Phuong Dao

According to our database, Phuong Dao authored at least 18 papers between 2008 and 2022.

Collaborative distances:

• Dijkstra number of three.
• Erdős number of two.

2022

N-Grammer: Augmenting Transformers with latent n-grams.

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

CoRR, 2022

2017

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 Wójtowicz, Sanna Madan, Roded Sharan, Teresa M. Przytycka

PLoS Comput. Biol., 2017

BeWith: A Between-Within Method for Module Discovery in Cancer using Integrated Analysis of Mutual Exclusivity, Co-occurrence and Functional Interactions (Extended Abstract).

Phuong Dao, Yoo-Ah Kim, Sanna Madan, Roded Sharan, Teresa M. Przytycka

Proceedings of the Research in Computational Molecular Biology, 2017

2016

Ups and Downs of Poised RNA Polymerase II in B-Cells.

Phuong Dao, Damian Wójtowicz, Steevenson Nelson, David Levens, Teresa M. Przytycka

PLoS Comput. Biol., 2016

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, Teresa M. Przytycka

Proceedings of the Research in Computational Molecular Biology - 20th Annual Conference, 2016

2015

MEMCover: integrated analysis of mutual exclusivity and functional network reveals dysregulated pathways across multiple cancer types.

Yoo-Ah Kim, Dong-Yeon Cho, Phuong Dao, Teresa M. Przytycka

Bioinform., 2015

2014

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 C. Collins, Evan E. Eichler, Süleyman Cenk Sahinalp

Bioinform., 2014

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, Süleyman Cenk Sahinalp

Proceedings of the Research in Computational Molecular Biology, 2014

2012

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 C. Collins, Süleyman Cenk Sahinalp

Proceedings of the Algorithms in Bioinformatics - 12th International Workshop, 2012

Assessing the Significance of Data Mining Results on Graphs with Feature Vectors.

Stephan Günnemann, Phuong Dao, Mohsen Jamali, Martin Ester

Proceedings of the 12th IEEE International Conference on Data Mining, 2012

2011

Optimally discriminative subnetwork markers predict response to chemotherapy.

Phuong Dao, Kendric Wang, Colin C. Collins, Martin Ester, Anna Lapuk, Süleyman Cenk Sahinalp

Bioinform., 2011

2010

Applicability Domains for Classification Problems: Benchmarking of Distance to Models for Ames Mutagenicity Set.

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

J. Chem. Inf. Model., 2010

PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes.

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

Bioinform., 2010

Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery.

Fereydoun Hormozdiari, Iman Hajirasouliha, Phuong Dao, Faraz Hach, Deniz Yörükoglu, Can Alkan, Evan E. Eichler, Süleyman Cenk Sahinalp

Bioinform., 2010

Inferring cancer subnetwork markers using density-constrained biclustering.

Phuong Dao, Recep Colak, Raheleh Salari, Flavia Moser, Elai Davicioni, Alexander Schönhuth, Martin Ester

Bioinform., 2010

2009

Quantifying Systemic Evolutionary Changes by Color Coding Confidence-Scored PPI Networks.

Phuong Dao, Alexander Schönhuth, Fereydoun Hormozdiari, Iman Hajirasouliha, Süleyman Cenk Sahinalp, Martin Ester

Proceedings of the Algorithms in Bioinformatics, 9th International Workshop, 2009

2008

Combinatorial QSAR Modeling of Chemical Toxicants Tested against Tetrahymena pyriformis.

Hao Zhu, Alexander Tropsha, Denis Fourches, Alexandre Varnek, Ester Papa, Paola Gramatica, Tomas Öberg, Phuong Dao, Artem Cherkasov, Igor V. Tetko

J. Chem. Inf. Model., 2008

Biomolecular network motif counting and discovery by color coding.

Noga Alon, Phuong Dao, Iman Hajirasouliha, Fereydoun Hormozdiari, Süleyman Cenk Sahinalp

Proceedings of the Proceedings 16th International Conference on Intelligent Systems for Molecular Biology (ISMB), 2008