genomics; high throughput sequencing; next generation sequencing; sequence analysis; transposon; RNAseq; motifs
Experiences & Accomplishments
The basic question: how does DNA work? DNA, plus epigenetic factors, has enough information to operate a complex organism. We really don't know much about how this works. 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. The common theme in this research is that DNA sequence guides DNA structure, which in turn restricts and enables gene function. Looking at spatial relationships across genomes and using transpsosons to query genomic sequence/structure relationships are two ways to address these questions. Current projects: Second- and third-generation sequencing (alignment, data analysis, mapping) Spatial relationships of genomic features and functional correlates RNAseq analysis Genometric Correlation Transposon mapping and transposon expression analysis Sequence biology: motifs, sequence content etc.
Honors & Awards
2016 Johns Hopkins University Professor’s Award for Teaching Excellence in Biomedical Sciences
- 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; 8(5):e1002529. Epub 2012 May 31.
- 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
- Harr JC, Luperchio TR, Wong X, Cohen E, Wheelan SJ, Reddy KL. Directed targeting of chromatin to the nuclear lamina is mediated by chromatin state and A-type lamins. J Cell Biol. 2015
- Norris AL, Kamiyama H, Makohon-Moore A, Pallavajjala A, Morsberger LA, Lee K, Batista D, Iacobuzio-Donahue CA, Lin MT, Klein AP, Hruban RH, Wheelan SJ, Eshleman JR. Transflip mutations produce deletions in pancreatic cancer. Genes Chromosomes Cancer. 2015
- Mularoni L, Zhou Y, Bowen T, Gangadharan S, Wheelan S‡, Boeke J‡. Retrotransposon Ty1 integration targets specifically positioned asymmetric nucleosomal DNA segments in tRNA hotspots. Genome Res. 2012; 22(4):693-703.