ADS-Publications

Jong-Hoon Park and Young-Rae Cho. "Computational drug repositioning with attention walking". Scientific Reports, 14:10072, 2024. [link]
Hoyeon Jeong, Young-Rae Cho, Jungsoo Gim, Seung-Kuy Cha, Maengsup Kim, and Dae Ryong Kang. "GraphMHC: Neoantigen prediction model applying the graph neural network to molecular structure". PLOS ONE, 19(3):e0291223, 2024. [link]
Yoonbee Kim, Young-Rae Cho. Predicting drug-gene-disease associations by tensor decomposition for network-based computation drug repositioning. Biomedicines, 11(7):1998, 2023. [link]
Yoonbee Kim, Yi-Sue Jung, Jong-Hoon Park, Seon-Jun Kim and Young-Rae Cho. Drug-disease association prediction using heterogeneous networks for computational drug repositioning. Biomolecules, 12(10):1497, 2022. [link]
Yoonbee Kim, Jong-Hoon Park and Young-Rae Cho. Network-based approaches for disease-gene association prediction using protein-protein interaction networks. International Journal of Molecular Sciences (IJMS), 23(13):7411, 2022. [link]
Yi-Sue Jung, Yoonbee Kim and Young-Rae Cho. Comparative analysis of network-based approaches and machine learning algorithms for predicting drug-target interactions. Methods, 198:19-31, 2022. [link]
Hoyeon Jeong, Yoonbee Kim, Yi-Sue Jung, Dae Ryong Kang and Young-Rae Cho. Entropy-based graph clustering of PPI networks for predicting overlapping functional modules of proteins. Entropy, 23(10):1271, 2021. [link]
Young-Rae Cho. Young-Rae Cho. Evaluation of cross-ontology association rules weighted by term specificity. International Journal of Data Mining and Bioinformatics (IJDMB), 24(3):258-268, 2020. [link]
Karel Kalecky, Rebecca Modisette, Samantha Pena, Young-Rae Cho and Joseph Taube. Integrative analysis of breast cancer profiles in TCGA by TNBC subgrouping reveals novel microRNA-specific clusters, including miR-17-92a, distinguishing basal-like 1 and basal-like 2 TNBC subtypes. BMC Cancer, 20:141 (2020). [link]
Sawal Maskey and Young-Rae Cho. LePrimAlign: local entropy-based alignment of PPI networks to predict conserved modules. BMC Genomics, 20:964 (2019). [link]
Karel Kalecky and Young-Rae Cho. PrimAlign: PrimAlign: PageRank-inspired Markovian alignment for large biological networks. Bioinformatics, 34(13):i537-i546 (2018). [link]
Jan Sladek and Young-Rae Cho. Evaluating the contributions of GO term properties to semantic similarity measurement. International Journal of Data Mining and Bioinformatics (IJDMB), 18(3):240-251 (2017). [link]
Yong Shui and Young-Rae Cho. Alignment of PPI networks using semantic similarity for conserved protein complex prediction. IEEE Transactions on Nanobioscience (TNB), 15(4):380-389 (2016). [link]
Young-Rae Cho, Yanan Xin and Greg Speegle. P-Finder: Reconstruction of signaling networks from protein-protein interactions and GO annotations. IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), 12(2):309-321 (2015). [link]
Slavka Jaromerska, Petr Praus and Young-Rae Cho. Distance-wise pathway discovery from protein-protein interaction networks weighted by semantic similarity. Journal of Bioinformatics and Computational Biology, 12(1):1450004 (2014). [link]
True Price, Francisco I Pena and Young-Rae Cho. Survey: Enhancing protein complex prediction in PPI networks with GO similarity weighting. Interdisciplinary Sciences: Computational Life Sciences, 5(3):196-210 (2013). [link]
Young-Rae Cho, Marco Mina, Yanxin Lu, Nayoung Kwon and Pietro H Guzzi. M-Finder: Uncovering functionally associated proteins from interactome data integrated with GO annotations. Proteome Science, 11(Suppl 1):S3 (2013). [link]
George Montanez and Young-Rae Cho. Predicting false positives of protein-protein interaction data by semantic similarity measures. Current Bioinformatics, 8(3):339-346 (2013). [link]
Tak C. Chiam and Young-Rae Cho. Accuracy improvement in protein complex prediction from protein interaction networks by refining cluster overlaps. Proteome Science, 10(Suppl 1):S3 (2012). [link]
Edward C. Kenley and Young-Rae Cho. Detecting protein complexes and functional modules from protein interaction networks: a graph entropy approach. Proteomics, 11(19):3835-3844 (2011). [link]
