■ International Journal Publications†Corresponding authors*First authors
  1. Seong Hee Choi*, Muralidharan Mani*, Jeonghwan Kim*, Wha Ja Cho, Thomas Martin, Jee Hyun Kim, Hun Su Chu, Won Jin Jeong, Young-Wook Won, Byung Ju Lee, Byungyong Ahn, Junil Kim†, Do Yong Jeon†, Jeong Woo Park†, "DRG2 is required for surface localization of PD-L1 and the efficacy of anti-PD-1 therapy", Accepted for publication in Cell Death Discovery (IF: 7.0) 14 May 2024
  2. Jongsu Lim, Chanho Park, Minjae Kim, Hyukhee Kim, Junil Kim, Dong-Sung Lee, "Advances in single-cell omics and multiomics for high-resolution molecular profiling", Experimental & Molecular Medicine (IF: 12.8), Vol. 56, Issue 3, 5 March 2024 [Link]
  3. Sujin Park, Jin Sun Heo, Seiya Mizuno, Min Woo Kim, Haein An, Eunji Hong, Min Gi Kang, Junil Kim, Rebecca Yun, Hyeyeon Park, Eun-Hye Noh, Min-Jung Lee, Kwiyeom Yoon, Pyunggang Kim, Minjung Son, Kyoungwha Pang, Jihee Lee, Jinah Park, Akira Ooshima, Tae-Jin Kim, Je Yeun Park, Kyung-Min Yang, Seung-Jae Myung, Hyun Bae, Kyung-Mi Lee, John Letterio, Seok Hee Park, Satoru Takahashi, Seong-Jin Kim "Tm4sf19 deficiency inhibits osteoclast multinucleation and prevents bone loss", Metabolism (IF: 13.934), Vol. 151, 155746, 1 Feb 2024 [Link]
  4. Hyeonkyu Kim, Hwisoo Choi, Daewon Lee†, Junil Kim† , "A review on gene regulatory network reconstruction algorithms based on single cell RNA sequencing", Genes and Genomics, Vol 46, Issue 1, 31 Jan 2024 (†Co-corresponding authors) [Link]
  5. Hyobin Kim, Cecilia Lövkvist, António Palma, Patrick Martin, Junil kim, Amit Kumar, Maria Leonor Peixoto, Esha Madan, Rajan Gogna, Kyoung Jae Won, "CellNeighborEX: Deciphering Neighbor-Dependent Gene Expression from Spatial Transcriptomics Data", Molecular Systems Biology (IF: 12.744), Vol. 19, e11670, 9 Nov 2023 [Link]
  6. Jahanzeb Saqib, Beomsu Park, Yunjung Jin, Junseo Seo, Jaewoo Mo, Junil Kim, "Identification of niche-specific gene signatures between malignant and tumor microenvironments by integrating single cell and spatial transcriptomics data", Genes, 14 (11), 2033, 1 Nov 2023 [Link]
  7. Rebecca Yun*, Eunji Hong*, Junil Kim*, Bora Park, Staci Jakyong Kim, Bona Lee, Yong Sang Song, Seong-Jin Kim, Sujin Park, Jin Muk Kang, "N-linked glycosylation is essential for anti-tumor activities of KIAA1324 in gastric cancer", Cell Death and Disease (IF: 9.705), Vol. 14, Article Number: 546, 23 Aug 2023 [Link]
  8. Junil Kim*, Michaela Mrugala Rothová*, Esha Madan*, Siyeon Rhee, Guangzheng Weng, António Palma, Linbu Liao, Eyal David, Ido Amit, Morteza Chalabi Hajkarim, Vignesh Vudatha, Andrés Gutiérrez-García, Eduardo Moreno, Robert Winn, Jose Trevino, Paul B. Fisher, Joshua M. Brickman, Rajan Gogna, Kyoung Jae Won, "Neighbor-specific gene expression revealed from physically interacting cells during mouse embryonic development", PNAS (IF: 12.777), Vol. 120, Issue 2, e2205371120, 3 Jan. 2023 (Google Scholar: 7 / Web of Science: 4) [Link]
  9. Do Yong Jeon, So Yeon Jeong, Ju Won Lee, Jeonghwan Kim, Jee Hyun Kim, Hun Su Chu, Won Jin Jeong, Byung Ju Lee, Byungyong Ahn, Junil Kim, Seong Hee Choi, Jeong Woo Park, "FOXO1 Is a Key Mediator of Glucocorticoid-Induced Expression of Tristetraprolin in MDA-MB-231 Breast Cancer Cells", International Journal of Molecular Sciences (IF: 6.208), Vol. 23, Issue 25, 13673, 8 Nov. 2022 [Link]
