Identification of hub biomarkers of myocardial infarction by single-cell sequencing, bioinformatics, and machine learning.

10.3389/fcvm.2022.939972

Front Cardiovasc Med

ncbi_col-pubmed

Identification of immune hub genes participating in the pathogenesis and progression of Vogt-Koyanagi-Harada disease.

10.3389/fimmu.2022.936707

ncbi_col-pubmed

Regulome-based characterization of drug activity across the human diseasome.

10.1038/s41540-022-00255-4

2015_NAR_Kibbe

NPJ Syst Biol Appl

10.1007/s00103-022-03591-2

2022_NAR_Schriml

Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz

Journal Article|Review

Graph representation learning in biomedicine and healthcare.

10.1038/s41551-022-00942-x

2012_NAR_Schriml

Journal Article|Review

Effective medical center finding during COVID-19 pandemic using a spatial DSS centered on ontology engineering.

10.1007/s10708-022-10777-3

2019_NAR_Schriml|2012_NAR_Schriml

A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology.

10.1186/s13326-022-00279-z

2022_NAR_Schriml

J Biomed Semantics

A network-based approach for isolating the chronic inflammation gene signatures underlying complex diseases towards finding new treatment opportunities.

10.3389/fphar.2022.995459

2019_NAR_Schriml

Assessment of DDAH1 and DDAH2 Contributions to Psychiatric Disorders via In Silico Methods.

10.3390/ijms231911902

2012_NAR_Schriml|2009_BMCG_Osborne

<i>Caulis Polygoni Multiflori</i> Accelerates Megakaryopoiesis and Thrombopoiesis via Activating PI3K/Akt and MEK/ERK Signaling Pathways.

10.3390/ph15101204

2012_NAR_Schriml

Pharmaceuticals (Basel)

Survival-based bioinformatics analysis to identify hub long non-coding RNAs along with lncRNA-miRNA-mRNA network for potential diagnosis/prognosis of thyroid cancer.

10.1007/s12079-022-00697-9

2019_NAR_Schriml

J Cell Commun Signal

Assessing equivalent and inverse change in genes between diverse experiments.

10.3389/fbinf.2022.893032

2012_NAR_Schriml

Modeling and integration of N-glycan biomarkers in a comprehensive biomarker data model.

10.1093/glycob/cwac046

Signatures of Co-Deregulated Genes and Their Transcriptional Regulators in Lung Cancer.

10.3390/ijms231810933

2015_NAR_Kibbe

Identification of the Diagnostic Biomarker VIPR1 in Hepatocellular Carcinoma Based on Machine Learning Algorithm.

10.1155/2022/2469592

2019_NAR_Schriml|2018_DMM_Bello|2012_NAR_Schriml

H19 may regulate the immune cell infiltration in carcinogenesis of gastric cancer through miR-378a-5p/SERPINH1 signaling.

10.1186/s12957-022-02760-6

2018_DMM_Bello

World J Surg Oncol

Integrating and formatting biomedical data as pre-calculated knowledge graph embeddings in the Bioteque.

10.1038/s41467-022-33026-0

2018_DMM_Bello

Fernández-Torras A

The Representation of Causality and Causation with Ontologies: A Systematic Literature Review.

10.5210/ojphi.v14i1.12577

2012_NAR_Schriml

Online J Public Health Inform

Journal Article|Review

Inferring human miRNA-disease associations via multiple kernel fusion on GCNII.

10.3389/fgene.2022.980497

2012_NAR_Schriml

Organization of gene programs revealed by unsupervised analysis of diverse gene-trait associations.

10.1093/nar/gkac413

2012_NAR_Schriml

Nucleic Acids Res

LeMeDISCO is a computational method for large-scale prediction &amp; molecular interpretation of disease comorbidity.

10.1038/s42003-022-03816-9

2012_NAR_Schriml

iPiDA-LTR: Identifying piwi-interacting RNA-disease associations based on Learning to Rank.

10.1371/journal.pcbi.1010404

2019_NAR_Schriml

PLoS Comput Biol

CCAS: One-stop and comprehensive annotation system for individual cancer genome at multi-omics level.

10.3389/fgene.2022.956781

2022_NAR_Schriml

Circulating microRNA signatures associated with disease severity and outcome in COVID-19 patients.

