DISEASES
DISEASES is a weekly updated web resource that integrates evidence on disease-gene associations from automatic text mining, manually curated literature, cancer mutation data, and genome-wide association studies. We further unify the evidence by assigning confidence scores that facilitate comparison of the different types and sources of evidence.
Description
More detailed information about this field from each metasource.
DISEASES is a weekly updated web resource that integrates evidence on disease-gene associations from automatic text mining, manually curated literature, cancer mutation data, and genome-wide association studies. We further unify the evidence by assigning confidence scores that facilitate comparison of the different types and sources of evidence.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:31:07.403080
Webpage:
https://diseases.jensenlab.org/Webpage
More detailed information about this field from each metasource.
https://diseases.jensenlab.org/
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:31:07.403080
Licence:
Name: CC-BY-4.0Licence name
More detailed information about this field from each metasource.
Publications:
Publications
More detailed information about this field from each metasource.
DISEASES: text mining and data integration of disease-gene associations
PMID: 25484339
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:07.403080
Publications
More detailed information about this field from each metasource.
DISEASES: text mining and data integration of disease-gene associations
PMID: 25484339
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:07.403080
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DISEASES: text mining and data integration of disease-gene associations
PubMed citations: 184.
184 articles citing: DISEASES: text mining and data integration of disease-gene associations
Rule-Based Information Extraction from Free-Text Pathology Reports Reveals Trends in South African Female Breast Cancer Molecular Subtypes and Ki67 Expression. PMID:35355821
The druggable schizophrenia genome: from repurposing opportunities to unexplored drug targets. PMID:35338153
LASSO Regression Modeling on Prediction of Medical Terms among Seafarers' Health Documents Using Tidy Text Mining. PMID:35324813
Multiomics Topic Modeling for Breast Cancer Classification. PMID:35267458
HDL-Associated Lipoproteins: Potential Prognostic Biomarkers for Gram-Negative Sepsis. PMID:35210815
PREGO: A Literature and Data-Mining Resource to Associate Microorganisms, Biological Processes, and Environment Types. PMID:35208748
New insights on familial colorectal cancer type X syndrome. PMID:35181726
Exploring the effects of genetic variation on gene regulation in cancer in the context of 3D genome structure. PMID:35176995
Resistance to Antimalarial Monotherapy Is Cyclic. PMID:35160232
Machine learning prediction and tau-based screening identifies potential Alzheimer's disease genes relevant to immunity. PMID:35149761
A knowledge graph to interpret clinical proteomics data. PMID:35102292
Discovering the key genes and important DNA methylation regions in breast cancer. PMID:35063044
Target Deconvolution of Fenofibrate in Nonalcoholic Fatty Liver Disease Using Bioinformatics Analysis. PMID:34988225
Prediction of lncRNA-disease association based on a Laplace normalized random walk with restart algorithm on heterogeneous networks. PMID:34983367
Dissociation of impulsive traits by subthalamic metabotropic glutamate receptor 4. PMID:34982027
Mining Early Life Risk and Resiliency Factors and Their Influences in Human Populations from PubMed: A Machine Learning Approach to Discover DOHaD Evidence. PMID:34834416
HumanNet v3: an improved database of human gene networks for disease research. PMID:34747468
Text Mining for Building Biomedical Networks Using Cancer as a Case Study. PMID:34680062
Deep post-GWAS analysis identifies potential risk genes and risk variants for Alzheimer's disease, providing new insights into its disease mechanisms. PMID:34654853
Towards a Consensus on Alzheimer's Disease Comorbidity? PMID:34640387
OnTheFly2.0: a text-mining web application for automated biomedical entity recognition, document annotation, network and functional enrichment analysis. PMID:34632381
Determining the immune environment of cutaneous T-cell lymphoma lesions through the assessment of lesional blood drops. PMID:34608214
Modelling Nonalcoholic Steatohepatitis In Vivo-A Close Transcriptomic Similarity Supports the Guinea Pig Disease Model. PMID:34572384
