Google Scholar page: https://scholar.google.com/citations?user=ZAclXEEAAAAJ 

PubMed in NCBI: https://pubmed.ncbi.nlm.nih.gov/?term=pora+kim&sort=date&size=200 

Selected Publications

(*co-first, **co-corresponding authors, ***corresponding author)

1. Himansu Kumar, Zikang Chen, Abayomi Adegunlehin, Loren Trowbridge, Leonardo Aguilar, Pora Kim***, KinaseFusionDB: an integrative knowledge of kinase fusion proteins in multi-scales, Briefings In Bioinformatics, https://doi.org/ 10.1093/bib/bbaf259 (2025) (Corresponding)

2. Himansu Kumar, Abayomi Adegunlehin, Zikang Chen, and Pora Kim***, FusionPub, a Therapeutic Landscape of Human Fusion Genes, Briefings In Bioinformatics, https//doi.org/10.1093/bib/bbaf145. (2025) (Corresponding)

3. Yuntao Yang, Himansu Kumar, Xie Yuhan, Zhao Li, Rongbin Li, Wenbo Chen, Chiamaka S. Diala, Meer A. Ali, Yi Xu, Albon Wu, Sayed-Rzgar Hosseini, Erfei Bi, Hongyu Zhao, Pora Kim**, Wenjin Zheng, ASpdb: an integrative knowledgebase of human protein isoforms from experimental and AI-predicted structures, Nucleic Acids Res. 2024 Nov 12: gkae1018, https://doi.org/10.1093/nar/gkae1018. (Co-corresponding)

4. Grant Wang, Xiaona Liu, Aoqi Wang, Jianguo Wen, Pora Kim, Qianqian Song, Xiaona Liu, Xiaobo Zhou, CRISPRoffT: comprehensive database of CRISPR/Cas off-targets, Nucleic Acids Res. 2024 November 11, doi:10.1093/nar/gkae1025

5. Tiangang Wang, Xuanmin Chen, Yujuan Han, Jiahao Yi, Xi Liu, Pora Kim, Liyu Huang, Kexin Huang, Xiaobo Zhou, scProAtlas: an atlas of multiplexed single-cell spatial proteomics imaging in human tissues, Nucleic Acids Res, 2024 November 11, doi:10.1093/nar/gkae990

6. Sijia Wu, Jiajin Zhang, Yanfei Wang, Xinyu Qin, Zhaocan Zhang, Zhennan Lu, Pora Kim, Xiaobo Zhou, Liyu Huang, metsDB: a knowledgebase of cancer metastasis at bulk, single-cell and spatial levels, Nucleic Acids Res. 2024 Oct 21:gkae916. doi: 10.1093/nar/gkae916.

7. Mengyuan Yang, Yuzhou Feng, Jiajia Liu, Hong Wang, Sijia Wu, Weiling Zhao, Pora Kim**, Xiaobo Zhou, SexAnnoDB, a knowledgebase of sex-specific regulations from multi-omics data of human cancers, Biology of Sex Differences. 2024 Aug 22;15(1):64. doi: 10.1186/s13293-024-00638-8. (Co-corresponding)

8. Himansu Kumar, Pora Kim***, Artificial intelligence in fusion protein three-dimensional structure prediction: Review and perspective, Clin Transl Med, 2024 Aug;14(8):e1789. doi: 10.1002/ctm2.1789.

9. Chengyuan Yang, Himansu Kumar, Pora Kim***, FusionNW, a potential clinical impact assessment of kinases in pan-cancer fusion gene network, Briefings in Bioinformatics. 2024 Jan 22;25(2):bbae097. doi: 10.1093/bib/bbae097. 

10. Xiaona Liu, Jiahao Y, Tiina Li, Jianguo Wen, Kexin Huang, Jiajia Liu, Grant Wang, Pora Kim**, Qianqian Song, Xiaobo Zhou, Nucleic Acids Res. DRMref: comprehensive reference map of drug resistance mechanisms in human cancer, 2023 Nov 20:gkad1087. doi: 10.1093/nar/gkad1087.

11. Kexin Huang, Xi Liu, Zhaocan Zhang, Tiangang Wang, Haixia Xu, Qingxuan Li, Yuhao Jia, Liyu Huang, Pora Kim**, Xiaobo Zhou, AgeAnnoMO: a knowledgebase of multi-omics annotation for animal aging, Nucleic Acids Res. 2023 Oct 18:gkad884. doi: 10.1093/nar/gkad884.