10.3389/fimmu.2022.968991

2015_NAR_Kibbe

Ten quick tips for biomarker discovery and validation analyses using machine learning.

10.1371/journal.pcbi.1010357

2012_NAR_Schriml

PLoS Comput Biol

A survey of genome-wide association studies, polygenic scores and UK Biobank highlights resources for autoimmune disease genetics.

10.3389/fimmu.2022.972107

2022_NAR_Schriml

Journal Article|Review

Identification and characterization of four immune-related signatures in keloid.

10.3389/fimmu.2022.942446

2018_DMM_Bello

Contribution of model organism phenotypes to the computational identification of human disease genes.

10.1242/dmm.049441

2022_NAR_Schriml

The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms.

10.12688/f1000research.110194.1

2012_NAR_Schriml

Gene Ontology: application and importance in functional annotation of the genomic data

10.1016/B978-0-323-89775-4.00015-8

2009_BMCG_Osborne

Bioinformatics: Methods and Applications

Book|Book Chapter

2-s2.0-85139302224

Support vector machine based disease classification model employing hasten eagle Cuculidae search optimization

10.1002/cpe.7259

2012_NAR_Schriml

Concurrency and Computation: Practice and Experience

2-s2.0-85136530394

Ontology-based categorization of clinical studies by their conditions

10.1016/j.jbi.2022.104235

2012_NAR_Schriml

Journal of Biomedical Informatics

2-s2.0-85140925219

Transcriptome and DNA methylome analyses reveal underlying mechanisms for the racial disparity in uterine fibroids

10.1172/jci.insight.160274

2012_NAR_Schriml

2-s2.0-85140418022

Biomedical Relation Extraction With Knowledge Graph-Based Recommendations

10.1109/JBHI.2022.3173558

2012_NAR_Schriml

IEEE Journal of Biomedical and Health Informatics

2-s2.0-85132523504

ConSIG: Consistent discovery of molecular signature from OMIC data

10.1093/bib/bbac253

2012_NAR_Schriml

Briefings in Bioinformatics

2-s2.0-85134720455

A Semantic Framework Supporting Multilayer Networks Analysis for Rare Diseases

10.4018/IJSWIS.297141

2012_NAR_Schriml

International Journal on Semantic Web and Information Systems

2-s2.0-85133127602

Graph Convolutional Auto-Encoders for Predicting Novel lncRNA-Disease Associations

10.1109/TCBB.2021.3070910

2012_NAR_Schriml

IEEE/ACM Transactions on Computational Biology and Bioinformatics

2-s2.0-85103890921

In Silico Databases and Tools for Drug Repurposing

10.1016/B978-0-12-816125-8.00024-9

2012_NAR_Schriml

In Silico Drug Design: Repurposing Techniques and Methodologies

Book|Book Chapter

2-s2.0-85137861293

Adding structured information to the ANVISA’s “Bulário Eletrônico”

2012_NAR_Schriml

SBSI 2015 - Proceedings of the Annual Conference on Brazilian Symposium on Information Systems, Information Systems: A Computer Socio-Technical Perspective

Conference Proceeding|Conference Paper

2-s2.0-85135286745

idenMD-NRF: A ranking framework for miRNA-disease association identification

10.1093/bib/bbac224

2015_NAR_Kibbe

Briefings in Bioinformatics

2-s2.0-85134636046

A comprehensive decision support model for online doctors ranking with interval-valued neutrosophic numbers

10.1111/itor.13208

2015_NAR_Kibbe

International Transactions in Operational Research

2-s2.0-85137565918

DeepIDA: Predicting Isoform-Disease Associations by Data Fusion and Deep Neural Networks

10.1109/TCBB.2021.3058801

2015_NAR_Kibbe

IEEE/ACM Transactions on Computational Biology and Bioinformatics

2-s2.0-85101488457

Overcoming Sparseness of Biomedical Networks to Identify Drug Repositioning Candidates

10.1109/TCBB.2021.3059807

2015_NAR_Kibbe|2012_NAR_Schriml

IEEE/ACM Transactions on Computational Biology and Bioinformatics

2-s2.0-85101288709

Bidirectional spreading activation method for finding human diseases relatedness using well formed disease ontology

10.4018/978-1-7998-1204-3.ch090

2015_NAR_Kibbe

Data Analytics in Medicine: Concepts, Methodologies, Tools, and Applications

Book|Book Chapter

2-s2.0-85137555437

Biomedical ontologies and their development, management, and applications in and beyond China

