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List of works by Daniel Domingo-Fernández

A Computational Approach for Mapping Heme Biology in the Context of Hemolytic Disorders

scientific article published on 06 March 2020

A Systems Biology Approach for Hypothesizing the Effect of Genetic Variants on Neuroimaging Features in Alzheimer’s Disease

scientific article

A computational approach for mapping heme biology in the context of hemolytic disorders

scholarly article

A systematic approach for identifying shared mechanisms in epilepsy and its comorbidities

preprint

A systematic approach for identifying shared mechanisms in epilepsy and its comorbidities

scientific article

BEL Commons: an environment for exploration and analysis of networks encoded in Biological Expression Language

preprint

BEL Commons: an environment for exploration and analysis of networks encoded in Biological Expression Language

scholarly article

BioKEEN: A library for learning and evaluating biological knowledge graph embeddings

preprint

BioKEEN: a library for learning and evaluating biological knowledge graph embeddings

scholarly article

CLEP: A Hybrid Data- and Knowledge- Driven Framework for Generating Patient Representations

preprint published on 04 November 2020

CLEP: a hybrid data- and knowledge-driven framework for generating patient representations

scientific article published in 2021

COVID-19 Knowledge Graph: a computable, multi-modal, cause-and-effect knowledge model of COVID-19 pathophysiology

scientific article published on 15 April 2020

COVID-19 Knowledge Graph: a computable, multi-modal, cause-and-effect knowledge model of COVID-19 pathophysiology

scientific article published on 25 September 2020

Causal reasoning over knowledge graphs leveraging drug-perturbed and disease-specific transcriptomic signatures for drug discovery

scientific article published on 25 February 2022

Challenges of Integrative Disease Modeling in Alzheimer's Disease

scholarly article

Clustering of Alzheimer's and Parkinson's disease based on genetic burden of shared molecular mechanisms

scientific article published on 05 November 2020

ComPath: An ecosystem for exploring, analyzing, and curating mappings across pathway databases

preprint

ComPath: an ecosystem for exploring, analyzing, and curating mappings across pathway databases

scholarly article

Corrigendum to “Machine Learning Based Prediction of COVID-19 Mortality Suggests Repositioning of Anticancer Drug for Treating Severe Cases”[Artificial Intelligence in Life Sciences] 1(2021), 100020

scientific article published in 2022

Corrigendum: The Impact of Pathway Database Choice on Statistical Enrichment Analysis and Predictive Modeling

scientific article published on 29 April 2020

Data-Driven Modeling of Knowledge Assemblies in Understanding Comorbidity Between Type 2 Diabetes Mellitus and Alzheimer's Disease

scientific article published on 08 September 2020

Drug2ways: Reasoning over causal paths in biological networks for drug discovery

scientific article published on 02 December 2020

Elucidating gene expression patterns across multiple biological contexts through a large-scale investigation of transcriptomic datasets

scientific article published on 01 January 2022

Elucidating gene expression patterns across multiple biological contexts through a large-scale investigation of transcriptomic datasets

scientific article published on 15 June 2022

Erratum: Publisher Correction: ComPath: an ecosystem for exploring, analyzing, and curating mappings across pathway databases

scientific article published on 07 March 2019

Extension of Roles in the ChEBI Ontology

scholarly article

Identifying Drug Repositioning Candidates using Comparative Mechanism Enrichment in Neurodegenerative Diseases ⬇️

conference poster

Identifying Drug Repositioning Candidates using Representation Learning on Heterogeneous Networks ⬇️

conference poster

Integration of Structured Biological Data Sources using Biological Expression Language

BioRxiv scholarly article describing Bio2BEL

Integrative data semantics through a model-enabled data stewardship

scientific article published in 2022

Maintenance and Enrichment of Disease Maps in Biological Expression Language ⬇️

conference poster

MultiPaths: a python framework for analyzing multi-layer biological networks using diffusion algorithms

scientific article published on 26 December 2020

Multimodal Mechanistic Signatures for Neurodegenerative Diseases (NeuroMMSig): a web server for mechanism enrichment

scientific article

PS4DR: a multimodal workflow for identification and prioritization of drugs based on pathway signatures

preprint

PS4DR: a multimodal workflow for identification and prioritization of drugs based on pathway signatures

scientific article published on 05 June 2020

PTSD Biomarker Database: deep dive metadatabase for PTSD biomarkers, visualizations and analysis tools

scientific article published on 01 January 2019

PathMe: Merging and exploring mechanistic pathway knowledge

PathMe: merging and exploring mechanistic pathway knowledge

scholarly article

Predicting Missing Links Using PyKEEN ⬇️

conference paper

ProtSTonKGs: A Sophisticated Transformer Trained on Protein Sequences, Text, and Knowledge Graphs ⬇️

RatVec: A General Approach for Low-dimensional Distributed Vector Representations via Domain-specific Rational Kernels ⬇️

Conference paper

Re-curation and Rational Enrichment of Knowledge Graphs in Biological Expression Language

BioRxiv article

Re-curation and rational enrichment of knowledge graphs in Biological Expression Language.

scientific article

STonKGs: A Sophisticated Transformer Trained on Biomedical Text and Knowledge Graphs

preprint published on 18 August 2021

STonKGs: A Sophisticated Transformer Trained on Biomedical Text and Knowledge Graphs

scientific article published on 5 January 2022

The Human Brain Pharmacome: An Overview ⬇️

conference poster

The Impact of Pathway Database Choice on Statistical Enrichment Analysis and Predictive Modeling

preprint

The Impact of Pathway Database Choice on Statistical Enrichment Analysis and Predictive Modeling

scientific article published on 22 November 2019

Towards a global investigation of transcriptomic signatures through co-expression networks and pathway knowledge for the identification of disease mechanisms

scientific article published on 11 June 2021

Towards a mechanism-based taxonomy of Alzheimer’s and Parkinson’s disease ⬇️

conference poster

Unifying the Identification of Biomedical Entities with the Bioregistry ⬇️

preprint published on 10 July 2022

Unifying the identification of biomedical entities with the Bioregistry ⬇️

scientific article published on 19 November 2022

Unravelling the debate on heme effects in COVID-19 infections

scientific article

Using Multi-Scale Genetic, Neuroimaging and Clinical Data for Predicting Alzheimer's Disease and Reconstruction of Relevant Biological Mechanisms

scientific article published in Scientific Reports

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