Publications (1st Author)

Figure 1

chromVAR: Inferring transcription factor variation from single-cell epigenomic data.

Schep AN, Wu B, Buenrostro JD, Greenleaf WJ. chromVAR: Inferring transcription factor variation from single-cell epigenomic data. BioRxiv 2017.

I developed chromVAR, an R package that enables interpretable analysis of sparse epigenomics data from single cell ATAC-seq or lightly sequenced bulk epigenomics data. The method finds sequence motifs or other genomic annotations associated with variation in chrommatin accessibility across cells or samples.



Figure 1

Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions

Schep AN, Buenrostro JD, Denny SK, Schwartz K, Sherlock G, Greenleaf WJ. Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions. Genome Res. 2015.

I developed a new method for determining nucleosome positioning using ATAC-seq data. The method takes advantage of the highly structured fragmentation pattern that can be observed around well-positioned nucleosomes. The algorithm is implemented as a python package named NucleoATAC.



Figure 1

A Comparative Analysis of Transcription Factor Expression during Metazoan Embryonic Development

Schep AN, Adryan B. A comparative analysis of transcription factor expression during metazoan embryonic development. PLoS One. 2013.

I used published in situ hybridization, microarray, and RNA-seq datasets to compare expression patterns of transcription factors during early embryonic development between different species. I show that TF expression appears to follow the hourglass model, in that expression is most similar between species mid-way through embryonic development, although for insects it appears there may be two distinct periods of maximal similarity.


Additional publications (co-author)

Single-cell epigenomics maps the continuous regulatory landscape of human hematopoietic differentiation.

Buenrostro JD, Corces R, Wu B, Schep AN, et al. Single-cell epigenomics maps the continuous regulatory landscape of human hematopoietic differentiation. BioRxiv 2017.

The genome-wide transcriptional response to varying RpoS levels in Escherichia coli K-12.

Wong GT, Bonocorra RP, Schep AN, et al. The genome-wide transcriptional response to varying RpoS levels in Escherichia coli K-12. Journal of Bacteriology 2017.

Nfib Promotes Metastasis through a Widespread Increase in Chromatin Accessibility.

Denny, SK, Yang D, et al. Nfib Promotes Metastasis through a Widespread Increase in Chromatin Accessbility. Cell 2016;166(2): 328-343.

Transcriptional repression by the proximal exonic region at the human TERT gene

Wong TC, Sokol ES, Schep AN, Punjiya M, Tran DA, Allan D, et al. Transcriptional repression by the proximal exonic region at the human TERT gene. Gene. 2011;486: 65–73.

Characterization of an Ultra-Conserved Putative cis-Regulatory Module at the Mammalian Telomerase Reverse Transcriptase Gene

Tran DA, Wong TC, Schep AN, Drewell RA. Characterization of an ultra-conserved putative cis-regulatory module at the mammalian telomerase reverse transcriptase gene. DNA Cell Biol. 2010;29: 499–508.

Identification and Characterization of Dynein Genes in Tetrahymena

Wilkes DE, Bennardo N, Chan CWC, Chang Y-L, Corpuz EO, DuMond J, et al. Identification and characterization of dynein genes in Tetrahymena. Methods Cell Biol. 2009;92: 11–30.

Additional writing (for a general audience)

What are the genetics behind congenital amusia (tone deafness)?


How is a human genome mapping performed?


How similar are humans to neanderthals and chimpanzees?


If two kids have same dad but their moms are sisters and the sisters are from same mom and dad, are the kids full siblings or half?