Prediction of Drug-Target Interactions for Drug Repositioning Only Based on Genomic Expression Similarity
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DOI: 10.1371/journal.pcbi.1003315
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- Michael J. Keiser & Vincent Setola & John J. Irwin & Christian Laggner & Atheir I. Abbas & Sandra J. Hufeisen & Niels H. Jensen & Michael B. Kuijer & Roberto C. Matos & Thuy B. Tran & Ryan Whaley & Ri, 2009. "Predicting new molecular targets for known drugs," Nature, Nature, vol. 462(7270), pages 175-181, November.
- Chao Chen & Kay Grennan & Judith Badner & Dandan Zhang & Elliot Gershon & Li Jin & Chunyu Liu, 2011. "Removing Batch Effects in Analysis of Expression Microarray Data: An Evaluation of Six Batch Adjustment Methods," PLOS ONE, Public Library of Science, vol. 6(2), pages 1-10, February.
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Cited by:
- Yong Liu & Min Wu & Chunyan Miao & Peilin Zhao & Xiao-Li Li, 2016. "Neighborhood Regularized Logistic Matrix Factorization for Drug-Target Interaction Prediction," PLOS Computational Biology, Public Library of Science, vol. 12(2), pages 1-26, February.
- Mao Shu & Xiaoli Zai & Beina Zhang & Rui Wang & Zhihua Lin, 2016. "Hypothyroidism Side Effect in Patients Treated with Sunitinib or Sorafenib: Clinical and Structural Analyses," PLOS ONE, Public Library of Science, vol. 11(1), pages 1-11, January.
- E Tejera & I Carrera & Karina Jimenes-Vargas & V Armijos-Jaramillo & A Sánchez-Rodríguez & M Cruz-Monteagudo & Y Perez-Castillo, 2019. "Cell fishing: A similarity based approach and machine learning strategy for multiple cell lines-compound sensitivity prediction," PLOS ONE, Public Library of Science, vol. 14(10), pages 1-11, October.
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