HR job title
- Professor
- Contact Info
- 1 979 845 6942
- Websites
- ORCiD
- 0000-0001-9328-1101
Yoon, Byung-Jun Professor
Positions
Dr. Yoon's main theoretical interests include objective-based uncertainty quantification, optimal experimental design (OED), machine learning, and signal processing. Application areas of interest include bioinformatics, computational network biology, and AI-driven drug/materials discovery.
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- Publications
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- Teaching
- Works By Students
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Overview
Publications
selected publications
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academic article
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Maddouri, O., Qian, X., & Yoon, B.
(2023).
Geometric Affinity Propagation for Clustering With Network Knowledge. 35(11), 11419-11436.
-
Frasch, M. G., Yoon, B., Helbing, D. L., Snir, G., Antonelli, M. C., & Bauer, R.
(2023).
Autism Spectrum Disorder: A Neuro-Immunometabolic Hypothesis of the Developmental Origins. Biology.
12(7), 914-914.
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Kim, W. S., Khot, M. I., Woo, H., Hong, S., Baek, D., Maisey, T., ... Park, S. I.
(2022).
AI-enabled, implantable, multichannel wireless telemetry for photodynamic therapy. 13(1), 2178.
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Maddouri, O., Qian, X., Alexander, F. J., Dougherty, E. R., & Yoon, B.
(2022).
Robust importance sampling for error estimation in the context of optimal Bayesian transfer learning. 3(3), 100428-100428.
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Maddouri, O., Qian, X., & Yoon, B.
(2022).
Deep graph representations embed network information for robust disease marker identification. Bioinformatics.
38(4), 1075-1086.
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Niu, P., Soto, M. J., Yoon, B., Dougherty, E. R., Alexander, F. J., Blaby, I., & Qian, X.
(2021).
TRIMER: Transcription Regulation Integrated with Metabolic Regulation. iScience.
24(11), 103218-103218.
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Woo, H., Hong, Y., Kwon, B., & Yoon, B.
(2021).
Accelerating Optimal Experimental Design for Robust Synchronization of Uncertain Kuramoto Oscillator Model Using Machine Learning. IEEE Transactions on Signal Processing.
69, 6473-6487.
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Hong, Y., Kwon, B., & Yoon, B.
(2021).
Optimal Experimental Design for Uncertain Systems Based on Coupled Differential Equations. IEEE Access.
9, 53804-53810.
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Yoon, B., Qian, X., & Dougherty, E. R.
(2021).
Quantifying the Multi-Objective Cost of Uncertainty. 9, 80351-80359.
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Zhao, G., Qian, X., Yoon, B., Alexander, F. J., & Dougherty, E. R.
(2020).
Model-Based Robust Filtering and Experimental Design for Stochastic Differential Equation Systems. 68, 3849-3859.
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Chen, C., Jeong, H., Qian, X., & Yoon, B.
(2019).
TOPAS: network-based structural alignment of RNA sequences. 35(17), 2941-2948.
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Yoon, B., Qian, X., Kahveci, T., & Pal, R.
(2019).
Selected research articles from the 2018 International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC). 20(Suppl 12), 316.
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Yoon, B., Qian, X., Kahveci, T., & Pal, R.
(2018).
Selected research articles from the 2017 International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC). 19(Suppl 3), 69.
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Kim, M., Zhang, H., Woloshuk, C., Shim, W., & Yoon, B.
(2018).
Computational Prediction of Pathogenic Network Modules in Fusarium verticillioides. IEEE/ACM Transactions on Computational Biology and Bioinformatics.
15(2), 506-515.
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Ghaffari, N., Arshad, O. A., Jeong, H., Thiltges, J., Criscitiello, M. F., Yoon, B., Datta, A., & Johnson, C. D.
(2018).
Examining De Novo Transcriptome Assemblies via a Quality Assessment Pipeline. 15(2), 494-505.
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Jeong, H., Qian, X., & Yoon, B.
(2017).
CUFID-query: accurate network querying through random walk based network flow estimation. BMC Bioinformatics.
18(Suppl 14), 500.
