Sri Ramya Donepudi
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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: Antimicrobial mitochondrial reactive oxygen species induction by lung epithelial immunometabolic modulation
Antimicrobial mitochondrial reactive oxygen species induction by lung epithelial immunometabolic modulation Open
Pneumonia is a worldwide threat, making discovery of novel means to combat lower respiratory tract infection an urgent need. Manipulating the lungs’ intrinsic host defenses by therapeutic delivery of certain pathogen-associated molecular p…
View article: Meta-omics profiling of the gut-lung axis illuminates metabolic networks and host-microbial interactions associated with elevated lung elastance in a murine model of obese allergic asthma
Meta-omics profiling of the gut-lung axis illuminates metabolic networks and host-microbial interactions associated with elevated lung elastance in a murine model of obese allergic asthma Open
Obesity and associated changes to the gut microbiome worsen airway inflammation and hyperresponsiveness in asthma. Obesogenic host-microbial metabolomes have altered production of metabolites that may influence lung function and inflammato…
View article: Supplementary Table S2 from Multi-omics Integration Analysis Robustly Predicts High-Grade Patient Survival and Identifies CPT1B Effect on Fatty Acid Metabolism in Bladder Cancer
Supplementary Table S2 from Multi-omics Integration Analysis Robustly Predicts High-Grade Patient Survival and Identifies CPT1B Effect on Fatty Acid Metabolism in Bladder Cancer Open
Supplementary Table S2. List of gene-specific primers used for q-PCR.
View article: Supplementary Table S2 from Multi-omics Integration Analysis Robustly Predicts High-Grade Patient Survival and Identifies CPT1B Effect on Fatty Acid Metabolism in Bladder Cancer
Supplementary Table S2 from Multi-omics Integration Analysis Robustly Predicts High-Grade Patient Survival and Identifies CPT1B Effect on Fatty Acid Metabolism in Bladder Cancer Open
Supplementary Table S2. List of gene-specific primers used for q-PCR.
View article: Supplemental legend from Multi-omics Integration Analysis Robustly Predicts High-Grade Patient Survival and Identifies CPT1B Effect on Fatty Acid Metabolism in Bladder Cancer
Supplemental legend from Multi-omics Integration Analysis Robustly Predicts High-Grade Patient Survival and Identifies CPT1B Effect on Fatty Acid Metabolism in Bladder Cancer Open
Supplemental legend
View article: Supplementary Figure S5 from Multi-omics Integration Analysis Robustly Predicts High-Grade Patient Survival and Identifies CPT1B Effect on Fatty Acid Metabolism in Bladder Cancer
Supplementary Figure S5 from Multi-omics Integration Analysis Robustly Predicts High-Grade Patient Survival and Identifies CPT1B Effect on Fatty Acid Metabolism in Bladder Cancer Open
Supplementary Figure S5. A) Survival analysis of the upregulated (11/27) gene signature in high grade BLCA from the Kim, Lindgren, Sjodahl, and TCGA coherts. B) Survival analysis of the upregulated (11/27) gene signature in low grade BLCA …
View article: Supplementary Figure S8 from Multi-omics Integration Analysis Robustly Predicts High-Grade Patient Survival and Identifies CPT1B Effect on Fatty Acid Metabolism in Bladder Cancer
Supplementary Figure S8 from Multi-omics Integration Analysis Robustly Predicts High-Grade Patient Survival and Identifies CPT1B Effect on Fatty Acid Metabolism in Bladder Cancer Open
Supplementary Figure S8. A) FAO activity in BLCA cell lines upon CPTB overexpression. B) mRNA expression of ATP8B2 and PLA2G4C in patients with BLCA and BLCA cell lines of different grades. mRNA levels were normalized to GAPDH internal con…
View article: Supplementary Table S7 from Multi-omics Integration Analysis Robustly Predicts High-Grade Patient Survival and Identifies CPT1B Effect on Fatty Acid Metabolism in Bladder Cancer
Supplementary Table S7 from Multi-omics Integration Analysis Robustly Predicts High-Grade Patient Survival and Identifies CPT1B Effect on Fatty Acid Metabolism in Bladder Cancer Open
Supplementary Table S7. Univariate and multivariate Cox proportional hazard regression models of the TCGA (A), Lindgren (B), Sjodahl (C), and Kim (D), data sets using CPT1B gene expression. Univariate Cox proportional hazard regression ana…
View article: Supplementary Tble S3 from Multi-omics Integration Analysis Robustly Predicts High-Grade Patient Survival and Identifies CPT1B Effect on Fatty Acid Metabolism in Bladder Cancer
Supplementary Tble S3 from Multi-omics Integration Analysis Robustly Predicts High-Grade Patient Survival and Identifies CPT1B Effect on Fatty Acid Metabolism in Bladder Cancer Open
Supplementary Table S3. Patient characteristics of bladder specimens used for the metabolomics and lipidomics profiling.
