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Johns Hopkins University
3400 N. Charles St.
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.
Gilpatrick T, Lee I, Graham JE, Raimondeau E, Bowen R, Heron A, Sedlazeck FJ, Timp W. Targeted Nanopore Sequencing with Cas9 for studies of methylation, structural variants and mutations [Internet]. bioRxiv. 2019 [cited 2019 May 8]. p. 604173. Available from: https://www.biorxiv.org/content/10.1101/604173v1
Lee I, Razaghi R, Gilpatrick T, Sadowski N, Sedlazeck F, Timp W. Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing [Internet]. bioRxiv. 2018 [cited 2019 Jan 13]. p. 504993. Available from: https://www.biorxiv.org/content/early/2018/12/22/504993.abstract
Workman RE, Tang A, Tang PS, Jain M, Tyson JR, Zuzarte PC, Gilpatrick T, Razaghi R, Quick J, Sadowski N, Holmes N, de Jesus JG, Jones K, Snutch TP, Loman NJ, Paten B, Loose MW, Simpson JT, Olsen HE, Brooks AN, Akeson M, Timp W. Nanopore native RNA sequencing of a human poly(A) transcriptome [Internet]. bioRxiv. 2018 [cited 2018 Nov 28]. p. 459529. Available from: https://www.biorxiv.org/content/early/2018/11/09/459529.article-metrics
Simner PJ, Antar AAR, Hao S, Gurtowski J, Tamma PD, Rock C, Opene BNA, Tekle T, Carroll KC, Schatz MC, Timp W. Antibiotic pressure on the acquisition and loss of antibiotic resistance genes in Klebsiella pneumoniae. J Antimicrob Chemother [Internet]. 2018 Apr; Available from: http://dx.doi.org/10.1093/jac/dky121 PMID: 29648629
Workman RE, Myrka AM, Wong GW, Tseng E, Welch KC, Timp W. Single-molecule, full-length transcript sequencing provides insight into the extreme metabolism of the ruby-throated hummingbird Archilochus colubris. Gigascience [Internet]. 2018 Mar;7(3). Available from: https://academic.oup.com/gigascience/article/7/3/giy009/4860431
Roach NP, Sadowski N, Alessi AF, Timp W, Taylor J, Kim JK. The full-length transcriptome of C. elegans using direct RNA sequencing [Internet]. bioRxiv. 2019 [cited 2019 Apr 7]. p. 598763. Available from: https://www.biorxiv.org/content/10.1101/598763v1
Simpson JT, Workman RE, Zuzarte PC, David M, Dursi LJ, Timp W. Detecting DNA cytosine methylation using nanopore sequencing. Nat Methods. 2017 Apr;14(4):407–410.
Miga KH, Koren S, Rhie A, Vollger MR, Gershman A, Bzikadze A, Brooks S, Howe E, Porubsky D, Logsdon GA, Schneider VA, Potapova T, Wood J, Chow W, Armstrong J, Fredrickson J, Pak E, Tigyi K, Kremitzki M, Markovic C, Maduro V, Dutra A, Bouffard GG, Chang AM, Hansen NF, Thibaud-Nissen F, Schmitt AD, Belton JM, Selvaraj S, Dennis MY, Soto DC, Sahasrabudhe R, Kaya G, Quick J, Loman NJ, Holmes N, Loose M, Surti U, Risques Ra, Graves Lindsay TA, Fulton R, Hall I, Paten B, Howe K, Timp W, Young A, Mullikin JC, Pevzner PA, Gerton JL, Sullivan BA, Eichler EE, and Phillippy AM. Telomereto- telomere assembly of a complete human X chromosome. bioRxiv 2019. DOI: 10.1101/735928.