Daniel Domingo-Fernández

28 papers A* 1Journal 23Unranked 3
YearRankTypeTitle / Venue / Authors
2024 J jnl
Curating, Collecting, and Cataloguing Global COVID-19 Datasets for the Aim of Predicting Personalized Risk.
Data
Sepehr Golriz Khatami, Astghik Sargsyan, Maria Francesca Russo, Daniel Domingo-Fernández, Andrea Zaliani, Abish Kaladharan, Priya Sethumadhavan, Sarah Mubeen, Yojana Gadiya, Reagon Karki, Stephan Gebel, Ram Kumar Ruppa Surulinathan, Vanessa Lage-Rupprecht, Saulius Archipovas, Geltrude Mingrone, Marc Jacobs, Carsten Claussen, Martin Hofmann-Apitius, Alpha Tom Kodamullil
2024 J jnl
Evaluating the generalizability of graph neural networks for predicting collision cross section.
J. Cheminformatics
Chloe Engler Hart, António J. Preto, Shaurya Chanana, David Healey, Tobias Kind, Daniel Domingo-Fernández
2024 J jnl
MARS: A neurosymbolic approach for interpretable drug discovery.
CoRR
Lauren Nicole Delong, Yojana Gadiya, Paola Galdi, Jacques D. Fleuriot, Daniel Domingo-Fernández
2023 A* conf
A Comprehensive Evaluation of Biomedical Entity Linking Models.
EMNLP
David Kartchner, Jennifer Deng, Shubham Lohiya, Tejasri Kopparthi, Prasanth Bathala, Daniel Domingo-Fernández, Cassie S. Mitchell
2023 J jnl
Exploring the known chemical space of the plant kingdom: insights into taxonomic patterns, knowledge gaps, and bioactive regions.
J. Cheminformatics
Daniel Domingo-Fernández, Yojana Gadiya, Sarah Mubeen, David Healey, Bryan H. Norman, Viswa Teja S. S. Colluru
2023 J jnl
On the correspondence between the transcriptomic response of a compound and its effects on its targets.
BMC Bioinform.
Chloe Engler Hart, Daniel Ence, David Healey, Daniel Domingo-Fernández
2022 J jnl
Causal reasoning over knowledge graphs leveraging drug-perturbed and disease-specific transcriptomic signatures for drug discovery.
PLoS Comput. Biol.
Daniel Domingo-Fernández, Yojana Gadiya, Abhishek Patel, Sarah Mubeen, Daniel Rivas-Barragan, Chris W. Diana, Biswapriya B. Misra, David Healey, John C. Rokicki, Viswa Teja S. S. Colluru
2022 J jnl
Elucidating gene expression patterns across multiple biological contexts through a large-scale investigation of transcriptomic datasets.
BMC Bioinform.
Rebeca Queiroz Figueiredo, Sara Díaz del Ser, Tamara Raschka, Martin Hofmann-Apitius, Alpha Tom Kodamullil, Sarah Mubeen, Daniel Domingo-Fernández
2022 J jnl
Ensembles of knowledge graph embedding models improve predictions for drug discovery.
Briefings Bioinform.
Daniel Rivas-Barragan, Daniel Domingo-Fernández, Yojana Gadiya, David Healey
2022 J jnl
Integrative data semantics through a model-enabled data stewardship.
Bioinform.
Philipp Wegner, Sebastian Schaaf, Mischa Uebachs, Daniel Domingo-Fernández, Yasamin Salimi, Stephan Gebel, Astghik Sargsyan, Colin Birkenbihl, Stephan Springstubbe, Thomas Klockgether, Juliane Fluck, Martin Hofmann-Apitius, Alpha Tom Kodamullil
2022 J jnl
On the influence of several factors on pathway enrichment analysis.
Briefings Bioinform.
Sarah Mubeen, Alpha Tom Kodamullil, Martin Hofmann-Apitius, Daniel Domingo-Fernández
2022 — conf
ProtSTonKGs: A Sophisticated Transformer Trained on Protein Sequences, Text, and Knowledge Graphs.
SWAT4HCLS
Helena Balabin, Charles Tapley Hoyt, Benjamin M. Gyori, John A. Bachman, Alpha Tom Kodamullil, Martin Hofmann-Apitius, Daniel Domingo-Fernández
2022 J jnl
STonKGs: a sophisticated transformer trained on biomedical text and knowledge graphs.
Bioinform.
Helena Balabin, Charles Tapley Hoyt, Colin Birkenbihl, Benjamin M. Gyori, John A. Bachman, Alpha Tom Kodamullil, Paul G. Plöger, Martin Hofmann-Apitius, Daniel Domingo-Fernández
2021 J jnl
CLEP: a hybrid data- and knowledge-driven framework for generating patient representations.
