| Year |
Citation |
Score |
| 2022 |
Cha J, Yu J, Cho JW, Hemberg M, Lee I. scHumanNet: a single-cell network analysis platform for the study of cell-type specificity of disease genes. Nucleic Acids Research. PMID 36350625 DOI: 10.1093/nar/gkac1042 |
0.305 |
|
| 2022 |
Baek S, Yang S, Lee I. COVID-GWAB: A Web-Based Prediction of COVID-19 Host Genes via Network Boosting of Genome-Wide Association Data. Biomolecules. 12. PMID 36291657 DOI: 10.3390/biom12101446 |
0.327 |
|
| 2021 |
Kim CY, Baek S, Cha J, Yang S, Kim E, Marcotte EM, Hart T, Lee I. HumanNet v3: an improved database of human gene networks for disease research. Nucleic Acids Research. PMID 34747468 DOI: 10.1093/nar/gkab1048 |
0.348 |
|
| 2020 |
Baek S, Lee I. Single-cell ATAC sequencing analysis: From data preprocessing to hypothesis generation. Computational and Structural Biotechnology Journal. 18: 1429-1439. PMID 32637041 DOI: 10.1016/J.Csbj.2020.06.012 |
0.386 |
|
| 2020 |
Lee S, Lee T, Yang S, Lee I. BarleyNet: A Network-Based Functional Omics Analysis Server for Cultivated Barley, L. Frontiers in Plant Science. 11: 98. PMID 32133024 DOI: 10.3389/Fpls.2020.00098 |
0.437 |
|
| 2020 |
Shim JE, Lee I. Construction of Functional Protein Networks Using Domain Profile Associations. Methods in Molecular Biology (Clifton, N.J.). 2074: 35-44. PMID 31583628 DOI: 10.1007/978-1-4939-9873-9_3 |
0.312 |
|
| 2019 |
Kim E, Bae D, Yang S, Ko G, Lee S, Lee B, Lee I. BiomeNet: A database for construction and analysis of functional interaction networks for any species with a sequenced genome. Bioinformatics (Oxford, England). PMID 31599923 DOI: 10.1093/Bioinformatics/Btz776 |
0.423 |
|
| 2019 |
Han H, Lee S, Lee I. NGSEA: Network-Based Gene Set Enrichment Analysis for Interpreting Gene Expression Phenotypes with Functional Gene Sets. Molecules and Cells. PMID 31307154 DOI: 10.14348/Molcells.2019.0065 |
0.395 |
|
| 2019 |
Shim JE, Kim JH, Shin J, Lee JE, Lee I. Pathway-specific protein domains are predictive for human diseases. Plos Computational Biology. 15: e1007052. PMID 31075101 DOI: 10.1371/Journal.Pcbi.1007052 |
0.351 |
|
| 2019 |
Lee T, Lee S, Yang S, Lee I. MaizeNet: A co-functional network for network-assisted systems genetics in Zea mays. The Plant Journal : For Cell and Molecular Biology. PMID 31006149 DOI: 10.1111/tpj.14341 |
0.366 |
|
| 2019 |
Kim H, Joe A, Lee M, Yang S, Ma X, Ronald PC, Lee I. A Genome-Scale Co-Functional Network of Xanthomonas Genes Can Accurately Reconstruct Regulatory Circuits Controlled by Two-Component Signaling Systems. Molecules and Cells. PMID 30759970 DOI: 10.14348/Molcells.2018.0403 |
0.463 |
|
| 2019 |
Han H, Lehner B, Lee I. Cancer Gene Discovery by Network Analysis of Somatic Mutations Using the MUFFINN Server. Methods in Molecular Biology (Clifton, N.J.). 1907: 37-50. PMID 30542989 DOI: 10.1007/978-1-4939-8967-6_3 |
0.378 |
|
| 2018 |
Hwang S, Kim CY, Yang S, Kim E, Hart T, Marcotte EM, Lee I. HumanNet v2: human gene networks for disease research. Nucleic Acids Research. PMID 30418591 DOI: 10.1093/Nar/Gky1126 |
0.44 |
|
| 2018 |
Kim CY, Lee M, Lee K, Yoon SS, Lee I. Network-based genetic investigation of virulence-associated phenotypes in methicillin-resistant Staphylococcus aureus. Scientific Reports. 8: 10796. PMID 30018396 DOI: 10.1038/S41598-018-29120-3 |
0.381 |
|
| 2018 |
