Siraj M. Ali
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View article: Deep learning predicts EGFR mutation status from histology images in non-small cell lung cancer
Deep learning predicts EGFR mutation status from histology images in non-small cell lung cancer Open
EGFR mutation screening in non-small cell lung cancer (NSCLC) remains variable globally and represents a significant care gap, despite international recommendations and molecular testing guidelines. Recently, the use of deep learning (DL) …
View article: 1347 AI-powered image-based spatial profiling of MET-mutated non-small cell lung cancer identifies immune-active MET exon 14 skipping subtypes as potential immunotherapy targets
1347 AI-powered image-based spatial profiling of MET-mutated non-small cell lung cancer identifies immune-active MET exon 14 skipping subtypes as potential immunotherapy targets Open
View article: 1098 Unveiling spatial correlation between cell surface targets and lymphocytes via artificial intelligence (AI)-powered quantitative immunohistochemistry (IHC) analysis
1098 Unveiling spatial correlation between cell surface targets and lymphocytes via artificial intelligence (AI)-powered quantitative immunohistochemistry (IHC) analysis Open
View article: Monitoring Tools in Conservative AIS Treatment: A Scoping Review Protocol
Monitoring Tools in Conservative AIS Treatment: A Scoping Review Protocol Open
View article: Collagen VII Is Associated with Airway Remodeling, Honeycombing, and Fibroblast Foci in Usual Interstitial Pneumonia/Idiopathic Pulmonary Fibrosis
Collagen VII Is Associated with Airway Remodeling, Honeycombing, and Fibroblast Foci in Usual Interstitial Pneumonia/Idiopathic Pulmonary Fibrosis Open
Collagen VII is an essential anchoring protein in the basement membrane zone, maintaining the attachment of stratified and pseudostratified epithelia to the underlying interstitial matrix. However, collagen VII is largely unexplored in nor…
View article: CORRELATION OF MULTIDETECTOR COMPUTED TOMOGRAPHY AND TRANSTHORACIC ECHOCARDIOGRAPHY IN THE DIAGNOSIS OF CONGENITAL CYANOTIC HEART DISEASES
CORRELATION OF MULTIDETECTOR COMPUTED TOMOGRAPHY AND TRANSTHORACIC ECHOCARDIOGRAPHY IN THE DIAGNOSIS OF CONGENITAL CYANOTIC HEART DISEASES Open
Background: Congenital Cyanotic Heart Diseases (CCHDs) are among the most common birth defects in newborns, with Tetralogy of Fallot (TOF) being the most frequent type, affecting about three in every 10,000 live births. Objective: This stu…
View article: A universal immunohistochemistry analyzer for generalizing AI-driven assessment of immunohistochemistry across immunostains and cancer types
A universal immunohistochemistry analyzer for generalizing AI-driven assessment of immunohistochemistry across immunostains and cancer types Open
Immunohistochemistry (IHC) is the common companion diagnostics in targeted therapies. However, quantifying protein expressions in IHC images present a significant challenge, due to variability in manual scoring and inherent subjective inte…
View article: Generalizing AI-driven Assessment of Immunohistochemistry across Immunostains and Cancer Types: A Universal Immunohistochemistry Analyzer
Generalizing AI-driven Assessment of Immunohistochemistry across Immunostains and Cancer Types: A Universal Immunohistochemistry Analyzer Open
Despite advancements in methodologies, immunohistochemistry (IHC) remains the most utilized ancillary test for histopathologic and companion diagnostics in targeted therapies. However, objective IHC assessment poses challenges. Artificial …
View article: Generalizing AI-driven Assessment of Immunohistochemistry across Immunostains and Cancer Types: A Universal Immunohistochemistry Analyzer
Generalizing AI-driven Assessment of Immunohistochemistry across Immunostains and Cancer Types: A Universal Immunohistochemistry Analyzer Open
Despite advancements in methodologies, immunohistochemistry (IHC) remains the most utilized ancillary test for histopathologic and companion diagnostics in targeted therapies. However, objective IHC assessment poses challenges. Artificial …
View article: Patient-specific 3D in vitro modeling and fluid dynamic analysis of primary pulmonary vein stenosis
Patient-specific 3D in vitro modeling and fluid dynamic analysis of primary pulmonary vein stenosis Open
Introduction Primary pulmonary vein stenosis (PVS) is a rare congenital heart disease that proves to be a clinical challenge due to the rapidly progressive disease course and high rates of treatment complications. PVS intervention is frequ…
