Taek-Kyun Kim, PhD

Bioinformatics Scientist

Taek-Kyun Kim currently works at the Hood-Price Lab for Systems Biomedicine, at the Institute for Systems Biology.

Taek-Kyun does research in Cell Biology, Cancer Research and Molecular Biology. Their current project is ‘Epigenetics of physical exercise.’

Cell Biology, Cancer Research, Molecular Biology

Cheung, V. G., N. Nowak, W. Jang, I. R. Kirsch, S. Zhao, X. N. Chen, T. S. Furey, et al. 2001. “Integration of Cytogenetic Landmarks into the Draft Sequence of the Human Genome.” Nature 409 (6822): 953–58. Cite
Gan, T. I., L. Rowen, R. Nesbitt, B. A. Roe, H. Wu, P. Hu, Z. Yao, U. J. Kim, T. O’Sickey, and M. Bina. 2002. “Genomic Organization of Human TCF12 Gene and Spliced MRNA Variants Producing Isoforms of Transcription Factor HTF4.” Cytogenet Genome Res 98 (4): 245–48. Cite
King, N. L., E. W. Deutsch, J. Ranish, A. I. Nesvizhskii, J. S. Eddes, P. Mallick, J. Eng, et al. 2006. “Analysis of the Saccharomyces Cerevisiae Proteome with PeptideAtlas.” Genome Biol 7 (11): R106. Cite
Heo, K., B. Kim, K. Kim, J. Choi, H. Kim, Y. Zhan, J. Ranish, and W. An. 2007. “Isolation and Characterization of Proteins Associated with Histone H3 Tails in Vivo.” J Biol Chem 282 (21): 15476–83. Cite
Choi, J., B. Kim, K. Heo, K. Kim, H. Kim, Y. Zhan, J. Ranish, and W. An. 2007. “Purification and Characterization of Cellular Proteins Associated with Histone H4 Tails.” J Biol Chem 282 (29): 21024–31. Cite
Kim, B., A. I. Nesvizhskii, P. G. Rani, S. Hahn, R. Aebersold, and J. Ranish. 2007. “The Transcription Elongation Factor TFIIS Is a Component of RNA Polymerase II Preinitiation Complexes.” Proc Natl Acad Sci U S A 104 (41): 16068–73. Cite
Jeong, S. K., M. S. Kwon, E. Y. Lee, H. J. Lee, S. Y. Cho, H. Kim, J. S. Yoo, et al. 2009. “BiomarkerDigger: A Versatile Disease Proteome Database and Analysis Platform for the Identification of Plasma Cancer Biomarkers.” Proteomics 9 (14): 3729–40. Cite
Peterson, A., L. Hohmann, L. Huang, B. Kim, J. K. Eng, and D. B. Martin. 2009. “Analysis of RP-HPLC Loading Conditions for Maximizing Peptide Identifications in Shotgun Proteomics.” J Proteome Res 8 (8): 4161–68. Cite
Milne, Caroline B., Pan-Jun Kim, James A. Eddy, and Nathan D. Price. 2009. “Accomplishments in Genome-Scale in Silico Modeling for Industrial and Medical Biotechnology.” Biotechnology Journal 4 (12): 1653–70. https://doi.org/10.1002/biot.200900234. Cite
Pfenning, A. R., T. K. Kim, J. M. Spotts, M. Hemberg, D. Su, and A. E. West. 2010. “Genome-Wide Identification of Calcium-Response Factor (CaRF) Binding Sites Predicts a Role in Regulation of Neuronal Signaling Pathways.” PLoS OnePLoS ONE 5 (5): e10870. Cite
Lin, B., A. Madan, J. G. Yoon, X. Fang, X. Yan, T. K. Kim, D. Hwang, L. Hood, and G. Foltz. 2010. “Massively Parallel Signature Sequencing and Bioinformatics Analysis Identifies Up-Regulation of TGFBI and SOX4 in Human Glioblastoma.” PLoS OnePLoS ONE 5 (4): e10210. Cite
Kim, Pan-Jun, and Nathan D. Price. 2010. “Macroscopic Kinetic Effect of Cell-to-Cell Variation in Biochemical Reactions.” Physical Review Letters 104 (14): 148103. Cite
