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Welcome
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Publications
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Research
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Teaching
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email
cedric.chauve [at] sfu.ca
office
(SFU) : SC K10516
Tel: (778) 782-7091
Fax: (778) 782-4947
mail address
Cedric Chauve
Dep. Mathematics, SFU
8888 University Drive
Burnaby, BC, V5A 1S6, Canada
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Supervised students and post-docs
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Postdocs
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Julien Courtiel (Spring 2015, SFU, Mathematics, joint supervision with Yann Ponty and Marni Mishna)
Research topics: RNA structures alignments
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Jérémie Lumbroso (2013, SFU, Mathematics, joint supervision with Marni Mishna)
Research topics: combinatorics, probabilistic counting
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Roland Wittler (2010, SFU, Mathematics)
Research topics: cancer genomics, comparative genomics.
Papers: BMC Bioinformatics 2011, CPM 2011,
J. Comp. Biol. (RECOMB-CG 2010 issue).
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Aida Ouangraoua (2008-2009, SFU, Mathematics, joint supervision with Anne Bergeron, UQAM).
Research topics: computational comparative genomics.
Papers: ISBRA 2009,
J. Comp Biol (RECOMB-CG 2009 issue),
J. Comput. Biol. (RECOMB-CG 2010 issue),
TCS 2011,
Bioinformatics 2011.
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Eric Fusy (2007-2008, SFU, Mathematics, PIMS-CNRS PDF,
joint supervision with Marni Mishna, SFU)
Research topics: graph families enumeration.
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Annie Chateau (2004-2006, UQAM, joint supervision with Anne
Bergeron, UQAM).
Research topics: computational comparative genomics.
Papers: WABI 2004,
RECOMB-CG 2006,
APBC 2007.
Graduate students, PhD
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Fang Zhang (2015-, PhD, SFU, MADD_Gen, joint supervision with Leonid Chindelevitch)
Research topics: computational epidemiology.
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Ehsan Hasghshenas (2014-, PhD, SFU, MADD_Gen, joint supervision with Cenk Sahinalp and Faraz Hach)
Research topics: algorithms for PacBio long reads.
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Nina Luhmann (2013-, PhD, Bielefeld, Didy, joint supervision with Jens Stoye and Roland Wittler)
Research topics: paleogenomics scaffolding
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Ashok Rajaraman (2011-2015, PhD, SFU, Mathematics)
Research topics: ancestral genomes reconstruction.
Papers:
thesis,
Bioinformatics 2012,
JOBIM 2013,
IWOCA 2013,
Bioinformatics 2013,
Science 2014.
TCBB 2016.
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Murray Patterson (2006-2011, PhD, UBC, Computer Science, joint supervision with Arvind Gupta and Jan Manuch)
Research topics: complexity of C1P variants.
Papers:
thesis,
EUROCOMB 2009,
DAM 2012,
CPM 2011,
J. Comp. Biol. (RECOMB-CG 2010 issue, paper 1),
J. Comp. Biol. (RECOMB-CG 2010 issue, paper 2).
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Jean-Philippe Doyon (2004-2010, PhD, Computer Science,
Université de Montréal, joint supervision with Sylvie
Hamel, UdM, and Hervé Philippe, UdM).
Research topics: algorithms for gene family evolution
Papers:
thesis,
RECOMB-CG 2007,
J. Comp Biol (RECOMB-CG 2007 issue),
RECOMB-CG 2008,
J. Comp Biol (RECOMB-CG 2008 issue),
Software Tools and Algorithms for Biological Systems 2011,
TCBB 2012.
Graduate students, MSc
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Alice Yue (2015-, MSc, SFU, MADD_Gen, joint supervision with Ryan Brinkman).
Research topics: flow cytometry algorithms.
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France Paquet-Nadeau (2015-, MSc, SFU, Mathematics, joint supervision with Marni Mishna)
Research topics: enumeration of seeds neighbourhoods.
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Akbar Raffiey (2014-, MSc, SFU, Mathematics, joint supervision with Jan Manuch and Ladislav Stacho)
Research topics: vertex ordering problems in computational biology.
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Maria Tamayo (2010-2013, MSc, SFU, Mathematics, joint supervision with Tamon Stephen)
Research topics: Tucker patterns
Papers:
thesis.
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Mehrnoush Malekesmaeili (2010-2012, MSc, SFU, Mathematics, senior supervision by Tamon Stephen)
Research topics: non-C1P matrices
Papers: thesis,
IPL 2012.