View article: Augmented interpretation of HER2, ER, and PR in breast cancer by artificial intelligence analyzer: enhancing interobserver agreement through a reader study of 201 cases
Augmented interpretation of HER2, ER, and PR in breast cancer by artificial intelligence analyzer: enhancing interobserver agreement through a reader study of 201 cases Open
Background Accurate classification of breast cancer molecular subtypes is crucial in determining treatment strategies and predicting clinical outcomes. This classification largely depends on the assessment of human epidermal growth factor …
View article: Inflamed immune phenotype predicts favorable clinical outcomes of immune checkpoint inhibitor therapy across multiple cancer types
Inflamed immune phenotype predicts favorable clinical outcomes of immune checkpoint inhibitor therapy across multiple cancer types Open
Background The inflamed immune phenotype (IIP), defined by enrichment of tumor-infiltrating lymphocytes (TILs) within intratumoral areas, is a promising tumor-agnostic biomarker of response to immune checkpoint inhibitor (ICI) therapy. How…
View article: Generalizing AI-Driven Assessment of Immunohistochemistry Across Immunostains and Cancer Types: A Universal Mmunohistochemistry Analyzer
Generalizing AI-Driven Assessment of Immunohistochemistry Across Immunostains and Cancer Types: A Universal Mmunohistochemistry Analyzer Open
View article: 1446 Pan-cancer methylation analysis reveals a significant correlation of immune-desert phenotype with methylation aberrancy
1446 Pan-cancer methylation analysis reveals a significant correlation of immune-desert phenotype with methylation aberrancy Open
Background Recently, the degree of methylation aberrancy, or methylation burden has shown inverse correlation with tumor immunogenicity measured by gene expression profile (GEP) reflecting activated immune cells across multiple cancer type…
View article: EP10.01-13 Evaluating Osimertinib Induced Pneumonitis in EGFR Advanced Lung Cancer in a Real World Clinical Practice.
EP10.01-13 Evaluating Osimertinib Induced Pneumonitis in EGFR Advanced Lung Cancer in a Real World Clinical Practice. Open
View article: 1293 Fragmented pattern of tumor mass is related to fibroblast activation mitigating spatial interaction between tumor and immune cells
1293 Fragmented pattern of tumor mass is related to fibroblast activation mitigating spatial interaction between tumor and immune cells Open
Background Microscopic tumor fragmentation has shown association with the immune landscape of tumor microenvironment (TME).1 The current study aimed to further investigate the effect of the tumor fragmentation index (TFI), defin…
View article: 961 Tumor-infiltrating lymphocytes in tumor microenvironment assessed by artificial intelligence powered H&E image analyzer is correlated with immunomodulatory subtype of triple-negative breast cancer
961 Tumor-infiltrating lymphocytes in tumor microenvironment assessed by artificial intelligence powered H&E image analyzer is correlated with immunomodulatory subtype of triple-negative breast cancer Open
Background Tumor-infiltrating lymphocytes (TILs) serve as both prognostic and predictive biomarker in triple-negative breast cancer (TNBC). TNBC exhibits six distinct molecular subtypes —basal-like 1, basal-like 2, mesenchymal, mesenchymal…
View article: 1308 Artificial intelligence (AI)-powered immune phenotyping based on programmed death ligand 1 (PD-L1) immunohistochemistry (IHC) in triple negative breast cancer (TNBC)
1308 Artificial intelligence (AI)-powered immune phenotyping based on programmed death ligand 1 (PD-L1) immunohistochemistry (IHC) in triple negative breast cancer (TNBC) Open
Background The tumor microenvironment has recently become important in cancer and immune phenotype (IP) has been proposed as a way to assess it. A variety of methods to assess IP in tumor tissue were proposed, mostly from histology slides …
View article: Data from The Genomics of Colorectal Cancer in Populations with African and European Ancestry
Data from The Genomics of Colorectal Cancer in Populations with African and European Ancestry Open
Black people have a higher incidence of colorectal cancer and worse survival rates when compared with white people. Comprehensive genomic profiling was performed in 46,140 colorectal adenocarcinoma cases. Ancestry-informative markers ident…
View article: Supplementary Figure from The Genomics of Colorectal Cancer in Populations with African and European Ancestry
Supplementary Figure from The Genomics of Colorectal Cancer in Populations with African and European Ancestry Open
