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Annex 3. Curriculum vitae – Research team

Annex 3.1. Ivan Brukner’s CV

Curriculum Vitae

Name

Ivan Brukner

Office Address

Hospital Ste-Justine, B479, 3175 Cote-Ste-Catherine, Montreal, Qc, H3T 1C5 & Jewish General Hospital, 3755 Côte-Sainte-Catherine Road, Montréal, Québec, Canada, H3T 1E2

Telephone [phone] ext. 3376

Fax [phone]
Date of Birth

13-11-1960

Social Insurance No.

279602379

Citizenship

Canadian and Serbian

Home Address

3754 av. Kent, Montreal, H3S1N3, QC, Canada

Spouse's Name

Maja Krajinovic

Children

Danko Brukner

Place of Birth

Novi Sad, Serbia

EDUCATION:
Undergraduate
Jovan Jovanovic Zmaj High School-Gymnasium, Novi Sad, Serbia, www.jjzmaj.edu.yu
Graduate
B.Sci Molecular Biology and Physiology, Faculty of Biology, University of Belgrade, 1985 http://www.bg.ac.yu/

(University courses and marks enclosed as a separate file)

M.Sci: Sequence-dependent structural variations of DNA revealed by DNase I, Molecular Biology, Faculty of Biology, University of Belgrade, Yugoslavia, 1990. Supervisor, Prof Dr Ana Savic
PhD: Structural polymorphisms of DNA, Molecular Biology, University of Belgrade, Yugoslavia, 1993. Supervisor Prof. Ana Savic
Research training
Graduate training

International Center for Genetic Engineering and Biotechnology (ICGEB/UNIDO), Trieste, Italy;

Practical Course: Computer Methods in Molecular biology, 1990, http://www.icgeb.trieste.it/home.html
Biochemistry and Biophysics Department, University of Trieste, Italy;

Project: Triple helix formation and DNA methylation (09/91–01/92), supervisors Drs Giorgio Manzini and Luigi Xodo, www.units.it/

EMBO fellowship, European Molecular Biology Organization Heidelberg, Germany;

Project: Biological Structures and Biocomputing Division, DNA-DNase I interactions (01/92-07/1992), supervised by Dr Dietrich Suck, http://www.embl-heidelberg.de/

Postgraduate training

ICGEB/UNIDO postdoctoral fellow: International Center for Genetic Engineering and Biotechnology, Trieste, Italy, Protein Structure and Function (07/1992-02/1995).

Project: sequence-dependent structural variations of DNA, supervised by Dr Sandor Pongor, http://www.icgeb.trieste.it/home.html
MRC post-doctoral fellow, Red Cross Society and Cancer Institute de Montreal (CIM), Montreal (03/1995-1997)

Project: DNA structural and functional elements: impact on recombination; topology of DNA and transfection capacity of vector supervised by Dr Pierre Chartrand, Director of CIM

APOINTMENTS and WORK EXPERIENCE
Teaching Assistant 1986-1991, University of Belgrade, Faculty of Biology, Department of Molecular Biology and Biochemistry, http://www.bg.ac.yu/
Assistant Professor, 1991, University of Belgrade, Faculty of Biology, Department of Molecular Biology and Biochemistry, http://www.bg.ac.yu/
Lady Davis Institute (07/1997-10/1998), McGill AIDS Center, Montreal, Research Associate;

Projects: monitoring cell distribution of non-nucleoside inhibitors of HIV RT, antisense effect of arabinonucleic acids, cloning and expression of HIV nucleocapside 7, supervised by Drs Michael Parniak and Masad Damha

Biochemistry Department, University of Montreal (10/1998–06/1999), Research Associate;

Project: Oligonucleotide Libraries, supervised by Prof Dr Robert Cedergren

Procrea Bioscience Inc, Montreal, Research and Development, (06/1999-05/2000), Research Associate;

Project: Cloning and expression of GFP-fused reporter genes relevant for beta oxidation of fatty acids, supervised by Dr Pierre Chartrand, www.procrea.com/

