Martin Hofmann-Apitius

Affiliations:
  • 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 84 papers between 2005 and 2024.

Collaborative distances:
  • Dijkstra number2 of four.
  • Erdős number3 of four.

Timeline

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Online presence:

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Bibliography

2024
Curating, Collecting, and Cataloguing Global COVID-19 Datasets for the Aim of Predicting Personalized Risk.
Data, 2024

2023
PEMT: a patent enrichment tool for drug discovery.
Bioinform., January, 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
Common data model for COVID-19 datasets.
Bioinform., December, 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

Integrative data semantics through a model-enabled data stewardship.
Bioinform., 2022

STonKGs: a sophisticated transformer trained on biomedical text and knowledge graphs.
Bioinform., 2022

On the influence of several factors on pathway enrichment analysis.
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

The COVID-19 Ontology.
Bioinform., 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
Drug2ways: Reasoning over causal paths in biological networks for drug discovery.
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

PathMe: merging and exploring mechanistic pathway knowledge.
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
BEL2ABM: agent-based simulation of static models in Biological Expression Language.
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
A new optimization phase for scientific workflow management systems.
Future Gener. Comput. Syst., 2014

Detecting miRNA Mentions and Relations in Biomedical Literature.
F1000Research, 2014

CSEO - the Cigarette Smoke Exposure Ontology.
J. Biomed. Semant., 2014

2013
'HypothesisFinder: ' A Strategy for the Detection of Speculative Statements in Scientific Text.
PLoS Comput. Biol., 2013

HuPSON: the human physiology simulation ontology.
J. Biomed. Semant., 2013

SCAI: Extracting drug-drug interactions using a rich feature vector.
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
Mining biomarker information in biomedical literature.
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

A new optimization phase for scientific workflow management systems.
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

PLIO: an ontology for formal description of protein-ligand interactions.
Bioinform., 2011

A Semantic Platform for Information Retrieval from E-Health Records.
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

A UNICORE Plugin for HPC-Enabled Scientific Workflows in Taverna 2.2.
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

Concept-Based Semi-Automatic Classification of Drugs.
J. Chem. Inf. Model., 2009

Identification of histone modifications in biomedical text for supporting epigenomic research.
BMC Bioinform., 2009

Patent Retrieval in Chemistry Based on Semantically Tagged Named Entities.
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

A Robust Framework for Rapid Deployment of a Virtual Screening Laboratory.
Proceedings of the Healthgrid Research, Innovation and Business Case - Proceedings of HealthGrid 2009, Berlin, Germany, 29 June, 2009

2008
Grid-Added Value to Address Malaria.
IEEE Trans. Inf. Technol. Biomed., 2008

Grid-enabled Virtual Screening Against Malaria.
J. Grid Comput., 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

Detection of IUPAC and IUPAC-like chemical names.
Proceedings of the Proceedings 16th International Conference on Intelligent Systems for Molecular Biology (ISMB), 2008

Virtual High Throughput Screening (vHTS) on an Optical High Speed Testbed.
Proceedings of the Global Healthgrid: e-Science Meets Biomedical Informatics, 2008


@neuLink: A Service-oriented Application for Biomedical Knowledge Discovery.
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
Virtual screening on large scale grids.
Parallel Comput., 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

Identifying gene-Specific Variations in Biomedical Text.
J. Bioinform. Comput. Biol., 2007

Understanding Cerebral Aneurysms - The @neurIST Project.
ERCIM News, 2007

Identification of new drug classification terms in textual resources.
Proceedings of the Proceedings 15th International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB), 2007

Automatic Recognition of Chemical Images.
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

Large Scale In Silico Screening on Grid Infrastructures
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

Demonstration of In Silico Docking at a Large Scale on Grid Infrastructure.
Proceedings of the Challenges and Opportunities of HealthGrids, 2006


Grid Added Value to Address Malaria.
Proceedings of the Sixth IEEE International Symposium on Cluster Computing and the Grid (CCGrid 2006), 2006

2005
GRID Computing.
Proceedings of the 35. Jahrestagung der Gesellschaft für Informatik, 2005


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