• 5681 Citations
  • 20 h-Index
20042019
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Research Output 2004 2019

2019

Comprehensive genome and transcriptome analyses reveal genetic relationship, selection signature, and transcriptome landscape of small-sized Korean native Jeju horse

Srikanth, K., Kim, N. Y., Park, W. C., Kim, J. M., Kim, K. D., Lee, K. T., Son, J. H., Chai, H. H., Choi, J. W., Jang, G. W., Kim, H., Ryu, Y. C., Nam, J. W., Park, J. E., Kim, J. M. & Lim, D., 2019 Dec 1, In : Scientific reports. 9, 1, 16672.

Research output: Contribution to journalArticle

Open Access
Gene Expression Profiling
Transcriptome
Horses
Genome
Single Nucleotide Polymorphism
1 Citation (Scopus)

En bloc and segmental deletions of human XIST reveal X chromosome inactivation-involving RNA elements

Lee, H. J., Gopalappa, R., Sunwoo, H., Choi, S. W., Ramakrishna, S., Lee, J. T., Kim, H. H. & Nam, J. W., 2019 May 7, In : Nucleic Acids Research. 47, 8, p. 3875-3887 13 p.

Research output: Contribution to journalArticle

Open Access
X Chromosome Inactivation
RNA
Exons
Guide RNA
High-Throughput Nucleotide Sequencing
1 Citation (Scopus)

HERES, a lncRNA that regulates canonical and noncanonical Wnt signaling pathways via interaction with EZH2

You, B. H., Yoon, J. H., Kang, H., Lee, E. K., Lee, S. K. & Nam, J. W., 2019 Dec 3, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 49, p. 24620-24629 10 p.

Research output: Contribution to journalArticle

Open Access
Long Noncoding RNA
Wnt Signaling Pathway
Esophageal Squamous Cell Carcinoma
Tumor Cell Line
Heterografts
1 Citation (Scopus)

HuR stabilizes a polyadenylated form of replication-dependent histone mRNAs under stress conditions

Ryu, I., Park, Y., Seo, J. W., Park, O. H., Ha, H., Nam, J. W. & Kim, Y. K., 2019 Jan 1, In : FASEB Journal. 33, 2, p. 2680-2693 14 p.

Research output: Contribution to journalArticle

Histones
Antigens
Messenger RNA
Poly A
Untranslated Regions
6 Citations (Scopus)

The small peptide world in long noncoding RNAs

Choi, S. W., Kim, H. W. & Nam, J. W., 2019 Sep 27, In : Briefings in Bioinformatics. 20, 5, p. 1853-1864 12 p.

Research output: Contribution to journalReview article

Open Access
Long Noncoding RNA
RNA
Peptides
Plant Genome
High-Throughput Nucleotide Sequencing
1 Citation (Scopus)

UPF1/SMG7-dependent microRNA-mediated gene regulation

Park, J., Seo, J. W., Ahn, N., Park, S., Hwang, J. & Nam, J. W., 2019 Dec 1, In : Nature Communications. 10, 1, 4181.

Research output: Contribution to journalArticle

Open Access
gene expression
MicroRNAs
Gene expression
Messenger RNA
RNA Stability
2018

Non-coding transcriptome maps across twenty tissues of the Korean Black Chicken, Yeonsan Ogye

Hong, H., Chai, H. H., Nam, K., Lim, D., Lee, K. T., Do, Y. J., Cho, C. Y. & Nam, J. W., 2018 Aug 10, In : International Journal of Molecular Sciences. 19, 8, d2359.

Research output: Contribution to journalArticle

chickens
Long Noncoding RNA
Transcriptome
genes
Chickens
1 Citation (Scopus)
Long Noncoding RNA
RNA-Binding Proteins
RNA
Sequencing
High Throughput
45 Citations (Scopus)

The long noncoding RNA LUCAT1 promotes tumorigenesis by controlling ubiquitination and stability of DNA methyltransferase 1 in esophageal squamous cell carcinoma

Yoon, J. H., You, B. H., Park, C. H., Kim, Y. J., Nam, J. W. & Lee, S. K., 2018 Mar 28, In : Cancer Letters. 417, p. 47-57 11 p.

