Afaf E.G. Osman
YOU?
Author Swipe
View article: Real-world outcomes associated with azacitidine and venetoclax in Myelodysplastic Syndromes
Real-world outcomes associated with azacitidine and venetoclax in Myelodysplastic Syndromes Open
Introduction: Myelodysplastic syndromes (MDS) are hematologic malignancies characterized by bone marrow failure and risk for progression to acute myeloid leukemia (AML). Treatment for MDS depends on patients' risk of transformation to AML …
View article: Epigenetic Modulation, Intratumoral Microbiome, and Immunity in Early-Onset Colorectal Cancer
Epigenetic Modulation, Intratumoral Microbiome, and Immunity in Early-Onset Colorectal Cancer Open
The incidence of colorectal cancer in young adults (age of diagnosis <50 years) has been rapidly increasing. Although ∼20% of early-onset colorectal cancer (EOCRC) cases are due to germline mutations, the etiology of the majority of EOC…
View article: DEEP LEARNING FOR MEDICAL IMAGE ANALYSIS: A REVOLUTION IN DIAGNOSTIC MEDICINE
DEEP LEARNING FOR MEDICAL IMAGE ANALYSIS: A REVOLUTION IN DIAGNOSTIC MEDICINE Open
Deep learning has revolutionized medical image analysis by enabling rapid, automated interpretation of complex imaging data. We propose a novel framework that combines a self‑configuring U‑Net backbone with integrated transformer‑style att…
View article: qcCHIP: an R package to identify clonal hematopoiesis variants using cohort-specific data characteristics
qcCHIP: an R package to identify clonal hematopoiesis variants using cohort-specific data characteristics Open
Summary Clonal hematopoiesis (CH) is a molecular biomarker associated with various adverse outcomes in both healthy individuals and those with underlying conditions, including cancer. Detecting CH usually involves genomic sequencing of ind…
View article: Predisposition to hematopoietic malignancies by deleterious germline CHEK2 variants
Predisposition to hematopoietic malignancies by deleterious germline CHEK2 variants Open
The role of germline CHEK2 variants in hematopoietic malignancies (HMs) is poorly understood. We examined pathogenic/likely pathogenic (P/LP) CHEK2 variants in patients with hereditary HMs (HHMs), a solid tumor risk cohort, public datasets…
View article: Epigenetic Modulation, Intra-tumoral Microbiome and Immunity in Early Onset Colorectal Cancer
Epigenetic Modulation, Intra-tumoral Microbiome and Immunity in Early Onset Colorectal Cancer Open
Background: The incidence of colorectal cancer (CRC) in young adults (age of diagnosis < 50 years old) has been rapidly increasing. Although ~20% of early-onset (EO) CRC cases are due to germline mutations, the etiology of the majority of …
View article: Table S2 from The Tumor Microbiome as a Predictor of Outcomes in Patients with Metastatic Melanoma Treated with Immune Checkpoint Inhibitors
Table S2 from The Tumor Microbiome as a Predictor of Outcomes in Patients with Metastatic Melanoma Treated with Immune Checkpoint Inhibitors Open
Modeling results for gene expression differences between responders and non-responders
View article: Table S5 from The Tumor Microbiome as a Predictor of Outcomes in Patients with Metastatic Melanoma Treated with Immune Checkpoint Inhibitors
Table S5 from The Tumor Microbiome as a Predictor of Outcomes in Patients with Metastatic Melanoma Treated with Immune Checkpoint Inhibitors Open
Correlations between microbe abundances and MSigDB Hallmark gene sets average Z scores
View article: Supplementary Data from The Tumor Microbiome Reacts to Hypoxia and Can Influence Response to Radiation Treatment in Colorectal Cancer
Supplementary Data from The Tumor Microbiome Reacts to Hypoxia and Can Influence Response to Radiation Treatment in Colorectal Cancer Open
Cox proportional hazards model results for the interaction terms between hypoxia (binary, low or high) with microbe relative abundance in COADREAD tumors treated with radiotherapy.
