Martin Hofmann-Apitius
Orcid: 0000-0001-9012-6720Affiliations:
- Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Sankt Augustin, Germany
- University of Bonn, Bonn-Aachen International Center for IT (B-IT), Germany
According to our database1,
Martin Hofmann-Apitius
authored at least 87 papers
between 2005 and 2024.
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Bibliography
2024
BMC Medical Informatics Decis. Mak., December, 2024
Dataset of miRNA-disease relations extracted from textual data using transformer-based neural networks.
Database J. Biol. Databases Curation, January, 2024
Curating, Collecting, and Cataloguing Global COVID-19 Datasets for the Aim of Predicting Personalized Risk.
Data, 2024
2023
Design of the formalized and integrated Alzheimer's Disease Ontology and its application in retrieving textual data via text mining.
Database J. Biol. Databases Curation, 2023
Comparative analysis of protein function text-based embeddings and their applicability to prediction tasks.
Proceedings of the 14th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences (SWAT4HCLS 2023), 2023
2022
GuiltyTargets: Prioritization of Novel Therapeutic Targets With Network Representation Learning.
IEEE ACM Trans. Comput. Biol. Bioinform., 2022
A hybrid approach unveils drug repurposing candidates targeting an Alzheimer pathophysiology mechanism.
Patterns, 2022
Deep Learning-based detection of psychiatric attributes from German mental health records.
Int. J. Medical Informatics, 2022
Elucidating gene expression patterns across multiple biological contexts through a large-scale investigation of transcriptomic datasets.
BMC Bioinform., 2022
Bioinform., 2022
STonKGs: a sophisticated transformer trained on biomedical text and knowledge graphs.
Bioinform., 2022
Briefings Bioinform., 2022
ProtSTonKGs: A Sophisticated Transformer Trained on Protein Sequences, Text, and Knowledge Graphs.
Proceedings of the 13th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences, 2022
2021
Bridging Scales in Alzheimer's Disease: Biological Framework for Brain Simulation With The Virtual Brain.
Frontiers Neuroinformatics, 2021
MultiPaths: a Python framework for analyzing multi-layer biological networks using diffusion algorithms.
Bioinform., 2021
COVID-19 Knowledge Graph: a computable, multi-modal, cause-and-effect knowledge model of COVID-19 pathophysiology.
Bioinform., 2021
CLEP: a hybrid data- and knowledge-driven framework for generating patient representations.
Bioinform., 2021
2020
PLoS Comput. Biol., 2020
Variational Autoencoder Modular Bayesian Networks for Simulation of Heterogeneous Clinical Study Data.
Frontiers Big Data, 2020
PS4DR: a multimodal workflow for identification and prioritization of drugs based on pathway signatures.
BMC Bioinform., 2020
CTO: A Community-Based Clinical Trial Ontology and Its Applications in PubChemRDF and SCAIView.
Proceedings of the 11th International Conference on Biomedical Ontologies (ICBO) joint with the 10th Workshop on Ontologies and Data in Life Sciences (ODLS) and part of the Bolzano Summer of Knowledge (BoSK 2020), 2020
2019
Quantifying mechanisms in neurodegenerative diseases (NDDs) using candidate mechanism perturbation amplitude (CMPA) algorithm.
BMC Bioinform., 2019
Re-curation and rational enrichment of knowledge graphs in Biological Expression Language.
Database J. Biol. Databases Curation, 2019
PTSD Biomarker Database: deep dive metadatabase for PTSD biomarkers, visualizations and analysis tools.
Database J. Biol. Databases Curation, 2019
2018
Bioinform., 2018
BEL Commons: an environment for exploration and analysis of networks encoded in Biological Expression Language.
Database J. Biol. Databases Curation, 2018
A systematic approach for identifying shared mechanisms in epilepsy and its comorbidities.
Database J. Biol. Databases Curation, 2018
Converting Alzheimer's Disease Map into a Heavyweight Ontology: A Formal Network to Integrate Data.
Proceedings of the Data Integration in the Life Sciences - 13th International Conference, 2018
2017
Multimodal mechanistic signatures for neurodegenerative diseases (NeuroMMSig): a web server for mechanism enrichment.
Bioinform., 2017
2016
NeuroRDF: semantic integration of highly curated data to prioritize biomarker candidates in Alzheimer's disease.
J. Biomed. Semant., 2016
Reasoning over genetic variance information in cause-and-effect models of neurodegenerative diseases.
Briefings Bioinform., 2016
2015
Construction of biological networks from unstructured information based on a semi-automated curation workflow.
Database J. Biol. Databases Curation, 2015
<i>NeuroTransDB</i>: highly curated and structured transcriptomic metadata for neurodegenerative diseases.