View article: Supplementary Figure S2 from Multi-omics Integration Analysis Robustly Predicts High-Grade Patient Survival and Identifies CPT1B Effect on Fatty Acid Metabolism in Bladder Cancer
Supplementary Figure S2 from Multi-omics Integration Analysis Robustly Predicts High-Grade Patient Survival and Identifies CPT1B Effect on Fatty Acid Metabolism in Bladder Cancer Open
Supplementary Figure S2. Chromatographic reproducibility of metabolomics of liver samples over three technical replicates identified by LC-MS using HILIC positive, HILIC negative, and reverse phase positive ionization modes. B) Chromatogra…
View article: Supplemental legend from Multi-omics Integration Analysis Robustly Predicts High-Grade Patient Survival and Identifies CPT1B Effect on Fatty Acid Metabolism in Bladder Cancer
Supplemental legend from Multi-omics Integration Analysis Robustly Predicts High-Grade Patient Survival and Identifies CPT1B Effect on Fatty Acid Metabolism in Bladder Cancer Open
Supplemental legend
View article: Supplementary Table S8. from Multi-omics Integration Analysis Robustly Predicts High-Grade Patient Survival and Identifies CPT1B Effect on Fatty Acid Metabolism in Bladder Cancer
Supplementary Table S8. from Multi-omics Integration Analysis Robustly Predicts High-Grade Patient Survival and Identifies CPT1B Effect on Fatty Acid Metabolism in Bladder Cancer Open
Supplementary Table S8. Patient characteristics of bladder specimens used for figure 4B, 4C, and 4G.
View article: Supplementary Figure S3 from Multi-omics Integration Analysis Robustly Predicts High-Grade Patient Survival and Identifies CPT1B Effect on Fatty Acid Metabolism in Bladder Cancer
Supplementary Figure S3 from Multi-omics Integration Analysis Robustly Predicts High-Grade Patient Survival and Identifies CPT1B Effect on Fatty Acid Metabolism in Bladder Cancer Open
Supplementary Figure S3. Flowchart of data acquisition for metabolites after unbiased metabolomics and lipidomics.
View article: Supplementary Table S6 from Multi-omics Integration Analysis Robustly Predicts High-Grade Patient Survival and Identifies CPT1B Effect on Fatty Acid Metabolism in Bladder Cancer
Supplementary Table S6 from Multi-omics Integration Analysis Robustly Predicts High-Grade Patient Survival and Identifies CPT1B Effect on Fatty Acid Metabolism in Bladder Cancer Open
Supplementary Table S6. Univariate and multivariate Cox proportional hazard regression models of the 27-gene signature using the Kim (A), Lindgren (B), Sjodahl (C), and TCGA (D) data sets. Univariate Cox proportional hazard regression anal…
View article: Supplementary Table S4 from Multi-omics Integration Analysis Robustly Predicts High-Grade Patient Survival and Identifies CPT1B Effect on Fatty Acid Metabolism in Bladder Cancer
Supplementary Table S4 from Multi-omics Integration Analysis Robustly Predicts High-Grade Patient Survival and Identifies CPT1B Effect on Fatty Acid Metabolism in Bladder Cancer Open
Supplementary Table S4. List of 519 differential metabolites, m/z, log fold change, and linear fold change.