View article: Table S3 from The Tumor Microbiome as a Predictor of Outcomes in Patients with Metastatic Melanoma Treated with Immune Checkpoint Inhibitors
Table S3 from The Tumor Microbiome as a Predictor of Outcomes in Patients with Metastatic Melanoma Treated with Immune Checkpoint Inhibitors Open
Model performance of 31 published gene expression signatures for predicting immunotherapy treatment response
View article: Figure S5 from The Tumor Microbiome as a Predictor of Outcomes in Patients with Metastatic Melanoma Treated with Immune Checkpoint Inhibitors
Figure S5 from The Tumor Microbiome as a Predictor of Outcomes in Patients with Metastatic Melanoma Treated with Immune Checkpoint Inhibitors Open
Comparison of alternate machine learning methods
View article: Table S1 from The Tumor Microbiome as a Predictor of Outcomes in Patients with Metastatic Melanoma Treated with Immune Checkpoint Inhibitors
Table S1 from The Tumor Microbiome as a Predictor of Outcomes in Patients with Metastatic Melanoma Treated with Immune Checkpoint Inhibitors Open
The list of published gene signatures compared between treatment responders and non-responders and to tumor microbe abundances.
View article: Supplementary Data from The Tumor Microbiome Reacts to Hypoxia and Can Influence Response to Radiation Treatment in Colorectal Cancer
Supplementary Data from The Tumor Microbiome Reacts to Hypoxia and Can Influence Response to Radiation Treatment in Colorectal Cancer Open
Numbers at risk for the association between survival and Fusobacterium canifelinum abundance in COADREAD tumors treated with radiation.
View article: Supplementary Tables Legend from The Tumor Microbiome Reacts to Hypoxia and Can Influence Response to Radiation Treatment in Colorectal Cancer
Supplementary Tables Legend from The Tumor Microbiome Reacts to Hypoxia and Can Influence Response to Radiation Treatment in Colorectal Cancer Open
Legend for Supplementary Tables
View article: Supplementary Data from The Tumor Microbiome Reacts to Hypoxia and Can Influence Response to Radiation Treatment in Colorectal Cancer
Supplementary Data from The Tumor Microbiome Reacts to Hypoxia and Can Influence Response to Radiation Treatment in Colorectal Cancer Open
Selected log2 fold change results for microbes found to be significantly enriched in hypoxic tumors in both mice and human subjects.
View article: Supplementary Data from The Tumor Microbiome Reacts to Hypoxia and Can Influence Response to Radiation Treatment in Colorectal Cancer
Supplementary Data from The Tumor Microbiome Reacts to Hypoxia and Can Influence Response to Radiation Treatment in Colorectal Cancer Open
Log2 fold changes of annotated Cutibacterium genes between hypoxic and normoxic tumors in nude and BALB/c mice.
View article: Figure S4 from The Tumor Microbiome as a Predictor of Outcomes in Patients with Metastatic Melanoma Treated with Immune Checkpoint Inhibitors
Figure S4 from The Tumor Microbiome as a Predictor of Outcomes in Patients with Metastatic Melanoma Treated with Immune Checkpoint Inhibitors Open
Comparison with TCGA for microbes most significantly enriched in response groups
View article: Supplementary Data from The Tumor Microbiome Reacts to Hypoxia and Can Influence Response to Radiation Treatment in Colorectal Cancer
Supplementary Data from The Tumor Microbiome Reacts to Hypoxia and Can Influence Response to Radiation Treatment in Colorectal Cancer Open
Correlations between tumor microbes enriched in hypoxic tumors in both mice and humans and deconvolved immune cell abundances.
View article: Supplementary Data from The Tumor Microbiome Reacts to Hypoxia and Can Influence Response to Radiation Treatment in Colorectal Cancer
Supplementary Data from The Tumor Microbiome Reacts to Hypoxia and Can Influence Response to Radiation Treatment in Colorectal Cancer Open
Fold-changes and adjusted p-values for all microbes associated with hypoxic or normoxic tumors in the ORIEN and TCGA datasets (associated with Figure 2A). Results of survival analyses of interactions between microbes and hypoxia in COADREA…
View article: Supplemental Figure S1 from The Tumor Microbiome Reacts to Hypoxia and Can Influence Response to Radiation Treatment in Colorectal Cancer
Supplemental Figure S1 from The Tumor Microbiome Reacts to Hypoxia and Can Influence Response to Radiation Treatment in Colorectal Cancer Open
Hypoxia scores by stage (A) or sex (B) for the ORIEN radiation-treated cohort.
