| 2024-05 |
Transcriptomic and metabolomic analysis unveils nanoplastic-induced gut barrier dysfunction via STAT1/6 and ERK pathways |
Environmental Research
|
| 2024-01 |
Integrative single-cell characterization of a frugivorous and an insectivorous bat kidney and pancreas |
Nature Communications
|
| 2023-01 |
Imputation of single-cell transcriptome data enables the reconstruction of networks predictive of breast cancer metastasis |
Computational and Structural Biotechnology Journal
|
| 2023-01 |
scHumanNet: a single-cell network analysis platform for the study of cell-type specificity of disease genes |
Nucleic Acids Research
|
| 2023-01 |
Deletion of PD-1 destabilizes the lineage identity and metabolic fitness of tumor-infiltrating regulatory T cells |
Nature Immunology
|
| 2022-10 |
HiFi metagenomic sequencing enables assembly of accurate and complete genomes from human gut microbiota |
Nature Communications
|
| 2022-10 |
COVID-GWAB: A Web-Based Prediction of COVID-19 Host Genes via Network Boosting of Genome-Wide Association Data |
Biomolecules
|
| 2022-09 |
The nucleolus is the site for inflammatory RNA decay during infection |
Nature communications
|
| 2022-06 |
Viral coinfection promotes tuberculosis immunopathogenesis by type I IFN signaling-dependent impediment of Th1 cell pulmonary influx |
NATURE COMMUNICATIONS
|
| 2022-01 |
HumanNet v3: an improved database of human gene networks for disease research |
Nucleic Acids Research
|
| 2022-01 |
The importance of enhancer methylation for epigenetic regulation of tumorigenesis in squamous lung cancer |
Experimental and Molecular Medicine
|
| 2021-12 |
Human reference gut microbiome catalog including newly assembled genomes from under-represented Asian metagenomes |
GENOME MEDICINE
|
| 2021-10 |
Dysregulation of TFH-B-TRM lymphocyte cooperation is associated with unfavorable anti-PD-1 responses in EGFR-mutant lung cancer |
NATURE COMMUNICATIONS
|
| 2021-07 |
Chaperone-like protein DAY plays critical roles in photomorphogenesis |
NATURE COMMUNICATIONS
|
| 2021-01 |
Systems biology analysis identifies TNFRSF9 as a functional marker of tumor-infiltrating regulatory T-cell enabling clinical outcome prediction in lung cancer |
Computational and Structural Biotechnology Journal
|
| 2020-11 |
Single-cell network biology for resolving cellular heterogeneity in human diseases |
EXPERIMENTAL AND MOLECULAR MEDICINE
|
| 2020-11 |
Tumor-infiltrating regulatory T-cell accumulation in the tumor microenvironment is mediated by IL33/ST2 signaling |
CANCER IMMUNOLOGY RESEARCH
|
| 2020-09 |
Genome-wide identification of differentially methylated promoters and enhancers associated with response to anti-PD-1 therapy in non-small cell lung cancer |
EXPERIMENTAL AND MOLECULAR MEDICINE
|
| 2020-06 |
Single-cell ATAC sequencing analysis: From data preprocessing to hypothesis generation |
Computational and Structural Biotechnology Journal
|
| 2020-03 |
BiomeNet: A database for construction and analysis of functional interaction networks for any species with a sequenced genome |
BIOINFORMATICS
|
| 2020-02 |
BarleyNet: A Network-Based Functional Omics Analysis Server for Cultivated Barley, Hordeum vulgare L. |
FRONTIERS IN PLANT SCIENCE
|
| 2020-02 |
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 |
GENOME MEDICINE
|
| 2020-01 |
VirtualCytometry: a webserver for evaluating immune cell differentiation using single-cell RNA sequencing data |
BIOINFORMATICS
|
| 2019-08 |
NGSEA: Network-Based Gene Set Enrichment Analysis for Interpreting Gene Expression Phenotypes with Functional Gene Sets |
MOLECULES AND CELLS
|
| 2019-08 |
MaizeNet: a co-functional network for network-assisted systems genetics in Zea mays |
PLANT JOURNAL
|
| 2019-07 |
Network Integrative Genomic and Transcriptomic Analysis of Carbapenem-Resistant Klebsiella pneumoniae Strains Identifies Genes for Antibiotic Resistance and Virulence |
mSystems
|
| 2019-05 |
Pathway-specific protein domains are predictive for human diseases |
