John N. Weinstein
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View article: The glutaminase activity of ASNS fuels glutamine metabolism in leukemia
The glutaminase activity of ASNS fuels glutamine metabolism in leukemia Open
Not available.
View article: The ASNS inhibitor ASX-173 potentiates L-asparaginase anticancer activity
The ASNS inhibitor ASX-173 potentiates L-asparaginase anticancer activity Open
Cancer cells reprogram metabolic pathways to meet increased energy and biosynthetic demands. Among those pathways, elevated asparagine metabolism regulated by asparagine synthetase (ASNS) has been linked to tumor progression in various can…
View article: Single-sample, multi-omic mass spectrometry for investigating mechanisms of drug toxicity
Single-sample, multi-omic mass spectrometry for investigating mechanisms of drug toxicity Open
Poor therapeutic index is a principal cause of drug attrition during development. A case in point is L-asparaginase (ASNase), an enzyme-drug approved for treatment of pediatric acute lymphoblastic leukemia (ALL) but too toxic for adults. T…
View article: Ion suppression correction and normalization for non-targeted metabolomics
Ion suppression correction and normalization for non-targeted metabolomics Open
Ion suppression is a major problem in mass spectrometry (MS)-based metabolomics; it can dramatically decrease measurement accuracy, precision, and sensitivity. Here we report a method, the IROA TruQuant Workflow, that uses a stable isotope…
View article: Somatic copy number deletion of chromosome 22q in papillary thyroid carcinoma
Somatic copy number deletion of chromosome 22q in papillary thyroid carcinoma Open
Deletion of the long q arm of chromosome 22 (22qDEL) is the most frequently identified recurrent somatic copy number alteration observed in papillary thyroid carcinoma (PTC). Since its role in PTC is not fully understood, we conducted a po…
View article: A deconvolution framework that uses single-cell sequencing plus a small benchmark data set for accurate analysis of cell type ratios in complex tissue samples
A deconvolution framework that uses single-cell sequencing plus a small benchmark data set for accurate analysis of cell type ratios in complex tissue samples Open
Bulk deconvolution with single-cell/nucleus RNA-seq data is critical for understanding heterogeneity in complex biological samples, yet the technological discrepancy across sequencing platforms limits deconvolution accuracy. To address thi…
View article: Ultra-Fast Multi-Organ Proteomics Unveils Tissue-Specific Mechanisms of Drug Efficacy and Toxicity
Ultra-Fast Multi-Organ Proteomics Unveils Tissue-Specific Mechanisms of Drug Efficacy and Toxicity Open
Rapid and comprehensive analysis of complex proteomes across large sample sets is vital for unlocking the potential of systems biology. We present UFP-MS, an ultra-fast mass spectrometry (MS) proteomics method that integrates narrow-window…
View article: Single-cell chromatin accessibility reveals malignant regulatory programs in primary human cancers
Single-cell chromatin accessibility reveals malignant regulatory programs in primary human cancers Open
To identify cancer-associated gene regulatory changes, we generated single-cell chromatin accessibility landscapes across eight tumor types as part of The Cancer Genome Atlas. Tumor chromatin accessibility is strongly influenced by copy nu…
View article: Supplementary Video S1 from Explore, Visualize, and Analyze Functional Cancer Proteomic Data Using the Cancer Proteome Atlas
Supplementary Video S1 from Explore, Visualize, and Analyze Functional Cancer Proteomic Data Using the Cancer Proteome Atlas Open
Tutorial video on how to use TCPA.
View article: Supplementary Video S1 from Explore, Visualize, and Analyze Functional Cancer Proteomic Data Using the Cancer Proteome Atlas
Supplementary Video S1 from Explore, Visualize, and Analyze Functional Cancer Proteomic Data Using the Cancer Proteome Atlas Open
Tutorial video on how to use TCPA.
View article: Supplementary Video S1 from Explore, Visualize, and Analyze Functional Cancer Proteomic Data Using the Cancer Proteome Atlas
Supplementary Video S1 from Explore, Visualize, and Analyze Functional Cancer Proteomic Data Using the Cancer Proteome Atlas Open
Narrated instructional overview video of the proteogenomics informatics resource.
View article: Supplementary Video S1 from Explore, Visualize, and Analyze Functional Cancer Proteomic Data Using the Cancer Proteome Atlas
Supplementary Video S1 from Explore, Visualize, and Analyze Functional Cancer Proteomic Data Using the Cancer Proteome Atlas Open
Narrated instructional overview video of the proteogenomics informatics resource.
View article: Data from Explore, Visualize, and Analyze Functional Cancer Proteomic Data Using the Cancer Proteome Atlas
Data from Explore, Visualize, and Analyze Functional Cancer Proteomic Data Using the Cancer Proteome Atlas Open
Reverse-phase protein arrays (RPPA) represent a powerful functional proteomic approach to elucidate cancer-related molecular mechanisms and to develop novel cancer therapies. To facilitate community-based investigation of the large-scale p…
View article: Data from Explore, Visualize, and Analyze Functional Cancer Proteomic Data Using the Cancer Proteome Atlas
Data from Explore, Visualize, and Analyze Functional Cancer Proteomic Data Using the Cancer Proteome Atlas Open
Reverse-phase protein arrays (RPPA) represent a powerful functional proteomic approach to elucidate cancer-related molecular mechanisms and to develop novel cancer therapies. To facilitate community-based investigation of the large-scale p…
View article: Supplementary Video 1 from A Galaxy Implementation of Next-Generation Clustered Heatmaps for Interactive Exploration of Molecular Profiling Data
Supplementary Video 1 from A Galaxy Implementation of Next-Generation Clustered Heatmaps for Interactive Exploration of Molecular Profiling Data Open
Key interactive capabilities of NG-CHMs
View article: Supplementary Figure S1 from A Galaxy Implementation of Next-Generation Clustered Heatmaps for Interactive Exploration of Molecular Profiling Data
Supplementary Figure S1 from A Galaxy Implementation of Next-Generation Clustered Heatmaps for Interactive Exploration of Molecular Profiling Data Open
Figure showing the NG-CHM Generator in the Galaxy bioinformatics platform.
