Timp, Winston

Assistant Professor
Biomedical Engineering
Lab Website

Clark Hall 118A
(410) 417-8467
wtimp@jhu.edu

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Johns Hopkins scholars, leaders celebrate faculty research awards

September 4, 2015

Scholars from across Johns Hopkins University’s 10 divisions gathered last night at the George Peabody Library to celebrate 60 innovative research projects that are being supported by the inaugural Catalyst and Discovery awards. Thirty-seven early career scholars (five of them from WSE) received Catalyst Awards and 23 cross-divisional faculty teams, which included 14 WSE faculty […]

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About

Education
  • Ph.D. 2007, Mass. Institute of Technology (MIT)
Experience
  • 2013 - Present:  Assistant Professor of Biomedical Engineering, Johns Hopkins University
  • 2007 - 2012:  Postdoctoral Fellow, Johns Hopkins University School of Medicine
Research Areas
  • Biology
  • Biophysics
  • Cancer
  • Clinical tools for human disease
  • Clinicla samples for diagnosis, surveillence, and treatment of human disease
  • Computational Biology
  • Diagnosis
  • Epigenome
  • Explore interesting questions about fundamental biological concepts using model systems
  • Genome
  • Hummingbird
  • Infectious Disease
  • Molecular Biology
  • Nanopore sequencing
  • Sequencing technologies
  • Transcriptome
Presentations
  • "Targeted DNA methylation in human cells using engineered {dCas9}-methyltransferases", Epigenetics and Bioengineering Conference.  Miami Florida, United States of America (the).  December 20, 2017
  • "Direct RNA and cDNA sequencing of the human transcriptome", Nanopore Community Meeting.  New York City New York, United States of America (the).  December 1, 2017
  • "Detecting Nucleotide Modifications Using Nanopore Sequencing", Invited Talk at NEB.  Ipswich MA, United States of America (the).  October 23, 2017
  • "Detecting nucleotide modifications using nanopore sequencing", JHU Pharmacology Departmental Seminar.  October 15, 2017
  • "Examining cancer with the {minION}: Methylation and structural variation", LabRoots Cancer Research and Oncology Virtual Event.  Boston Massachusetts, United States of America (the).  October 12, 2017
  • "Nanopore sequencing for exploration of infectious disease", JHU Microbiome Seminar.  October 1, 2017
  • "Measuring DNA methylation with the minION", London Calling.  London, England.  May 1, 2017
  • "Assembly and analysis of concurrent XDR and HMV K. pneumo substrains using nanopore sequencing", Sequencing Finishing and Analysis in the Future.  Santa Fe, NM.  May 1, 2017
  • "Detecting nucleotide modifications using nanopore sequencing", Advanced DNA Sequencing Technology Development.  Boston, MA.  May 1, 2017
  • "Direct RNA vs cDNA sequencing of C. elegans transcriptome", London Calling.  London, England.  May 1, 2017
  • "Nanopore sequencing: Methylation and structural variant calling", American Association for Cancer Research: ONT Workshop.  Washington, DC.  April 1, 2017
  • "Iso-seq transcriptome analysis of hummingbird Archilochis Colubris", Advances in Genome Biology and Technology.  Hollywood, FL.  February 1, 2017
  • "Antimicrobial resistance detection in Illumina and nanopore sequencing", Advances in Genome Biology and Technology (AGBT).  Hollywood, FL.  February 1, 2017
  • "Targeted nanopore sequencing for phased variant detection", Advanced in Genome Biology and Technology.  Hollywood, FL.  February 1, 2017