View article: Supplementary Data from The Tumor Microbiome Reacts to Hypoxia and Can Influence Response to Radiation Treatment in Colorectal Cancer
Supplementary Data from The Tumor Microbiome Reacts to Hypoxia and Can Influence Response to Radiation Treatment in Colorectal Cancer Open
Differences in the tumor microbes in low and high hypoxia mouse tumors.
View article: Supplementary Data from The Tumor Microbiome Reacts to Hypoxia and Can Influence Response to Radiation Treatment in Colorectal Cancer
Supplementary Data from The Tumor Microbiome Reacts to Hypoxia and Can Influence Response to Radiation Treatment in Colorectal Cancer Open
Differences in the immune cell populations, estimated by RNAseq, within high and low hypoxia mouse tumors, combining the nude and BALB/c mice.
View article: Supplementary Data from The Tumor Microbiome Reacts to Hypoxia and Can Influence Response to Radiation Treatment in Colorectal Cancer
Supplementary Data from The Tumor Microbiome Reacts to Hypoxia and Can Influence Response to Radiation Treatment in Colorectal Cancer Open
Numbers at risk for the association between low and high hypoxia in COAD and READ tumors (associated with the Kaplan-Meier curve shown in Figure 1D).
View article: Supplemental Figure S2 from The Tumor Microbiome Reacts to Hypoxia and Can Influence Response to Radiation Treatment in Colorectal Cancer
Supplemental Figure S2 from The Tumor Microbiome Reacts to Hypoxia and Can Influence Response to Radiation Treatment in Colorectal Cancer Open
Boxplots comparing immune fractions in low and high hypoxia groups in the ORIEN radiation cohort, displaying cells with significantly different abundance with an adjusted p-value <0.05.
View article: Supplementary Data from The Tumor Microbiome Reacts to Hypoxia and Can Influence Response to Radiation Treatment in Colorectal Cancer
Supplementary Data from The Tumor Microbiome Reacts to Hypoxia and Can Influence Response to Radiation Treatment in Colorectal Cancer Open
Demographic variables stratified by low and high hypoxia scores, showing no significant differences to be controlled for in the Cox proportional hazards model described in Figure 1D.
View article: Figure S1 from The Tumor Microbiome as a Predictor of Outcomes in Patients with Metastatic Melanoma Treated with Immune Checkpoint Inhibitors
Figure S1 from The Tumor Microbiome as a Predictor of Outcomes in Patients with Metastatic Melanoma Treated with Immune Checkpoint Inhibitors Open
Association of CIBERSORT cell types with the response to ICIs
View article: Supplementary Data from The Tumor Microbiome Reacts to Hypoxia and Can Influence Response to Radiation Treatment in Colorectal Cancer
Supplementary Data from The Tumor Microbiome Reacts to Hypoxia and Can Influence Response to Radiation Treatment in Colorectal Cancer Open
Differences in the immune cell populations, estimated by RNAseq, within high and low hypoxia mouse tumors, separated by mouse strain.
View article: Supplemental Figure S4 from The Tumor Microbiome Reacts to Hypoxia and Can Influence Response to Radiation Treatment in Colorectal Cancer
Supplemental Figure S4 from The Tumor Microbiome Reacts to Hypoxia and Can Influence Response to Radiation Treatment in Colorectal Cancer Open
Boxplots showing the immune cell fractions for immune cells with significantly different expression in high and low hypoxia mouse samples at p-value <0.05. No differences remained significant after correction for multiple hypothesis testin…
View article: Table S4 from The Tumor Microbiome as a Predictor of Outcomes in Patients with Metastatic Melanoma Treated with Immune Checkpoint Inhibitors
Table S4 from The Tumor Microbiome as a Predictor of Outcomes in Patients with Metastatic Melanoma Treated with Immune Checkpoint Inhibitors Open
Modeling results for the microbes enriched in the tumors responsive or not-responsive to immunotherapy
View article: Supplemental Figure S3 from The Tumor Microbiome Reacts to Hypoxia and Can Influence Response to Radiation Treatment in Colorectal Cancer
Supplemental Figure S3 from The Tumor Microbiome Reacts to Hypoxia and Can Influence Response to Radiation Treatment in Colorectal Cancer Open
Boxplot comparing Fusobacterium counts in low and high hypoxia 16s samples.