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Items: 31

1.

Applying Rapid Whole Genome Sequencing to Predict Phenotypic Antimicrobial Susceptibility Testing Results Among Carbapenem-Resistant Klebsiella pneumoniae Clinical Isolates.

Tamma PD, Fan Y, Bergman Y, Pertea G, Kazmi A, Lewis S, Carroll KC, Schatz MC, Timp W, Simner PJ.

Antimicrob Agents Chemother. 2018 Oct 29. pii: AAC.01923-18. doi: 10.1128/AAC.01923-18. [Epub ahead of print]

PMID:
30373801
2.

A Loss of Epigenetic Control Can Promote Cell Death through Reversing the Balance of Pathways in a Signaling Network.

Vanaja KG, Timp W, Feinberg AP, Levchenko A.

Mol Cell. 2018 Oct 4;72(1):60-70.e3. doi: 10.1016/j.molcel.2018.08.025. Epub 2018 Sep 20.

PMID:
30244832
3.

Antibiotic pressure on the acquisition and loss of antibiotic resistance genes in Klebsiella pneumoniae.

Simner PJ, Antar AAR, Hao S, Gurtowski J, Tamma PD, Rock C, Opene BNA, Tekle T, Carroll KC, Schatz MC, Timp W.

J Antimicrob Chemother. 2018 Apr 10. doi: 10.1093/jac/dky121. [Epub ahead of print]

PMID:
29648629
4.

Single-molecule, full-length transcript sequencing provides insight into the extreme metabolism of the ruby-throated hummingbird Archilochus colubris.

Workman RE, Myrka AM, Wong GW, Tseng E, Welch KC Jr, Timp W.

Gigascience. 2018 Mar 1;7(3):1-12. doi: 10.1093/gigascience/giy009.

5.

Successful Treatment of Persistent Burkholderia cepacia Complex Bacteremia with Ceftazidime-Avibactam.

Tamma PD, Fan Y, Bergman Y, Sick-Samuels AC, Hsu AJ, Timp W, Simner PJ, Prokesch BC, Greenberg DE.

Antimicrob Agents Chemother. 2018 Mar 27;62(4). pii: e02213-17. doi: 10.1128/AAC.02213-17. Print 2018 Apr.

6.

Whole genome DNA methylation sequencing of the chicken retina, cornea and brain.

Lee I, Rasoul BA, Holub AS, Lejeune A, Enke RA, Timp W.

Sci Data. 2017 Oct 10;4:170148. doi: 10.1038/sdata.2017.148.

7.

First Draft Genome Sequence of the Pathogenic Fungus Lomentospora prolificans (Formerly Scedosporium prolificans).

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.

G3 (Bethesda). 2017 Nov 6;7(11):3831-3836. doi: 10.1534/g3.117.300107.

8.

Multiplexed analysis of fixed tissue RNA using Ligation in situ Hybridization.

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.

Nucleic Acids Res. 2017 Aug 21;45(14):e128. doi: 10.1093/nar/gkx471.

9.

Targeted DNA methylation in human cells using engineered dCas9-methyltransferases.

Xiong T, Meister GE, Workman RE, Kato NC, Spellberg MJ, Turker F, Timp W, Ostermeier M, Novina CD.

Sci Rep. 2017 Jul 27;7(1):6732. doi: 10.1038/s41598-017-06757-0.

10.

Presence of Human Hepegivirus-1 in a Cohort of People Who Inject Drugs.

Kandathil AJ, Breitwieser FP, Sachithanandham J, Robinson M, Mehta SH, Timp W, Salzberg SL, Thomas DL, Balagopal A.

Ann Intern Med. 2017 Jul 4;167(1):1-7. doi: 10.7326/M17-0085. Epub 2017 Jun 6.

11.

Detecting DNA cytosine methylation using nanopore sequencing.

Simpson JT, Workman RE, Zuzarte PC, David M, Dursi LJ, Timp W.

Nat Methods. 2017 Apr;14(4):407-410. doi: 10.1038/nmeth.4184. Epub 2017 Feb 20.

PMID:
28218898
12.

Nanopore sequencing detects structural variants in cancer.

Norris AL, Workman RE, Fan Y, Eshleman JR, Timp W.

Cancer Biol Ther. 2016;17(3):246-53. doi: 10.1080/15384047.2016.1139236. Epub 2016 Jan 19.

13.

Large hypomethylated blocks as a universal defining epigenetic alteration in human solid tumors.

Timp W, Bravo HC, McDonald OG, Goggins M, Umbricht C, Zeiger M, Feinberg AP, Irizarry RA.

Genome Med. 2014 Aug 26;6(8):61. doi: 10.1186/s13073-014-0061-y. eCollection 2014.

14.

Epigenetic memory emerging from integrated transcription bursts.

Kurz V, Nelson EM, Perry N, Timp W, Timp G.

Biophys J. 2013 Sep 17;105(6):1526-32. doi: 10.1016/j.bpj.2013.08.010.

15.

Cancer as a dysregulated epigenome allowing cellular growth advantage at the expense of the host.

Timp W, Feinberg AP.

