BIOINFORMATICS & GENOMICS

A hybrid transcriptome assembly reveals coding and non-coding landscapes in Drosophila hemocytes, Kyung-Tae Lee*, Bumsik Cho*, Daewon Lee, Sunggyu Yoon, Hobin Do, Jaeseong Han, Ms. Hansoll Na, Sangho Yoon, Mingyu Shin, Jiwon Shim#, Jin-Wu Nam#  In revision.

Daewon Lee, Ferdinand Koranteng, Nuri Cha, Sangho Yoon, Kyung-Tae Lee, Jin-Wu Nam, Young V. Kwon, Jiwon Shim, Mitochondrial metabolic remodeling drives innate immune activation in Drosophila hemocyte, bioRxiv 2026.03.23.713618, 2026.

JE Park, MT Nguyen, J Kim, CH Lee, JW Nam, H Chung, MK Park, JY Lee, NSD family-mediated H3K36 methylation in human cancer: mechanisms and therapeutic opportunities, Biomedicines 13 (11), 2749, 2025.

Seokju Park*, Sung-Ho Park*, Jin-Seon Oh, Yung-Kyun Noh, Junho K Hur#, Jin-Wu Nam#, shRNAI: a deep neural network for the design of highly potent shRNAs, Molecular Therapy Nucleic Acid 36(4):102738, 2025. Dec. 9.

Yeolhoe Kim*, Kyung-Tae Lee*, ...., Jin Won Cho, Eungene C. Yi, Jin-Wu Nam#, Won-Ho Yang#, O-GlcNAcylation of NONO regulates paraspeckle component assembly and contributes to colon cancer cell proliferation, Cell Death Discovery, 11:234, 2025

Seo-Won Choi and Jin-Wu Nam, Optimal design of synthetic circular RNAs. Experimental & Molecular Medicine, 2024. doi.org/10.1038/s12276-024-01251-w

Kyungtae Lee*, Inez K.A. Pranoto*, Soon-Young Kim,  Hee-Joo Choi, Ngoc Bao To, Hansong Chae, Jeong-Yeon Lee, Jung-Eun Kim, Young Kwon#, and Jin-Wu Nam# Comparative Interactome Analysis of α-arrestin Families in Human and Drosophila, eLife, 2024. Jan. https://doi.org/10.7554/eLife.88328.4

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Sangho Yoon and Jin-Wu Nam, Clustering malignant cell states using universally variable genes, Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad460.

Sang-Ho Yoon, Bumsik Cho, Daewon Lee, Hanji Kim, Jiwon Shim#, and Jin-Wu Nam#. Molecular Traces of Drosophila Hemocyte Evolution, Plos Genetics, 19(12):e1011077, 2023.12.

Dohun Yi, Jin-Wu Nam#, and Hyobin Jeong#. Toward functional interpretation of somatic structural variations: bulk and single-cell approaches.  Briefings in Bioinformatics, bbad297, 2023.

Jang-il Sohn*, Min-Hak Choi*, Dohun Yi*, A Vipin Menon, Yeon Jeong Kim, Junehawk Lee, Jung Woo Park, Sungkyu Kyung, Seung-Ho Shin, Byunggook Na, Je-Gun Joung, Sungroh Yoon, Young Seok Ju, Min Sun Yeom, Youngil Koh, Sung-Soo Yoon, Daehyun Baek, Tae-Min Kim, and Jin-Wu Nam, Ultrafast prediction of somatic structural variations by filtering out reads matched to pan-genome k-mer sets. Nat. Biomed. Eng 7, 853–866, 2023.   Nature Community Blog

*Highlight: Nature Biomed. Eng. https://www.nature.com/articles/s41551-023-01039-9

Seokju Park*, Hee Doo Yang*, Jwa-Won Seo, Jin-Wu Nam#, and Sukwoo Nam#. hnRNPC induces isoform shifts in miR-21-5p leading to cancer development, EMM 54:812–824 2022

Eun-Gyeong Park, Sung-Jin Pyo, Youixi Cui, Sang-Ho Yoon, and Jin-Wu Nam. Tumor Immune Microenvironment lncRNAs, Briefings in Bioinfo. 23(1):bbab504, 2022

Sukjun Kim, Soyoung Kim, Hee Ryung Chang, Doyeon Kim, Junehee Park, Narae Son, Joori Park, Minhyuk Yoon, Gwangung Chae, Young-Kook Kim, V. Narry Kim, Yoon Ki Kim, Jin-Wu Nam, Chanseok Shin#, and Daehyun Baek#. The regulatory impact of RNA-binding proteins on microRNA targeting, Nature Communs. 12:5057, 2021.

