Nigara Falls 2008

 

PHUONG DAO


I am a PhD student at School of Computing Science at Simon Fraser University. My research interests are in Bioinformatics and Computional Biology. I am supervised by Dr. Martin Ester and Dr. S. Cenk Sahinalp. I also obtained my master degree under supervision of Dr. S. Cenk Sahinalp in Fall 2008.

Currently, I am doing research at Lab for Computational Biology and Data Mining Lab. Besides, I enjoy collaborating with Dr. Colin Collins's group at Vancouver Prostate Center.

You can contact me by myid (at) cs (dot) sfu (dot) ca where myid is pdao.


 


Research Interests

  • Analysis and Modeling of Biomolecular Networks
  • Systems Biology Approaches to Genotype-Phenotype Relationships
  • Graph Mining and Graph Algorithms

Awards and Honors

Sep 2011–Sep 2012
 NSERC Alexander Graham Bell Canada Graduate Scholarship
Sep 2010–Sep 2012
 PIMS Graduate Training in Mathematical Biology Fellowship
Jan 2008, May 2010, Jan 2011
 Simon Fraser University Graduate Fellowship
May 2010–Sep 2010
 MITACS Accerlerate Internship Program
Jan 2009
 Simon Fraser University Graduate Entrance Scholarship
Sep 2006
 University Medal in Computer Science, Carleton University
2004-2006
 Carleton University Incourse Scholarship
2004-2006
 Carleton University Dean List
2000
 Gold Medal at 30/4 Olympiads in Informatics

 

Publications

  • Proteome Network Emulating Models
Phuong Dao, Fereydoun Hormozdiari, Iman Hajirasouliha, Martin Ester, S. Cenk Sahinalp
A chapter in Functional Coherence of Molecular Networks, edited by Mehmet Koyuturk, Shankar Subramaniam and Ananth Grama; Springer, 1st Edition (September 30, 2011)
Phuong Dao*, Kendric Wang*, Colin Collins, Martin Ester, Anna Lapuk**, S. Cenk Sahinalp**
19th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2011)
 Also: to appear in Bioinformatics
* Joint first authorship ** Corresponding author
SOFTWARE PACKAGE AND DATASETS
Fereydoun Hormozdiari, Can Alkan, Mario Ventura, Iman Hajirasouliha, Maika Malig, Faraz Hach, Deniz Yorukoglu, Phuong Dao, Marzieh Bakhshi, S. Cenk Sahinalp, Evan E. Eichler.
Genome Research 2011. 21: 840-849
Cherkasov et al.
Journal of Proteome Research, 2011, 10 (3), pp 11391150.
Phuong Dao*, Recep Colak*, Raheleh Salari, Flavia Moser, Elai Davicioni, Alexander Schonhuth**, Martin Ester**
9th European Conference on Computational Biology (ECCB 2010)
 Also: Bioinformatics 26(13): 1608-1615 (2010)
* Joint first authorship, **Corresponding author
SOFTWARE PACKAGE
Fereydoun Hormozdiari, Iman Hajirasouliha, Phuong Dao, Faraz Hach, Deniz Yorukoglu, Can Alkan, Evan E. Eichler, S. Cenk Sahinalp
ISMB'10 (18th Annual International Conference Intelligent Systems for Molecular Biology), Boston, USA, July 11-13 2010
with Cherkasov, A. and others
Journal of Proteome Research DOI: 10.1021/pr100918u
Yu N.Y., Wagner J.R., Laird M.R., Melli G., Rey S., Lo R., Dao P., Sahinalp S.C., Ester M., Foster L.J., Brinkman F.S.L.
Bioinformatics 26(18): (2010)
Phuong Dao, Alexander Schonhuth, Fereydoun Hormozdiari, Iman Hajirasouliha, S. Cenk Sahinalp and Martin Ester
9th Workshop on Algorithms on Bioinformatics (WABI 2009)
Phuong Dao, Farhad Hormozdiari, Hossein Jowhari, Kendall Byler, Artem Cherkasov, S.Cenk Sahinalp
8th Annual Conference on Computational Systems Bioinformatics (CSB 2009)
  • Protein Interaction Network Comparison via Network Motif Counting
Phuong Dao, M.Sc. Thesis, Simon Fraser University, Canada, Fall 2008
Noga Alon, Phuong Dao, Iman Hajirasouliha, Fereydoun Hormozdiari and S.Cenk Sahinalp
16th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2008)
Also: Bioinformatics 2008 24: i32-i40; doi:10.1093/bioinformatics/btn173 abstract
with Hao Zhu, Alexander Tropsha, Denis Fourches, Alexandre Varnek, Ester Papa, Paola Gramatica, Tomas Öberg, Phuong Dao, Artem Cherkasov, and Igor V. Tetko 
Journal of Chemical Information and Modelling 48(4):766-84 (April 2008)

 

Research and Teaching Experience
Summer 2009 – Present Research Assistant, School of Computing Science, Simon Fraser University

Doing research at Lab for Computational Biology and Data Mining Lab
Spring 2009 Teaching Assistant, School of Computing Science, Simon Fraser University

TA for Discrete Mathematics, MACM 101
Spring 2007 – Fall 2008 Research Assistant, School of Computing Science, Simon Fraser University

Doing research at Lab for Computational Biology
Fall 2006 Teaching Assistant, School of Computing Science, Simon Fraser University

TA for Data Structures and Algorithms, CMPT 307
Summer 2006 Teaching Assistant, School of Computer Science, Carleton University

TA for Design and Analysis of Algorithms I, COMP 3804
Spring 2004 – Summer 2006 Teaching Assistant, School of Mathematics and Statistics, Carleton University

TA for Calculus I, II, Linear Algebra I, II and Precalculus

Presentations

  • Optimally Discriminative Subnetwork Markers Predict Response to Chemotherapy, 19th Annual International Conference on Intelligent Systems for Molecular Biology, September 2011, Vienna, Austria.
  • Inferring cancer subnetwork markers using density-constrained biclustering, MITACS Workshop on Biological Network and Systems Biology, January 2011.
  • Inferring cancer subnetwork markers using density-constrained biclustering, 9th European Conference on Computational Biology, September 2010, Canada.
  • Protein-Protein interaction network comparison via efficient network motif counting, PIMS International Graduate Training Centre (IGTC) in Mathematical Biology, October 2010, Canada.
  • Protein-Protein interaction network comparison via efficient network motif counting, Center for Mathematics and Computer Science (CWI), September 2010, The Netherlands.
  • Protein-Protein interaction network comparison via efficient network motif counting, Poster presentation at Workshop in Biomolecular Interaction Networks: Function and Disease 2010, Quebec, Canada.
  • Protein-Protein interaction network comparison via efficient network motif counting, Bioinformatics for Combating Infectious Diseases, December 2009, Simon Fraser University.
  • Quantifying Systemic Evolutionary Changes by Color Coding Confidence-Scored PPI Networks, 9th Workshop on Algorithms in Bioinformatics, University of Pennsylvania, September 2009.
  • Improved Small Molecule Activity Determination via Centroid Nearest Neighbors Classification, 8th Annual International Conference on Computational Systems Bioinformatics, Stanford University, August 2009.
  • Biomolecular Network Motif Counting and Discovery by Color Coding, Simon Fraser University, Burnaby, Canada, October 2008.
  • Small Molecules Classification and Similarity Search, Simon Fraser University, Burnaby, Canada, April 2008.