Seungchan Kim, Ph.D.

Seungchan Kim, Ph.D.

Chief Scientist & Executive Professor

Publications

Refereed Journal Articles

  1. Kirillova A, Sethuraman M, Dong X, … Kim S, Chan SY. (2025). Reversal of inflammatory reprogramming by vasodilator agents in pulmonary hypertension. ERJ Open Research, 11(1): 00486-2024.
  2. Tai YY, Yu Q, Tang Y, … Kim S, Chan SY. (2024). Allele-specific control of rodent and human lncRNA KMT2E-AS1 promotes hypoxic endothelial pathology in pulmonary hypertension. Sci Transl Med, 16(729):eadd2029.
  3. Feng M, … Kim S, McConkey D, Choi W. (2023). Identification of Lineage-specific Transcriptional Factor-defined Molecular Subtypes in Small Cell Bladder Cancer. European Urology. https://doi.org/10.1016/j.eururo.2023.05.023.
  4. Feng M, Matoso A, … Kim S, McConkey D, Choi W. (2023). Identification of Lineage-specific Transcriptional Factor-defined Molecular Subtypes in Small Cell Bladder Cancer. European Urology.
  5. Nwosu L, Li X, Qian L, Kim S, Dong X. (2022). Calibrated bagging deep learning for image semantic segmentation: A case study on COVID-19 chest X-ray image. PLoS ONE.
  6. Nakamura K, Zhu Z, … Kim S, … Goel A. (2022). An exosome-based transcriptomic signature for noninvasive, early detection of patients with pancreatic ductal adenocarcinoma. Gastroenterology.
  7. Negi V, Yang J, … Kim S, Chan SY. (2021). Computational repurposing of therapeutic small molecules from cancer to pulmonary hypertension. Sci Adv, 7(43):eabh3794.
  8. Craig DW, … Kim S, … Van Keuren-Jensen K. (2021). RNA sequencing of whole blood reveals early alterations in immune cells and gene expression in Parkinson’s disease. Nature Aging, 1, 734-747.
  9. Culley MK, … Kim S, … Chan SY. (2021). Frataxin deficiency promotes endothelial senescence in pulmonary hypertension. J Clin Invest, 136459.
  10. Woodcock C, … Kim S, … Chan SY. (2021). Matrix Stiffening Induces a Pathogenic QKI-miR-7-SRSF1 Signaling Axis in Pulmonary Arterial Endothelial Cells. Am J Physiol Lung Cell Mol Physiol, 320(5):L726-L738.
  11. Sun W, Tang Y, … Kim S, … Chan SY. (2020). SCUBE1 Controls BMPR2-Relevant Pulmonary Endothelial Function: Implications for Diagnostic Marker Development in Pulmonary Arterial Hypertension. JACC Basic to Translational Science, 5(11): 1073–1092.
  12. Kalani MYS, … Kim S, Keuren-Jensen KV. (2020). Extracellular microRNAs in blood differentiate between ischaemic and haemorrhagic stroke subtypes. Journal of Extracellular Vesicles, 9(1).
  13. Berens ME, … Kim S, … Ginty F. (2019). Multiscale, multimodal analysis of tumor heterogeneity in IDH1 mutant vs wild-type diffuse gliomas. PLoS ONE, 14(12): e0219724.
  14. Halperin RF, … Kim S, Byron SA. (2019). Leveraging Spatial Variation in Tumor Purity for Improved Somatic Variant Calling of Archival Tumor Only Samples. Frontiers in Oncology, 9: 119.
  15. Stearman RS, … Kim S, … Geraci MW. (2019). Systems Analysis of the Human Pulmonary Arterial Hypertension Lung Transcriptome. Am J Respir Cell Mol Biol, 60(6):637-649.
  16. Sima C, Hua J, Bittner ML, Kim S, Dougherty ER. (2018). Phenotype Classification Using Moment Features of Single-Cell Data. Cancer Informatics.
  17. Bell JB, … Kim S, … Platanias LC. (2018). Differential Response of Glioma Stem Cells to Arsenic Trioxide Therapy Is Regulated by MNK1 and mRNA Translation. Mol Cancer Res, 16(1):32-46.
  18. Halperin RF, … Kim S, Craig DW. (2017). A method to reduce ancestry related germline false positives in tumor only somatic variant calling. BMC Medical Genomics, 10:61.
