Application of weighted gene co-expression network analysis to identify the hub genes in H1N1.
PMID:34336131
HGNChelper: identification and correction of invalid gene symbols for human and mouse.
PMID:33564398
A review of computational drug repositioning: strategies, approaches, opportunities, challenges, and directions.
PMID:33431024
A dichotomy of gene regulatory associations during the activated B-cell to plasmablast transition.
PMID:32843533
netNMF-sc: leveraging gene-gene interactions for imputation and dimensionality reduction in single-cell expression analysis.
PMID:31992614
A Novel Discovery: Holistic Efficacy at the Special Organ Level of Pungent Flavored Compounds from Pungent Traditional Chinese Medicine.
PMID:30754631
Module Analysis Captures Pancancer Genetically and Epigenetically Deregulated Cancer Driver Genes for Smoking and Antiviral Response.
PMID:29331675
Drug repurposing for the treatment of glioblastoma multiforme.
PMID:29179732
Non-Small Cell Lung Cancer Radiogenomics Map Identifies Relationships between Molecular and Imaging Phenotypes with Prognostic Implications.
PMID:28727543
The CINSARC signature as a prognostic marker for clinical outcome in multiple neoplasms.
PMID:28710396
annoPeak: a web application to annotate and visualize peaks from ChIP-seq/ChIP-exo-seq.
PMID:28169395
The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins.
PMID:27374120
Network Analysis Identifies Proinflammatory Plasma Cell Polarization for Secretion of ISG15 in Human Autoimmunity.
PMID:27357150
Finding New Order in Biological Functions from the Network Structure of Gene Annotations.
PMID:26588252
Gene expression meta-analysis reveals immune response convergence on the IFNγ-STAT1-IRF1 axis and adaptive immune resistance mechanisms in lymphoma.
PMID:26362649
Inhibition of Thrombopoietin/Mpl Signaling in Adult Hematopoiesis Identifies New Candidates for Hematopoietic Stem Cell Maintenance.
PMID:26147434
DSigDB: drug signatures database for gene set analysis.
PMID:25990557
Pancancer analysis of DNA methylation-driven genes using MethylMix.
PMID:25631659
Transcriptional coexpression network reveals the involvement of varying stem cell features with different dysregulations in different gastric cancer subtypes.
PMID:24917244
Pathway and network analysis in proteomics.
PMID:24911777
SPIB and BATF provide alternate determinants of IRF4 occupancy in diffuse large B-cell lymphoma linked to disease heterogeneity.
PMID:24875472
Annotation enrichment analysis: an alternative method for evaluating the functional properties of gene sets.
PMID:24569707
Identification of ovarian cancer driver genes by using module network integration of multi-omics data.
PMID:24511378
Polymorphic cytochrome P450 enzymes (CYPs) and their role in personalized therapy.
PMID:24340040
Reverse causal reasoning: applying qualitative causal knowledge to the interpretation of high-throughput data.
PMID:24266983
Confero: an integrated contrast data and gene set platform for computational analysis and biological interpretation of omics data.
PMID:23895370
Network2Canvas: network visualization on a canvas with enrichment analysis.
PMID:23749960
GeneSetDB: A comprehensive meta-database, statistical and visualisation framework for gene set analysis.
PMID:23650583
Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool.
PMID:23586463
Stem cell-like gene expression in ovarian cancer predicts type II subtype and prognosis.
PMID:23536770
A microarray platform-independent classification tool for cell of origin class allows comparative analysis of gene expression in diffuse large B-cell lymphoma.
PMID:23424639
Identifying master regulators of cancer and their downstream targets by integrating genomic and epigenomic features.
PMID:23424118
A data similarity-based strategy for meta-analysis of transcriptional profiles in cancer.
PMID:23383020
Exact statistical tests for the intersection of independent lists of genes.
PMID:23335952
Expression profiling of archival tumors for long-term health studies.
PMID:23136189
Transcriptional data: a new gateway to drug repositioning?
PMID:22897878
Silencing of Irf7 pathways in breast cancer cells promotes bone metastasis through immune escape.
PMID:22820642
iBBiG: iterative binary bi-clustering of gene sets.
PMID:22789589
Integration of breast cancer gene signatures based on graph centrality.
PMID:22784616
Genes2FANs: connecting genes through functional association networks.
PMID:22748121
Prognostic PET 18F-FDG uptake imaging features are associated with major oncogenomic alterations in patients with resected non-small cell lung cancer.
PMID:22710433
Network- and attribute-based classifiers can prioritize genes and pathways for autism spectrum disorders and intellectual disability.
PMID:22499558
Liverome: a curated database of liver cancer-related gene signatures with self-contained context information.
PMID:22369201
Angiogenic mRNA and microRNA gene expression signature predicts a novel subtype of serous ovarian cancer.
PMID:22348002
A three-gene model to robustly identify breast cancer molecular subtypes.
PMID:22262870
Comprehensive literature review and statistical considerations for microarray meta-analysis.
PMID:22262733
Characterization and clinical evaluation of CD10+ stroma cells in the breast cancer microenvironment.
PMID:22235100
The Stem Cell Discovery Engine: an integrated repository and analysis system for cancer stem cell comparisons.
PMID:22121217
GeneSigDB: a manually curated database and resource for analysis of gene expression signatures.
PMID:22110038
Predictive networks: a flexible, open source, web application for integration and analysis of human gene networks.
PMID:22096235
SIGNATURE: a workbench for gene expression signature analysis.
PMID:22078435
Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments.
PMID:22064864
Network based consensus gene signatures for biomarker discovery in breast cancer.
PMID:22046239
3DSwap: curated knowledgebase of proteins involved in 3D domain swapping.
PMID:21959866
Integrative computational biology for cancer research.
PMID:21691773
Protein-network modeling of prostate cancer gene signatures reveals essential pathways in disease recurrence.
PMID:21672909
Molecular signatures database (MSigDB) 3.0.
PMID:21546393
Conceptual aspects of large meta-analyses with publicly available microarray data: a case study in oncology.
PMID:21423405
Breast cancer biomarker discovery in the functional genomic age: a systematic review of 42 gene expression signatures.
PMID:21082037
A novel tissue-specific meta-analysis approach for gene expression predictions, initiated with a mammalian gene expression testis database.
PMID:20699007
Discovering causal signaling pathways through gene-expression patterns.
PMID:20494976
Data reporting standards: making the things we use better.
PMID:19939294