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(Near) COMPLETE LIST of publications.

Ph.D. Thesis

Signal Processing Methods for Genomic Sequence Analysis
Byung-Jun Yoon, Ph.D. Thesis, California Institute of Technology, Electrical Engineering, 2007. (Defended Nov. 2006) [CaltechThesis: A Caltech Library Service]

Journal Publications

34 Optimal experimental design for gene regulatory networks in the presence of uncertainty [NEW]
Roozbeh Dehghannasiri, Byung-Jun Yoon, and Edward R. Dougherty, IEEE/ACM Transactions on Computational Biology and Bioinformatics, accepted.
[preprint]
33 Effective estimation of node-to-node correspondence between different graphs [NEW]
Hyundoo Jeong and Byung-Jun Yoon, IEEE Signal Processing Letters, accepted.
[preprint]
32 Simultaneous identification of robust synergistic subnetwork markers for effective cancer prognosis [NEW]
Navadon Khunlertgit and Byung-Jun Yoon, EURASIP Journal on Bioinformatics and Systems Biology, 2014:19, 2014.
[preprint] [supplementary data] [EURASIP BSB]
31 Sequence alignment by passing messages [NEW]
Byung-Jun Yoon, BMC Genomics, 15(Suppl 1):S14, 2014.
[preprint] [BMC Genomics]
30 SMETANA: accurate and scalable algorithm for probabilistic alignment of large-scale biological networks [NEW]
Sayed Mohammad Ebrahim Sahraeian and Byung-Jun Yoon, PLoS One, 8(7): e67995, 2013. doi:10.1371/journal.pone.0067995
[preprint] [supplementary data] [PLoS One]
29 Quantifying the objective cost of uncertainty in complex dynamical systems [NEW]
Byung-Jun Yoon, Xiaoning Qian, and Edward R. Dougherty, IEEE Transactions on Signal Processing, vol. 61, no. 9, pp. 2256-2266, May 2013.
[preprint] [IEEExplore]
28 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 [NEW]
Mohammad Shahrokh Esfahani, Jason Knight, Amin Zollanvari, Byung-Jun Yoon, and Edward R. Dougherty, Pattern Recognition, vol. 46, no. 10, pp. 2783–2797, 2013.
[preprint] [supplementary data] [Pattern Recognition]
27 Identification of robust pathway markers for cancer through rank-based pathway activity inference [NEW]
Navadon Khunlertgit and Byung-Jun Yoon, Advances in Bioinformatics, vol. 2013, Article ID 618461, 8 pages, 2013. doi:10.1155/2013/618461.
[preprint] [supplementary data] [Advances in Bioinformatics]
26 Adaptive reference update (ARU) algorithm: a stochastic search algorithm for efficient optimization of multi-drug cocktails
Mansuck Kim and Byung-Jun Yoon, BMC Genomics, 13(Suppl 6):S12, 2012.
[preprint] [supplementary data] [BMC Genomics]
25 A network synthesis model for generating protein interaction network families
Sayed Mohammad Ebrahim Sahraeian and Byung-Jun Yoon, PLoS One, 7(8): e41474, 2012. doi:10.1371/journal.pone.0041474
[preprint] [supplementary data] [PLoS One]
24 RESQUE: Network reduction using semi-Markov random walk scores for efficient queryin g of biological networks
Sayed Mohammad Ebrahim Sahraeian and Byung-Jun Yoon, Bioinformatics, 28 (16): 2129-2136, 2012. doi:10.1093/bioinformatics/bts341
[preprint] [supplementary data] [Bioinformatics] [RECOMB extended abstract]
23 Comparative analysis of biological networks: hidden Markov model and Markov chain-based approach
Byung-Jun Yoon, Xiaoning Qian, and Sayed Mohammad Ebrahim Sahraeian, IEEE Signal Processing Magazine, Special Issue on Genomic and Proteomic Signal Processing in Biomolecular Pathways, 29(1):22-34, 2012.
[preprint] [IEEExplore]
22 Probabilistic reconstruction of the tumor progression process in gene regulatory networks in the presence of uncertainty
Mohammad Shahrokh Esfahani, Byung-Jun Yoon, and Edward R. Dougherty, BMC Bioinformatics, 12(Suppl 8):S9, 2011.
[preprint] [BMC Bioinformatics]
21 Enhancing the accuracy of HMM-based conserved pathway prediction using global correspondence scores
Xiaoning Qian, Sayed Mohammad Ebrahim Sahraeian, and Byung-Jun Yoon, BMC Bioinformatics, 12(Suppl 8):S6, 2011.
[preprint] [supplementary material] [BMC Bioinformatics]
20 PicXAA-Web: a web-based platform for non-progressive maximum expected accuracy alignment of multiple biological sequences
Sayed Mohammad Ebrahim Sahraeian and Byung-Jun Yoon, Nucleic Acids Research, 39 (Suppl 2): W8-W12, 2011.
[PicXAA-Web Server] [Nucleic Acids Research]