10.1097/JBR.0000000000000051

2015_NAR_Kibbe

Journal of Bio-X Research

2-s2.0-85113395977

Rule Based Medicine Recommendation for Skin Diseases Using Ontology with Semantic Information

10.1007/978-3-031-12638-3_31

2015_MG_Schriml

Communications in Computer and Information Science

Book Series|Conference Paper

2-s2.0-85135898427

Identification of Biomarkers in Intracranial Aneurysm and Their Immune Infiltration Characteristics

10.1016/j.wneu.2022.06.138

2018_DMM_Bello

World Neurosurgery

2-s2.0-85135348017

Using FlyBase: A Database of Drosophila Genes and Genetics

10.1007/978-1-0716-2541-5_1

2018_DMM_Bello

Methods in Molecular Biology

Book Series|Book Chapter

2-s2.0-85136639786

A Novel Tightly Coupled Information System for Research Data Management

10.3390/electronics11193196

2019_NAR_Schriml

Electronics (Switzerland)

2-s2.0-85139868482

Paving the way for enriched metadata of linguistic linked data

10.3233/SW-222994

2019_NAR_Schriml

2-s2.0-85140839697

Online in silico validation of disease and gene sets, clusterings or subnetworks with DIGEST

10.1093/bib/bbac247

2019_NAR_Schriml

Briefings in Bioinformatics

2-s2.0-85134721065

Artificial Intelligence in Bioinformatics: From Omics Analysis to Deep Learning and Network Mining

10.1016/C2019-0-04920-5

2019_NAR_Schriml|2012_NAR_Schriml

Artificial Intelligence in Bioinformatics: From Omics Analysis to Deep Learning and Network Mining

2-s2.0-85138931915

https://ceur-ws.org/Vol-3204/paper_5.pdf

2019_NAR_Schriml

CEUR Workshop Proceedings

Conference Proceeding|Conference Paper

2-s2.0-85138226596

Fine-Grained ICD Code Assignment Using Ontology-Based Classification

http://www.cis.umassd.edu/~hxu/Papers/UMD/2019/CP/IEEE-IRI22-Carberry-Xu.pdf

10.1109/IRI54793.2022.00058

2019_NAR_Schriml

Proceedings - 2022 IEEE 23rd International Conference on Information Reuse and Integration for Data Science, IRI 2022

Conference Proceeding|Conference Paper

2-s2.0-85139018761

Leipzig Health Atlas

The Leipzig Health Atlas-An open platform to present, archive and share bio-medical data, analyses and models online

10.1055/a-1914-1985

2019_NAR_Schriml|2015_MG_Schriml|2012_NAR_Schriml

Methods of Information in Medicine

2-s2.0-85136156537

A Review: Biological Insights on Knowledge Graphs

10.1007/978-3-031-15743-1_36

2022_NAR_Schriml

Communications in Computer and Information Science

Book Series|Conference Paper

2-s2.0-85137987064

EBOCA: Evidences for BiOmedical Concepts Association Ontology

https://arxiv.org/pdf/2208.01093.pdf

10.1007/978-3-031-17105-5_11

2022_NAR_Schriml

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Book Series|Conference Paper

2-s2.0-85140489445

A community approach to the cancer-variant-interpretation bottleneck.

10.1038/s43018-022-00379-w

ncbi_col-pubmed

Human Health Exposure Analysis Resource (HHEAR): A model for incorporating the exposome into health studies.

10.1016/j.ijheh.2021.113768

Int J Hyg Environ Health

Journal Article|Review

ncbi_col-pubmed

The Children's Health Exposure Analysis Resource: enabling research into the environmental influences on children's health outcomes.

