Rohit Chandwani
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View article: Stochastic Activation of Enhancers in the Innate Immune Response by the Histone Demethylase JMJD2D
Stochastic Activation of Enhancers in the Innate Immune Response by the Histone Demethylase JMJD2D Open
The architecture of chromatin is complex and plays a substantial role in all of the biological processes involving DNA. In particular, transcriptional activation depends on the interplay of dozens of chromatin modifiers to establish an epi…
View article: The Spatial Atlas of Human Anatomy (SAHA): A Multimodal Subcellular-Resolution Reference Across Human Organs
The Spatial Atlas of Human Anatomy (SAHA): A Multimodal Subcellular-Resolution Reference Across Human Organs Open
The Spatial Atlas of Human Anatomy (SAHA) represents the first multimodal, subcellular- resolution reference of healthy adult human tissues across multiple organ systems. Integrating spatial transcriptomics, proteomics, and histological fe…
View article: Molecular dynamics driving phenotypic divergence among KRAS mutants in pancreatic tumorigenesis
Molecular dynamics driving phenotypic divergence among KRAS mutants in pancreatic tumorigenesis Open
Inflammation in the pancreas drives acinar-to-ductal metaplasia (ADM), a progenitor-like state that can be hijacked by mutant Kras in the formation of pancreatic cancer (PDAC). How these cell fate decisions vary according to KRAS mutation …
View article: Pan-Cancer PDOs Preserve Tumor Heterogeneity and Uncover Therapeutic Vulnerabilities
Pan-Cancer PDOs Preserve Tumor Heterogeneity and Uncover Therapeutic Vulnerabilities Open
We developed a tumor-matched, pan-cancer patient-derived organoid (PDO) platform comprising 220 PDOs from 190 patients across 15 cancer types to advance functional precision oncology. Our comprehensively characterized PDOs showed 93% histo…
View article: PRRX1 Has Functional Roles in Pancreatic Acinar to Ductal Metaplasia and Carcinogenesis
PRRX1 Has Functional Roles in Pancreatic Acinar to Ductal Metaplasia and Carcinogenesis Open
View article: FRA1 controls acinar cell plasticity during murine Kras-induced pancreatic acinar to ductal metaplasia
FRA1 controls acinar cell plasticity during murine Kras-induced pancreatic acinar to ductal metaplasia Open
View article: Supplementary Figure S1 from A Novel Approach to Quantify Heterogeneity of Intrahepatic Cholangiocarcinoma: The Hidden-Genome Classifier
Supplementary Figure S1 from A Novel Approach to Quantify Heterogeneity of Intrahepatic Cholangiocarcinoma: The Hidden-Genome Classifier Open
Supplementary Figure S1 One-versus-rest precision-recall area under the curve (AUC) of each class and the overall accuracy of the three-class model (A) and the two-class model (B). EHC: extrahepatic cholangiocarcinoma; GBC: gallbladder can…
View article: Supplementary Table S8 from A Novel Approach to Quantify Heterogeneity of Intrahepatic Cholangiocarcinoma: The Hidden-Genome Classifier
Supplementary Table S8 from A Novel Approach to Quantify Heterogeneity of Intrahepatic Cholangiocarcinoma: The Hidden-Genome Classifier Open
Histologic subtypes of biliary-class and HCC-class intrahepatic cholangiocarcinoma (IHC).
View article: Supplementary Table S1 from A Novel Approach to Quantify Heterogeneity of Intrahepatic Cholangiocarcinoma: The Hidden-Genome Classifier
Supplementary Table S1 from A Novel Approach to Quantify Heterogeneity of Intrahepatic Cholangiocarcinoma: The Hidden-Genome Classifier Open
Genes (n = 341) common to all MSK-IMPACT panels.
View article: Data from A Novel Approach to Quantify Heterogeneity of Intrahepatic Cholangiocarcinoma: The Hidden-Genome Classifier
Data from A Novel Approach to Quantify Heterogeneity of Intrahepatic Cholangiocarcinoma: The Hidden-Genome Classifier Open
Purpose:Intrahepatic cholangiocarcinoma (IHC) is a heterogeneous tumor. The hidden-genome classifier, a supervised machine learning–based algorithm, was used to quantify tumor heterogeneity and improve classification.Experimental Design:A …
View article: Supplementary Figure S3 from A Novel Approach to Quantify Heterogeneity of Intrahepatic Cholangiocarcinoma: The Hidden-Genome Classifier
Supplementary Figure S3 from A Novel Approach to Quantify Heterogeneity of Intrahepatic Cholangiocarcinoma: The Hidden-Genome Classifier Open
Supplementary Figure S3 Overall survival stratified by biliary class in non-resected patients (A) and resected patients (B) without IDH1 mutations or FGFR2 fusion. Interaction between the presence of any IDH1 or FGFR2 mutation and the geno…
View article: Supplementary Table S7 from A Novel Approach to Quantify Heterogeneity of Intrahepatic Cholangiocarcinoma: The Hidden-Genome Classifier
Supplementary Table S7 from A Novel Approach to Quantify Heterogeneity of Intrahepatic Cholangiocarcinoma: The Hidden-Genome Classifier Open
Incidence of IDH1 mutations and FGF2 fusions in biliary-aligned intrahepatic cholangiocarcinoma (IHC) and hepatocellular carcinoma (HCC)-aligned IHC.