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Chen, C., Qian, X., & Yoon, B.
(2017).
Effective computational detection of piRNAs using n-gram models and support vector machine. BMC Bioinformatics.
18(Suppl 14), 517.
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Chen, C., Ghaffari, N., Qian, X., & Yoon, B.
(2017).
Optimal hybrid sequencing and assembly: Feasibility conditions for accurate genome reconstruction and cost minimization strategy. Computational Biology and Chemistry.
69, 153-163.
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Jeong, H., & Yoon, B.
(2017).
SEQUOIA: significance enhanced network querying through context-sensitive random walk and minimization of network conductance. BMC Systems Biology.
11(Suppl 3), 20.
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Yoon, B., Qian, X., & Kahveci, T.
(2017).
Selected research articles from the 2016 International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC). BMC Bioinformatics.
18(Suppl 4), 159.
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Jeong, H., Qian, X., & Yoon, B.
(2016).
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.
-
Khunlertgit, N., & Yoon, B.
(2016).
Incorporating topological information for predicting robust cancer subnetwork markers in human protein-protein interaction network. BMC Bioinformatics.
17(Suppl 13), 351.
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Kim, M., Zhang, H., Woloshuk, C., Shim, W., & Yoon, B.
(2015).
Computational identification of genetic subnetwork modules associated with maize defense response to Fusarium verticillioides. BMC Bioinformatics.
16 Suppl 13(Suppl 13), S12.
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Dehghannasiri, R., Yoon, B., & Dougherty, E. R.
(2015).
Efficient experimental design for uncertainty reduction in gene regulatory networks. BMC Bioinformatics.
16 Suppl 13(Suppl 13), S2.
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Jeong, H., & Yoon, B.
(2015).
Effective Estimation of Node-to-Node Correspondence Between Different Graphs. 22(6), 661-665.
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Broumand, A., Esfahani, M. S., Yoon, B., & Dougherty, E. R.
(2015).
Discrete optimal Bayesian classification with error-conditioned sequential sampling. Pattern Recognition.
48(11), 3766-3782.
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Dehghannasiri, R., Yoon, B., & Dougherty, E. R.
(2015).
Erratum to: Efficient experimental design for uncertainty reduction in gene regulatory networks. BMC Bioinformatics.
16(1), 410.
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Jeong, H., & Yoon, B.
(2015).
Accurate multiple network alignment through context-sensitive random walk. BMC Systems Biology.
9 Suppl 1(Suppl 1), S7-S7.
-
Yoon, B.
(2014).
Sequence alignment by passing messages. BMC GENOMICS.
15(Suppl 1), s14-8.
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Yoon, B.
(2014).
Sequence alignment by passing messages. BMC GENOMICS.
15 Suppl 1(Suppl 1), S14.
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Khunlertgit, N., & Yoon, B.
(2014).
Simultaneous identification of robust synergistic subnetwork markers for effective cancer prognosis. EURASIP Journal on Bioinformatics and Systems Biology.
2014(1), 19-10.
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Sahraeian, S., & Yoon, B.
(2014).
PicXAA: A Probabilistic Scheme for Finding the Maximum Expected Accuracy Alignment of Multiple Biological Sequences. 1079, 203-210.
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Sahraeian, S., & Yoon, B.
(2014).
PicXAA: a probabilistic scheme for finding the maximum expected accuracy alignment of multiple biological sequences. Methods in molecular biology (Clifton, N.J.).
1079, 203-210.
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Sahraeian, S., & Yoon, B.
(2013).
SMETANA: accurate and scalable algorithm for probabilistic alignment of large-scale biological networks. PLoS ONE.
8(7), e67995-e67995.
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Yoon, B., Qian, X., & Dougherty, E. R.
(2013).
Quantifying the Objective Cost of Uncertainty in Complex Dynamical Systems. 61(9), 2256-2266.
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Esfahani, M. S., Knight, J., Zollanvari, A., Yoon, B., & Dougherty, E. R.
(2013).
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.
46(10), 2783-2797.
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Khunlertgit, N., & Yoon, B.
(2013).
