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Dumitru Brinza Dumitru Brinza
Postdoctoral Associate, UCSD and Burnham Inst.

Department of Computer Science and Engineering
University of California at San Diego
9500 Gilman Drive M/C 0404
La Jolla, CA 92093-0404, USA
phone: 858-822-2496
e-mail:  dima@cs.ucsd.edu
web:http://www.cs.ucsd.edu/~dbrinza
Research: Computational biology, Bioinformatics, Algorithms, Discrete optimization, Proteomics, Ad-hoc wireless and Sensors networks.
  GSU Outstanding Graduate Research Award, 2006
  GSU Molecular Basis of Disease Fellowship, 2005/2006/2007
  Computational Genomics Conf. Travel & Registr. Awards, 2006
  Genetic Analysis Workshop 15 Scholarship, by Illumina, 2006
Postdoctoral advisor:
Pavel Pevzner
Ph.D advisor:
Alexander Zelikovsky
Education:
Ph.D in Computer Science (Bioinformatics)
Dept. of Computer Science, Georgia State University, USA, 2007
B.S. in Applied Mathematics , Specializing in Computer Science and Optimization Methods Dept. of Mathematics and Cybernetics, Moldova State University, 2002.
Refereed Journal Articles and Book Chapters:
  		•  Brinza, D. and Zelikovsky, A. (2007) `Design and Validation of Methods Searching for Risk Factors in Genotype Case-Control Studies', Journal of Computational Biology (JCB), pdf, ppt.
  		• Ilja M. Nolte, Andre R. de Vries, Geert T. Spijker, Ritsert C. Jansen, Dumitru Brinza, Alexander Zelikovsky, and Gerard J. te Meerman (2007) `Association testing by haplotype-sharing methods applicable to whole-genome analysis', BioMed Central (BMC), 1(Suppl 1):S129.
  		• Brinza, D., He, J., and Zelikovsky, A. (2007) `Optimization Methods for Genotype Data Analysis in Epidemiological Studies', book chapter in Bioinformatics Algorithms: Techniques and Applications, January 2007, pdf.
  		• Brinza, D. and Zelikovsky, A. (2007) `2SNP: Scalable Phasing Method for Trios and Unrelated Individuals', Journal of IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), invited, January 2007, pdf.
  		• Brinza, D. and Zelikovsky, A. (2006) `2SNP: Scalable Phasing Based on 2-SNP Haplotypes', BIOINFORMATICS , pdf
    Pub 2006 Feb 1;22(3):371-3. Epub 2005 Nov 15
  		• Brinza, D., He, J., Mao, W. and Zelikovsky, A. (2005) `Family Trio Phasing and Missing Data Recovery', International Journal Bioinformatics Research and Applications, IJBRA'05 Vol. 1, No.2 pp. 221 - 229, pdf, pdf2.

