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Last modified at 2022-12-07T12:59:38+09:00


Lee, Kanggeun, Dongbin Cho, Jinho Jang, Kang Choi, Hyoung-oh Jeong, Jiwon Seo, Won-Ki Jeong, and Semin Lee. "RAMP: response-aware multi-task learning with contrastive regularization for cancer drug response prediction." Briefings in Bioinformatics (2022).

Jeong, Hyoung-oh, Hayoon Lee, Hyemin Kim, Jinho Jang, Seunghoon Kim, Taejoo Hwang, David Whee-Young Choi et al. "Cellular plasticity and immune microenvironment of malignant pleural effusion are associated with EGFR-TKI resistance in non–small-cell lung carcinoma." Iscience 25, no. 11 (2022): 105358.

Yoon, Meesun, Hyo Kyung Lee, Eun Young Park, Jin Hee Kim, Jong Hoon Lee, Young Seok Kim, Hak Jae Kim et al. "Randomized multicenter phase II trial of prophylactic irradiation of para‐aortic lymph nodes in advanced cervical cancer according to tumor hypoxia: Korean Radiation Oncology Group (KROG 07‐01) study." International Journal of Cancer (2022).

Ju, Min Kyung, Joo Rak Lee, Yeonsong Choi, Seon Young Park, Hee Jung Sul, Hee Jin Chung, Soyeong An, et al. "PWWP2B Promotes DNA End Resection and Homologous Recombination." EMBO reports, 2022.


Lee, Eungyung, Suhyun Park, Sunwoo Um, Seunghoon Kim, Jaewoong Lee, Jinho Jang, Hyoung-oh Jeong, Jonghyun Shin, Jihoon Kang, Semin Lee, and Taesung Jeong. 2021. "Microbiome of Saliva and Plaque in Children According to Age and Dental Caries Experience" Diagnostics 11, no. 8: 1324.

Kim, Miok, Yong Ki Min, Jinho Jang, Hyejin Park, Semin Lee, and Chang Hoon Lee. "Single-cell RNA sequencing reveals distinct cellular factors for response to immunotherapy targeting CD73 and PD-1 in colorectal cancer." Journal for ImmunoTherapy of Cancer 9, no. 7 (2021): e002503.

Sohn, Sung-Hwa, Hee Jung Sul, Yeonsong Choi, Semin Lee, Bum Jun Kim, Hyeong Su Kim, Youngho Koh, and Dae Young Zang. "An integrated mRNA–microRNA regulatory network identified INHBA and has-miR-135a-5p as predictors of gastric cancer recurrence." Molecular & Cellular Toxicology (2021): 1-8.


Kim, Ji-Yeon, Hyoung-Oh Jeong, Dae Seog Heo, Bhumsuk Keam, Kyung Chul Moon, Cheol Kwak, Jinho Jang et al. "Treatment strategy for papillary renal cell carcinoma type 2: a case series of seven patients treated based on next generation sequencing data." Annals of Translational Medicine 8, no. 21 (2020).

Kim, Eun-Hye, Seunghoon Kim, Hyun-Joo Kim, Hyoung-oh Jeong, Jaewoong Lee, Jinho Jang, Ji-Young Joo et al. "Prediction of Chronic Periodontitis Severity Using Machine Learning Models Based On Salivary Bacterial Copy Number." Frontiers in Cellular and Infection Microbiology 10 (2020): 698.

Cheon, Chong Kun, Yeoun Joo Lee, Sukdong Yoo, Jung Hee Lee, Jeong Eun Lee, Hyun Ji Kim, Yeonsong Choi, Semin Lee, and Ju Young Yoon. "Delineation of the genetic and clinical spectrum, including candidate genes, of monogenic diabetes: a multicenter study in South Korea." Journal of Pediatric Endocrinology and Metabolism 1, no. ahead-of-print (2020).

Hwang, Taejoo, Shelley Reh, Yerkin Dunbayev, Yi Zhong, Yoko Takata, Jianjun Shen, Kevin M. McBride et al. "Defining the mutation signatures of DNA polymerase θ in cancer genomes." NAR cancer 2, no. 3 (2020): zcaa017.