  10. Jihee Lee, Kyoungwha Pang, Junil Kim, Eunji Hong, Jeeyun Lee, Hee Jin Cho, Jinah Park, Minjung Son, Sihyun Park, Min-Jung Lee, Akira Ooshima, Kyung-Soon Park, Han-Kwang Yang, Kyung-Min Yang, Seong-Jin Kim, “ESRP1-regulated isoform switching of LRRFIP2 determines metastasis of gastric cancer”, Nature Communications (IF: 17.69), Vol. 13, 6274, 28 Oct. 2022 (Google Scholar: 14 / Web of Science: 10) [Link]
  11. Dongha Kim*, Junil Kim*, Young Suk Yu, Yong Ryoul Kim, Sung-hee Baek, Kyoung-Jae Won, “Systemic approaches using single cell transcriptome reveal that C/EBPγ regulates autophagy under amino acid starved condition”, Nucleic Acids Research (IF: 19.160), Vol. 50, Issue 13, 7298-7309, 22 July 2022 (Google Scholar: 5 / Web of Science: 3) [Link]
  12. Xiaodun Yang*, Jeffrey C. Raum*, Junil Kim*, Reynold Yu, Juxiang Yang, Gabriella Rice, Changhong Li, Kyoung-Jae Won, Diana E. Stanescu, and Doris A. Stoffers, “A PDX1 cistrome and single-cell transcriptome resource of the developing pancreas”, Development (IF: 6.862), Vol. 149, Issue 13, dev200432, 29 June 2022 (Google Scholar: 3 / Web of Science: 2)  [Link]
  13. Kyoungwha Pang, Jihee Lee, Junil Kim, Jinah Park, Yuna Park, Eunji Hong, Haein An, Akira Ooshima, Minjung Son, Kyung-Soon Park, Jae-Hyu Cho, Cheol Lee, Yong Sang Song, Kyung Min Yang, and Seong-Jin Kim, “Degradation of DRAK1 by CUL3/SPOP E3 Ubiquitin ligase promotes tumor growth of paclitaxel-resistant cervical cancer cells”, Cell Death and Disease (IF: 9.705), Vol. 13, Article Number: 169, 22 Feb 2022 (Google Scholar: 15 / Web of Science: 10) [Link]
  14. Guangzheng Weng, Junil Kim†, and Kyoung Jae Won†, "VeTra: a tool for trajectory inference based on RNA velocity", Bioinformatics (IF: 6.931), Vol. 37, Issue 20, p3509-3513, 15 Oct. 2021. (Google Scholar: 20 / Web of Science: 12) [Link]
  15. Juxiang Yang, Batoul Hammoud, Changhong Li, Abigail Ridler; Daphne Yau, Junil Kim, Kyoung-Jae Won, Charles A Stanley, Toshinori Hoshi, Diana Elena Stanescu, "Decreased KATP channel activity contributes to the low glucose threshold for insulin secretion in the early postnatal period", Endocrinology, Vol. 162, Issue 9, bqab121 , 1 Sept. 2021. (Google Scholar: 21 / Web of Science: 10) [Link]
  16. Junil Kim, Simon T. Jakobsen, Kedar N. Natarajan, Kyoung Jae Won, “TENET: Gene network reconstruction using transfer entropy reveals key regulatory factors from single cell transcriptomic data”, Nucleic Acids Research (IF: 19.160), Vol. 49, Issue 1, e1-e1, 11 Jan. 2021. (Google Scholar: 34 / Web of Science: 19) [Link]
  17. Tomoya Sakamoto, Timothy R Matsuura, Shibiao Wan, David M Ryba, Junil Kim, Kyoung Jae Won, Ling Lai, Christopher Petucci, Nataliya Petrenko, Kiran Musunuru, Rick B Vega, and Daniel P Kelly, “A Critical Role for Estrogen-Related Receptor Signaling in Cardiac Maturation", Circulation Research (IF: 23.213), Vol. 126, No 12, 1685-1702, March 2020. (Google Scholar: 95 / Web of Science: 66) [Link]
  18. Shibiao Wan, Junil Kim, Kyoung Jae Won, “SHARP: hyper-fast and accurate processing of single-cell RNA-seq data via ensemble random projection”, Genome Research (IF: 9.438), Vol. 30, Issue 2, 205-213, Jan. 2020. (Google Scholar: 64 / Web of Science: 46) [Link]