Sang-Ho Yoon , Seo-Won Choi , Suk Woo Nam , Kyoung Bun Lee#, and Jin-Wu Nam#. Preoperative immune landscape predisposes adverse outcomes in hepatocellular carcinoma patients with liver transplantation, npj Precision Oncology 5:27, 2021.

Eunkyeong Jang, Somi Cho, Sungjin Pyo, Jin-Wu Nam, Jeehee Youn. An inflammatory loop between spleen-derived myeloid cells and CD4+ T cells leads to accumulation of long-lived plasma cells that exacerbates lupus autoimmunity, Frontiers In Immunology, 12:631472, 2021 Feb-11.

Bumsik Cho*, Sang-Ho Yoon*, Daewon Lee, Ferdinand Koranteng, Sudhir Gopal Tattikota, Nuri Cha, Mingyu Shin, Hobin Do, Yanhui Hu, Sue Young Oh, Seok Joon Moon, Norbert Perrimon, Jin-Wu Nam#, Jiwon Shim#. Single-cell transcriptome maps of myeloid blood cell lineages in Drosophila, Nature Comm., 11:4483, 2020.

Vipin Menon, Jangil Sohn, and Jin-Wu Nam. CGD: Comprehensive Guide Designer for CRISPR-Cas Systems, Computational and Structural Biotechnology Journal, 18:814-820, 2020.

My Kieu Ha, Sook Jin Kwon, Jang‐Sik Choi, Nguyen Thanh Nguyen, Jaewoo Song, Yangsoon Lee, Young‐Eun Kim, Incheol Shin, Jin‐Wu Nam, Tae Hyun Yoon. Mass Cytometry and Single‐Cell RNA‐seq Profiling of the Heterogeneity in Human Peripheral Blood Mononuclear Cells Interacting with Silver Nanoparticles, Small, 16(21):, 2020. 

Sudhir Gopal Tattikpta, Yanhui Hu, Yifang Liu, Bumsik Cho, Vibtor Barrera, Michael Steinbaugh, Sang-Ho Yoon, Aram Comjean, Fangge Li, Franz Dervis, Ruei-Jiun Hung, Jin-Wu Nam, Shannan Ho Sui, Jiwon Shim, Norbert Perrimon. A Single-cell survey of Drosophila blood, elife, 9:e54818, 2020.

Bo-Hyun You*, Jung-Ho Yoon*, Hoin Kang, Eun Kyung Lee, Sang Kil Lee#, and Jin-Wu Nam#. HERES, a IncRNA that Regulates Canonical and Noncanonical Wnt Signaling Pathways via Interaction with EZH2, PNAS, 116(49):24620-24629, 2019. 

Krishnamoorthy Srikanth, Nam-Young Kim, Woncheoul Park, Jae-Min Kim, Kwon-Do Kim, Kyung-Tai Lee, Ju-Hwan Son, Han-Ha Chai, Jung-Woo Choi, Gul-Won Jang, Heebal Kim, Youn-Chul Ryu, Jin-Wu Nam, Jong-Eun Park, Jun-Mo Kim & Dajeong Lim. Comprehensive genome and transcriptome analyses reveal genetic relationship, selection signature, and transcriptome landscape of small-sized Korean native Jeju, Scientific Reports, 9(1):16672, 2019. 

Jun-Bean Park, Jae-Hoon Choi, Jin-Wu Nam, Hyung-Kwan Kim, Yun-Sang Lee, Jae Min Jeong, Yong-Jin Kim, Jin Chul Paeng and Seung-Pyo Lee. Assesment of inflammation in pulmonary artery hypertension by 68Ga-Mannosylated Human serum  albumin, American journal of Respiratory and Critical Care Medicine, 201(1):95-106, 2020. 