Jeon, Sungwon, Youngjune Bhak, Yeonsong Choi, Yeonsu Jeon, Seunghoon Kim, Jaeyoung Jang, Jinho Jang et al. "Korean Genome Project: 1094 Korean personal genomes with clinical information." Science Advances 6, no. 22 (2020): eaaz7835.

Weber, Jessica A., Seung Gu Park, Victor Luria, Sungwon Jeon, Hak-Min Kim, Yeonsu Jeon, Youngjune Bhak, Semin Lee et al. "The whale shark genome reveals how genomic and physiological properties scale with body size." Proceedings of the National Academy of Sciences 117, no. 34 (2020): 20662-20671.

Kim, Sangin, Nalae Kang, Su Hyung Park, James Wells, Taejoo Hwang, Eunjin Ryu, Byung-gyu Kim et al. "ATAD5 restricts R-loop formation through PCNA unloading and RNA helicase maintenance at the replication fork." Nucleic acids research 48, no. 13 (2020): 7218-7238.

Choi, Sun Sil, Sang Kwon Lee, Joong Kwan Kim, Hye-Kyung Park, Eujin Lee, Jinho Jang, Yo Han Lee et al. "Flightless-1 inhibits ER stress-induced apoptosis in colorectal cancer cells by regulating Ca 2+ homeostasis." Experimental & Molecular Medicine (2020): 1-11.

Lim, Minji, Juhee Park, Alarice C. Lowe, Hyoung-oh Jeong, Semin Lee, Hee Chul Park, Kyusang Lee, Gwang Ha Kim, Mi-Hyun Kim, and Yoon-Kyoung Cho. "A lab-on-a-disc platform enables serial monitoring of individual CTCs associated with tumor progression during EGFR-targeted therapy for patients with NSCLC." Theranostics 10, no. 12 (2020): 5181.

Seidualy, Madina, Asta Blazyte, Sungwon Jeon, Youngjune Bhak, Yeonsu Jeon, Jungeun Kim, Anders Eriksson, Semin Lee et al. "Decoding a highly mixed Kazakh genome." Human genetics 139, no. 5 (2020): 557-568.

Lee, Yu Geon, Yeji Nam, Kyeong Jin Shin, Sora Yoon, Weon Seo Park, Jae Young Joung, Jeong Kon Seo, Semin Lee et al. "Androgen-induced expression of DRP1 regulates mitochondrial metabolic reprogramming in prostate cancer." Cancer Letters 471 (2020): 72-87.


Kim, Hui-Su, Sungwon Jeon, Changjae Kim, Yeon Kyung Kim, Yun Sung Cho, Jungeun Kim, Asta Blazyte, Andrea Manica, Semin Lee, and Jong Bhak. "Chromosome-scale assembly comparison of the Korean Reference Genome KOREF from PromethION and PacBio with Hi-C mapping information." GigaScience 8, no. 12 (2019): giz125.

Lee, Kanggeun, Hyoung-oh Jeong, Semin Lee, and Won-Ki Jeong. "CPEM: Accurate cancer type classification based on somatic alterations using an ensemble of a random forest and a deep neural network." Scientific reports 9, no. 1 (2019): 1-9.

Bhak, Youngjune, Hyoung-oh Jeong, Yun Sung Cho, Sungwon Jeon, Juok Cho, Jeong-An Gim, Yeonsu Jeon et al. "Depression and suicide risk prediction models using blood-derived multi-omics data." Translational psychiatry 9, no. 1 (2019): 1-8.

Zhang, Yiqun, Lixing Yang, Melanie Kucherlapati, Angela Hadjipanayis, Angeliki Pantazi, Christopher A. Bristow, Eunjung Alice Lee et al. "Global impact of somatic structural variation on the DNA methylome of human cancers." Genome biology 20, no. 1 (2019): 209.

Yang, Lixing, Su Wang, Jake June-Koo Lee, Semin Lee, Eunjung Lee, Eve Shinbrot, David A. Wheeler, Raju Kucherlapati, and Peter J. Park. "An enhanced genetic model of colorectal cancer progression history." Genome biology 20, no. 1 (2019): 1-17.