Lee T, Lee I. araGWAB: Network-based boosting of genome-wide association studies in Arabidopsis thaliana. Scientific Reports. 8: 2925. PMID 29440686 DOI: 10.1038/s41598-018-21301-4 |
0.308 |
|
| 2017 |
Shim JE, Lee T, Lee I. From sequencing data to gene functions: co-functional network approaches. Animal Cells and Systems. 21: 77-83. PMID 30460054 DOI: 10.1080/19768354.2017.1284156 |
0.469 |
|
| 2017 |
Han H, Cho JW, Lee S, Yun A, Kim H, Bae D, Yang S, Kim CY, Lee M, Kim E, Lee S, Kang B, Jeong D, Kim Y, Jeon HN, ... ... Lee I, et al. TRRUST v2: an expanded reference database of human and mouse transcriptional regulatory interactions. Nucleic Acids Research. PMID 29087512 DOI: 10.1093/Nar/Gkx1013 |
0.305 |
|
| 2017 |
Lee T, Lee I. AraNet: A Network Biology Server for Arabidopsis thaliana and Other Non-Model Plant Species. Methods in Molecular Biology (Clifton, N.J.). 1629: 225-238. PMID 28623589 DOI: 10.1007/978-1-4939-7125-1_15 |
0.451 |
|
| 2017 |
Kim E, Lee I. Network-Based Gene Function Prediction in Mouse and Other Model Vertebrates Using MouseNet Server. Methods in Molecular Biology (Clifton, N.J.). 1611: 183-198. PMID 28451980 DOI: 10.1007/978-1-4939-7015-5_14 |
0.363 |
|
| 2017 |
Lee T, Hwang S, Kim CY, Shim H, Kim H, Ronald PC, Marcotte EM, Lee I. WheatNet: A genome-scale functional network for hexaploid bread wheat, Triticum aestivum. Molecular Plant. PMID 28450181 DOI: 10.1016/J.Molp.2017.04.006 |
0.387 |
|
| 2017 |
Shim JE, Bang C, Yang S, Lee T, Hwang S, Kim CY, Singh-Blom UM, Marcotte EM, Lee I. GWAB: a web server for the network-based boosting of human genome-wide association data. Nucleic Acids Research. PMID 28449091 DOI: 10.1093/Nar/Gkx284 |
0.417 |
|
| 2017 |
Jang K, Kim K, Cho A, Lee I, Choi JK. Network perturbation by recurrent regulatory variants in cancer. Plos Computational Biology. 13: e1005449. PMID 28333928 DOI: 10.1371/Journal.Pcbi.1005449 |
0.388 |
|
| 2017 |
Shin J, Lee I. Construction of Functional Gene Networks Using Phylogenetic Profiles. Methods in Molecular Biology (Clifton, N.J.). 1526: 87-98. PMID 27896737 DOI: 10.1007/978-1-4939-6613-4_5 |
0.407 |
|
| 2017 |
Kim CY, Lee I. Functional gene networks based on the gene neighborhood in metagenomes Animal Cells and Systems. 21: 301-306. DOI: 10.1080/19768354.2017.1382388 |
0.485 |
|
| 2016 |
Shim H, Kim JH, Kim CY, Hwang S, Kim H, Yang S, Lee JE, Lee I. Function-driven discovery of disease genes in zebrafish using an integrated genomics big data resource. Nucleic Acids Research. 44: 9611-9623. PMID 27903883 DOI: 10.1093/nar/gkw897 |
0.337 |
|
| 2016 |
Yang S, Kim CY, Hwang S, Kim E, Kim H, Shim H, Lee I. COEXPEDIA: exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH). Nucleic Acids Research. PMID 27679477 DOI: 10.1093/Nar/Gkw868 |
0.331 |
|
| 2016 |
Kim E, Hwang S, Lee I. SoyNet: a database of co-functional networks for soybean Glycine max. Nucleic Acids Research. PMID 27492285 DOI: 10.1093/Nar/Gkw704 |
0.457 |
|
| 2016 |
Cho A, Shim JE, Kim E, Supek F, Lehner B, Lee I. MUFFINN: cancer gene discovery via network analysis of somatic mutation data. Genome Biology. 17: 129. PMID 27333808 DOI: 10.1186/S13059-016-0989-X |
0.368 |
|
| 2016 |
Shim JE, Lee I. Weighted mutual information analysis substantially improves domain-based functional network models. Bioinformatics (Oxford, England). PMID 27207946 DOI: 10.1093/Bioinformatics/Btw320 |
0.338 |
|
| 2016 |