TCF7L2 lncRNA: a link between bipolar disorder and body mass index through glucocorticoid signaling. PMID:34535768
Repurposing new drug candidates and identifying crucial molecules underlying PCOS Pathogenesis Based On Bioinformatics Analysis. PMID:34480296
Cost-Effective Mapping of Genetic Interactions in Mammalian Cells. PMID:34434222
ELMO1 signaling is a promoter of osteoclast function and bone loss. PMID:34404802
FLAME: A Web Tool for Functional and Literature Enrichment Analysis of Multiple Gene Lists. PMID:34356520
TrendyGenes, a computational pipeline for the detection of literature trends in academia and drug discovery. PMID:34344904
Discovering and Summarizing Relationships Between Chemicals, Genes, Proteins, and Diseases in PubChem. PMID:34322655
Insights into the molecular mechanisms of Huangqi decoction on liver fibrosis via computational systems pharmacology approaches. PMID:34301291
DES-Tcell is a knowledgebase for exploring immunology-related literature. PMID:34253812
Identifying ceRNA Networks Associated With the Susceptibility and Persistence of Atrial Fibrillation Through Weighted Gene Co-Expression Network Analysis. PMID:34249084
Identification of viral-mediated pathogenic mechanisms in neurodegenerative diseases using network-based approaches. PMID:34237135
Genome-wide association study of stimulant dependence. PMID:34226506
Identification of SARS-CoV-2-induced pathways reveals drug repurposing strategies. PMID:34193418
Advancing clinical genomics and precision medicine with GVViZ: FAIR bioinformatics platform for variable gene-disease annotation, visualization, and expression analysis. PMID:34174938
Transcriptomic analysis of primate placentas and novel rhesus trophoblast cell lines informs investigations of human placentation. PMID:34154587
Reconstruction of the miR-506-Quaking axis in Idiopathic Pulmonary Fibrosis using integrative multi-source bioinformatics. PMID:34127686
Contribution of genetic ancestry and polygenic risk score in meeting vitamin B12 needs in healthy Brazilian children and adolescents. PMID:34099811
2-kupl: mapping-free variant detection from DNA-seq data of matched samples. PMID:34090332
Reciprocal priming between receptor tyrosine kinases at recycling endosomes orchestrates cellular signalling outputs. PMID:34086370
Transcriptome Profiling of Embryonic Retinal Pigment Epithelium Reprogramming. PMID:34072522
Serum lncRNAs in early pregnancy as potential biomarkers for the prediction of pregnancy-induced hypertension, including preeclampsia. PMID:33868785
Whole-exome sequencing identifies genes associated with Tourette's disorder in multiplex families. PMID:33837273
Reprogramming enriches for somatic cell clones with small-scale mutations in cancer-associated genes. PMID:33831558
Hepatic transcriptional profile reveals the role of diet and genetic backgrounds on metabolic traits in female progenitor strains of the Collaborative Cross. PMID:33818129
Disease Modeling and Disease Gene Discovery in Cardiomyopathies: A Molecular Study of Induced Pluripotent Stem Cell Generated Cardiomyocytes. PMID:33805011
Predicting Lyme Disease From Patients' Peripheral Blood Mononuclear Cells Profiled With RNA-Sequencing. PMID:33763080
A network-based machine-learning framework to identify both functional modules and disease genes. PMID:33409574
Integrative analysis of long extracellular RNAs reveals a detection panel of noncoding RNAs for liver cancer. PMID:33391469
Epigenetic Variation Analysis Leads to Biomarker Discovery in Gastric Adenocarcinoma. PMID:33363566
A Topic Modeling Analysis of TCGA Breast and Lung Cancer Transcriptomic Data. PMID:33339347
Identification of Novel Potential Genes Involved in Cancer by Integrated Comparative Analyses. PMID:33334055
Oncology and Pharmacogenomics Insights in Polycystic Ovary Syndrome: An Integrative Analysis. PMID:33329391
Whole-exome sequencing of non-BRCA1/BRCA2 mutation carrier cases at high-risk for hereditary breast/ovarian cancer. PMID:33326660
Genome-wide identification of major genes and genomic prediction using high-density and text-mined gene-based SNP panels in Hanwoo (Korean cattle). PMID:33264312
Cellular Mechanisms Triggered by the Cotreatment of Resveratrol and Doxorubicin in Breast Cancer: A Translational In Vitro-In Silico Model. PMID:33204396
Pathway information extracted from 25 years of pathway figures. PMID:33168034
Systematic Analysis of Protein-Protein and Gene-Environment Interactions to Decipher the Cognitive Mechanisms of Autism Spectrum Disorder. PMID:33165687