Young-Rae Cho and Aidong Zhang. Mining protein interactome networks to measure interaction reliability and select hub proteins. International Journal of Knowledge Discovery in Bioinformatics (IJKDB), 1(3):20-35 (2010). [link]
Young-Rae Cho and Aidong Zhang. Identification of functional hubs and modules by converting interactome networks into hierarchical ordering of proteins. BMC Bioinformatics, 11(Suppl 3):S3 (2010). [link]
Young-Rae Cho and Aidong Zhang. Predicting function by frequent functional association pattern mining in protein interaction networks. IEEE Transactions on Information Technology in Biomedicine (TITB), 14(1):30-36 (2010). [link]
Lei Shi, Young-Rae Cho and Aidong Zhang. Prediction of protein function from connectivity of protein interaction networks. International Journal of Computational Bioscience, 1(1):4-12 (2010). [link]
Young-Rae Cho, Aidong Zhang and Xian Xu. Semantic similarity based feature extraction from microarray expression data. International Journal of Data Mining and Bioinformatics (IJDMB), 3(3):333-345 (2009). [link]
Young-Rae Cho, Lei Shi and Aidong Zhang. A probabilistic framework to predict protein function from interaction data integrated with semantic knowledge. BMC Bioinformatics, 9:392 (2008). [link]
Young-Rae Cho, Lei Shi, Murali Ramanathan and Aidong Zhang. Functional module detection by functional flow pattern minining in protein interaction networks. BMC Bioinformatics, 9(Suppl 10):O1 (2008). [link]
Woochang Hwang, Young-Rae Cho, Aidong Zhang and Murali Ramanathan. CASCADE: a novel quasi all path-based network analysis algorithm for clustering biological interactions. BMC Bioinformatics, 9:64 (2008). [link]
Young-Rae Cho, Woochang Hwang, Murali Ramanathan and Aidong Zhang. Semantic integration to identify overlapping functional modules in protein interaction networks. BMC Bioinformatics, 8:265 (2007). [link]
Woochang Hwang, Young-Rae Cho, Aidong Zhang and Murali Ramanathan. A novel functional module detection algorithm for protein-protein interaction networks. Algorithms for Molecular Biology, 1:24 (2006). [link]

Sawal Maskey and Young-Rae Cho. Survey of biological network alignment: cross-species analysis of conserved systems. Proceedings of IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2019), 2090-2096. [link]
Joseph Huang, Collin Rapp and Young-Rae Cho. Mining cross-ontology weighted association rules between GO and HPO. Proceedings of IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2017), 1706-1711. [link]
Yong Shui and Young-Rae Cho. Filtering Association Rules in Gene Ontology Based on Term Specificity. Proceedings of IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2016), 1314-1321. [link]
Qiaoli Hu and Young-Rae Cho. An integrative measure of graph- and vector-based semantic similarity using information content distance. Proceedings of IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2015), 517-522. [link]
Lizhu Ma and Young-Rae Cho. Semantic mapping to align PPI networks and predict conserved protein complexes. Proceedings of IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2015), 1608-1613. [link]
Yanan Xin and Young-Rae Cho. Effective prediction of signaling pathways from protein-protein interaction networks using network motifs. Proceedings of ISCA International Conference on Bioinformatics and Computational Biology (BICoB 2015).
Young-Rae Cho and Slavka Jaromerska. Prediction of signaling networks by information propagation on protein-protein interaction networks integrated with GO annotations. Proceedings of IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2013), 172-132. [link]
Yilan Bai, Greg Speegle and Young-Rae Cho. Signaling pathway prediction by path frequency in protein-protein interaction networks. Proceedings of IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2013). [link]
Greg Speegle, Yilan Bai and Young-Rae Cho. Extending local similarity indexes with kNN for link prediction. Proceedings of International Conference on Data Mining (DMIN 2013).