Identification of Robust Pathway Markers for Cancer through Rank-Based Pathway Activity Inference. Advances in Bioinformatics.
2013, 618461-8.
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Dougherty, E. R., Yoon, B., Qian, X., & Pal, R.
(2012).
Special Issue on Genomic Signal Processing FOREWORD. 20(4), VII-VIII.
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Sahraeian, S., & Yoon, B.
(2012).
A network synthesis model for generating protein interaction network families. PLoS ONE.
7(8), e41474-e41474.
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Sahraeian, S., & Yoon, B.
(2012).
RESQUE: network reduction using semi-Markov random walk scores for efficient querying of biological networks. Bioinformatics.
28(16), 2129-2136.
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Yoon, B., Qian, X., & Sahraeian, S.
(2012).
Comparative Analysis of Biological Networks: Hidden Markov model and Markov chain-based approach. IEEE Signal Processing Magazine.
29(1), 22-34.
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Qian, X., Sahraeian, S., & Yoon, B.
(2011).
Enhancing the accuracy of HMM-based conserved pathway prediction using global correspondence scores. BMC Bioinformatics.
12 Suppl 10(Suppl 10), S6.
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Esfahani, M. S., Yoon, B., & Dougherty, E. R.
(2011).
Probabilistic reconstruction of the tumor progression process in gene regulatory networks in the presence of uncertainty. BMC Bioinformatics.
12 Suppl 10(Suppl 10), S9.
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Sahraeian, S., & Yoon, B.
(2011).
PicXAA-Web: a web-based platform for non-progressive maximum expected accuracy alignment of multiple biological sequences. Nucleic Acids Research (NAR).
39(Web Server issue), W8-12.
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Qian, X., & Yoon, B.
(2011).
Comparative analysis of protein interaction networks reveals that conserved pathways are susceptible to HIV-1 interception. BMC Bioinformatics.
12 Suppl 1(Suppl 1), S19.
-
Yoon, B.
(2011).
Enhanced stochastic optimization algorithm for finding effective multi-target therapeutics. 12 Suppl 1(Suppl 1), S18.
-
Sahraeian, S., & Yoon, B.
(2011).
PicXAA-R: efficient structural alignment of multiple RNA sequences using a greedy approach. 12 Suppl 1(Suppl 1), S38.
-
Sahraeian, S., & Yoon, B.
(2011).
A Novel Low-Complexity HMM Similarity Measure. 18(2), 87-90.
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Wang, Y., Brahmakshatriya, V., Zhu, H., Lupiani, B., Reddy, S. M., Yoon, B., ... Zhou, H.
(2010).
Identification of differentially expressed miRNAs in chicken lung and trachea with avian influenza virus infection by a deep sequencing approach (vol 11, pg 373, 2010). BMC GENOMICS.
11(1), 373.
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Braga-Neto, U., Kuang, R., Lahdesmaki, H., Vikalo, H., & Yoon, B.
(2010).
Genomic Signal Processing. 2010(1), 137263.
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Su, J., Yoon, B., & Dougherty, E. R.
(2010).
Identification of diagnostic subnetwork markers for cancer in human protein-protein interaction network. BMC Bioinformatics.
11 Suppl 6(Suppl 6), S8.
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Sahraeian, S., & Yoon, B.
(2010).
PicXAA: greedy probabilistic construction of maximum expected accuracy alignment of multiple sequences. Nucleic Acids Research (NAR).
38(15), 4917-4928.
-
Su, J., Yoon, B., & Dougherty, E. R.
(2009).
Accurate and reliable cancer classification based on probabilistic inference of pathway activity. PLoS ONE.
4(12), e8161-e8161.
-
Qian, X., & Yoon, B.
(2009).
Effective identification of conserved pathways in biological networks using hidden Markov models. PLoS ONE.
4(12), e8070-e8070.
-
Yoon, B.
(2009).
Efficient alignment of RNAs with pseudoknots using sequence alignment constraints. EURASIP Journal on Bioinformatics and Systems Biology.
2009(1), 491074-13.
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Qian, X., Sze, S., & Yoon, B.
(2009).