Signal Gene Inc, Montreal, Research and Development, Scientist, 05/2000-10/2001, DNA arrays;

Projects: RNA-related techniques, in vitro transcription, in vitro translation, NASBA isothermal amplification, cloning and expression of GFP-fused reporter assay for genes involved in apoptotic pathway, Director of Research and Development Dr Larry Malek

Genizon Inc., Montreal, Research and Development, (2001-2003) Senior Scientist,

Projects: Ligation Based Genotyping, Long Range PCR, Whole Genome Amplification procedures, construction of cloning system based on inactivation of suicidal gene (ccdt), expressed under arabinose promoter (pBAD derivative), Director of Research and Development: Dr Bruno Paquin

CHU Sainte-Justine, Research Center, Montreal Senior Research Associate, (2003-now),

Projects: Whole Genome Amplification over small genomes or degraded DNA; Selection of robust diagnostic probes using in vitro evolution, supervised by Drs Damian Labuda and Maja Krajinovic

Clinical Laboratory of Jewish General Hospital – Microbiology and Immunology, Montreal, (2007-now), Senior Research associate;

Project: Clostridium Difficile, sample processing and assay development, supervised by Dr Andre Dascal, www.jgh.ca

SPECIAL HONORS, AWARDS, RECOGNITION
Contribution of the year 1995: Curved DNA without AA-TT dinucleotide step: effect of ions, 1995, Biological Structure and Dynamics, NY, Albany.
EMBO Heidelberg, fellowship, (01/92- 07/1992)
ICGEB/UNIDO, Italy, post-doctoral fellowship, (07/1992-02/1995)
MRC-CIHR, Montreal, post-doctoral fellowship (1996-1998)

Invited Lectures, Talks, Presentations
1. DNA bending, bendability and curvature: Biological Structure and Dynamics, Volumes One and Two

The Proceedings of the Ninth Conversation held at The University-SUNY Albany, NY, June 20-24, 1995.

2. Generating aptamers from complex biological mixtures/fluids: Differential SELEX, University of Sherbooke, Department of Biochemistry, Medical Faculty, 1998.
3. Using combinatorial oligonucleotide approach in medicine: applications in diagnostic and therapy, St-Justine Hopital, Montreal, 1998.
4. New diagnostic-relevant oligonucleotide probes, Innogenetics, Gent, Belgium, 2003, http://www.innogenetics.com/
OTHER CONTRIBUTIONS

Journals Reviews
Current Drugs (5), Analytical Biochemistry (32) and European Biochemistry (2)
Grant Reviews and Panel Member
Current Drugs International panel of evaluators for new drugs and patents under development (08/1996–2001).
External expert for EC project proposals (DNA arrays, molecular biology and biotechnology, European Union Commission, (October, 2003-2007)).
Professional and Scientific Contributions
Confidential Disclosure Agreements (CDA) with Invitrogen (US) 1997, AmershamBioscience (US) 2003, HySeq (US), 2000, Affymetrics (US), 2000, Digene (US), 2003; Innogenetics (EU), 2003, GE Bioscience (2006); Complete Genomics, (2008).
Patents:
1. Brukner, I., Belmaaza, A. and Noureddine, R: SELECTIVE TECHNIQUE FOR RAPID IDENTIFICATION OF PROTEINS AND GENES AND USES THEREOF (US 6.331.777), PolyGene, Montreal, 1997.
2. Paquin, B, Brukner, I., Tremblay, G.: PROCESS FOR THE GENERATION OF OLIGONUCLEOTIDE LIBRARIES (OLs) REPRESENTATIVE OF GENOMES OR EXPRESSED mRNAs (cDNAs) AND USES THEREOF (EP 12810.62 US 12810.63 and CA 12810.61), University of Montreal,1999.
3. Brukner, I., Belouchi, A. and Paquin, B US patent pending: PRIMER DESIGN FOR REMOVING BACKGROUND IN AMPLIFICATION BASED ON RANDOM PRIMING, Gallielo Genomics Inc, 2003
4. Brukner, I , Krajinovic, M and Labuda, D. (2006) US patent pending: AMPLIFICATION OF NUCLEIC ACID SEQUENCES, St Justine Hospital-UNIVALOR # 60/750,049; Filed 12-14-2005.
5. Brukner, I , Krajinovic, M and Labuda, D. (2006-now) Provisional US patent application # 60/882,153: NUCLEIC ACID PROBES, METHODS FOR THEIR PREPARATION AND USES THEREOF; WO-2008017162; Filed 08-11-2006).

