Publications
* Co-first author, # Co-correspondance
AI-aided design of shRNAmir/shRNA
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, bioRxiv.
CircRNA Biogenetics and Synthesis (review)
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
Comparative Interactome Analysis of α-arrestins
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
Single-cell Clustering using Universally Variable Genes
Sangho Yoon and Jin-Wu Nam, Clustering malignant cell states using universally variable genes, Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad460.
Hemocyte Evolution at Single-cell Level
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.
SVs at Bulk and Single-cell Levels (review)
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.
ETCHING: SV Caller
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
isomiR regulation
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
TIME lncRNAs
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
RBP-miRNA Targeting
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.
HCC TIME Deconvolution
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.
Mouse Myeloid-derived Suppressor Cells
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.
Single cell analysis of fly lymph gland
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.
gRNA Designer
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.
Mass-cytometry & scRNAs-eq - Nanoparticle Toxicity
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.
Single cell analysis of fly bloods
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.
HERES-Wnt signaling regulator
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.
Genome and Transcriptome Analyses of Jejuma
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.
Assessment of inflammation in Pulmonary Artey Hypertension
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.
UPF1-mediated miRNA targeting
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.
Functional Elements of Human XIST
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.
ARE-mediated mRNA decay
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.
The small peptide in LncRNAs
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.
Transcriptome Analysis of Non-Foamy cells in Atherosclerotic Murine Models
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.
HSF2 and lncRNAs in black tissues
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.
Ogye draft genome and transcriptomes
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.
LUCAT1 in ESCC
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.
lncRNA annotation
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.
De Novo Whole Genome Assembly
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.
DROSHA self-regulation
Dooyoung Lee, Jin-Wu Nam, and Chanseok Shin. DROSHA targets its own transcript to modulate alternative splicing, RNA, 23(7):1035-1047, 2017.
Targeted Exomse Sequencing in TN-Breast Cancer
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.
Co-assembly of Transcriptome
Bo-Hyun You, Sang-Ho Yoon, and Jin-Wu Nam. High-Confidence Coding and Noncoding Transcriptome Maps, Genome Res, 27(6):1050-1062, 2017.
miRNA-mediated silencing of mRNA-like lncRNAs
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.
Endogenous Cpf1 efficiency predictor
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.
Network-based Tumour Purity
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.
Parkinson’s disease therapy by NSCs expanded with LIN28A
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.
Bifunctional RNAs-Review
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.
Pseudo-Reference-Based Assembly of Vertebrate Transcriptomes
Kyoungwoo Nam*, Heesu Jeong*, Jin-Wu Nam. Pseudo-Reference-Based Assembly of Vertebrate Transcriptomes, Genes, 7(3)E10, 2016.
microRNAs in stem cell differentiation
Jiwon Shim, Jin-Wu Nam. The expression and functional roles of microRNAs in stem cell differentiation, BMB Reports, 49(1):3-10, 2016.
micoRNA-362-3p/329 as tumor suppressor
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.
GETUTR
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.
TargetScan 7.0
Vikram Agarwal, George W. Bell, Jin-Wu Nam, David P.Bartel. Predicting effective microRNA target sites in mammalian mRNAs, eLife, 4:e05005, 2015.
Cell-type specific miRNA targeting
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.
miRNA-mediated cleavage target
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.
lncRNAs in C. elegans
J.-W. Nam and D. Bartel. Long non-coding RNAs in C.elegans, Genome Research, 22:2529-2540, 2012.
Centered sites of miRNAs
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.
The common miR-8/miR-200 targeting
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.
Book chapter
B.-T Zhang and J.-W. Nam. Supervised learning approach for microRNA studies, Machine Learning in Bioinformatics, Chapter 16, John Wiley & Sons, 2008.
miR-29 and cancer
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.
GWAS
J.H. Namkung, J.-W. Nam, and TS Park. Identification of eQTL by the interaction analysis using genetic algorithm, BMC proc.
The tertiary structure of pre-miRNA
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.
Plant miRNAs
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.
miRNA-mRNA biclustering
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.
Pre-miRNA structure
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.
PromiRII: miRNA prediction
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.
miTarget: miRNA target prediction
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.
Review: genomics of miRNA
V.N. Kim and J.-W. Nam. Genomics of microRNA, Trends in Genetics, 22(3):165-173, 2006.
SNP: ERCC2
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.
ProMiR: miRNA prediction
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.
Confrence proceeding
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.
C. elegans miRNA targets
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.
miRNA precursor prediction
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.
DNA computing
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.
Genetic programming
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.