  19. Junil Kim, Diana E. Stanescu, and Kyoung Jae Won, “CellBIC: Bimodality-based top-down clustering of single-cell RNA sequencing data reveals hierarchical structure of the cell type", Nucleic Acids Research (IF: 19.160), Vol. 46, Issue 21, e124, 30 Nov. 2018. (Google Scholar: 16 / Web of Science: 12) [Link]
  20. Sujin Park, Kyung-Min Yang, Yuna Park, Eunji Hong, Chang Pyo Hong, Jinah Park, Kyoungwha Pang, Jihee Lee, Bora Park, Siyoung Lee, Haein An, Mi-Kyung Kwak, Junil Kim, Jin Muk Kang, Pyunggang Kim, Yang Xiao, Guangjun Nie, Akira Ooshima, and Seong-Jin Kim “Identification of Epithelial-Mesenchymal Transition-related Target Genes Induced by the Mutation of Smad3 Linker Phosphorylation”, Journal of Cancer Prevention, Vol. 23, Issue 2, 107, Jun. 2018. (Google Scholar: 12 / Web of Science: 10) [Link]
  21. Jinah Park, Junil Kim, Bora Park, Kyung-Min Yang, Eun Jin Sun, Cristina E. Tognon, Poul H. Sorenson, and Seong-Jin Kim, “Novel identification of STAT1 as a crucial mediator of ETV6-NTRK3-induced tumorigenesis”, Oncogene (IF: 8.756), Vol. 37, 2270-2284, Feb. 2018. (Google Scholar: 14 / Web of Science: 9) [Link]
  22. Kyung-Min Yang, Eunjin Bae, Sung Gwe Ahn, Kyoungwha Pang, Yuna Park, Jinah Park, Jihee Lee, Akira Ooshima, Bora Park, Junil Kim, Yungshin Jung, Satoru Takahashi, Joon Jeong, Seok Hee Park, Seong-Jin Kim, “Co-chaperone BAG2 Determines the Pro-oncogenic Role of Cathepsin B in Triple-Negative Breast Cancer Cells”, Cell Reports (IF: 9.995), Vol. 21, Issue 10, 2952-2964, Dec. 2017. (Google Scholar: 51 / Web of Science: 42) [Link]
  23. Junil Kim, Sujin Park, Haein An, Ji-Young Choi, Myung-Sook Choi, Sang-Woon Choi, Seong-Jin Kim, “Differential Tissue-specific and Pathway-specific Anti-obesity Effects of Green Tea and Taeumjowitang, a Traditional Korean Medicine, in Mice”, Journal of Cancer Prevention, Vol. 22, Issue 3, 147, Sep. 2017. [Link]
  24. Ji-Young Choi, Robin McGregor, Eun-Young Kwon, Ye jin Kim, Youngji Han, Jung Han Yoon-Park, Ki Won Lee, Seong-Jin Kim, Junil Kim, Jong Won Yun, and Myung-Sook Choi, "The metabolic response to a high-fat diet reveals obesity-prone and -resistant phenotypes in mice with distinct mRNA-seq transcriptome profiles", International Journal of Obesity (IF: 5.095), Vol. 40, 1452-1460, Sep. 2016. (Google Scholar: 30 / Web of Science: 19) [Link]
  25. Jong-Eun Kim*, Dasom Song*, Junil Kim*, Jina Choi, Jong Rhan Kim, Hyun-Sun Yoon, Jung-Soo Bae, Mira Han, Sein Lee, Ji Eun Shin, Ji Sun Hong, Dayoung Song, Seong-Jin Kim, Myung-Jin Son, Sang-Woon Choi,  Jin Ho Chung, Tae-Aug Kim, and Ki Won Lee, "Oral supplementation with cocoa extract reduces UVB-induced wrinkles in hairless mouse skin", Journal of Investigative Dermatology (IF: 8.551), Vol. 136, Issue 5, 1012-1021, May 2016. (Google Scholar: 40 / Web of Science: 26) [Link]
  26. Sang Woon Choi, Jina Choi, Junil Kim, Yuri Kim, Simonetta Friso, “Walnut Substantially Alters the DNA Methylation Profile in Colon Cancer Stem Cells”, The FASEB Journal, Vol. 30, Issue S1, 912.5-912.5, April 2016. (Google Scholar: 2 / Web of Science: 0) [Link]
  27. Junil Kim, Seong-Jin Kim, and Kazuhito Naka, "Transcriptome sequencing of hematopoietic stem cells and chronic myelogenous leukemia stem cells", Genomics Data, Vol. 7, 57-59, March 2016. (Google Scholar: 3 / Web of Science: 3) [Link]