Nat Rev Cancer. 2013 Jul;13(7):497-510. doi: 10.1038/nrc3486. Epub 2013 Jun 13. Review.

16.

DNA base-calling from a nanopore using a Viterbi algorithm.

Timp W, Comer J, Aksimentiev A.

Biophys J. 2012 May 16;102(10):L37-9. doi: 10.1016/j.bpj.2012.04.009. Epub 2012 May 15.

17.

Using a nanopore for single molecule detection and single cell transfection.

Nelson EM, Kurz V, Shim J, Timp W, Timp G.

Analyst. 2012 Jul 7;137(13):3020-7. doi: 10.1039/c2an35571j. Epub 2012 May 29.

18.

Genome-scale epigenetic reprogramming during epithelial-to-mesenchymal transition.

McDonald OG, Wu H, Timp W, Doi A, Feinberg AP.

Nat Struct Mol Biol. 2011 Jul 3;18(8):867-74. doi: 10.1038/nsmb.2084.

19.

Increased methylation variation in epigenetic domains across cancer types.

Hansen KD, Timp W, Bravo HC, Sabunciyan S, Langmead B, McDonald OG, Wen B, Wu H, Liu Y, Diep D, Briem E, Zhang K, Irizarry RA, Feinberg AP.

Nat Genet. 2011 Jun 26;43(8):768-75. doi: 10.1038/ng.865.

20.

Nanopore Sequencing: Electrical Measurements of the Code of Life.

Timp W, Mirsaidov UM, Wang D, Comer J, Aksimentiev A, Timp G.

IEEE Trans Nanotechnol. 2010 May 1;9(3):281-294.

21.

Molecular diagnostics for personal medicine using a nanopore.

Mirsaidov UM, Wang D, Timp W, Timp G.

Wiley Interdiscip Rev Nanomed Nanobiotechnol. 2010 Jul-Aug;2(4):367-81. doi: 10.1002/wnan.86. Review.

22.

Jamming prokaryotic cell-to-cell communications in a model biofilm.

Timp W, Mirsaidov U, Matsudaira P, Timp G.

Lab Chip. 2009 Apr 7;9(7):925-34. doi: 10.1039/b810157d. Epub 2008 Dec 11.

PMID:
19294303
23.

Nanoelectromechanics of methylated DNA in a synthetic nanopore.

Mirsaidov U, Timp W, Zou X, Dimitrov V, Schulten K, Feinberg AP, Timp G.

Biophys J. 2009 Feb 18;96(4):L32-4. doi: 10.1016/j.bpj.2008.12.3760.

24.

A new link between epigenetic progenitor lesions in cancer and the dynamics of signal transduction.

Timp W, Levchenko A, Feinberg AP.

Cell Cycle. 2009 Feb 1;8(3):383-90. Epub 2009 Feb 3. Review.

PMID:
19177016
25.

Chapter 14: Electron microscopy of hydrated samples.

Timp W, Matsudaira P.

Methods Cell Biol. 2008;89:391-407. doi: 10.1016/S0091-679X(08)00614-6.

PMID:
19118683
26.

Live cell lithography: using optical tweezers to create synthetic tissue.

Mirsaidov U, Scrimgeour J, Timp W, Beck K, Mir M, Matsudaira P, Timp G.

Lab Chip. 2008 Dec;8(12):2174-81. doi: 10.1039/b807987k. Epub 2008 Oct 1.

PMID:
19023484
27.

Optimal optical trap for bacterial viability.

Mirsaidov U, Timp W, Timp K, Mir M, Matsudaira P, Timp G.

Phys Rev E Stat Nonlin Soft Matter Phys. 2008 Aug;78(2 Pt 1):021910. Epub 2008 Aug 25.

PMID:
18850868
28.

Enhanced sensitivity to IGF-II signaling links loss of imprinting of IGF2 to increased cell proliferation and tumor risk.

Kaneda A, Wang CJ, Cheong R, Timp W, Onyango P, Wen B, Iacobuzio-Donahue CA, Ohlsson R, Andraos R, Pearson MA, Sharov AA, Longo DL, Ko MS, Levchenko A, Feinberg AP.

Proc Natl Acad Sci U S A. 2007 Dec 26;104(52):20926-31. Epub 2007 Dec 17.

29.

Nucleic acid and protein mass mapping by live-cell deep-ultraviolet microscopy.

Zeskind BJ, Jordan CD, Timp W, Trapani L, Waller G, Horodincu V, Ehrlich DJ, Matsudaira P.

Nat Methods. 2007 Jul;4(7):567-9. Epub 2007 Jun 3.

PMID:
17546037
30.

Wet electron microscopy with quantum dots.

Timp W, Watson N, Sabban A, Zik O, Matsudaira P.

Biotechniques. 2006 Sep;41(3):295-8.

31.

Laser-guided assembly of heterotypic three-dimensional living cell microarrays.

Akselrod GM, Timp W, Mirsaidov U, Zhao Q, Li C, Timp R, Timp K, Matsudaira P, Timp G.

Biophys J. 2006 Nov 1;91(9):3465-73. Epub 2006 Aug 4.

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