• 4501 Citations
  • 26 h-Index
19952020

Research output per year

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Research Output

2020

BarleyNet: A Network-Based Functional Omics Analysis Server for Cultivated Barley, Hordeum vulgare L.

Lee, S., Lee, T., Yang, S. & Lee, I., 2020 Feb 18, In : Frontiers in Plant Science. 11, 98.

Research output: Contribution to journalArticle

Open Access

BiomeNet: A database for construction and analysis of functional interaction networks for any species with a sequenced genome

Kim, E., Bae, D., Yang, S., Ko, G., Lee, S., Lee, B., Lee, I. & Wren, J., 2020 Mar 1, In : Bioinformatics. 36, 5, p. 1584-1589 6 p.

Research output: Contribution to journalArticle

Open Access
1 Citation (Scopus)

Construction of functional protein networks using domain profile associations

Shim, J. E. & Lee, I., 2020, Methods in Molecular Biology. Humana Press Inc., p. 35-44 10 p. (Methods in Molecular Biology; vol. 2074).

Research output: Chapter in Book/Report/Conference proceedingChapter

1 Citation (Scopus)

Single-cell ATAC sequencing analysis: From data preprocessing to hypothesis generation

Baek, S. & Lee, I., 2020, In : Computational and Structural Biotechnology Journal. 18, p. 1429-1439 11 p.

Research output: Contribution to journalReview article

Open Access

Single-cell transcriptome analysis reveals TOX as a promoting factor for T cell exhaustion and a predictor for anti-PD-1 responses in human cancer

Kim, K., Park, S., Park, S. Y., Kim, G., Park, S. M., Cho, J. W., Kim, D. H., Park, Y. M., Koh, Y. W., Kim, H. R., Ha, S. J. & Lee, I., 2020 Feb 28, In : Genome Medicine. 12, 1, 22.

Research output: Contribution to journalArticle

Open Access
2 Citations (Scopus)
2019

A genome-scale co-functional network of xanthomonas genes can accurately reconstruct regulatory circuits controlled by two-component signaling systems

Kim, H., Joe, A., Lee, M., Yang, S., Ma, X., Ronald, P. C. & Lee, I., 2019, In : Molecules and cells. 42, 2, p. 166-174 9 p.

Research output: Contribution to journalArticle

2 Citations (Scopus)

Cancer Gene Discovery by Network Analysis of Somatic Mutations Using the MUFFINN Server

Han, H., Lehner, B. & Lee, I., 2019, Methods in Molecular Biology. Humana Press Inc., p. 37-50 14 p. (Methods in Molecular Biology; vol. 1907).

Research output: Chapter in Book/Report/Conference proceedingChapter

HumanNet v2: Human gene networks for disease research

Hwang, S., Kim, C. Y., Yang, S., Kim, E., Hart, T., Marcotte, E. M. & Lee, I., 2019 Jan 8, In : Nucleic acids research. 47, D1, p. D573-D580

Research output: Contribution to journalArticle

17 Citations (Scopus)

MaizeNet: a co-functional network for network-assisted systems genetics in Zea mays

Lee, T., Lee, S., Yang, S. & Lee, I., 2019 Aug, In : Plant Journal. 99, 3, p. 571-582 12 p.

Research output: Contribution to journalArticle

5 Citations (Scopus)

NGSEA: Network-Based Gene Set Enrichment Analysis for Interpreting Gene Expression Phenotypes with Functional Gene Sets

Han, H., Lee, S. & Lee, I., 2019 Aug 31, In : Molecules and cells. 42, 8, p. 579-588 10 p.

Research output: Contribution to journalArticle

2 Citations (Scopus)

Pathway-specific protein domains are predictive for human diseases

Shim, J. E., Kim, J. H., Shin, J., Lee, J. E. & Lee, I., 2019 May, In : PLoS computational biology. 15, 5, e1007052.

Research output: Contribution to journalArticle

Open Access
1 Citation (Scopus)
2018

AraGWAB: Network-based boosting of genome-wide association studies in Arabidopsis thaliana

Lee, T. & Lee, I., 2018 Dec 1, In : Scientific reports. 8, 1, 2925.

Research output: Contribution to journalArticle

10 Citations (Scopus)

Direct Conversion of Mouse Fibroblasts into Cholangiocyte Progenitor Cells

Lim, K. T., Kim, J., Hwang, S. I., Zhang, L., Han, H., Bae, D., Kim, K. P., Hu, Y. P., Schöler, H. R., Lee, I., Hui, L. & Han, D. W., 2018 May 8, In : Stem Cell Reports. 10, 5, p. 1522-1536 15 p.