  28. Junil Kim, Eun-Young Kwon, Sujin Park, Jeong-Rae Kim, Sang-woon Choi, Myung Sook Cho, and Seong-Jin Kim, "Integrative systems analysis of diet-induced obesity identified a critical transition in the transcriptomes of the murine liver and epididymal white adipose tissue", International Journal of Obesity (IF: 5.095), Vol. 40, 338-345, Feb. 2016. (Google Scholar: 8 / Web of Science: 5) [Link]
  29. Yung-Keun Kwon, Junil Kim, and Kwang-Hyun Cho, "Dynamical Robustness Against Multiple Mutations in Signaling Networks", IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 13, Issue 5, 996-1002, Oct. 2015. (Google Scholar: 14 / Web of Science: 6) [Link]
  30. Kazuhito Naka, Yoshie Jomen, Kaori Ishihara, Junil Kim, Takahiro Ishimoto, Eunjin Bae, Robert Mohney, Steven M. Stirdivant, Hiroko Oshima, Masanobu Oshima, Dong-Wook Kim, Hiromitsu Nakauchi, Yoshihiro Takihara, yukio kato, Akira Ooshima, and Seong-Jin Kim, "Dipeptide species regulate p38MAPK-Smad3 signalling to maintain chronic myelogenous leukaemia stem cells", Nature Communications (IF: 14.919), Vol. 6, 8039, Aug. 2015. (Google Scholar: 58 / Web of Science: 45) [Link]
  31. Jin Muk Kang, Sujin Park, Staci Jakyong Kim, Hyojung Kim, Bona Lee, Junil Kim, Jinah Park, Shin Tae Kim, Han-Kwang Yang, Woo Ho Kim, and Seong-Jin Kim, "KIAA1324 suppresses gastric cancer progression by inhibiting the oncoprotein GRP78", Cancer Research (IF: 12.701), Vol. 75, 3087, June 2015. (Google Scholar: 90 / Web of Science: 42) [Link]
  32. Ho Sung Lee*, Myung-Jin Goh*, Junil Kim*, Taejun Choi, Hae Kwang Lee, Yong Ju Na, and Kwang-Hyun Cho, "A systems-biological study on the identification of safe and effective molecular targets for the reduction of ultraviolet B-induced skin pigmentation", Scientific Reports, Vol. 5, 10305, May 2015. (Google Scholar: 30 / Web of Science: 19) [Link]
  33. Bona Lee, Kwiyeom Yoon, Sunghoon Lee, Jin Muk Kang, Junil Kim, Sung Han Shim, Hak-Min Kim, Sanghoon Song, Kazuhito Naka, An Keun Kim, Han-Kwang Yang, and Seong-Jin Kim, “Homozygous deletions at 3p22, 5p14, 6q15, and 9p21 result in aberrant expression of tumor suppressor genes in gastric cancer”, Genes, Chromosomes, and Cancer, Vol. 54, Issue 3, 141-155, March 2015. (Google Scholar: 20 / Web of Science: 13) [Link]
  34. Junil Kim, Drieke Vandamme, Jeong-Rae Kim, Amaya Garcia Munoz, Walter Kolch, and Kwang-Hyun Cho, “Robustness and evolvability of the human signaling network”, Vol. 10, Issue 7, e1003763, PLoS Computational Biology, July 2014. (Google Scholar: 32 / Web of Science: 19) [Link]
  35. Junil Kim, Sang-Min Park, and Kwang-Hyun Cho, “Discovery of a kernel for controlling biomolecular regulatory networks”, Scientific Reports, Vol. 3, 2223, July 2013. (Google Scholar: 119 / Web of Science: 72) [Link]
  36. Junil Kim, Minsoo Choi, Jeong-Rae Kim, Hua Jin, V. Narry Kim, and Kwang-Hyun Cho, "The Co-regulation Mechanism of Transcription Factors in the Human Gene Regulatory Network", Nucleic Acids Research (IF: 19.160), Vol. 40, No. 18, pp. 8849-8861, Oct 2012. (Google Scholar: 31 / Web of Science: 17) [Link]