    Refereed Conference Articles:
  		•  Brinza, D. and Zelikovsky, A. (2007) `Risk Factor Searching Heuristics for SNP Case-Control Studies',Proc. of IEEE International conference on Bioinformatics and Biomedicine (BIBM 2007), to appear, pdf.
  		• Brinza, D. and Zelikovsky, A. (2007) `Discrete Methods for Association Search an Status Prediction in Genotype Case-Control Studies', Proc. of IEEE 7-th International Symposium on BioInformatics and BioEngineering (BIBE'07), pdf.
  		• Brinza, D. and Zelikovsky, A. (2006) `Combinatorial Analysis of Disease Association and Susceptibility for Rheumatoid Arthritis SNP Data', Travel Award, Proc. of 15-th Genetic Analysis Workshop (GAW15), 13:6-11, pdf.
  		• Andre R. de Vries, Ilja M. Nolte, Geert T. Spijker, Dumitru Brinza, Alexander Zelikovsky, and Gerard J. te Meerman (2006) `Cross Haplotype Sharing Statistic: Haplotype length based method for whole genome association testing', Proc. of 15-th Genetic Analysis Workshop (GAW15), 13:16-21, pdf.
  		• Brinza, D., He, J. and Zelikovsky, A. (2006) `Combinatorial Search Methods for Multi-SNP Disease Association', Proc. International Conf. of the IEEE Engineering in Medicine and Biology (EMBC'06), pp. 5802-5805, pdf, ppt.
  		• Brinza, D. and Zelikovsky, A. (2006) `Combinatorial Methods for Disease Association Search and Susceptibility Prediction', 6th Workshop on Algorithms in BioInformatics (WABI 2006), Lecture Notes in Bioinformatics 4175,p286-297, pdf, ppt.
  		• Brinza, D., Perelygin, A., Brinton, M. and Zelikovsky, A. (2006) `Search for multi-SNP Disease Association', The Fifth International Conference on Bioinformatics of Genome Regulation and Structure (BGRS'06), pp. 122–125, pdf, ppt.
  		• Brinza, D. and Zelikovsky, A. (2006) `DEEPS: Deterministic Energy-Efficient Protocol for Sensor networks', ACIS International Workshop on Self-Assembling Wireless Networks (SAWN'06), Proc. of SNPD 2006, pp. 261-266 pdf.
  		• Brinza, D. and Zelikovsky, A. (2006) `Phasing of 2-SNP Genotypes based on Non-Random Mating Model', International Workshop on Bioinformatics Research and Applications (IWBRA'06), Proc. of ICCS 2006, LNCS 3992, pp. 767–774, pdf.
  		• Mao, W., Brinza, D., Hundewale, N., Gremalschi, S. and Zelikovsky, A. (2006) `Genotype Susceptibility and Integrated Risk Factors for Complex Diseases', Proc. IEEE Intl Conf on Granular Computing (GRC 2006), pp. 754-757 pdf.
  		• Altun, G., Hu, H.-J., Brinza, D., Harrison, R.W., Zelikovsky, A. and Pan, Y. (2006) `Hybrid SVM kernels for protein secondary structure prediction', Proc. IEEE Intl Conf on Granular Computing (GRC 2006), pp. 762-765, pdf.
  		• Brinza, D., Calinescu, G., Tongngam, S. and Zelikovsky, A. (2005) `Energy-Efficient Continuous and Event-Driven Monitoring', 2nd IEEE International Conference on Mobile Ad-Hoc and Sensor Systems (MASS'05), 10.1109/MAHSS. 2005.1542792, pdf.
  		• Mao, W., He, J., Brinza, D. and Zelikovsky, A. (2005) `A Combinatorial Method for Predicting Genetic Susceptibility to Complex Diseases', International Conference of the IEEE Engineering In Medicine and Biology Society (EMBC'05),pp. 224-227, pdf.
  		• Brinza, D., He, J., Mao, W. and Zelikovsky, A. (2005) `Phasing and Missing Data Recovery in Family Trios', International Workshop on Bioinformatics Research and Applications (IWBRA'05),Proc. of ICCS 2005 LNCS 3515, pp. 1011-1019, pdf.
  		• Brinza, D., Hincu, G., (2002) `Design of multithread algorithm for Simplex method', Moldova State University Journal, pp. 17-32.
  		• Brinza, D., Savcenco, V., Bercu, I. and Magariu, N. (1998) `Developing of an Algorithms Builder', Publication in Moldova State University Journal, pp. 9-11, html.

