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Author: Yoon, Byung-Jun

Noushin Ghaffari, Osama A. Arshad, Hyundoo Jeong, John Thiltges, Michael F. Criscitiello, Byung-Jun Yoon, Aniruddha Datta, Charles D. Johnson, "Examining de novo transcriptome assemblies via a quality assessment pipeline", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 15, no. 2, pp. 494-505, 2018.  (Journal Publication)  [More Details]  [Online]

Mansuck Kim, Huan Zhang, Charles Woloshuk, Won-Bo Shim, and Byung-Jun Yoon, "Computational Prediction of Pathogenic Network Modules in Fusarium verticillioides", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 15, no. 2, pp. 506 – 515, 2018  (Journal Publication)  [More Details]  [Online]

Man Kim, Huan Zhang, Huijuan Yan, Byung-Jun Yoon, and Won-Bo Shim, "Characterizing co-expression networks underpinning maize stalk rot virulence in Fusarium verticillioidesthrough computational subnetwork module analyses", Scientific Reports, accepted.  (Journal Publication)  [More Details]  [Online]

Hyundoo Jeong, Xiaoning Qian, and Byung-Jun Yoon, "CUFID-query: accurate network querying through estimation of network flow between query and target networks based on random walk", BMC Bioinformatics, 18(Suppl 14):500, 2017  (Journal Publication)  [More Details]  [Online]

Hyundoo Jeong, Xiaoning Qian, and Byung-Jun Yoon, "CUFID-query: accurate network querying through estimation of network flow between query and target networks based on random walk", BMC Bioinformatics, 18(Suppl 14):500, 2017  (Journal Publication)  [More Details]  [Online]

Hyundoo Jeong and Byung-Jun Yoon, "SEQUOIA: Significance enhanced network querying through context-sensitive random walk and minimization of network conductance", BMC Systems Biology, 11(Suppl 3):20, 2017.  (Journal Publication)  [More Details]  [Online]

Chun-Chi Chen, Xiaoning Qian, and Byung-Jun Yoon, "Effective computational detection of piRNAs using n-gram models and support vector machine", BMC Bioinformatics, 18(Suppl 14):517. 2017.  (Journal Publication)  [More Details]  [Online]

Chun-Chi Chen, Noushin Ghaffari, Xiaoning Qian, and Byung-Jun Yoon, "Optimal hybrid sequencing and assembly: feasibility conditions for accurate genome reconstruction and cost minimization strategy", Computational Biology and Chemistry, 69, pp. 153–163, 2017  (Journal Publication)  [More Details]  [Online]

Navadon Khunlertgit and Byung-Jun Yoon, "Incorporating topological information for predicting robust cancer subnetwork markers in human protein-protein interaction network", BMC Bioinformatics, 17(Suppl 13):351, 2016  (Journal Publication)  [More Details]  [Online]

Hyundoo Jeong, Xiaoning Qian, and Byung-Jun Yoon, "Effective comparative analysis of protein-protein interaction networks by measuring the steady-state network flow using a Markov model", BMC Bioinformatics, 17(Suppl 13):395, 2016.  (Journal Publication)  [More Details]  [Online]

Roozbeh Dehghannasiri, Byung-Jun Yoon, and Edward R. Dougherty, "Efficient experimental design for uncertainty reduction in gene regulatory networks", BMC Bioinformatics, 16(Suppl 13):S2, 2015.  (Journal Publication)  [More Details]  [Online]

Roozbeh Dehghannasiri, Byung-Jun Yoon, and Edward R. Dougherty, "Optimal experimental design for gene regulatory networks in the presence of uncertainty", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.12, no.4, pp.938-950, 2015.  (Journal Publication)  [More Details]  [Online]

N. Ghaffari, O. A. Arshad, H. Jeong, J. Thiltges, M. F. Criscitiello, B.-J. Yoon, A. Datta and C. D. Johnson, "Examining De Novo Transcriptome Assemblies via a Quality Assessment Pipeline",   (Journal Publication)  [More Details]  [Online]

Mansuck Kim, Huan Zhang, Charles Woloshuk, Won-Bo Shim, and Byung-Jun Yoon, "Computational identification of genetic subnetwork modules associated with maize defense response to Fusarium verticillioides", BMC Bioinformatics, 16(Suppl 13):S12, 2015.  (Journal Publication)  [More Details]  [Online]

Hyundoo Jeong and Byung-Jun Yoon, "Accurate multiple network alignment through context-sensitive random walk", BMC Systems Biology, 9(Suppl 1):S7, 2015.  (Journal Publication)  [More Details]  [Online]

Navadon Khunlertgit and Byung-Jun Yoon, "Simultaneous identification of robust synergistic subnetwork markers for effective cancer prognosis", EURASIP Journal on Bioinformatics and Systems Biology, 2014:19, 2014.  (Journal Publication)  [More Details]  [Online]

Byung-Jun Yoon, "Sequence alignment by passing messages", BMC Genomics, 15(Suppl 1):S14, 2014.  (Journal Publication)  [More Details]  [Online]

Sayed Mohammad Ebrahim Sahraeian and Byung-Jun Yoon,, "SMETANA: accurate and scalable algorithm for probabilistic alignment of large-scale biological networks", PLoS One, 8(7): e67995, 2013.  (Journal Publication)  [More Details]  [Online]

Navadon Khunlertgit and Byung-Jun Yoon, "Identification of robust pathway markers for cancer through rank-based pathway activity inference", Advances in Bioinformatics, vol. 2013, Article ID 618461, 8 pages, 2013.  (Journal Publication)  [More Details]  [Online]

Mohammad Shahrokh Esfahania, Jason Knighta, Amin Zollanvaria, Byung-Jun Yoona, Edward R. Dougherty, "Classifier design given an uncertainty class of feature distributions via regularized maximum likelihood and the incorporation of biological pathway knowledge in steady-state phenotype classification", Pattern Recognition Volume 46, Issue 10, October 2013, Pages 2783–2797  (Journal Publication)  [More Details]  [Online]

Byung-Jun Yoon, Xiaoning Qian, and Edward R. Dougherty, "Quantifying the objective cost of uncertainty in complex dynamical systems", IEEE Transactions on Signal Processing, vol. 61, no. 9, pp. 2256-2266, May 2013  (Journal Publication)  [More Details]  [Online]

Byung-Jun Yoon, Xiaoning Qian, Sayed Mohammad Ebrahim Sahraeian, "Comparative analysis of biological networks using Markov chains and hidden Markov models", IEEE Signal Processing Magazine, Special Issue on Genomic and Proteomic Signal Processing in Biomolecular Pathways, 29(1): 22--34, 2012.  (Journal Publication)  [More Details]  [Online]

Esfahani, M. S., Yoon, B-J., and Dougherty, E. R., "Probabilistic Reconstruction of the Tumor Progression Process in Gene Regulatory Networks in the Presence of Uncertainty", BMC Bioinformatics, 12(Suppl 10):S9, October, 2011  (Journal Publication)  [More Details]  [Online]

Byung-Jun Yoon, "Hidden Markov Models and their Applications in Biological Sequence Analysis", Curr Genomics. 2009 September; 10(6): 402–415  (Journal Publication)  [More Details]  [Online]

Xiaoning Qian , Sing-Hoi Sze, Byung-Jun Yoon, "Querying pathways in protein interaction networks based on hidden Markov models", Journal of Computational Biology, 16(2):145--157, 2009  (Journal Publication)  [More Details]  [Online]