Park, Jung-Eun, Jinho Jang, Eun Ji Lee, Su Jung Kim, Hyun Ju Yoo, Semin Lee, and Min-Ji Kang. "Potential involvement of Drosophila flightless-1 in carbohydrate metabolism." BMB reports 51, no. 9 (2018): 462.

Zhang, Yiqun, Lixing Yang, Melanie Kucherlapati, Fengju Chen, Angela Hadjipanayis, Angeliki Pantazi, Christopher A. Bristow, Semin Lee et al. "A pan-cancer compendium of genes deregulated by somatic genomic rearrangement across more than 1,400 cases." Cell reports 24, no. 2 (2018): 515-527.

Fan, Jean, Hae-Ock Lee, Soohyun Lee, Da-eun Ryu, Semin Lee, Catherine Xue, Seok Jin Kim et al. "Linking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq data." Genome research 28, no. 8 (2018): 1217-1227.

Phi, Ji Hoon, Ae Kyung Park, Semin Lee, Seung Ah Choi, In-Pyo Baek, Pora Kim, Eun-Hye Kim et al. "Genomic analysis reveals secondary glioblastoma after radiotherapy in a subset of recurrent medulloblastomas." Acta neuropathologica 135, no. 6 (2018): 939-953.


Kim, Jungeun, Jessica A. Weber, Sungwoong Jho, Jinho Jang, JeHoon Jun, Yun Sung Cho, Hak-Min Kim et al. "KoVariome: Korean National Standard Reference Variome database of whole genomes with comprehensive SNV, indel, CNV, and SV analyses." Scientific reports 8, no. 1 (2018): 1-14.

Cho, Yun Sung, Hyunho Kim, Hak-Min Kim, Sungwoong Jho, JeHoon Jun, Yong Joo Lee, Kyun Shik Chae, Semin Lee et al. "An ethnically relevant consensus Korean reference genome is a step towards personal reference genomes (vol 7, 13637, 2016)." NATURE COMMUNICATIONS 8 (2017).

Robertson, A. Gordon, Juliann Shih, Christina Yau, Ewan A. Gibb, Junna Oba, Karen L. Mungall, Julian M. Hess, Semin Lee et al. "Integrative analysis identifies four molecular and clinical subsets in uveal melanoma." Cancer cell 32, no. 2 (2017): 204-220.

Zhang, Yiqun, Patrick Kwok-Shing Ng, Melanie Kucherlapati, Fengju Chen, Yuexin Liu, Yiu Huen Tsang, Guillermo de Velasco, Semin Lee et al. "A pan-cancer proteogenomic atlas of PI3K/AKT/mTOR pathway alterations." Cancer cell 31, no. 6 (2017): 820-832.

Cancer Genome Atlas Research Network (Semin Lee). "Integrated genomic and molecular characterization of cervical cancer." Nature 543, no. 7645 (2017): 378-384.

Cancer Genome Atlas Research Network (Semin Lee). "Integrated genomic characterization of oesophageal carcinoma." Nature 541, no. 7636 (2017): 169-175.


Cho, Yun Sung, Hyunho Kim, Hak-Min Kim, Sungwoong Jho, JeHoon Jun, Yong Joo Lee, Kyun Shik Chae, Semin Lee et al. "An ethnically relevant consensus Korean reference genome is a step towards personal reference genomes." Nature communications 7, no. 1 (2016): 1-13.

Kim, Soonok, Yun Sung Cho, Hak-Min Kim, Oksung Chung, Hyunho Kim, Sungwoong Jho, Hong Seomun, Semin Lee et al. "Comparison of carnivore, omnivore, and herbivore mammalian genomes with a new leopard assembly." Genome biology 17, no. 1 (2016): 1-12.

Xi, Ruibin, Semin Lee, Yuchao Xia, Tae-Min Kim, and Peter J. Park. "Copy number analysis of whole-genome data using BIC-seq2 and its application to detection of cancer susceptibility variants." Nucleic acids research 44, no. 13 (2016): 6274-6286.

Ceccarelli, M., F. P. Barthel, T. M. Malta, T. S. Sabedot, S. R. Salama, B. A. Murray, O. Morozova et al. "TCGA Research Network., Noushmehr H, Iavarone A, Verhaak RG. Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma." Cell 164, no. 3 (2016): 550-63.