Milne, Caroline B., James A. Eddy, Ravali Raju, Soroush Ardekani, Pan-Jun Kim, Ryan S. Senger, Yong-Su Jin, Hans P. Blaschek, and Nathan D. Price. 2011. “Metabolic Network Reconstruction and Genome-Scale Model of Butanol-Producing Strain Clostridium Beijerinckii NCIMB 8052.” BMC Systems Biology 5. https://doi.org/10.1186/1752-0509-5-130. Cite
Kim, Y., T. K. Kim, J. Yoo, S. You, I. Lee, G. Carlson, L. Hood, S. Choi, and D. Hwang. 2011. “Principal Network Analysis: Identification of Subnetworks Representing Major Dynamics Using Gene Expression Data.” Bioinformatics 27 (3): 391–98. Cite
Kim, Pan-Jun, and Nathan D. Price. 2011. “Genetic Co-Occurrence Network across Sequenced Microbes.” PLoS Computational Biology 7 (12). https://doi.org/10.1371/journal.pcbi.1002340. Cite
Paik, Y. K., S. K. Jeong, G. S. Omenn, M. Uhlen, S. Hanash, S. Y. Cho, H. J. Lee, et al. 2012. “The Chromosome-Centric Human Proteome Project for Cataloging Proteins Encoded in the Genome.” Nature Biotechnology 30 (3): 221–23. Cite
You, Sungyong, Chul-Soo Cho, Inyoul Lee, Leroy Hood, Daehee Hwang, and Wan-Uk Kim. 2012. “A Systems Approach to Rheumatoid Arthritis.” PLoS One 7: e51508. https://doi.org/10.1371/journal.pone.0051508. Cite
Ombrello, Michael J., Elaine F. Remmers, Guangping Sun, Alexandra F. Freeman, Shrimati Datta, Parizad Torabi-Parizi, Naeha Subramanian, et al. 2012. “Cold Urticaria, Immunodeficiency, and Autoimmunity Related to PLCG2 Deletions.” N Engl J Med 366 (January): 330–38. https://doi.org/10.1056/NEJMoa1102140. Cite Download
Lee, Geun-Shik, Naeha Subramanian, Andrew I. Kim, Ivona Aksentijevich, Raphaela Goldbach-Mansky, David B. Sacks, Ronald N. Germain, Daniel L. Kastner, and Jae Jin Chae. 2012. “The Calcium-Sensing Receptor Regulates the NLRP3 Inflammasome through Ca2+ and CAMP.” Nature 492 (December): 123–27. https://doi.org/10.1038/nature11588. Cite Download
Sung, Jaeyun, Pan-Jun Kim, Shuyi Ma, Cory C. Funk, Andrew T. Magis, Yuliang Wang, Leroy Hood, Donald Geman, and Nathan D. Price. 2013. “Multi-Study Integration of Brain Cancer Transcriptomes Reveals Organ-Level Molecular Signatures.” PLoS Computational Biology 9 (7). https://doi.org/10.1371/journal.pcbi.1003148. Cite
Liu, S., H. Im, A. Bairoch, M. Cristofanilli, R. Chen, E. W. Deutsch, S. Dalton, et al. 2013. “A Chromosome-Centric Human Proteome Project (C-HPP) to Characterize the Sets of Proteins Encoded in Chromosome 17.” Journal of Proteome Research 12 (1): 45–57. Cite
Mirzaei, H., T. A. Knijnenburg, B. Kim, M. Robinson, P. Picotti, G. W. Carter, S. Li, et al. 2013. “Systematic Measurement of Transcription Factor-DNA Interactions by Targeted Mass Spectrometry Identifies Candidate Gene Regulatory Proteins.” Proceedings of the National Academy of Sciences of the United States of America 110 (9): 3645–50. Cite
Dong, Yiran, Charu Gupta Kumar, Nicholas Chia, Pan-Jun Kim, Philip A. Miller, Nathan D. Price, Isaac K. O. Cann, et al. 2013. “Halomonas Sulfidaeris-Dominated Microbial Community Inhabits a 1.8 Km-Deep Subsurface Cambrian Sandstone Reservoir.” Environ Microbiol, November. https://doi.org/10.1111/1462-2920.12325. Cite
Gierman, Hinco J., Kristen Fortney, Jared C. Roach, Natalie S. Coles, Hong Li, Gustavo Glusman, Glenn J. Markov, et al. 2014. “Whole-Genome Sequencing of the World’s Oldest People.” PloS One 9 (11): e112430. https://doi.org/10.1371/journal.pone.0112430. Cite
