Publications

Journal Publications 

* equal contribution

2023

  • Kim J, Lee M*, Seok J*, “Deep learning model with L1 penalty for predicting breast cancer metastasis using gene expression data”, Machine Learning-Science and Technology. 2023.
  • Kim I, Lee M*, Seok J*, “ICEGAN: Inverse Covariance Estimating Generative Adversarial Network”, Machine Learning-Science and Technology. 2023.
  • Seo J, Kim I, Seok J, “Grid-wise simulation acceleration of the electromagnetic fields of 2D optical devices using super-resolution”, Scientific Reports. 2023.

2022

  • Choi S*, Joo HJ*, Kim Y, Kim J-H, Seok J, “Conversion of Automated 12-Lead Electrocardiogram Interpretations to OMOP CDM Vocabulary”, Applied Clinical Informatics. 2022.
  • Kim W, Kim S, Lee M*, Seok J*, “Inverse design of nanophotonic devices using generative adversarial networks”, Engineering Applications of Artificial Intelligence. 2022.
  • Hwang H-S, Lee M*, Seok J*, “Deep reinforcement learning with a critic-value-based branch tree for the inverse design of two-dimensional optical devices”, Applied Soft Computing. 2022.
  • Ahn H, Lee S, Ko H, Kim M, Han S-W*, Seok J*, “Searching similar weather maps using convolutional autoencoder and satellite images”, ICT Express. 2022.
  • Kim I, Park SJ, Jeong C, Shim M, Kim DS, Kim G-T, Seok J, “Simulator acceleration and inverse design of fin field-effect transistors using machine learning”, Scientific Reports. 2022.

2021

  • Seo J-W, Lee YH, Tae DH, Park SH, Moon J-Y, Jeong KH, Kim C-D, Chung BH, Park JB, Kim YH, Seok J, Joo SH, Lee SH, Lee JS, Lee S-H “Non-Invasive Diagnosis for Acute Rejection Using Urinary mRNA Signature Reflecting Allograft Status in Kidney Transplantation”, Frontiers in Immunology. 2021.
  • Lee YH, Seo J-W, Kim M, Tae D, Seok J, Kim YG, Lee S-H, Kim JS, Hwang HS, Jeong K-H, Moon J-Y “Urinary mRNA Signatures as Predictors of Renal Function Decline in Patients With Biopsy-Proven Diabetic Kidney Disease”, Frontiers in endocrinology. 2021.
  • Lee M, Seok J, “Estimation with Uncertainty via Conditional Generative Adversarial Networks”, Sensors. 2021.

2020

  • Kim Y*, Lee J*, Choi S, Lee J, Kim J, Seok J**, Joo H**, “Validation of deep learning natural language processing algorithm for keyword extraction from pathology reports in electronic health records”, Scientific Reports. 2020.
  • Kim Y, Seok J, “Network estimation for censored time-to-event data for multiple events based on multivariate survival analysis”, PLOS One. 2020.
  • Kim W, Seok J, “Simulation Acceleration for Transmittance of Electromagnetic Waves in 2D Slit Arrays Using Deep Learning”, Scientific Reports. 2020.
  • Ko EJ, Seo J-W, Kim KW, Kim B-M, Cho J-H, Kim C-D, Seok J, Yang CW, Lee S-H, Chung HB, “Phenotype and Molecular Signature of CD8+ T Cell Subsets in T cell-Mediated Rejections After Kidney Transplantation”, PLOS One. 2020.
  • Lee M, Tae D, Choi JH, Jung H-Y, Seok J, “Improved Recurrent Generative Adversarial Networks with Regularization Techniques and a Controllable Framework”, Information Sciences. 2020.
  • Choi JY, Choi S, Lee M, Park YS, Sung JS, Chang WJ, Kim JW, Choi YJ, Kim J, Kim D-S, Lee S-H, Seok J, Park KH, Kim SH, Lim YH, “Clinical Implication of Concordant or Discordant Genomic Profiling Between Primary and Matched Metastatic Tissues in Patients With Colorectal Cancer”, Cancer Research and Treatment. 2020.
  • Lee HK, Park WH, Kang YC, Kang S, Im S, Park S, Kim JT, Lee M, Seok J, Oh M-S, Choi HS, Pak YK, “Serum Biomarkers From Cell-Based Assays for AhRL and MIS Strongly Predicted the Future Development of Diabetes in a Large Community-Based Prospective Study in Korea”, Scientific Reports. 2020.
  • Yun H*, Lee M*, Kang YS, Seok J, “Portfolio Management via Two-stage Deep Learning with A Joint Cost”, Expert Systems with Applications. 2020.

