Martin Hofmann-Apitius

According to our database1, Martin Hofmann-Apitius authored at least 56 papers between 2005 and 2019.

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



In proceedings 
PhD thesis 





PathMe: merging and exploring mechanistic pathway knowledge.
BMC Bioinformatics, 2019

BEL2ABM: agent-based simulation of static models in Biological Expression Language.
Bioinformatics, 2018

BEL Commons: an environment for exploration and analysis of networks encoded in Biological Expression Language.
Database, 2018

A systematic approach for identifying shared mechanisms in epilepsy and its comorbidities.
Database, 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

Multimodal mechanistic signatures for neurodegenerative diseases (NeuroMMSig): a web server for mechanism enrichment.
Bioinformatics, 2017

NeuroRDF: semantic integration of highly curated data to prioritize biomarker candidates in Alzheimer's disease.
J. Biomedical Semantics, 2016

Reasoning over genetic variance information in cause-and-effect models of neurodegenerative diseases.
Briefings in Bioinformatics, 2016

Construction of biological networks from unstructured information based on a semi-automated curation workflow.
Database, 2015

NeuroTransDB: highly curated and structured transcriptomic metadata for neurodegenerative diseases.
Database, 2015

A new optimization phase for scientific workflow management systems.
Future Generation Comp. Syst., 2014

CSEO - the Cigarette Smoke Exposure Ontology.
J. Biomedical Semantics, 2014

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

HuPSON: the human physiology simulation ontology.
J. Biomedical Semantics, 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

Mining biomarker information in biomedical literature.
BMC Med. Inf. & Decision Making, 2012

Development of a benchmark corpus to support the automatic extraction of drug-related adverse effects from medical case reports.
Journal of Biomedical 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

Challenges in the association of human single nucleotide polymorphism mentions with unique database identifiers.
BMC Bioinformatics, 2011

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

DockFlow: Achieving interoperability of protein docking tools across heterogeneous Grid middleware.
IJAHUC, 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

Direct use of information extraction from scientific text for modeling and simulation in the life sciences.
Library Hi Tech, 2009

Concept-Based Semi-Automatic Classification of Drugs.
Journal of Chemical Information and Modeling, 2009

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

Grid-Added Value to Address Malaria.
IEEE Trans. Information Technology in Biomedicine, 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 Bioinformatics, 2008

OSIRISv1.2: A named entity recognition system for sequence variants of genes in biomedical literature.
BMC Bioinformatics, 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

Virtual screening on large scale grids.
Parallel Computing, 2007

Alternative to Consensus ScoringA New Approach Toward the Qualitative Combination of Docking Algorithms.
Journal of Chemical Information and Modeling, 2007

Design of New Plasmepsin Inhibitors: A Virtual High Throughput Screening Approach on the EGEE Grid.
Journal of Chemical Information and Modeling, 2007

Identifying gene-Specific Variations in Biomedical Text.
J. Bioinformatics and Computational Biology, 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

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

GRID Computing.
Proceedings of the INFORMATIK 2005, 2005