Hwang S, Kim CY, Ji SG, Go J, Kim H, Yang S, Kim HJ, Cho A, Yoon SS, Lee I. Network-assisted investigation of virulence and antibiotic-resistance systems in Pseudomonas aeruginosa. Scientific Reports. 6: 26223. PMID 27194047 DOI: 10.1038/Srep26223 |
0.38 |
|
| 2016 |
Kim SM, Kim JW, Kwak TH, Park SW, Kim KP, Park H, Lim KT, Kang K, Kim J, Yang JH, Han H, Lee I, Hyun JK, Bae YM, Schöler HR, et al. Generation of Integration-free Induced Neural Stem Cells from Mouse Fibroblasts. The Journal of Biological Chemistry. PMID 27189941 DOI: 10.1074/Jbc.M115.713578 |
0.318 |
|
| 2015 |
Hwang S, Kim E, Lee I, Marcotte EM. Systematic comparison of variant calling pipelines using gold standard personal exome variants. Scientific Reports. 5: 17875. PMID 26639839 DOI: 10.1038/Srep17875 |
0.337 |
|
| 2015 |
Kim E, Hwang S, Kim H, Shim H, Kang B, Yang S, Shim JH, Shin SY, Marcotte EM, Lee I. MouseNet v2: a database of gene networks for studying the laboratory mouse and eight other model vertebrates. Nucleic Acids Research. PMID 26527726 DOI: 10.1093/Nar/Gkv1155 |
0.478 |
|
| 2015 |
Shin J, Lee I. Co-Inheritance Analysis within the Domains of Life Substantially Improves Network Inference by Phylogenetic Profiling. Plos One. 10: e0139006. PMID 26394049 DOI: 10.1371/Journal.Pone.0139006 |
0.405 |
|
| 2015 |
Shim JE, Hwang S, Lee I. Pathway-Dependent Effectiveness of Network Algorithms for Gene Prioritization. Plos One. 10: e0130589. PMID 26091506 DOI: 10.1371/Journal.Pone.0130589 |
0.408 |
|
| 2015 |
Shin J, Yang S, Kim E, Kim CY, Shim H, Cho A, Kim H, Hwang S, Shim JE, Lee I. FlyNet: a versatile network prioritization server for the Drosophila community. Nucleic Acids Research. 43: W91-7. PMID 25943544 DOI: 10.1093/Nar/Gkv453 |
0.457 |
|
| 2015 |
Lee I, Mockler TC. Editorial overview: genome studies and molecular genetics: data-driven approaches to genotype-to-phenotype studies in crops. Current Opinion in Plant Biology. 24: iv-vi. PMID 25817324 DOI: 10.1016/J.Pbi.2015.03.001 |
0.307 |
|
| 2015 |
Lee T, Oh T, Yang S, Shin J, Hwang S, Kim CY, Kim H, Shim H, Shim JE, Ronald PC, Lee I. RiceNet v2: an improved network prioritization server for rice genes. Nucleic Acids Research. 43: W122-7. PMID 25813048 DOI: 10.1093/nar/gkv253 |
0.351 |
|
| 2015 |
Kim H, Jung KW, Maeng S, Chen YL, Shin J, Shim JE, Hwang S, Janbon G, Kim T, Heitman J, Bahn YS, Lee I. Network-assisted genetic dissection of pathogenicity and drug resistance in the opportunistic human pathogenic fungus Cryptococcus neoformans. Scientific Reports. 5: 8767. PMID 25739925 DOI: 10.1038/Srep08767 |
0.421 |
|
| 2015 |
Lee T, Kim H, Lee I. Network-assisted crop systems genetics: network inference and integrative analysis. Current Opinion in Plant Biology. 24: 61-70. PMID 25698380 DOI: 10.1016/j.pbi.2015.02.001 |
0.339 |
|
| 2015 |
Kim T, Dreher K, Nilo-Poyanco R, Lee I, Fiehn O, Lange BM, Nikolau BJ, Sumner L, Welti R, Wurtele ES, Rhee SY. Patterns of metabolite changes identified from large-scale gene perturbations in Arabidopsis using a genome-scale metabolic network. Plant Physiology. 167: 1685-98. PMID 25670818 DOI: 10.1104/Pp.114.252361 |
0.386 |
|
| 2015 |
Kim H, Shim JE, Shin J, Lee I. EcoliNet: a database of cofunctional gene network for Escherichia coli. Database : the Journal of Biological Databases and Curation. 2015. PMID 25650278 DOI: 10.1093/Database/Bav001 |
0.467 |
|
| 2015 |
