Publications

Journal Publications


  1. 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, accepted. [NEW]
  2. Chun-Chi Chen, Xiaoning Qian, and Byung-Jun Yoon, “Effective computational detection of piRNAs using n-gram models and support vector machine,” BMC Bioinformatics, accepted. [NEW]
  3. 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. [NEW]
  4. 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. [NEW]
  5. 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.
    * Best Paper Runner-Up, 13th MCBIOS Conference, Memphis, Tennessee, USA, March 2016.
  6. 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.
  7. 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.
  8. 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.
    * Best Paper Award, 12th MCBIOS Conference, Little Rock, Arkansas, USA, March 2015.
  9. 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, accepted.
  10. 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, accepted.
  11. Ariana Broumand, Mohammad Shahrokh Esfahani, Byung-Jun Yoon, Edward R. Dougherty, “Discrete optimal Bayesian classification with error-conditioned sequential sampling,” Pattern Recognition, vol. 48, no. 11, pp 3766–3782, 2015.
  12. 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.
  13. Hyundoo Jeong and Byung-Jun Yoon, “Accurate multiple network alignment through context-sensitive random walk,” BMC Systems Biology, 9(Suppl 1):S7, 2015.
  14. Hyundoo Jeong and Byung-Jun Yoon, “Effective estimation of node-to-node correspondence between different graphs,” IEEE Signal Processing Letters, vol. 22, no. 6, pp. 661-665, 2015.
  15. 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.
  16. Byung-Jun Yoon, “Sequence alignment by passing messages,” BMC Genomics, 15(Suppl 1):S14, 2014.
  17. 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.
  18. 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.
  19. Mohammad Shahrokh Esfahani, Jason Knight, Amin Zollanvari, Byung-Jun Yoon, and 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, vol. 46, no. 10, pp. 2783–2797, 2013.
  20. 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.
  21. Mansuck Kim and Byung-Jun Yoon, “Adaptive reference update (ARU) algorithm: a stochastic search algorithm for efficient optimization of multi-drug cocktails,” BMC Genomics, 13(Suppl 6):S12, 2012.
  22. Sayed Mohammad Ebrahim Sahraeian and Byung-Jun Yoon, “A network synthesis model for generating protein interaction network families,”
    PLoS One, 7(8): e41474, 2012.
  23. Sayed Mohammad Ebrahim Sahraeian and Byung-Jun Yoon, “RESQUE: Network reduction using semi-Markov random walk scores for efficient querying of biological networks,” Bioinformatics, 28 (16): 2129-2136, 2012.
  24. Byung-Jun Yoon, Xiaoning Qian, and Sayed Mohammad Ebrahim Sahraeian, “Comparative analysis of biological networks: hidden Markov model and Markov chain-based approach,” IEEE Signal Processing Magazine, 29(1):22-34, 2012.
  25. Mohammad Shahrokh Esfahani, Byung-Jun Yoon, and Edward R. Dougherty, “Probabilistic reconstruction of the tumor progression process in gene regulatory networks in the presence of uncertainty,” BMC Bioinformatics, 12(Suppl 8):S9, 2011.
  26. Xiaoning Qian, Sayed Mohammad Ebrahim Sahraeian, and Byung-Jun Yoon, “Enhancing the accuracy of HMM-based conserved pathway prediction using global correspondence scores,” BMC Bioinformatics, 12(Suppl 8):S6, 2011.
  27. Sayed Mohammad Ebrahim Sahraeian and Byung-Jun Yoon, “PicXAA-Web: a web-based platform for non-progressive maximum expected accuracy alignment of multiple biological sequences,” Nucleic Acids Research, 39 (Suppl 2): W8-W12, 2011.
  28. Xiaoning Qian and Byung-Jun Yoon, “Comparative analysis of protein interaction networks reveals that conserved pathways are susceptible to HIV-1 interception,” BMC Bioinformatics, 12(Suppl 1):S19, 2011.
  29. Sayed Mohammad Ebrahim Sahraeian and Byung-Jun Yoon, “PicXAA-R: efficient structural alignment of multiple RNA sequences using a greedy approach,” BMC Bioinformatics, 12(Suppl 1):S38, 2011.
