Sarah Wheelan

Associate Professor


1550 Orleans Street
David H. Koch Cancer Research Building 2, Room 1M51
Baltimore MD 21287

Department of Oncology

Molecular Biology and Genetics; Joint Appointment, Biostatistics, Bloomberg School of Public Health

Molecular genetics is built on the assumption that DNA sequence alone is sufficient to direct a cell’s creation, operation, and fate. While this assumption must be modified to accommodate epigenetic phenomena, it is at least clear that the information contained solely in the sequence of the genome is massive and complex. We use sequence alignment algorithms, phylogenetics, and sequence modeling to form hypotheses about historic and current roles of DNA features. High-throughput techniques such as microarrays and second generation sequencing can provide the large volume of information needed to test those hypotheses, though the analysis of data from these experiments is far from routine. Our current projects are diverse but at the core they share a focus on creating new techniques for mathematical analysis and biological interpretation of high-throughput sequencing data and other high-dimensional biological datasets. Since sequence analysis is a very broadly applicable technique, we have been involved in projects ranging from analyses of cancer genomes to in-depth analysis of the dog transcriptome, to mapping transposon insertions using sequencing methods in several organisms. I am one of the PIs of the Center for Computational Genomics, a multidisciplinary center that incorporates graduate-level teaching, postgraduate teaching, and interactive research. The center was founded in an effort to organize the current Hopkins faculty doing genomics, genetics, biostatistics, and computational biology work and to recruit new students and faculty to make Hopkins a leader in the field. We have a deep commitment both to research and to teaching, as the two are closely intertwined. I am co-director of the Experimental and Computational Genomics Core in the department of Oncology. We have an Illumina Novaseq, an Illumina MiSeq, and an Ion Torrent, and we run an extremely wide range of sequencing experiments, on an equally wide range of organisms. Creating high-quality data as well as analysis and presentation of these results is our priority. I teach a class, offered through the School of Public Health, on computational biology from a practical, algorithmic perspective (Analysis of Biological Sequences, 140.638). There are no prerequisites for the course and it generally draws a wide range of students, credit and noncredit, from many programs.

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

Avigdor BE, Beierl K, Gocke CD, Zabransky DJ, Cravero K, Kyker-Snowman, K, Button B, Chu D, Croessmann S, Cochran RL, Connolly RM, Park BH, Cimino-Mathews A, Wheelan SJ. Whole exome sequencing of metaplastic breast carcinoma indicates monoclonality with associated ductal carcinoma component. Clinical Cancer Research 2017

Ling JP, Chhabra R, Merran JD, Schaughency PM, Wheelan SJ, Corden JL, Wong PC. PTBP1 and PTBP2 Repress Nonconserved Cryptic Exons. Cell Rep. 2016

Lee SS, Bohrson C, Pike AM, Wheelan SJ, Greider CW. ATM Kinase Is Required for Telomere Elongation in Mouse and Human Cells. Cell Rep. 2015

Wilton R, Budavari T, Langmead B, Wheelan SJ, Salzberg SL, Szalay AS. Arioc: high-throughput read alignment with GPU-accelerated exploration of the seed-and-extend search space. PeerJ. 2015