View article: Supplementary Table S1 from A Novel Approach to Quantify Heterogeneity of Intrahepatic Cholangiocarcinoma: The Hidden-Genome Classifier
Supplementary Table S1 from A Novel Approach to Quantify Heterogeneity of Intrahepatic Cholangiocarcinoma: The Hidden-Genome Classifier Open
Genes (n = 341) common to all MSK-IMPACT panels.
View article: Supplementary Table S6 from A Novel Approach to Quantify Heterogeneity of Intrahepatic Cholangiocarcinoma: The Hidden-Genome Classifier
Supplementary Table S6 from A Novel Approach to Quantify Heterogeneity of Intrahepatic Cholangiocarcinoma: The Hidden-Genome Classifier Open
Incidence of the key genetic alterations observed in intrahepatic cholangiocarcinoma classified based on the biliary score.
View article: Supplementary Table S5 from A Novel Approach to Quantify Heterogeneity of Intrahepatic Cholangiocarcinoma: The Hidden-Genome Classifier
Supplementary Table S5 from A Novel Approach to Quantify Heterogeneity of Intrahepatic Cholangiocarcinoma: The Hidden-Genome Classifier Open
Comparison of clinicopathologic characteristics of IHC genomic subclasses.
View article: Supplementary Table S2 from A Novel Approach to Quantify Heterogeneity of Intrahepatic Cholangiocarcinoma: The Hidden-Genome Classifier
Supplementary Table S2 from A Novel Approach to Quantify Heterogeneity of Intrahepatic Cholangiocarcinoma: The Hidden-Genome Classifier Open
Prevalence of genes altered in 10% or more cases.
View article: Supplementary Figure S2 from A Novel Approach to Quantify Heterogeneity of Intrahepatic Cholangiocarcinoma: The Hidden-Genome Classifier
Supplementary Figure S2 from A Novel Approach to Quantify Heterogeneity of Intrahepatic Cholangiocarcinoma: The Hidden-Genome Classifier Open
Supplementary Figure S2 The genomic alterations in extrahepatic biliary tumors and hepatocellular carcinoma are visualized using two-dimensional embeddings of the lasso-selected active genetic predictors in the training data, which include…
View article: Supplementary Table S8 from A Novel Approach to Quantify Heterogeneity of Intrahepatic Cholangiocarcinoma: The Hidden-Genome Classifier
Supplementary Table S8 from A Novel Approach to Quantify Heterogeneity of Intrahepatic Cholangiocarcinoma: The Hidden-Genome Classifier Open
Histologic subtypes of biliary-class and HCC-class intrahepatic cholangiocarcinoma (IHC).
View article: Supplementary Table S2 from A Novel Approach to Quantify Heterogeneity of Intrahepatic Cholangiocarcinoma: The Hidden-Genome Classifier
Supplementary Table S2 from A Novel Approach to Quantify Heterogeneity of Intrahepatic Cholangiocarcinoma: The Hidden-Genome Classifier Open
Prevalence of genes altered in 10% or more cases.
View article: Supplementary Table S6 from A Novel Approach to Quantify Heterogeneity of Intrahepatic Cholangiocarcinoma: The Hidden-Genome Classifier
Supplementary Table S6 from A Novel Approach to Quantify Heterogeneity of Intrahepatic Cholangiocarcinoma: The Hidden-Genome Classifier Open
Incidence of the key genetic alterations observed in intrahepatic cholangiocarcinoma classified based on the biliary score.
