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.

Scientific Reports · May 25, 2026Peer-reviewedGenomics

Fatty Acid Oxidation Suppression Reprograms Fibroblasts in Fibrostenotic Crohns Disease

Jihad Jihad Aljabban, Ayesh Awad, Benjamin D. McMichael, Valerie Gartner, Viguna Thomas, Bingfang Huan, David Weaver, Grace Lian, Caroline Beasley, Gwen W. Lau, Sophie Silverstein, Muneera Rehana Kapadia, Anna C. Salvador, Florian Rieder, Jessica E. Thaxton, , Shehzad Z. Sheikh

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

bioRxiv · May 10, 2026 · PreprintGenomics

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

Nina C. Nishiyama, Sophie Silverstein, Kimberly Darlington, Meaghan M. Kennedy Ng, Katelyn Clough, Mikaela J. Bauer, Caroline Beasley, Akshatha Bharadwaj, Rajee Ganesan, Muneera Rehana Kapadia, Gwen W. Lau, Grace Lian, Reza Rahbar, Timothy S. Sadiq, Matthew R. Schaner, , Terrence S. Furey

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

bioRxiv · Oct 14, 2024 · PreprintGenomics

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

Alexandria J. Shumway, Michael T. Shanahan, Émilie Hollville, Kevin Chen, Caroline Beasley, Jonathan Villanueva, Sara Albert, Grace Lian, Moises R. Cure, Matthew R. Schaner, Lee‐Ching Zhu, Surekha Bantumilli, Mohanish Deshmukh, Terrence S. Furey, Shehzad Z. Sheikh, Praveen Sethupathy

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.

JCI Insight · Feb 21, 2024Peer-reviewedGenomics

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

Kevin A. Chen, Nina C. Nishiyama, Meaghan M. Kennedy Ng, Alexandria J. Shumway, Chinmaya U. Joisa, Matthew R. Schaner, Grace Lian, Caroline Beasley, Lee‐Ching Zhu, Surekha Bantumilli, Muneera Rehana Kapadia, Shawn M. Gomez, Terrence S. Furey, Shehzad Z. Sheikh

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

Scientific Reports · Feb 1, 2024Peer-reviewedBioinformatics

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

Matt Kanke, Meaghan M. Kennedy Ng, Sean V. Connelly, Matthew R. Schaner, Michael T. Shanahan, Elisabeth A. Wolber, Caroline Beasley, Grace Lian, Animesh Jain, Millie D. Long, Edward L. Barnes, Hans H. Herfarth, Kim L. Isaacs, Jonathan J. Hansen, Muneera Rehana Kapadia, , Praveen Sethupathy

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.

bioRxiv · Jan 13, 2021 · PreprintGenomics

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

Takahiko Toyonaga, Kenza C. Araba, Meaghan M. Kennedy Ng, Benjamin P. Keith, Elisabeth A. Wolber, Caroline Beasley, Erin C. Steinbach, Matthew R. Schaner, Animesh Jain, Millie D. Long, Edward L. Barnes, Hans H. Herfarth, Kim L. Isaacs, Jonathan J. Hansen, Muneera Rehana Kapadia, , Shehzad Z. Sheikh

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

bioRxiv · Nov 24, 2020 · PreprintGenomics