(Near) COMPLETE LIST of publications.
Ph.D. Thesis | |
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Signal Processing Methods for Genomic Sequence Analysis Byung-Jun Yoon, Ph.D. Thesis, California Institute of Technology, Electrical Engineering, 2007. (Defended Nov. 2006) |
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Journal Publications | |
| 23 |
Comparative analysis of biological networks: hidden Markov model and Markov chain-based approach
[NEW]
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
[NEW]
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
[NEW]
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
[NEW]
Sayed Mohammad Ebrahim Sahraeian and Byung-Jun Yoon, Nucleic Acids Research, doi:10.1093/nar/gkr244, 2011. [PicXAA-Web Server] [Nucleic Acids Research] |
| 19 |
Comparative analysis of protein interaction networks reveals that conserved pathways are susceptible to HIV-1 interception
[NEW]
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
[NEW]
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
[NEW]
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 | |
| 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. [NEW] [preprint:extended abstract] |
| 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: Jan.23.2012