Research output: Contribution to journalArticle

2 Citations (Scopus)

Network-based genetic investigation of virulence-associated phenotypes in methicillin-resistant Staphylococcus aureus

Kim, C. Y., Lee, M., Lee, K., Yoon, S. S. & Lee, I., 2018 Dec 1, In : Scientific reports. 8, 1, 10796.

Research output: Contribution to journalArticle

2 Citations (Scopus)

TRRUST v2: An expanded reference database of human and mouse transcriptional regulatory interactions

Han, H., Cho, J. W., Lee, S., Yun, A., Kim, H., Bae, D., Yang, S., Kim, C. Y., Lee, M., Kim, E., Lee, S., Kang, B., Jeong, D., Kim, Y., Jeon, H. N., Jung, H., Nam, S., Chung, M., Kim, J. H. & Lee, I., 2018 Jan 1, In : Nucleic acids research. 46, D1, p. D380-D386

Research output: Contribution to journalArticle

148 Citations (Scopus)
2017

AraNet: A network biology server for Arabidopsis thaliana and other non-model plant species

Lee, T. & Lee, I., 2017, Methods in Molecular Biology. Humana Press Inc., p. 225-238 14 p. (Methods in Molecular Biology; vol. 1629).

Research output: Chapter in Book/Report/Conference proceedingChapter

4 Citations (Scopus)

COEXPEDIA: Exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH)

Yang, S., Kim, C. Y., Hwang, S., Kim, E., Kim, H., Shim, H. & Lee, I., 2017 Jan 1, In : Nucleic acids research. 45, D1, p. D389-D396

Research output: Contribution to journalArticle

23 Citations (Scopus)

Construction of functional gene networks using phylogenetic profiles

Shin, J. & Lee, I., 2017, Methods in Molecular Biology. Humana Press Inc., p. 87-98 12 p. (Methods in Molecular Biology; vol. 1526).

Research output: Chapter in Book/Report/Conference proceedingChapter

6 Citations (Scopus)

From sequencing data to gene functions: co-functional network approaches

Shim, J. E., Lee, T. & Lee, I., 2017 Mar 4, In : Animal Cells and Systems. 21, 2, p. 77-83 7 p.

Research output: Contribution to journalReview article

13 Citations (Scopus)

Functional gene networks based on the gene neighborhood in metagenomes

Kim, C. Y. & Lee, I., 2017 Sep 3, In : Animal Cells and Systems. 21, 5, p. 301-306 6 p.

Research output: Contribution to journalArticle

6 Citations (Scopus)

GWAB: A web server for the network-based boosting of human genome-wide association data

Shim, J. E., Bang, C., Yang, S., Lee, T., Hwang, S., Kim, C. Y., Singh-Blom, U. M., Marcotte, E. M. & Lee, I., 2017 Jul 3, In : Nucleic acids research. 45, W1, p. W154-W161

Research output: Contribution to journalArticle

18 Citations (Scopus)

Network-based gene function prediction in mouse and other model vertebrates using mousenet server

Kim, E. & Lee, I., 2017, Methods in Molecular Biology. Humana Press Inc., p. 183-198 16 p. (Methods in Molecular Biology; vol. 1611).

Research output: Chapter in Book/Report/Conference proceedingChapter

1 Citation (Scopus)

Network perturbation by recurrent regulatory variants in cancer

Jang, K., Kim, K., Cho, A., Lee, I. & Choi, J. K., 2017 Mar, In : PLoS computational biology. 13, 3, e1005449.

Research output: Contribution to journalArticle

3 Citations (Scopus)

SoyNet: A database of co-functional networks for soybean Glycine max

Kim, E., Hwang, S. & Lee, I., 2017 Jan 1, In : Nucleic acids research. 45, D1, p. D1082-D1089

Research output: Contribution to journalArticle

20 Citations (Scopus)

TomatoNet: A Genome-wide Co-functional Network for Unveiling Complex Traits of Tomato, a Model Crop for Fleshy Fruits

Kim, H., Kim, B. S., Shim, J. E., Hwang, S., Yang, S., Kim, E., Iyer-Pascuzzi, A. S. & Lee, I., 2017 Apr 3, In : Molecular Plant. 10, 4, p. 652-655 4 p.