    Poster and Oral Presentations:
  		•  Brinza, D. and Zelikovsky, A. (2007) ` Discrete Optimization Approach to Disease Association Search and Susceptibility Prediction Problems', Workshop on Discrete Mathematical Problems in Computational Biomedicine (DIMACS'07), ppt.
  		• Brinza, D., Astrovskaya, I., and Zelikovsky, A. (2007) `Greedy Approach to Reliable Disease Susceptibility Prediction', International Symposium on Bioinformatics Research and Applications (ISBRA'07), pdf.
  		• Gremalschi, S., Brinza, D., and Zelikovsky, A. (2007) `Model Fitting Disease Susceptibility Prediction Methods', 2nd Annual Computational and Systems Biology Symposium (CSBS 2007), ppt.
  		• Astrovskaya, I., Westbrooks, K., Brinza, D., and Zelikovsky, A. (2007) `Methods for Searching Atomic Risk Factors in Case-Control Studies', 2nd Annual Computational and Systems Biology Symposium (CSBS 2007), ppt.
  		• Brinza, D. and Zelikovsky, A. (2007) `Design and Validation of Methods Searching for Risk Factors in Genotype Case-Control Studies', The Third RECOMB Satellite Conference on SNPs & Haplotype Analysis (SNPHAP 2007), pdf, ppt.
  		• Brinza, D. and Zelikovsky, A. (2006) `Case(Control)-Free Multi-SNP Combinations in Case-Control Studies', Algorithmic Biology 2006, at University of California, San Diego, pdf, ppt, ppt.
  		• Brinza, D. and Zelikovsky, A. (2006) `Combinatorial Analysis of Disease Association and Susceptibility for Rheumatoid Arthritis SNP Data', Proc. of 15-th Genetic Analysis Workshop (GAW15), Travel Award, pdf.
  		• Brinza, D. and Zelikovsky, A. (2006) `Combinatorial methods for disease association search and susceptibility prediction', Proc. of 9-th Conference of Computational Genomics (CG'06), Travel Award, pdf.
  		• Barkhash, A., Perelygin, A., Brinza, D., Pilipenko, P., Bogdanova, YU., Romaschenko, A., Voevoda, M. and Brinton, M. (2006) `GENETIC RESISTANCE TO FLAVIVIRUSES', Genomics Proteomics Bioinformatics & Nanotechnologies for Medicine (GPBM'06), pdf.
  		• Brinza, D. and Zelikovsky, A. (2006) `Combinatorial Search Methods for Genotypes Associated with Lung Cancer', Mollecular Basis of Disease Symphosium (MBD'06), ppt.
  		• Barkhash, A., Perelygin, A., Brinza, D., Pilipenko, P., Bogdanova, YU., Romaschenko, A., Voevoda, M. and Brinton, M. (2006) `VARIABILITY IN THE 2’-5’ OLIGOADENYLATE SYNTHETASE (OAS) GENE CLUSTER IS ASSOCIATED WITH SEVERITY OF TICK-BORNE ENCEPHALITIS VIRUS-INDUCED DISEASE IN RUSSIAN PATIENTS', 9-th Southeastern Regional Virology Conference 2006, pdf.
     Brinza, D. and Zelikovsky, A. (2005) `2SNP: New Scalable Phasing Method', The Fifth Georgia TECH International Conference on Bioinformatics (GTICB'05), - best poster award - pdf.
  		• Brinza, D. and Zelikovsky, A. (2005) `2SNP: New Scalable Phasing Method', The Second SECABC Fall Workshop ON Biocomputing (SECABC'05), pdf.
  		• Brinza, D. and Zelikovsky, A. (2005) `New 2-SNP Statistics method for Phasing and Missing data recovery', Georgia State Biotech Symposium.
  		• Brinza, D., He, J., Mao, W. and Zelikovsky, A. (2005) `Family Trio Phasing and Missing Data Recovery', Research in Computational Molecular Biology (RECOMB'05), pdf, pdf.
  		• Brinza, D., Calinescu, G. and Zelikovsky, A. (2004) `Energy-Efficient Continuous and Event-Driven Monitoring', Georgia Electronic Design Center Industry Advisory Board (GEDC IAB'04), ppt.
  		• Brinza, D., Derado, G., Aznita, R., Li, Y. and Zelikovsky, A. (2004) `Energy efficient protocols for ad-hoc static networks', Georgia Electronic Design Center Industry Advisory Board (GEDC IAB'04), ppt.

