Lista de obras -

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.

artículo científico publicado en 2007

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

artículo científico publicado en 2014

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

artículo científico publicado en 2008

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

artículo científico publicado en 2016

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

artículo científico publicado en 2007

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

artículo científico publicado en 2016

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

artículo científico publicado en 2014

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

artículo científico publicado en 2017

Assessment of effectiveness of the network-guided genetic screen

artículo científico publicado en 2010

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

artículo científico publicado en 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

artículo científico publicado en 2007

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

artículo científico publicado en 2017

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

artículo científico publicado en 2019

Characterising and predicting haploinsufficiency in the human genome.

artículo científico publicado en 2010

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

artículo científico publicado en 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

artículo científico publicado en 2017

Construction of Functional Protein Networks Using Domain Profile Associations

artículo científico publicado en 2020

Direct Conversion of Mouse Fibroblasts into Cholangiocyte Progenitor Cells

artículo científico publicado en 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

artículo científico publicado en 2021

EcoliNet: a database of cofunctional gene network for Escherichia coli

artículo científico publicado en 2015

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

artículo científico publicado en 2015

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

artículo científico publicado en 2009

FlyNet: a versatile network prioritization server for the Drosophila community

artículo científico publicado en 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

artículo científico publicado en 2016

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.

artículo científico publicado en 2017

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

artículo científico publicado en 2016

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

artículo científico publicado en 2011

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

artículo científico publicado en 2021

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

artículo científico publicado en 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

artículo científico publicado en 2021

Integrating functional genomics data

scientific article published on 01 January 2008

Introduction. Progresses in genome informatics

artículo científico publicado en 2011

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

artículo científico publicado el 17 de mayo de 2013

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

artículo científico publicado en 2014

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

artículo científico publicado en 2016

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

artículo científico publicado en 2019

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

artículo científico publicado en 2012

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

artículo científico publicado en 2016

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

artículo científico publicado en 2015

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

artículo científico publicado en 2015

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

artículo científico publicado en 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.

artículo científico publicado en 2019

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

Network perturbation by recurrent regulatory variants in cancer

artículo científico publicado en 2017

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

artículo científico publicado en 2017

Network-assisted approaches for human disease research

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

artículo científico publicado en 2015

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

artículo científico publicado en 2015

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

artículo científico publicado en 2016

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

artículo científico publicado en 2018

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

artículo científico publicado en 2008

Pathway-Dependent Effectiveness of Network Algorithms for Gene Prioritization

artículo científico publicado en 2015

Pathway-specific protein domains are predictive for human diseases.

artículo científico publicado en 2019

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

artículo científico publicado en 2015

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

artículo científico publicado en 2003

Predicting genetic modifier loci using functional gene networks

artículo científico publicado en 2010

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

artículo científico publicado en 2011

Probabilistic functional gene societies ⬇️

artículo científico publicado el 31 de enero de 2011

Protein interaction networks from yeast to human

artículo científico publicado en 2004

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

artículo científico publicado el 26 de diciembre de 2012

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

artículo científico publicado en 2010

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

artículo científico publicado en 2009

RiceNet v2: an improved network prioritization server for rice genes

artículo científico publicado en 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.

artículo científico publicado en 2016

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

artículo científico publicado en 2015

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

artículo científico publicado el 25 de agosto de 2011

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

artículo científico publicado en 2017

TRRUST: a reference database of human transcriptional regulatory interactions

artículo científico publicado en 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

artículo científico publicado en 2016

Towards establishment of a rice stress response interactome

artículo científico publicado en 2011

Towards understanding how molecular networks evolve in plants ⬇️

artículo científico publicado el 24 de enero de 2012

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

artículo científico publicado en 2020

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

artículo científico publicado en 2020

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

artículo científico publicado en 2016

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

artículo científico publicado en 2017

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

artículo científico publicado en 2014

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

artículo científico publicado en 2013

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

artículo científico publicado en 2018

Lista de obras de

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