    * Best Paper Award, 9th Asia Pacific Bioinformatics Conference (APBC), Incheon, Korea, January 2011.
  30. Byung-Jun Yoon, “Enhanced stochastic optimization algorithm for finding effective multi-target therapeutics,” BMC Bioinformatics, 12(Suppl 1):S18, 2011.
  31. Sayed Mohammad Ebrahim Sahraeian and Byung-Jun Yoon, “A novel low-complexity HMM similarity measure,” IEEE Signal Processing Letters, vol.18, no.2, pp. 87-90, Feb. 2011.
  32. Junjie Su, Byung-Jun Yoon, and Edward R. Dougherty, “Identification of diagnostic subnetwork markers for cancer in human protein-protein interaction network,” BMC Bioinformatics, 11(Suppl 6):S8, 2010.
  33. Sayed Mohammad Ebrahim Sahraeian and Byung-Jun Yoon, “PicXAA: greedy probabilistic construction of maximum expected accuracy alignment of multiple sequences,” Nucleic Acids Research, 38(15): 4917-4928, 2010.
  34. Junjie Su, Byung-Jun Yoon, and Edward R. Dougherty, “Accurate and reliable cancer classification based on probabilistic inference of pathway activity,” PLoS One, 4(12): e8161, 2009.
  35. Xiaoning Qian and Byung-Jun Yoon, “Effective identification of conserved pathways in biological networks using hidden Markov models,” PLoS One, 4(12): e8070, 2009.
  36. Ying Wang, Vinayak Brahmakshatriya, Huifeng Zhu, Blanca Lupiani, Sanjay M. Reddy, Byung-Jun Yoon, Preethi H. Gunaratne, Jong Hwan Kim, Rui Chen, Junjun Wang, and Huaijun Zhou, “Identification of differentially expressed miRNAs in chicken lung and trachea after avian influenza virus infection by a deep sequencing approach,” BMC Genomics, 10:512, 2009.
  37. Byung-Jun Yoon, “Hidden Markov models and their applications in biological sequence analysis,” Current Genomics, vol. 10, no. 6, pp. 402-415, Sep. 2009.
  38. Byung-Jun Yoon, “Efficient alignment of RNAs with pseudoknots using sequence alignment constraints,” EURASIP Journal on Bioinformatics and Systems Biology, vol. 2009, Article ID 491074, 13 pages, 2009.
  39. Xiaoning Qian, Sing-Hoi Sze, and Byung-Jun Yoon, “Querying pathways in protein interaction networks based on hidden Markov models,” Journal of Computational Biology, vol. 16, no. 2, pp. 145-157, Feb. 2009.
  40. Byung-Jun Yoon and P. P. Vaidyanathan, “Fast structural alignment of RNAs by optimizing the adjoining order of profile-csHMMs,” IEEE Journal of Selected Topics in Signal Processing, vol. 2, pp. 400-411, June 2008.
  41. Byung-Jun Yoon and P. P. Vaidyanathan, “Structural alignment of RNAs using profile-csHMMs and its application to RNA homology search: Overview and new results,” IEEE Transactions on Automatic Control (Joint Special Issue on Systems Biology with IEEE Transactions on Circuits and Systems: Part-I), vol. 53, pp. 10-25, Jan. 2008.
  42. Byung-Jun Yoon and P. P. Vaidyanathan, “Computational identification and analysis of noncoding RNAs – Unearthing the buried treasures in the genome,” IEEE Signal Processing Magazine, vol. 24, no. 1, pp. 64-74, Jan. 2007.
  43. Byung-Jun Yoon and P. P. Vaidyanathan, “Context-sensitive hidden Markov models for modeling long-range dependencies in symbol sequences,” IEEE Transactions on Signal Processing, vol. 54, pp. 4169-4184, Nov. 2006.
  44. Byung-Jun Yoon and Henrique S. Malvar, “A practical approach for the design of nonuniform lapped transforms,” IEEE Signal Processing Letters, vol. 13, pp. 469-452, Aug. 2006.
  45. Byung-Jun Yoon and P. P. Vaidyanathan, “A multirate DSP model for estimation of discrete probability density functions,” IEEE Transactions on Signal Processing, vol. 53, pp. 252-264, Jan. 2005.