Querying pathways in protein interaction networks based on hidden Markov models. Journal of Computational Biology.
16(2), 145-157.
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Yoon, B.
(2009).
Hidden Markov Models and their Applications in Biological Sequence Analysis. Current Genomics.
10(6), 402-415.
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Wang, Y., Brahmakshatriya, V., Zhu, H., Lupiani, B., Reddy, S. M., Yoon, B., ... Zhou, H.
(2009).
Identification of differentially expressed miRNAs in chicken lung and trachea with avian influenza virus infection by a deep sequencing approach. BMC GENOMICS.
10(1), 512.
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Yoon, B., & Vaidyanathan, P. P.
(2008).
Fast Structural Alignment of RNAs by Optimizing the Adjoining Order of Profile-csHMMs. IEEE Journal of Selected Topics in Signal Processing.
2(3), 400-411.
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Yoon, B., & Vaidyanathan, P. P.
(2008).
Structural Alignment of RNAs Using Profile-csHMMs and Its Application to RNA Homology Search: Overview and New Results. IEEE Transactions on Automatic Control.
53(Special Issue), 10-25.
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Yoon, B., & Vaidyanathan, P. P.
(2007).
Computational identification and analysis of noncoding RNAs - Unearthing the buried treasures in the genorne. IEEE Signal Processing Magazine.
24(1), 64-74.
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Yoon, B., & Vaidyanathan, P. P.
(2006).
Context-Sensitive Hidden Markov Models for Modeling Long-Range Dependencies in Symbol Sequences. IEEE Transactions on Signal Processing.
54(11), 4169-4184.
-
Yoon, B., & Malvar, H. S.
(2006).
A Practical Approach for the Design of Nonuniform Lapped Transforms. IEEE Signal Processing Letters.
13(8), 469-472.
-
Yoon, B., & Vaidyanathan, P. P.
(2005).
A Multirate DSP Model for Estimation of Discrete Probability Density Functions. IEEE Transactions on Signal Processing.
53(1), 252-264.
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Vaidyanathan, P. P., & Yoon, B.
(2002).
Digital filters for gene prediction applications. Conference record / Asilomar Conference on Signals, Systems & Computers. Asilomar Conference on Signals, Systems & Computers.
1, 306-310 vol.1-310.
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Kim, W. S., Liu, J., Li, Q., Hong, S., Qi, K., Cherukuri, R., ... Park, S. I.
AI-Driven Battery-Free Dual-Channel Wireless Optogenetics for High-Throughput Automation of Behavioral Analysis
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Chong, P., Yoon, B., Lai, D., Lee, J., & He, S.
Comparison of Global and United States Social Determinants in COVID-19 Vaccination Rates
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Maddouri, O., Qian, X., & Yoon, B.
(2023).
Geometric Affinity Propagation for Clustering With Network Knowledge. 35(11), 11419-11436.
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conference paper
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Zhao, G., Dougherty, E. R., Yoon, B., Alexander, F. J., & Qian, X.
(2021).
Bayesian Active Learning by Soft Mean Objective Cost of Uncertainty
-
Zhao, G., Dougherty, E. R., Yoon, B., Alexander, F. J., & Qian, X.
(2021).
Efficient Active Learning for Gaussian Process Classification by Error Reduction. Advances in Neural Information Processing Systems.
-
Wang, Y., Jeong, H., Yoon, B., & Qian, X.
(2020).
ClusterM: a scalable algorithm for computational prediction of conserved protein complexes across multiple protein interaction networks. BMC GENOMICS.
615.
-
Yoon, B., Qian, X., & Kahveci, T.
(2017).
CNB-MAC'17. 750-750.
-
Hilton, A., Hilton, A., Kim, M., Ortiz, C., Woloshuk, C., Yoon, B., & Shim, W.
(2016).
Computational and functional analyses of MADS-box transcription factor-mediated regulation of fumonisin biosynthesis in Fusarium verticillioides. Phytopathology.
157-158.
-
Zhang, H., Zhang, H., Kim, M., Yan, H., Yoon, B., & Shim, W.
(2016).
