Paul Dallaire’s Curriculum Vitae
March 2005
Département d’Informatique et de recherche opérationnelle
Université de Montréal
CP 6128, succ. Centre-Ville
Montréal, Québec, H3C-3J7 Canada
dallaire@iro.umontreal.ca
p.dallaire@sympatico.ca
Languages: French, English, c++.
University degrees
PhD in Computer Science. Université de Montréal. (ongoing)
miRNA discovery and siRNA construction.
Supervisor Dr. François Major (UofM).
Masters in Computer Science. Université de Montréal. (2001)
Oligonucleotides selection for DNA chips using splash trees. Efficiently solving the K Empty
Neighborhood problem.
Supervisor Dr. François Major (UofM),
co-supervisor Dr. Maureen O’Connor-McCourt (BRI/NRCC).
bioinformatics, algorithm desing, parsers, high dimensions clustering, PCA.
Masters in Virology and Immunology. Institut Armand-Frappier. (1994)
Effects of the 5’ untranslated region of the turnip mosaic potyvirus RNA on translation initiation.
Supervisor Dr. Jean-François Laliberté. Virology dept.
molecular biology, transgenic plants, eukaryote translation.
B.Sc. Biochemistry. Université du Québec à Trois-Rivières (1991)
Bioinformatics and Laboratory experience
Celmed Biosciences Inc., Montréal
Bioinformatician (2002-2003)
Bioinformatics group management. Focus on modeling of systems to promote discovery and support pre-clinical
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and clinical product development. Reconcile divergent requirements.
Key Responsibilities include :
• Plan the bioinformatics effort under FDA regulations constraints.
• Survey scientific landscape on system’s biology and give presentations.
• Interact productively with CSO, VPs, Lab directors, group leaders, focus students’ efforts and
extensively collaborate with University parties.
• Formulate internal requirements, meet with major hardware, software, validation and customized
solutions providers, evaluate proposals.
• Design and prototype ddb, a small generic LIMS for discovery activities.
Genevision/Warnex, Laval
Bioinformatician (June 2000 - April 2002)
C++, Perl, tools automation, suffix-trees, graph algorithms, gapless alignments, Linux, HTML, budgeting,
supervising, interacting with researchers, systems deployment and administration.
Key Responsibilities include :
• Run the bioinformatics effort.
• Establish strategies for bioinformatics problem solving with emphasis on marker discovery.
• Buy, budget, integrate hardware and software resources (Linux cluster, servers, workstations) and
management, planning for growth.
• Interact productively with molecular biologists and microbiologist.
• Program bioinformatics solutions on Linux.
• Supervise a small staff and a Master’s students efforts on tools parallelization.
National Research Council Canada. Biotechnology Research Institute. Montréal
Bioinformatics specialist. Computer Staff level 2 (2001, part time, term contract.)
Dr. Enrico Purisima’s laboratory. Modeling group. Health sector.
C++, Perl, interaction with researchers.
• Interact with group leaders and other researchers in the health sector on the subjects of
bioinformatics.
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• Tools (blast/fasta/clustal/web, EMBOSS, GCG, etc) automation using Perl to digest and dissect
ESTs and predicted genes.
• Write computer programs to solve selected bioinformatics problems when tools automation proves
insufficient.
Research Assistant and Technical Officer (1993-1994, 1995-1996, 1996-1997) PENCE, McGill
Dr. Maureen O’Connor-McCourt’s laboratory. Receptors group. Health sector.
radio ligands competitions, isotopic iodination, cell culture, PCR, cloning, sequencing, phage display, BIAcore,
windows C++ programming, RNA extractions, cDNA synthesis.
• Hunt for TGF-β type II homologs.
• TGF-α agonists research using phage-display.
• SPR-plot software development.
University of Québec in Trois-Rivières
Internship Pulp and paper research center. (1989-1990)
De-inking process optimization. aqueous phase electrophoresis.
Internship Research center on membrane biotechnologies. (1988-1989).
Liposomes isothermal surface charge measurements. biochemistry and electro-chemistry
Teaching experience
Instructor Initiation to bioinformatics DESI. UofM (automn 2003).
Instructor Programming II (using Java) CS dept. UofM (winter 2003).
Teaching assistant Programming using Java for non programmers UofM.(summer 2000).
Teaching assistant Data structures (using C++) CS dept. UofM (winter 2000).
Teaching assistant Programming II (using Java) CS dept. UofM (fall 1999).