10.1097/MOP.0000000000000491

Journal Article|Review

ncbi_col-pubmed

DFELMDA: Identification of miRNA–disease associations via deep forest ensemble learning based on autoencoder

Identification of miRNA–disease associations via deep forest ensemble learning based on autoencoder

10.1093/bib/bbac104

2012_NAR_Schriml

Briefings in Bioinformatics

2-s2.0-85130766184

Review on predicting pairwise relationships between human microbes, drugs and diseases: from biological data to computational models

10.1093/bib/bbac080

2012_NAR_Schriml

Briefings in Bioinformatics

2-s2.0-85130355161

A Network-Based Analysis of Disease Modules from a Taxonomic Perspective

10.1109/JBHI.2021.3106787

2012_NAR_Schriml

IEEE Journal of Biomedical and Health Informatics

2-s2.0-85128489347

Integrated Transcriptomics and Reverse Pharmacophore Mapping-based Network Pharmacology to Explore the Mechanisms of Natural Compounds against Doxorubicin-induced Cardiotoxicity

10.2174/1386207324666210816122629

2012_NAR_Schriml

Combinatorial Chemistry and High Throughput Screening

2-s2.0-85135242548

Digital Humanities and Portuguese Processing: a research pathway

2012_NAR_Schriml

CEUR Workshop Proceedings

Conference Proceeding|Conference Paper

2-s2.0-85129204256

Survey of Various Statistical Numerical and Machine Learning Ontological Models on Infectious Disease Ontology

10.1002/9781119785620.ch17

2012_NAR_Schriml

Data Analytics in Bioinformatics: A Machine Learning Perspective

Book|Book Chapter

2-s2.0-85131172660

iLncDA-LTR: Identification of lncRNA-disease associations by learning to rank

http://bliulab.net/iLncDA-LTR/

iLncDA-LTR: Identification of lncRNA-disease associations by learning to rank

10.1016/j.compbiomed.2022.105605

2015_NAR_Kibbe

Computers in Biology and Medicine

2-s2.0-85130325784

Analysis of Causal Relationships in Integrated Ontologies of Diseases, Phenotypes, and Radiological Diagnosis

10.3233/SHTI220074

2015_NAR_Kibbe; 2012_NAR_Schriml

Studies in Health Technology and Informatics

Book Series|Conference Paper

scopus; ncbi_col-pubmed

2-s2.0-85131504249

Applying Transformer Models for Disease Named Entity Recognition

10.1109/ICARC54489.2022.9754023

2015_NAR_Kibbe

ICARC 2022 - 2nd International Conference on Advanced Research in Computing: Towards a Digitally Empowered Society

Conference Proceeding|Conference Paper

2-s2.0-85128916847

Evaluating and extending the Informed Consent Ontology for representing permissions from the clinical domain

10.3233/AO-210260

2015_NAR_Kibbe

Applied Ontology

2-s2.0-85130367681

Drug Repurposing for Rare Orphan Diseases Using Machine Learning Techniques

10.32473/flairs.v35i.130653

2015_NAR_Kibbe

Manicavasagam R

Proceedings of the International Florida Artificial Intelligence Research Society Conference, FLAIRS

Conference Proceeding|Conference Paper

2-s2.0-85131130227

iCircDA-LTR: identification of circRNA-disease associations based on Learning to Rank

10.1093/bioinformatics/btab334

2015_NAR_Kibbe

2-s2.0-85119015623

Ontology Driven Cross-Linked Domain Data Integration and Spatial Semantic Multi Criteria Query System for Geospatial Public Health

10.4018/978-1-5225-8054-6.ch032

2015_MG_Schriml

Geospatial Intelligence: Concepts, Methodologies, Tools, and Applications

Book|Book Chapter

2-s2.0-85129038433

Transcriptome meta-analysis of valproic acid exposure in human embryonic stem cells

10.1016/j.euroneuro.2022.04.008

2018_DMM_Bello

European Neuropsychopharmacology

2-s2.0-85131051182

MDADP: A Webserver Integrating Database and Prediction Tools for Microbe-Disease Associations

10.1109/JBHI.2022.3156166

2019_NAR_Schriml

IEEE Journal of Biomedical and Health Informatics

2-s2.0-85126325796

Research on LncRNA and Disease Associations Prediction Base on Data Mining

10.1088/1742-6596/2219/1/012029

2019_NAR_Schriml

Journal of Physics: Conference Series

Conference Proceeding|Conference Paper

2-s2.0-85130508715

Automated intelligent online healthcare ontology Integration

10.1109/ICCI54321.2022.9756070

2019_NAR_Schriml

5th International Conference on Computing and Informatics, ICCI 2022

Conference Proceeding|Conference Paper

2-s2.0-85129395870

The Organ-Disease Annotations (ODiseA) Database of Hereditary Diseases and Inflicted Tissues

10.1016/j.jmb.2022.167619

2022_NAR_Schriml

Journal of Molecular Biology

2-s2.0-85130310784

SeEn: Sequential enriched datasets for sequence-aware recommendations.

