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View article: 1241 Self-supervised representation learning enables genomic pediction at single-organoid resolution
1241 Self-supervised representation learning enables genomic pediction at single-organoid resolution Open
View article: Methods to Measure NLR Oligomerization I: Size Exclusion Chromatography, Co-immunoprecipitation, and Cross-Linking
Methods to Measure NLR Oligomerization I: Size Exclusion Chromatography, Co-immunoprecipitation, and Cross-Linking Open
View article: 1283 Applying machine vision to empower preclinical development of immunotherapies in patient-derived organoid models of solid tumors
1283 Applying machine vision to empower preclinical development of immunotherapies in patient-derived organoid models of solid tumors Open
Background Paradigm shifting next-generation immuno-oncology therapeutics such as CAR-T cells and bispecific engagers are rapidly gaining interest as investigational therapies. However, the discovery and preclinical development of these th…
View article: Integration of tumor extrinsic and intrinsic features associates with immunotherapy response in non-small cell lung cancer
Integration of tumor extrinsic and intrinsic features associates with immunotherapy response in non-small cell lung cancer Open
The efficacy of immune checkpoint blockade (ICB) varies greatly among metastatic non-small cell lung cancer (NSCLC) patients. Loss of heterozygosity at the HLA-I locus (HLA-LOH) has been identified as an important immune escape mechanism. …
View article: Correction: Refining colorectal cancer classification and clinical stratification through a single-cell atlas
Correction: Refining colorectal cancer classification and clinical stratification through a single-cell atlas Open
View article: Refining colorectal cancer classification and clinical stratification through a single-cell atlas
Refining colorectal cancer classification and clinical stratification through a single-cell atlas Open
View article: Additional file 7 of Refining colorectal cancer classification and clinical stratification through a single-cell atlas
Additional file 7 of Refining colorectal cancer classification and clinical stratification through a single-cell atlas Open
Additional file 7: Table S6. List of significant differentially expressed genes from Fibroblast.
View article: Additional file 3 of Refining colorectal cancer classification and clinical stratification through a single-cell atlas
Additional file 3 of Refining colorectal cancer classification and clinical stratification through a single-cell atlas Open
Additional file 3: Table S2. Cell count by cell type and patient from stromal, immune and Epithelial compartments.
View article: Additional file 8 of Refining colorectal cancer classification and clinical stratification through a single-cell atlas
Additional file 8 of Refining colorectal cancer classification and clinical stratification through a single-cell atlas Open
Additional file 8: Table S7. The P-values for pairwise t-tests comparisons (with Benjamani-Hochberg correction) of cell abundance across CMS.
View article: Additional file 6 of Refining colorectal cancer classification and clinical stratification through a single-cell atlas
Additional file 6 of Refining colorectal cancer classification and clinical stratification through a single-cell atlas Open
Additional file 6: Table S5. List of significant Pseudo Bulk differentially expressed genes in CMS from malignant cells.
View article: Additional file 12 of Refining colorectal cancer classification and clinical stratification through a single-cell atlas
Additional file 12 of Refining colorectal cancer classification and clinical stratification through a single-cell atlas Open
Additional file 12: Table S11. List of proportional hazard assumption ratio for survival from the samples in GSE17536 [45] and GSE39582 [48.
View article: Additional file 10 of Refining colorectal cancer classification and clinical stratification through a single-cell atlas
Additional file 10 of Refining colorectal cancer classification and clinical stratification through a single-cell atlas Open
Additional file 10: Table S9. List of significant differentially expressed genes from T-cells.
View article: Additional file 9 of Refining colorectal cancer classification and clinical stratification through a single-cell atlas
Additional file 9 of Refining colorectal cancer classification and clinical stratification through a single-cell atlas Open
Additional file 9: Table S8. List of significant differentially expressed genes from Myeloid cells.
View article: Additional file 2 of Refining colorectal cancer classification and clinical stratification through a single-cell atlas
Additional file 2 of Refining colorectal cancer classification and clinical stratification through a single-cell atlas Open
Additional file 2: Table S1. Patient information, CMS classification and mutational status.
View article: Additional file 5 of Refining colorectal cancer classification and clinical stratification through a single-cell atlas
Additional file 5 of Refining colorectal cancer classification and clinical stratification through a single-cell atlas Open
Additional file 5: Table S4. Cell count by CMS subtype and patient from Epithelial compartments of Lee et al. 2020 [18] data and Our CRC data.
