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Author Details

Daniel Domingo-Fern??ndez
Fraunhofer Institute for Algorithms and Scientific Computing (SCAI)
2017
36
11
PMIDPaper TitleJournal TitlePublished Year
36462601Integrative analysis to identify shared mechanisms between schizophrenia and bipolar disorder and their comorbidities.Prog Neuropsychopharmacol Biol Psychiatry2023
37681175MultiGML: Multimodal graph machine learning for prediction of adverse drug events.Heliyon2023
34986221STonKGs: a sophisticated transformer trained on biomedical text and knowledge graphs.Bioinformatics2022
35705903Elucidating gene expression patterns across multiple biological contexts through a large-scale investigation of transcriptomic datasets.BMC Bioinformatics2022
35598021ADataViewer: exploring semantically harmonized Alzheimer's disease cohort datasets.Alzheimers Res Ther2022
36402838Unifying the identification of biomedical entities with the Bioregistry.Sci Data2022
35156080Corrigendum to "Machine Learning Based Prediction of COVID-19 Mortality Suggests Repositioning of Anticancer Drug for Treating Severe Cases"[Artificial Intelligence in Life Sciences] 1(2021), 100020.Artif Intell Life Sci2022
35213534Causal reasoning over knowledge graphs leveraging drug-perturbed and disease-specific transcriptomic signatures for drug discovery.PLoS Comput Biol2022
32976572COVID-19 Knowledge Graph: a computable, multi-modal, cause-and-effect knowledge model of COVID-19 pathophysiology.Bioinformatics2021
33925394Linking COVID-19 and Heme-Driven Pathophysiologies: A Combined Computational-Experimental Approach.Biomolecules2021
33554913A Systems Biology Approach for Hypothesizing the Effect of Genetic Variants on Neuroimaging Features in Alzheimer's Disease.J Alzheimers Dis2021
34988543Machine Learning Based Prediction of COVID-19 Mortality Suggests Repositioning of Anticancer Drug for Treating Severe Cases.Artif Intell Life Sci2021
34707117Using predictive machine learning models for drug response simulation by calibrating patient-specific pathway signatures.NPJ Syst Biol Appl2021
34568823DecoPath: a web application for decoding pathway enrichment analysis.NAR Genom Bioinform2021
33964127CLEP: a hybrid data- and knowledge-driven framework for generating patient representations.Bioinformatics2021
34040048A method for the rational selection of drug repurposing candidates from multimodal knowledge harmonization.Sci Rep2021
34197603Towards a global investigation of transcriptomic signatures through co-expression networks and pathway knowledge for the identification of disease mechanisms.Nucleic Acids Res2021
33367476MultiPaths: a Python framework for analyzing multi-layer biological networks using diffusion algorithms.Bioinformatics2021
32411185Corrigendum: The Impact of Pathway Database Choice on Statistical Enrichment Analysis and Predictive Modeling.Front Genet2020
31993440Challenges of Integrative Disease Modeling in Alzheimer's Disease.Front Mol Biosci2020
33344750Evaluating the Alzheimer's disease data landscape.Alzheimers Dement (N Y)2020
33154531Clustering of Alzheimer's and Parkinson's disease based on genetic burden of shared molecular mechanisms.Sci Rep2020
33264280Drug2ways: Reasoning over causal paths in biological networks for drug discovery.PLoS Comput Biol2020
32925069Data-Driven Modeling of Knowledge Assemblies in Understanding Comorbidity Between Type 2 Diabetes Mellitus and Alzheimer's Disease.J Alzheimers Dis2020
32503412PS4DR: a multimodal workflow for identification and prioritization of drugs based on pathway signatures.BMC Bioinformatics2020
32211383A Computational Approach for Mapping Heme Biology in the Context of Hemolytic Disorders.Front Bioeng Biotechnol2020
30768158BioKEEN: a library for learning and evaluating biological knowledge graph embeddings.Bioinformatics2019
31824580The Impact of Pathway Database Choice on Statistical Enrichment Analysis and Predictive Modeling.Front Genet2019
31260040PTSD Biomarker Database: deep dive metadatabase for PTSD biomarkers, visualizations and analysis tools.Database (Oxford)2019
31225582Re-curation and rational enrichment of knowledge graphs in Biological Expression Language.Database (Oxford)2019
31092193PathMe: merging and exploring mechanistic pathway knowledge.BMC Bioinformatics2019
30564458ComPath: an ecosystem for exploring, analyzing, and curating mappings across pathway databases.NPJ Syst Biol Appl2018
30042519Using Multi-Scale Genetic, Neuroimaging and Clinical Data for Predicting Alzheimer's Disease and Reconstruction of Relevant Biological Mechanisms.Sci Rep2018
29873705A systematic approach for identifying shared mechanisms in epilepsy and its comorbidities.Database (Oxford)2018
30576488BEL Commons: an environment for exploration and analysis of networks encoded in Biological Expression Language.Database (Oxford)2018
28651363Multimodal mechanistic signatures for neurodegenerative diseases (NeuroMMSig): a web server for mechanism enrichment.Bioinformatics2017
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Collaborators

Martin Hofmann-Apitius
Co-authored papers 30
Alpha Tom Kodamullil
Co-authored papers 15
Charles Tapley Hoyt
Harvard Medical School
Co-authored papers 15
Holger Fr??hlich
Bonn-Aachen International Center for IT (B-IT), University of Bonn
Co-authored papers 7
Christian Ebeling
Co-authored papers 3
Benjamin M Gyori
Khoury College of Computer Sciences, Northeastern University
Co-authored papers 3
Anandhi Iyappan
Fraunhofer Institute for Algorithms and Scientific Computing (Fraunhofer SCAI)
Co-authored papers 3
Sumit Madan
Co-authored papers 2
Deepak R Unni
Lawrence Berkeley National Laboratory
Co-authored papers 1
Donald Winston
Polyneme LLC
Co-authored papers 1
Julie A McMurry
University of Colorado - Anschutz Medical Campus
Co-authored papers 1
Manuel C Peitsch
Philip Morris International Research Laboratories Pte. Ltd
Co-authored papers 1
Sayoni Das
University College London
Co-authored papers 1
Meghan Balk
University of Arizona
Co-authored papers 1
Tiago Lubiana
School of Pharmaceutical Sciences, University of Sao Paulo
Co-authored papers 1
Nicolas Matentzoglu
Co-authored papers 1
Tiffany J Callahan
Columbia University
Co-authored papers 1
Julia Hoeng
Vectura Fertin Pharma
Co-authored papers 1
Daniel S Himmelstein
University of Pennsylvania
Co-authored papers 1
Melissa A Haendel
Co-authored papers 1
Mufassra Naz
Fraunhofer Institute for Algorithms and Scientific Computing
Co-authored papers 1
Simon Lovestone
Janssen Medical Ltd
Co-authored papers 1
Klas Karis
Harvard Medical School
Co-authored papers 1
Sierra A T Moxon
Lawrence Berkeley National Laboratory
Co-authored papers 1
John Kunze
University of California berkeley
Co-authored papers 1
Adriano Rutz
School of Pharmaceutical Sciences, University of Geneva
Co-authored papers 1
Christopher J Mungall
International Society for Biocuration, Lawrence Berkeley National Laboratory, University of Edinburgh, University of Edinburgh School of Biological Sciences
Co-authored papers 1
Neal G Ravindra
Yale University School
Co-authored papers 1
Roland Eils
Berlin Institute of Health (BIH) and Charite
Co-authored papers 1
Egon L Willighagen
Maastricht University
Co-authored papers 1
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