Nam, Jae-Yong, Nayoung KD Kim, Sang Cheol Kim, Je-Gun Joung, Ruibin Xi, Semin Lee, Peter J. Park, and Woong-Yang Park. "Evaluation of somatic copy number estimation tools for whole-exome sequencing data." Briefings in bioinformatics 17, no. 2 (2016): 185-192.


De Los Angeles, Alejandro, Francesco Ferrari, Yuko Fujiwara, Ronald Mathieu, Soohyun Lee, Semin Lee, Ho-Chou Tu et al. "Failure to replicate the STAP cell phenomenon." Nature 525, no. 7570 (2015): E6-E9.

Alioto, Tyler S., Ivo Buchhalter, Sophia Derdak, Barbara Hutter, Matthew D. Eldridge, Eivind Hovig, Lawrence E. Heisler, Semin Lee et al. "A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing." Nature communications 6, no. 1 (2015): 1-13.

Abeshouse, Adam, Jaeil Ahn, Rehan Akbani, Adrian Ally, Samirkumar Amin, Christopher D. Andry, Matti Annala, Semin Lee et al. "The molecular taxonomy of primary prostate cancer." Cell 163, no. 4 (2015): 1011-1025.

Lodato, Michael A., Mollie B. Woodworth, Semin Lee, Gilad D. Evrony, Bhaven K. Mehta, Amir Karger, Soohyun Lee et al. "Somatic mutation in single human neurons tracks developmental and transcriptional history." Science 350, no. 6256 (2015): 94-98.

De Los Angeles, Alejandro, Francesco Ferrari, Yuko Fujiwara, Ronald Mathieu, Soohyun Lee, Semin Lee, Ho-Chou Tu et al. "Failure to replicate the STAP cell phenomenon." Nature 525, no. 7570 (2015): E6-E9.

Akbani, Rehan, Kadir C. Akdemir, B. Arman Aksoy, Monique Albert, Adrian Ally, Samirkumar B. Amin, Harindra Arachchi, Semin Lee et al. "Genomic classification of cutaneous melanoma." Cell 161, no. 7 (2015): 1681-1696.

Cancer Genome Atlas Research Network (Semin Lee). "Comprehensive, integrative genomic analysis of diffuse lower-grade gliomas." New England Journal of Medicine 372, no. 26 (2015): 2481-2498.

Kapanidou, Maria, Semin Lee, and Victor M. Bolanos-Garcia. "BubR1 kinase: protection against aneuploidy and premature aging." Trends in molecular medicine 21, no. 6 (2015): 364-372.

Cancer Genome Atlas Network (Semin Lee). "Comprehensive genomic characterization of head and neck squamous cell carcinomas." Nature 517, no. 7536 (2015): 576-582.


Agrawal, Nishant, Rehan Akbani, B. áArman Aksoy, Adrian Ally, Harindra Arachchi, SylviaáL Asa, J. áTodd Auman, Semin Lee et al. "Integrated genomic characterization of papillary thyroid carcinoma." Cell 159, no. 3 (2014): 676-690.

Lee, Semin, and Victor M. Bolanos-Garcia. "The dynamics of signal amplification by macromolecular assemblies for the control of chromosome segregation." Frontiers in Physiology 5 (2014): 368.

Parfenov, Michael, Chandra Sekhar Pedamallu, Nils Gehlenborg, Samuel S. Freeman, Ludmila Danilova, Christopher A. Bristow, Semin Lee et al. "Characterization of HPV and host genome interactions in primary head and neck cancers." Proceedings of the National Academy of Sciences 111, no. 43 (2014): 15544-15549.

Davis, Caleb F., Christopher J. Ricketts, Min Wang, Lixing Yang, Andrew D. Cherniack, Hui Shen, Christian Buhay, Semin Lee et al. "The somatic genomic landscape of chromophobe renal cell carcinoma." Cancer cell 26, no. 3 (2014): 319-330.

Cancer Genome Atlas Research Network (Semin Lee). "Comprehensive molecular profiling of lung adenocarcinoma." Nature 511, no. 7511 (2014): 543-550.