View article: Supplementary Table S1 from Multi-omics Integration Analysis Robustly Predicts High-Grade Patient Survival and Identifies CPT1B Effect on Fatty Acid Metabolism in Bladder Cancer
Supplementary Table S1 from Multi-omics Integration Analysis Robustly Predicts High-Grade Patient Survival and Identifies CPT1B Effect on Fatty Acid Metabolism in Bladder Cancer Open
Supplementary Table S1. List of internal standards for metabololomics and lipidomics, spiked across the various profiling platforms.
View article: Supplementary Table S1 from Multi-omics Integration Analysis Robustly Predicts High-Grade Patient Survival and Identifies CPT1B Effect on Fatty Acid Metabolism in Bladder Cancer
Supplementary Table S1 from Multi-omics Integration Analysis Robustly Predicts High-Grade Patient Survival and Identifies CPT1B Effect on Fatty Acid Metabolism in Bladder Cancer Open
Supplementary Table S1. List of internal standards for metabololomics and lipidomics, spiked across the various profiling platforms.
View article: Supplementary Figure S8 from Multi-omics Integration Analysis Robustly Predicts High-Grade Patient Survival and Identifies CPT1B Effect on Fatty Acid Metabolism in Bladder Cancer
Supplementary Figure S8 from Multi-omics Integration Analysis Robustly Predicts High-Grade Patient Survival and Identifies CPT1B Effect on Fatty Acid Metabolism in Bladder Cancer Open
Supplementary Figure S8. A) FAO activity in BLCA cell lines upon CPTB overexpression. B) mRNA expression of ATP8B2 and PLA2G4C in patients with BLCA and BLCA cell lines of different grades. mRNA levels were normalized to GAPDH internal con…
View article: Supplementary Figure S6 from Multi-omics Integration Analysis Robustly Predicts High-Grade Patient Survival and Identifies CPT1B Effect on Fatty Acid Metabolism in Bladder Cancer
Supplementary Figure S6 from Multi-omics Integration Analysis Robustly Predicts High-Grade Patient Survival and Identifies CPT1B Effect on Fatty Acid Metabolism in Bladder Cancer Open
Supplementary Figure S6. Survival analysis of individual downregulated genes showed poor prognosis associated with CPT1B and PIGB in the Lindgren and Sjodahl cohorts; PLA2G4A in the Lindgren cohort; PIGV in the Kim and Sjodahl cohorts; ATP…
View article: Supplementary Table S4 from Multi-omics Integration Analysis Robustly Predicts High-Grade Patient Survival and Identifies CPT1B Effect on Fatty Acid Metabolism in Bladder Cancer
Supplementary Table S4 from Multi-omics Integration Analysis Robustly Predicts High-Grade Patient Survival and Identifies CPT1B Effect on Fatty Acid Metabolism in Bladder Cancer Open
Supplementary Table S4. List of 519 differential metabolites, m/z, log fold change, and linear fold change.
View article: Supplement Table S5 from Multi-omics Integration Analysis Robustly Predicts High-Grade Patient Survival and Identifies CPT1B Effect on Fatty Acid Metabolism in Bladder Cancer
Supplement Table S5 from Multi-omics Integration Analysis Robustly Predicts High-Grade Patient Survival and Identifies CPT1B Effect on Fatty Acid Metabolism in Bladder Cancer Open
Supplement Table S5. List of differential lipids and their classification.
View article: Supplementary Figure S3 from Multi-omics Integration Analysis Robustly Predicts High-Grade Patient Survival and Identifies CPT1B Effect on Fatty Acid Metabolism in Bladder Cancer
Supplementary Figure S3 from Multi-omics Integration Analysis Robustly Predicts High-Grade Patient Survival and Identifies CPT1B Effect on Fatty Acid Metabolism in Bladder Cancer Open
Supplementary Figure S3. Flowchart of data acquisition for metabolites after unbiased metabolomics and lipidomics.
