Phuong Dao

19 papers A* 1A 1B 3C 2Journal 12
YearRankTypeTitle / Venue / Authors
2022 J jnl
N-Grammer: Augmenting Transformers with latent n-grams.
CoRR
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
2017 B conf
BeWith: A Between-Within Method for Module Discovery in Cancer using Integrated Analysis of Mutual Exclusivity, Co-occurrence and Functional Interactions (Extended Abstract).
RECOMB
Phuong Dao, Yoo-Ah Kim, Sanna Madan, Roded Sharan, Teresa M. Przytycka
2017 J jnl
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.
Phuong Dao, Yoo-Ah Kim, Damian Wójtowicz, Sanna Madan, Roded Sharan, Teresa M. Przytycka
2016 B conf
AptaTRACE: Elucidating Sequence-Structure Binding Motifs by Uncovering Selection Trends in HT-SELEX Experiments.
RECOMB
Phuong Dao, Jan Hoinka, Yijie Wang, Mayumi Takahashi, Jiehua Zhou, Fabrizio Costa, John Rossi, John Burnett, Rolf Backofen, Teresa M. Przytycka
2016 J jnl
AptaTRACE: Elucidating Sequence-Structure Binding Motifs by Uncovering Selection Trends in HT-SELEX Experiments.
CoRR
Phuong Dao, Jan Hoinka, Yijie Wang, Mayumi Takahashi, Jiehua Zhou, Fabrizio Costa, John Rossi, John Burnett, Rolf Backofen, Teresa M. Przytycka
2016 J jnl
Ups and Downs of Poised RNA Polymerase II in B-Cells.
PLoS Comput. Biol.
Phuong Dao, Damian Wójtowicz, Steevenson Nelson, David Levens, Teresa M. Przytycka
2015 J jnl
MEMCover: integrated analysis of mutual exclusivity and functional network reveals dysregulated pathways across multiple cancer types.
Bioinform.
Yoo-Ah Kim, Dong-Yeon Cho, Phuong Dao, Teresa M. Przytycka
2014 B conf
HIT'nDRIVE: Multi-driver Gene Prioritization Based on Hitting Time.
RECOMB
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
2014 J jnl
ORMAN: Optimal resolution of ambiguous RNA-Seq multimappings in the presence of novel isoforms.
Bioinform.
Phuong Dao, Ibrahim Numanagic, Yen-Yi Lin, Faraz Hach, Emre Karakoç, Nilgun Donmez, Colin C. Collins, Evan E. Eichler, Süleyman Cenk Sahinalp
2012 A* conf
Assessing the Significance of Data Mining Results on Graphs with Feature Vectors.
ICDM
Stephan Günnemann, Phuong Dao, Mohsen Jamali, Martin Ester
2012 C conf
CLIIQ: Accurate Comparative Detection and Quantification of Expressed Isoforms in a Population.
WABI
Yen-Yi Lin, Phuong Dao, Faraz Hach, Marzieh Bakhshi, Fan Mo, Anna Lapuk, Colin C. Collins, Süleyman Cenk Sahinalp
2011 J jnl
Optimally discriminative subnetwork markers predict response to chemotherapy.
Bioinform.
Phuong Dao, Kendric Wang, Colin C. Collins, Martin Ester, Anna Lapuk, Süleyman Cenk Sahinalp
2010 J jnl
Applicability Domains for Classification Problems: Benchmarking of Distance to Models for Ames Mutagenicity Set.
J. Chem. Inf. Model.
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 M. 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
2010 J jnl
Inferring cancer subnetwork markers using density-constrained biclustering.
Bioinform.
Phuong Dao, Recep Colak, Raheleh Salari, Flavia Moser, Elai Davicioni, Alexander Schönhuth, Martin Ester
2010 J jnl
Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery.
Bioinform.
Fereydoun Hormozdiari, Iman Hajirasouliha, Phuong Dao, Faraz Hach, Deniz Yörükoglu, Can Alkan, Evan E. Eichler, Süleyman Cenk Sahinalp
2010 J jnl
PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes.
Bioinform.
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
2009 C conf
Quantifying Systemic Evolutionary Changes by Color Coding Confidence-Scored PPI Networks.
WABI
Phuong Dao, Alexander Schönhuth, Fereydoun Hormozdiari, Iman Hajirasouliha, Süleyman Cenk Sahinalp, Martin Ester
2008 A conf
Biomolecular network motif counting and discovery by color coding.
ISMB
Noga Alon, Phuong Dao, Iman Hajirasouliha, Fereydoun Hormozdiari, Süleyman Cenk Sahinalp
2008 J jnl
Combinatorial QSAR Modeling of Chemical Toxicants Tested against Tetrahymena pyriformis.
J. Chem. Inf. Model.
Hao Zhu, Alexander Tropsha, Denis Fourches, Alexandre Varnek, Ester Papa, Paola Gramatica, Tomas Öberg, Phuong Dao, Artem Cherkasov, Igor V. Tetko