12. Yangyang Luo, Jingjing Guo, Jianguo Wen, Weiling Zhao, Kexin Huang, Yang Liu, Grant Wang, Ruihan Luo, Ting Niu, Yuzhou Feng, Haixia Xu, Pora Kim**, Xiaobo Zhou , StemDriver: a knowledgebase of gene functions for hematopoietic stem cell fate determination, Nucleic Acids Res. 2023 Nov 11:gkad1063. doi: 10.1093/nar/gkad1063.

13. Yuzhou Feng, Jiahao Yi, Lin Yang, Yanfei Wang, Jianguo Wen, Weiling Zhao, Pora Kim**, Xiaobo Zhou, COV2Var, a function annotation database of SARS-CoV-2 genetic variation, Nucleic Acids Res. 2023 Oct 28:gkad958. doi: 10.1093/nar/gkad958. (Co-corresponding)

14. Himansu Kumar, Lin-Ya Tang, Chengyuan Yang, Pora Kim***, FusionPDB: a knowledgebase of human Fusion Proteins. Nucleic Acids Res. 2023 Oct 23. https://doi.org/10.1093/nar/gkad920.

15. Himansu Kumar, Ruihan Luo, Jianguo Wen, Chengyuan Yang, Xiaobo Zhou, Pora Kim***, FusionNeoAntigen: a resource of fusion gene-specific neoantigens, Nucleic Acids Res. 2023 Oct 23:gkad922. doi: 10.1093/nar/gkad922. (Corresponding)

16. Pora Kim***, Himansu Kumar, Chengyuan Yang, Ruihan Luo, Jiajia Liu, Xiaobo Zhou, Systematic investigation of the homology sequences around the human fusion gene breakpoints in pan-cancer - bioinformatics study for a potential link to MMEJ. Briefings in Bioinformatics. 2023 Aug 26;bbad314. doi: 10.1093/bib/bbad314. (Corresponding)

17. Yuzhou Feng, Mengyuan Yang, Zhiwei Fan, Weiling Zhao, Pora Kim**, Xiaobo Zhou, COVIDanno, COVID-19 annotation in human. Frontiers in Microbiology. 2023 Jul 11;14:1129103. doi: 10.3389/fmicb.2023.1129103. (Co-corresponding)

18. Sijia Wu, Qiuping Xue, Mengyuan Yang, Yanfei Wang, Pora Kim**, Xiaobo Zhou**, Liyu Huang**, Genetic control of RNA editing in neurodegenerative disease, Brief Bioinform, 2023 Jan 21;bbad007. doi: 10.1093/bib/bbad007

19. Zhiwei Fan, Yangyang Luo, Huifen Lu, Tiangang Wang, YuZhou Feng, Weiling Zhao, Pora Kim**, Xiaobo Zhou, SPASCER: spatial transcriptomics annotation at single-cell resolution, Nucleic Acids Res. 2022 Oct 16:gkac889. doi: 10.1093/nar/gkac889

20. Kexin Huang, Hoaran Gong, Jingjing Guan, Lingxiao Zhang, Changbao Hu, Weiling Zhao, Liyu Huang, Wei Zhang, Pora Kim**, Xiaobo Zhou, AgeAnno: a knowledgebase of single-cell annotation of aging in human, Nucleic Acids Res. 2022 Oct 6:gkac847. doi: 10.1093/nar/gkac847.

21. Pora Kim***, Hua Tan, Jiajia Liu, Himansu Kumar, Xiaobo Zhou, FusionAI, a DNA-sequence-based deep learning protocol reduces the false positives of human fusion gene prediction, STAR Protoc. 2022 Feb 28;3(1):101185. doi: 10.1016/j.xpro.2022.101185. eCollection 2022 Mar 18.

22. Mengyuan Yang, Huifen Lu, Jiajia Liu, Sijia Wu, Pora Kim**, and Xiaobo Zhou, lncRNAfunc: a knowledgebase of lncRNA functional in human cancer, Nucleic Acids Res. doi.org/10.1093/nar/gkab1035, 2021 Nov 17 (Co-Corresponding)

23. Pora Kim***, Hua Tan, Jiajia Liu, Haeseung Lee, Hyesoo Jung, Himanshu Kumar, and Xiaobo Zhou, FusionGDB 2.0: fusion gene annotation updates aided by deep learning, Nucleic Acids Res. doi: 10.1093/nar/gkab1056, 2021 Nov 10 (Corresponding)

24. Pora Kim**, Hua Tan, Jiajia Liu, Mengyuan Yang, and Xiaobo Zhou, FusionAI: Predicting Fusion Breakpoint from DNA Sequence with Deep Learning, iScience, doi: 10.1016/j.isci.2021.103164, 2021 Oct 22 (Co-Corresponding)