Wang, Lanfeng, Oliver Limbo, Jia Fei, Lu Chen, Bong Kim, Jie Luo, Jenny Chong, et al. 2014. “Regulation of the Rhp26ERCC6/CSB Chromatin Remodeler by a Novel Conserved Leucine Latch Motif.” Proceedings of the National Academy of Sciences of the United States of America 111 (52): 18566–71. https://doi.org/10.1073/pnas.1420227112. Cite
Zelter, A., M. Bonomi, J. O. Kim, N. T. Umbreit, M. R. Hoopmann, R. Johnson, M. Riffle, et al. 2015. “The Molecular Architecture of the Dam1 Kinetochore Complex Is Defined by Cross-Linking Based Structural Modelling.” Nature Communications 6: 8673. https://doi.org/10.1038/ncomms9673. Cite
Caron, E., L. Espona, D. J. Kowalewski, H. Schuster, N. Ternette, A. Alpizar, R. B. Schittenhelm, et al. 2015. “An Open-Source Computational and Data Resource to Analyze Digital Maps of Immunopeptidomes.” ELife 4. https://doi.org/10.7554/eLife.07661. Cite
Xue, Min, Wei Wei, Yapeng Su, Jungwoo Kim, Young Shik Shin, Wilson X. Mai, David A. Nathanson, and James R. Heath. 2015. “Chemical Methods for the Simultaneous Quantitation of Metabolites and Proteins from Single Cells.” Journal of the American Chemical Society 137 (12): 4066–69. https://doi.org/10.1021/jacs.5b00944. Cite
Lee, H. J., J. M. Kim, K. H. Kim, J. I. Heo, S. J. Kwak, and J. A. Han. 2015. “Genotoxic Stress/P53-Induced DNAJB9 Inhibits the pro-Apoptotic Function of P53.” Cell Death and Differentiation 22 (1): 86–95. Cite
Ichiyama, Kenji, Tingting Chen, Xiaohu Wang, Xiaowei Yan, Byung-Seok Kim, Shinya Tanaka, Delphine Ndiaye-Lobry, et al. 2015. “The Methylcytosine Dioxygenase Tet2 Promotes DNA Demethylation and Activation of Cytokine Gene Expression in T Cells.” Immunity 42 (April): 613–26. https://doi.org/10.1016/j.immuni.2015.03.005. Cite
He, Yuqing, Juanjuan Lin, Yuanlin Ding, Guodong Liu, Yanhong Luo, Mingyuan Huang, Chengkai Xu, et al. 2015. “A Systematic Study on Dysregulated MicroRNAs in Cervical Cancer Development.” Int J Cancer, May. https://doi.org/10.1002/ijc.29618. Cite
He, Y., J. R. Chevillet, G. Liu, T. K. Kim, and K. Wang. 2015. “The Effects of MicroRNA on the Absorption, Distribution, Metabolism and Excretion of Drugs.” Br J Pharmacol 172 (June): 2733–47. https://doi.org/10.1111/bph.12968. Cite
Cancer Genome Atlas Research Network, Daniel J. Brat, Roel G. W. Verhaak, Kenneth D. Aldape, W. K. Alfred Yung, Sofie R. Salama, Lee A. D. Cooper, et al. 2015. “Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas.” The New England Journal of Medicine 372 (26): 2481–98. https://doi.org/10.1056/NEJMoa1402121. Cite
He, Y., J. Lin, D. Kong, M. Huang, C. Xu, T. K. Kim, A. Etheridge, Y. Luo, Y. Ding, and K. Wang. 2015. “Current State of Circulating MicroRNAs as Cancer Biomarkers.” Clinical Chemistry 61 (September): 1138–55. https://doi.org/10.1373/clinchem.2015.241190. Cite
Lee, J. M., K. H. Kim, A. Shin, M. J. Chao, K. Abu Elneel, T. Gillis, J. S. Mysore, et al. 2015. “Sequence-Level Analysis of the Major European Huntington Disease Haplotype.” American Journal of Human Genetics 97 (September): 435–44. https://doi.org/10.1016/j.ajhg.2015.07.017. Cite