Research output: Contribution to journalLetter

7 Citations (Scopus)

WheatNet: a Genome-Scale Functional Network for Hexaploid Bread Wheat, Triticum aestivum

Lee, T., Hwang, S., Kim, C. Y., Shim, H., Kim, H., Ronald, P. C., Marcotte, E. M. & Lee, I., 2017 Aug 7, In : Molecular Plant. 10, 8, p. 1133-1136 4 p.

Research output: Contribution to journalLetter

7 Citations (Scopus)
2016

An integrated systems biology approach identifies positive cofactor 4 as a factor that increases reprogramming efficiency

Jo, J., Hwang, S., Kim, H. J., Hong, S., Lee, J. E., Lee, S. G., Baek, A., Han, H., Lee, J. I., Lee, I. & Lee, D. R., 2016, In : Nucleic acids research. 44, 3, p. 1203-1215 13 p.

Research output: Contribution to journalArticle

7 Citations (Scopus)

A single gene of a commensal microbe affects host susceptibility to enteric infection

Yoon, M. Y., Min, K. B., Lee, K. M., Yoon, Y., Kim, Y., Oh, Y. T., Lee, K., Chun, J., Kim, B. Y., Yoon, S. H., Lee, I., Kim, C. Y. & Yoon, S. S., 2016 May 13, In : Nature communications. 7, 11606.

Research output: Contribution to journalArticle

11 Citations (Scopus)

Function-driven discovery of disease genes in zebrafish using an integrated genomics big data resource

Shim, H., Kim, J. H., Kim, C. Y., Hwang, S., Kim, H., Yang, S., Lee, J. E. & Lee, I., 2016, In : Nucleic acids research. 44, 20, p. 9611-9623 13 p.

Research output: Contribution to journalArticle

10 Citations (Scopus)

Generation of integration-free induced neural stem cells from mouse fibroblasts

Kim, S. M., Kim, J. W., Kwak, T. H., Park, S. W., Kim, K. P., Park, H., Lim, K. T., Kang, K., Kim, J., Yang, J. H., Han, H., Lee, I., Hyun, J. K., Bae, Y. M., Schöler, H. R., Lee, H. T. & Han, D. W., 2016 Jul 1, In : Journal of Biological Chemistry. 291, 27, p. 14199-14212 14 p.

Research output: Contribution to journalArticle

19 Citations (Scopus)

Microvesicles from brain-extract-treated mesenchymal stem cells improve neurological functions in a rat model of ischemic stroke

Lee, J. Y., Kim, E., Choi, S. M., Kim, D. W., Kim, K. P., Lee, I. & Kim, H. S., 2016 Sep 9, In : Scientific reports. 6, 33038.

Research output: Contribution to journalArticle

25 Citations (Scopus)

MouseNet v2: A database of gene networks for studying the laboratory mouse and eight other model vertebrates

Kim, E., Hwang, S., Kim, H., Shim, H., Kang, B., Yang, S., Shim, J. H., Shin, S. Y., Marcotte, E. M. & Lee, I., 2016, In : Nucleic acids research. 44, D1, p. D848-D854

Research output: Contribution to journalArticle

20 Citations (Scopus)

MUFFINN: Cancer gene discovery via network analysis of somatic mutation data

Cho, A., Shim, J. E., Kim, E., Supek, F., Lehner, B. & Lee, I., 2016 Jun 23, In : Genome biology. 17, 1, 129.

Research output: Contribution to journalArticle

61 Citations (Scopus)

Network-assisted investigation of virulence and antibiotic-resistance systems in Pseudomonas aeruginosa

Hwang, S., Kim, C. Y., Ji, S. G., Go, J., Kim, H., Yang, S., Kim, H. J., Cho, A., Yoon, S. S. & Lee, I., 2016 May 19, In : Scientific reports. 6, 26223.

Research output: Contribution to journalArticle

15 Citations (Scopus)

Weighted mutual information analysis substantially improves domain-based functional network models

Shim, J. E. & Lee, I., 2016 Sep 15, In : Bioinformatics. 32, 18, p. 2824-2830 7 p.

Research output: Contribution to journalArticle

11 Citations (Scopus)
2015

AraNet v2: An improved database of co-functional gene networks for the study of Arabidopsis thaliana and 27 other nonmodel plant species

Lee, T., Yang, S., Kim, E., Ko, Y., Hwang, S., Shin, J., Shim, J. E., Shim, H., Kim, H., Kim, C. & Lee, I., 2015 Jan 15, In : Nucleic acids research. 43, D1, p. D996-D1002

Research output: Contribution to journalArticle

68 Citations (Scopus)

Co-inheritance analysis within the domains of life substantially improves network inference by phylogenetic profiling

Shin, J. & Lee, I., 2015 Sep 22, In : PloS one. 10, 9, e0139006.