Research output: Contribution to journalArticle

Long Noncoding RNA
Ubiquitination
Methyltransferases
Carcinogenesis
DNA
26 Citations (Scopus)

The present and future of de novo whole-genome assembly

Sohn, J. I. & Nam, J. W., 2018 Jan 1, In : Briefings in Bioinformatics. 19, 1, p. 23-40 18 p., bbw096.

Research output: Contribution to journalArticle

Genes
Genome
Budgets
Chromosomes
Guidelines
27 Citations (Scopus)

Transcriptome analysis reveals nonfoamy rather than foamy plaque macrophages are proinflammatory in atherosclerotic murine models

Kim, K., Shim, D., Lee, J. S., Zaitsev, K., Williams, J. W., Kim, K. W., Jang, M. Y., Jang, H. S., Yun, T. J., Lee, S. H., Yoon, W. K., Prat, A., Seidah, N. G., Choi, J., Lee, S. P., Yoon, S. H., Nam, J. W., Seong, J. K., Oh, G. T., Randolph, G. J. & 3 others, Artyomov, M. N., Cheong, C. & Choi, J. H., 2018 Jan 1, In : Circulation Research. 123, 10, p. 1127-1142 16 p.

Research output: Contribution to journalArticle

Gene Expression Profiling
Macrophages
Lipids
Tunica Intima
RNA Sequence Analysis
2 Citations (Scopus)

Whole genome and transcriptome maps of the entirely black native Korean chicken breed Yeonsan Ogye

Sohn, J. I., Nam, K., Hong, H., Kim, J. M., Lim, D., Lee, K. T., Do, Y. J., Cho, C. Y., Kim, N., Chai, H. H. & Nam, J. W., 2018 Jan 1, In : GigaScience. 7, 7, p. 1-14 14 p.

Research output: Contribution to journalArticle

Transcriptome
Chickens
Genes
Genome
Hyperpigmentation
2017
7 Citations (Scopus)

DROSHA targets its own transcript to modulate alternative splicing

Lee, D., Nam, J. W. & Shin, C., 2017 Jul, In : RNA. 23, 7, p. 1035-1047 13 p.

Research output: Contribution to journalArticle

Alternative Splicing
MicroRNAs
Exons
Microcomputers
Ribonuclease III
19 Citations (Scopus)

High-confidence coding and noncoding transcriptome maps

You, B. H., Yoon, S. H. & Nam, J. W., 2017 Jun, In : Genome Research. 27, 6, p. 1050-1062 13 p.

Research output: Contribution to journalArticle

Transcriptome
RNA Sequence Analysis
Long Noncoding RNA
Genome
High-Throughput Nucleotide Sequencing
86 Citations (Scopus)

In vivo high-throughput profiling of CRISPR-Cpf1 activity

Kim, H. K., Song, M., Lee, J., Menon, A. V., Jung, S., Kang, Y. M., Choi, J. W., Woo, E., Koh, H. C., Nam, J-W. & Kim, H., 2017 Feb 1, In : Nature Methods. 14, 2, p. 153-159 7 p.

Research output: Contribution to journalArticle

Francisella
Clustered Regularly Interspaced Short Palindromic Repeats
Prevotella
Throughput
CRISPR-Associated Proteins
3 Citations (Scopus)
Long Noncoding RNA
Zebrafish
MicroRNAs
Embryonic Structures
Messenger RNA
5 Citations (Scopus)

Targeted exome sequencing of Korean triple-negative breast cancer reveals homozygous deletions associated with poor prognosis of adjuvant chemotherapy-treated patients

Jeong, H. M., Kim, R. N., Kwon, M. J., Oh, E., Han, J., Lee, S. K., Choi, J. S., Park, S., Nam, S. J., Gong, G. Y., Nam, J. W., Choi, D. H., Lee, H., Nam, B. H., Choi, Y. L. & Shin, Y. K., 2017 Sep 1, In : Oncotarget. 8, 37, p. 61538-61550 13 p.

