List of works - Insuk Lee

A Genome-Scale Co-Functional Network of Genes Can Accurately Reconstruct Regulatory Circuits Controlled by Two-Component Signaling Systems

article

A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality.

scientific article

A probabilistic functional network of yeast genes

scientific article published on 01 November 2004

A showcase of future plant biology: moving towards next-generation plant genetics assisted by genome sequencing and systems biology

scientific article published on 23 May 2014

A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans.

scientific article published on 27 January 2008

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

scientific article

An improved, bias-reduced probabilistic functional gene network of baker's yeast, Saccharomyces cerevisiae

scientific article

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

scientific article published on 5 January 2016

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

scientific article

AraNet: A Network Biology Server for Arabidopsis thaliana and Other Non-Model Plant Species

scientific article published on January 2017

Assessment of effectiveness of the network-guided genetic screen

scientific article published on 9 August 2010

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

scientific article published on 18 February 2020

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

scientific article published on 01 March 2020

Broad network-based predictability of Saccharomyces cerevisiae gene loss-of-function phenotypes

scientific article

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

scientific article (publication date: 4 January 2017)

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

scientific article published on 01 January 2019

Characterising and predicting haploinsufficiency in the human genome.

scientific article

Co-Inheritance Analysis within the Domains of Life Substantially Improves Network Inference by Phylogenetic Profiling

scientific article published on 22 September 2015

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

scientific article published on 01 January 2014

Construction of Functional Gene Networks Using Phylogenetic Profiles

scientific article published on January 2017

Construction of Functional Protein Networks Using Domain Profile Associations

scientific article published on 01 January 2020

Direct Conversion of Mouse Fibroblasts into Cholangiocyte Progenitor Cells

scientific article published on 27 March 2018

Dysregulation of T<sub>FH</sub>-B-T<sub>RM</sub> lymphocyte cooperation is associated with unfavorable anti-PD-1 responses in EGFR-mutant lung cancer

scientific article published on 18 October 2021

EcoliNet: a database of cofunctional gene network for Escherichia coli

scientific article

Editorial overview: genome studies and molecular genetics: data-driven approaches to genotype-to-phenotype studies in crops

scientific article

Effects of functional bias on supervised learning of a gene network model.

scientific article published on January 2009

FlyNet: a versatile network prioritization server for the Drosophila community

scientific article published on 5 May 2015

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

article

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

scientific article

Functional gene networks based on the gene neighborhood in metagenomes

article

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

scientific article

Generation of Integration-free Induced Neural Stem Cells from Mouse Fibroblasts

scientific article published on 04 May 2016

Genetic dissection of the biotic stress response using a genome-scale gene network for rice.

scientific article published on 31 October 2011

Genome-Wide Association Studies in Arabidopsis thaliana: Statistical Analysis and Network-Based Augmentation of Signals

scientific article published on 01 January 2021

Genome-wide identification of differentially methylated promoters and enhancers associated with response to anti-PD-1 therapy in non-small cell lung cancer

scientific article published on 02 September 2020

HumanNet v2: human gene networks for disease research

scientific article published on 01 January 2019

HumanNet v3: an improved database of human gene networks for disease research

scientific article published on 19 October 2021

Integrating functional genomics data

scientific article published on 01 January 2008

Introduction. Progresses in genome informatics

scientific article published on 01 December 2011

JiffyNet: a web-based instant protein network modeler for newly sequenced species ⬇️

scientific article published on May 17, 2013

MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network.

scientific article

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

scientific article

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

scientific article published on 16 May 2019

Metabolomics as a Hypothesis-Generating Functional Genomics Tool for the Annotation of Arabidopsis thaliana Genes of "Unknown Function"

scientific article

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

scientific article published on 09 September 2016

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

scientific article published on 20 March 2015

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

scientific article

Movement imagery-related lateralization of event-related (de)synchronization (ERD/ERS): motor-imagery duration effects

scientific article published on 25 August 2010

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

scientific article published on 01 August 2019

Network Integrative Genomic and Transcriptomic Analysis of Carbapenem-Resistant Klebsiella pneumoniae Strains Identifies Genes for Antibiotic Resistance and Virulence.

scientific article published on 21 May 2019

Network approaches to the genetic dissection of phenotypes in animals and humans

Network perturbation by recurrent regulatory variants in cancer

scientific article

Network-Based Gene Function Prediction in Mouse and Other Model Vertebrates Using MouseNet Server

scientific article published on January 2017

Network-assisted approaches for human disease research

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

scientific article

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

scientific article

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

scientific article published on 19 May 2016

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

scientific article published on 17 July 2018

Network-guided genetic screening: building, testing and using gene networks to predict gene function

scientific article published on 29 April 2008

Pathway-Dependent Effectiveness of Network Algorithms for Gene Prioritization

scientific article published on 19 June 2015

Pathway-specific protein domains are predictive for human diseases.

scientific article published on 10 May 2019

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

scientific article

Patterns of sequence conservation at termini of long terminal repeat (LTR) retrotransposons and DNA transposons in the human genome: lessons from phage Mu.

scientific article

Predicting genetic modifier loci using functional gene networks

scientific article

Prioritizing candidate disease genes by network-based boosting of genome-wide association data.

scientific article

Probabilistic functional gene societies ⬇️

scientific article published on January 31, 2011

Protein interaction networks from yeast to human

scientific article (publication date: June 2004)