TCRD and Pharos 2021: mining the human proteome for disease biology. PMID:33156327
Finding disease modules for cancer and COVID-19 in gene co-expression networks with the Core&Peel method. PMID:33077837
Named Entity Recognition and Relation Detection for Biomedical Information Extraction. PMID:32984300
Deciphering the Plasma Proteome of Type 2 Diabetes. PMID:32928870
Incorporating prior knowledge into regularized regression. PMID:32915960
Neurological manifestations of COVID-19: available evidences and a new paradigm. PMID:32839951
A guide to writing systematic reviews of rare disease treatments to generate FAIR-compliant datasets: building a Treatabolome. PMID:32787960
RGS6 Mediates Effects of Voluntary Running on Adult Hippocampal Neurogenesis. PMID:32755589
DAnkrd49 and Bdbt act via Casein kinase Iε to regulate planar polarity in Drosophila. PMID:32750048
PertInInt: An Integrative, Analytical Approach to Rapidly Uncover Cancer Driver Genes with Perturbed Interactions and Functionalities. PMID:32711844
Proteomics analysis of FUS mutant human motoneurons reveals altered regulation of cytoskeleton and other ALS-linked proteins via 3'UTR binding. PMID:32678235
Ecological Sensing Through Taste and Chemosensation Mediates Inflammation: A Biological Anthropological Approach. PMID:32647890
Study of genetic correlation between children's sleep and obesity. PMID:32555314
Semantic text mining in early drug discovery for type 2 diabetes. PMID:32542027
Human gene and disease associations for clinical-genomics and precision medicine research. PMID:32508008
Metabolomics and Multi-Omics Integration: A Survey of Computational Methods and Resources. PMID:32429287
PDZ Domains as Drug Targets. PMID:32313833
Oral lichen planus interactome reveals CXCR4 and CXCL12 as candidate therapeutic targets. PMID:32214134
Translating traditional herbal formulas into modern drugs: a network-based analysis of Xiaoyao decoction. PMID:32190105
AllEnricher: a comprehensive gene set function enrichment tool for both model and non-model species. PMID:32183716
DISNET: a framework for extracting phenotypic disease information from public sources. PMID:32110491
An integrative analysis of genome-wide association study and regulatory SNP annotation datasets identified candidate genes for bipolar disorder. PMID:32009227
Comparative Genomic Mapping Implicates LRRK2 for Intellectual Disability and Autism at 12q12, and HDHD1, as Well as PNPLA4, for X-Linked Intellectual Disability at Xp22.31. PMID:31963867
Combined network pharmacology and virtual reverse pharmacology approaches for identification of potential targets to treat vascular dementia. PMID:31937840
Combining lexical and context features for automatic ontology extension. PMID:31931870
Mechanistic insights into transcription factor cooperativity and its impact on protein-phenotype interactions. PMID:31913281
How to Illuminate the Druggable Genome Using Pharos. PMID:31898878
Common Neurodegeneration-Associated Proteins Are Physiologically Expressed by Human B Lymphocytes and Are Interconnected via the Inflammation/Autophagy-Related Proteins TRAF6 and SQSTM1. PMID:31824497
PCOSBase: a manually curated database of polycystic ovarian syndrome. PMID:31725861
Inferring Disease-Associated MicroRNAs Using Semi-supervised Multi-Label Graph Convolutional Networks. PMID:31605942
Debutant iOS app and gene-disease complexities in clinical genomics and precision medicine. PMID:31586224
Applying citizen science to gene, drug and disease relationship extraction from biomedical abstracts. PMID:31504205
Distinct signatures of lung cancer types: aberrant mucin O-glycosylation and compromised immune response. PMID:31429720
A machine-compiled database of genome-wide association studies. PMID:31350405
NGSEA: Network-Based Gene Set Enrichment Analysis for Interpreting Gene Expression Phenotypes with Functional Gene Sets. PMID:31307154
Integrating biomedical research and electronic health records to create knowledge-based biologically meaningful machine-readable embeddings. PMID:31292438
A systematic approach to orient the human protein-protein interaction network. PMID:31289271
Prioritizing target-disease associations with novel safety and efficacy scoring methods. PMID:31285471
Exploring the dark genome: implications for precision medicine. PMID:31270560
Protein-Protein Interaction Network Analysis Reveals Several Diseases Highly Associated with Polycystic Ovarian Syndrome. PMID:31216618
CoCoScore: context-aware co-occurrence scoring for text mining applications using distant supervision. PMID:31199464
