Martin Hofmann-Apitius

Publication Activity (10 Years)

Years Active: 2006-2024
Publications (10 Years): 35

Top Topics

Neurodegenerative Diseases

Workflow Management

Unstructured Information

Top Venues

Database J. Biol. Databases Curation

Briefings Bioinform.

Publications

Sumit Madan, Manuel Lentzen, Johannes Brandt, Daniel Rueckert, Martin Hofmann-Apitius, Holger Fröhlich
Transformer models in biomedicine. BMC Medical Informatics Decis. Mak. 24 (1) (2024)
Sumit Madan, Lisa Kühnel, Holger Fröhlich, Martin Hofmann-Apitius, Juliane Fluck
Dataset of miRNA-disease relations extracted from textual data using transformer-based neural networks. Database J. Biol. Databases Curation 2024 (2024)
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) (2024)
Rohitha Ravinder, Leyla Jael Castro, Martin Hofmann-Apitius, Dietrich Rebholz-Schuhmann
Comparative analysis of protein function text-based embeddings and their applicability to prediction tasks. SWAT4HCLS (2023)
Bide Zhang, Vanessa Lage-Rupprecht, Philipp Wegner, Astghik Sargsyan, Stephan Gebel, Marc Jacobs, Jürgen Klein, Martin Hofmann-Apitius, Alpha Tom Kodamullil
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 (2023)
Yojana Gadiya, Andrea Zaliani, Philip Gribbon, Martin Hofmann-Apitius
PEMT: a patent enrichment tool for drug discovery. Bioinform. 39 (1) (2023)
Vanessa Lage-Rupprecht, Bruce Schultz, Justus Dick, Marcin Namysl, Andrea Zaliani, Stephan Gebel, Ole Pless, Jeanette Reinshagen, Bernhard Ellinger, Christian Ebeling, Alexander M. Esser, Marc Jacobs, Carsten Claussen, Martin Hofmann-Apitius
A hybrid approach unveils drug repurposing candidates targeting an Alzheimer pathophysiology mechanism. Patterns 3 (3) (2022)
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)
Philipp Wegner, Geena Mariya Jose, Vanessa Lage-Rupprecht, Sepehr Golriz Khatami, Bide Zhang, Stephan Springstubbe, Marc Jacobs, Thomas Linden, Cindy Ku, Bruce Schultz, Martin Hofmann-Apitius, Alpha Tom Kodamullil
Common data model for COVID-19 datasets. Bioinform. 38 (24) (2022)
Ozlem Muslu, Charles Tapley Hoyt, Mauricio Lacerda, Martin Hofmann-Apitius, Holger Fröhlich
GuiltyTargets: Prioritization of Novel Therapeutic Targets With Network Representation Learning. IEEE ACM Trans. Comput. Biol. Bioinform. 19 (1) (2022)
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) (2022)
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)
Sumit Madan, Fabian Julius Zimmer, Helena Balabin, Sebastian Schaaf, Holger Fröhlich, Juliane Fluck, Irene Neuner, Klaus Mathiak, Martin Hofmann-Apitius, Pegah Sarkheil
Deep Learning-based detection of psychiatric attributes from German mental health records. Int. J. Medical Informatics 161 (2022)
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) (2022)
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) (2022)
Leon Stefanovski, Jil Mona Meier, Roopa Pai, Paul Triebkorn, Tristram Lett, Leon Martin, Konstantin Bülau, Martin Hofmann-Apitius, Ana Solodkin, Anthony Randal McIntosh, Petra Ritter
Bridging Scales in Alzheimer's Disease: Biological Framework for Brain Simulation With The Virtual Brain. Frontiers Neuroinformatics 15 (2021)
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) (2021)
Astghik Sargsyan, Alpha Tom Kodamullil, Shounak Baksi, Johannes Darms, Sumit Madan, Stephan Gebel, Oliver Keminer, Geena Mariya Jose, Helena Balabin, Lauren Nicole Delong, Manfred Kohler, Marc Jacobs, Martin Hofmann-Apitius
The COVID-19 Ontology. Bioinform. 36 (24) (2021)
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) (2021)
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) (2021)
Luise Gootjes-Dreesbach, Meemansa Sood, Akrishta Sahay, Martin Hofmann-Apitius, Holger Fröhlich
Variational Autoencoder Modular Bayesian Networks for Simulation of Heterogeneous Clinical Study Data. Frontiers Big Data 3 (2020)
Asiyah Yu Lin, Stephan Gebel, Qingliang Leon Li, Sumit Madan, Johannes Darms, Evan Bolton, Barry Smith, Martin Hofmann-Apitius, Yongqun Oliver He, Alpha Tom Kodamullil
CTO: A Community-Based Clinical Trial Ontology and Its Applications in PubChemRDF and SCAIView. ICBO/ODLS (2020)