19 Comparative analysis of protein interaction networks reveals that conserved pathways are susceptible to HIV-1 interception
Xiaoning Qian and Byung-Jun Yoon, BMC Bioinformatics, 12(Suppl 1):S19, 2011.
[preprint] [BMC Bioinformatics]
18 PicXAA-R: efficient structural alignment of multiple RNA sequences using a greedy approach
Sayed Mohammad Ebrahim Sahraeian and Byung-Jun Yoon, BMC Bioinformatics, 12(Suppl 1):S38, 2011.
[preprint] [BMC Bioinformatics]
17 Enhanced stochastic optimization algorithm for finding effective multi-target therapeutics
Byung-Jun Yoon, BMC Bioinformatics, 12(Suppl 1):S18, 2011.
[preprint] [BMC Bioinformatics]
16 A novel low-complexity HMM similarity measure
Sayed Mohammad Ebrahim Sahraeian and Byung-Jun Yoon, IEEE Signal Processing Letters, vol.18, no.2, pp. 87-90, Feb. 2011.
[preprint] [IEEExplore]
15 Identification of diagnostic subnetwork markers for cancer in human protein-protein interaction network
Junjie Su, Byung-Jun Yoon, and Edward R. Dougherty, BMC Bioinformatics, 11(Suppl 6):S8, 2010.
[BMC Bioinformatics]
14 PicXAA: greedy probabilistic construction of maximum expected accuracy alignment of multiple sequences
Sayed Mohammad Ebrahim Sahraeian and Byung-Jun Yoon, Nucleic Acids Research, 38(15): 4917-4928, 2010.
[Nucleic Acids Research]
13 Accurate and reliable cancer classification based on probabilistic inference of pathway activity
Junjie Su, Byung-Jun Yoon, and Edward R. Dougherty, PLoS One, 4(12): e8161. doi:10.1371/journal.pone.0008161, 2009.
[preprint] [PLoS One]
12 Effective identification of conserved pathways in biological networks using hidden Markov models
Xiaoning Qian and Byung-Jun Yoon, PLoS One, 4(12): e8070. doi:10.1371/journal.pone.0008070, 2009.
[preprint] [PLoS One]
11 Identification of differentially expressed miRNAs in chicken lung and trachea after avian influenza virus infection by a deep sequencing approach
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, BMC Genomics, 10:512, 2009.
[BMC Genomics]
10 Hidden Markov models and their applications in biological sequence analysis
Byung-Jun Yoon, Current Genomics, vol. 10, no. 6, pp. 402-415, Sep. 2009.
[preprint] [PubMed Central]
9 Efficient alignment of RNAs with pseudoknots using sequence alignment constraints
Byung-Jun Yoon, EURASIP Journal on Bioinformatics and Systems Biology, vol. 2009, Article ID 491074, 13 pages, 2009.
[preprint] [EURASIP BSB]
8 Querying pathways in protein interaction networks based on hidden Markov models
Xiaoning Qian, Sing-Hoi Sze, and Byung-Jun Yoon, Journal of Computational Biology, vol. 16, no. 2, pp. 145-157, Feb. 2009.
[preprint] [JCB]
7 Fast structural alignment of RNAs by optimizing the adjoining order of profile-csHMMs
Byung-Jun Yoon and P. P. Vaidyanathan, IEEE Journal of Selected Topics in Signal Processing, vol. 2, pp. 400-411, June 2008.
[preprint] [IEEExplore]
6 Structural alignment of RNAs using profile-csHMMs and its application to RNA homology search: Overview and new results
Byung-Jun Yoon and P. P. Vaidyanathan, 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.
[preprint] [IEEExplore]
5 Computational identification and analysis of noncoding RNAs - Unearthing the buried treasures in the genome
Byung-Jun Yoon and P. P. Vaidyanathan, IEEE Signal Processing Magazine, Special Issue on Signal Processing Methods in Genomics and Proteomics, vol. 24, no. 1, pp. 64-74, Jan. 2007.
[preprint] [IEEExplore]
4 Context-sensitive hidden Markov models for modeling long-range dependencies in symbol sequences
Byung-Jun Yoon and P. P. Vaidyanathan, IEEE Transactions on Signal Processing, vol. 54, pp. 4169-4184, Nov. 2006.
[preprint] [IEEE Xplore]
3 A practical approach for the design of nonuniform lapped transforms
Byung-Jun Yoon and Henrique S. Malvar, IEEE Signal Processing Letters, vol. 13, pp. 469-452, Aug. 2006.
[preprint] [IEEE Xplore]
2 A multirate DSP model for estimation of discrete probability density functions
Byung-Jun Yoon and P. P. Vaidyanathan, IEEE Transactions on Signal Processing, vol. 53, pp. 252-264, Jan. 2005.
[preprint] [IEEE Xplore]
1 The role of signal-processing concepts in genomics and proteomics
P. P. Vaidyanathan and Byung-Jun Yoon, Journal of the Franklin Institute (invited paper), Special Issue on Genomics, vol. 341, pp. 111-135, 2004.
[preprint]

