John K. Simmons
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View article: The Data Distillery: A Graph Framework for Semantic Integration and Querying of Biomedical Data
The Data Distillery: A Graph Framework for Semantic Integration and Querying of Biomedical Data Open
The Data Distillery Knowledge Graph (DDKG) is a framework for semantic integration and querying of biomedical data across domains. Built for the NIH Common Fund Data Ecosystem, it supports translational research by linking clinical and exp…
View article: Large-scale human myeloma cell line small molecule compound screen dataset
Large-scale human myeloma cell line small molecule compound screen dataset Open
Multiple myeloma, a hematopoietic malignancy of terminally differentiated B cells, is the second most common hematological malignancy after leukemia. While patients have benefited from numerous advances in treatment in recent years resulti…
View article: Homo Sapiens Chromosomal Location Ontology: A Framework for Genomic Data in Biomedical Knowledge Graphs
Homo Sapiens Chromosomal Location Ontology: A Framework for Genomic Data in Biomedical Knowledge Graphs Open
The Homo sapiens Chromosomal Location Ontology (HSCLO) is designed to facilitate the integration of human genomic features into biomedical knowledge graphs from releases GRCh37 and GRCh38 at multiple resolutions. HSCLO comprises two distin…
View article: Petagraph: A large-scale unifying knowledge graph framework for integrating biomolecular and biomedical data
Petagraph: A large-scale unifying knowledge graph framework for integrating biomolecular and biomedical data Open
Over the past decade, there has been substantial growth in both the quantity and complexity of available biomedical data. In order to more efficiently harness this extensive data and alleviate challenges associated with integration of mult…
View article: Comprehensive NGS profiling to enable detection of ALK gene rearrangements and MET amplifications in non-small cell lung cancer
Comprehensive NGS profiling to enable detection of ALK gene rearrangements and MET amplifications in non-small cell lung cancer Open
Introduction Next-generation sequencing (NGS) is currently widely used for biomarker studies and molecular profiling to identify concurrent alterations that can lead to the better characterization of a tumor’s molecular landscape. However,…
View article: Data from Cooperative Targets of Combined mTOR/HDAC Inhibition Promote MYC Degradation
Data from Cooperative Targets of Combined mTOR/HDAC Inhibition Promote MYC Degradation Open
Cancer treatments often require combinations of molecularly targeted agents to be effective. mTORi (rapamycin) and HDACi (MS-275/entinostat) inhibitors have been shown to be effective in limiting tumor growth, and here we define part of th…
View article: SupplementalFigures 1-4, Tables from Hypomorphic mTOR Downregulates CDK6 and Delays Thymic Pre-T LBL Tumorigenesis
SupplementalFigures 1-4, Tables from Hypomorphic mTOR Downregulates CDK6 and Delays Thymic Pre-T LBL Tumorigenesis Open
Supplemental Figures S1-S4 + two supp. tables
View article: supplementary methods from Cooperative Targets of Combined mTOR/HDAC Inhibition Promote MYC Degradation
supplementary methods from Cooperative Targets of Combined mTOR/HDAC Inhibition Promote MYC Degradation Open
supplementary statistical methods and primer sequences
View article: Supplementary Figures from Cooperative Targets of Combined mTOR/HDAC Inhibition Promote MYC Degradation
Supplementary Figures from Cooperative Targets of Combined mTOR/HDAC Inhibition Promote MYC Degradation Open
Figures S1-S7
View article: Data from Hypomorphic mTOR Downregulates CDK6 and Delays Thymic Pre-T LBL Tumorigenesis
Data from Hypomorphic mTOR Downregulates CDK6 and Delays Thymic Pre-T LBL Tumorigenesis Open
