Fusion Gene Studies
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bullet point Publication relating to the fusion genes

2024
- Himansu Kumar, Pora Kim***, Artificial intelligence in fusion protein three-dimensional structure prediction: Review and perspective, Clinical and Translational Medicine. 2024 Aug, doi.org/10.1002/ctm2.1789.
- 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.
- 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.
- 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.

2023
- 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.

2022
- Pora Kim***, Hua Tan, Jiajia Liu, Haeseung Lee, Hyesoo Jung, Himanshu Kumar, Xiaobo Zhou, FusionGDB 2.0: fusion gene annotation updates aided by deep learning, Nucleic Acids Research. 2022 Jan 7;50(D1):D1221-D1230. doi: 10.1093/nar/gkab1056.
- 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.

2021
- Pora Kim**, Hua Tan, Jiajia Liu, Mengyuan Yang, Xiaobo Zhou, FusionAI: Predicting fusion breakpoint from DNA sequence with deep learning, iScience2021 Sep 25;24(10):103164. doi: 10.1016/j.isci.2021.103164. eCollection 2021 Oct 22.

2020
- Pora Kim, Hanyang Li, Junmei Wang, Zhongming Zhao, Landscape of drug-resistance mutations in kinase regulatory hotspots. Briefings in Bioinformatics. doi: 10.1093/bib/bbaa108. 2020 Jun 8.
- Pora Kim**, Yiya Ke, and Xiaobo Zhou, FGviewer: an online visualization tool for functional features of human fusion genes. Nucleic Acids Research. 48(W1):W313-W320, July 2020.

2019
- Pora Kim, Ye Eun Jang, Sanghyuk Lee, FusionScan: accurate prediction of fusion genes from RNA-Seq data, Genomics & Informatics, 17(3):e33, 2019.
- Pora Kim and Xiaobo Zhou, FusionGDB: fusion gene annotation DataBase, Nucleic Acids Research, 47(D1):D994-D1004, January 2019.

2018
- Ji Hoon Phi, Ae Kyung Park, Semin Lee, Seung Ah Choi, In-Pyo Baek, Pora Kim, Eun-Hye Kim, Hee Chul Park, Byung Chul Kim, Jong Bhak, Sung-Hye Park, Ji Yeoun Lee, Kyu‑Chang Wang, Dong-Seok Kim, Kyu Won Shim, Se Hoon Kim, Chae‑Yong Kim, Seung-Ki Kim, Genomic analysis reveals secondary glioblastoma after radiotherapy in a subset of recurrent medulloblastomas, Acta Neuropathologica, 135(6):939-953, June 2018.
- 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, April 2018.

2017
- 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, November 2017.
- 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, January 2018.
- 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, May 2018.
- 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, January 2017.

2016
- 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, June 2016.

2015
- 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, July 2015.

2013
- 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.

2012
- 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, June 2012.

2010
- 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, January 2010.

2006
- Namshin Kim, Pora Kim, Seungyoon Nam, Seokmin Shin, and Sanghyuk Lee, ChimerDB - a knowledgebase for fusion sequences, Nucleic Acids Research, 34, D21-24, January 2006.

2005
- 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, January 2005.