Shehzad Z. Sheikh

Transcriptome-wide Differential Expression and Splicing in Inflammatory Bowel Disease Patients

The paper identifies differential expression and splicing in IBD patients, showing distinct molecular mechanisms in CD and UC.

Reference-guided Genome Assembly of Long Non-coding RNA Transcripts reveals Target Genes Associated With Crohn's Disease

The paper identifies differentially expressed lncRNAs in Crohn's disease using genome-guided RNA-seq and links them to nearby protein-coding genes involved in immune response and tissue regeneration.

Fatty Acid Oxidation Suppression Reprograms Fibroblasts in Fibrostenotic Crohns Disease

The paper identifies impaired fatty acid oxidation in fibroblasts from fibrostenotic Crohn's disease patients and links it to intestinal fibrosis.

eQTL in diseased colon tissue identifies novel target genes associated with IBD

The paper identifies novel target genes associated with IBD by analyzing eQTL in diseased colon tissue and comparing them to non-IBD eQTL.

CoVar: A generalizable machine learning approach to identify the coordinated regulators driving variational gene expression

CoVar identifies coordinated regulators driving gene expression changes by analyzing network connectivity in perturbed data, revealing key genes missed by differential expression alone.

Aberrant miR-29 is a predictive feature of severe phenotypes in pediatric Crohn's disease

The paper identifies miR-29 as a predictive marker for severe phenotypes in pediatric Crohn's disease through miRNA analysis and validation in mice and human patients.

Linking Gene Expression to Clinical Outcomes in Pediatric Crohn's Disease Using Machine Learning

The paper uses machine learning to predict clinical outcomes in pediatric Crohn's disease by analyzing gene expression from ileal and colonic tissues.

Single-cell analysis of colonic epithelium reveals unexpected shifts in cellular composition and molecular phenotype in treatment-naiïve adult Crohn's disease

The paper uses single-cell analysis to compare colonic epithelial cells in Crohn's disease and control patients, revealing shifts in cell composition and gene expression patterns.

Increased Colonic Expression of ACE2 Associates with Poor Prognosis in Crohn's disease

The paper finds that increased colonic ACE2 expression in Crohn's disease patients is associated with a higher risk of surgery within 5 years.

Colonic Epithelial miR-31 Associates with the Development of Crohn’s Phenotypes

This study identifies miR-31 as a marker that stratifies Crohn’s disease patients into two subtypes with distinct clinical outcomes.