Bioinform.
Vinay Srinivas Bharadhwaj, Mehdi Ali, Colin Birkenbihl, Sarah Mubeen, Jens Lehmann, Martin Hofmann-Apitius, Charles Tapley Hoyt, Daniel Domingo-Fernández
2021 J jnl
COVID-19 Knowledge Graph: a computable, multi-modal, cause-and-effect knowledge model of COVID-19 pathophysiology.
Bioinform.
Daniel Domingo-Fernández, Shounak Baksi, Bruce Schultz, Yojana Gadiya, Reagon Karki, Tamara Raschka, Christian Ebeling, Martin Hofmann-Apitius, Alpha Tom Kodamullil
2021 J jnl
MultiPaths: a Python framework for analyzing multi-layer biological networks using diffusion algorithms.
Bioinform.
Josep Marín-Llaó, Sarah Mubeen, Alexandre Perera-Lluna, Martin Hofmann-Apitius, Sergio Picart-Armada, Daniel Domingo-Fernández
2020 J jnl
Drug2ways: Reasoning over causal paths in biological networks for drug discovery.
PLoS Comput. Biol.
Daniel Rivas-Barragan, Sarah Mubeen, Francesc Guim Bernat, Martin Hofmann-Apitius, Daniel Domingo-Fernández
2020 J jnl
PS4DR: a multimodal workflow for identification and prioritization of drugs based on pathway signatures.
BMC Bioinform.
Mohammad Asif Emon, Daniel Domingo-Fernández, Charles Tapley Hoyt, Martin Hofmann-Apitius
2019 J jnl
BioKEEN: a library for learning and evaluating biological knowledge graph embeddings.
Bioinform.
Mehdi Ali, Charles Tapley Hoyt, Daniel Domingo-Fernández, Jens Lehmann, Hajira Jabeen
2019 — —
Computational Analysis of Pathophysiological Mechanisms Based on Pathway Modeling
Daniel Domingo-Fernández
2019 J jnl
PTSD Biomarker Database: deep dive metadatabase for PTSD biomarkers, visualizations and analysis tools.
Database J. Biol. Databases Curation
Daniel Domingo-Fernández, Allison Provost, Alpha Tom Kodamullil, Josep Marín-Llaó, Heather Lasseter, Kristophe Diaz, Nikolaos P. Daskalakis, Lee Lancashire, Martin Hofmann-Apitius, Magali Haas
2019 J jnl
PathMe: merging and exploring mechanistic pathway knowledge.
BMC Bioinform.
Daniel Domingo-Fernández, Sarah Mubeen, Josep Marín-Llaó, Charles Tapley Hoyt, Martin Hofmann-Apitius
2019 — conf
Predicting Missing Links Using PyKEEN.
ISWC (Satellites)
Mehdi Ali, Charles Tapley Hoyt, Daniel Domingo-Fernández, Jens Lehmann
2019 — conf
RatVec: A General Approach for Low-dimensional Distributed Vector Representations via Rational Kernels.
LWDA
Eduardo Brito, Bogdan Georgiev, Daniel Domingo-Fernández, Charles Tapley Hoyt, Christian Bauckhage
2019 J jnl
Re-curation and rational enrichment of knowledge graphs in Biological Expression Language.
Database J. Biol. Databases Curation
Charles Tapley Hoyt, Daniel Domingo-Fernández, Rana Aldisi, Lingling Xu, Kristian Kolpeja, Sandra Spalek, Esther Wollert, John A. Bachman, Benjamin M. Gyori, Patrick Greene, Martin Hofmann-Apitius
2018 J jnl
A systematic approach for identifying shared mechanisms in epilepsy and its comorbidities.
Database J. Biol. Databases Curation
Charles Tapley Hoyt, Daniel Domingo-Fernández, Nora Balzer, Anka Güldenpfennig, Martin Hofmann-Apitius
2018 J jnl
BEL Commons: an environment for exploration and analysis of networks encoded in Biological Expression Language.
Database J. Biol. Databases Curation
Charles Tapley Hoyt, Daniel Domingo-Fernández, Martin Hofmann-Apitius
2017 J jnl
Multimodal mechanistic signatures for neurodegenerative diseases (NeuroMMSig): a web server for mechanism enrichment.
Bioinform.
Daniel Domingo-Fernández, Alpha Tom Kodamullil, Anandhi Iyappan, Mufassra Naz, Mohammad Asif Emon, Tamara Raschka, Reagon Karki, Stephan Springstubbe, Christian Ebeling, Martin Hofmann-Apitius