  19. Tran H, Speyer G, Kiefer J, Kim S. (2017). Contextualization of Drug-Mediator Relations Using Evidence Networks. BMC Bioinformatics, 18 (Suppl 7): 252.
  20. Yeri A, … Kim S, … Van Keuren-Jensen K. (2017). Total Extracellular Small RNA Profiles from Plasma, Saliva, and Urine of Healthy Subjects. Scientific Reports, 7: 44061.
  21. Vitucci M, … Kim S, … Miller CR. (2017). Genomic profiles of low-grade murine gliomas evolve during progression to glioblastoma. Neuro Oncology, 19(9):1237-1247.
  22. Cancer Target Discovery and Development Network. (2016). Transforming Big Data into Cancer-Relevant Insight. Mol Cancer Res, 14(8):675-82.
  23. Legendre CR, … Kim S, Salhia B. (2016). Pathway implications of aberrant global methylation in adrenocortical cancer. PLoS ONE, 11(3):e0150629.
  24. Zheng S, … Kim S, … Verhaak RGW. (2016). Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma. Cancer Cell, 30(2):363.
  25. Tibes R, … Kim S, … Shea TC. (2014). Phase I study of the novel Cdc2/CDK1 and AKT inhibitor terameprocol in patients with advanced leukemias. Invest New Drugs.
  26. Staren ED, … Kim S, … Markman M. (2014). Initial experience with genomic profiling of heavily pretreated breast cancers. Annals of Surgical Oncology, 21(10): 3216-22.
  27. Verdicchio M, Kim S. (2014). Template-Based Intervention in Boolean Network Models of Biological Systems. EURASIP Bioinformatics and Systems Biology, 2014:11.
  28. Joy A, Ramesh A, … Kim S, Feuerstein BG. (2014). AKT Pathway Genes Define 5 Prognostic Subgroups in Glioblastoma. PLoS One, 9(7):e100827.
  29. Paoloni M, … Kim S, … Trent J. (2014). Prospective molecular profiling of canine cancers… PLoS One.
  30. Jung S, Kim S. (2014). EDDY: A novel statistical gene set test method to detect differential genetic dependencies. Nucleic Acids Res, 42(7): e60.
  31. Choi W, … Kim S, … McConkey DJ. (2014). Identification of distinct basal and luminal subsets of human bladder cancers with different sensitivities to frontline chemotherapy. Cancer Cell, 25(2): 152-165.
  32. Burgos KL, … Kim S, … Keuren-Jensen KV. (2013). Identification of extracellular miRNA in human cerebrospinal fluid by next-generation sequencing. RNA, 19(5):712-22.
  33. Jung S, Verdicchio M, … Kim S. (2013). Learning Contextual Gene Set Interaction Networks of Cancer with Condition Specificity. BMC Genomics, 14(1):110.
  34. Baker AS, … Kim S, … Fonseca R. (2013). Uncovering the Biology of Multiple Myeloma Among African Americans. Blood, 121(16):3147-52.
  35. Jung S, Kim S, … Salhia B. (2012). DNA Methylation in Multiple Myeloma is Weakly Associated with Gene Transcription. PLoS One, 7(12):e52626.
  36. Loftus JC, … Kim S, … Tran NL. (2012). miRNA Expression Profiling in Migrating Glioblastoma Cells. PLoS One, 7(6):e39818.
  37. Arora S, … Kim S, Weiss GJ. (2011). MicroRNA-328 is associated with Non-small Cell Lung Cancer (NSCLC) Brain Metastasis. Int J Cancer, 129(11):2621-31.
  38. Nasser S, Cunliffe H, Black M, Kim S. (2011). Context-specific Gene Regulatory Networks Subdivide Intrinsic Subtypes of Breast Cancer. BMC Bioinformatics, 12(Suppl 2):S3.
  39. Nasser S, … Kim S. (2011). Biomarkers Associated with Metastasis of Lung Cancer to Brain Predict Patient Survival. Int J Data Mining and Bioinformatics, 5(3): 287-307.
  40. Bryce D, Verdicchio M, Kim S. (2010). Planning Interventions in Biological Networks. ACM Trans Intell Syst Technol, 1(2):11.
  41. Gowda T, Vrudhula S, Kim S. (2009). Prediction of Pair-wise Gene Interaction Using Threshold Logic. Ann NY Acad Sci, 1158:276-86.
