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2020 – today
- 2022
[i2]Aurko Roy, Rohan Anil, Guangda Lai, Benjamin Lee, Jeffrey Zhao, Shuyuan Zhang, Shibo Wang, Ye Zhang, Shen Wu, Rigel Swavely, Tao Yu, Phuong Dao, Christopher Fifty, Zhifeng Chen, Yonghui Wu:
N-Grammer: Augmenting Transformers with latent n-grams. CoRR abs/2207.06366 (2022)
2010 – 2019
- 2017
- [j10]Phuong Dao
, Yoo-Ah Kim, Damian Wójtowicz, Sanna Madan, Roded Sharan, Teresa M. Przytycka:
BeWith: A Between-Within method to discover relationships between cancer modules via integrated analysis of mutual exclusivity, co-occurrence and functional interactions. PLoS Comput. Biol. 13(10) (2017) - [c7]Phuong Dao, Yoo-Ah Kim, Sanna Madan, Roded Sharan, Teresa M. Przytycka:
BeWith: A Between-Within Method for Module Discovery in Cancer using Integrated Analysis of Mutual Exclusivity, Co-occurrence and Functional Interactions (Extended Abstract). RECOMB 2017: 370-371 - 2016
- [j9]Phuong Dao, Damian Wójtowicz, Steevenson Nelson, David Levens, Teresa M. Przytycka:
Ups and Downs of Poised RNA Polymerase II in B-Cells. PLoS Comput. Biol. 12(4) (2016) - [c6]Phuong Dao, Jan Hoinka, Yijie Wang, Mayumi Takahashi, Jiehua Zhou, Fabrizio Costa, John Rossi, John Burnett, Rolf Backofen, Teresa M. Przytycka:
AptaTRACE: Elucidating Sequence-Structure Binding Motifs by Uncovering Selection Trends in HT-SELEX Experiments. RECOMB 2016: 261-262 - [i1]Phuong Dao, Jan Hoinka, Yijie Wang, Mayumi Takahashi, Jiehua Zhou, Fabrizio Costa, John Rossi, John Burnett, Rolf Backofen, Teresa M. Przytycka:
AptaTRACE: Elucidating Sequence-Structure Binding Motifs by Uncovering Selection Trends in HT-SELEX Experiments. CoRR abs/1604.03081 (2016) - 2015
- [j8]Yoo-Ah Kim, Dong-Yeon Cho, Phuong Dao, Teresa M. Przytycka:
MEMCover: integrated analysis of mutual exclusivity and functional network reveals dysregulated pathways across multiple cancer types. Bioinform. 31(12): 284-292 (2015) - 2014
- [j7]Phuong Dao, Ibrahim Numanagic, Yen-Yi Lin, Faraz Hach, Emre Karakoç, Nilgun Donmez, Colin C. Collins, Evan E. Eichler, Süleyman Cenk Sahinalp:
ORMAN: Optimal resolution of ambiguous RNA-Seq multimappings in the presence of novel isoforms. Bioinform. 30(5): 644-651 (2014) - [c5]Raunak Shrestha, Ermin Hodzic, Jake Yeung, Kendric Wang, Thomas Sauerwald, Phuong Dao, Shawn Anderson, Himisha Beltran, Mark A. Rubin, Colin C. Collins, Gholamreza Haffari, Süleyman Cenk Sahinalp:
HIT'nDRIVE: Multi-driver Gene Prioritization Based on Hitting Time. RECOMB 2014: 293-306 - 2012
- [c4]Stephan Günnemann, Phuong Dao, Mohsen Jamali, Martin Ester:
Assessing the Significance of Data Mining Results on Graphs with Feature Vectors. ICDM 2012: 270-279 - [c3]Yen-Yi Lin, Phuong Dao, Faraz Hach, Marzieh Bakhshi, Fan Mo, Anna Lapuk, Colin C. Collins, Süleyman Cenk Sahinalp:
CLIIQ: Accurate Comparative Detection and Quantification of Expressed Isoforms in a Population. WABI 2012: 178-189 - 2011
- [j6]Phuong Dao, Kendric Wang, Colin C. Collins, Martin Ester, Anna Lapuk, Süleyman Cenk Sahinalp:
Optimally discriminative subnetwork markers predict response to chemotherapy. Bioinform. 27(13): 205-213 (2011) - 2010
- [j5]Fereydoun Hormozdiari, Iman Hajirasouliha, Phuong Dao, Faraz Hach, Deniz Yörükoglu, Can Alkan, Evan E. Eichler, Süleyman Cenk Sahinalp:
Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery. Bioinform. 26(12): 350-357 (2010) - [j4]Nancy Y. Yu, James R. Wagner, Matthew R. Laird, Gabor Melli, Sébastien Rey, Raymond Lo, Phuong Dao, Süleyman Cenk Sahinalp, Martin Ester, Leonard J. Foster, Fiona S. L. Brinkman:
PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes. Bioinform. 26(13): 1608-1615 (2010) - [j3]Phuong Dao, Recep Colak, Raheleh Salari, Flavia Moser, Elai Davicioni, Alexander Schönhuth, Martin Ester:
Inferring cancer subnetwork markers using density-constrained biclustering. Bioinform. 26(18) (2010) - [j2]Iurii Sushko, Sergii Novotarskyi, Robert Körner, Anil Kumar Pandey, Artem Cherkasov, Jiazhong Li, Paola Gramatica, Katja Hansen, Timon Schroeter, Klaus-Robert Müller, Lili Xi, Huanxiang Liu, Xiaojun Yao, Tomas Öberg, Farhad Hormozdiari, Phuong Dao, Süleyman Cenk Sahinalp, Roberto Todeschini, Pavel G. Polishchuk, Anatoly G. Artemenko, Victor Kuzmin, Todd Martin, Douglas M. Young, Denis Fourches, Eugene N. Muratov, Alexander Tropsha, Igor I. Baskin, Dragos Horvath, Gilles Marcou, Christophe Muller, Alexandre Varnek, Volodymyr V. Prokopenko, Igor V. Tetko:
Applicability Domains for Classification Problems: Benchmarking of Distance to Models for Ames Mutagenicity Set. J. Chem. Inf. Model. 50(12): 2094-2111 (2010)
2000 – 2009
- 2009
- [c2]Phuong Dao, Alexander Schönhuth, Fereydoun Hormozdiari, Iman Hajirasouliha, Süleyman Cenk Sahinalp, Martin Ester:
Quantifying Systemic Evolutionary Changes by Color Coding Confidence-Scored PPI Networks. WABI 2009: 37-48 - 2008
- [j1]Hao Zhu, Alexander Tropsha, Denis Fourches, Alexandre Varnek, Ester Papa, Paola Gramatica, Tomas Öberg, Phuong Dao, Artem Cherkasov, Igor V. Tetko:
Combinatorial QSAR Modeling of Chemical Toxicants Tested against Tetrahymena pyriformis. J. Chem. Inf. Model. 48(4): 766-784 (2008) - [c1]Noga Alon, Phuong Dao, Iman Hajirasouliha, Fereydoun Hormozdiari, Süleyman Cenk Sahinalp:
Biomolecular network motif counting and discovery by color coding. ISMB 2008: 241-249
Coauthor Index
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