Database J. Biol. Databases Curation, 2015
2014
Future Gener. Comput. Syst., 2014
2013
'HypothesisFinder: ' A Strategy for the Detection of Speculative Statements in Scientific Text.
PLoS Comput. Biol., 2013
Proceedings of the 7th International Workshop on Semantic Evaluation, 2013
BEL Networks Derived from Qualitative Translations of BioNLP Shared Task Annotations.
Proceedings of the 2013 Workshop on Biomedical Natural Language Processing, 2013
2012
BMC Medical Informatics Decis. Mak., 2012
Development of a benchmark corpus to support the automatic extraction of drug-related adverse effects from medical case reports.
J. Biomed. Informatics, 2012
ADO: A formal ontology for understanding structure of information and domain knowledge of Alzheimer's disease.
Proceedings of the 3rd International Conference on Biomedical Ontology (ICBO 2012), 2012
Proceedings of the 8th IEEE International Conference on E-Science, 2012
2011
Challenges in the association of human single nucleotide polymorphism mentions with unique database identifiers.
BMC Bioinform., 2011
Bioinform., 2011
Proceedings of The Twentieth Text REtrieval Conference, 2011
Information Retrieval Framework for Technology Survey in Biomedical and Chemistry Literature.
Proceedings of The Twentieth Text REtrieval Conference, 2011
Proceedings of the World Congress on Services, 2011
2010
DockFlow: Achieving interoperability of protein docking tools across heterogeneous Grid middleware.
Int. J. Ad Hoc Ubiquitous Comput., 2010
Prior Art Search in Chemistry Patents Based On Semantic Concepts and Co-Citation Analysis.
Proceedings of The Nineteenth Text REtrieval Conference, 2010
Abstracts versus Full Texts and Patents: A Quantitative Analysis of Biomedical Entities.
Proceedings of the Advances in Multidisciplinary Retrieval, 2010
2009
Direct use of information extraction from scientific text for modeling and simulation in the life sciences.
Libr. Hi Tech, 2009
Identification of histone modifications in biomedical text for supporting epigenomic research.
BMC Bioinform., 2009
Proceedings of The Eighteenth Text REtrieval Conference, 2009
DockFlow - a prototypic PharmaGrid for Virtual Screening Integrating Four Different Docking Tools.
Proceedings of the Healthgrid Research, Innovation and Business Case - Proceedings of HealthGrid 2009, Berlin, Germany, 29 June, 2009
Proceedings of the Healthgrid Research, Innovation and Business Case - Proceedings of HealthGrid 2009, Berlin, Germany, 29 June, 2009
2008
Public microarray repository semantic annotation with ontologies employing text mining and expression profile correlation.
BMC Bioinform., 2008
OSIRISv1.2: A named entity recognition system for sequence variants of genes in biomedical literature.
BMC Bioinform., 2008
Proceedings of the Proceedings 16th International Conference on Intelligent Systems for Molecular Biology (ISMB), 2008
Proceedings of the Global Healthgrid: e-Science Meets Biomedical Informatics, 2008
Proceedings of the Global Healthgrid: e-Science Meets Biomedical Informatics, 2008
Proceedings of the Global Healthgrid: e-Science Meets Biomedical Informatics, 2008
@neurIST - Towards a System Architecture for Advanced Disease Management through Integration of Heterogeneous Data, Computing, and Complex Processing Services.
Proceedings of the Twenty-First IEEE International Symposium on Computer-Based Medical Systems, 2008
Initial Results on Knowledge Discovery and Decision Support for Intracranial Aneurysms.
Proceedings of the First International Conference on Health Informatics, 2008
2007
Alternative to Consensus ScoringA New Approach Toward the Qualitative Combination of Docking Algorithms.
J. Chem. Inf. Model., 2007
Design of New Plasmepsin Inhibitors: A Virtual High Throughput Screening Approach on the EGEE Grid.
J. Chem. Inf. Model., 2007
J. Bioinform. Comput. Biol., 2007
Proceedings of the Proceedings 15th International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB), 2007
Proceedings of the Eight Mexican International Conference in Current Trends in Computer Science, 2007
2006
Integration and mining of malaria molecular, functional and pharmacological data: how far are we from a chemogenomic knowledge space?
CoRR, 2006
Biomedical and Chemical Named Entity Recognition with Conditional Random Fields: The Advantage of Dictionary Features.
Proceedings of the Second International Symposium on Semantic Mining in Biomedicine, 2006
Proceedings of the Challenges and Opportunities of HealthGrids, 2006
Proceedings of the Sixth IEEE International Symposium on Cluster Computing and the Grid (CCGrid 2006), 2006
2005
Proceedings of the 35. Jahrestagung der Gesellschaft für Informatik, 2005