 

2019

  • Lee M, Han SW, Seok J, “Prediction of survival risks with adjusted gene expression through risk-gene networks”, Bioinformatics. 2019.
  • Lee M, Seok J, “Controllable Generative Adversarial Network”, IEEE Access. 2019.
  • Lee K*, Lee M*, Seok J, Han SW “Regression-Based Network Estimation for High-Dimensional Genetic Data”, Journal of Computational Biology. 2019.

2018

  • Tae D, Seok J “mEBT: multiple-matching Evidence-based Translator of Murine Genomic Responses for Human Immunity Studies.” Bioinformatics. 2018.
  • Kim Y, Kang YS, Seok J “GAIT: Gene expression Analysis for Interval Time”,  Bioinformatics. 2018.
  • Lee M, Kang YS, Seok J “The estimation of probability distribution for factor variables with many categorical values”,  Plos One. 2018.

2017

  • Lee M*, Seok J*, Tae D, Zhong H, Han SW “A Comparison of Two-Stage Approaches Based on Penalized Regression for Estimating Gene Networks”,  Journal of Computational Biology. 2017.PubMed
  • Han SW, Kim SH, Seok J, Yoon J, Zhong H  “Estimation of directed subnetworks in ultra high dimensional data for gene network problems”,  Statistics and its Interface. 2017.

2015

  • Seok J, Xu W, Davis RW, Xiao W “RASA: Robust Alternative Splicing Analysis for Human Transcriptome Arrays”,  Sci. Rep. 2015.PubMed
  • Seok J and Kang Y.S.” Mutual Information between Discrete Variables with Many Categories using Recursive Adaptive Partitioning.” Sci. Rep. 2015.PubMed
  • Seok J, Davis RW, Xiao W. “A hybrid approach of gene sets and single genes for the prediction of survival risks with gene expression data.” PLoS One. 2015.PubMed
  • Seok J.. “Evidence-based translation for the genomic responses of murine models for the study of human immunity.” PLoS One. 2015.PubMed
  • Warren HS, Tompkins RG, Moldawer LL, Seok J, Xu W, Mindrinos MN, Maier RV, Xiao W, Davis RW. “Mice are not men.”, Proc Natl Acad Sci U S A. 2015. PubMed

