Daniel Domingo-Fernández

发表

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

Martin Hofmann-Apitius, Charles Tapley Hoyt, Sarah Mubeen, 2020, Frontiers in Genetics.

The COVID-19 PHARMACOME: Rational Selection of Drug Repurposing Candidates from Multimodal Knowledge Harmonization

Martin Hofmann-Apitius, Andrea Zaliani, Reagon Karki, 2020, bioRxiv.

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

Martin Hofmann-Apitius, Alexandre Perera-Lluna, Sarah Mubeen, 2020, bioRxiv.

Using predictive machine learning models for drug response simulation by calibrating patient-specific pathway signatures

Martin Hofmann-Apitius, Alpha Tom Kodamullil, Sarah Mubeen, 2020, bioRxiv.

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

Martin Hofmann-Apitius, Alpha Tom Kodamullil, Daniel Domingo-Fernández, 2019, Database J. Biol. Databases Curation.

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

Martin Hofmann-Apitius, Charles Tapley Hoyt, Daniel Domingo-Fernández, 2018, bioRxiv.

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

Martin Hofmann-Apitius, Charles Tapley Hoyt, Daniel Domingo-Fernández, 2019, npj Systems Biology and Applications.

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

Mohammad Asif Emon, Martin Hofmann-Apitius, Charles Tapley Hoyt, 2020, BMC Bioinformatics.

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

Martin Hofmann-Apitius, Benjamin M. Gyori, Charles Tapley Hoyt, 2019, bioRxiv.

Predicting Missing Links Using PyKEEN

Jens Lehmann, Charles Tapley Hoyt, Daniel Domingo-Fernández, 2019, ISWC Satellites.

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

Martin Hofmann-Apitius, Charles Tapley Hoyt, Daniel Domingo-Fernández, 2018, npj Systems Biology and Applications.

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

Christian Bauckhage, Eduardo Brito, Charles Tapley Hoyt, 2019, LWDA.

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

Martin Hofmann-Apitius, Charles Tapley Hoyt, Daniel Domingo-Fernández, 2018 .

PathMe: merging and exploring mechanistic pathway knowledge

Martin Hofmann-Apitius, Charles Tapley Hoyt, Sarah Mubeen, 2018, BMC Bioinformatics.

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

Martin Hofmann-Apitius, Sarah Mubeen, Daniel Domingo-Fernández, 2020, bioRxiv.

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

Martin Hofmann-Apitius, Charles Tapley Hoyt, Daniel Domingo-Fernández, 2018, bioRxiv.

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

Martin Hofmann-Apitius, Sarah Mubeen, Daniel Domingo-Fernández, 2020, PLoS computational biology.

Challenges of Integrative Disease Modeling in Alzheimer's Disease

Martin Hofmann-Apitius, Charles Tapley Hoyt, Daniel Domingo-Fernández, 2020, Frontiers in Molecular Biosciences.

Multimodal mechanistic signatures for neurodegenerative diseases (NeuroMMSig): a web server for mechanism enrichment

Mohammad Asif Emon, Martin Hofmann-Apitius, Reagon Karki, 2017, Bioinform..

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

Martin Hofmann-Apitius, Reagon Karki, Alpha Tom Kodamullil, 2020, bioRxiv.

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

Martin Hofmann-Apitius, Jens Lehmann, Charles Tapley Hoyt, 2020, bioRxiv.

Integration of Structured Biological Data Sources using Biological Expression Language

Martin Hofmann-Apitius, Charles Tapley Hoyt, Sarah Mubeen, 2019, bioRxiv.

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

Jens Lehmann, Charles Tapley Hoyt, Daniel Domingo-Fernández, 2019, Bioinform..

Extension of Roles in the ChEBI Ontology

Charles Tapley Hoyt, Daniel Domingo-Fernández, Christopher J. Mungall, 2020 .

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

Martin Hofmann-Apitius, Reagon Karki, Alpha Tom Kodamullil, 2020, bioRxiv.

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

Martin Hofmann-Apitius, Jens Lehmann, Charles Tapley Hoyt, 2021, Bioinform..

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

Mohammad Asif Emon, Martin Hofmann-Apitius, Holger Fröhlich, 2018, Scientific Reports.