  • "Investigating extreme metabolism using the ruby-throated hummingbird transcriptome", Plant and Animal Genome Meeting: PacBio Workshop.  San Diego, CA.  January 1, 2017
  • "Iso-seq transcriptome analysis of hummingbird Archilochis Colubris", Plant and Animal Genome Meeting (PAG).  San Diego, CA.  January 1, 2017
  • "Structural variation detection on human DNA using targeted sequencing", Nanopore Community Meeting.  New York City, NY.  December 1, 2016
  • "Measuring DNA methylation with the minION", Nanopore Community Meeting.  New York City, NY.  December 1, 2016
  • "Site-Specific DNA Methylation Using Engineered dCas9-Methyltransferases", American Institute of Chemical Engineers National Meeting.  San Francisco, CA.  November 14, 2016
  • "The link between human telomerase reverse transcriptase (hTERT) promoter methylation status and alternative splicing in thyroid cancer", American Thyroid Association Meeting.  Denver, CO.  September 1, 2016
  • "Influenza monitoring and surveillance using nanopore sequencing", Options IX for the Control of Influenza (ISIRV).  Chicago, IL.  August 1, 2016
  • "RNA-programmed DNA methylation", 2016 Synthetic Biology: Engineering, Evolution & Design (SEED).  Chicago, IL.  July 19, 2016
  • "An extreme metabolism: Iso-seq analysis of the ruby-throated hummingbird", Pacific Biosystems User Group Meeting.  Baltimore, MD.  June 1, 2016
  • "Applications of nanopore sequencing for infectious disease detection", London Calling.  London, England.  June 1, 2016
  • "Methylation, microbiome and mobile elements: Applications of the minION", Department of Bioengineering.  College Park, MD.  April 1, 2016
  • "Measuring cytosine methylation using the minION", Advanced in Genome Biology and Technology (AGBT).  Orlando, FL.  February 1, 2016
  • "Nanopore sequencing detects structural variants in cancer", Advanced in Genome Biology and Technology (AGBT).  Orglando, FL.  February 1, 2016
  • "An Extreme Metabolism: Iso-Seq analysis of the Ruby-Throated Hummingbird Transcriptome.", Plant and Animal Genome Meeting.  San Diego, CA, USA.  January 12, 2016
  • "Methylation, Microbiome and Mobile Elements: Applications of the MinION.", MinION Community Meeting.  New York Genome Center, New York, NY, USA.  December 4, 2015
  • "Application and optimization of ATAC-seq for comparison of tumor-normal epigenetic state", Biomedical Engineering Society (BMES).  Tampa, FL.  October 1, 2015
  • "Unique molecular indexes to remove PCR bias in bisulfite sequencing", American Society of Human Genetics.  Baltimore, MD.  October 1, 2015
  • "Towards reliable detecting structural variants with nanopore sequencing", American Society of Human Genetics.  Baltimore, MD.  October 1, 2015
  • "Nanopore Based DNA Analysis: Sequencing and Beyond.", Invited Talk at Center for NanoScience and Technology.  South Bend, IN, USA.  July 20, 2015
  • "Modified base detection using Oxford Nanopore", London Calling.  London, England.  May 1, 2015
  • "Nanopore Based DNA Analysis: Sequencing and Beyond.", Invited talk in Division of Molecular Pathology.  Baltimore, MD, USA.  March 25, 2015
  • "Adenine and cytosine methylation sequencing on the minION", Advances in Genome Biology and Technology (AGBT).  Marco Island, FL.  February 1, 2015
  • "Exploration of cytosine methylation effects on protein-DNA binding", Biophysical Society.  Baltimore, MD.  February 1, 2015
  • "Nanopore Based DNA Analysis: Sequencing and Beyond", 8th Annual Young Investigators Symposium on Genomics and Bioinformatics.  Baltimore, MD, 21218.  October 30, 2014
