Publications

Publication List (in reverse chronological order)  Lab members highlighted in bold:

Lee I, Rasoul BA, Holub AS, Lejeune A, Enke RA§, Timp W§. Whole genome DNA methylation sequencing of the chicken retina, cornea and brain. Scientific Data. 2017 Oct 10;4:sdata2017148.

Luo R, Zimin A, Workman R, Fan Y, Pertea G, Grossman N, Wear MP, Jia B, Miller H, Casadevall A, Timp W, Zhang SX, Salzberg SL. First Draft Genome Sequence of the Pathogenic Fungus Lomentospora prolificans (formerly Scedosporium prolificans). G3 (Bethesda). 2017 Sep 29; PMID: 28963165

Xiong T, Meister GE, Workman RE, Kato NC, Spellberg MJ, Turker F, Timp W, Ostermeier M, Novina CD. Targeted DNA methylation in human cells using engineered dCas9-methyltransferases. Sci Rep [Internet]. 2017 Jul 27;7. PMCID: PMC5532369

Credle JJ, Itoh CY, Yuan T, Sharma R, Scott ER, Workman RE, Fan Y, Housseau F, Llosa NJ, Bell WR, Miller H, Zhang SX, Timp W, Larman HB. Multiplexed analysis of fixed tissue RNA using Ligation in situ Hybridization. Nucleic Acids Res. 2017 Aug 21;45(14):e128. PMID: 28854731

Kandathil AJ, Breitwieser FP, Sachithanandham J, Robinson M, Mehta SH, Timp W, Salzberg SL, Thomas DL, Balagopal A. Presence of Human Hepegivirus-1 in a Cohort of People Who Inject Drugs. Ann Intern Med. 2017 Jul 4;167(1):1–7. PMID: 28586923

Workman RE, Myrka AM, Tseng E, Wong GW, Welch KC§, Timp W.§ Single molecule, full-length transcript sequencing provides insight into the extreme metabolism of ruby-throated hummingbird Archilochus colubris. bioRxiv. 2017 Mar 15;117218.

Simpson JT§, Workman RE, Zuzarte PC, David M, Dursi LJ, Timp W§. Detecting DNA cytosine methylation using nanopore sequencing. Nat Meth. 2017 Apr;14(4):407–410. PMID: 28218898

Norris AL, Workman RE, Fan Y, Eshleman JR, Timp W.§. Nanopore sequencing detects structural variants in cancer. Cancer Biology & Therapy. 2016 Jan 19;0(0):1–8. PMID: 26787508

Timp W, Nice AM, Nelson EM, Kurz V, McKelvey K, Timp G. Think Small: Nanopores for Sensing and Synthesis. IEEE Access. 2014;2:1396–1408.

Timp W, Bravo HC, McDonald OG, Goggins M, Umbricht C, Zeiger M, Feinberg AP, Irizarry RA. Large hypomethylated blocks as a universal defining epigenetic alteration in human solid tumors. Genome Med. 2014;6(8):61. PMCID: PMC4154522

Timp W, Feinberg AP. Cancer as a dysregulated epigenome allowing cellular growth advantage at the expense of the host. Nat Rev Cancer. 2013 Jul;13(7):497–510.

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 Journal102, 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 and Molecular Biology. 10.1038/nsmb.2084. (PMID: 21725293)

Hansen, K.D.*, W. Timp*, H.C. Bravo*, S. Sabunciyan*, B. Langmead*, O.G. McDonald, B. Wen, H. Wu, 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. doi: 10.1038/ng.865. (PMID: 21706001)

Timp, W., U. M. Mirsaidov, D. 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. (PMID: 21572978)

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. (PMID: 19217843)

Timp, W., A. Levchenko, and A. P. Feinberg. 2009. A New Link Between Epigenetic Progenitor Lesions in Cancer and the Dynamics of Signal Transduction. Cell Cycle 8 (3):383-390. (PMID: 19177016)

Timp, W., and P. Matsudaira. 2008. Electron Microscopy of Hydrated Samples. In Biophysical Tools for Biologists, Vol 2: In Vivo Techniques. San Diego: Elsevier Academic Press Inc. (PMID: 19118683)

Timp, W., U. Mirsaidov, P. Matsudaira, and G. Timp. 2009. Jamming prokaryotic cell-to-cell communications in a model biofilm. Lab on a Chip 9:925-934. (PMID: 19294303)

Mirsaidov, U., J. Scrimgeour, W. Timp, K. Beck, M. Mir, P. Matsudaira, and G. Timp. 2008. Live cell lithography: Using optical tweezers to create synthetic tissue. Lab on a Chip 8 (12):2174-2181. (PMID: 19023484)

Mirsaidov, U,* W. Timp*, K. Timp, M. Mir, P. Matsudaira, and G. Timp. 2008. Optimal optical trap for bacterial viability. Physical Review E 78 (2):7. (PMID: 18850868)

Kaneda, A., C. J. Wang, R. Cheong, W. Timp, P. Onyango, B. Wen, C. A. Lacobuzio-Donahuel, R. Ohlsson, R. Andraos, M. A. Pearson, A. A. Sharov, D. L. Longol, M. S. H. Ko, A. Levchenko, and A. P. Feinberg. 2007. Enhanced sensitivity to IGF-II signalling links loss of imprinting of IGF2 to increased cell proliferation and tumour risk. Proceedings of the National Academy of Sciences of the United States of America 104 (52):20926-20931. (PMID: 18087038)

Zeskind, B.J., C.D. Jordan, W. Timp, D.J. Ehrlich, and P. Matsudaira. 2007. Mapping Nucleic Acid and Protein Mass in Live Cells by Deep Ultraviolet Microscopy. Nature Methods 4: 567-569. (PMID: 17546037)

Akselrod, G. M., W. Timp, Q. Zhao, C. Li, U. Mirsaidov, R. Timp, K. Timp, P. Matsudaira, and G. Timp. 2006. Laser-Guided Assembly of Heterotypic 3D Living Cell Microarrays. Biophysical Journal 91 (9):3456-3464. (Cover Article) (PMID: 16891375)

Timp, W., N. Watson, A. Sabban, O. Zik, and P. Matsudaira. 2006. Wet Electron Microscopy with Quantum Dots. Biotechniques 41 (3):295-298. (PMID: 16989089)

Tennant, D. M., G. L. Timp, L. E. Ocola, M. Green, T. Sorsch, A. Kornblit, F. Klemens, R. Kleiman, Y. Kim, and W. Timp. 1999. Progress toward a 30 nm silicon metal-oxide-semiconductor gate technology. Journal of Vacuum Science & Technology B 17 (6):3158-3163. 

O’Malley, M. L., G. L. Timp, W. Timp, S. V. Moccio, J. P. Garno, and R. N. Kleiman. 1999. Electrical simulation of scanning capacitance microscopy imaging of the pn junction with semiconductor probe tips. Applied Physics Letters 74 (24):3672-3674.