Web tutorial Static CORBA 2.2 using C++ on Linux with omniORB. CS dept. UofM (winter 1998).
(retired)
Guest speaker Involved introduction to set photography. École du show-business.(winter 1996).
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Software
ddb (2002, ongoing) The Discovery DataBase is a secure, web based generic LIMS targetted at
supporting discovery activities in a laboratory in a user friendly and graphical view. Ddb is based on
Open Source software, in particular Tomcat (jsp and servlets). The system tracks experiment types,
products storage, samples and alliquots, user roles, data generators, data role and type, events, etc. Ddb
also converts files on the fly (fcs to excel and the likes) for presentation. Ddb acts as a hub between
various OS, equipements, types of users and tools through a dynamic XML interface and manages
backups. (this code is proprietary.)
cpf (2001) Given a potentially large set of PCR primer pairs and a fasta formatted stream of DNA, Check
Primers Fast will find all PCR products potentially amplified by any of the pairs (or their reverse
complement) and generate a set of web pages describing hits. User selectable mismatches number
(reasonable value) between oligonucleotides and target sequences. This software proved valuable for
building PCR DNA chips and on other occasions. Using all 10 CPU’s on NRC’s Sun Enterprise server,
thousands of primer pairs are validated against refseq in less than 5 minutes. Excellent results can also be
achieved on Linux boxes if sufficient RAM is provided. (Linux/sun, C++, SMP machines.)
aleas3 (2001) Uses Splash trees (as introduced in my Masters thesis) with randomization of input to
locate K-unique fixed length mers in sets of DNA sequences potentially suitable for oligonucleotides
DNA chips (or arrays) fabrication. Outputs a blastable fasta formatted stream of candidates or a
colorized HTML file. (Linux, C++).
moligs (2001) Restricted version of aleas3 based on different ideas (hashing). Extremely rapid but usable
only on a limited set of conditions. (Linux/SunOS, C++).
gbp and friends (2000) A GenBank Parser complemented with a suite developed during my Masters
but while interested to other projects. Object oriented wrappers for genbank and swissprot dataformats.
Also includes some of EMBOSS’s programs output parsers, blast drivers and other goodies. Hardly
usable by anybody else before documentation is done. (C++, flex, Linux, GNU.)
uniks (2000-2001) Extraction of markers (with errors) for subsets of sequences starting with unaligned
DNA sequences. C++, Linux, HTML, suffix-trees, graph algorithms. (proprietary, patentability currently
under investigation)
cronblast (1999) blast email alerting system for community of users. cgi, c++, shell. (restricted access,
retired code)
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SPRplot and SPRlink (1998) Data visualization and point picking tool for Excel and Visual-Basic used
in a numeric integration tool developed for BIAcore data analysis. Significant user base. C++, Borland
windows (3.1, 95, NT), dll.
(SPRevolution’s data GUI: http://www.bri.nrc.ca/csrg/equipf.htm#biacore).
Favored software tools and languages
greatest things are free emacs, CVS, gcc, GNU/Linux, forte, Tomcat, postgresql, SAPDB, other
unices.
fluent C++, Java, SQL, C, shell, make, flex, web, CORBA.
familiarity Perl, assembly (x86), Qt, OpenGL, prolog, Ada95.
Scientific publications
Tang, X.-B., Dallaire, P., Hoyt, D.W., Sykes, B.D., O’Connor-McCourt, M.D. and Malcolm, B.A. (1997)
Construction of Transforming Growth Factor-a (TGF-a) Phage Library and Identification of High
Binders of Epidermal Growth Factor Receptor (EGFR) by Phage Display. J. Biochem., 122:686-690
Basso J, Dallaire P, Charest PJ, Devantier Y, Laliberté JF (1995) Evidence for an internal ribosome entry
site within the 5’ non-translated region of the turnip mosaic potyvirus RNA. J. Gen. Virol. 75: 3157-3165.
Presentation and poster. PENCE annual 1995. TGF-alpha and phage display.
Posters on TuMV’s 5’UTR in 1993: ICTV (Glasgow, Scotland), Plant/Microbe interaction Rutgers
University (NJ, USA), ACFAS (Rimouski, Québec).
Stays, formations, symposiums
I had the good fortune to participate to a number of formations, stays and collaborations. Topics include:
molecular modeling, BIAcore, combinatorial chemistry, phage display, biolistic DNA transfer,
distributed programming with CORBA, algorithmic approaches to gene discovery, bioinformatics, etc.
Other things I enjoy doing
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• Play with my child.
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