Phuong Dao
Phuong Dao
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PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes
NY Yu, JR Wagner, MR Laird, G Melli, S Rey, R Lo, P Dao, SC Sahinalp, ...
Bioinformatics 26 (13), 1608-1615, 2010
Single-cell map of diverse immune phenotypes in the breast tumor microenvironment
E Azizi, AJ Carr, G Plitas, AE Cornish, C Konopacki, S Prabhakaran, ...
Cell 174 (5), 1293-1308. e36, 2018
Gemini: a family of highly capable multimodal models
G Team, R Anil, S Borgeaud, Y Wu, JB Alayrac, J Yu, R Soricut, ...
arXiv preprint arXiv:2312.11805, 2023
Combinatorial QSAR modeling of chemical toxicants tested against Tetrahymena pyriformis
H Zhu, A Tropsha, D Fourches, A Varnek, E Papa, P Gramatica, T Oberg, ...
Journal of chemical information and modeling 48 (4), 766-784, 2008
Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery
F Hormozdiari, I Hajirasouliha, P Dao, F Hach, D Yorukoglu, C Alkan, ...
Bioinformatics 26 (12), i350-i357, 2010
Applicability domains for classification problems: benchmarking of distance to models for Ames mutagenicity set
I Sushko, S Novotarskyi, R Körner, AK Pandey, A Cherkasov, J Li, ...
Journal of chemical information and modeling 50 (12), 2094-2111, 2010
Biomolecular network motif counting and discovery by color coding
N Alon, P Dao, I Hajirasouliha, F Hormozdiari, SC Sahinalp
Bioinformatics 24 (13), i241-i249, 2008
Large scale analysis of the mutational landscape in HT-SELEX improves aptamer discovery
J Hoinka, A Berezhnoy, P Dao, ZE Sauna, E Gilboa, TM Przytycka
Nucleic acids research 43 (12), 5699-5707, 2015
Optimally discriminative subnetwork markers predict response to chemotherapy
P Dao, K Wang, C Collins, M Ester, A Lapuk, SC Sahinalp
Bioinformatics 27 (13), i205-i213, 2011
Alu repeat discovery and characterization within human genomes
F Hormozdiari, C Alkan, M Ventura, I Hajirasouliha, M Malig, F Hach, ...
Genome research 21 (6), 840-849, 2011
MEMCover: integrated analysis of mutual exclusivity and functional network reveals dysregulated pathways across multiple cancer types
YA Kim, DY Cho, P Dao, TM Przytycka
Bioinformatics 31 (12), i284-i292, 2015
Mapping the Protein Interaction Network in Methicillin-Resistant Staphylococcus aureus
A Cherkasov, M Hsing, R Zoraghi, LJ Foster, RH See, N Stoynov, J Jiang, ...
Journal of proteome research 10 (3), 1139-1150, 2011
Inferring cancer subnetwork markers using density-constrained biclustering
P Dao, R Colak, R Salari, F Moser, E Davicioni, A Schönhuth, M Ester
Bioinformatics 26 (18), i625-i631, 2010
AptaTRACE elucidates RNA sequence-structure motifs from selection trends in HT-SELEX experiments
P Dao, J Hoinka, M Takahashi, J Zhou, M Ho, Y Wang, F Costa, JJ Rossi, ...
Cell systems 3 (1), 62-70, 2016
CLIIQ: Accurate Comparative Detection and Quantification of Expressed Isoforms in a Population
YY Lin, P Dao, F Hach, M Bakhshi, F Mo, A Lapuk, C Collins, S Sahinalp
Algorithms in Bioinformatics, 178-189, 2012
Natural genetic variation reveals key features of epigenetic and transcriptional memory in virus-specific CD8 T cells
J van der Veeken, Y Zhong, R Sharma, L Mazutis, P Dao, D Pe’er, ...
Immunity 50 (5), 1202-1217. e7, 2019
BeWith: A Between-Within method to discover relationships between cancer modules via integrated analysis of mutual exclusivity, co-occurrence and functional interactions
P Dao, YA Kim, D Wojtowicz, S Madan, R Sharan, TM Przytycka
PLoS computational biology 13 (10), e1005695, 2017
HIT'nDRIVE: patient-specific multidriver gene prioritization for precision oncology
R Shrestha, E Hodzic, T Sauerwald, P Dao, K Wang, J Yeung, ...
Genome research 27 (9), 1573-1588, 2017
Open community challenge reveals molecular network modules with key roles in diseases
S Choobdar, ME Ahsen, J Crawford, M Tomasoni, T Fang, D Lamparter, ...
bioRxiv, 265553, 2018
ORMAN: optimal resolution of ambiguous RNA-Seq multimappings in the presence of novel isoforms
P Dao, I Numanagić, YY Lin, F Hach, E Karakoc, N Donmez, C Collins, ...
Bioinformatics 30 (5), 644-651, 2014
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