Phuong Dao

2013-today

• BeWith: A Between-Within method to discover relationships between cancer modules via integrated analysis of mutual exclusivity, co-occurrence and functional interactions
  Phuong Dao*, Yoo-Ah Kim*, Damian Wojtowicz, Sanna Madan, Roded Sharan, Teresa M. Przytycka
  To appear at Plos Computational Biology (2017).
  
  
  
• HIT'nDRIVE: Patient-specific multi-driver gene prioritization for precision oncology
  Raunak Shrestha, Ermin Hodzic, Thomas Sauerwald, Phuong Dao, Kendric Wang, Jake Yeung, Shawn Anderson, Fabio Vandin, Gholamreza Haffari, Colin C Collins and Cenk Sahinalp
  Genome research 27 (9), 1573-1588 (2017).
  
  
  
• AptaTRACE: Elucidating Sequence-Structure Binding Motifs by Uncovering Selection Trends in HT-SELEX Experiments
  Phuong Dao*, Jan Hoinka*, Yijie Wang, Mayumi Takahashi, Jiehua Zhou, Fabrizio Costa, John Rossi, John Burnett, Rolf Backofen and Teresa Przytycka.
  Research in Computational Molecular Biology (RECOMB) 2016.
  
  
  
• AptaGUI—A Graphical User Interface for the Efficient Analysis of HT-SELEX Data
  Jan Hoinka, Phuong Dao and Teresa M Przytycka
  Molecular Therapy Nucleic Acids (2015) 4, e257; doi:10.1038/mtna.2015.26
  
  
  
• Large scale analysis of the mutational landscape in HT-SELEX improves aptamer discovery
  Jan Hoinka, Alexey Berezhnoy, Phuong Dao, Zuben E. Sauna, Eli Gilboa and Teresa M. Przytycka
  Nucl. Acids Res. (13 July 2015) 43 (12): 5699-5707.
  
  
  
• MEMCover: integrated analysis of mutual exclusivity and functional network reveals dysregulated pathways across multiple cancer types
  Yoo-Ah Kim, Dong-Yeon Cho, Phuong Dao and Teresa M. Przytycka
  Bioinformatics (2015) 31 (12): i284-i292.
  
  
  
• HIT’nDRIVE: Multi-driver Gene Prioritization Based on Hitting Time
  Raunak Shrestha, Ermin Hodzic, Jake Yeung, Kendric Wang, Thomas Sauerwald, Phuong Dao, Shawn Anderson, Himisha Beltran, Mark A. Rubin, Colin C. Collins, Gholamreza Haffari, S. Cenk Sahinalp
  Research in Computational Molecular Biology (RECOMB) 2014: 293-306.
  
  
  
• ORMAN: Optimal resolution of ambiguous RNA-Seq multimappings in the presence of novel isoforms
  Phuong Dao*, Ibrahim Numanagic*, Yen-Yi Lin*, Faraz Hach*, Emre Karakoç, Nilgun Donmez, Colin Collins, Evan E. Eichler, S. Cenk Sahinalp
  Bioinformatics (2014) 30 (5): 644-651.
  
  
  

2008-2012

• Whole-transcriptome profiling of thyroid nodules identifies expression-based signatures for accurate thyroid cancer diagnosis
  Sam M. Wiseman, Zaid Haddad, Blair Walker, Ismael A. Vergara, Thomas Sierocinski, Anamaria Crisan, Mercedeh Ghadessi, Phuong Dao, Benedikt Zimmermann, Timothy J. Triche, Nicholas Erho, and Elai Davicioni
  The Journal of Clinical Endocrinology & Metabolism 98 (10), 4072-4079
  
  
  
• Assessing the Significance of Data Mining Results on Graphs with Feature Vectors
  Stephan Gunnemann, Phuong Dao, Mohsen Jamali, Martin Ester
  IEEE 12th International Conference on Data Mining (ICDM) 2012, 270-279.
  