Selected Conference Publications

32 Sequence alignment by passing messages [NEW]
Byung-Jun Yoon, Asia Pacific Bioinformatics Conference (APBC), Shanghai, China, January 2014.
[preprint] [BMC Genomics]
31 RESQUE: Network reduction using semi-Markov random walk scores for efficient querying of biological networks
Sayed Mohammad Ebrahim Sahraeian and Byung-Jun Yoon, 16th Annual International Conference on Research in Computational Molecular Biology (RECOMB), Barcelona, April 2012.
[RECOMB extended abstract] [preprint] [supplementary data]
30 Comparative analysis of protein interaction networks reveals that conserved pathways are susceptible to HIV-1 interception
Xiaoning Qian and Byung-Jun Yoon, Asia Pacific Bioinformatics Conference (APBC), Incheon, Korea, January 2011.
[preprint] [BMC Bioinformatics]
29 PicXAA-R: efficient structural alignment of multiple RNA sequences using a greedy approach
Sayed Mohammad Ebrahim Sahraeian and Byung-Jun Yoon, Asia Pacific Bioinformatics Conference (APBC), Incheon, Korea, January 2011.
[preprint] [BMC Bioinformatics]
28 Enhanced stochastic optimization algorithm for finding effective multi-target therapeutics
Byung-Jun Yoon, Asia Pacific Bioinformatics Conference (APBC), Incheon, Korea, January 2011.
[preprint] [BMC Bioinformatics]
27 Shape matching based on graph alignment using hidden Markov models
Xiaoning Qian and Byung-Jun Yoon, IEEE International Conference on Acoustics, Speech, and Signal Processing (ICASSP), Dallas, TX, March 2010.
[preprint]
26 Identifying reliable subnetwork markers in protein-protein interaction network for classification of breast cancer metastasis
Junjie Su and Byung-Jun Yoon, IEEE International Conference on Acoustics, Speech, and Signal Processing (ICASSP), Dallas, TX, March 2010.
[preprint]
25 Accurate and reliable cancer classification based on probabilistic inference of pathway activity
Junjie Su, Byung-Jun Yoon, and Edward R. Dougherty, RECOMB Systems Biology, Boston, MA, Dec. 2009.
[preprint] [PLoS One]
24 Effective identification of conserved pathways in biological networks using hidden Markov models
Xiaoning Qian and Byung-Jun Yoon, RECOMB Systems Biology, Boston, MA, Dec. 2009.
[preprint] [PLoS One]
23 Simple alignment constraints for efficient alignment of RNA sequences using family-specifi models
Byung-Jun Yoon, IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS), Minneapolis, MN, May 2009.
[preprint]
22 Identification of differentially expressed miRNAs in chicken lung and trachea after avian influenza virus infection by Solexa sequencer
Ying Wang, Vinayak Brahmakshatriya, Blanca Lupiani, Sanjay Reddy, Byung-Jun Yoon, Huifeng Zhu, Preethi Gunaratne, Rui Chen, and Huaijun Zhou, International Plant and Animal Genome Conference (PAG-XVII), San Diego, CA, Jan. 2009.
21 Querying pathways in protein interaction networks based on hidden Markov models
Xiaoning Qian, Sing-Hoi Sze, and Byung-Jun Yoon, RECOMB Systems Biology, Boston, MA, Oct. 2008.
[preprint] [JCB]
20 A simple method for finding structurally similar RNAs using two-dimensional discrete convolution
Byung-Jun Yoon, IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS), Phoenix, AZ, June 2008.
[preprint]
19 Coding overcomplete representations of audio using the MCLT
Byung-Jun Yoon and Henrique S. Malvar, Data Compression Conference (DCC), Snowbird, Utah, Mar. 2008.
[preprint]
18 Effective annotation of noncoding RNA families using profile context-sensitive HMMs
Byung-Jun Yoon, IEEE International Symposium on Communications, Control and Signal Processing (ISCCSP), St. Julians, Malta, Mar. 2008.
[preprint]
17 Fast structural similarity search of noncoding RNAs based on matched filtering of stem patterns
Byung-Jun Yoon and P. P. Vaidyanathan, Proc. 41st Asilomar Conference on Signals, Systems, and Computers, Monterey, CA, Nov. 2007.
[preprint]
16 Fast search of sequences with complex symbol correlations using profile context-sensitive HMMs and pre-screening filters