Luo, J., P. Cimermancic, S. Viswanath, C. C. Ebmeier, B. Kim, M. Dehecq, V. Raman, et al. 2015. “Architecture of the Human and Yeast General Transcription and DNA Repair Factor TFIIH.” Molecular Cell 59 (September): 794–806. https://doi.org/10.1016/j.molcel.2015.07.016. Cite
Kim, T. K., A. Bheda-Malge, Y. Lin, K. Sreekrishna, R. Adams, M. K. Robinson, C. C. Bascom, J. P. Tiesman, R. J. Isfort, and R. Gelinas. 2015. “A Systems Approach to Understanding Human Rhinovirus and Influenza Virus Infection.” Virology 486 (December): 146–57. https://doi.org/10.1016/j.virol.2015.08.014. Cite
Daude, Nathalie, Inyoul Lee, Taek-Kyun Kim, Christopher Janus, John Paul Glaves, Hristina Gapeshina, Jing Yang, et al. 2016. “A Common Phenotype Polymorphism in Mammalian Brains Defined by Concomitant Production of Prolactin and Growth Hormone.” PloS One 11 (2): e0149410. https://doi.org/10.1371/journal.pone.0149410. Cite
McPhillie, Martin, Ying Zhou, Kamal El Bissati, Jitender Dubey, Hernan Lorenzi, Michael Capper, Amanda K. Lukens, et al. 2016. “New Paradigms for Understanding and Step Changes in Treating Active and Chronic, Persistent Apicomplexan Infections.” Scientific Reports 6: 29179. https://doi.org/10.1038/srep29179. Cite
Lee, L. James, Zhaogang Yang, Mohammad Rahman, Junyu Ma, Kwang Joo Kwak, Joseph McElroy, Konstantin Shilo, et al. 2016. “Extracellular MRNA Detected by Tethered Lipoplex Nanoparticle Biochip for Lung Adenocarcinoma Detection.” American Journal of Respiratory and Critical Care Medicine 193 (12): 1431–33. https://doi.org/10.1164/rccm.201511-2129LE. Cite
Wu, Shenghui, Taek-Kyun Kim, Xiaogang Wu, Kelsey Scherler, David Baxter, Kai Wang, Ruth E. Krasnow, Terry Reed, and Jun Dai. 2016. “Circulating MicroRNAs and Life Expectancy Among Identical Twins.” Annals of Human Genetics 80 (5): 247–56. https://doi.org/10.1111/ahg.12160. Cite
Zheng, Siyuan, Andrew D. Cherniack, Ninad Dewal, Richard A. Moffitt, Ludmila Danilova, Bradley A. Murray, Antonio M. Lerario, et al. 2016. “Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma.” Cancer Cell 29 (5): 723–36. https://doi.org/10.1016/j.ccell.2016.04.002. Cite
Qin, Shizhen, Yong Zhou, Li Gray, Ulrike Kusebauch, Laurence McEvoy, Daniel J. Antoine, Lucy Hampson, et al. 2016. “Identification of Organ-Enriched Protein Biomarkers of Acute Liver Injury by Targeted Quantitative Proteomics of Blood in Acetaminophen- and Carbon-Tetrachloride-Treated Mouse Models and Acetaminophen Overdose Patients.” Journal of Proteome Research. https://doi.org/10.1021/acs.jproteome.6b00547. Cite
Wei, Wei, Young Shik Shin, Min Xue, Tomoo Matsutani, Kenta Masui, Huijun Yang, Shiro Ikegami, et al. 2016. “Single-Cell Phosphoproteomics Resolves Adaptive Signaling Dynamics and Informs Targeted Combination Therapy in Glioblastoma.” Cancer Cell 29 (4): 563–73. https://doi.org/10.1016/j.ccell.2016.03.012. Cite
Stittrich, Anna B, Justin Ashworth, Mude Shi, Max Robinson, Denise Mauldin, Mary E Brunkow, Shameek Biswas, et al. 2016. “Genomic Architecture of Inflammatory Bowel Disease in Five Families with Multiple Affected Individuals.” Human Genome Variation 3 (January): 15060. https://doi.org/10.1038/hgv.2015.60. Cite