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News & Announcements

International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC 2014) will be held in Newport Beach, CA, on September 20, 2014. The workshop will be organized in conjunction with the 5th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics (ACM-BCB 2014). [NEW]
CNB-MAC-2014 Website:
Call for Papers: [Download]
RESQUE, a fast and accurate reduction-based network querying algorithm is now available for download. Visit [RESQUE] to download the source code of RESQUE.
NAPAbench, a comprehensive benchmark for network alignment is now available at [NAPAbench]. You can download both the benchmark dataset as well as the software (and source code) that was used to generate the synthetic network families in the dataset.

Short Bio

Current Position Associate Professor
Texas A&M University, College Station, TX
Department of Electrical & Computer Engineering
Genomic Signal Processing (GSP) Lab
Center for Bioinformatics & Genomic Systems Engineering (CBGSE)
Education Ph.D., California Institute of Technology, Electrical Engineering, 2007.
M.S., California Institute of Technology, Electrical Engineering, 2002.
B.S.E. (summa cum laude), Seoul National University, Electrical Engineering, 1998.
Work Experience Post-Doc, California Institute of Technology, Electrical Engineering, Dec.2006-Oct.2007.
Microsoft Research, Intern, Summer 2004, 2005, 2006.
SecureSoft Inc./Junghwa Systems Inc., Software Developer, 1998-2001.
Awards & Honors NSF CAREER Award, National Science Foundation, 2011.
Best Paper Award, Asia Pacific Bioinformatics Conference (APBC2011), Jan. 2011.
SLATE Teaching Excellence Award, Texas A&M University, 2009.
Microsoft Research PhD Fellowship, Microsoft Research, 2004.
Paper Award (2nd place), Student Paper Contest, Asilomar Conference on Signals, Systems, and Computers, 2003.
Killgore Fellowship, California Institute of Technology, 2001.
Doctoral Scholarship, The Korea Foundation for Advanced Studies (KFAS), 2001.

Research Interests

Genomic Signal Processing (GSP), Bioinformatics, and Systems Biology
Probabilistic Graphical Models & Algorithms, and Their Application in Computational Biology
Noncoding RNA (ncRNA) Prediction, RNA Sequence Analysis
Network Biology & Comparative Analysis of Biological Networks

Selected Publications

1 Sequence alignment by passing messages [NEW]
Byung-Jun Yoon, BMC Genomics, 15(Suppl 1):S14, 2014.
[preprint] [BMC Genomics]
2 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]
3 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]
4 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]
5 RESQUE: Network reduction using semi-Markov random walk scores for efficient querying 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]
6 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]
7 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]
8 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]
9 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]
10 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]
** To see the complete list of publications, visit the [publication] section.


Mailing Address Dept. of Electrical & Computer Engineering
Texas A&M University, MS 3128
College Station, TX 77843, USA
Email byung jun (only bold characters)
Office Location Wisenbaker Engineering Building (WEB) 205L

Last update: Sep.1.2014