Supplementary Figure from The Genomics of Colorectal Cancer in Populations with African and European Ancestry
View article: Supplementary Figure from The Genomics of Colorectal Cancer in Populations with African and European Ancestry
Supplementary Figure from The Genomics of Colorectal Cancer in Populations with African and European Ancestry Open
Supplementary Figure from The Genomics of Colorectal Cancer in Populations with African and European Ancestry
View article: Data from The Genomics of Colorectal Cancer in Populations with African and European Ancestry
Data from The Genomics of Colorectal Cancer in Populations with African and European Ancestry Open
Black people have a higher incidence of colorectal cancer and worse survival rates when compared with white people. Comprehensive genomic profiling was performed in 46,140 colorectal adenocarcinoma cases. Ancestry-informative markers ident…
View article: Supplementary Figure from The Genomics of Colorectal Cancer in Populations with African and European Ancestry
Supplementary Figure from The Genomics of Colorectal Cancer in Populations with African and European Ancestry Open
Supplementary Figure from The Genomics of Colorectal Cancer in Populations with African and European Ancestry
View article: Supplementary Figure from The Genomics of Colorectal Cancer in Populations with African and European Ancestry
Supplementary Figure from The Genomics of Colorectal Cancer in Populations with African and European Ancestry Open
Supplementary Figure from The Genomics of Colorectal Cancer in Populations with African and European Ancestry
View article: Data from <i>EGFR</i> Kinase Domain Duplication (<i>EGFR</i>-KDD) Is a Novel Oncogenic Driver in Lung Cancer That Is Clinically Responsive to Afatinib
Data from <i>EGFR</i> Kinase Domain Duplication (<i>EGFR</i>-KDD) Is a Novel Oncogenic Driver in Lung Cancer That Is Clinically Responsive to Afatinib Open
Oncogenic EGFR mutations are found in 10% to 35% of lung adenocarcinomas. Such mutations, which present most commonly as small in-frame deletions in exon 19 or point mutations in exon 21 (L858R), confer sensitivity to EGFR tyrosine …
View article: Supplementary Figure S3 from Comprehensive Genomic Profiling of Pancreatic Acinar Cell Carcinomas Identifies Recurrent <i>RAF</i> Fusions and Frequent Inactivation of DNA Repair Genes
Supplementary Figure S3 from Comprehensive Genomic Profiling of Pancreatic Acinar Cell Carcinomas Identifies Recurrent <i>RAF</i> Fusions and Frequent Inactivation of DNA Repair Genes Open
Supplementary Fig. S3: Co-mutation across all PACC tumors.
View article: Data from Targeted Next Generation Sequencing Identifies Markers of Response to PD-1 Blockade
Data from Targeted Next Generation Sequencing Identifies Markers of Response to PD-1 Blockade Open
Therapeutic antibodies blocking programmed death-1 and its ligand (PD-1/PD-L1) induce durable responses in a substantial fraction of melanoma patients. We sought to determine whether the number and/or type of mutations identified using a n…
View article: Data from Activation of MET via Diverse Exon 14 Splicing Alterations Occurs in Multiple Tumor Types and Confers Clinical Sensitivity to MET Inhibitors
Data from Activation of MET via Diverse Exon 14 Splicing Alterations Occurs in Multiple Tumor Types and Confers Clinical Sensitivity to MET Inhibitors Open
Focal amplification and activating point mutation of the MET gene are well-characterized oncogenic drivers that confer susceptibility to targeted MET inhibitors. Recurrent somatic splice site alterations at MET exon 14 (ME…
View article: Supplementary Table S1A - S1B from Comprehensive Genomic Profiling of Pancreatic Acinar Cell Carcinomas Identifies Recurrent <i>RAF</i> Fusions and Frequent Inactivation of DNA Repair Genes
Supplementary Table S1A - S1B from Comprehensive Genomic Profiling of Pancreatic Acinar Cell Carcinomas Identifies Recurrent <i>RAF</i> Fusions and Frequent Inactivation of DNA Repair Genes Open
Supplementary Table S1A: Genes analyzed for base substitutions, short insertions/deletions, and copy number alterations (DNA). Supplementary Table S1B: Genes analyzed for rearrangements (DNA).
View article: Supplementary Figure S2 from Comprehensive Genomic Profiling of Pancreatic Acinar Cell Carcinomas Identifies Recurrent <i>RAF</i> Fusions and Frequent Inactivation of DNA Repair Genes
Supplementary Figure S2 from Comprehensive Genomic Profiling of Pancreatic Acinar Cell Carcinomas Identifies Recurrent <i>RAF</i> Fusions and Frequent Inactivation of DNA Repair Genes Open
Supplementary Fig. S2: Loss of function mutations in select tumor suppressor genes.