View article: Additional file 4 of Refining colorectal cancer classification and clinical stratification through a single-cell atlas
Additional file 4 of Refining colorectal cancer classification and clinical stratification through a single-cell atlas Open
Additional file 4: Table S3. Cell counts by cell subtypes and samples from stromal and immune and epithelial compartments.
View article: Additional file 14 of Refining colorectal cancer classification and clinical stratification through a single-cell atlas
Additional file 14 of Refining colorectal cancer classification and clinical stratification through a single-cell atlas Open
Additional file 14: Table S13. Pathway analysis on the customized collection of 51 CRC-related gene sets.
View article: Additional file 13 of Refining colorectal cancer classification and clinical stratification through a single-cell atlas
Additional file 13 of Refining colorectal cancer classification and clinical stratification through a single-cell atlas Open
Additional file 13: Table S12. Multivariate-Cox regression analysis.
View article: Additional file 11 of Refining colorectal cancer classification and clinical stratification through a single-cell atlas
Additional file 11 of Refining colorectal cancer classification and clinical stratification through a single-cell atlas Open
Additional file 11: Table S10. Continuous subtype scoring across cell type (GSE39582 [45], GSE17536 [48]).
View article: 62 Applying machine vision to empower preclinical development of cell engager and adoptive cell therapeutics in patient-derived organoid models of solid tumors
62 Applying machine vision to empower preclinical development of cell engager and adoptive cell therapeutics in patient-derived organoid models of solid tumors Open
Background Cell engager and adoptive cell therapeutics have emerged as efficacious and durable treatments in patients with B-cell malignancies. Though many analogous strategies are under development in solid tumors, none have received appr…
View article: Redefining colorectal cancer classification and clinical stratification through a single-cell atlas
Redefining colorectal cancer classification and clinical stratification through a single-cell atlas Open
Colorectal cancer (CRC), a disease of high incidence and mortality, has had few treatment advances owing to a large degree of inter- and intratumoral heterogeneity. Attempts to classify subtypes of colorectal cancer to develop treatment st…
View article: An in vitro model of hepatic steatosis using lipid loaded induced pluripotent stem cell derived hepatocyte like cells
An in vitro model of hepatic steatosis using lipid loaded induced pluripotent stem cell derived hepatocyte like cells Open
Hepatic steatosis is a metabolic disease, characterized by selective and progressive accumulation of lipids in liver, leading to progressive non-alcoholic fatty liver disease (NAFLD), non-alcoholic steatohepatitis (NASH), and cirrhosis. Th…
View article: The PYRIN domain-only protein POP2 inhibits inflammasome priming and activation
The PYRIN domain-only protein POP2 inhibits inflammasome priming and activation Open
View article: Lymphocytic hypophysitis in nonpregnant middle-aged females mimicking pituitary adenoma
Lymphocytic hypophysitis in nonpregnant middle-aged females mimicking pituitary adenoma Open
View article: Measuring NLR Oligomerization I: Size Exclusion Chromatography, Co-immunoprecipitation, and Cross-Linking
Measuring NLR Oligomerization I: Size Exclusion Chromatography, Co-immunoprecipitation, and Cross-Linking Open
View article: Conditional deletion of caspase-8 in macrophages alters macrophage activation in a RIPK-dependent manner
Conditional deletion of caspase-8 in macrophages alters macrophage activation in a RIPK-dependent manner Open
These data demonstrate that caspase-8 functions uniquely in macrophages by controlling the response to TLR activation and macrophage polarization in an RIPK-dependent manner.
View article: The PYRIN Domain-only Protein POP1 Inhibits Inflammasome Assembly and Ameliorates Inflammatory Disease
The PYRIN Domain-only Protein POP1 Inhibits Inflammasome Assembly and Ameliorates Inflammatory Disease Open
View article: Additional file 2: Table S2. of Conditional deletion of caspase-8 in macrophages alters macrophage activation in a RIPK-dependent manner
Additional file 2: Table S2. of Conditional deletion of caspase-8 in macrophages alters macrophage activation in a RIPK-dependent manner Open
ANOVA comparison data from Affymetrix QuantiGene 2.0 custom panel 21522 for analysis of macrophage polarization. (XLS 68 kb)