Jeongyoon Park*, Jwa-Won Seo*, Narae Ahn, Seokju Park, Jungwook Hwang#, and Jin-Wu Nam#.UPF1/SMG7-dependent MicroRNA-mediated Gene Regulation, Nature Communications, 10(1):4181, 2019. 

Hyeon Lee*, Rama Gopalappa, Hongjae Sunwoo*, Seowon Choi, Suresh Ramakrishna, Jeannie Lee, Hyongbum (Henry) Kim#,  Jin-Wu Nam#. En bloc and segmental deletions of human XIST reveal X chromosome inactivation- involving RNA elements, Nucleic Acids Res, 47(8):3875-3887, 2019.

Incheol Ryu, Yeonkyoung Park, Jwa-Won Seo, Ok Hyun Park, Hongseok Ha, Jin-Wu Nam and Yoon Ki Kim. HuR stabilizes a polydenylated form of replication-dependent histone mRNas under stress conditions, FASEB, 33(2):2680-2693, 2019. 

Seo-Won Choi*, Hyunwoo Kim*, and Jin-Wu Nam. The small peptide world in long non-coding RNAs, Briefings in Bioinformatics, 20(5):1853-1864, 2019.

Kyeongdae Kim , Dahee Shim , Jun Seong Lee , Konstantin Zaitsev , Jesse W Williams , Ki-Wook Kim , Man-Young Jang , Hyung Seok Jang , Tae Jin Yun , Seung Hyun Lee , Won Kee Yoon , Annik Prat , Nabil G Seidah , Jungsoon Choi , Seung-Pyo Lee , Sang-Ho Yoon , Jin Wu Nam , Je Kyung Seong, Goo Taeg Oh , Gwendalyn Randolph , Maxim N Artyomov , Cheolho Cheong , and Jae-Hoon Choi . Transcriptome Analysis Reveals Non-Foamy Rather than Foamy Plaque Macrophages Are Pro-Inflammatory in Atherosclerotic Murine Models, Circulation Res, 123(10) :1127-1142, 2018. 

Hyosun Hong*, Han-Ha Chai*, Kyoungwoo Nam, Dajeong Lim, Kyung-Tai Lee, Yoon Jung Do, Chang-Yeon Cho and Jin-Wu Nam. HSF2 Co-regulates Protein-coding and Long Non-coding RNA Genes Specific to Black Tissues of the Black Chicken, Yeonsan Ogye , International Journal of Molecular Sciences, 19(8):E2359, 2018.

Jang-il Sohn*, Kyoungwoo Nam*, Hyosun Hong*, Jun-Mo Kim*,  Dajeong Lim, Kyung-Tai Lee, Yoon Jung Do, Chang Yeon Cho, Namshin Kim, Han-Ha Chai# and Jin-Wu Nam#. Whole genome and transcriptome maps of the entirely black native Korean chicken breed Yeonsan Ogye , GigaSciences, 7(7):giy086, 2018. 

Jung-Ho Yoon, Bo-Hyun You, Chan Hyuk Park, Yeong Jin Kim, Jin-Wu Nam, and Sang Kil Lee. The long noncoding RNA LUCAT1 promotes tumorigenesis by controlling ubiquitination and stability of DNA methyltransferase 1 in esophageal squamous cell carcinoma, Cancer Letters, 417:47-57, 2018.

Seo-Won Choi and Jin-Wu Nam. TERIUS: accurate prediction of lncRNA via high-throughput sequencing data representing RNA binding protein association, BMC Bioinformatics, 19(1):14, 2018. 

Jang-il Sohn and Jin-Wu Nam. The Present and Future of De Novo Whole Genome Assembly, Briefings in Bioinformatics , 19(1):23-40, 2018.

Dooyoung Lee, Jin-Wu Nam, and Chanseok Shin. DROSHA targets its own transcript to modulate alternative splicing, RNA, 23(7):1035-1047, 2017.

Hae Min Jeong, Ryong Nam Kim, Mi Jeong Kwon, Ensel Oh, Jinil Han, Se Kyung Lee, Jong-Sun Choi, Sara Park, Seok Jin Nam, Gyung Yup Gong, Jin Wu Nam, Doo Ho Choi, Hannah Lee, Byung-Ho Nam, Yoon-La Choi and Young Kee Shin. Targeted exome sequencing of Korean triple-negative breast cancer reveals homozygous deletions associated with poor prognosis of adjuvant chemotherapy-treated patients, Oncotarget, 8(37):61538-61550, 2017.