  37. Jeong-Rae Kim, Junil Kim, Yung-Keun Kwon, Hwang-Yeol Lee, Pat Heslop-Harrison, and Kwang-Hyun Cho, "Reduction of complex signaling networks to a representative kernel", Science Signaling (IF: 8.192), Vol. 4, Issue 175, pp. Ra35, May 2011. (Google Scholar: 64 / Web of Science: 53) [Link]
  38. Tae-Hwan Kim*, Junil Kim*, Pat Heslop-Harrison, and Kwang-Hyun Cho, "Evolutionary design principles and functional characteristics based on kingdom-specific network motifs", Bioinformatics (IF: 6.931), Vol. 27, No. 2, pp. 245-251, Jan. 2011. (Google Scholar: 24 / Web of Science: 14) [Link]
  39. Jungsoo Gim*, Ho-Shik Kim*, Junil Kim*, Minsoo Choi, Jeong-Rae Kim, Yeun Jun Chung, and Kwang-Hyun Cho, "A system-level investigation into the cellular toxic response mechanism mediated by AhR signal transduction pathway", Bioinformatics (IF: 6.931), Vol. 26, No. 17, pp. 2169-2175, Sep. 2010. (Google Scholar: 17 / Web of Science: 11) [Link]
  40. Junil Kim, Tae-Geon Kim, Sung Hoon Jung, Jeong-Rae Kim, Taesung Park, Pat Heslop-Harrison, and Kwang-Hyun Cho, "Evolutionary design principles of modules that control cellular differentiation: Consequences for hysteresis and multistationarity", Bioinformatics (IF: 6.931), Vol. 24, No. 13, pp. 1516-1522, July 2008. (Google Scholar: 20 / Web of Science: 13) [Link]
  41. Shinuk Kim, Junil Kim, and Kwang-Hyun Cho, "Inferring gene regulatory networks from temporal expression profiles under time-delay and noise", Computational Biology and Chemistry, Vol. 31, Issue 4, pp. 239-245, Aug. 2007. (Google Scholar: 66 / Web of Science: 45) [Link]
  42. Kwang-Hyun Cho, Sang-Mok Choo, Sung Hoon Jung, Jeong-Rae Kim, H. S. Choi, and Junil Kim, "Reverse Engineering of Gene Regulatory Networks", IET Systems Biology, Vol. 1, No. 3, pp. 149-163, May 2007. (Google Scholar: 157 / Web of Science: 76) [Link]
  ■ Issued Patents
  1. Y.J. Na, M.J. Goh, H.K. Lee, J.C. Cho, K.-H. Cho, J. Kim, H.-S. Lee, and T.-J Choi, (AMOREPASIFIC Co., KAIST), Screening method of melanin synthesis control factor, device thereof and screening method of whitening material using the same, Korea Patent No. 10-2026290 (Sep. 23, 2019).
 ■ Invited talk
  • Invited Speaker at the Spatial Biology Congress Asia, Singapore, Nov 07-08, 2023 Talk Title: "Identification of Neighbour-Specific Gene Signatures Between Malignant and Tumour microenvironments by Integrating Single Cell and Spatial transcriptomics data
  • Invited Speaker at the KEYSTONE SYMPOSIA on Molecular and Cellular Biology: Single Cell Biology, Breckenridge, Colorado, USA, Jan. 13-17, 2019. Talk Title: “Reconstruction of gene regulatory network from pseudo-time ordered single-cell RNA sequencing data using conditional mutual information”
  • Plenary talk at the 6th Seoul International Congress of Endocrinology and Metabolism 2018, Seoul, Korea, April 19-22, 2018. Talk title: “Bimodality-based top-down clustering of single-cell RNA sequencing data reveals type 2 diabetes and age specific beta cell signatures”
  • Invited Speaker at KSBSB2014 Yonsei University, Seoul, Korea, Nov. 14, 2014. Talk title: “Mathematical modeling of human gene regulatory network”
  • Invited Speaker at ICSB2011 Heidelberg/Mannheim, Germany, Aug. 2011. Talk title: “Decomposition of Human Signaling Network into Two Modules: Evolvable Core and Robust Neighbor”