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Faculty & Research


Sarah Wheelan

Department Affiliation Primary: Oncology
Secondary: Molecular Biology & Genetics
RankAssociate Professor
Phone Numbers410-502-7754
School of Medicine Address1550 Orleans Street
David H. Koch Cancer Research Building 2, Room 1M51
Baltimore MD 21287
Link to Lab Homepage
Sarah Wheelan

Research Topic: Computational Biology, Genomics, and Sequence Alignment

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 Next Generation Genome Sequencing Center, in the department of Oncology. We have two SOLiD 4.0 instruments, two SOLiD 5500 instruments, an Ion Torrent, and (soon) two Illumina sequencers, 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.​


Mularoni L, Zhou Y, Bowen T, Gangadharan S, Wheelan SJ*, Boeke J*. Retrotransposon Ty1 integration targets specifically positioned asymmetric nucleosomal DNA segments in tRNA hotspots. Genome Res. 2012 Jan 9.
PubMed Reference
Creamer TJ, Darby MM, Jamonnak N, Schaughency P, Hao H, Wheelan SJ, Corden JL. Transcriptome-Wide Binding Sites for Components of the Saccharomyces cerevisiae Non-Poly(A) Termination Pathway: Nrd1, Nab3, and Sen1. PLoS Genet 7(10): e1002329. 2011.
PubMed Reference
Tyekucheva S, Yolken R, McCombie R, Parla J, Kramer M, Wheelan SJ*, Sabunciyan S*. Establishing the baseline level of repetitive element expression in the human cortex. BMC Genomics. 2011 Oct 10;12(1):495.
PubMed Reference
Niranjan TS, Adamczyk A, Corrada Bravo H, Wheelan SJ, Irizarry R, Wang T. Effective Detection of Rare Variants in Pooled DNA Samples using SRFIM and Cross-Pool Tailcurve Analysis. Genome Biology, 2011 Sep 28;12(9):R9.
PubMed Reference
Jamonnak N, Creamer T, Darby M, Schaughency P, Wheelan SJ, Corden J. Yeast Nrd1, Nab3 and Sen1 transcriptome-wide binding maps suggest multiple roles in post-transcriptional RNA processing. RNA, 2011 Sep 27.
PubMed Reference
Sobreira NLM, Gnanakkan V, Walsh M, Marosy B, Wohler E, Thomas G, Hoover-Fong JE, Hamosh A, Wheelan SJ, Valle D. Characterization of Complex Chromosomal Rearrangements by Targeted Capture and Next-Generation Sequencing. 2011 Genome Research, epub September 2, 2011.
PubMed Reference
Hong SH, Skaist AM, Wheelan SJ, Friedman AD. AP-1 protein induction during monopoiesis favors C/EBP:AP-1 heterodimerization over C/EBP homodimerization to stimulate FosB transcription. J Leukoc Biol. 2011.
PubMed Reference
Murthy S, Hayward GS, Wheelan SJ, Forman MS, Ahn JH, Pass RF, Arav-Boger R. Detection of a single identical cytomegalovirus (CMV) strain in recently seroconverted young women. PLoS One. 2011 Jan 10;6(1):e15949.
PubMed Reference