PI3K/AKT/mTOR pathway hyperactivation is frequent in T-cell acute lymphoblastic leukemia/lymphoma (T-ALL/LBL). To model inhibition of mTOR, pre–T-cell lymphoblastic leukemia/lymphoma (pre-T LBL) tumor development was monitored in mice with…
View article: supplementary methods from Cooperative Targets of Combined mTOR/HDAC Inhibition Promote MYC Degradation
supplementary methods from Cooperative Targets of Combined mTOR/HDAC Inhibition Promote MYC Degradation Open
supplementary statistical methods and primer sequences
View article: Data from Hypomorphic mTOR Downregulates CDK6 and Delays Thymic Pre-T LBL Tumorigenesis
Data from Hypomorphic mTOR Downregulates CDK6 and Delays Thymic Pre-T LBL Tumorigenesis Open
PI3K/AKT/mTOR pathway hyperactivation is frequent in T-cell acute lymphoblastic leukemia/lymphoma (T-ALL/LBL). To model inhibition of mTOR, pre–T-cell lymphoblastic leukemia/lymphoma (pre-T LBL) tumor development was monitored in mice with…
View article: Supplementary Figures from Cooperative Targets of Combined mTOR/HDAC Inhibition Promote MYC Degradation
Supplementary Figures from Cooperative Targets of Combined mTOR/HDAC Inhibition Promote MYC Degradation Open
Figures S1-S7
View article: Supplementary Table 1 from Cooperative Targets of Combined mTOR/HDAC Inhibition Promote MYC Degradation
Supplementary Table 1 from Cooperative Targets of Combined mTOR/HDAC Inhibition Promote MYC Degradation Open
Statistical Data and SNPS
View article: SupplementalFigures 1-4, Tables from Hypomorphic mTOR Downregulates CDK6 and Delays Thymic Pre-T LBL Tumorigenesis
SupplementalFigures 1-4, Tables from Hypomorphic mTOR Downregulates CDK6 and Delays Thymic Pre-T LBL Tumorigenesis Open
Supplemental Figures S1-S4 + two supp. tables
View article: Data from Cooperative Targets of Combined mTOR/HDAC Inhibition Promote MYC Degradation
Data from Cooperative Targets of Combined mTOR/HDAC Inhibition Promote MYC Degradation Open
Cancer treatments often require combinations of molecularly targeted agents to be effective. mTORi (rapamycin) and HDACi (MS-275/entinostat) inhibitors have been shown to be effective in limiting tumor growth, and here we define part of th…
View article: Supplementary Table 1 from Cooperative Targets of Combined mTOR/HDAC Inhibition Promote MYC Degradation
Supplementary Table 1 from Cooperative Targets of Combined mTOR/HDAC Inhibition Promote MYC Degradation Open
Statistical Data and SNPS
View article: Supplementary Tables S1-S15 from Metastatic Colorectal Cancer Treatment Response Evaluation by Ultra-Deep Sequencing of Cell-Free DNA and Matched White Blood Cells
Supplementary Tables S1-S15 from Metastatic Colorectal Cancer Treatment Response Evaluation by Ultra-Deep Sequencing of Cell-Free DNA and Matched White Blood Cells Open
The Supplementary Tables file consists of Supplementary Tables 1 to 15 belonging to the manuscript "Metastatic colorectal cancer treatment response evaluation by ultra-deep sequencing of cell-free DNA and matched white blood cells"
View article: Data from Metastatic Colorectal Cancer Treatment Response Evaluation by Ultra-Deep Sequencing of Cell-Free DNA and Matched White Blood Cells
Data from Metastatic Colorectal Cancer Treatment Response Evaluation by Ultra-Deep Sequencing of Cell-Free DNA and Matched White Blood Cells Open
Purpose:Circulating tumor DNA (ctDNA) has the potential to guide therapy selection and monitor treatment response in patients with metastatic cancer. However, germline and clonal hematopoiesis–associated alterations can confound identifica…
View article: Supplementary Data S1 from Metastatic Colorectal Cancer Treatment Response Evaluation by Ultra-Deep Sequencing of Cell-Free DNA and Matched White Blood Cells
Supplementary Data S1 from Metastatic Colorectal Cancer Treatment Response Evaluation by Ultra-Deep Sequencing of Cell-Free DNA and Matched White Blood Cells Open
Supplementary Data 1 shows an overview of ctDNA dynamics, treatments, and radiological response measurements per patient.