Bo-Hyun You, Sang-Ho Yoon, and Jin-Wu Nam. High-Confidence Coding and Noncoding Transcriptome Maps, Genome Res,  27(6):1050-1062, 2017. 

Kyung-Tae Lee and Jin-Wu Nam.  Post-transcriptional and translational regulation of mRNA-like long non-coding RNAs by microRNAs in early developmental stages of zebrafish embryos, BMB Rep, 50(4):226-231, 2017. 

Hui Kwon Kim, Myungjae Song, Jinu Lee, Adrussery. Vipin Menon, Soobin Jung, Young-Mook Kang, Euijeon Woo, Jin-Wu Nam, and Hyongbum (Henry) Kim. In vivo high-throughput profiling of CRISPR-Cpf1 activity based on target sequence composition, Nature Methods, 14(2):153-159, 2017. 

Youngjune Park, Sangsoo Lim, Jin-Wu Nam, and Sun Kim. Measuring intratumor heterogeneity by network entropy using RNA-seq data, Sci. Rep, 6:37767, 2016.

Yong-Hee Rhee, Tae-Ho Kim, A-Young Jo, Mi-Yoon Chang, Chang-Hwan Park,Sang-Mi Kim, Jae-Jin Song, Sang-Min Oh, Sang-Hoon Yi, Hyeon Ho Kim, Bo-Hyun You, Jin-Wu Nam, and Sang-Hun Lee. LIN28A enhances the therapeutic potential of cultured neural stem cells in a Parkinson’s disease model, Brain, 139(10):2722-2739, 2016. 

Jin-Wu Nam, Seo-Won Choi, and Bo-Hyun You. Incredible RNA: Dual Functions of Coding and Noncoding, Mol. Cells, 39(5):367-374, 2016. 

Kyoungwoo Nam*, Heesu Jeong*, Jin-Wu Nam. Pseudo-Reference-Based Assembly of Vertebrate Transcriptomes, Genes, 7(3)E10, 2016.

Jiwon Shim, Jin-Wu Nam. The expression and functional roles of microRNAs in stem cell differentiation, BMB Reports, 49(1):3-10, 2016.

Hoin Kang, Chongtae Kim, Heejin Lee, Jun Gi Rho, Jwa-Won Seo, Jin-Wu Nam, Woo Keun Song, Suk Woo Nam, Wook Kim and Eun Kyung Lee. Downregulation of microRNA-362-3p and microRNA-329 promotes tumor progression in human breast cancer, Cell Death & Diff, 23(3):484-495, 2016. 

MinHyeok Kim, Bo-Hyun You, and Jin Wu Nam. Global Estimation of the 3' Untranslated Region Landscape Using RNA Sequencing, Methods, 83:111-117, 2015. 

Vikram Agarwal, George W. Bell, Jin-Wu Nam, David P.Bartel. Predicting effective microRNA target sites in mammalian mRNAs, eLife, 4:e05005, 2015. 

J.-W. Nam, O. Rissland, D. Kopstein, V. Agarwal, C. Jan, M. Yildrim and D. Bartel. Global analyses of the effect of different cellular contexts on microRNA targeting, Mol Cell, 53(6):1031-1043, 2014. 

June Hyun Park, Soungyub Ahn, Soyoung Kim, Junho Lee, Jin-Wu Nam*, Chanseok Shin*. Degradome sequencing reveals an endogenous microRNA target in C. elegans, FEBS Letters, 587(2013):964-969, 2013. 

J.-W. Nam and D. Bartel. Long non-coding RNAs in C.elegans, Genome Research, 22:2529-2540, 2012. 

C.Shin*, J.-W. Nam*, K.Farh*, R.Chiang, A.Shkumatava, and D.Bartel. Expanding the MicroRNA Targeting Code: A Novel Type of Site with Centered Pairing, Mol Cell, 38(6):789-802, 2010. 