Cancer Genome Atlas Research Network (Semin Lee), and Analysis Working Group. "Comprehensive molecular characterization of gastric adenocarcinoma." Nature 513, no. 7517 (2014): 202-209.

Cancer Genome Atlas Research Network (Semin Lee). "Comprehensive molecular characterization of urothelial bladder carcinoma." Nature 507, no. 7492 (2014): 315-322.


Brennan, Cameron W., Roel GW Verhaak, Aaron McKenna, Benito Campos, Houtan Noushmehr, Sofie R. Salama, Siyuan Zheng, Semin Lee et al. "The somatic genomic landscape of glioblastoma." Cell 155, no. 2 (2013): 462-477.

Weinstein, John N., Eric A. Collisson, Gordon B. Mills, Kenna R. Mills Shaw, Brad A. Ozenberger, Kyle Ellrott, Ilya Shmulevich, Chris Sander, Joshua M. Stuart, and Cancer Genome Atlas Research Network (Semin Lee). "The cancer genome atlas pan-cancer analysis project." Nature genetics 45, no. 10 (2013): 1113.

Levine, Douglas A., and Cancer Genome Atlas Research Network (Semin Lee). "Integrated genomic characterization of endometrial carcinoma." Nature 497, no. 7447 (2013): 67-73.


Xi, Ruibin, Semin Lee, and Peter J. Park. "A survey of copy‐number variation detection tools based on high‐throughput sequencing data." Current protocols in human genetics 75, no. 1 (2012): 7-19.

Cancer Genome Atlas Research Network (Semin Lee). "Comprehensive genomic characterization of squamous cell lung cancers." Nature 489, no. 7417 (2012): 519.

Cancer Genome Atlas Network (Semin Lee). "Comprehensive molecular characterization of human colon and rectal cancer." Nature 487, no. 7407 (2012): 330.


Lee, Semin, Philippe Thebault, Luca Freschi, Sylvie Beaufils, Tom L. Blundell, Christian R. Landry, Victor M. Bolanos-Garcia, and Sabine Elowe. "Characterization of spindle checkpoint kinase Mps1 reveals domain with functional and structural similarities to tetratricopeptide repeat motifs of Bub1 and BubR1 checkpoint kinases." Journal of Biological Chemistry 287, no. 8 (2012): 5988-6001.


Lee, Semin, Alan Brown, William Ross Pitt, Alicia Perez Higueruelo, Sungsam Gong, George Richard Bickerton, Adrian Schreyer, Duangrudee Tanramluk, Alison Baylay, and Tom Leon Blundell. "Structural interactomics: informatics approaches to aid the interpretation of genetic variation and the development of novel therapeutics." Molecular Biosystems 5, no. 12 (2009): 1456-1472.

Gong, Sungsam, Catherine L. Worth, G. Richard J. Bickerton, Semin Lee, Duangrudee Tanramluk, and Tom L. Blundell. "Structural and functional restraints in the evolution of protein families and superfamilies." Biochemical Society Transactions 37, no. 4 (2009): 727-733.

Lee, Semin, and Tom L. Blundell. "Ulla: a program for calculating environment-specific amino acid substitution tables." Bioinformatics 25, no. 15 (2009): 1976-1977.

Lee, Semin, and Tom L. Blundell. "BIPA: a database for protein–nucleic acid interaction in 3D structures." Bioinformatics 25, no. 12 (2009): 1559-1560.


Worth, Catherine L., G. Richard J. Bickerton, Adrian Schreyer, Julia R. Forman, Tammy MK Cheng, Semin Lee, Sungsam Gong, David F. Burke, and Tom L. Blundell. "A structural bioinformatics approach to the analysis of nonsynonymous single nucleotide polymorphisms (nsSNPs) and their relation to disease." Journal of bioinformatics and computational biology 5, no. 06 (2007): 1297-1318.


Park, Daeui, Semin Lee, Dan Bolser, Michael Schroeder, Michael Lappe, Donghoon Oh, and Jong Bhak. "Comparative interactomics analysis of protein family interaction networks using PSIMAP (protein structural interactome map)." Bioinformatics 21, no. 15 (2005): 3234-3240.