Enhancing our understanding of Fusarium maize stalk rot pathogenesis through gene association subnetwork module analyses. Phytopathology.
18-18.
-
Yan, H., Zhang, H., Kim, M., Yoon, B., & Shim, W.
(2016).
Evaluation of Rice Varieties for Resistance for Autumn Decline in Arkansas. Phytopathology.
150-150.
-
Shim, W., Kim, M., Zhang, H., Yan, H., Yoon, B., Payne, G., & Woloshuk, C.
(2016).
Identifying new genetic targets for maize ear rot and mycotoxin control through computational subnetwork module analyses. Phytopathology.
177-177.
-
Wang, Y., Yoon, B., & Qian, X.
(2016).
CO-SEGMENTATION OF MULTIPLE IMAGES THROUGH RANDOM WALK ON GRAPHS. Proceedings of the ... IEEE International Conference on Acoustics, Speech, and Signal Processing / sponsored by the Institute of Electrical and Electronics Engineers Signal Processing Society. ICASSP (Conference).
1811-1815.
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Jeong, H., & Yoon, B.
(2016).
SEQUOIA. 535-536.
-
Kim, M., Yoon, B., & Shim, W.
(2016).
Systematic computational network-based analysis to predict subnetwork modules associated with pathogenicity and fumonisins in Fusarium verticillioides. Phytopathology.
157-157.
-
Dehghannasiri, R., Yoon, B., & Dougherty, E. R.
(2015).
Optimal Experimental Design for Gene Regulatory Networks in the Presence of Uncertainty. IEEE/ACM Transactions on Computational Biology and Bioinformatics.
938-950.
-
Ghaffari, N., Arshad, O. A., Jeong, H., Thiltges, J., Criscitiello, M. F., Yoon, B., Datta, A., & Johnson, C. D.
(2014).
De novo Transcriptome Assemblies and Annotation for Pacific Whiteleg Shrimp. 1342-1343.
-
Dehghannasiri, R., Yoon, B., & Dougherty, E. R.
(2014).
Computationally Efficient Experimental Design Strategy for Reducing Gene Network Uncertainty. 1380-1381.
-
Raja, P. J., Jacob, J., Yoon, B., Bartholomeusz, G., & Rao, A.
(2013).
AUTOMATED IMAGE ANALYSIS AND INFERENCE OF GENE FUNCTION FROM HIGH - CONTENT SCREENS. European Signal Processing Conference.
-
Dehghannasiri, R., Yoon, B., & Dougherty, E. R.
(2013).
Designing Experiments for Optimal Reduction of Uncertainty in Gene Regulatory Networks. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
88-89.
-
Khunlertgit, N., & Yoon, B.
(2013).
Finding Robust Subnetwork Markers that Improve Cross-Dataset Performance of Cancer Classification. 94-94.
-
Sahraeian, S., & Yoon, B.
(2012).
RESQUE: Network Reduction Using Semi-Markov Random Walk Scores for Efficient Querying of Biological Networks (Extended Abstract). Lecture Notes in Computer Science.
239-240.
-
Qian, X., Yoon, B., & Dougherty, E. R.
(2012).
STRUCTURAL INTERVENTION OF GENE REGULATORY NETWORKS BY GENERAL RANK-K MATRIX PERTURBATION. Proceedings of the ... IEEE International Conference on Acoustics, Speech, and Signal Processing / sponsored by the Institute of Electrical and Electronics Engineers Signal Processing Society. ICASSP (Conference).
729-732.
-
Nikooienejad, A., Metz, R., Yoon, B., & Johnson, C. D.
(2012).
Fast DNA Barcode Generating Algorithm Using Radix Coding Method. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
26-30.
-
Khunlertgit, N., & Yoon, B.
(2012).
Finding Robust Pathway Markers for Cancer Classification. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
147-150.
-
Kim, M., & Yoon, B.
(2012).
Adaptive reference update (ARU) algorithm. A stochastic search algorithm for efficient optimization of multi-drug cocktails. BMC GENOMICS.
S12-S12.
-
Kim, M., & Yoon, B. J.
(2011).
Efficient combinatorial drug optimization through stochastic search. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
33-35.
