Zoheb Khan
About Me
I am an incoming doctoral student in Biology at New York University, starting in Fall 2026. I graduated from the University of Chicago in 2022 with a B.A. in Genetics. After graduation, I worked as a bioinformatician in the Moskowitz Lab, where I studied Hedgehog signaling-dependent gene regulatory networks that govern the timing and lineage specification of cardiac and neural progenitor differentiation.
My Research
In the Moskowitz Lab, I studied how Hedgehog signaling shapes differentiation timing and lineage specification in iPSC-derived cardiac and neural progenitors, including comparisons of trisomy 21 and matched disomy cells across developmental time.
I integrated time-course RNA-seq with chromatin accessibility and transcription-factor binding data to identify candidate regulators of developmental timing and cell-fate commitment.
Selected projects
- Developmental timing of cardiac progenitor differentiation in Down syndrome.
Comparing trisomy 21 and matched disomy iPSC-derived cardiac progenitors across differentiation time points to identify shifts in transcriptional maturation.
- Transcription factor-dependent neurotransmitter subtype specification in iPSC-derived neuronal differentiation.
Studying temporal gene regulatory programs that distinguish excitatory VGLUT1/VGLUT2 and inhibitory GlyT2/VGAT neuronal subtype programs.
- Hedgehog-dependent gene regulatory control of progenitor differentiation timing and fate.
Integrating time-course expression and chromatin data to identify GLI1-dependent transcription factors and cis-regulatory elements that regulate the timing and fate of cardiac and neural progenitor differentiation.
Research Interests
I am interested in using transcriptomic and regulatory-genomic approaches, including RNA-seq, ATAC-seq, ChIP-seq, CUT&RUN, and single-nucleus RNA-seq, to investigate the gene regulatory logic underlying developmental timing and cell-fate decisions. In particular, I want to understand how transcription factors, chromatin state and conformation, and cis-regulatory elements determine when progenitor cells terminally differentiate and which fates they adopt.
R packages and functions
I have recently made more of an effort in my free time to clearly and reproducibly document my library of personal functions and workflows that I have accumulated across the various bioinformatics projects I have worked on. To this end, I have documented and organized around half of these scripts and workflows in the repositories that I have listed below. Each repository has an associated tutorial/vignette site, except where noted. Feel free to clone/fork/adapt any of my scripts or workflows to your use case. Please contact me at zohebkhan600@gmail.com if you have questions.
Principal components analysis-based time-course maturation score
Places bulk RNA-seq samples along a reference differentiation time course by projecting them onto a PCA trajectory fitted through timepoint centroids.
Gene Set Enrichment Analysis ranked waterfall plots
Plots precomputed GSEA results as NES-ranked waterfalls, volcanoes, and cross-contrast scatter plots.
encodeUtils
An R package for searching the ENCODE Portal, downloading and verifying files, and recording their provenance.
Control-matched bulk RNA-seq single sample gene set scoring
Single sample control expression-matched gene set scoring for bulk RNA-seq.
biocontext
A macOS terminal UI for answering Bioconductor package questions from local documentation and exact package source, with citations for the supporting file, line range, package version, and Bioconductor release.
Publications
Burnicka-Turek, O., Trampel, K., Laforest, B., Broman, M., Yang, X., Khan, Z., Rytkin, E., Li, B., Schaffer, E., Gadek, M., Shen, K., Efimov, I., & Moskowitz, I. Coordinated Tbx3/Tbx5 transcriptional control of the adult ventricular conduction system. eLife, 2025.
Broman, M., Nadadur, R., Perez-Cervantes, C., Burnicka-Turek, O., Lazarevic, S., Gams, A., Laforest, B., Steimle, J., Iddir, S., Wang, Z., Smith, L., Mazurek, S., Olivey, H., Zhou, P., Gadek, M., Shen, K., Khan, Z., et al. A genomic link from heart failure to atrial fibrillation risk: FOG2 modulates a TBX5/GATA4-dependent atrial gene regulatory network. Circulation, 2024.
Khan, Z., Hamandi, M., Khan, H., DiMaio, J., & Evans, M. Convergent epicardial-endocardial ablation for treatment of long-standing persistent atrial fibrillation: A review of literature. Journal of Cardiac Surgery, 2020.