Publications

Articles in peer reviewed journals.
Drmanac, R., Labat, I., Brukner, I. and Crkvenjakov, R (1989): Sequencing of megabase plus DNA by hybridization: Theory of the Method, Genomics, 4, 114-128.
Brukner, I., Jurukovski, V. and Savic, A. (1990): Sequence-dependent structural variations of DNA revealed by DNase I, Nucleic Acids Res. 18, 891-894.
Brukner, I., Jurukovski, V., Konstantinovic, M. and Savic, A. (1991): Curved DNA without AA/TT dinucleotide step, Nucleic Acids Res. 19, 3549-3551.
Brukner, I., Dlakic, M., Savic, A., Susic, S., Pongor, S. and Suck, D. (1993): Evidence for opposite groove-directed curvature of GGGCCC and AAAAA sequence elements, Nucleic Acids Res. 21, 1025-1029.
Brukner, I., Susic, S., Dlakic, M., Savic, A. and Pongor S. (1994): Physiological concentration of Mg2+ ions induces a strong macroscopic curvature in GGGCCC-containing DNA, J.Mol. Biol. 236, 26-32.
Wolf, E., Brukner, I. and Suck, D. (1995): Mutation analysis of DNase I-DNA interaction: design, expression and characterization of a DNaseI loop-insertion mutant with altered sequence selectivity, Protein Engineering 8, 283-291.
Brukner, I., Sanchez, R., Suck, D. and Pongor, S. (1995): Sequence-dependent bending propensity of DNA as revealed by DNaseI: parameters for trinucleotides, EMBO J., 14, 1812-1818.
Brukner, I., Sanchez, R., Suck, D. and Pongor, S. (1995): Trinucleotide Models for DNA Bending Propensity: Comparison of Models Based on DNaseI Digestion and Nucleosome Packing Data, J. Biomol. Stuct. Dyn., 13, 309-317.
Brukner, I., Belmaaza A. and Chartrand, P. (1997) Differential behavior of curved DNA upon untwisting, Proc. Natl. Acad. Sci. USA, 94, 403-406.
Damha, M.J., Wilds, C. J., Noronha, A., Brukner, I., Borkow , G. and Parniak, M.A. (1998) Hybrids of RNA and Arabinonucleic Acids (ANA and 2’F-ANA) are Substrates of Ribonuclease H, JACS, 120, 12976-12977.
Brukner, I. & Tremblay G. (2000) RNA targeting by antisense oligonucleotides strongly depends on protein-oligonucleotide interaction: new in vitro assay, Biochemistry. 39(37):11463-6.
Brukner, I., Tremblay, G. & Paquin, B. (2002) The generation of amplifiable genome-specific oligonucleotide probes-libraries, BioTechniques, 33:874-882.
Brukner, I., Paquin, B., Belouchi, M., Labuda, D. and Krajinovic, M. (2005) Decrease of self-priming by random oligonucleotides increase the performance of whole genome amplification, Analytical Biochemistry, 339(2):345-7.
Brukner, I., Labuda, D. and Krajinovic, M. (2006) Phi29-based amplification of small genomes. Analytical Biochemistry, 354(1):154-6.
Brukner, I., El-Ramahi1 R, Gorska-Flipot, I., Krajinovic, M. and Labuda, D (2007) An in vitro selection scheme for oligonucleotide probes to discriminate between closely related DNA sequences, Nucl Acids Res. 2007;35(9):e66.
Brukner, I., El-Ramahi; R., Jacob Sawicki; J., Gorska-Flipot, I., Krajinovic, M. and Labuda, D.(2007) Hybridization assay for typing high risk Human Papillomaviruses performed at ambient temperature, Journal of Clinical Virology, 39 (2):113-8.
Brukner I, Krajinovic M, Dascal A, Labuda D. (2007) A protocol for the in vitro selection of specific oligonucleotide probes for high-resolution DNA typing. Nature Protoc. ;2 (11):2807-14.