  
  
• CLIIQ: Accurate Comparative Detection and Quantification of Expressed Isoforms in a Population
  Yen-Yi Lin*, Phuong Dao*, Faraz Hach*, Marzieh Bakhshi, Fan Mo, Anna Lapuk, Colin Collins, S. Cenk Sahinalp
  12th International Workshop on Algorithms in Bioinformatics (WABI) 2012, 178-189.
  
  
  
• Proteome Network Emulating Models
  Phuong Dao, Fereydoun Hormozdiari, Iman Hajirasouliha, Martin Ester, S Cenk Sahinalp
  A chapter in Functional Coherence of Molecular Networks in Bioinformatics published in 2012, page 69-95.
  
  
  
• Optimally discriminative subnetwork markers predict response to chemotherapy
  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.
  Bioinformatics (2011) 27 (13): i205-i213.
  
  
  
• Alu repeat discovery and characterization within human genomes
  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.
  
  
  
• Mapping the Protein Interaction Network in Methicillin-Resistant Staphylococcus aureus
  Artem Cherkasov, Michael Hsing, Roya Zoraghi, Leonard J Foster, Raymond H See, Nikolay Stoynov, Jihong Jiang, Sukhbir Kaur, Tian Lian, Linda Jackson, Huansheng Gong, Rick Swayze, Emily Amandoron, Farhad Hormozdiari, Phuong Dao, Cenk Sahinalp, Osvaldo Santos-Filho, Peter Axerio-Cilies, Kendall Byler, William R McMaster, Robert C Brunham, B Brett Finlay, Neil E Reiner
  Journal of Proteome Research, 2011, 10 (3), pp 1139–1150.
  
  
  
• Applicability domains for classification problems: benchmarking of distance to models for Ames mutagenicity set
  Iurii Sushko et al.
  Journal of Chemical Information Modeling, 2010, 50 (12), pp 2094–2111
  
  
  
• Inferring cancer subnetwork markers using density-constrained biclustering
  Phuong Dao*, Recep Colak*, Raheleh Salari*, Flavia Moser*, Elai Davicioni, Alexander Schönhuth, Martin Ester
  European Conference on Computational Biology (ECCB) 2010. Bioinformatics (2010) 26 (18): i625-i631.
  
  
  
• PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes
  Nancy Yu, James R Wagner, Matthew R Laird, Gabor Melli, Sébastien Rey, Raymond Lo, Phuong Dao, S Cenk Sahinalp, Martin Ester, Leonard J Foster, Fiona SL Brinkman
  Bioinformatics (2010) 26 (13): 1608-1615.
  
  
  
• Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery
  Fereydoun Hormozdiari, Iman Hajirasouliha, Phuong Dao, Faraz Hach, Deniz Yorukoglu, Can Alkan, Evan E Eichler, S Cenk Sahinalp
  18th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) 2010.
  Bioinformatics (2010) 26 (12): i350-i357.
  
  
  
• Quantifying systemic evolutionary changes by color coding confidence-scored PPI networks
  Phuong Dao, Alexander Schönhuth, Fereydoun Hormozdiari, Iman Hajirasouliha, S. Cenk Sahinalp, Martin Ester
  9th International Workshop on Algorithms in Bioinformatics (WABI) 2009, page 37-48.
  
  
  
• Improved small molecule activity determination via centroid nearest neighbors classification
  Phuong Dao*, Farhad Hormozdiari*, Hossein Jowhari and S.Cenk Sahinalp
  9th Annual International Conference Computational Systems Bioinformatics (CSB) 2009.
  
  
  
• Biomolecular network motif counting and discovery by color coding
  Noga Alon, Phuong Dao, Iman Hajirasouliha, Fereydoun Hormozdiari, S Cenk Sahinalp
  16th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) 2008.
  Bioinformatics (2008) 24 (13): i241-i249.