View article: Supplementary Figures S1-S15 from Metastatic Colorectal Cancer Treatment Response Evaluation by Ultra-Deep Sequencing of Cell-Free DNA and Matched White Blood Cells
Supplementary Figures S1-S15 from Metastatic Colorectal Cancer Treatment Response Evaluation by Ultra-Deep Sequencing of Cell-Free DNA and Matched White Blood Cells Open
The Supplementary Figures file consists of Supplementary Figures 1 to 15 belonging to the manuscript: "Metastatic colorectal cancer treatment response evaluation by ultra-deep sequencing of cell-free DNA and matched white blood cells"
View article: Supplementary Tables S1-S15 from Metastatic Colorectal Cancer Treatment Response Evaluation by Ultra-Deep Sequencing of Cell-Free DNA and Matched White Blood Cells
Supplementary Tables S1-S15 from Metastatic Colorectal Cancer Treatment Response Evaluation by Ultra-Deep Sequencing of Cell-Free DNA and Matched White Blood Cells Open
The Supplementary Tables file consists of Supplementary Tables 1 to 15 belonging to the manuscript "Metastatic colorectal cancer treatment response evaluation by ultra-deep sequencing of cell-free DNA and matched white blood cells"
View article: Data from Metastatic Colorectal Cancer Treatment Response Evaluation by Ultra-Deep Sequencing of Cell-Free DNA and Matched White Blood Cells
Data from Metastatic Colorectal Cancer Treatment Response Evaluation by Ultra-Deep Sequencing of Cell-Free DNA and Matched White Blood Cells Open
Purpose:Circulating tumor DNA (ctDNA) has the potential to guide therapy selection and monitor treatment response in patients with metastatic cancer. However, germline and clonal hematopoiesis–associated alterations can confound identifica…
View article: Supplementary Data S1 from Metastatic Colorectal Cancer Treatment Response Evaluation by Ultra-Deep Sequencing of Cell-Free DNA and Matched White Blood Cells
Supplementary Data S1 from Metastatic Colorectal Cancer Treatment Response Evaluation by Ultra-Deep Sequencing of Cell-Free DNA and Matched White Blood Cells Open
Supplementary Data 1 shows an overview of ctDNA dynamics, treatments, and radiological response measurements per patient.
View article: Supplementary Figures S1-S15 from Metastatic Colorectal Cancer Treatment Response Evaluation by Ultra-Deep Sequencing of Cell-Free DNA and Matched White Blood Cells
Supplementary Figures S1-S15 from Metastatic Colorectal Cancer Treatment Response Evaluation by Ultra-Deep Sequencing of Cell-Free DNA and Matched White Blood Cells Open
The Supplementary Figures file consists of Supplementary Figures 1 to 15 belonging to the manuscript: "Metastatic colorectal cancer treatment response evaluation by ultra-deep sequencing of cell-free DNA and matched white blood cells"
View article: Metastatic Colorectal Cancer Treatment Response Evaluation by Ultra-Deep Sequencing of Cell-Free DNA and Matched White Blood Cells
Metastatic Colorectal Cancer Treatment Response Evaluation by Ultra-Deep Sequencing of Cell-Free DNA and Matched White Blood Cells Open
Purpose: Circulating tumor DNA (ctDNA) has the potential to guide therapy selection and monitor treatment response in patients with metastatic cancer. However, germline and clonal hematopoiesis–associated alterations can confound identific…
View article: Validation of a Circulating Tumor <scp>DNA</scp>-Based <scp>Next-Generation</scp> Sequencing Assay in a Cohort of Patients with Solid tumors: A Proposed Solution for Decentralized Plasma Testing
Validation of a Circulating Tumor <span>DNA</span>-Based <span>Next-Generation</span> Sequencing Assay in a Cohort of Patients with Solid tumors: A Proposed Solution for Decentralized Plasma Testing Open
Background Characterization of circulating tumor DNA (ctDNA) has been integrated into clinical practice. Although labs have standardized validation procedures to develop single locus tests, the efficacy of on-site plasma-based next-generat…