-
Yoon, B. J.
(2011).
Finding effective subnetwork markers for cancer by passing messages. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
95-96.
-
Sahraeian, S., & Yoon, B. J.
(2011).
Probabilistic consistency transformation for multiple alignment of biological networks. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
52-53.
-
Qian, X., Yoon, B., & Dougherty, E. R.
(2011).
UNCERTAINTY-BASED ESSENTIALITY IN GENE REGULATORY NETWORKS. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
17-20.
-
Qian, X., & Yoon, B.
(2011).
CONTOUR-BASED HIDDEN MARKOV MODEL TO SEGMENT 2D ULTRASOUND IMAGES. Proceedings of the ... IEEE International Conference on Acoustics, Speech, and Signal Processing / sponsored by the Institute of Electrical and Electronics Engineers Signal Processing Society. ICASSP (Conference).
705-708.
-
Esfahani, M. S., Zollanvari, A., Yoon, B., & Dougherty, E. R.
(2011).
Designing Enhanced Classifiers Using Prior Process Knowledge: Regularized Maximum-Likelihood. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
91-94.
-
Sahraeian, S., & Yoon, B.
(2011).
FAST NETWORK QUERYING ALGORITHM FOR SEARCHING LARGE-SCALE BIOLOGICAL NETWORKS. Proceedings of the ... IEEE International Conference on Acoustics, Speech, and Signal Processing / sponsored by the Institute of Electrical and Electronics Engineers Signal Processing Society. ICASSP (Conference).
6008-6011.
-
Qian, X., & Yoon, B.
(2010).
SHAPE MATCHING BASED ON GRAPH ALIGNMENT USING HIDDEN MARKOV MODELS. Proceedings of the ... IEEE International Conference on Acoustics, Speech, and Signal Processing / sponsored by the Institute of Electrical and Electronics Engineers Signal Processing Society. ICASSP (Conference).
934-937.
-
Su, J., & Yoon, B.
(2010).
IDENTIFYING RELIABLE SUBNETWORK MARKERS IN PROTEIN-PROTEIN INTERACTION NETWORK FOR CLASSIFICATION OF BREAST CANCER METASTASIS. Proceedings of the ... IEEE International Conference on Acoustics, Speech, and Signal Processing / sponsored by the Institute of Electrical and Electronics Engineers Signal Processing Society. ICASSP (Conference).
525-528.
-
Yoon, B.
(2009).
SIMPLE ALIGNMENT CONSTRAINTS FOR EFFICIENT ALIGNMENT OF RNA SEQUENCES USING FAMILY-SPECIFIC MODELS. 1-3.
-
Yoon, B.
(2008).
A SIMPLE METHOD FOR FINDING STRUCTURALLY SIMILAR RNAS USING TWO-DIMENSIONAL DISCRETE CONVOLUTION. 1-3.
-
Yoon, B., & Malvar, H. S.
(2008).
Coding Overcomplete Representations of Audio using the MCLT. Data Compression Conference Proceedings.
152-161.
-
Yoon, B.
(2008).
Effective Annotation of Noncoding RNA Families Using Profile Context-Sensitive HMMs. 1193-1198.
-
Yoon, B., Tashev, I., & Acero, A.
(2007).
Robust Adaptive Beamforming Algorithm using Instantaneous Direction of Arrival with Enhanced Noise Suppression Capability. Proceedings of the ... IEEE International Conference on Acoustics, Speech, and Signal Processing / sponsored by the Institute of Electrical and Electronics Engineers Signal Processing Society. ICASSP (Conference).
i-133-i-136.
-
Yoon, B., & Vaidyanathan, P. P.
(2007).
Fast Search of Sequences with Complex Symbol Correlations using Profile Context-Sensitive HMMS and Pre-Screening Filters. Proceedings of the ... IEEE International Conference on Acoustics, Speech, and Signal Processing / sponsored by the Institute of Electrical and Electronics Engineers Signal Processing Society. ICASSP (Conference).
i-345-i-348.
-
Yoon, B., & Vaidyanathan, P. P.
(2007).
