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Refereed Publications: J. Pel, D. Broemeling, L. Mai, H-L. Poon, G. Tropini, R.L. Warren, R.A. Holt, and A. Marziali “Non-linear Electrophoretic Response Yields a Unique Parameter for Separation of Biomolecules” published online in PNAS August 17, 2009 (PDF) (Supp Material) Daniel Branton, David W Deamer, Andre Marziali, Hagan Bayley, Steven A Benner, Thomas Butler, Massimiliano Di Ventra, Slaven Garaj, Andrew Hibbs, Xiaohua Huang, Stevan B Jovanovich, Predrag S Krstic, Stuart Lindsay, Xinsheng Sean Ling, Carlos H Mastrangelo, Amit Meller, John S Oliver, Yuriy V Pershin, J Michael Ramsey, Robert Riehn, Gautam V Soni, Vincent Tabard-Cossa, Meni Wanunu, Matthew Wiggin and Jeffery A Schloss, "The potential and challenges of nanopore sequencing", Nature Biotechnology 26, 1146 (2008).[PDF] Matthew Wiggin, Carolina Tropini, Vincent Tabard-Cossa, Nahid N. Jetha, and Andre Marziali, "Nonexponential Kinetics of DNA Escape from a-Hemolysin Nanopores", Biophysical Journal 95, 5317 (2008). Nahid N. Jetha, Matthew Wiggin, and Andre Marziali, “Forming an α-hemolysin nanopore for single molecule analysis”, Chapter 16A, Microfluids, Nanotechnologies, and Physical Science in Separation, Detection, Manipulation, and Analysis of Biomolecules, invited submission, in press (2008) Nahid N. Jetha, Matthew Wiggin, and Andre Marziali, Nanopore Force Spectroscopy on DNA Duplexes”, Chapter 16B, Microfluids, Nanotechnologies, and Physical Science in Separation, Detection, Manipulation, and Analysis of Biomolecules, invited submission, in press (2008) D. Broemeling , J. Pel, D. Gunn, L. Mai, J. Thompson, H. Poon, A. Marziali, “An Instrument for Automated Purification of Nucliec Acids from Contaminated Forensic Sample ” JALA, 2008, 13, 40-48 (PDF) Dylan Gunn, Jared Slobodan, Cheyenne Kamran, Justin Tzou, David Broemeling, Diponkar Banerjee and Andre Marziali "A Novel Applicator Design for Contact-Free Delivery of Aqueous Reagent to Individual Biopsies in a Tissue Microarray", Journal of the Association for Laboratory Automation. 12: 277-283, 2007 (PDF) Vincent Tabard-Cossa, Dhruti Trivedi, Matthew Wiggin, Nahid N Jetha and Andre Marziali, "Noise analysis and reduction in solid-state nanopores", Nanotechnology, 18, 305505, 2007 (PDF) C. Tropini and A. Marziali, "Parallel multi-nanopore force spectroscopy for DNA analysis", Biophysical Journal, 92, 1632-1637 (2007). (PDF) N. N. Jetha, A. Marziali. "Liquid-Handling Technology and the Method of Electrostatic Drop Transfer to Improve Dispensing Performance". Journal of the Association for Laboratory Automation. 11: 278-280 (2006) (PDF) Elisabeth Maurer-Spurej, Keddie Brown, Audrey Labrie, Andre Marziali and Otto Glatter "Portable dynamic light scattering instrument and method for the measurement of blood platelet suspensions", Phys. Med. Biol., 51 3747–3758, July 2006 (PDF) N. Jetha and A. Marziali, “An Electrostatic Device For Active Transfer Of Sub-Microliter Samples From Syringe Pipettors”, BioTechniques, 40: 148-151 FEB 2006 (PDF) *Duane E Smailus, Marco A Marra, Andre Marziali, Robert A Holt, “Simple, robust methods for high-throughput nanoliter-scale DNA sequencing”, Genome Research, 2005, 15: 1447 - 1450 R. Coope, A. Marziali, “Contaminant-induced current decline in capillary