Automated assessment of biological database assertions using the scientific literature. PMID:31035936
The Promoter Regions of Intellectual Disability-Associated Genes Are Uniquely Enriched in LTR Sequences of the MER41 Primate-Specific Endogenous Retrovirus: An Evolutionary Connection Between Immunity and Cognition. PMID:31031802
Genome sequencing analysis of blood cells identifies germline haplotypes strongly associated with drug resistance in osteosarcoma patients. PMID:30991985
Measuring the importance of vertices in the weighted human disease network. PMID:30901770
Design, implementation, and operation of a rapid, robust named entity recognition web service. PMID:30850898
How to Develop a Drug Target Ontology: KNowledge Acquisition and Representation Methodology (KNARM). PMID:30848456
Global Genetics Research in Prostate Cancer: A Text Mining and Computational Network Theory Approach. PMID:30838019
Genetic meta-analysis of diagnosed Alzheimer's disease identifies new risk loci and implicates Aβ, tau, immunity and lipid processing. PMID:30820047
Identifying Windows of Susceptibility by Temporal Gene Analysis. PMID:30809014
Analyzing a co-occurrence gene-interaction network to identify disease-gene association. PMID:30736752
Selective Estrogen Receptor Modulators Enhance CNS Remyelination Independent of Estrogen Receptors. PMID:30696729
Translating cancer genomics into precision medicine with artificial intelligence: applications, challenges and future perspectives. PMID:30671672
A noncanonical role for the engulfment gene ELMO1 in neutrophils that promotes inflammatory arthritis. PMID:30643265
Proteins Altered by Surgical Weight Loss Highlight Biomarkers of Insulin Resistance in the Community. PMID:30580566
ALS mutations of FUS suppress protein translation and disrupt the regulation of nonsense-mediated decay. PMID:30455313
Cytoscape StringApp: Network Analysis and Visualization of Proteomics Data. PMID:30450911
HumanNet v2: human gene networks for disease research. PMID:30418591
Uncovering new disease indications for G-protein coupled receptors and their endogenous ligands. PMID:30285606
HACER: an atlas of human active enhancers to interpret regulatory variants. PMID:30247654
Searching the overlap between network modules with specific betweeness (S2B) and its application to cross-disease analysis. PMID:30068933
Automatic extraction of gene-disease associations from literature using joint ensemble learning. PMID:30048465
Using data-driven sublanguage pattern mining to induce knowledge models: application in medical image reports knowledge representation. PMID:29980203
Controllability in an islet specific regulatory network identifies the transcriptional factor NFATC4, which regulates Type 2 Diabetes associated genes. PMID:29977601
Network-based association analysis to infer new disease-gene relationships using large-scale protein interactions. PMID:29949603
Computational analysis of mRNA expression profiling in the inner ear reveals candidate transcription factors associated with proliferation, differentiation, and deafness. PMID:29929553
ILDgenDB: integrated genetic knowledge resource for interstitial lung diseases (ILDs). PMID:29897484
Multiclass classification for skin cancer profiling based on the integration of heterogeneous gene expression series. PMID:29750795
Phenotype Instance Verification and Evaluation Tool (PIVET): A Scaled Phenotype Evidence Generation Framework Using Web-Based Medical Literature. PMID:29728351
ParaBTM: A Parallel Processing Framework for Biomedical Text Mining on Supercomputers. PMID:29702574
Navigating the disease landscape: knowledge representations for contextualizing molecular signatures. PMID:29684165
A Systems Approach to Refine Disease Taxonomy by Integrating Phenotypic and Molecular Networks. PMID:29669699
TISSUES 2.0: an integrative web resource on mammalian tissue expression. PMID:29617745
Unexplored therapeutic opportunities in the human genome. PMID:29472638
A comprehensive and quantitative comparison of text-mining in 15 million full-text articles versus their corresponding abstracts. PMID:29447159
Inverse changes in plasma tetranectin and titin levels in patients with type 2 diabetes mellitus: a potential predictor of acute myocardial infarction? PMID:29417940
The research on gene-disease association based on text-mining of PubMed. PMID:29415654
Toppar: an interactive browser for viewing association study results. PMID:29325066