Gorska-Flipot I, Sawick J, Gaboury LA, Krajinovic M, Labuda D, Brukner I, Rouleau D, Ghattas G, Franco EL, Coutlée F. Newly-isolated HPV97, related to HPV18 and 45 is frequently detected in HIV-positive men from the Montreal area. Int J Cancer. 2008, 122(5):1195-7.

Krajinovic, M. and Brukner, I. (2008) Further insight into the markers of methotrexate resistance in childhood acute lymphoblastic leukemia patients. Personilized Medicine; 5 (4), 2008, 325-329.
Technical reports and books
Gabrielian, A., Vlahovicek, K., Munteanu, M., Gromiha, M, Brukner, I., Sanchez, R. and Pongor, S. (1998) Prediction of bendability and curvature in genomic DNA in Biomolecular Structures & Dynamics, Adenine Press
Brukner, I. C-1027 (2000) Taiho Pharmaceutical Co Ltd. Current Opinion in Oncologic, Endocrine & Metabolic Investigational Drugs 2 (3), 344-352.
Brukner, I. (2001) OvaRex AltaRex, IDdrugs, 4 (4), 457-462.
Brukner, I. (2001) INGN-201. Introgen Therapeutics. Curr Opin Investig Drugs, 2 (12):1776-85.
Reviews
Brukner, I. and Pongor, S. (1995): A trinucleotide Model for Sequence-Dependent DNA Bending Propensity, Biological Structure and Dynamics, 2, 289-294.
Abstracts and conference presentations
Sawicki J, Gaboury LA, Krajinovic M, Labuda D, Brukner I, Coutlée F, Gorska I (2006) Cloning strategy of a new type of Human Papilloma Virus from a clinical sample with mixed HPV infection. 23 International Papillomavirus Conference and Workshop, Prague
Developing genome resources for Clostridium difficile V Forgetta, MT Oughton, I Brukner, A Villeneuve, G Levesque, C Nagy, J Dias, V Magrini, M Hickenbotham, K Haub, C Markovic, J Nelson, E Mardis, A Dascal, K Dewar; poster presentation at Genome Canada annual conference, Quebec City, October 2007
Al-Shakfa F, Brukner I, St-Onge G, Moghrabi A, Krajinovic M (2008) Pharmacogenetics of DHFR in childhood ALL. 1st Annual Canadian Human Genetics Conference, 9-12 avril, St-Sauveur, Canada.
Al-Shakfa F, Brukner I, St-Onge G, Moghrabi A, Krajinovic M (2008) Pharmacogenetics of DHRF in childhood ALL. Les Journées Génétiques RMGA, May 14-16, Québec, Canada
Al-Shakfa F, Brukner I, St-Onge G, Moghrabi A, Krajinovic M (2008) Pharmacogenetics of DHFR in childhood ALL. IXth World Conference on Clinical Pharmacology and Therapeutics - CPT2008 July 27 - August 1, Québec City, Canada.
MT Oughton, V Forgetta, I Brukner, A Villeneuve, G Levesque, C Nagy, J Dias, V Magrini, M Hickenbotham, K Haub, C Markovic, J Nelson, E Mardis, A Dascal, K Dewar; (2008) Comparative genomics analysis of Clostridium difficile: improving methods for detection, epidemiology, therapeutics and understanding pathogenicity poster presentation at AMMI Canada/CACMID annual conference
Brukner I, Krajinovic M, Labuda D (2008) Robust performance of in vitro generated hybridizations probes: suitable for different nucleic-acid based diagnostic-detection platforms. XX International Congress of Genetics, July 12-17, Berlin, Germany.