Young-Rae Cho, Tak C. Chiam and Yanxin Lu. M-Finder: Functional association mining from protein interaction networks weighted by semantic similarity. Proceedings of IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2012), 95-100. [link]
Francisco I. Pena and Young-Rae Cho. Improvements of graph entropy approach to detect protein complexes by ontological analysis of PPIs. Proceedings of IEEE International Conference on Bioinformatics and Biomedicine - Workshops (BIBMW 2012), 211-217. [link]
George D. Montanez and Young-Rae Cho. Assessing reliability of protein-protein interactions by Gene Ontology integration. Proceedings of IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB 2012), 21-27. [link]
Edward C. Kenley and Young-Rae Cho. Entropy-based graph clustering: application to biological and social networks. Proceedings of IEEE International Conference on Data Mining (ICDM 2011), 1116-1121. [link]
Nicholas Soltau and Young-Rae Cho. Assessment of cluster overlaps to improve accuracy of module detection from PPI networks. Proceedings of IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2011), 569-573. [link]
Edward C. Kenley, Lyles Kirk and Young-Rae Cho. Differentiating party and date hubs in protein interaction networks using semantic similarity measures. Proceedings of ACM International Conference on Bioinformatics and Computational Biology (BCB 2011), 641-645. [link]
Hao Lian, Chengsen Song, and Young-Rae Cho. Decomposing protein interactome networks by graph entropy. Proceedings of IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2010), 585-589. [link]
Young-Rae Cho. Topological analysis of structural roles of proteins in interactome networks. Proceedings of ACM International Conference on Bioinformatics and Computational Biology (BCB 2010), 587-593. [link]
Lei Shi, Young-Rae Cho, and Aidong Zhang. Functional flow simulation based analysis of protein interaction network. Proceedings of IEEE International Conference on Bioinformatics and Bioengineering (BIBE 2010), 144-149. [link]
Young-Rae Cho, Lei Shi and Aidong Zhang. flowNet: Flow-based approach for efficient analysis of complex biological networks. Proceedings of IEEE International Conference on Data Mining (ICDM 2009), 91-100. [link]
Pritam Chanda, Young-Rae Cho, Aidong Zhang and Murali Ramanathan. Mining of attribute interactions using information theoretic metrics. Proceedings of IEEE International Conference on Data Mining - Workshops (ICDMW 2009), 350-355. [link]
Young-Rae Cho and Aidong Zhang. Restructuring protein interaction networks to reveal structural hubs and functional organizations. Proceedings of IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2009), 105-110. [link]
Lei Shi, Young-Rae Cho, and Aidong Zhang. ANN based protein function prediction using integrated protein-protein interaction data. Proceedings of ISIBM International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing (IJCSB 2009), 271-277. [link]
Young-Rae Cho and Aidong Zhang. Discovering frequent patterns of functional associations in protein interaction networks for function prediction. Proceedings of IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2008), 59-65. [link]
Young-Rae Cho, Xian Xu, Woochang Hwang and Aidong Zhang. Feature extraction from microarray expression data by integration of semantic knowledge. Proceedings of IEEE International Conference on Machine Learning and Application (ICMLA 2007), 606-611. [link]
Young-Rae Cho, Woochang Hwang and Aidong Zhang. Assessing reliability of protein-protein interactions by semantic data integration. Proceedings of IEEE International Conference on Data Mining - Workshops (ICDMW 2007), 83-88. [link]
Young-Rae Cho, Woochang Hwang and Aidong Zhang. Optimizing flow-based modularization by iterative centroid search in protein interaction networks. Proceedings of IEEE International Conference on Bioinformatics and Bioengineering (BIBE 2007), 342-349. [link]
Woochang Hwang, Taehyoung Kim, Young-Rae Cho, Aidong Zhang and Murali Ramanathan. SIGN: reliable protein interaction identification by integrating the similarity in GO and the similarity in protein interaction networks. Proceedings of IEEE International Conference on Bioinformatics and Bioengineering (BIBE 2007), 1384-1388. [link]
Young-Rae Cho, Woochang Hwang and Aidong Zhang. Modularization of protein interaction networks by incorporating Gene Ontology annotations. Proceedings of IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB 2007), 233-238. [link]
Young-Rae Cho, Woochang Hwang and Aidong Zhang. Identification of overlapping functional modules in protein interaction networks: information flow-based approach. Proceedings of IEEE International Conference on Data Mining - Workshops (ICDMW 2006), 147-152. [link]
Young-Rae Cho, Woochang Hwang and Aidong Zhang. Efficient modularization of weighted protein interaction networks using k-hop graph reduction.. Proceedings of IEEE Symposium on Bioinformatics and Bioengineering (BIBE 2006), 289-298. [link]
Woochang Hwang, Young-Rae Cho, Aidong Zhang and Murali Ramanathan. Signal transduction model based functional module detection algorithm for protein-protein interaction networks. Proceedings of SIGKDD Workshop on Data Mining in Bioinformatics (BIOKDD 2006), 3-12.
Young-Rae Cho, Woochang Hwang, Aidong Zhang and Murali Ramanathan. Assessing hierarchical modularity in protein interaction networks. Proceedings of LSS Computational Systems Bioinformatics Conference - Posters (CSB 2006).

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