Lee T, Yang S, Kim E, Ko Y, Hwang S, Shin J, Shim JE, Shim H, Kim H, Kim C, Lee I. AraNet v2: an improved database of co-functional gene networks for the study of Arabidopsis thaliana and 27 other nonmodel plant species. Nucleic Acids Research. 43: D996-1002. PMID 25355510 DOI: 10.1093/Nar/Gku1053 |
0.462 |
|
| 2015 |
Shim JE, Lee I. Network-assisted approaches for human disease research Animal Cells and Systems. 19: 231-235. DOI: 10.1080/19768354.2015.1074108 |
0.372 |
|
| 2014 |
Cho A, Shin J, Hwang S, Kim C, Shim H, Kim H, Kim H, Lee I. WormNet v3: a network-assisted hypothesis-generating server for Caenorhabditis elegans. Nucleic Acids Research. 42: W76-82. PMID 24813450 DOI: 10.1093/Nar/Gku367 |
0.465 |
|
| 2014 |
Shin J, Lee T, Kim H, Lee I. Complementarity between distance- and probability-based methods of gene neighbourhood identification for pathway reconstruction. Molecular Biosystems. 10: 24-9. PMID 24194096 DOI: 10.1039/C3Mb70366E |
0.352 |
|
| 2014 |
Kim H, Shin J, Kim E, Kim H, Hwang S, Shim JE, Lee I. YeastNet v3: a public database of data-specific and integrated functional gene networks for Saccharomyces cerevisiae. Nucleic Acids Research. 42: D731-6. PMID 24165882 DOI: 10.1093/nar/gkt981 |
0.373 |
|
| 2013 |
Kim E, Kim H, Lee I. JiffyNet: a web-based instant protein network modeler for newly sequenced species. Nucleic Acids Research. 41: W192-7. PMID 23685435 DOI: 10.1093/Nar/Gkt419 |
0.426 |
|
| 2013 |
Lee I. Network approaches to the genetic dissection of phenotypes in animals and humans Animal Cells and Systems. 17: 75-79. DOI: 10.1080/19768354.2013.789076 |
0.348 |
|
| 2012 |
Wang PI, Hwang S, Kincaid RP, Sullivan CS, Lee I, Marcotte EM. RIDDLE: reflective diffusion and local extension reveal functional associations for unannotated gene sets via proximity in a gene network. Genome Biology. 13: R125. PMID 23268829 DOI: 10.1186/Gb-2012-13-12-R125 |
0.319 |
|
| 2012 |
Quanbeck SM, Brachova L, Campbell AA, Guan X, Perera A, He K, Rhee SY, Bais P, Dickerson JA, Dixon P, Wohlgemuth G, Fiehn O, Barkan L, Lange I, Lange BM, ... Lee I, et al. Metabolomics as a Hypothesis-Generating Functional Genomics Tool for the Annotation of Arabidopsis thaliana Genes of "Unknown Function". Frontiers in Plant Science. 3: 15. PMID 22645570 DOI: 10.3389/Fpls.2012.00015 |
0.423 |
|
| 2011 |
Lee I, Seo YS, Coltrane D, Hwang S, Oh T, Marcotte EM, Ronald PC. Genetic dissection of the biotic stress response using a genome-scale gene network for rice. Proceedings of the National Academy of Sciences of the United States of America. 108: 18548-53. PMID 22042862 DOI: 10.1073/Pnas.1110384108 |
0.365 |
|
| 2011 |
Hwang S, Rhee SY, Marcotte EM, Lee I. Systematic prediction of gene function in Arabidopsis thaliana using a probabilistic functional gene network. Nature Protocols. 6: 1429-42. PMID 21886106 DOI: 10.1038/Nprot.2011.372 |
0.315 |
|
| 2011 |
Lee I, Blom UM, Wang PI, Shim JE, Marcotte EM. Prioritizing candidate disease genes by network-based boosting of genome-wide association data. Genome Research. 21: 1109-21. PMID 21536720 DOI: 10.1101/Gr.118992.110 |
0.362 |
|
| 2011 |
Lee I. Probabilistic functional gene societies. Progress in Biophysics and Molecular Biology. 106: 435-42. PMID 21281658 DOI: 10.1016/J.Pbiomolbio.2011.01.003 |
0.447 |
|
| 2010 |