PLOS COMPUTATIONAL BIOLOGY
|
| 2019-02 |
A Genome-Scale Co-Functional Network of Xanthomonas Genes Can Accurately Reconstruct Regulatory Circuits Controlled by Two-Component Signaling Systems |
MOLECULES AND CELLS
|
| 2019-01 |
HumanNet v2: Human gene networks for disease research |
NUCLEIC ACIDS RESEARCH
|
| 2018-07 |
Network-based genetic investigation of virulence-associated phenotypes in methicillin-resistant Staphylococcus aureus |
SCIENTIFIC REPORTS
|
| 2018-03 |
Direct Conversion of Mouse Fibroblasts into Cholangiocyte Progenitor Cells |
STEM CELL REPORTS
|
| 2018-02 |
araGWAB: Network-based boosting of genome-wide association studies in Arabidopsis thaliana |
SCIENTIFIC REPORTS
|
| 2018-01 |
TRRUST v2: An expanded reference database of human and mouse transcriptional regulatory interactions |
NUCLEIC ACIDS RESEARCH
|
| 2017-09 |
Functional gene networks based on the gene neighborhood in metagenomes |
ANIMAL CELLS AND SYSTEMS
|
| 2017-08 |
WheatNet: A genome-scale functional network for hexaploid bread wheat, Triticum aestivum |
MOLECULAR PLANT
|
| 2017-04 |
GWAB: a web server for the network-based boosting of human genome-wide association data |
NUCLEIC ACIDS RESEARCH
|
| 2017-04 |
TomatoNet: A Genome-wide Co-functional Network for Unveiling Complex Traits of Tomato a Model Crop for Fleshy Fruits |
MOLECULAR PLANT
|
| 2017-03 |
Network perturbation by recurrent regulatory variants in cancer |
PLOS COMPUTATIONAL BIOLOGY
|
| 2017-02 |
From sequencing data to gene functions: co-functional network approaches |
ANIMAL CELLS AND SYSTEMS
|
| 2017-01 |
COEXPEDIA: exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH) |
NUCLEIC ACIDS RESEARCH
|
| 2017-01 |
SoyNet: a database of co-functional networks for soybean Glycine max |
NUCLEIC ACIDS RESEARCH
|
| 2016-11 |
Function-driven discovery of disease genes in zebrafish using an integrated genomics big data resource |
NUCLEIC ACIDS RESEARCH
|
| 2016-09 |
Microvesicles from brain-extract-treated mesenchymal stem cells improve neurological functions in a rat model of ischemic stroke |
SCIENTIFIC REPORTS
|
| 2016-09 |
Weighted mutual information analysis substantially improves domain-based functional network models |
BIOINFORMATICS
|
| 2016-07 |
Generation of Integration-free Induced Neural Stem Cells from Mouse Fibroblasts |
JOURNAL OF BIOLOGICAL CHEMISTRY
|
| 2016-06 |
MUFFINN: cancer gene discovery via network analysis of somatic mutation data |
GENOME BIOLOGY
|
| 2016-05 |
Network-assisted investigation of virulence and antibiotic-resistance systems in Pseudomonas aeruginosa |
SCIENTIFIC REPORTS
|
| 2016-05 |
A single gene of a commensal microbe affects host susceptibility to enteric infection |
NATURE COMMUNICATIONS
|
| 2016-02 |
An integrated systems biology approach identifies positive cofactor 4 as a factor that increases reprogramming efficiency |
NUCLEIC ACIDS RESEARCH
|
| 2016-01 |
MouseNet v2: a database of gene networks for studying the laboratory mouse and eight other model vertebrates |
NUCLEIC ACIDS RESEARCH
|
| 2015-12 |
Systematic comparison of variant calling pipelines using gold standard personal exome variants |
SCIENTIFIC REPORTS
|
| 2015-09 |
Co-Inheritance Analysis within the Domains of Life Substantially Improves Network Inference by Phylogenetic Profiling |
PLOS ONE
|
| 2015-08 |
Network-assisted approaches for human disease research |
ANIMAL CELLS AND SYSTEMS
|
| 2015-07 |
RiceNet v2: an improved network prioritization server for rice genes |
NUCLEIC ACIDS RESEARCH
|
| 2015-07 |
FlyNet: a versatile network prioritization server for the Drosophila community |
NUCLEIC ACIDS RESEARCH
|
| 2015-06 |
Pathway-Dependent Effectiveness of Network Algorithms for Gene Prioritization |
PLOS ONE
|
| 2015-06 |
TRRUST: a reference database of human transcriptional regulatory interactions |
SCIENTIFIC REPORTS
|
| 2015-04 |
Editorial overview: Genome studies and molecular genetics: data-driven approaches to genotype-to-phenotype studies in crops |