Research output: Contribution to journalArticle

Triple Negative Breast Neoplasms
Exome
Adjuvant Chemotherapy
DNA Repair
Sequence Deletion
2016
38 Citations (Scopus)

Downregulation of microRNA-362-3p and microRNA-329 promotes tumor progression in human breast cancer

Kang, H., Kim, C., Lee, H., Rho, J. G., Seo, J. W., Nam, J. W., Song, W. K., Nam, S. W., Kim, W. & Lee, E. K., 2016 Mar 1, In : Cell Death and Differentiation. 23, 3, p. 484-495 12 p.

Research output: Contribution to journalArticle

MicroRNAs
Down-Regulation
Breast Neoplasms
Neoplasms
DNA Methylation
31 Citations (Scopus)

Incredible RNA: Dual functions of coding and noncoding

Nam, J. W., Choi, S. W. & You, B. H., 2016 May 1, In : Molecules and Cells. 39, 5, p. 367-374 8 p.

Research output: Contribution to journalReview article

RNA
Long Noncoding RNA
Untranslated RNA
Gene Regulatory Networks
Open Reading Frames
6 Citations (Scopus)

LIN28A enhances the therapeutic potential of cultured neural stem cells in a Parkinson's disease model

Rhee, Y. H., Kim, T. H., Jo, A. Y., Chang, M. Y., Park, C. H., Kim, S. M., Song, J. J., Oh, S. M., Yi, S. H., Kim, H. H., You, B. H., Nam, J. W. & Lee, S. H., 2016 Oct 1, In : Brain. 139, 10, p. 2722-2739 18 p.

Research output: Contribution to journalArticle

Neural Stem Cells
Parkinson Disease
Mesencephalon
Dopaminergic Neurons
Therapeutics
11 Citations (Scopus)

Measuring intratumor heterogeneity by network entropy using RNA-seq data

Park, Y., Lim, S., Nam, J. W. & Kim, S., 2016 Nov 24, In : Scientific reports. 6, 37767.

Research output: Contribution to journalArticle

Entropy
Clonal Evolution
Transcriptome
RNA
Neoplasms

Pseudo-reference-based assembly of vertebrate transcriptomes

Nam, K., Jeong, H. & Nam, J. W., 2016 Feb 24, In : Genes. 7, 3, 10.

Research output: Contribution to journalArticle

Transcriptome
Vertebrates
Ducks
Genome
Chickens
5 Citations (Scopus)

The expression and functional roles of microRNAs in stem cell differentiation

Shim, J. & Nam, J. W., 2016 Jan 1, In : BMB reports. 49, 1, p. 3-10 8 p.

Research output: Contribution to journalShort survey

Stem cells
MicroRNAs
Cell Differentiation
Stem Cells
Cytology
2015
18 Citations (Scopus)

Global estimation of the 3' untranslated region landscape using RNA sequencing

Kim, M. H., You, B. H. & Nam, J. W., 2015 Jul 15, In : Methods. 83, p. 111-117 7 p.

Research output: Contribution to journalArticle

RNA Sequence Analysis
3' Untranslated Regions
RNA
Poly A
Messenger RNA
1737 Citations (Scopus)

Predicting effective microRNA target sites in mammalian mRNAs

Agarwal, V., Bell, G. W., Nam, J. W. & Bartel, D. P., 2015 Aug 12, In : eLife. 4, AUGUST2015, e05005.

Research output: Contribution to journalArticle

MicroRNAs
Messenger RNA
Crosslinking
Gene Regulatory Networks
Seed
2014
127 Citations (Scopus)

Global analyses of the effect of different cellular contexts on microRNA targeting

Nam, J. W., Rissland, O. S., Koppstein, D., Abreu-Goodger, C., Jan, C. H., Agarwal, V., Yildirim, M. A., Rodriguez, A. & Bartel, D. P., 2014 Mar 20, In : Molecular Cell. 53, 6, p. 1031-1043 13 p.

Research output: Contribution to journalArticle

MicroRNAs
3' Untranslated Regions
Protein Isoforms
Cell Line
Genes
2013
7 Citations (Scopus)

Degradome sequencing reveals an endogenous microRNA target in C. elegans

Park, J. H., Ahn, S., Kim, S., Lee, J., Nam, J. W. & Shin, C., 2013 Apr 2, In : FEBS Letters. 587, 7, p. 964-969 6 p.