  46. P. P. Vaidyanathan and Byung-Jun Yoon, “The role of signal-processing concepts in genomics and proteomics,” Journal of the Franklin Institute (invited paper), vol. 341, pp. 111-135, 2004.

Selected Conference Publications


  1. Hyundoo Jeong and Byung-Jun Yoon, “Accurate multiple network alignment through context-sensitive random walk,” Asia Pacific Bioinformatics Conference (APBC), HsinChu, Taiwan, January 2015.
  2. Byung-Jun Yoon, “Sequence alignment by passing messages,” Asia Pacific Bioinformatics Conference (APBC), Shanghai, China, January 2014.
  3. Sayed Mohammad Ebrahim Sahraeian and Byung-Jun Yoon, “RESQUE: Network reduction using semi-Markov random walk scores for efficient querying of biological networks,” Annual International Conference on Research in Computational Molecular Biology (RECOMB), Barcelona, April 2012.
  4. Sayed Mohammad Ebrahim Sahraeian and Byung-Jun Yoon, “PicXAA-R: efficient structural alignment of multiple RNA sequences using a greedy approach,” Asia Pacific Bioinformatics Conference (APBC), Incheon, Korea, January 2011.
  5. Byung-Jun Yoon, “Enhanced stochastic optimization algorithm for finding effective multi-target therapeutics,” Asia Pacific Bioinformatics Conference (APBC), Incheon, Korea, January 2011.
  6. Xiaoning Qian and Byung-Jun Yoon, “Comparative analysis of protein interaction networks reveals that conserved pathways are susceptible to HIV-1 interception,” Asia Pacific Bioinformatics Conference (APBC), Incheon, Korea, January 2011.
  7. Xiaoning Qian and Byung-Jun Yoon, “Shape matching based on graph alignment using hidden Markov models,” IEEE International Conference on Acoustics, Speech, and Signal Processing (ICASSP), Dallas, TX, March 2010.
  8. Junjie Su and Byung-Jun Yoon, “Identifying reliable subnetwork markers in protein-protein interaction network for classification of breast cancer metastasis,” IEEE International Conference on Acoustics, Speech, and Signal Processing (ICASSP), Dallas, TX, March 2010.
  9. Junjie Su, Byung-Jun Yoon, and Edward R. Dougherty, “Accurate and reliable cancer classification based on probabilistic inference of pathway activity,” RECOMB Systems Biology, Boston, MA, Dec. 2009.
  10. Xiaoning Qian and Byung-Jun Yoon, “Effective identification of conserved pathways in biological networks using hidden Markov models,” RECOMB Systems Biology, Boston, MA, Dec. 2009.
  11. Xiaoning Qian, Sing-Hoi Sze, and Byung-Jun Yoon, “Querying pathways in protein interaction networks based on hidden Markov models,” RECOMB Systems Biology, Boston, MA, Oct. 2008.
  12. Byung-Jun Yoon, Ivan Tashev, and Alex Acero, “Robust adaptive beamforming algorithm using instantaneous direction of arrival with enhanced noise suppression capability,” IEEE International Conference on Acoustics, Speech, and Signal Processing (ICASSP), Honolulu, HI, April 2007.
  13. Byung-Jun Yoon and P. P. Vaidyanathan, “Profile context-sensitive HMMs for probabilistic modeling of sequences with complex correlations,” IEEE International Conference on Acoustics, Speech, and Signal Processing (ICASSP), Toulouse, May 2006.
  14. Byung-Jun Yoon and P. P. Vaidyanathan, “HMM with auxiliary memory: a new tool for modeling RNA secondary structures,” Asilomar Conference on Signals, Systems, and Computers, Monterey, CA, Nov. 2004.
  15. Byung-Jun Yoon and P. P. Vaidyanathan, “Wavelet-based denoising by customized thresholding,” IEEE International Conference on Acoustics, Speech, and Signal Processing (ICASSP), Montreal, May 2004.
  16. P. P. Vaidyanathan and Byung-Jun Yoon, “Digital filters for gene prediction applications,” Asilomar Conference on Signals, Systems, and Computers, Monterey, CA, Nov. 2002.
  17. P. P. Vaidyanathan and Byung-Jun Yoon, “Gene and exon prediction using allpass-based filters,” IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS), Raleigh, NC, Oct. 2002.
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