CURRENT OPINION IN PLANT BIOLOGY
|
| 2015-04 |
Patterns of metabolite changes identified from large-scale gene perturbations in arabidopsis using a genome-scale metabolic network |
PLANT PHYSIOLOGY
|
| 2015-04 |
Network-assisted crop systems genetics: Network inference and integrative analysis |
CURRENT OPINION IN PLANT BIOLOGY
|
| 2015-03 |
Modes of interaction between individuals dominate the topologies of real world networks |
PLOS ONE
|
| 2015-03 |
Network-assisted genetic dissection of pathogenicity and drug resistance in the opportunistic human pathogenic fungus Cryptococcus neoformans |
SCIENTIFIC REPORTS
|
| 2015-02 |
EcoliNet: a database of cofunctional gene network for Escherichia coli |
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
|
| 2015-01 |
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
|
| 2014-07 |
MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network |
NUCLEIC ACIDS RESEARCH
|
| 2014-07 |
WormNet v3: a network-assisted hypothesis-generating server for Caenorhabditis elegans |
NUCLEIC ACIDS RESEARCH
|
| 2014-05 |
A showcase of future plant biology: moving towards next-generation plant genetics assisted by genome sequencing and systems biology |
GENOME BIOLOGY
|
| 2014-01 |
Complementarity between distance- and probability-based methods of gene neighbourhood identification for pathway reconstruction |
MOLECULAR BIOSYSTEMS
|
| 2014-01 |
YeastNet v3: a public database of data-specific and integrated functional gene networks for Saccharomyces cerevisiae |
NUCLEIC ACIDS RESEARCH
|
| 2013-07 |
JiffyNet: a web-based instant protein network modeler for newly sequenced species |
NUCLEIC ACIDS RESEARCH
|
| 2013-04 |
Network approaches to the genetic dissection of phenotypes in animals and humans |
ANIMAL CELLS AND SYSTEMS
|
| 2012-12 |
RIDDLE: Reflective diffusion and local extension reveal functional associations for unannotated gene sets via proximity in a gene network |
GENOME BIOLOGY
|
| 2012-04 |
Towards understanding how molecular networks evolve in plants |
CURRENT OPINION IN PLANT BIOLOGY
|
| 2012-02 |
Metabolomics as a hypothesis-generating functional genomics tool for the annotation of Arabidopsis thaliana genes of "unknown function" |
FRONTIERS IN PLANT SCIENCE
|
| 2011-11 |
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
|
| 2011-09 |
Systematic prediction of gene function in Arabidopsis thaliana using a probabilistic functional gene network |
NATURE PROTOCOLS
|
| 2011-08 |
Probabilistic functional gene societies |
PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY
|
| 2011-07 |
Prioritizing candidate disease genes by network-based boosting of genome-wide association data |
GENOME RESEARCH
|
| 2011-04 |
Towards Establishment of a Rice Stress Response Interactome |
PLOS GENETICS
|
| 2010-10 |
Characterising and Predicting Haploinsufficiency in the Human Genome |
PLOS GENETICS
|
| 2010-09 |
Assessment of effectiveness of the network-guided genetic screen |
Molecular Biosystems
|
| 2010-08 |
Predicting genetic modifier loci using functional gene networks |
Genome research
|
| 2010-02 |
Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana |
Nature Biotechnology
|
| 2009-10 |
Rational Extension of the Ribosome Biogenesis Pathway Using Network-Guided Genetics |
Plos Biology
|
| 2009-10 |
The planar cell polarity effector Fuz is essential for targeted membrane trafficking, ciliogenesis and mouse embryonic development |
Nature Cell Biology
|
| 2008-08 |
Network-guided genetic screening: building, testing, and using gene networks to predict gene function |
BRIEF. FUNCT. GENOMIC. PROTEOMIC.
|
| 2008-02 |
A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans |
Nature Genetics
|
| 2007-10 |
An improved, bias-reduced probabilistic functional gene network of baker's yeast, Saccharomyces cerevisiae |
PLoS One
|
| 2007-07 |
A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality |
BMC BIOINFORMATICS
|