S. Hyun*, J.H. Lee*, H. J*. J.-W. Nam, B.J. Namkoong, G. Lee, J. Chung, V.N. Kim. Conserved MicroRNA miR-8/miR-200 and Its Target USH/FOG2 Control Growth by Regulating PI3K, Cell, 139(6):1096-1108, 2009. 

B.-T Zhang and J.-W. Nam. Supervised learning approach for microRNA studies, Machine Learning in Bioinformatics, Chapter 16, John Wiley & Sons, 2008.

S. Y. Park*, J. H. Lee*, M. Ha, J.-W. Nam and V. N. Kim. miR-29 miRNAs activate p53 by targeting p85a and CDC42, Nature Structural and Molecular Biology, 16(1):23-29, 2008. 

J.H. Namkung, J.-W. Nam, and TS Park. Identification of eQTL by the interaction analysis using genetic algorithm, BMC proc.

J.-W. Nam, I.-H. Lee, K.-B. Hwang, S.-B. Park, and B.-T. Zhang. Dinucleotide step parameterization of pre-miRNAs using multi-objective evolutionary algorithms, EvoBio, 4447:176-186, 2007. 

M. Oh, H. Lee, Y.-K. Kim, J.-W. Nam, J.-K. Rhee, B.-T. Zhang, V.N. Kim, I. Lee. Identification and characterization of small RNAs from vernalized Arabidopsis thaliana, Journal of Plant Biology, 50(5):562-572, 2007. 

J.-G. Joung, K.-B.Hwang, J.-W. Nam, S.-J. Kim, B.-T. Zhang. Discovery of microRNA-mRNA modules via population-based probabilistic learning, Bioinformatics, 23:1141-1147, 2007. 

J. Han, Y.T. Kim, K.-H Yeom, J.-W. Nam, I.H. Hur, Je-keun Rhee, B.-T. Zhang and V.N. Kim. Molecular basis for the recognition and processing of primary microRNA by Drosha, Cell, 125:887-901, 2006. 

J.-W. Nam*, J.H.Kim*, S.K.Kim, B.-T. Zhang. ProMiR II: a web server for the probabilistic prediction of clustered, nonclustered, conserved and nonconserved microRNAs, Nucleic Acids Research, 34:W455-W458, 2006. 

J.-W. Nam*, S.K. Kim* Je-Keun Rhee, W.J. Lee, B.-T. Zhang. miTarget: microRNA target-gene prediction using a Support Vector Machine, BMC Bioinformatics, 7(1):411, 2006. 

V.N. Kim and J.-W. Nam. Genomics of microRNA, Trends in Genetics, 22(3):165-173, 2006. 

SA Lee, KM Lee, WY Park, B Kim, J.-W. Nam, KY Yoo,  DY Noh, SH Ahn, A Hironen, D Kang. Obesity and genetic polymorphism of ERCC2 and ERCC2 as modifiers of risk of breast cancer, Exp. Mol. Med, 37(2):86-90, 2006.  

J.-W. Nam, K.R. Shin, J.J. Han, Y.T. Lee, V.N. Kim and B.T.Zhang. Human miRNA prediction through probabilistic co-learning of sequence and structure, Nucleic Acids Research, 33(11):3570-3581, 2005. 

S.K. Kim, J.-W. Nam, W.J. Lee, B.T. Zhang. A Kernel Method for MicroRNA Target Prediction Using Sensible Data and Position-Based Features. IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB 2005), pp. 46-52, 2005.

W.J. Lee, J.-W. Nam, S.K. Kim, B.T. Zhang. Identification of C.elegans MicroRNA Targets Using a Kernel Method, Genomics and Informatics, 3(1):15-23, 2005. 

J.-W. Nam, W.J. Lee, B.T. ZHANG. Computational Methods for Identification of Human microRNA Precursors, Lecture Notes in Artificial Intelligence, vol 3157, 2005. 

E.-J. Park, J.-W. Nam, I.-H. Lee, and B.-T. Zhang Solving the monkey and banana problem using DNA computing. Preliminary Proceedings of the Tenth International Meeting on DNA Computing (DNA10), p.452, 2004.

J.-W. Nam, Joung, J.-G., Ahn, Y.S. and Zhang, B.-T. Two-Step Genetic Programming for Optimization of RNA Common-Structure, Lecture Notes in Computer Science, vol 3005, 73-83, 2004.