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Joanne Macdonald
Associate Research Scientist
650 W168th St, BB1019, New York, NY 10032
Phone: (212)305-0351
Fax: (212)305-3475
Email: jm2236@columbia.edu

Academic Qualification

PhD

Training

• 2004-Present, Molecular engineering and biocomputing, experimental therapeutics, medical diagnostics and biological imaging
  Division of Experimental Therapeutics and Clinical Pharmacology, Department of Medicine, Columbia University, New York, USA
  
• 2002-2004 Postdoctoral Research Scientist, 2 years, West Nile, SARS and Borna disease virus pathogenesis and diagnosis
  Jerome L. and Dawn Greene Infectious Disease Laboratory, Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, USA
  
• 1998-2002 PHD, 4 years (Awarded 12 June 2003), Thesis - Flaviviral small nonstructural proteins and their interactions
  Arbovirus Research Laboratory, Department of Microbiology and Parasitology, School of Molecular and Microbial Sciences, University of Queensland, Brisbane, Australia
  
• 1997-1998 Research Assistant, 8 months, Iron-regulating genes of Pseudomonas aeruginosa
  Department of Chemistry, University of Queensland, Brisbane, Australia
  
• 1996-1997 Honours Class I, 1 year, Thesis - An antigenic and genetic investigation into the phylogeny of Edge Hill virus
  Department of Microbiology and Parasitology, University of Queensland, Brisbane, Australia
  
• 1996 Technical officer, 6 months, Routine microbiological testing of meat and bone meal
  CSIRO, Division of Food Science and Technology, Brisbane, Australia.
  
• 1993-1996 Bachelor of Science, 3 years, University of Queensland, Brisbane, Australia
• 1995 Undergraduate project, 6 months, Edge Hill virus antigenicity
  Department of Microbiology and Parasitology, University of Queensland, Brisbane, Australia.
• 1994-1995 Undergraduate summer project, 3 months, Cholera toxin co-regulated pillus distribution
• Department of Microbiology and Parasitology, University of Queensland, Brisbane, Australia.

Discipiline

Cybernetics, Molecular Diagnostics & Engineering, Molecular Virology

Research Interests

Molecular Computation: Logic gate circuits and game-playing automata.

• IN THE NEWS! MAYA-II was published 07 October 2006. Maya-II is a second-generation molecular automaton (a molecular array of YES and ANDNOT gates) that plays tic-tac-toe.

• Molecular Diagnostics: Rapid computational arrays for multiplex SNP detection (including A-i mutations), viral lineage attribution (including West Nile virus and Avian Influenza virus), and small molecule discrimination (including Vasopressin).
• Molecular Engineering: Artificial enzymes for substance abuse; Vasopressin partial agonists to treat vasodilatory shock.
• Molecular Virology: West Nile virus replication; Edge Hill virus phylogeny
  

Honors And Awards

• 2006 Young scientist registration bursary Genomes to Systems Conference 2006, Manchester, U.K.
• 2001-2002 PHD completion scholarship University of Queensland, Brisbane, Australia.
• 2001 Young scientist grant 6th International Symposium on Positive Strand RNA viruses, Paris, France.
• 2000 Best student oral presentation 8th Arbovirus research in Australia, 4th Mosquito control association of Australia International symposium, Stradbroke Island, Australia
• 1998-2001 Australian postgraduate award University of Queensland, Brisbane, Australia.
• 1997 Becton Dickinson award, runner up Queensland Branch, Australian Society for Microbiology, Brisbane, Australia
  

Publications

• Joanne Macdonald (2007) DNA-based calculators with 7-segment displays. The 13th International Meeting on DNA Computing, Memphis, Tennessee, June 2007, Session E3
  