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Ahmad Mahmoody Ghaidary (2009-2011, MSc, SFU, Mathematics, joint supervision with Ladislav Stacho)
Research topics: DCJ median algorithms
Papers:
thesis,
poster (RECOMB-CG 2010, IWOCA 2011),
ArXiV 1111.5872.
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Ashok Rajaraman (2009-2011, MSc, SFU, Mathematics)
Research topics: ancestral protein-protein interaction networks
Thesis.
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Vivija You (2007-2009, MSc, SFU, Mathematics)
Research topics: The Consecutive-Ones Property
Papers: thesis, RECOMB-CG 2009,
J. Comput. Biol. (RECOMB-CG 2009 issue).
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Jacob Post (2006-2009, MSc, Computer Science, SFU, joint
supervision with Pavol Hell, SFU).
Research topics: Combinatorics of arc diagrams, Ferrers fillings, Young tableaux and lattice paths.
Papers: thesis (defense), FPSAC 2010.
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Karine St-Onge (2004-2006, MSc, Computer Science, UQAM, joint
supervision with Anne Bergeron, UQAM).
Research topics: Conserved gene clusters in bacterial genomes
Papers: thesis,
CompBioNets 2005.
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Valentin Guignon (2004-2006, MSc, Bioinformatics,
Université de Montréal, joint supervision with Sylvie
Hamel, UdM)
Research topics: Comparison of RNA secondary structures
Papers: thesis,
SPIRE 2005,
poster ISMB 2008,
TCS 2011.
Undergraduate students
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Jake Turner (Summer 2014, SFU, Mathematics, NSERC USRA, joint supervision with Tamon Stephen)
Research topics: Tucker patterns.
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Rosemary McCloskey (Summer 2011, SFU, Mathematics, NSERC USRA, joint supervision with Marni Mishna)
Research topics: Combinatorics of common interval trees.
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Bradley Jones (Summer 2011 to Spring 2012, SFU, Mathematics, VPR USRA)
Research topics: Efficient implementation of ancestral genome reconstruction methods.
Papers: Bioinformatics 2012.
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Ryan Coghlan (Fall 2009, SFU, Mathematics, joint supervision with Tamon Stephen)
Research topics: A program to decide the gapped-C1P property.
Papers: poster RECOMB-CG 2010.
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Ryan Coghlan and Saehee Choi (Summer 2009, SFU, Mathematics, NSERC USRA, joint supervision with Tamon Stephen)
Research topics: On the 1-C1P property for ancestral genome reconstruction
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Andrew McPherson (Summer 2008, SFU, Mathematics, NSERC USRA)
Research topics: Ancestral genome reconstruction
Papers: ISBRA 2009.
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Huiyi Lu (Summer 2007, SFU, Mathematics, NSERC USRA)
Research topics: Metagenomics
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Yannick Gingras (Summer 2005, UQAM, Computer Science, NSERC USRA, joint
supervision with Anne Bergeron, UQAM)
Research topics: Whole genome synteny comparison
Papers: poster RECOMB-CG 2005.
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Hadrien-Charles David (Summer 2004, UQAM, Computer Science, LaCIM USRA)
Research topics: PQ-trees and conserved intervals
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Patrick Simard (Summer 2003, UQAM, Mathematics, NSERC USRA)
Research topics: GPI-anchors detection using HMM
Papers: poster HUPO 2003.
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Guy Larochelle (Summer 2003, UQAM, Computer Science, NSERC USRA)
Research topics: RNA secondary structures pattern matching
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Karine St-Onge (Summer 2002, UQAM, Computer Science, NSERC USRA, joint
supervision with Anne Bergeron, UQAM)
Research topics: evolution scenarios with gene duplication.
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Alexis Musanganya (Summer 2002, UQAM, Computer Science, LaCIM USRA)
Research topics: sorting by reversals
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Jean-Philippe Beauchamps (Summer 2002, UQAM, Mathematics, LaCIM USRA, joint
supervision with Pierre Leroux, UQAM)
Research topics: random generation of planar cacti
Software: GenCacti
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Karine St-Onge (Summer 2001, UQAM, Computer Science, NSERC USRA, joint
supervision with Anne Bergeron, UQAM)
Research topics: sorting by reversals
Papers: JOBIM 2002,
poster RECOMB 2002.
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