10.1038/s41597-022-01598-7

2019_NAR_Schriml

PheNominal: an EHR-integrated web application for structured deep phenotyping at the point of care.

10.1186/s12911-022-01927-1

2012_NAR_Schriml

BMC Med Inform Decis Mak

Transcriptomic and proteomic retinal pigment epithelium signatures of age-related macular degeneration.

10.1038/s41467-022-31707-4

2019_NAR_Schriml; 2012_NAR_Schriml

https://www.cbrc.kaust.edu.sa/des-amyloidosis/home/

DES-Amyloidoses "Amyloidoses through the looking-glass": A knowledgebase developed for exploring and linking information related to human amyloid-related diseases.

10.1371/journal.pone.0271737

2015_NAR_Kibbe

Follistatin-like 1 and its paralogs in heart development and cardiovascular disease.

10.1007/s10741-022-10262-6

2019_NAR_Schriml

Journal Article|Review

https://pubmed.ncbi.nlm.nih.gov/35857363

An Urban Population Health Observatory for Disease Causal Pathway Analysis and Decision Support: Underlying Explainable Artificial Intelligence Model.

2012_NAR_Schriml

Characterizing and explaining the impact of disease-associated mutations in proteins without known structures or structural homologs.

10.1093/bib/bbac187

2022_NAR_Schriml

The Core Human Microbiome: Does It Exist and How Can We Find It? A Critical Review of the Concept.

10.3390/nu14142872

2012_NAR_Schriml

Journal Article|Review

PharMeBINet: Pharmacological Medical Biochemical Network

https://pharmebi.net/

The heterogeneous pharmacological medical biochemical network PharMeBINet.

10.1038/s41597-022-01510-3

2019_NAR_Schriml

An Integrated Bioinformatics Analysis towards the Identification of Diagnostic, Prognostic, and Predictive Key Biomarkers for Urinary Bladder Cancer.

10.3390/cancers14143358

2019_NAR_Schriml

Virofree, an Herbal Medicine-Based Formula, Interrupts the Viral Infection of Delta and Omicron Variants of SARS-CoV-2.

10.3389/fphar.2022.905197

2019_NAR_Schriml; 2009_BIX_Du

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9313348

Prediction of circRNA-Disease Associations Based on the Combination of Multi-Head Graph Attention Network and Graph Convolutional Network.

10.3390/biom12070932

2012_NAR_Schriml

Whole-genome sequencing reveals host factors underlying critical COVID-19.

10.1038/s41586-022-04576-6

2012_NAR_Schriml

Common genetic variation associated with Mendelian disease severity revealed through cryptic phenotype analysis.

10.1038/s41467-022-31030-y

2019_NAR_Schriml

From drug repositioning to target repositioning: prediction of therapeutic targets using genetically perturbed transcriptomic signatures.

10.1093/bioinformatics/btac240

2015_NAR_Kibbe

Omics-based integrated analysis identified IKZF2 as a biomarker associated with lupus nephritis.

10.1038/s41598-022-13336-5

2012_NAR_Schriml

Journal Article|Meta-Analysis

HemI 2.0: Heat map Illustrator 2.0

https://hemi.biocuckoo.org/

HemI 2.0: an online service for heatmap illustration.

10.1093/nar/gkac480

2019_NAR_Schriml

Nucleic Acids Res

https://github.com/armando2603/GeMI

GeMI: interactive interface for transformer-based Genomic Metadata Integration.

10.1093/database/baac036

2019_NAR_Schriml

Database (Oxford)

http://139.224.212.120:18095/

AnthraxKP: a knowledge graph-based, Anthrax Knowledge Portal mined from biomedical literature.

10.1093/database/baac037

2012_NAR_Schriml

Database (Oxford)

Expediting knowledge acquisition by a web framework for Knowledge Graph Exploration and Visualization (KGEV): case studies on COVID-19 and Human Phenotype Ontology.

10.1186/s12911-022-01848-z

2019_NAR_Schriml

BMC Med Inform Decis Mak

Diagnostic genes and immune infiltration analysis of colorectal cancer determined by LASSO and SVM machine learning methods: a bioinformatics analysis.

10.21037/jgo-22-536

2019_NAR_Schriml

J Gastrointest Oncol