Huang N, Lee I, Marcotte EM, Hurles ME. Characterising and predicting haploinsufficiency in the human genome. Plos Genetics. 6: e1001154. PMID 20976243 DOI: 10.1371/Journal.Pgen.1001154 |
0.437 |
|
| 2010 |
Lee I, Lehner B, Vavouri T, Shin J, Fraser AG, Marcotte EM. Predicting genetic modifier loci using functional gene networks. Genome Research. 20: 1143-53. PMID 20538624 DOI: 10.1101/Gr.102749.109 |
0.435 |
|
| 2010 |
Lee I, Ambaru B, Thakkar P, Marcotte EM, Rhee SY. Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana. Nature Biotechnology. 28: 149-56. PMID 20118918 DOI: 10.1038/Nbt.1603 |
0.439 |
|
| 2009 |
Li Z, Lee I, Moradi E, Hung NJ, Johnson AW, Marcotte EM. Rational extension of the ribosome biogenesis pathway using network-guided genetics. Plos Biology. 7: e1000213. PMID 19806183 DOI: 10.1371/Journal.Pbio.1000213 |
0.422 |
|
| 2009 |
Lee I, Marcotte EM. Effects of functional bias on supervised learning of a gene network model. Methods in Molecular Biology (Clifton, N.J.). 541: 463-75. PMID 19381535 DOI: 10.1007/978-1-59745-243-4_20 |
0.41 |
|
| 2008 |
Lee I, Marcotte EM. Integrating functional genomics data. Methods in Molecular Biology (Clifton, N.J.). 453: 267-78. PMID 18712309 DOI: 10.1007/978-1-60327-429-6_14 |
0.374 |
|
| 2008 |
Lehner B, Lee I. Network-guided genetic screening: building, testing and using gene networks to predict gene function. Briefings in Functional Genomics & Proteomics. 7: 217-27. PMID 18445637 DOI: 10.1093/Bfgp/Eln020 |
0.452 |
|
| 2008 |
Lee I, Lehner B, Crombie C, Wong W, Fraser AG, Marcotte EM. A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans. Nature Genetics. 40: 181-8. PMID 18223650 DOI: 10.1038/Ng.2007.70 |
0.443 |
|
| 2007 |
McGary KL, Lee I, Marcotte EM. Broad network-based predictability of Saccharomyces cerevisiae gene loss-of-function phenotypes. Genome Biology. 8: R258. PMID 18053250 DOI: 10.1186/Gb-2007-8-12-R258 |
0.447 |
|
| 2007 |
Lee I, Li Z, Marcotte EM. An improved, bias-reduced probabilistic functional gene network of baker's yeast, Saccharomyces cerevisiae. Plos One. 2: e988. PMID 17912365 DOI: 10.1371/Journal.Pone.0000988 |
0.461 |
|
| 2007 |
Hart GT, Lee I, Marcotte ER. A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality. Bmc Bioinformatics. 8: 236. PMID 17605818 DOI: 10.1186/1471-2105-8-236 |
0.302 |
|
| 2004 |
Lee I, Date SV, Adai AT, Marcotte EM. A probabilistic functional network of yeast genes. Science (New York, N.Y.). 306: 1555-8. PMID 15567862 DOI: 10.1126/Science.1099511 |
0.462 |
|
| 2004 |
Bork P, Jensen LJ, von Mering C, Ramani AK, Lee I, Marcotte EM. Protein interaction networks from yeast to human. Current Opinion in Structural Biology. 14: 292-9. PMID 15193308 DOI: 10.1016/J.Sbi.2004.05.003 |
0.359 |
|
| 2003 |
Lee I, Harshey RM. Patterns of sequence conservation at termini of long terminal repeat (LTR) retrotransposons and DNA transposons in the human genome: lessons from phage Mu. Nucleic Acids Research. 31: 4531-40. PMID 12888514 DOI: 10.1093/Nar/Gkg499 |
0.566 |
|
| 2003 |
Lee I, Harshey RM. The conserved CA/TG motif at Mu termini: T specifies stable transpososome assembly. Journal of Molecular Biology. 330: 261-75. PMID 12823966 DOI: 10.1016/S0022-2836(03)00574-6 |
0.553 |
|
| 2001 |
Lee I, Harshey RM. Importance of the conserved CA dinucleotide at Mu termini. Journal of Molecular Biology. 314: 433-44. PMID 11846557 DOI: 10.1006/Jmbi.2001.5177 |
0.548 |
|
| Show low-probability matches. |