  • "Nanopore Based DNA Analysis: Sequencing and Beyond", Mid-Atlantic DNA Nanotechnology Symposium.  Baltimore, MD, USA.  August 8, 2014
  • "Bedside Genomics: The Promise of Nanopore Sequencing", IEEE Webinar.  Internet.  March 26, 2014
  • "Minimizing the effects of bias in next-generation bisulfite sequencing", Advanced in Genome Biology & Technology (AGBT).  Marco Island, FL.  February 1, 2014
  • "A Unified View of Cancer as a Disease of Epigenetic Instability.", Invited Talk at Department of Bioengineering UIC.  Chicago, IL, USA.  September 6, 2013
  • "A Unified View of Cancer as a Disease of Epigenetic Instability", Invited Talk at Cold Spring Harbor Lab.  Cold Spring Harbor, NY, USA.  July 10, 2013
  • "A Unified View of Cancer as a Disease of Epigenetic Instability", Gordon Research Conference on Cancer Genetics & Epigenetics.  Lucca, Italy.  April 21, 2013
  • "Nanopore Sequencing Using A Hidden Markov Model For Base-calling", Biophysical Society Meeting.  Philadelphia, PA, USA.  February 4, 2013
  • "Optimizing a protocol for bisulfite library creation on the ion torrent", Ion World.  Boston, MA.  January 1, 2013

Publications

Journal Articles
  • Tamma PD, Fan Y, Bergman Y, Sick-Samuels AC, Hsu AJ, Timp W, Simner PJ, Prokesch BC, Greenberg DE (2018).  Successful treatment of persistent Burkholderia cepacia complex bacteremia with ceftazidime-avibactam.  Antimicrobial Agents and Chemotherapy.  62(4).
  • Xiong T, Meister GE, Workman RE, Kato NC, Spellberg MJ, Turker F, Timp W, Ostermeier M, Novina CD (2017).  Targeted DNA methylation in human cells using engineered dCas9-methyltransferases.  Scientific Reports.  7(1).
  • 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 (2017).  First draft genome sequence of the pathogenic fungus Lomentospora prolificans (formerly Scedosporium prolificans).  G3: Genes, Genomes, Genetics.  7(11).
  • Lee I, Rasoul BA, Holub AS, Lejeune A, Enke RA, Timp W (2017).  Data Descriptor: Whole genome DNA methylation sequencing of the chicken retina, cornea and brain.  Scientific Data.  4.
  • 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 (2017).  Multiplexed analysis of fixed tissue RNA using Ligation in situ Hybridization.  Nucleic acids research.  45(14).
  • Kandathil AJ, Breitwieser FP, Sachithanandham J, Robinson M, Mehta SH, Timp W, Salzberg SL, Thomas DL, Balagopal A (2017).  Presence of human hepegivirus-1 in a cohort of people who inject drugs.  Annals of Internal Medicine.  167(1).
  • Simpson JT, Workman RE, Zuzarte PC, David M, Dursi LJ, Timp W (2017).  Detecting DNA cytosine methylation using nanopore sequencing.  Nature Methods.  (4).
  • Norris AL, Workman RE, Fan Y, Eshleman JR, Timp W (2016).  Nanopore sequencing detects structural variants in cancer.  Cancer Biology and Therapy.  17(3).
  • Norris AL, Workman RE, Fan Y, Eshleman JR, Timp W (2016).  Nanopore sequencing detects structural variants in cancer..  Cancer biology & therapy.  0.
  • Timp W, Nice A, Nelson E, Kurz V, McKelvey K, Timp G (2014).  Think Small: Nanopores for Sensing and Synthesis.  IEEE Access.  2.  1396-1408.
  • Timp W, Bravo HC, McDonald OG, Goggins M, Umbricht C, Zeiger M, Feinberg AP, Irizarry RA (2014).  Large hypomethylated blocks as a universal defining epigenetic alteration in human solid tumors.  Genome Medicine.  6(8).
  • Timp W, Nice AM, Nelson EM, Kurz V, McKelvey K, Timp G (2014).  Think small: Nanopores for sensing and synthesis.  IEEE Access.  2.