RIDDLE: reflective diffusion and local extension reveal functional associations for unannotated gene sets via proximity in a gene network ⬇️

scientific article published on December 26, 2012

Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana

scientific article

Rational extension of the ribosome biogenesis pathway using network-guided genetics

scientific article

RiceNet v2: an improved network prioritization server for rice genes

scientific article published on 26 March 2015

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

scientific article published on 12 June 2020

Single-cell network biology for resolving cellular heterogeneity in human diseases

scientific article published on 26 November 2020

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

scientific article published on 28 February 2020

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

scientific article published on 04 August 2016

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

scientific article

Systematic prediction of gene function in Arabidopsis thaliana using a probabilistic functional gene network ⬇️

scientific article published on August 25, 2011

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

scientific article published on 26 October 2017

TRRUST: a reference database of human transcriptional regulatory interactions

scientific article published on 12 June 2015

The conserved CA/TG motif at Mu termini: T specifies stable transpososome assembly

scientific article published on 01 July 2003

The planar cell polarity effector Fuz is essential for targeted membrane trafficking, ciliogenesis and mouse embryonic development

scientific journal article

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

scientific article published on 29 November 2016

Towards establishment of a rice stress response interactome

scientific article

Towards understanding how molecular networks evolve in plants ⬇️

scientific article published on January 24, 2012

Tumor-Infiltrating Regulatory T Cell Accumulation in the Tumor Microenvironment is Mediated by IL33/ST2 Signaling

scientific article published on 02 September 2020

VirtualCytometry: a webserver for evaluating immune cell differentiation using single-cell RNA sequencing data

scientific article published on 01 January 2020

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

scientific article

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

scientific article published on 24 April 2017

WormNet v3: a network-assisted hypothesis-generating server for Caenorhabditis elegans

scientific article

YeastNet v3: a public database of data-specific and integrated functional gene networks for Saccharomyces cerevisiae

scientific article

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

scientific article published on 13 February 2018

List of works by Insuk Lee

A Genome-Scale Co-Functional Network of Genes Can Accurately Reconstruct Regulatory Circuits Controlled by Two-Component Signaling Systems

A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality.

A probabilistic functional network of yeast genes

A showcase of future plant biology: moving towards next-generation plant genetics assisted by genome sequencing and systems biology

A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans.

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

An improved, bias-reduced probabilistic functional gene network of baker's yeast, Saccharomyces cerevisiae

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

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

AraNet: A Network Biology Server for Arabidopsis thaliana and Other Non-Model Plant Species

Assessment of effectiveness of the network-guided genetic screen

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

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

Broad network-based predictability of Saccharomyces cerevisiae gene loss-of-function phenotypes

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

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

Characterising and predicting haploinsufficiency in the human genome.

Co-Inheritance Analysis within the Domains of Life Substantially Improves Network Inference by Phylogenetic Profiling

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

Construction of Functional Gene Networks Using Phylogenetic Profiles

Construction of Functional Protein Networks Using Domain Profile Associations

Direct Conversion of Mouse Fibroblasts into Cholangiocyte Progenitor Cells

Dysregulation of T<sub>FH</sub>-B-T<sub>RM</sub> lymphocyte cooperation is associated with unfavorable anti-PD-1 responses in EGFR-mutant lung cancer

EcoliNet: a database of cofunctional gene network for Escherichia coli

Editorial overview: genome studies and molecular genetics: data-driven approaches to genotype-to-phenotype studies in crops

Effects of functional bias on supervised learning of a gene network model.

FlyNet: a versatile network prioritization server for the Drosophila community

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

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

Functional gene networks based on the gene neighborhood in metagenomes

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

Generation of Integration-free Induced Neural Stem Cells from Mouse Fibroblasts

Genetic dissection of the biotic stress response using a genome-scale gene network for rice.

Genome-Wide Association Studies in Arabidopsis thaliana: Statistical Analysis and Network-Based Augmentation of Signals

Genome-wide identification of differentially methylated promoters and enhancers associated with response to anti-PD-1 therapy in non-small cell lung cancer

HumanNet v2: human gene networks for disease research

HumanNet v3: an improved database of human gene networks for disease research

Integrating functional genomics data

Introduction. Progresses in genome informatics

JiffyNet: a web-based instant protein network modeler for newly sequenced species ⬇️

MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network.

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

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

Metabolomics as a Hypothesis-Generating Functional Genomics Tool for the Annotation of Arabidopsis thaliana Genes of "Unknown Function"

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

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

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

Movement imagery-related lateralization of event-related (de)synchronization (ERD/ERS): motor-imagery duration effects

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

Network Integrative Genomic and Transcriptomic Analysis of Carbapenem-Resistant Klebsiella pneumoniae Strains Identifies Genes for Antibiotic Resistance and Virulence.

Network approaches to the genetic dissection of phenotypes in animals and humans

Network perturbation by recurrent regulatory variants in cancer

Network-Based Gene Function Prediction in Mouse and Other Model Vertebrates Using MouseNet Server

Network-assisted approaches for human disease research

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

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

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

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

Network-guided genetic screening: building, testing and using gene networks to predict gene function

Pathway-Dependent Effectiveness of Network Algorithms for Gene Prioritization

Pathway-specific protein domains are predictive for human diseases.

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

Patterns of sequence conservation at termini of long terminal repeat (LTR) retrotransposons and DNA transposons in the human genome: lessons from phage Mu.

Predicting genetic modifier loci using functional gene networks

Prioritizing candidate disease genes by network-based boosting of genome-wide association data.

Probabilistic functional gene societies ⬇️

Protein interaction networks from yeast to human

RIDDLE: reflective diffusion and local extension reveal functional associations for unannotated gene sets via proximity in a gene network ⬇️

Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana

Rational extension of the ribosome biogenesis pathway using network-guided genetics

RiceNet v2: an improved network prioritization server for rice genes

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

Single-cell network biology for resolving cellular heterogeneity in human diseases

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

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

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

Systematic prediction of gene function in Arabidopsis thaliana using a probabilistic functional gene network ⬇️

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

TRRUST: a reference database of human transcriptional regulatory interactions