Biotea: semantics for Pubmed Central. PMID:29312824
CRISPR Screens Uncover Genes that Regulate Target Cell Sensitivity to the Morphogen Sonic Hedgehog. PMID:29290584
Prioritizing chronic obstructive pulmonary disease (COPD) candidate genes in COPD-related networks. PMID:29262568
PedAM: a database for Pediatric Disease Annotation and Medicine. PMID:29126123
Drug target ontology to classify and integrate drug discovery data. PMID:29122012
Context-dependent compensation among phosphatidylserine-recognition receptors. PMID:29116131
eRAM: encyclopedia of rare disease annotations for precision medicine. PMID:29106618
HEDD: Human Enhancer Disease Database. PMID:29077884
miRandola 2017: a curated knowledge base of non-invasive biomarkers. PMID:29036351
SciLite: a platform for displaying text-mined annotations as a means to link research articles with biological data. PMID:28948232
Systematic integration of biomedical knowledge prioritizes drugs for repurposing. PMID:28936969
Chronic obstructive pulmonary disease candidate gene prioritization based on metabolic networks and functional information. PMID:28873096
In silico prediction of novel therapeutic targets using gene-disease association data. PMID:28851378
Rational confederation of genes and diseases: NGS interpretation via GeneCards, MalaCards and VarElect. PMID:28830434
PheKnow-Cloud: A Tool for Evaluating High-Throughput Phenotype Candidates using Online Medical Literature. PMID:28815124
Reverse Nearest Neighbor Search on a Protein-Protein Interaction Network to Infer Protein-Disease Associations. PMID:28757797
Towards a more molecular taxonomy of disease. PMID:28750648
Landscape and variation of novel retroduplications in 26 human populations. PMID:28662076
Literature evidence in open targets - a target validation platform. PMID:28587637
GWAB: a web server for the network-based boosting of human genome-wide association data. PMID:28449091
TIN-X: target importance and novelty explorer. PMID:28398460
Klinefelter syndrome comorbidities linked to increased X chromosome gene dosage and altered protein interactome activity. PMID:28369266
In silico prediction of lncRNA function using tissue specific and evolutionary conserved expression. PMID:28361701
Cross-Species Genome-Wide Identification of Evolutionary Conserved MicroProteins. PMID:28338802
A Review of Recent Advancement in Integrating Omics Data with Literature Mining towards Biomedical Discoveries. PMID:28331849
Disease Risk Assessment Using a Voronoi-Based Network Analysis of Genes and Variants Scores. PMID:28326099
An analysis of disease-gene relationship from Medline abstracts by DigSee. PMID:28054646
The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible. PMID:27924014
MalaCards: an amalgamated human disease compendium with diverse clinical and genetic annotation and structured search. PMID:27899610
Extraction and analysis of signatures from the Gene Expression Omnibus by the crowd. PMID:27667448
The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation. PMID:27664130
Overview of the interactive task in BioCreative V. PMID:27589961
DTMiner: identification of potential disease targets through biomedical literature mining. PMID:27506226
Challenges in identifying cancer genes by analysis of exome sequencing data. PMID:27417679
The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. PMID:27374120
An integer programming framework for inferring disease complexes from network data. PMID:27307626
Genetic and neuroendocrine regulation of the postpartum brain. PMID:27184829
Utilizing yeast chemogenomic profiles for the prediction of pharmacogenomic associations in humans. PMID:27025271
Integrative Single-Cell Transcriptomics Reveals Molecular Networks Defining Neuronal Maturation During Postnatal Neurogenesis. PMID:26989163
Enhancer methylation dynamics contribute to cancer plasticity and patient mortality. PMID:26907635
EXTRACT: interactive extraction of environment metadata and term suggestion for metagenomic sample annotation. PMID:26896844
DDA: A Novel Network-Based Scoring Method to Identify Disease-Disease Associations. PMID:26673408
Lynx: a knowledge base and an analytical workbench for integrative medicine. PMID:26590263
Data integration of structured and unstructured sources for assigning clinical codes to patient stays. PMID:26316458
HOODS: finding context-specific neighborhoods of proteins, chemicals and diseases. PMID:26157625
Comprehensive comparison of large-scale tissue expression datasets. PMID:26157623
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