Daniel Domingo-Fernández

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 25

Top Topics

Gene Expression

Graph Embedding

Top Venues

Database J. Biol. Databases Curation

Briefings Bioinform.

Publications

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
Curating, Collecting, and Cataloguing Global COVID-19 Datasets for the Aim of Predicting Personalized Risk. Data 9 (2) (2024)
David Kartchner, Jennifer Deng, Shubham Lohiya, Tejasri Kopparthi, Prasanth Bathala, Daniel Domingo-Fernández, Cassie S. Mitchell
A Comprehensive Evaluation of Biomedical Entity Linking Models. EMNLP (2023)
Chloe Engler Hart, Daniel Ence, David Healey, Daniel Domingo-Fernández
On the correspondence between the transcriptomic response of a compound and its effects on its targets. BMC Bioinform. 24 (1) (2023)
Daniel Domingo-Fernández, Yojana Gadiya, Sarah Mubeen, David Healey, Bryan H. Norman, Viswa Teja S. S. Colluru
Exploring the known chemical space of the plant kingdom: insights into taxonomic patterns, knowledge gaps, and bioactive regions. J. Cheminformatics 15 (1) (2023)
Sarah Mubeen, Alpha Tom Kodamullil, Martin Hofmann-Apitius, Daniel Domingo-Fernández
On the influence of several factors on pathway enrichment analysis. Briefings Bioinform. 23 (3) (2022)
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
Integrative data semantics through a model-enabled data stewardship. Bioinform. 38 (15) (2022)
Helena Balabin, Charles Tapley Hoyt, Benjamin M. Gyori, John A. Bachman, Alpha Tom Kodamullil, Martin Hofmann-Apitius, Daniel Domingo-Fernández
ProtSTonKGs: A Sophisticated Transformer Trained on Protein Sequences, Text, and Knowledge Graphs. SWAT4HCLS (2022)
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
Causal reasoning over knowledge graphs leveraging drug-perturbed and disease-specific transcriptomic signatures for drug discovery. PLoS Comput. Biol. 18 (2) (2022)
Daniel Rivas-Barragan, Daniel Domingo-Fernández, Yojana Gadiya, David Healey
Ensembles of knowledge graph embedding models improve predictions for drug discovery. Briefings Bioinform. 23 (6) (2022)
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
STonKGs: a sophisticated transformer trained on biomedical text and knowledge graphs. Bioinform. 38 (6) (2022)
Rebeca Queiroz Figueiredo, Sara Díaz del Ser, Tamara Raschka, Martin Hofmann-Apitius, Alpha Tom Kodamullil, Sarah Mubeen, Daniel Domingo-Fernández
Elucidating gene expression patterns across multiple biological contexts through a large-scale investigation of transcriptomic datasets. BMC Bioinform. 23 (1) (2022)
Josep Marín-Llaó, Sarah Mubeen, Alexandre Perera-Lluna, Martin Hofmann-Apitius, Sergio Picart-Armada, Daniel Domingo-Fernández
MultiPaths: a Python framework for analyzing multi-layer biological networks using diffusion algorithms. Bioinform. 37 (1) (2021)
Daniel Domingo-Fernández, Shounak Baksi, Bruce Schultz, Yojana Gadiya, Reagon Karki, Tamara Raschka, Christian Ebeling, Martin Hofmann-Apitius, Alpha Tom Kodamullil
COVID-19 Knowledge Graph: a computable, multi-modal, cause-and-effect knowledge model of COVID-19 pathophysiology. Bioinform. 37 (9) (2021)
Vinay Srinivas Bharadhwaj, Mehdi Ali, Colin Birkenbihl, Sarah Mubeen, Jens Lehmann, Martin Hofmann-Apitius, Charles Tapley Hoyt, Daniel Domingo-Fernández
CLEP: a hybrid data- and knowledge-driven framework for generating patient representations. Bioinform. 37 (19) (2021)
Mohammad Asif Emon, Daniel Domingo-Fernández, Charles Tapley Hoyt, Martin Hofmann-Apitius
PS4DR: a multimodal workflow for identification and prioritization of drugs based on pathway signatures. BMC Bioinform. 21 (1) (2020)
Daniel Rivas-Barragan, Sarah Mubeen, Francesc Guim Bernat, Martin Hofmann-Apitius, Daniel Domingo-Fernández
Drug2ways: Reasoning over causal paths in biological networks for drug discovery. PLoS Comput. Biol. 16 (12) (2020)
Eduardo Brito, Bogdan Georgiev, Daniel Domingo-Fernández, Charles Tapley Hoyt, Christian Bauckhage
RatVec: A General Approach for Low-dimensional Distributed Vector Representations via Rational Kernels. LWDA (2019)
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
Re-curation and rational enrichment of knowledge graphs in Biological Expression Language. Database J. Biol. Databases Curation 2019 (2019)
Mehdi Ali, Charles Tapley Hoyt, Daniel Domingo-Fernández, Jens Lehmann, Hajira Jabeen
BioKEEN: a library for learning and evaluating biological knowledge graph embeddings. Bioinform. 35 (18) (2019)
Mehdi Ali, Charles Tapley Hoyt, Daniel Domingo-Fernández, Jens Lehmann
Predicting Missing Links Using PyKEEN. ISWC (Satellites) (2019)
Daniel Domingo-Fernández, Sarah Mubeen, Josep Marín-Llaó, Charles Tapley Hoyt, Martin Hofmann-Apitius
PathMe: merging and exploring mechanistic pathway knowledge. BMC Bioinform. 20 (1) (2019)
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
PTSD Biomarker Database: deep dive metadatabase for PTSD biomarkers, visualizations and analysis tools. Database J. Biol. Databases Curation 2019 (2019)
Charles Tapley Hoyt, Daniel Domingo-Fernández, Martin Hofmann-Apitius
BEL Commons: an environment for exploration and analysis of networks encoded in Biological Expression Language. Database J. Biol. Databases Curation 2018 (2018)
Charles Tapley Hoyt, Daniel Domingo-Fernández, Nora Balzer, Anka Güldenpfennig, Martin Hofmann-Apitius
A systematic approach for identifying shared mechanisms in epilepsy and its comorbidities. Database J. Biol. Databases Curation 2018 (2018)
Daniel Domingo-Fernández, Alpha Tom Kodamullil, Anandhi Iyappan, Mufassra Naz, Mohammad Asif Emon, Tamara Raschka, Reagon Karki, Stephan Springstubbe, Christian Ebeling, Martin Hofmann-Apitius
Multimodal mechanistic signatures for neurodegenerative diseases (NeuroMMSig): a web server for mechanism enrichment. Bioinform. 33 (22) (2017)