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Zanvyl Krieger School of Arts & Sciences
3400 N. Charles Street
Baltimore, MD 21218
Sequencing Technology Development and Application to Genetics, Epigenetics and Transcriptomics
My lab’s focus is in the development and application of sequencing technologies to gain a deeper understanding of biology and a more accurate set of clinical tools for human disease. We integrate biophysics, molecular biology and computational biology to create new tools for exploring the epigenome and genome. Leveraging these tools, we then explore interesting questions about fundamental biological concepts using model systems. We apply our newfound knowledge and toolset to clinical samples for diagnosis, surveillance and treatment of human disease. Recent projects range from diagnosis of infectious disease using nanopore sequencing, to developing new tools to characterize the genome and epigenome of cancer, to reading the transcriptome of the hummingbird.
Timp W, Feinberg AP. Cancer as a dysregulated epigenome allowing cellular growth advantage at the expense of the host. Nature Reviews Cancer. 2013 Jul;13(7):497–510.
Kurz V, Nelson EM, Perry N, Timp W, Timp G. Epigenetic Memory Emerging from Integrated Transcription Bursts. Biophysical Journal. 2013 Sep 17;105(6):1526–1532.
Nelson, E.M., V. Kurz, J. Shim, W. Timp, G. Timp. 2012. Using a Nanopore for Single Molecule Detection and Single Cell Transfection. The Analyst 137: 3020–3027. doi:10.1039/C2AN35571J.
Timp, W., J. Comer, A. Aksimentiev. 2012. DNA Base-calling via nanopore sequencing using a Viterbi algorithm. Biophysical Journal 102, L37–L39.
McDonald, O. G., H. Wu, W. Timp, A. Doi, and A. P. Feinberg. 2011. Genome-scale epigenetic reprogramming during epithelial-to-mesenchymal transition. Nature Structural & Molecular Biology 18 (8):867–74.
Hansen, K. D., W. Timp, H. C. Bravo, S. Sabunciyan, B. Langmead, O. G. McDonald, B. Wen, H. Wu, Y. Liu, D. Diep, E. Briem, K. Zhang, R. A. Irizarry, and A. P. Feinberg. 2011. Increased methylation variation in epigenetic domains across cancer types. Nature Genetics 43 (8):768–75.
Timp, W., U. M. Mirsaidov, Deqiang Wang, J. Comer, A. Aksimentiev, and G. Timp. 2010. Nanopore Sequencing: Electrical Measurements of the Code of Life. Nanotechnology, IEEE Transactions on 9 (3):281–294.
Mirsaidov, U., W. Timp, X. Zou, V. Dimitrov, K. Schulten, A. P. Feinberg, and G. Timp. 2009. Nanoelectromechanics of Methylated DNA in a Synthetic Nanopore. Biophysical Journal 96 (4):L32–L34.