Fast Structural Similarity Search of Noncoding RNAs Based on Matched Filtering of Stem Patterns. Conference record / Asilomar Conference on Signals, Systems & Computers. Asilomar Conference on Signals, Systems & Computers.
44-48.
-
Yoon, B. J., & Vaidyanathan, P. P.
(2006).
Profile context-sensitive HMMS for probabilistic modeling of sequences with complex correlations. Proceedings of the ... IEEE International Conference on Acoustics, Speech, and Signal Processing / sponsored by the Institute of Electrical and Electronics Engineers Signal Processing Society. ICASSP (Conference).
-
Yoon, B., & Vaidyanathan, P. P.
(2006).
Modeling and Identification of Alternative Folding in Regulatory RNAS using Context-Sensitive HMMS. 21-22.
-
Yoon, B. J., & Vaidyanathan, P. P.
(2005).
An overview of the role of context-sensitive HMMS in the prediction of ncrna genes. 1378-1383.
-
Yoon, B., & Vaidyanathan, P. P.
(2005).
Optimal Alignment Algorithm for Context-Sensitive Hidden Markov Models. Proceedings of the ... IEEE International Conference on Acoustics, Speech, and Signal Processing / sponsored by the Institute of Electrical and Electronics Engineers Signal Processing Society. ICASSP (Conference).
iv-293-iv-296.
-
Yoon, B. J., & Vaidyanathan, P. P.
(2004).
HMM with auxiliary memory: A new tool for modeling RNA secondary structures. Conference record / Asilomar Conference on Signals, Systems & Computers. Asilomar Conference on Signals, Systems & Computers.
1651-1655.
-
Yoon, B. J., & Vaidyanathan, P. P.
(2004).
Identification of CpG islands using a bank of IIR lowpass filters. 315-319.
-
Yoon, B. J., & Vaidyanathan, P. P.
(2004).
Rna secondary structure prediction using context-sensitive hidden markov models
-
Yoon, B. J., & Vaidyanathan, P. P.
(2004).
Wavelet-based denoising by customized thresholding. Proceedings of the ... IEEE International Conference on Acoustics, Speech, and Signal Processing / sponsored by the Institute of Electrical and Electronics Engineers Signal Processing Society. ICASSP (Conference).
-
Yoon, B. J., & Vaidyanathan, P. P.
(2004).
Discrete pdf estimation in the presence of noise. IEEE International Symposium on Circuits and Systems.
-
Vaidyanathan, P. P., & Yoon, B.
(2004).
The role of signal-processing concepts in genomics and proteomics. Journal of the Franklin Institute.
111-135.
-
Yoon, B. J., & Vaidyanathan, P. P.
(2003).
Improved estimation of discrete probability density functions using multirate models. Conference record / Asilomar Conference on Signals, Systems & Computers. Asilomar Conference on Signals, Systems & Computers.
1188-1192.
-
Vaidyanathan, P. P., & Yoon, B. J.
(2003).
Discrete Probability Density Estimation Using Multirate DSP Models. Proceedings of the ... IEEE International Conference on Acoustics, Speech, and Signal Processing / sponsored by the Institute of Electrical and Electronics Engineers Signal Processing Society. ICASSP (Conference).
477-480.
-
Vaidyanathan, P. P., & Yoon, B.
(2003).
Discrete Probability Density Estimation Using Multirate DSP Models. Proceedings / IEEE International Conference on Multimedia and Expo. IEEE International Conference on Multimedia and Expo.
i-853-i-856-I856.
-
Zhao, G., Dougherty, E. R., Yoon, B., Alexander, F. J., & Qian, X.
(2021).
Bayesian Active Learning by Soft Mean Objective Cost of Uncertainty
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institutional repository document
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Pouchard, L., Reyes, K. G., Alexander, F. J., & Yoon, B.
(2023).
A Rigorous Uncertainty-Aware Quantification Framework Is Essential for Reproducible and Replicable Machine Learning Workflows
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Niu, P., Soto, M. J., Huang, S., Yoon, B., Dougherty, E. R., Alexander, F. J., Blaby, I., & Qian, X.