25. Mengyuan Yang, Ke Yiya, Pora Kim**, and Xiaobo Zhou. ExonSkipAD provides the functional genomic landscape of exon skipping event in Alzheimer's disease. Briefings in Bioinformatics. 2021 Jan 26. doi: 10.1093/bib/bbaa438 (Co-Corresponding)

26. Sijia Wu, Mengyuan Yang, Pora Kim,** and Xiaobo Zhou. ADeditome provides the genomic landscape of RNA A-to-I editing in Alzheimer's disease. Briefings in Bioinformatics. 2021 Jan 6. doi: 10.1093/bib/bbaa384. (Co-Corresponding)

27. Pora Kim, Hanyang Li, Junmei Wang, Zhongming Zhao, Landscape of drug-resistance mutations in kinase regulatory hotspots. Briefings in Bioinformatics. 2020 Jun 8. doi: 10.1093/bib/bbaa108

28. Hua Tan, Pora Kim*, Peiqing Sun, Xiaobo Zhou, miRactDB characterizes miRNA-gene relation switch between normal and cancer tissues across pan-cancer. Briefings in Bioinformatics. Briefings in Bioinformatics. 2020 May 20. doi: 10.1093/bib/bbaa089. (Co-First)

29. Pora Kim**, Yiya Ke, and Xiaobo Zhou, FGviewer: an online visualization tool for functional features of human fusion genes. Nucleic Acids Research. 2020 May 18. doi: 10.1093/nar/gkaa364. (Co-Corresponding)

30. Pora Kim**, Mengyuan Yang, Yiya Ke, Weiling Zhao, Xiaobo Zhou**, ExonSkipDB: functional annotation of exon skipping event in human, Nucleic Acids Research, doi: 10.1093/nar/gkz917, 48(D1):D896-D907 (Co-Corresponding)

31. Pora Kim, Ye Eun Jang, Sanghyuk Lee, FusionScan: accurate prediction of fusion genes from RNA-Seq data, Genomics & Informatics, 17(3):e33, 2019

32. Pora Kim and Xiaobo Zhou, FusionGDB: fusion gene annotation DataBase, Nucleic Acids Research, 47(D1):D994-D1004, 2019 Jan 8

33. Theo A. Knijnenburg,Linghua Wang, Michael T. Zimmermann, Nyasha Chambwe, Galen F. Gao, Andrew D. Cherniack, Huihui Fan, Hui Shen, Gregory P. Way, Casey S. Greene, Yuexin Liu, Rehan Akbani,Bin Feng, Lawrence A. Donehower, Chase Miller, Yang Shen, Mostafa Karimi, Haoran Chen, Pora Kim, Peilin Jia, Eve Shinbrot, Shaojun Zhang, Jianfang Liu, Hai Hu, Matthew H. Bailey, Christina Yau, Denise Wolf, Zhongming Zhao, John N. Weinstein, Lei Li, Li Ding, Gordon B. Mills, Peter W. Laird, David A. Wheeler, Ilya Shmulevich, The Cancer Genome Atlas Research Network, Raymond J. Monnat, Jr.,Yonghong Xiao, Chen Wang, Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas, Cell Reports, 23(1):239-254, 2018 Apr 3

34. Hua Sun, Pora Kim, Peilin Jia, Ae Kyung Park, Han Liang and Zhongming Zhao, Distinct telomere length and molecular signatures in seminoma and non-seminoma of testicular germ cell tumor, Briefings in Bioinformatics, doi: 10.1093/bib/bby020, 2018 Mar 20

35. Pora Kim, Leomar Y. Ballester and Zhongming Zhao, Domain retention in transcription factor fusion genes and its biological and clinical implications: a pan-cancer study, Oncotarget, 8(66):110103-110117, 2017 Nov 24

36. Pora Kim, Aekyung Park, Guangchun Han, Hua Sun, Peilin Jia, and Zhongming Zhao, TissGDB: tissue-specific gene database in cancer, Nucleic Acids Research, 46(D1):D1031-D1038, 2018 Jan 4

37. Pora Kim, Peilin Jia, Zhongming Zhao, Kinase impact assessment in the landscape of fusion genes that retain kinase domains: a pan-cancer study, Briefings in Bioinformatics, 19(3):450-460, 2018 May 1

38. Pora Kim, Junfei Zhao, Lu Pinyi, and Zhongming Zhao, mutLBSgeneDB: mutated Ligand Binding Site gene DataBase, Nucleic Acids Research, 45(D1):D256-D263, 2017 Jan 4

