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Sarah Jo Wheelan, M.D., Ph.D.

Headshot of Sarah Jo Wheelan
  • Associate Professor of Oncology

Research Interests

DNA sequence-structure-function relationships; chromatin architecture, particularly related to cancer genomics; sequence analysis and alignment algorithms ...read more

Background

Dr. Wheelan's medical training, and her 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 tackling the intricate puzzles that modern biology has uncovered.

Her recent work has focused on DNA sequence-structure-function relationships. The 3D structure of chromatin in the nucleus is nonrandom, regulatory, and fascinatingly complex. There are a number of ways to query this both experimentally and computationally, including but not limited to sequencing approaches.

She is deeply committed to teaching; as director of the Center for Computational Genomics, she helps organize an annual workshop (Practical Genomics) as well as a symposium, seminar series, and short courses. She teaches courses on computational biology algorithms and methods in both the medical school and the school of public health.

As co-director of the Experimental and Computational Genomics Core in the Sidney Kimmel Comprehensive Cancer Center (and director for bioinformatics), she helps design, execute, and analyze a variety of sequencing experiments.

...read more

Titles

  • Associate Professor of Oncology
  • Associate Professor of Molecular Biology and Genetics

Departments / Divisions

Centers & Institutes

Education

Degrees

  • M.D.; Johns Hopkins University School of Medicine (Maryland) (2003)
  • Ph.D.; Johns Hopkins University School of Medicine (Maryland) (2003)
  • B.A.; University of Colorado (Boulder) (Colorado) (1995)

Research & Publications

Research Summary

Dr. Wheelan's medical training, and her 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 tackling the intricate puzzles that modern biology has uncovered.

Her recent work has focused on DNA sequence-structure-function relationships. The 3D structure of chromatin in the nucleus is nonrandom, regulatory, and fascinatingly complex. There are a number of ways to query this both experimentally and computationally, including but not limited to sequencing approaches.

She is deeply committed to teaching; as director of the Center for Computational Genomics, she helps organize an annual workshop (Practical Genomics) as well as a symposium, seminar series, and short courses. She teaches courses on computational biology algorithms and methods in both the medical school and the school of public health.

As co-director of the Experimental and Computational Genomics Core in the Sidney Kimmel Comprehensive Cancer Center (and director for bioinformatics), she helps design, execute, and analyze a variety of sequencing experiments.

Clinical Trials

Learn more about clinical trials at the Johns Hopkins Kimmel Cancer Center.

Selected Publications

View all on PubMed

Esopi D, Graham MK, Brosnan-Cashman JA, Meyers J, Vaghasia A, Gupta A, Kumar B, Haffner MC, Heaphy CM, De Marzo AM, Meeker AK, Nelson WG, Wheelan SJ, Yegnasubramanian S. Pervasive promoter hypermethylation of silenced TERT alleles in human cancers. Cell Oncol (Dordr). 2020

Wilton R, Wheelan SJ, Szalay AS, Salzberg SL. The Terabase Search Engine: a large-scale relational database of short-read sequences. Bioinformatics. 2019

Kyker-Snowman K, Erlanger Avigdor B, Nasim M, Cimino-Mathews A, Wheelan SJ, Argani P, Park BH. A primary breast cancer with distinct foci of estrogen receptor-alpha positive and negative cells derived from the same clonal origin as revealed by whole exome sequencing. Breast Cancer Res Treat. 2018

Avigdor BE, Cimino-Mathews A, DeMarzo AM, Hicks JL, Shin J, Sukumar S, Fetting J, Argani P, Park BH, Wheelan SJ. Mutational profiles of breast cancer metastases from a rapid autopsy series reveal multiple evolutionary trajectories. JCI Insight. 2017

Favorov A, Mularoni L, Cope LM, Medvedeva Y, Mironov AA, Makeev VJ, Wheelan SJ. Exploring massive, genome scale datasets with the GenometriCorr package. PLoS Computational Biology. 2012

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