Publications

Single-allele chromatin tracing reveals cytokine-dependent super-enhancer repositioning in CD4+ T cells

Jay, A., Zhou, Y., Yoon, S., Abeje, B.N, Chandra, A., Michieletto, M.F., Wald, J., Henao-Mejia, J., Raj, A., Faryabi, R.B., Vahedi, G.

Immunity

2026

Lineage-determining transcription factors constrain cohesin to drive multi-enhancer oncogene regulation

Zhou* Y, Jay* A, Burget N, Friedrich T, Yoon S, Alsing J, Nir G, Grosschedl R, Vahedi# G, Faryabi# RB. # co-corresponding, * co-first authors

Nature Cell Biology

2025

Joint profiling of gene expression and chromatin accessibility in pancreatic lymph nodes and spleens in human type 1 diabetes

Abedi* M, Rai* P, Zhou* Y, Liu C, Johnson I, Chandra A, Fasolino M, Rostami S, Wang W, Min Z, Li Y, Yu M, Jay A, Lian V, Silverman M, Kaestner KH, Naji A, Faryabi# RB, Vahedi# G. # co-corresponding, * co-first authors

Science Immunology

2025

Single-Allele Chromatin Tracing Reveals Genomic Clustering of Paralogous Transcription Factors as a Mechanism for Developmental Robustness in T Cells

Jay, A., Zhou, Y., Yoon, S., Abeje, B., Chandra, A., Wald, J., Raj, A., Faryabi, RB, Vahedi, G.

biorXiv

2025

The epigenetic landscape of fate decisions in T cells

Jay, A., Pondevida, CM, and Vahedi, G.

Nature Immunology

2025

Modeling type 1 diabetes progression using machine learning and single-cell transcriptomic measurements in human islets

Patil, A. R., Schug, J., Liu, C., Lahori, D., Descamps, H.C., the Human Pancreas Analysis Consortium, Naji, A., Kaestner, K.H., Faryabi, R.B. and Vahedi, G.

Cell Reports Medicine

2024

Intrinsically disordered domain of transcription factor TCF-1 is required for T cell developmental fidelity

Goldman N, Chandra A, Johnson I, Sullivan MA, Patil AR, Vanderbeck A, Jay A, Zhou Y, Ferrari EK, Mayne L, Aguilan J, Xue HH, Faryabi RB, Wherry EJ, Sidoli S, Maillard I and Vahedi G.

Nature Immunology

2023

Quantitative control of Ets1 dosage by a multi-enhancer hub promotes Th1 cell differentiation and protects from allergic inflammation

Chandra*, A., Yoon*, S., Michieletto*, M.F., Goldman, N., Ferrari, E., Abedi, M., Johnson, I., Fasolino, M., Pham, K., Joannas, L., Kee, B., Henao-Mejia# J., and Vahedi#, G.
*co-first authors
#co-corresponding authors

Immunity

2023

Single-cell expression profiling of islets generated by the Human Pancreas Analysis Program

Patil AR, Schug J, Naji A, Kaestner KH, Faryabi RB, Vahedi G.

Nature Metabolism

2023