  • Timp W, Bravo HC, McDonald OG, Goggins M, Umbricht C, Zeiger M, Feinberg AP, Irizarry R (2014).  Large hypomethylated blocks as a universal defining epigenetic alteration in human solid tumors..  Genome medicine.  6(8).  61.
  • Kurz V, Nelson EM, Perry N, Timp W, Timp G (2013).  Epigenetic memory emerging from integrated transcription bursts.  Biophysical Journal.  105(6).
  • Kurz V, Nelson EM, Perry N, Timp W, Timp G (2013).  Epigenetic memory emerging from integrated transcription bursts..  Biophysical journal.  105(6).  1526-32.
  • Timp W, Feinberg AP (2013).  Cancer as a dysregulated epigenome allowing cellular growth advantage at the expense of the host.  Nature Reviews Cancer.  13(7).
  • Timp W, Feinberg AP (2013).  Cancer as a dysregulated epigenome allowing cellular growth advantage at the expense of the host.  Nature Reviews. Cancer.  13(7).  497-510.
  • Nelson EM, Kurz V, Shim J, Timp W, Timp G (2012).  Using a nanopore for single molecule detection and single cell transfection.  Analyst.  137(13).
  • Nelson EM, Kurz V, Shim J, Timp W, Timp G (2012).  Using a nanopore for single molecule detection and single cell transfection..  The Analyst.  137(13).  3020-7.
  • Timp W, Comer J, Aksimentiev A (2012).  DNA base-calling from a nanopore using a viterbi algorithm.  Biophysical Journal.  102(10).
  • McDonald OG, Wu H, Timp W, Doi A, Feinberg AP (2011).  Genome-scale epigenetic reprogramming during epithelial-to-mesenchymal transition.  Nature Structural and Molecular Biology.  18(8).
  • 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 (2011).  Increased methylation variation in epigenetic domains across cancer types.  Nature Genetics.  43(8).
  • McDonald OG, Wu H, Timp W, Doi A, Feinberg AP (2011).  Genome-scale epigenetic reprogramming during epithelial-to-mesenchymal transition..  Nature structural & molecular biology.  18(8).  867-74.
  • Hansen KD, Timp W, Bravo HC, Sabunciyan S, Langmead B, McDonald OG, Wen B, Wu H, Liu Y, Diep D, others (2011).  Increased methylation variation in epigenetic domains across cancer types.  Nature genetics.  43(8).  768-775.
  • Mirsaidov UM, Wang D, Timp W, Timp G (2010).  Molecular diagnostics for personal medicine using a nanopore.  Wiley Interdisciplinary Reviews: Nanomedicine and Nanobiotechnology.  2(4).
  • Timp W, Mirsaidov UM, Wang D, Comer J, Aksimentiev A, Timp G (2010).  Nanopore Sequencing: Electrical Measurements of the Code of Life..  IEEE transactions on nanotechnology.  9(3).  281-294.
  • Timp W, Mirsaidov UM, Wang D, Comer J, Aksimentiev A, Timp G (2010).  Nanopore sequencing: Electrical measurements of the code of life.  IEEE Transactions on Nanotechnology.  9(3).
  • Timp W, Mirsaidov U, Matsudaira P, Timp G (2009).  Jamming prokaryotic cell-to-cell communications in a model biofilm..  Lab on a chip.  9(7).  925-34.
  • Timp W, Mirsaidov U, Matsudaira P, Timp G (2009).  Jamming prokaryotic cell-to-cell communications in a model biofilm.  Lab on a Chip - Miniaturisation for Chemistry and Biology.  9(7).
  • Mirsaidov U, Timp W, Zou X, Dimitrov V, Schulten K, Feinberg AP, Timp G (2009).  Nanoelectromechanics of methylated DNA in a synthetic nanopore.  Biophysical Journal.  96(4).
  • Timp W, Levchenko A, Feinberg AP (2009).  A new link between epigenetic progenitor lesions in cancer and the dynamics of signal transduction.  Cell Cycle.  8(3).