39. Myunggyo Lee, Kyubum Lee, Namhee Yu, Insu Jang, Ikjung Choi, Pora Kim, Ye Eun Jang, Byounggun Kim, Sunkyu Kim, Byungwook Lee, Jaewoo Kang, and Sanghyuk Lee, ChimerDB 3.0: an enhanced database for fusion genes from cancer transcriptome and literature data mining, Nucleic Acids Research, 45(D1):D784-D789, 2017 Jan 4

40. Hae Young Yoo, Pora Kim*, Won Seong Kim, Seung Ho Lee, Sangok Kim, So Young Kang, Hye Yoon Jang, Jong-Eun Lee, Jaesang Kim, Seok Jin Kim, Young Hyeh Ko, and Sanghyuk Lee, Frequent CTLA4-CD28 Gene Fusion In Diverse Types Of T Cell Lymphoma, Haematologica, 101(6):757-63, 2016 Jun (Co-First)

41. Min Zhao, Pora Kim, Ramkrishna Mitra, Junfei Zhao, and Zhongming Zhao, TSGgene2.0: a literature-based database of tumor suppressor genes for pan-cancer analysis, Nucleic Acids Research, 44(D1):D1023-31, 2016 Jan 4.

42. Pora Kim*, Feixiong Cheng, Junfei Zhao, and Zhongming Zhao, ccmGDB: a database for cancer cell metabolism genes, Nucleic Acids Research, 44(D1):D959-68, 2016 Jan 4

43. Yeonjoo Jung, Seunghui Yong, Pora Kim, Hee-Young Lee, Yeonhwa Jung, Juhee Keum, Sanghyuk Lee, Jhingook Kim, and Jaesang Kim, VAMP2-NRG1 fusion gene is a novel oncogenic driver of non-small cell adenocarcinoma, Journal of Thoracic Oncology, 10(7)1107-11, 2015 Jul

44. Timothy O’Brien, Peilin Jia, Junfeng Xia, Uma Saxena, Hailing Jin, Huy Vuong, Pora Kim, Qingguo Wang, Martin Aryee, Mari Mino-Kenudson, Jeffrey Engelman, Long P. Le, A. John Iafrate, Rebecca S. Heist, William Pao, and Zhongming Zhao, Inconsistency and features of single nucleotide variants detected in whole exome sequencing versus transcriptome sequencing: A case study in lung cancer, Methods, S1046-2023(15)00162-0, 2015 Jul 15

45. Sang Cheol Kim, Yeonjoo Jung, Jinah Park, Sooyoung Cho, Chaehwa Seo, Jaesang Kim, Pora Kim, Jehwan Park, Jihae Seo, Jiwoong Kim, Seongjin Park, Insu Jang, Namshin Kim, Jin Ok Yang, Byungwook Lee, Kyoohyoung Rho, Yeonhwa Jung, Juhee Keum, Jinseon Lee, Jungho Han, Sangeun Kang, Sujin Bae, So-Jung Choi, Sujin Kim, Jong-Eun Lee, Wankyu Kim, Jhingook Kim, and Sanghyuk Lee, A high-dimensional, deep-sequencing study of lung adenocarcinoma in female never-smokers, PLoS One, 8(2):e55596, 2013

46. Yeonjoo Jung, Pora Kim*, Yeonhwa Jung, Juhee Keum, Soon-Nam Kim, Yong Soo Choi, In-Gu Do, Jinseon Lee, So-Jung Choi, Sujin Kim, Jong-Eun Lee, Jhingook Kim, Sanghyuk Lee, and Jaesang Kim, Discovery of ALK-PTPN3 gene fusion from human non-small cell lung carcinoma cell line using next generation RNA sequencing, Genes, Chromosomes and Cancer, 51(6), 590-597, 2012 Jun (Co-First)

47. Pora Kim, Suhyeon Yoon, Namshin Kim, Sanghyun Lee, Minjeong Ko, Haeseung Lee, Hyunjung Kang, Jaesang Kim, and Sanghyuk Lee, ChimerDB 2.0 - a knowledgebase for fusion genes updated, Nucleic Acids Research, 38, D81-85, 2010 Jan

48. Pora Kim, S. Jun Oh, and Sanghyuk Lee, Deducing isoform abundance from exon junction microarray, Genomics & Informatics, 4(1), 33-39, 2006

49. Pora Kim, Namshin Kim, Younghee Lee, Bumjin Kim, Youngah Shin, and Sanghyuk Lee, ECgene: genome annotation for alternative splicing, Nucleic Acids Research, 33, D75-79, 2005 Jan 1