    Refereeing:
    IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2007
    International Conference on Combinatorial Optimization and Applications (COCOA), 2007
    International Computing and Combinatorics Conference (COCOON), 2007
    International Symposium Bioinformatics Research and Applications (ISBRA), 2007
    International Journal of Data Mining and Bioinformatics, 2007
    IEEE Transactions on NanoBioscience, 2006
    IIEEE IEEE/ACM Transactions on Computational Biology and Bioinformatics(TCBB), 2006
    International Workshop Bioinformatics Research and Applications(IWBRA), 2006
    International Journal Bioinformatics Research and Applications(IJBRA), 2006
    First International Workshop on Mobile Ad-hoc and Ubiquitous Sensor Networks (MASN’05)
    IEEE Journal Systems, Man and Cybernetics, 2005
    IEEE Journal on Selected Areas in Communications, 2005

    Professional Service:
    PC member, IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2007
    Poster-Chair on International Symposium on Bioinformatics Research and Applications (ISBRA), 2007
    Co-Chair on International Workshop on Bioinformatics Research and Applications (IWBRA), 2006
    Conference Assistant IEEE Intl Conf on Granular Computing (GRC), 2006
    Technical Committee Second SECABC Fall Workshop on Biocomputing, 2005

    Teaching:
    Spring 2006: CSC4520/6520 Design and Analysis of Algorithms.
    Honors:
    • 2006 Genetic Analysis Workshop 15 Scholarship $1,600, sponsored by Illumina, St. Pete Beach, USA.
    • 2006 Computational Genomics Conf. Travel & Registr. Awards $1,500, Virginia Bioinformatics Inst., Virginia Tech, USA.
    • 2006 Molecular Basis of Disease Fellowship $22,000, GSU, Atlanta, USA.
    • 2006 Outstanding Graduate Research Award, GSU, Atlanta, USA.
    • 2005 Molecular Basis of Disease Fellowship $22,000, GSU, Atlanta, USA.
    • 2004 Georgia State University Scholarship $14,000, Atlanta, USA.
    • 2002 Moldova State University Stipend in commemoration of Professor Gherman, Chisinau, Moldova.
    • 2001 Soros stipend of grade III., Chisinau, Moldova.
    • 1999 First place in the Student's Olympiad in Math, Chisinau, Moldova.
    • 1998 Third place in the International Student's Olympiad in Computer Science, Chisinau, Moldova.
    • 1997 Moldova State University Scholarship, Chisinau, Moldova.
    • 1997 Participant of European Athletics Championship, Athens, Greece.
    • 1997-2001 Moldova Champion in javelin-throwing, Chisinau, Moldova.
    • 1997 First place in the Moldova competition in Computer Science, Chisinau, Moldova.
    • 1997 Second place in the Moldova competition in Physics, Chisinau, Moldova.
    • 1997 Third place in the Romania competition in Physics, Iasi, Romania.
    Speaking Languages: English, Russian(native), French, Romanian(native).

    Professional Experience:
    • 2007-0000 Postdoctoral Associate, CSE Department at UCSD, and Burnham Institute, San Diego, USA.
    • 2004-2007 Research Assistant, Department Computer Science, Georgia State University, Atlanta, USA.
    • 2002-2004 Software Engineer, Unisim-Soft S.R.L Copmany, Chisinau, Moldova.
    • 2001-2002 Senior Software Engineer, National Bank of Moldova, Chisinau, Moldova.
    • 2000-2001 Senior Software Engineer, Republican Center of Informatics and Calculus, Chisinau, Moldova.

    Certificates:

    Oracle PL/SQL Developer
    C Programmer
    Java1 Programmer
    Relational Database Management System Concepts

    Expertise:
    • Applications: Oracle 8i/10i, JBuilder, C++Builder, Delphi, MS Office, Microsoft Visual Basic, Adobe Photoshop, CorelDraw, 3D MAX, Apache, Toad, AutoCad, Macromedia Flash, MathLab, MySQL, MSSQL, Eclipse.
    • Languages: C/C++, Java, Assembler, PSP, JSP, PL/SQL, XML/XSL, HTML, JavaScript, DHTML, Delphi(Pascal), VB, COM, ActiveX, ASP, Perl, OODB, MPI, PVM.
    • Operating Systems: Dos/Windows 98/NT/2000/XP, UNIX, Linux, Solaris.
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