array electrophoresis”, Electrophoresis, 2005, 26, 11, 2128-2137 A. Marziali, J. Pel, D. Bizzotto, L. Whitehead, “Novel Electrophoresis Mechanism Based On Synchronous Alternating Drag Perturbation” Electrophoresis, 2005, 26, 82-90 (PDF) J. Nakane, M. Wiggin, A. Marziali, “A nano-sensor for trans-membrane capture and identification of single nucleic acid molecules” Biophysical Journal, 87: 615-621 July 2004. (PDF) Martin Krzywinski1, John Wallis2, Claudia Gösele3,4, Ian Bosdet1, Readman Chiu1, Tina Graves2, Oliver Hummel3, Dan Layman2, Carrie Mathewson1, Natasja Wye1, Baoli Zhu5, Derek Albracht2, Jennifer Asano1, Sarah Barber1, Mabel Brown-John1, Susanna Chan1, Steve Chand1, Alison Cloutier1, Jonathon Davito2, Chris Fjell1, Tony Gaige2, Detlev Ganten3, Noreen Girn1, Kurtis Guggenheimer, Heinz Himmelbauer4, Thomas Kreitler3,4, Stephen Leach1, Darlene Lee1, Hans Lehrach4, Andre Marziali, Michael Mayo1, Kelly Mead2, Teika Olson1, Pawan Pandoh1, Anna-Liisa Prabhu1, Heesun Shin1, Jason Thompson, Miranda Tsai1, Jason Walker2, George Yang1, Mandeep Sekhon2, LaDeana Hillier2, Heike Zimdahl3,4, Kazutoyo Osoegawa5, Shaying Zhao6, Asim Siddiqui1, Pieter J. de Jong5, Wes Warren2, Elaine Mardis2, John D. McPherson2, Rick Wilson2, Norbert Hübner3, Steven Jones1, Marco Marra1, Jacqueline Schein1,7, “Integrated and Sequence-Ordered BAC and YAC-based Physical Maps for the Rat Genome”, Genome Research, 14 (4): 766-779 APR 2004 (PDF) J. Nakane, M. Akeson, and A. Marziali, “Nanopore sensors for macromolecule analysis”, invited review for Journal of Physics: Condensed Matter, 2003, 15: R1365–R1393 (PDF) J. Thompson, T. Pugh, K. Guggenheimer, A. Safarpour, A. Christie, J. Pel, S. Chow, A. Marziali, “Facilitated Loading Of Horizontal Gels Using A Capillary Gel Comb”, BioTechniques, 2003, 34:814-818 (PDF) Wenonah A. Vercoutere , Stephen Winters-Hilt, Veronica S. DeGuzman, David Deamer , Sam Ridino , Joseph T. Rodgers, Hugh E. Olsen , Andre Marziali, and Mark Akeson, Discrimination Among Individual Watson-Crick Base-Pairs at the Termini of Single DNA Hairpin Molecules” Nucleic Acids Research, 2003, Vol. 31, 4, 1311-1318 (PDF) Greg Vatcher, Duane Smailus, Martin Krzywinski, Ran Guin, Jeff Stott, Miranda Tsai, Susanna Chan, Pawan Pandoh, George Yang, Jennifer Asano, Teika Olson, Anna-Liisa Prabhu, Robin Coope, Andre Marziali, Jacquie Schein, Steven Jones, and Marco Marra, “Resuspension of DNA Sequencing Reaction Products in Agarose Increases Sequence Quality on an Automated Sequencer”, BioTechniques, 2002 Sep;33(3):532-4, 536, 538-9 (PDF) J.Nakane, M. Akeson, A. Marziali, “Evaluation of nanopores as candidates for electronic analyte detection”, invited submission, Electrophoresis 2002, 23,2592–2601 (PDF) A. Marziali and M. Akeson, " New DNA Sequencing Methods", Annu. Rev. of Biomed. Eng. 2001, 3:195-223. (PDF) Jonathan Nakane, David Broemeling, Roger Donaldson, Andre Marziali, Thomas D. Willis, Matthew O’Keefe, and Ronald W. Davis**, "A Method For Parallel, Automated, Thermal Cycling Of Sub-Microliter Samples", Genome Res. 2001 11: 441-447. 