  42. Gowda T, Vrudhula S, Kim S. (2009). Modeling of Gene Regulatory Network Dynamics Using Threshold Logic. Ann NY Acad Sci, 1158:71-81.
  43. Tari L, Baral C, Kim S. (2009). Fuzzy c-means clustering with prior biological knowledge. J Biomed Inform, 42(1):74-81.
  44. Stephan EA, … Kim S, … Demeure MJ. (2008). Adrenocortical carcinoma survival rates correlated to genomic copy number variants. Mol Cancer Ther, 7(2): 425-431.
  45. Brun M, Kim S, Choi W, Dougherty ER. (2007). Comparison of gene regulatory networks via steady-state trajectories. EURASIP J Bioinform Syst Biol, 82702.
  46. Chng WJ, … Kim S, … Fonseca R. (2007). Molecular Dissection Of Hyperdiploid Multiple Myeloma Using Gene Expression Profiling. Cancer Res, 67: 2982-2989.
  47. Liu W, … Kim S, … Xu J. (2007). Germline copy number polymorphisms involving larger than 100 kb are uncommon in normal subjects. Prostate, 67, 227-233.
  48. Goutsias J, Kim S. (2006). Stochastic transcriptional regulatory systems with time delays: a mean-field approximation. J Comput Biol, 13, 1049-1076.
  49. Zhang X, Kim S, Wang T, Baral C. (2006). Joint learning of logic relationships for studying protein function using phylogenetic profiles. IEEE Trans Signal Process, 54, 2427-2435.
  50. Silva PJS, … Kim S, … Dougherty ER. (2005). Feature selection algorithms to find strong genes. Pattern Recognit Lett, 26, 1444-1453.
  51. Hashimoto RF, Kim S, … Dougherty ER. (2004). Growing genetic regulatory networks from seed genes. Bioinformatics, 20, 1241-1247.
  52. Goutsias J, Kim S. (2004). A Nonlinear Discrete Dynamical System for Transcriptional Regulation. Biophys J, 86: 1922-1945.
  53. Bomprezzi R, … Kim S, … Trent J. (2003). Gene expression profile in multiple sclerosis patients. Hum Mol Genet, 12, 2191-2199.
  54. Brun M, Sabbagh DL, Kim S, Dougherty ER. (2003). Corrected small-sample estimation of the Bayes error. Bioinformatics, 19, 944-951.
  55. Kobayashi T, … Kim S, … Zhang W. (2003). Microarray reveals differences in both tumors and vascular specific gene expression… Cancer Res, 63, 60-66.
  56. Morikawa J, … Kim S, … Kobayashi T. (2003). Identification of signature genes by microarray for acute myeloid leukemia… Int J Oncol, 23, 617-625.
  57. Dougherty ER, … Kim S, … Trent JM. (2002). Inference from clustering with application to gene-expression microarrays. J Comput Biol, 9, 105-126.
  58. Kim S, Dougherty ER, … Trent JM. (2002). Strong feature sets from small samples. J Comput Biol, 9, 127-146.
  59. Kim S, Dougherty ER, … Zhang W. (2002). Identification of combination gene sets for glioma classification. Mol Cancer Ther, 1, 1229-1236.
  60. Kim S, … Dougherty ER, … Suh EB. (2002). Can Markov chain models mimic biological regulation? J Biol Systems, 10, 337-358.
  61. Shmulevich I, Dougherty ER, Kim S, Zhang W. (2002). Probabilistic Boolean Networks: a rule-based uncertainty model for gene regulatory networks. Bioinformatics, 18, 261-274.
  62. Dougherty ER, … Kim S, Brun M. (2001). Multiresolution Analysis for Optimal Binary Filters. J Math Imaging Vis, 14, 53–72.
  63. Dougherty ER, Kim S, Chen Y. (2000). Coefficient of determination in nonlinear signal processing. Signal Processing, 80, 2219-2235.
  64. Kim S, … Trent JM. (2000). A General Nonlinear Framework for the Analysis of Gene Interaction via Expression Array. J Biomed Opt, 5, 411-424.
  65. Kim S, … Trent JM. (2000). Multivariate measurement of gene-expression relationships. Genomics, 67, 201-209.
  66. Baeg S, … Kim S, … Shah R. (1999). Unsupervised Morphological Granulometric Texture Segmentation of Digital Mammograms. J Electron Imaging, 8(1), 65-75.

