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Dr. Sarah Wheelan

M.D., Ph.D.

Bioinformatics algorithms gene regulation microarrary design and analysis transposon biology


Assistant Professor, Oncology Biostatistics

Joint Appointment, Biostatistics, Bloomberg School of Public Health


M.D., Johns Hopkins University, Baltimore, MD Ph.D., Human Genetics, Johns Hopkins University, Baltimore, MD

Research Summary

Dr. Wheelan's graduate training in bioinformatics at NCBI, coupled with her longstanding interest and experience in both biology and mathematics, has equipped her to address modern biological questions from an analytical perspective. Whether through the use of publicly available software or custom-coded programs, she enjoys solving puzzles and welcome collaborations with researchers of all types.

Her recent work has focused on microarrays, transposons, and gene regulation.

Microarrays are physically very simple; strands of DNA are deposited onto a solid substrate and the resulting array can be used to uncover the types and amounts of DNA or RNA in a sample of interest. Microarrays can be used in somewhat conventional ways to query gene expression and genomic structure (deletions and duplications) and also in more specialized realms such as transposon localization. This extremely useful and flexible high-throughput technique is evolving quickly, so that the most cutting-edge arrays have many millions of probes available, and new uses for microarrays are being reported almost continually.

Dr. Wheelan is interested in microarray design from both a biological and algorithmic standpoint. Working with Jef Boeke, Francisco Martínez-Murillo, and Rafael Irizarry, she developed an innovative double-tiling microarray design; this effectively doubles the number of probes available on any given microarray. Custom microarray design is an art and a science — special-purpose algorithms are often required for each individual design. Depending on the array manufacturer, there are sequence-based constraints on probes; biological constraints must also be considered, for example, the probe sequences must be unique in the genome(s) to be queried.

Dr. Wheelan is also interested in transposon biology. Transposons, mobile genetic elements that constitute varying and often quite significant fractions of every known genome, can either cause disease on their own through transposition or retrotransposition, or can serve as linkage markers for nearby disease genes. Having helped develop a new microarray technique for localizing transposons in any given genome, she is excited to pursue this research further.

Finally, Dr. Wheelan is interested in computational methods for uncovering regulatory mechanisms for gene expression.

Journal Citations

Huang, C.R.; Schneider, A.M.; Lu, Y.; Niranjan, T.; Shen, P.; Robinson, M.A.; Steranka, J.P.; Valle, D.; Civin, C.I.; Wang, T.; Wheelan, S.J.; Ji, H.; Boeke, J.D.; Burns, K.H. Mobile interspersed repeats are major structural variants in the human genome. Cell. 2010 Jun 25;141(7):1171-1182.


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