Daniel Domingo Fernández

AETIONOMY – Developing a »mechanism-based taxonomy« of Alzheimer´s and Parkinson´s Disease

The AETIONOMY concept foresees a primary role of the taxonomy in
i) describing and organizing the indication-specific data in the data cube, in
ii) linking the data to disease models that are based on causal and correlative relationships and in
iii) support of reasoning over the knowledge that is explicitly represented in related ontologies or knowledge-based disease models.

• https://www.aetionomy.eu/

Human Brain Pharmacome

This project aims to integrate quantitative chemical information with mechanistic models of complex neurodegenerative disease in order to identify and propose drug repurposing candidates.

• https://pharmacome.scai.fraunhofer.de/

PTSD Biomarker Database

PTSD Biomarker Database is the first resource aiming to capture and organize biomarker knowledge in this PTSD. This database was developed as result of a collaboration effort by Fraunhofer SCAI and Cohen Veterans Bioscience.

• https://ptsd.scai.fraunhofer.de/

NeuroMMSig

NeuroMMSig is a web application enabling the novel paradigm of mechanism enrichment. Through NeuroMMSig, we offer the scientific community over 200 subgraphs representing the knowledge around well-established disease-specific mechanisms involved in three major neurological disorders (Alzheimer's disease, Parkinson's disease, and epilepsy).

• http://neurommsig.scai.fraunhofer.de

BEL4IMOCEDE

Data- And Knowledge-Driven Approaches for the Identification of novel molecular and cellular determinants of psychiatric and neurological conditions using BEL modeling framework. This work is the result of a collaboration between raunhofer SCAI and Boehringer Ingelheim.

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

Daniel Domingo-Fernández, Charles Tapley Hoyt, Carlos Bobis Álvarez, Josep Marín-Llaó, and Martin Hofmann-Apitius. npj Systems Biology and Applications, Volume 4, 43, (2018). https://doi.org/10.1038/s41540-018-0078-8
 

PathMe: Merging and exploring mechanistic pathway knowledge

Daniel Domingo-Fernández, Sarah Mubeen, Josep Marín-Llaó, Charles Tapley Hoyt, and Martin Hofmann-Apitius. BMC Bioinformatics, Volume 20, Article number 243 (2019). https://doi.org/10.1186/s12859-019-2863-9

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

Daniel Domingo-Fernández, Alpha Tom Kodamullil, Anandhi Iyappan, Mufassra Naz, Mohammad Asif Emon, Tamara Raschka, Reagon Karki, Stephan Springstubbe, Christian Ebeling, and Martin Hofmann-Apitius. Bioinformatics, Volume 33, Issue 22, Pages 3679–3681 (2017). https://doi.org/10.1093/bioinformatics/btx399.

PTSD Biomarker Database: Deep Dive Meta-database for PTSD Biomarkers, Visualizations, and Analysis Tools

Daniel Domingo-Fernández, Allison Provost, Alpha Tom Kodamullil, Josep Marín-Llaó, Heather Lasseter, Kristophe Diaz, Lee Lancashire, Martin Hofmann-Apitius, and Magali Haas. Database: The Journal of Biological Databases and Curation, Volume 2019, baz081 (2019). https://doi.org/10.1093/database/baz081.

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

Shashank Khanna, Daniel Domingo-Fernández, Anandhi Iyappan, Mohammad Asif Emon, Martin Hofmann-Apitius, and Holger Fröhlich. Scientific Reports, Volume 8, Article number: 11173 (2018). https://doi.org/10.1038/s41598-018-29433-3.

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

Charles Tapley Hoyt, Daniel Domingo-Fernández, Nora Balzer, Anka Gueldenpfennig, and Martin Hofmann-Apitius. Database: The Journal of Biological Databases and Curation, Volume 2018, bay050 (2018). https://doi.org/10.1093/database/bay050.

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

Charles Tapley Hoyt, Daniel Domingo-Fernández, and Martin Hofmann-Apitius. Database: The Journal of Biological Databases and Curation, Volume 2018, bay126 (2018). https://doi.org/10.1093/database/bay126.

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

Charles Tapley Hoyt, Daniel Domingo-Fernández, Rana Aldisi, Lingling Xu, Kristian Kolpeja, Sandra Spalek, Esther Wollert, John Bachman, Benjamin Gyori, Patrick Greene, and Martin Hofmann-Apitius. Database: The Journal of Biological Databases and Curation, Volume 2019, baz068 (2019). https://doi.org/10.1093/database/baz068.

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

Mehdi Ali, Charles Tapley Hoyt, Daniel Domingo-Fernández, Jens Lehmann, and Hajira Jabeen. Bioinformatics, btz117, (2019). https://doi.org/10.1093/bioinformatics/btz117.