Research output: Contribution to journalArticle

MicroRNAs
Caenorhabditis elegans
RNA Cleavage
Messenger RNA
3' Untranslated Regions
2012
132 Citations (Scopus)

Long noncoding RNAs in C. elegans

Nam, J. W. & Bartel, D. P., 2012 Dec 1, In : Genome Research. 22, 12, p. 2529-2540 12 p.

Research output: Contribution to journalArticle

Long Noncoding RNA
Spermatozoa
Messenger RNA
Proteins
Caenorhabditis elegans
2010
404 Citations (Scopus)

Expanding the microRNA targeting code: functional sites with centered pairing.

Shin, C., Nam, J-W., Farh, K. K. H., Chiang, H. R., Shkumatava, A. & Bartel, D. P., 2010 Jan 1, In : Molecular Cell. 38, 6, p. 789-802 14 p.

Research output: Contribution to journalArticle

MicroRNAs
Seeds
Messenger RNA
Cultured Cells
Brain
2009
196 Citations (Scopus)

Conserved MicroRNA miR-8/miR-200 and Its Target USH/FOG2 Control Growth by Regulating PI3K

Hyun, S., Lee, J. H., Jin, H., Nam, J-W., Namkoong, B., Lee, G., Chung, J. & Kim, V. N., 2009 Dec 11, In : Cell. 139, 6, p. 1096-1108 13 p.

Research output: Contribution to journalArticle

MicroRNAs
Phosphatidylinositol 3-Kinases
Diptera
Fat Body
Fats
467 Citations (Scopus)

miR-29 miRNAs activate p53 by targeting p85α and CDC42

Park, S. Y., Lee, J. H., Ha, M., Nam, J. W. & Kim, V. N., 2009 Jan 1, In : Nature Structural and Molecular Biology. 16, 1, p. 23-29 7 p.

Research output: Contribution to journalArticle

MicroRNAs
rho GTP-Binding Proteins
Phosphatidylinositol 3-Kinases
Up-Regulation
Apoptosis
2008

Supervised Learning Methods for MicroRNA Studies

Zhang, B. T. & Nam, J-W., 2008 Apr 21, Machine Learning in Bioinformatics. John Wiley & Sons, Inc., p. 339-365 27 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Supervised learning
MicroRNAs
Learning
2007

Dinucleotide step parameterization of pre-miRNAs using multi-objective evolutionary algorithms

Nam, J-W., Lee, I. H., Hwang, K. B., Park, S. B. & Zhang, B. T., 2007 Dec 1, Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics - 5th European Conference, EvoBIO 2007, Proceedings. p. 176-186 11 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 4447 LNCS).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

MicroRNA
Multi-objective Evolutionary Algorithm
Parameterization
RNA
MicroRNAs
124 Citations (Scopus)

Discovery of microRNA-mRNA modules via population-based probabilistic learning

Joung, J. G., Hwang, K. B., Nam, J. W., Kim, S. J. & Zhang, B. T., 2007 May 1, In : Bioinformatics. 23, 9, p. 1141-1147 7 p.

Research output: Contribution to journalArticle

MicroRNA
MicroRNAs
Messenger RNA
Learning
Module
34 Citations (Scopus)

Genetic polymorphism of XRCC3 Thr241Met and breast cancer risk: Case-control study in Korean women and meta-analysis of 12 studies

Lee, S. A., Lee, K. M., Park, S. K., Choi, J. Y., Kim, B., Nam, J-W., Yoo, K. Y., Noh, D. Y., Ahn, S. H. & Kang, D., 2007 Jun 1, In : Breast Cancer Research and Treatment. 103, 1, p. 71-76 6 p.

Research output: Contribution to journalArticle

Genetic Polymorphisms
Meta-Analysis
Case-Control Studies
Genotype
Breast Neoplasms
5 Citations (Scopus)

Identification and characterization of small RNAs from vernalized Arabidopsis thaliana

Oh, M., Lee, H., Kim, Y. K., Nam, J. W., Rhee, J. K., Zhang, B. T., Kim, V. N. & Lee, I., 2007 Oct 31, In : Journal of Plant Biology. 50, 5, p. 562-572 11 p.

Research output: Contribution to journalArticle

Arabidopsis thaliana
RNA
vernalization
small interfering RNA
microRNA
2006
676 Citations (Scopus)

Genomics of microRNA

Kim, V. N. & Nam, J. W., 2006 Mar 1, In : Trends in Genetics. 22, 3, p. 165-173 9 p.