Byung-Jun Yoon and P. P. Vaidyanathan, Proc. 32nd IEEE International Conference on Acoustics, Speech, and Signal Processing (ICASSP), Honolulu, HI, April 2007.
[preprint]
15 Robust adaptive beamforming algorithm using instantaneous direction of arrival with enhanced noise suppression capability
Byung-Jun Yoon, Ivan Tashev, and Alex Acero, Proc. 32nd IEEE International Conference on Acoustics, Speech, and Signal Processing (ICASSP), Honolulu, HI, April 2007.
[preprint]
14 Modeling and identification of alternative folding in regulatory RNAs using context-sensitive HMMs
Byung-Jun Yoon and P. P. Vaidyanathan, IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS), College Station, Texas, May 2006.
[preprint]
13 Profile context-sensitive HMMs for probabilistic modeling of sequences with complex correlations
Byung-Jun Yoon and P. P. Vaidyanathan, Proc. 31st IEEE International Conference on Acoustics, Speech, and Signal Processing (ICASSP), Toulouse, May 2006.
[preprint]
12 An overview of the role of context-sensitive HMMs in the prediction of ncRNA genes
Byung-Jun Yoon and P. P. Vaidyanathan, IEEE Workshop on Statistical Signal Processing (SSP), Bordeaux, France, July 2005.
[preprint]
11 Scoring algorithm for context-sensitive HMMs with application to RNA secondary structure analysis
Byung-Jun Yoon and P. P. Vaidyanathan, IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS), Newport, RI, May 2005.
[preprint]
10 Optimal alignment algorithm for context-sensitive hidden Markov models
Byung-Jun Yoon and P. P. Vaidyanathan, Proc. 30th IEEE International Conference on Acoustics, Speech, and Signal Processing (ICASSP), Philadelphia, Mar. 2005.
[preprint]
9 RNA secondary structure prediction using context-sensitive hidden Markov models
Byung-Jun Yoon and P. P. Vaidyanathan, Proc. International Workshop on Biomedical Circuits and Systems (BioCAS), Singapore, Dec. 2004.
[preprint]
8 HMM with auxiliary memory: a new tool for modeling RNA secondary structures
Byung-Jun Yoon and P. P. Vaidyanathan, Proc. 38th Asilomar Conference on Signals, Systems, and Computers, Monterey, CA, Nov. 2004.
[preprint]
7 Identification of CpG islands using a bank of IIR lowpass filters
Byung-Jun Yoon and P. P. Vaidyanathan, Proc. 11th Digital Signal Processing Workshop, Taos Ski Valley, New Mexico, Aug. 2004.
[preprint]
6 Wavelet-based denoising by customized thresholding
Byung-Jun Yoon and P. P. Vaidyanathan, Proc. 29th IEEE International Conference on Acoustics, Speech, and Signal Processing (ICASSP), Montreal, May 2004.
[preprint]
5 Discrete PDF estimation in the presence of noise
Byung-Jun Yoon and P. P. Vaidyanathan, Proc. International Symposium on Circuits and Systems (ISCAS), Vancouver, May 2004.
[preprint]
4 Improved estimation of discrete probability density functions using multirate models
Byung-Jun Yoon and P. P. Vaidyanathan, Proc. 37th Asilomar Conference on Signals, Systems, and Computers, Monterey, CA, Nov. 2003.
[preprint]
3 Discrete probability density estimation using multirate DSP models
P. P. Vaidyanathan and Byung-Jun Yoon, Proc. 28th IEEE International Conference on Acoustics, Speech, and Signal Processing (ICASSP), Hong Kong, Apr. 2003.
[preprint]
2 Digital filters for gene prediction applications
P. P. Vaidyanathan and Byung-Jun Yoon, Proc. 36th Asilomar Conference on Signals, Systems, and Computers, Monterey, CA, Nov. 2002.
[preprint]
1 Gene and exon prediction using allpass-based filters
P. P. Vaidyanathan and Byung-Jun Yoon, IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS), Raleigh, NC, Oct. 2002.
[preprint]

Technical Reports

2 The design of nonuniform lapped transforms
Byung-Jun Yoon and Henrique S. Malvar, Microsoft Research Technical Report TR-2005-116, Sep. 2005.
[technical report]
1 Non-parametric estimation of discrete probability density functions using multirate DSP models
Byung-Jun Yoon and P. P. Vaidyanathan, Technical Report, Dept. of Electrical Engineering, California Institute of Technology, May 2003.


Last update: Nov.20.2014