immunotherapeutic Implications of Polyamine Metabolism
Supplementary Tables S1-S17 from Interrogation of T Cell–enriched Tumors Reveals Prognostic and Immunotherapeutic Implications of Polyamine Metabolism Open
Supplementary Tables
View article: Supplementary Tables S1-S17 from Interrogation of T Cell–enriched Tumors Reveals Prognostic and Immunotherapeutic Implications of Polyamine Metabolism
Supplementary Tables S1-S17 from Interrogation of T Cell–enriched Tumors Reveals Prognostic and Immunotherapeutic Implications of Polyamine Metabolism Open
Supplementary Tables
View article: A mechanistic simulation of molecular cell states over time
A mechanistic simulation of molecular cell states over time Open
Computer simulations of cell behaviors and dynamics allow for investigation of aspects of cellular biology with a ground truth that is currently difficult or impossible to generate from experimentally generated profiling data. Here, we pre…
View article: Transcriptomic forecasting with neural ODEs
Transcriptomic forecasting with neural ODEs Open
Single cell transcriptomics technologies can uncover changes in the molecular states that underlie cellular phenotypes. However, understanding the dynamic cellular processes requires extending from inferring trajectories from snapshots of …
View article: PanIN and CAF Transitions in Pancreatic Carcinogenesis Revealed with Spatial Data Integration
PanIN and CAF Transitions in Pancreatic Carcinogenesis Revealed with Spatial Data Integration Open
Spatial transcriptomics (ST) is a powerful new approach to characterize the cellular and molecular architecture of the tumor microenvironment. Previous single-cell RNA-sequencing (scRNA-seq) studies of pancreatic ductal adenocarcinoma (PDA…
View article: Interrogation of T Cell–enriched Tumors Reveals Prognostic and Immunotherapeutic Implications of Polyamine Metabolism
Interrogation of T Cell–enriched Tumors Reveals Prognostic and Immunotherapeutic Implications of Polyamine Metabolism Open
Metabolic features of the tumor microenvironment (TME) antagonize antitumor immunity. We hypothesized that T cell–infiltrated (Thi) tumors with a known antigen should exhibit superior clinical outcomes, though some fare worse given unfavor…
View article: BoolODE Simulated Time Series within Single Cells
BoolODE Simulated Time Series within Single Cells Open
BoolODE was designed to simulate single-cell expression data sets on the basis of a network of gene-gene interactions (Pratapa et al., 2020). We applied it here to generate expression simulated expression levels at 800 time points within t…
View article: BoolODE Simulated Time Series with single gene KO
BoolODE Simulated Time Series with single gene KO Open
BoolODE was designed to simulate single-cell expression data sets on the basis of a network of gene-gene interactions (Pratapa et al., 2020). To simulate data sets with gene KOs, the simulations were allowed to run for 101 time points, at …
View article: hTERT RPE cells scEU-seq AnnData
hTERT RPE cells scEU-seq AnnData Open
A scEU-seq data set from immortalized human retinal pigment epithelium (RPE) cells, published by (Battich et al., 2020).
View article: Interrogation of T Cell-Enriched Tumors Reveals Prognostic and Immunotherapeutic Implications of Polyamine Metabolism
Interrogation of T Cell-Enriched Tumors Reveals Prognostic and Immunotherapeutic Implications of Polyamine Metabolism Open
Background The presence of cytotoxic tumor infiltrating lymphocytes (TILs) and antigen (e.g., viral, tumor neoantigens) enhances anti-tumor immunity. However, features including recruitment of tolerogenic cell types, nutrient-depletion, an…
View article: Evaluating the impact of age on immune checkpoint therapy biomarkers
Evaluating the impact of age on immune checkpoint therapy biomarkers Open
Both tumors and aging alter the immune landscape of tissues. These interactions may play an important role in tumor progression among elderly patients and may suggest considerations for patient care. We leverage large-scale genomic and cli…
View article: Additional file 5 of Multi-omic profiling of lung and liver tumor microenvironments of metastatic pancreatic cancer reveals site-specific immune regulatory pathways
Additional file 5 of Multi-omic profiling of lung and liver tumor microenvironments of metastatic pancreatic cancer reveals site-specific immune regulatory pathways Open
Additional file 5: Table S4. 2nd Mass Cytometry Antibody Panel.
View article: Additional file 6 of Multi-omic profiling of lung and liver tumor microenvironments of metastatic pancreatic cancer reveals site-specific immune regulatory pathways
Additional file 6 of Multi-omic profiling of lung and liver tumor microenvironments of metastatic pancreatic cancer reveals site-specific immune regulatory pathways Open
Additional file 6: Table S5. Mass Cytometry Cell Subset Annotation for 2nd Panel Data.
View article: Additional file 4 of Multi-omic profiling of lung and liver tumor microenvironments of metastatic pancreatic cancer reveals site-specific immune regulatory pathways
Additional file 4 of Multi-omic profiling of lung and liver tumor microenvironments of metastatic pancreatic cancer reveals site-specific immune regulatory pathways Open
Additional file 4: Table S3. Mass Cytometry T Cell Subset Annotation from 1st Panel Data.
View article: Additional file 7 of Multi-omic profiling of lung and liver tumor microenvironments of metastatic pancreatic cancer reveals site-specific immune regulatory pathways
Additional file 7 of Multi-omic profiling of lung and liver tumor microenvironments of metastatic pancreatic cancer reveals site-specific immune regulatory pathways Open
Additional file 7: Table S6. Rapid Autopsy Samples Additional Detail.
View article: Additional file 2 of Multi-omic profiling of lung and liver tumor microenvironments of metastatic pancreatic cancer reveals site-specific immune regulatory pathways
Additional file 2 of Multi-omic profiling of lung and liver tumor microenvironments of metastatic pancreatic cancer reveals site-specific immune regulatory pathways Open
Additional file 2: Table S1. 1st Mass Cytometry Antibody Panel.