View article: Supplementary Video 2 from A Galaxy Implementation of Next-Generation Clustered Heatmaps for Interactive Exploration of Molecular Profiling Data
Supplementary Video 2 from A Galaxy Implementation of Next-Generation Clustered Heatmaps for Interactive Exploration of Molecular Profiling Data Open
NG-CHMs within Galaxy
View article: Supplementary Figure S1 from A Galaxy Implementation of Next-Generation Clustered Heatmaps for Interactive Exploration of Molecular Profiling Data
Supplementary Figure S1 from A Galaxy Implementation of Next-Generation Clustered Heatmaps for Interactive Exploration of Molecular Profiling Data Open
Figure showing the NG-CHM Generator in the Galaxy bioinformatics platform.
View article: Supplementary Video 2 from A Galaxy Implementation of Next-Generation Clustered Heatmaps for Interactive Exploration of Molecular Profiling Data
Supplementary Video 2 from A Galaxy Implementation of Next-Generation Clustered Heatmaps for Interactive Exploration of Molecular Profiling Data Open
NG-CHMs within Galaxy
View article: Data from A Galaxy Implementation of Next-Generation Clustered Heatmaps for Interactive Exploration of Molecular Profiling Data
Data from A Galaxy Implementation of Next-Generation Clustered Heatmaps for Interactive Exploration of Molecular Profiling Data Open
Clustered heatmaps are the most frequently used graphics for visualization of molecular profiling data in biology. However, they are generally rendered as static, or only modestly interactive, images. We have now used recent advances in we…
View article: Supplementary Video 1 from A Galaxy Implementation of Next-Generation Clustered Heatmaps for Interactive Exploration of Molecular Profiling Data
Supplementary Video 1 from A Galaxy Implementation of Next-Generation Clustered Heatmaps for Interactive Exploration of Molecular Profiling Data Open
Key interactive capabilities of NG-CHMs
View article: WITHDRAWN
WITHDRAWN Open
View article: T-Cell Lymphoma Masquerading as Cellular Mediated Rejection in a Heart Transplant Patient
T-Cell Lymphoma Masquerading as Cellular Mediated Rejection in a Heart Transplant Patient Open
View article: An IROA Workflow for correction and normalization of ion suppression in mass spectrometry-based metabolomic profiling data
An IROA Workflow for correction and normalization of ion suppression in mass spectrometry-based metabolomic profiling data Open
View article: RETRACTED: Liu et al. Prediction of Ovarian Cancer Response to Therapy Based on Deep Learning Analysis of Histopathology Images. Cancers 2023, 15, 4044
RETRACTED: Liu et al. Prediction of Ovarian Cancer Response to Therapy Based on Deep Learning Analysis of Histopathology Images. Cancers 2023, 15, 4044 Open
The journal and authors wish to retract the article entitled ‘Prediction of Ovarian Cancer Response to Therapy Based on Deep Learning Analysis of Histopathology Images’ cited above [...]
View article: PCA-Plus: Enhanced principal component analysis with illustrative applications to batch effects and their quantitation
PCA-Plus: Enhanced principal component analysis with illustrative applications to batch effects and their quantitation Open
Background Principal component analysis (PCA), a standard approach to analysis and visualization of large datasets, is commonly used in biomedical research for detecting similarities and differences among groups of samples. We initially us…
View article: DeMixSC: a deconvolution framework that uses single-cell sequencing plus a small benchmark dataset for improved analysis of cell-type ratios in complex tissue samples
DeMixSC: a deconvolution framework that uses single-cell sequencing plus a small benchmark dataset for improved analysis of cell-type ratios in complex tissue samples Open
Bulk deconvolution with single-cell/nucleus RNA-seq data is critical for understanding heterogeneity in complex biological samples, yet the technological discrepancy across sequencing platforms limits deconvolution accuracy. To address thi…
View article: RETRACTED: Prediction of Ovarian Cancer Response to Therapy Based on Deep Learning Analysis of Histopathology Images
RETRACTED: Prediction of Ovarian Cancer Response to Therapy Based on Deep Learning Analysis of Histopathology Images Open
Background: Ovarian cancer remains the leading gynecological cause of cancer mortality. Predicting the sensitivity of ovarian cancer to chemotherapy at the time of pathological diagnosis is a goal of precision medicine research that we hav…
View article: Ether phospholipids are required for mitochondrial reactive oxygen species homeostasis
Ether phospholipids are required for mitochondrial reactive oxygen species homeostasis Open
Mitochondria are hubs where bioenergetics, redox homeostasis, and anabolic metabolism pathways integrate through a tightly coordinated flux of metabolites. The contributions of mitochondrial metabolism to tumor growth and therapy resistanc…
View article: Data from Proteomic Profiling Identifies Dysregulated Pathways in Small Cell Lung Cancer and Novel Therapeutic Targets Including PARP1
Data from Proteomic Profiling Identifies Dysregulated Pathways in Small Cell Lung Cancer and Novel Therapeutic Targets Including PARP1 Open
Small cell lung cancer (SCLC) is an aggressive malignancy distinct from non–small cell lung cancer (NSCLC) in its metastatic potential and treatment response. Using an integrative proteomic and transcriptomic analysis, we investigated mole…