2601 (PDF) Athanasios Theologis, Joseph R. Ecker, Curtis J. Palm, Nancy A. Federspiel, Samir Kaul, Owen White, Jose Alonso,Hootan Alta, Rina Araujo, Cheryl L. Bowman, Shelise Y. Brooks,Eugen Buehler, April Chan, Qimin Chao, Huaming Chen, Rosa F. Cheuk, Christina W. Chin, Mike K. Chung, Lane Conn, Aaron B. Conway, Andrew R. Conway, Todd H. Creasy, Ken Dewar,Patrick Dunn, Pelin Etgu, Tamara V. Feldblyum, Ji Dong Feng, BettyFong, ClaireY.Fujii, John E. Gill, Andrew D. Goldsmith, BrianHaas, Nancy F. Hansen, Beth Hughes, Lucas Huizar, Jonathan L. Hunter, Jennifer Jenkins, Chanda Johnson-Hopson, Shehnaz Khan, Elizabeth Khaykin, Christopher J. Kim, Hean L. Koo, Irina Kremenetskaia, David B. Kurtz, Andrea Kwan, Bao Lam, Stephanie Langin-Hooper, Andrew Lee, Jeong M. Lee, Catherine A. Lenz, Joycelyn. H. Li, YaPing Li, Xiaoying Lin, Shirley X. Liu, Zhaoying A. Liu, Jason S. Luros, Rama Maiti, Andre Marziali, Jennifer Militscher, Molly Miranda, Michelle Nguyen, William C. Nierman, Brian I. Osborne, Grace Pai, Jeremy Peterson, Paul K. Pham, Michael Rizzo, Timothy Rooney, Don Rowley, Hitomi Sakano, Steven L. Salzberg, Jody R. Schwartz, Paul Shinn, Audrey M. Southwick, Hui Sun, Luke J. Tallon, Gabriel Tambunga, Mitsue J. Toriumi, Christopher D. Town, Teresa Utterback, Susan Van Aken, Maria Vaysberg, Valentina S. Vysotskaia, Michelle Walker, Dongying Wu, Guixia Yu, Claire M. Fraser, J. Craig Venter & Ronald W. Davis, “Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana”, Nature 408, 816 - 820 (2000) (PDF) Andre Marziali, Thomas D. Willis, Nancy A. Federspiel, and Ronald W. Davis, “An Automated Sample Preparation System for Large Scale DNA Sequencing” Genome Res. 1999 9: 457-462. (PDF) Andre Marziali, Thomas D. Willis, and Ronald W. Davis, “An Arrayable Flow-Through Microcentrifuge for High Throughput Instrumentation”,Proc. Natl. Acad. Sci. USA 1999 Jan 5;96(1):61‑66 (this paper elicited a commentary: “Laue, T.M., “An arrayable flow-through microcentrifuge for high-throughput instrumentation–a matter of scale”,Proc. Natl. Acad. Sci. USA Vol. 96, p. 1163, February 1999) (PDF) (Commentary) A. Marziali, Nancy Federspiel, and Ron Davis, “Automation for the Arabidopsis Genome Sequencing Project”, Trends in Plant Science, Feb. 1997, Vol. 2, No. 2. (PDF) MARZIALI A, SMITH TI, SCHWETTMAN HA " WAVELENGTH SHIFTING IN THE STANFORD FEL" NUCL INSTRUM METH A 358: (1-3) 252-255 APR 11 1995 (PDF) A. Marziali and T.I. Smith, "Demonstration of Wavelength Stabilization in a Free Electron Laser", I.E.E.E. Journal of Quantum Electronics, vol. 30, no.9, September 1994. (PDF) MARZIALI A, SMITH TI " FEEDBACK STABILIZATION OF THE SCA FEL WAVELENGTH" NUCL INSTRUM METH A 331: (1-3) 59-61 JUL 1 1993 A. Marziali, H.A. Schwettman, J.G. Hatmaker, M.W. Hiller, H.G. Cambell, R. Sinko, M.W. Hamilton, C.G. Coghill, R. Dunham, J.L. Light, Carroll Allcock, "Fabrication Methods of the Superconducting Injector Cavities for the Stanford University Free Electron Laser", I.E.E.E. Trans. Magn., 27(2) p1916, March 1991.
Non-Refereed Publications: Jon Nakane, "Detection and Analysis of Nucleic Acids Using Nanometerscale Pores" PhD Thesis, UBC Applied Biophysics Lab, 2006 (PDF) Robin Coope , "Contaminant-Induced Current Decline in Capillary Array Electrophoresis" PhD Thesis, UBC Applied Biophysics Lab, 2006 (PDF) Joel Pel, "A Novel Electrophoretic Mechanism and Separation Parameter for Selective Nucleic Acid Concentration Based on SCODA" PhD Thesis, UBC Applied Biophysics Lab, 2009 (PDF)
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