Research output: Contribution to journalArticle

12 Citations (Scopus)

EcoliNet: A database of cofunctional gene network for Escherichia coli

Kim, H., Shim, J. E., Shin, J. & Lee, I., 2015, In : Database. 2015, bav001.

Research output: Contribution to journalArticle

11 Citations (Scopus)
1 Citation (Scopus)

FlyNet: A versatile network prioritization server for the Drosophila community

Shin, J., Yang, S., Kim, E., Kim, C. Y., Shim, H., Cho, A., Kim, H., Hwang, S., Shim, J. E. & Lee, I., 2015, In : Nucleic acids research. 43, W1, p. W91-W97

Research output: Contribution to journalArticle

10 Citations (Scopus)

Modes of interaction between individuals dominate the topologies of real world networks

Lee, I., Kim, E. & Marcotte, E. M., 2015 Mar 20, In : PloS one. 10, 3, e0121248.

Research output: Contribution to journalArticle

3 Citations (Scopus)

Network-assisted approaches for human disease research

Shim, J. E. & Lee, I., 2015 Jul 4, In : Animal Cells and Systems. 19, 4, p. 231-235 5 p.

Research output: Contribution to journalArticle

9 Citations (Scopus)

Network-assisted crop systems genetics: Network inference and integrative analysis

Lee, T., Kim, H. & Lee, I., 2015 Apr 1, In : Current Opinion in Plant Biology. 24, p. 61-70 10 p.

Research output: Contribution to journalReview article

26 Citations (Scopus)

Network-assisted genetic dissection of pathogenicity and drug resistance in the opportunistic human pathogenic fungus Cryptococcus neoformans

Kim, H., Jung, K. W., Maeng, S., Chen, Y. L., Shin, J., Shim, J. E., Hwang, S., Janbon, G., Kim, T., Heitman, J., Bahn, Y. S. & Lee, I., 2015, In : Scientific reports. 5, 8767.

Research output: Contribution to journalArticle

19 Citations (Scopus)

Pathway-dependent effectiveness of network algorithms for gene prioritization

Shim, J. E., Hwang, S. & Lee, I., 2015 Jun 19, In : PloS one. 10, 6, e0130589.

Research output: Contribution to journalArticle

12 Citations (Scopus)

Patterns of metabolite changes identified from large-scale gene perturbations in arabidopsis using a genome-scale metabolic network

Kim, T., Dreher, K., Nilo-Poyanco, R., Lee, I., Fiehn, O., Lange, B. M., Nikolau, B. J., Sumner, L., Welti, R., Wurtele, E. S. & Rhee, S. Y., 2015 Apr 1, In : Plant physiology. 167, 4, p. 1685-1698 14 p.

Research output: Contribution to journalArticle

19 Citations (Scopus)

RiceNet v2: An improved network prioritization server for rice genes

Lee, T., Oh, T., Yang, S., Shin, J., Hwang, S., Kim, C. Y., Kim, H., Shim, H., Shim, J. E., Ronald, P. C. & Lee, I., 2015, In : Nucleic acids research. 43, W1, p. W122-W127

Research output: Contribution to journalArticle

43 Citations (Scopus)

Systematic comparison of variant calling pipelines using gold standard personal exome variants

Hwang, S., Kim, E., Lee, I. & Marcotte, E. M., 2015 Dec 7, In : Scientific reports. 5, 17875.

Research output: Contribution to journalArticle

132 Citations (Scopus)

TRRUST: A reference database of human transcriptional regulatory interactions

Han, H., Shim, H., Shin, D., Shim, J. E., Ko, Y., Shin, J., Kim, H., Cho, A., Kim, E., Lee, T., Kim, H., Kim, K., Yang, S., Bae, D., Yun, A., Kim, S., Kim, C. Y., Cho, H. J., Kang, B., Shin, S. & 1 others, Lee, I., 2015 Jun 12, In : Scientific reports. 5, 11432.

Research output: Contribution to journalArticle

135 Citations (Scopus)
2014

Complementarity between distance- and probability-based methods of gene neighbourhood identification for pathway reconstruction

Shin, J., Lee, T., Kim, H. & Lee, I., 2014 Jan, In : Molecular BioSystems. 10, 1, p. 24-29 6 p.

Research output: Contribution to journalArticle

21 Citations (Scopus)