(2022).
Sensitivity analysis of genome-scale metabolic flux prediction
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Kim, W. S., Liu, J., Li, Q., Hong, S., Qi, K., Cherukuri, R., ... Park, S. I.
(2021).
AI-driven high-throughput automation of behavioral analysis and dual-channel wireless optogenetics for multiplexing brain dynamics
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Niu, P., Soto, M. J., Yoon, B., Dougherty, E. R., Alexander, F. J., Blaby, I., & Qian, X.
(2021).
TRIMER: Transcription Regulation Integrated with MEtabolic Regulation
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Yoon, B., Qian, X., & Dougherty, E. R.
(2020).
Quantifying the multi-objective cost of uncertainty
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Hong, Y., Kwon, B., & Yoon, B.
(2020).
Optimal Experimental Design for Uncertain Systems Based on Coupled Differential Equations
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Pouchard, L., Reyes, K. G., Alexander, F. J., & Yoon, B.
(2023).
A Rigorous Uncertainty-Aware Quantification Framework Is Essential for Reproducible and Replicable Machine Learning Workflows
Research
principal investigator on
- Brookhaven Science Associates - Joint Assignment Agreement awarded by Brookhaven National Laboratory - (Upton, New York, United States) 2019 - 2021
- Elements: Software: Autonomous, Robust, and Optimal In-Silico Experimental Design Platform for Accelerating Innovations in Materials Discovery awarded by National Science Foundation - (Arlington, Virginia, United States) 2018 - 2021
- FFATA: CAREER: Models and Algorithms for Comparative Analysis of Biological Networks awarded by National Science Foundation - (Arlington, Virginia, United States) 2012 - 2018
- International Workshop on Computational Network Biology: Modeling,-Analysis, and Control (CNB-MAC 2016) awarded by National Science Foundation - (Arlington, Virginia, United States) 2016 - 2017
co-principal investigator on
- EAGER: Identifying Blockmodel Functional Modules across Multiple Networks awarded by National Science Foundation - (Arlington, Virginia, United States) 2014 - 2017
- International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC 2015) awarded by National Science Foundation - (Arlington, Virginia, United States) 2015
Teaching
teaching activities
- ECEN314 Signals And Systems Instructor
- ECEN485 Directed Studies Instructor
- ECEN491 Research Instructor
- ECEN644 Discrete-time Systems Instructor
- ECEN684 Professional Internship Instructor
- ECEN684 Professional Internship: In-ab Instructor
- ECEN685 Directed Studies Instructor
- ECEN689 Sptp:adv Prob Graphical Mdl Instructor
- ECEN691 Research Instructor
- ECEN760 Intro Prob Graphical Mdl Instructor
Works By Students
chaired theses and dissertations
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Khunlertgit, Navadon (2016-11). Improvement of Reproducibility in Cancer Classification Based on Pathway Markers and Subnetwork Markers.
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Kim, Mansuck (2016-02). Computational Identification of Functional Modules and Hub Genes Involved in Pathogenicity-Associated or Defense Response on Fusarium Verticillioides-Maize Interactions.
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Nikooienejad, Amir (2013-07). Presence / Absence Marker Discovery in RAD Markers for Multiplexed Samples in the Context of Next-Generation Sequencing.
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Sahraeian, Sayed 1983- (2013-01). Probabilistic Approaches in Comparative Analysis of Biological Networks and Sequences.
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Su, Junjie (2012-02). Accurate and Reliable Cancer Classi cation Based on Pathway-Markers and Subnetwork-Markers.
Background
education and training
- Ph.D. in Electrical Engineering, California Institute of Technology - (Pasadena, California, United States) 2007
- M.S. in Electrical Engineering, California Institute of Technology - (Pasadena, California, United States) 2002
- B.S.E. in Electrical Engineering, Seoul National University - (Seoul, South Korea) 1998
awards and honors
Contact
first name
- Byung-Jun
has last name
- Yoon
mailing address
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Texas A&M University
Electrical Engineering
3128 TAMU
College Station, TX 77843-3128
USA
Other
- bjyoon@tamu.edu