Research output: Contribution to journalReview article

Genomics
MicroRNAs
Plant Viruses
Messenger RNA
RNA Stability
163 Citations (Scopus)

miTarget: MicroRNA target gene prediction using a support vector machine

Kim, S. K., Nam, J. W., Rhee, J. K., Lee, W. J. & Zhang, B. T., 2006 Sep 18, In : BMC Bioinformatics. 7, 411.

Research output: Contribution to journalArticle

MicroRNA
MicroRNAs
Support vector machines
Support Vector Machine
Genes
1009 Citations (Scopus)

Molecular Basis for the Recognition of Primary microRNAs by the Drosha-DGCR8 Complex

Han, J., Lee, Y., Yeom, K. H., Nam, J. W., Heo, I., Rhee, J. K., Sohn, S. Y., Cho, Y., Zhang, B. T. & Kim, V. N., 2006 Jun 2, In : Cell. 125, 5, p. 887-901 15 p.

Research output: Contribution to journalArticle

MicroRNAs
RNA Interference
Anchors
Small Interfering RNA
RNA
52 Citations (Scopus)

ProMiR II: A web server for the probabilistic prediction of clustered, nonclustered, conserved and nonconserved microRNAs

Nam, J. W., Kim, J., Kim, S. K. & Zhang, B. T., 2006 Jul 1, In : Nucleic Acids Research. 34, WEB. SERV. ISS., p. W455-W458

Research output: Contribution to journalArticle

MicroRNAs
Viral Genome
Entropy
Statistical Models
Human Genome
2005
6 Citations (Scopus)

A kernel method for MicroRNA target prediction using sensible data and position-based features

Kim, S. K., Nam, J. W., Lee, W. J. & Zhang, B. T., 2005 Dec 1, Proceedings of the 2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB '05. 1594897. (Proceedings of the 2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB '05; vol. 2005).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Seed
Animals
Computational methods
RNA
Feature extraction
163 Citations (Scopus)

Human microRNA prediction through a probabilistic co-learning model of sequence and structure

Nam, J. W., Shin, K. R., Han, J., Lee, Y., Kim, V. N. & Zhang, B. T., 2005 Oct 18, In : Nucleic Acids Research. 33, 11, p. 3570-3581 12 p.

Research output: Contribution to journalArticle

MicroRNAs
Learning
Genes
Chromosomes, Human, Pair 19
Chromosomes, Human, Pair 16
30 Citations (Scopus)

Obesity and genetic polymorphism of ERCC2 and ERCC4 as modifiers of risk of breast cancer

Lee, S. A., Lee, K. M., Park, W. Y., Kim, B., Nam, J., Yoo, K. Y., Noh, D. Y., Ahn, S. H., Hirvonen, A. & Kang, D., 2005 Apr 30, In : Experimental and Molecular Medicine. 37, 2, p. 86-90 5 p.

Research output: Contribution to journalArticle

Genetic Polymorphisms
Polymorphism
Obesity
Breast Neoplasms
Genotype
2004
4 Citations (Scopus)

Computational methods for identification of human microRNA precursors

Nam, J-W., Lee, W. J. & Zhang, B. T., 2004 Dec 1, In : Lecture Notes in Artificial Intelligence (Subseries of Lecture Notes in Computer Science). 3157, p. 732-741 10 p.

Research output: Contribution to journalConference article

MicroRNA
Computational methods
RNA
Precursor
Computational Methods
5 Citations (Scopus)

Two-step genetic programming for optimization of RNA common-structure

Nam, J. W., Joung, J. G., Ahn, Y. S. & Zhang, B. T., 2004 Jan 1, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Raidl, G. R., Cagnoni, S., Johnson, C. G., Corne, D. W., Drechsler, R., Smith, G. D., Jin, Y., Machado, P., Rothlauf, F., Branke, J., Marchiori, E. & Squillero, G. (eds.). Springer Verlag, p. 73-83 11 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 3005).

Research output: Chapter in Book/Report/Conference proceedingChapter

Genetic programming
Genetic Programming
RNA
Grammar
Optimization