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ORCIDDaniel Domingo-Fernández
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2020 – today
- 2024
[j22]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): 25 (2024)- [j21]Chloe Engler Hart, António J. Preto, Shaurya Chanana, David Healey, Tobias Kind, Daniel Domingo-Fernández:
Evaluating the generalizability of graph neural networks for predicting collision cross section. J. Cheminformatics 16(1): 105 (2024) - [d1]Vinay Srinivas Bharadhwaj, Mehdi Ali, Colin Birkenbihl, Sarah Mubeen, Jens Lehmann, Martin Hofmann-Apitius, Charles Tapley Hoyt, Daniel Domingo-Fernández:
CLEP. Zenodo, 2024
- [i1]Lauren Nicole Delong, Yojana Gadiya, Paola Galdi, Jacques D. Fleuriot, Daniel Domingo-Fernández:
MARS: A neurosymbolic approach for interpretable drug discovery. CoRR abs/2410.05289 (2024) - 2023
- [j20]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): 207 (2023) - [j19]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): 107 (2023) - [c4]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: 14462-14478 - 2022
- [j18]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) - [j17]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) - [j16]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): 1648-1656 (2022) - [j15]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): 3850-3852 (2022) - [j14]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): 231 (2022) - [j13]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) - [c3]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: 103-107 - 2021
- [j12]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): 137-139 (2021) - [j11]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): 1332-1334 (2021) - [j10]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): 3311-3318 (2021) - 2020
- [j9]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): 231 (2020) - [j8]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)
2010 – 2019
- 2019
- [b1]Daniel Domingo-Fernández:
Computational Analysis of Pathophysiological Mechanisms Based on Pathway Modeling. University of Bonn, Germany, 2019 - [j7]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: baz068 (2019) - [j6]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: baz081 (2019) - [j5]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): 3538-3540 (2019) - [j4]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): 243:1-243:12 (2019) - [c2]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: 74-78 - [c1]Mehdi Ali, Charles Tapley Hoyt, Daniel Domingo-Fernández, Jens Lehmann:
Predicting Missing Links Using PyKEEN. ISWC (Satellites) 2019: 245-248 - 2018
- [j3]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: bay050 (2018) - [j2]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: bay126 (2018) - 2017
- [j1]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): 3679-3681 (2017)
Coauthor Index
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