  • Timp W, Levchenko A, Feinberg AP (2009).  A new link between epigenetic progenitor lesions in cancer and the dynamics of signal transduction..  Cell cycle (Georgetown, Tex.).  8(3).  383-90.
  • Timp W, Levchenko A, Feinberg AP (2009).  A new link between epigenetic progenitor lesions in cancer and the dynamics of signal transduction.  Cell Cycle (Georgetown, Tex.).  8(3).  383-390.
  • Timp W, Matsudaira P (2008).  Chapter 14 Electron Microscopy of Hydrated Samples.  Methods in Cell Biology.  89.
  • Timp W, Mirsaidov U, Timp G (2008).  Stretching genes.  AIChE Annual Meeting, Conference Proceedings.
  • Mirsaidov U, Scrimgeour J, Timp W, Beck K, Mir M, Matsudaira P, Timp G (2008).  Live cell lithography: using optical tweezers to create synthetic tissue..  Lab on a chip.  8(12).  2174-81.
  • Mirsaidov U, Scrimgeour J, Timp W, Beck K, Mir M, Matsudaira P, Timp G (2008).  Live cell lithography: Using optical tweezers to create synthetic tissue.  Lab on a Chip - Miniaturisation for Chemistry and Biology.  8(12).
  • Mirsaidov U, Timp W, Timp K, Mir M, Matsudaira P, Timp G (2008).  Optimal optical trap for bacterial viability.  Physical Review E - Statistical, Nonlinear, and Soft Matter Physics.  78(2).
  • Mirsaidov U, Timp W, Timp K, Mir M, Matsudaira P, Timp G (2008).  Optimal optical trap for bacterial viability..  Physical review. E, Statistical, nonlinear, and soft matter physics.  78(2 Pt 1).  021910.
  • Timp W, Matsudaira P (2008).  Chapter 14: Electron microscopy of hydrated samples..  Methods in cell biology.  89.  391-407.
  • 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 MSH, Levchenko A, Feinberg AP (2007).  Enhanced sensitivity to IGF-II signaling links loss of imprinting of IGF2 to increased cell proliferation and tumor risk.  Proceedings of the National Academy of Sciences of the United States of America.  104(52).
  • Kaneda A, Wang C, 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 (2007).  Enhanced sensitivity to IGF-II signaling links loss of imprinting of IGF2 to increased cell proliferation and tumor risk..  Proceedings of the National Academy of Sciences of the United States of America.  104(52).  20926-31.
  • Zeskind BJ, Jordan CD, Timp W, Trapani L, Waller G, Horodincu V, Ehrlich DJ, Matsudaira P (2007).  Nucleic acid and protein mass mapping by live-cell deep-ultraviolet microscopy..  Nature methods.  4(7).  567-9.
  • Zeskind BJ, Jordan CD, Timp W, Trapani L, Waller G, Horodincu V, Ehrlich DJ, Matsudaira P (2007).  Nucleic acid and protein mass mapping by live-cell deep-ultraviolet microscopy.  Nature Methods.  4(7).
  • Akselrod GM, Timp W, Mirsaidov U, Zhao Q, Li C, Timp R, Timp K, Matsudaira P, Timp GL (2006).  Laser-guided assembly of heterotypic three-dimensional living cell microarrays.  Biophysical Journal.  91(9).
  • Akselrod GM, Timp W, Mirsaidov U, Zhao Q, Li C, Timp R, Timp K, Matsudaira P, Timp G (2006).  Laser-guided assembly of heterotypic three-dimensional living cell microarrays..  Biophysical journal.  91(9).  3465-73.
  • Timp W, Watson N, Sabban A, Zik O, Matsudaira P (2006).  Wet electron microscopy with quantum dots.  BioTechniques.  41(3).
  • Timp W, Watson N, Sabban A, Zik O, Matsudaira P (2006).  Wet electron microscopy with quantum dots..  BioTechniques.  41(3).  295-8.