View article: Supplementary Figure S1 from A Novel Approach to Quantify Heterogeneity of Intrahepatic Cholangiocarcinoma: The Hidden-Genome Classifier
Supplementary Figure S1 from A Novel Approach to Quantify Heterogeneity of Intrahepatic Cholangiocarcinoma: The Hidden-Genome Classifier Open
Supplementary Figure S1 One-versus-rest precision-recall area under the curve (AUC) of each class and the overall accuracy of the three-class model (A) and the two-class model (B). EHC: extrahepatic cholangiocarcinoma; GBC: gallbladder can…
View article: Supplementary Table S4 from A Novel Approach to Quantify Heterogeneity of Intrahepatic Cholangiocarcinoma: The Hidden-Genome Classifier
Supplementary Table S4 from A Novel Approach to Quantify Heterogeneity of Intrahepatic Cholangiocarcinoma: The Hidden-Genome Classifier Open
This table reports the lasso-selected active genetic predictors of the hidden-genome model. The predictive power is represented by the GBC/EHC odds ratio (OR) or HCC OR. The max OR is the greater of the two values. The Shannon-Jensen impor…
View article: Supplementary Table S7 from A Novel Approach to Quantify Heterogeneity of Intrahepatic Cholangiocarcinoma: The Hidden-Genome Classifier
Supplementary Table S7 from A Novel Approach to Quantify Heterogeneity of Intrahepatic Cholangiocarcinoma: The Hidden-Genome Classifier Open
Incidence of IDH1 mutations and FGF2 fusions in biliary-aligned intrahepatic cholangiocarcinoma (IHC) and hepatocellular carcinoma (HCC)-aligned IHC.
View article: Supplementary Table S5 from A Novel Approach to Quantify Heterogeneity of Intrahepatic Cholangiocarcinoma: The Hidden-Genome Classifier
Supplementary Table S5 from A Novel Approach to Quantify Heterogeneity of Intrahepatic Cholangiocarcinoma: The Hidden-Genome Classifier Open
Comparison of clinicopathologic characteristics of IHC genomic subclasses.
View article: Supplementary Table S3 from A Novel Approach to Quantify Heterogeneity of Intrahepatic Cholangiocarcinoma: The Hidden-Genome Classifier
Supplementary Table S3 from A Novel Approach to Quantify Heterogeneity of Intrahepatic Cholangiocarcinoma: The Hidden-Genome Classifier Open
Genetic pathway alterations.
View article: Data from A Novel Approach to Quantify Heterogeneity of Intrahepatic Cholangiocarcinoma: The Hidden-Genome Classifier
Data from A Novel Approach to Quantify Heterogeneity of Intrahepatic Cholangiocarcinoma: The Hidden-Genome Classifier Open
Purpose:Intrahepatic cholangiocarcinoma (IHC) is a heterogeneous tumor. The hidden-genome classifier, a supervised machine learning–based algorithm, was used to quantify tumor heterogeneity and improve classification.Experimental Design:A …
View article: Supplementary Table S3 from A Novel Approach to Quantify Heterogeneity of Intrahepatic Cholangiocarcinoma: The Hidden-Genome Classifier
Supplementary Table S3 from A Novel Approach to Quantify Heterogeneity of Intrahepatic Cholangiocarcinoma: The Hidden-Genome Classifier Open
Genetic pathway alterations.
View article: Supplementary Table S4 from A Novel Approach to Quantify Heterogeneity of Intrahepatic Cholangiocarcinoma: The Hidden-Genome Classifier
Supplementary Table S4 from A Novel Approach to Quantify Heterogeneity of Intrahepatic Cholangiocarcinoma: The Hidden-Genome Classifier Open
This table reports the lasso-selected active genetic predictors of the hidden-genome model. The predictive power is represented by the GBC/EHC odds ratio (OR) or HCC OR. The max OR is the greater of the two values. The Shannon-Jensen impor…
View article: Supplementary Figure S2 from A Novel Approach to Quantify Heterogeneity of Intrahepatic Cholangiocarcinoma: The Hidden-Genome Classifier
Supplementary Figure S2 from A Novel Approach to Quantify Heterogeneity of Intrahepatic Cholangiocarcinoma: The Hidden-Genome Classifier Open
Supplementary Figure S2 The genomic alterations in extrahepatic biliary tumors and hepatocellular carcinoma are visualized using two-dimensional embeddings of the lasso-selected active genetic predictors in the training data, which include…
View article: Supplementary Figure S3 from A Novel Approach to Quantify Heterogeneity of Intrahepatic Cholangiocarcinoma: The Hidden-Genome Classifier
Supplementary Figure S3 from A Novel Approach to Quantify Heterogeneity of Intrahepatic Cholangiocarcinoma: The Hidden-Genome Classifier Open
Supplementary Figure S3 Overall survival stratified by biliary class in non-resected patients (A) and resected patients (B) without IDH1 mutations or FGFR2 fusion. Interaction between the presence of any IDH1 or FGFR2 mutation and the geno…