View article: Data from Multi-omics Integration Analysis Robustly Predicts High-Grade Patient Survival and Identifies CPT1B Effect on Fatty Acid Metabolism in Bladder Cancer
Data from Multi-omics Integration Analysis Robustly Predicts High-Grade Patient Survival and Identifies CPT1B Effect on Fatty Acid Metabolism in Bladder Cancer Open
Purpose:The perturbation of metabolic pathways in high-grade bladder cancer has not been investigated. We aimed to identify a metabolic signature in high-grade bladder cancer by integrating unbiased metabolomics, lipidomics, and transcript…
View article: Supplementary Table S7 from Multi-omics Integration Analysis Robustly Predicts High-Grade Patient Survival and Identifies CPT1B Effect on Fatty Acid Metabolism in Bladder Cancer
Supplementary Table S7 from Multi-omics Integration Analysis Robustly Predicts High-Grade Patient Survival and Identifies CPT1B Effect on Fatty Acid Metabolism in Bladder Cancer Open
Supplementary Table S7. Univariate and multivariate Cox proportional hazard regression models of the TCGA (A), Lindgren (B), Sjodahl (C), and Kim (D), data sets using CPT1B gene expression. Univariate Cox proportional hazard regression ana…
View article: Supplementary Figure S1 from Multi-omics Integration Analysis Robustly Predicts High-Grade Patient Survival and Identifies CPT1B Effect on Fatty Acid Metabolism in Bladder Cancer
Supplementary Figure S1 from Multi-omics Integration Analysis Robustly Predicts High-Grade Patient Survival and Identifies CPT1B Effect on Fatty Acid Metabolism in Bladder Cancer Open
Supplementary Figure S1. A) Quality control of 519 metabolites across three biological replicates of pooled liver sample extracts and run in hydrophilic interaction liquid chromatography (HILIC) positive, HILIC negative, and reverse phase …
View article: Supplementary Table S8. from Multi-omics Integration Analysis Robustly Predicts High-Grade Patient Survival and Identifies CPT1B Effect on Fatty Acid Metabolism in Bladder Cancer
Supplementary Table S8. from Multi-omics Integration Analysis Robustly Predicts High-Grade Patient Survival and Identifies CPT1B Effect on Fatty Acid Metabolism in Bladder Cancer Open
Supplementary Table S8. Patient characteristics of bladder specimens used for figure 4B, 4C, and 4G.
View article: Supplementary Figure S5 from Multi-omics Integration Analysis Robustly Predicts High-Grade Patient Survival and Identifies CPT1B Effect on Fatty Acid Metabolism in Bladder Cancer
Supplementary Figure S5 from Multi-omics Integration Analysis Robustly Predicts High-Grade Patient Survival and Identifies CPT1B Effect on Fatty Acid Metabolism in Bladder Cancer Open
Supplementary Figure S5. A) Survival analysis of the upregulated (11/27) gene signature in high grade BLCA from the Kim, Lindgren, Sjodahl, and TCGA coherts. B) Survival analysis of the upregulated (11/27) gene signature in low grade BLCA …
View article: Supplementary Figure S4 from Multi-omics Integration Analysis Robustly Predicts High-Grade Patient Survival and Identifies CPT1B Effect on Fatty Acid Metabolism in Bladder Cancer
Supplementary Figure S4 from Multi-omics Integration Analysis Robustly Predicts High-Grade Patient Survival and Identifies CPT1B Effect on Fatty Acid Metabolism in Bladder Cancer Open
Supplementary Figure S4. A) Survival analysis of the upregulated (11/27) gene signature in high grade BLCA from the Kim, Lindgren, Sjodahl, and TCGA coherts. B) Survival analysis of the upregulated (11/27) gene signature in low grade BLCA …