Johns Hopkins University
3400 N. Charles St.
Baltimore, MD 21218
My lab’s focus is on 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. Our research integrates the principles of biophysics, molecular biology, and computational biology to create new tools for exploring the epigenome and genome of various lifeforms, ranging in size from the flu virus to hummingbirds to California redwoods. Based on the knowledge gained from these studies, we apply their toolsets to clinical samples for the diagnosis, surveillance, and treatment of human disease.
A. Gershman, T. G. Romer, Y. Fan, R. Razaghi, W. A. Smith, and W. Timp, “De novo genome assembly of the tobacco hornworm moth (Manduca sexta),” G3 Genes|Genomes|Genetics, vol. 11, no. 1, Feb. 2021, jkaa047. eprint: https://academic. oup.com/g3journal/article-pdf/11/1/jkaa047/36183075/jkaa047.pdf.
I. Lee, R. Razaghi, T. Gilpatrick, M. Molnar, A. Gershman, N. Sadowski, F. J. Sedlazeck, K. D. Hansen, J. T. Simpson, and W. Timp, “Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing,” Nature Methods, vol. 17, no. 12, pp. 1191–1199, Dec. 2020.
S. Kovaka, Y. Fan, B. Ni, W. Timp, and M. C. Schatz, “Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED,” Nature Biotechnology, pp. 1–11, Nov. 30, 2020.
K. H. Miga, S. Koren, A. Rhie, M. R. Vollger, A. Gershman, A. Bzikadze, S. Brooks, E. Howe, D. Porubsky, G. A. Logsdon, V. A. Schneider, T. Potapova, J. Wood, W. Chow, J. Armstrong, J. Fredrickson, E. Pak, K. Tigyi, M. Kremitzki, C. Markovic, V. Maduro, A. Dutra, G. G. Bouffard, A. M. Chang, N. F. Hansen, A. B. Wilfert, F. Thibaud-Nissen, A. D. Schmitt, J.-M. Belton, S. Selvaraj, M. Y. Dennis, D. C. Soto, R. Sahasrabudhe, G. Kaya, J. Quick, N. J. Loman, N. Holmes, M. Loose, U. Surti, R. a. Risques, T. A. G. Lindsay, R. Fulton, I. Hall, B. Paten, K. Howe, W. Timp, A. Young, J. C. Mullikin, P. A. Pevzner, J. L. Gerton, B. A. Sullivan, E. E. Eichler, and A. M. Phillippy, “Telomere-to-telomere assembly of a complete human X chromosome,” en, Nature, pp. 1–9, Jul. 2020
R. Yee, F. P. Breitwieser, S. Hao, B. N. Opene, R. E. Workman, P. D. Tamma, J. Dien-Bard, W. Timp, and P. J. Simner, “Metagenomic next-generation sequencing of rectal swabs for the surveillance of antimicrobial-resistant organisms on the Illumina Miseq and Oxford MinION platforms,” European Journal of Clinical Microbiology & Infectious Diseases, Aug. 2020.
T. Gilpatrick, I. Lee, J. E. Graham, E. Raimondeau, R. Bowen, A. Heron, B. Downs, S. Sukumar, F. J. Sedlazeck, and W. Timp, “Targeted nanopore sequencing with Cas9-guided adapter ligation,” Nature Biotechnology, Feb. 2020.
R. E. Workman*, A. D. Tang*, P. S. Tang*, M. Jain*, J. R. Tyson*, R. Razaghi*, P. C. Zuzarte, T. Gilpatrick, A. Payne, J. Quick, N. Sadowski, N. Holmes, J. G. de Jesus, K. L. Jones, C. M. Soulette, T. P. Snutch, N. Loman, B. Paten, M. Loose, J. T. Simpson, H. E. Olsen, A. N. Brooks, M. Akeson§, and W. Timp, “Nanopore native RNA sequencing of a human poly(A) transcriptome,” Nature Methods, pp. 1–9, Nov. 2019.
J. T. Simpson§, R. E. Workman, P. C. Zuzarte, M. David, L. J. Dursi, and W. Timp, “Detecting DNA cytosine methylation using nanopore sequencing,” Nature Methods, vol. 14, no. 4, pp. 407–410, Apr. 2017.