Refereed Conference Articles

  1. Peng S, … Kim S, Dhruv H. (2019). Probing glioblastoma and its microenvironment using single-nucleus and single-cell sequencing. IEEE BIBM 2019, San Diego, USA.
  2. Speyer G, … Kim S. (2018). GPU-accelerated differential dependency network analysis. PDP 2018.
  3. Speyer G, … Kim S. (2017). Differential Pathway Dependency Discovery Associated with Drug Response across Cancer Cell Lines. Pacific Symposium on Biocomputing, 22:497-508.
  4. Speyer G, … Kim S. (2016). Knowledge-Assisted Approach to Identify Pathways with Differential Dependencies. Pacific Symposium on Biocomputing, 21:33-44.
  5. Jung S, Kim S. (2013). Identifying Potential Subtypes of Melanoma based on Pathway Activity Profiles. TBC/ISCB-Asia 2013, Seoul, Korea.
  6. Ramesh A, Nasser S, Kim S. (2011). Systematic Validation of Computationally Predicted Interaction Networks. WCSB 2011, Zurich.
  7. Jung S, … Kim S. (2011). Learning Contextual Gene Set Interaction Networks of Glioblastoma. WCSB 2011, Zurich.
  8. Verdicchio M, Kim S. (2011). Identifying Targets for Intervention by Analyzing Basins of Attraction. PSB 2011, Hawaii.
  9. Nasser S, … Kim S. (2010). Context-specific Gene Regulatory Networks Subdivide Intrinsic Subtypes of Breast Cancer. DTMBIO 2010.
  10. Ramesh A, … Kim S. (2010). Clustering Context-Specific Gene Regulatory Networks. PSB 2010.
  11. Nasser S, … Kim S. (2009). Identifying MiRNA and Imaging Features Associated with Metastasis of Lung Cancer. IEEE BIBM 2009. (Best Paper Award).
  12. Nasser S, … Kim S. (2009). In-silico conditioning of microRNA to identify potential biomarkers. IEEE GENSIPS 2009.
  13. Sen I, … Kim S. (2009). Context-Specific Gene Regulations in Cancer Gene Expression Data. PSB 2009.
  14. Gowda T, … Kim S. (2008). Threshold Logic Gene Regulatory Model. BIODEVICES 2008.
  15. Tembe W, … Kim S. (2008). Parallel programming to identify cellular contexts. IEEE GENSIPS 2008.
  16. Bryce D, Kim S. (2007). Planning for Gene Regulatory Network Intervention. IJCAI 07.
  17. Chung TH, Kim S. (2007). Prioritizing molecular signatures by combining aCGH and global gene expression profiling. IEEE GENSIPS 2007.
  18. Gowda T, … Kim S. (2007). Threshold Logic Gene Regulatory Networks. IEEE GENSIPS 2007.
  19. Kim S, … Bittner ML. (2007). Learning context-specific gene regulatory networks via in-silico conditioning. IEEE GENSIPS 2007.
  20. Kim S, … Bittner ML. (2007). Mining Molecular Contexts of Cancer via In-Silico Conditioning. CSB 2007.
  21. Henkel Z, Kim S. (2007). Learning Gene Regulatory Networks with the Finite State Linear Model. DREAM 2.
  22. Bryce D, Kim S. (2006). Planning for Gene Regulatory Network Intervention. IEEE/NLM Life Science Systems and Applications Workshop.
  23. Chung TH, Kim S. (2006). Quantization of Global Gene Expression Data. ICMLA 2006.
  24. Kim S, Tak Y, Tari L. (2006). Mining Gene Expression Profiles with Biological Prior Knowledge. IEEE/NLM Life Science Systems & Applications Workshop.
  25. Baral C, … Kim S, … Ramakrishnan I. (2005). BioLog: A Browser-based Collaboration… DILS 2005.
  26. Zhang X, Baral C, Kim S. (2005). An algorithm to learn causal connection between genes… AIME 05.
  27. Kim S, … Bittner M. (2005). Cellular contexts from gene expression profile. IEEE GENSIPS 2005.
  28. Dougherty ER, Kim S, … Brun M. (2000). Multiresolution Filter Design. SPIE Nonlinear Image Processing XI.
  29. Kim S, … Trent JM. (2000). Automated analysis of multivariate nonlinear gene relations… SPIE.
  30. Dougherty ER, … Kim S, … Trent JM. (2001). Time Series Inference from Clustering. SPIE.
  31. Chen Y, … Kim S, … Bittner ML. (2000). Estimating the Reliability of Inferences… BIST.
  32. Dougherty ER, Kim S, … Trent JM. (2000). Image Analysis and Signal Processing for cDNA Microarrays. CERH/NIEHS Symposium.
  33. Dougherty ER, … Kim S, Brun M. (2000). Multiresolution Filter Design. SPIE.
  34. Kim S, … Trent JM. (2000). Automated analysis of multivariate nonlinear gene relations… SPIE.
  35. Dougherty ER, Kim S, … Trent JM. (2000). Nonlinear stochastic determination for gene expressions… The Microarray Meeting.
  36. Dougherty ER, … Kim S, … Trent JM. (1999). Nonlinear Filters in Genomic Control. NSIP’99.
  37. Kim S, Batman S, Dougherty ER. (1998). A Fast Run-Length-Based Algorithm for One-Dimensional Flat Opening. SPIE.

Patents

  1. Kim S. Methods of Assessing A Risk Of Cancer Progression. US 8911940 B2 (2014).
  2. Kim S. Quantifying Gene Relatedness Nonlinear Prediction of Gene Expression Levels. US 7003403 B1 (2006). (Pending applications omitted for brevity, see full CV)

Book Chapters

  1. Bryce D, Kim S. (2010). Planning Interventions for Gene Regulatory Networks… Computational Methodologies in Gene Regulatory Networks.
  2. Kim S, et al. (2005). Integrated Approach for Computational Systems Biology. Genomic Signal Processing and Statistics.
  3. Suh EB, … Kim S, … Martino RL. (2002). Parallel Computation and Visualization Tools… Computational and Statistical Approaches To Genomics.