~ 2014

  • Seok J, Tian L, Wong WH. “Density estimation on multivariate censored data with optional Pólya tree”, Biostatistics, 2014. PubMed
  • Seok J*, Warren HS*, Cuenca AG*, Mindrinos MN, Baker HV, Xu W, Richards DR, McDonald-Smith GP, Gao H, Hennessy L, Finnerty CC, López CM, Honari S, Moore EE, Minei JP, Cuschieri J, Bankey PE, Johnson JL, Sperry J, Nathens AB, Billiar TR, West MA, Jeschke MG, Klein MB, Gamelli RL, Gibran NS, Brownstein BH, Miller-Graziano C, Calvano SE, Mason PH, Cobb JP, Rahme LG, Lowry SF, Maier RV, Moldawer LL, Herndon DN, Davis RW, Xiao W, Tompkins RG; the Inflammation and Host Response to Injury, Large Scale Collaborative Research Program. “Gene response in mouse models poorly mimics severe human inflammatory diseases”, Proc. Natl. Acad. Sci. U S A., 2013. PubMed
  • Cuenca AG, Gentile LF, Lopez MC, Ungaro R, Liu H, Xiao W, Seok J, Mindrinos MN, Ang D, Ozrazgat Baslanti T, Bihorac A, Efron PA, Cuschieri J, Warren HS, Tompkins RG, Maier RV, Baker HV, Moldawer LL; the Inflammation and Host Response to Injury Collaborative Research Program. “Development of a genomic metric that can be rapidly used to predict clinical outcome in severely injured trauma patients”, Crit. Care Med., 2013.  PubMed
  • Xu W, Gao H, Seok J, Wihelmy J, Mindrinos MN, Davis RW, Xiao W. “Coding SNPs as intrinsic markers for sample tracking in large-scale transcriptome studies”, BioTechniques, 2012.PubMed
  • Seok J, Xu W, Gao H, Davis RW, Xiao W. “JETTA: junction and exon toolkits for transcriptome analysis”, Bioinformatics, 2012.PubMed
  • Seok J*, Xu W*, Jiang H, Davis RW, Xiao W. “Knowledge-based reconstruction of mRNA transcripts with short sequencing reads for transcriptome research”, PLoS One, 2012.PubMed
  • Xiao W*, Mindrinos MN*, Seok J*, Cuschieri J*, Cuenca AG, Gao H, Hayden DL, Hennessy L, Moore EE, Minei JP, Bankey PE, Johnson JL, Sperry J, Nathens AB, Billiar TR, West MA, Brownstein BH, Mason PH, Baker HV, Finnerty CC, Jeschke MG, López MC, Klein MB, Gamelli RL, Gibran NS, Arnoldo B, Xu W, Zhang Y, Calvano SE, McDonald-Smith GP, Schoenfeld DA, Storey JD, Cobb JP, Warren HS, Moldawer LL, Herndon DN, Lowry SF, Maier RV, Davis RW, Tompkins RG; Inflammation and Host Response to Injury Large-Scale Collaborative Research Program. “A genomic storm in critically injured humans”, J. Exp. Med., 2011. (Research Highlight in Nature Reviews Immunology)PubMed
  • Luciani MG*, Seok J*, Sayeed A, Champion S, Goodson WH, Jeffrey SS, Xiao W, Mindrinos M, Davis RW, Dairkee SH. “Distinctive responsiveness to stromal signaling accompanies histologic grade programming of cancer cells”, PLoS One, 2011.PubMed
  • Xu W*, Seok J*, Mindrinos MN*, Schweitzer AC, Jiang H, Wilhelmy J, Clark TA, Kapur K, Xing Y, Faham M, Storey JD, Moldawer LL, Maier RV, Tompkins RG, Wong WH, Davis RW, Xiao W; Inflammation and Host Response to Injury Large-Scale Collaborative Research Program. “Human transcriptome array for high-throughput clinical studies”, Proc. Natl. Acad. Sci. U S A., 2011. (See the press release on Business Wire)PubMed
  • Seok J, Kaushal A, Davis RW, Xiao W. “Knowledge-based analysis of microarrays for the discovery of transcriptional regulation relationships”,BMC Bioinformatics, 2010.PubMed
  • Seok J, Xiao W, Moldawer LL, Davis RW, Covert MW. “A dynamic network of transcription in LPS-treated human subjects”, BMC Syst. Biol., 2009. (selected as “the Most Interesting Papers” by Faculty of 1000 in Biology)PubMed
  • Lin L, Liu S, Brockway H, Seok J, Jiang P, Wong WH, Xing Y. “Using high-density exon arrays to profile gene expression in closely related species”, Nucleic Acids Res., 2009.PubMed
  • Dairkee SH, Seok J, Champion S, Sayeed A, Mindrinos M, Xiao W, Davis RW, Goodson WH. “Bisphenol A induces a profile of tumor aggressiveness in high-risk cells from breast cancer patients”, Cancer Res., 2008.PubMed