• Joanne Macdonald, Yang Li, Marko Sutovic, Harvey Lederman, Kiran Pendri, Wanhong Lu, Benjamin L. Andrews, Darko Stefanovic, and Milan N. Stojanovic (2006) Medium Scale Integration of Molecular Logic Gates in an Automaton. Nano Letters, 6 (11), 2598 -2603.
• Yashin R., Macdonald J., Korkina O., Stojanovic M.N., Rudchenko S. (May 2006) Flow Cytometry Analysis of Modular Aptameric Sensors Conjugated to Microspheres. ISAC XXIII International Congress, Québec, Canada. Poster P240.
• Macdonald J., Li Y., Sutovic M., Stefanovic D., Stojanovic M.N. (March 2006) Oligonucleotide-detecting automata for games and genome analysis. Genomes to Systems Conference, Manchester, U.K. Poster BN-2.
• Macdonald J., Stefanovic D., and Stojanovic M.N. (2006) Solution-Phase Molecular-Scale Computation With Deoxyribozyme-Based Logic Gates and Fluorescent Readouts, in Methods in Molecular Biology, vol 335: Fluorescent energy transfer nucleic acid probes: designs and protocols (Didenko, V.V., Ed.) Chapter 22, pp 343-363, Humana Press Inc., Totowa, NJ.
• Lederman H., Macdonald J., Stefanovic D., Stojanovic M.N. (2006) Deoxyribozyme-Based Three-Input Logic Gates and Construction of a Molecular Full Adder. Biochemistry. 45(4):1194-9.
• Macdonald J., Tonry J., Hall R.A., Williams B., Palacios G., Mundrigi A.S., Jabado O., Briese T., Travassos Da Rosa A.P.A., Clark D., Tesh R.B., Lipkin W.I. (2005) NS1 protein secretion during the acute phase of West Nile virus infection. Journal of Virology. 22:13924-33.
• Stojanovic M.N., Semova S., Kolpashchikov D., Macdonald J., Morgan C., Stefanovic D., (2005) Deoxyribozyme-Based Ligase Logic Gates and Their Initial Circuits. Journal of the American Chemical Society, 127(19):6914-5.
• Macdonald J., Terry T.D., Harris J.M., Mackenzie J.M., and Hall R.A. (2001). Phage display and the study of flaviviral protein interactions. 6th International Symposium on Positive Strand RNA viruses, Paris, France. Poster P2-02.
• Pyke A.T., Williams D.T., Nisbet D.J., van den Hurk A.F., Taylor C.T., Johansen C.A., Macdonald J., Hall R.A., Simmons R.J., Mason R.J.V., Lee J.M., Ritchie S.A., Smith G.A., and Mackenzie J.S. (2001). The appearance of a second genotype of Japanese encephalitis virus in the Australasian region. American Journal of Tropical Medicine and Hygiene, 65(6):747-753.
• Macdonald J., Broom A.K., Doggett S.L., Mackenzie J.S., Phillips D.A., Poidinger M., Russell R.C., Young P.R. and Hall R.A. (2001) The phylogeny of Edge Hill virus. Arbovirus Research in Australia 8:225-230.
• Nisbet D.J., Hall R.A., Johansen C.A., Macdonald J., Paru J., Ritchie S.A., Saleh S., Van den Hurk A.F., Zborowski P. and Mackenzie J.S. (2001). Isolation of Sepik virus from Papua New Guinea. Arbovirus Research in Australia 8:263-266.
• Johansen C.A., van den Hurk A.F., Ritchie S.A., Zborowski P., Nisbet D.J., Paru R., Bockarie M.J., Macdonald J., Drew A.C., Khromykh T.I., Mackenzie J.S. (2000). Isolation of Japanese encephalitis virus from mosquitoes (Diptera: Culicidae) collected in the Western Province of Papua New Guinea, 1997-1998. American Journal of Tropical Medicine and Hygiene. 62(5):631-8.
• Peake J., Hall R.A., Mackenzie J.S., Broom A.K., Poidinger M. (1997) An investigation into the phylogeny of Edge Hill virus. Microbiology Australia 18(4):Oral presentation A79.

Press

• 01 October 2007, Molecular computation and MAYA-II featured in Biotechnology Healthcare review by Bob Carlson
• 01 March 2007, MAYA-II and applications featured in Journal of Chemical Education 84(3):378 review by Angela G. King
• 31 December 2006, Columbia University In Vivo Newsletter write up of MAYA-II
• 12 December 2006, IEEE Computer publication reports on MAYA-II (.pdf file)
• 30 October 2006, MAYA-II featured in Information Week: University Researchers Break Ground In Molecular Computing
• 18 October 2006, MAYA-II featured in Scientific American: DNA Computer Plays Complete Game of Tic-Tac-Toe
• 18 October 2006, MAYA-II mentioned in Yahoo News, India: DNA computer is tic-tac-toe champ
• 18 October 2006, MAYA-II featured at the Inquirer: DNA computer manages noughts and crosses. Always wins, eventually
• 17 October 2006, MAYA-II comments at Slashdot: Researchers Debut DNA-Powered Computer
• 17 October 2006, MAYA-II featured at New Scientist: 'DNA computer' is unbeatable at tic-tac-toe
• 16 October 2006, MAYA-II featured at www.Engadget.com: Meet Maya II the new DNA computer that can play tic-tac-toe
• 16 October 2006, American Chemical Society (ACS) issues press release on our second-generation Tic-Tac-Toe Molecular Automaton MAYA-II: DNA computing targets West Nile Virus, other deadly diseases
• 11 October 2006, MAYA-II automaton featured at www.Nanowerk.com: Molecular automaton plays tic-tac-toe
• 04 August 2006, New Scientist feature on MAYA-II and combinatorial arrays: DNA processors cash in on silicon's weaknesses
  

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