  • Timp G, Bude J, Baumann F, Bourdelle KK, Boone T, Garno J, Ghetti A, Green M, Gossmann H, Kim Y, Kleiman R, Kornblit A, Klemens F, Moccio S, Muller D, Rosamilia J, Silverman P, Sorsch T, Timp W, Tennant D, Tung R, Weir B (2000).  The relentless march of the MOSFET gate oxide thickness to zero.  Microelectronics Reliability.  40(4-5).
  • Tennant DM, Timp GL, Ocola LE, Green M, Sorsch T, Kornblit A, Klemens F, Kleiman R, Muller DA, Kim Y, Timp W (2000).  Gate technology issues for silicon MOS nanotransistors.  Materials Research Society Symposium - Proceedings.  584.
  • Tennant DM, Timp GL, Ocola LE, Green M, Sorsch T, Kornblit A, Klemens F, Kleiman R, Kim Y, Timp W (1999).  Progress toward a 30 nm silicon metal-oxide-semiconductor gate technology.  Journal of Vacuum Science and Technology B: Microelectronics and Nanometer Structures.  17(6).
  • O'Malley ML, Timp GL, Timp W, Moccio SV, Garno JP, Kleiman RN (1999).  Electrical simulation of scanning capacitance microscopy imaging of the pn junction with semiconductor probe tips.  Applied Physics Letters.  74(24).
  • Garno JP, Kleiman RN, Moccio SV, O’Malley ML, Timp GL, Timp W (1999).  Electrical simulation of scanning capacitance microscopy imaging of the pn junction with semiconductor probe tips.  Applied Physics Letters.  74(24).  3672-3674.
  • Timp W, O'Malley ML, Kleiman RN, Garno JP (1998).  Two-dimensional dopant profiling of a 60 nm gate length nMOSFET using scanning capacitance microscopy.  Technical Digest - International Electron Devices Meeting.
  • Kleiman RN, O'Malley ML, Baumann FH, Garno JP, Timp WG, Timp GL (1998).  Direct channel length determination of sub-100 nm MOS devices using scanning capacitance microscopy.  Digest of Technical Papers - Symposium on VLSI Technology.
  • Sorsch T, Timp W, Baumann FH, Bogart KHA, Boone T, Donnelly VM, Green M, Evans-Lutterodt K, Kim CY, Moccio S, Rosamilia J, Sapjeta J, Silverman P, Weir B, Timp G (1998).  Ultra-thin, 1.0-3.0 nm, gate oxides for high performance sub-100 nm technology.  Digest of Technical Papers - Symposium on VLSI Technology.
Book Chapters
  • Nelson EM, Mirsaidov U, Sarveswaran K, Perry N, Kurz V, Timp W, Timp G (2015).  Ecology of a Simple Synthetic Biofilm.  The Physical Basis of Bacterial Quorum Communication.  Springer New York.  205-226.
Conference Proceedings
  • Garno J, Kleiman R, O’Malley M, Timp W (1998).  Two-dimensional dopant profiling of a 60 nm gate length nMOSFET using scanning capacitance microscopy.  Electron Devices Meeting, 1998. IEDM '98. Technical Digest., International.  555-558.
  • Baumann F, Bogart K, Boone T, Donnelly V, Evans-Lutterodt K, Green M, Kim C, Moccio S, Rosamilia J, Sapjeta J, Silvermann P, Sorsch T, Timp G, Timp W, Weir B (1998).  Ultra-thin, 1.0-3.0 nm, gate oxides for high performance sub-100 nm technology.  1998 Symposium on VLSI Technology, 1998. Digest of Technical Papers.  222-223.
Patents
  • Timp W  "Characterizing Stretched Polynucleotides in a Synthetic Nanopassage", 2011.
  • Timp W  "Detecting and Sorting Methylated DNA Using a Synthetic Nanopore", 2009.
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