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) (2020)
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)
Reagon Karki, Alpha Tom Kodamullil, Charles Tapley Hoyt, Martin Hofmann-Apitius
Quantifying mechanisms in neurodegenerative diseases (NDDs) using candidate mechanism perturbation amplitude (CMPA) algorithm. BMC Bioinform. 20 (1) (2019)
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 (2019)
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) (2019)
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 (2019)
Michaela Gündel, Charles Tapley Hoyt, Martin Hofmann-Apitius
BEL2ABM: agent-based simulation of static models in Biological Expression Language. Bioinform. 34 (13) (2018)
Vincent Henry, Ivan Moszer, Olivier Dameron, Marie-Claude Potier, Martin Hofmann-Apitius, Olivier Colliot
Converting Alzheimer's Disease Map into a Heavyweight Ontology: A Formal Network to Integrate Data. DILS (2018)
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 (2018)
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 (2018)
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) (2017)
Mufassra Naz, Alpha Tom Kodamullil, Martin Hofmann-Apitius
Reasoning over genetic variance information in cause-and-effect models of neurodegenerative diseases. Briefings Bioinform. 17 (3) (2016)
Anandhi Iyappan, Shweta Bagewadi Kawalia, Tamara Raschka, Martin Hofmann-Apitius, Philipp Senger
NeuroRDF: semantic integration of highly curated data to prioritize biomarker candidates in Alzheimer's disease. J. Biomed. Semant. 7 (2016)
Justyna Szostak, Sam Ansari, Sumit Madan, Juliane Fluck, Marja Talikka, Anita Iskandar, Hector De Leon, Martin Hofmann-Apitius, Manuel C. Peitsch, Julia Hoeng
Construction of biological networks from unstructured information based on a semi-automated curation workflow. Database J. Biol. Databases Curation 2015 (2015)
Shweta Bagewadi Kawalia, Subash Adhikari, Anjani Dhrangadhariya, Afroza Khanam Irin, Christian Ebeling, Aishwarya Alex Namasivayam, Matthew Page, Martin Hofmann-Apitius, Philipp Senger
: highly curated and structured transcriptomic metadata for neurodegenerative diseases. Database J. Biol. Databases Curation 2015 (2015)
Sonja Holl, Olav Zimmermann, Magnus Palmblad, Yassene Mohammed, Martin Hofmann-Apitius
A new optimization phase for scientific workflow management systems. Future Gener. Comput. Syst. 36 (2014)
Shweta Bagewadi Kawalia, Tamara Bobic, Martin Hofmann-Apitius, Juliane Fluck, Roman Klinger
Detecting miRNA Mentions and Relations in Biomedical Literature. F1000Research 3 (2014)
Erfan Younesi, Sam Ansari, Michaela Gündel, Shiva Ahmadi, Chris Coggins, Julia Hoeng, Martin Hofmann-Apitius, Manuel C. Peitsch
CSEO - the Cigarette Smoke Exposure Ontology. J. Biomed. Semant. 5 (2014)
Ashutosh Malhotra, Erfan Younesi, Harsha Gurulingappa, Martin Hofmann-Apitius
'HypothesisFinder: ' A Strategy for the Detection of Speculative Statements in Scientific Text. PLoS Comput. Biol. 9 (7) (2013)
Michaela Gündel, Erfan Younesi, Ashutosh Malhotra, Jiali Wang, Hui Li, Bijun Zhang, Bernard de Bono, Heinz-Theodor Mevissen, Martin Hofmann-Apitius
HuPSON: the human physiology simulation ontology. J. Biomed. Semant. 4 (2013)
Juliane Fluck, Alexander Klenner, Sumit Madan, Sam Ansari, Tamara Bobic, Julia Hoeng, Martin Hofmann-Apitius, Manuel C. Peitsch
BEL Networks Derived from Qualitative Translations of BioNLP Shared Task Annotations. BioNLP@ACL (2013)
Tamara Bobic, Juliane Fluck, Martin Hofmann-Apitius
SCAI: Extracting drug-drug interactions using a rich feature vector. SemEval@NAACL-HLT (2013)
Ashutosh Malhotra, Michaela Gündel, Martin Hofmann-Apitius
ADO: A formal ontology for understanding structure of information and domain knowledge of Alzheimer's disease. ICBO (2012)
Sonja Holl, Olav Zimmermann, Martin Hofmann-Apitius
A new optimization phase for scientific workflow management systems. eScience (2012)
Erfan Younesi, Luca Toldo, Bernd Müller, Christoph M. Friedrich, Natalia Novac, Alexander Scheer, Martin Hofmann-Apitius, Juliane Fluck
Mining biomarker information in biomedical literature. BMC Medical Informatics Decis. Mak. 12 (2012)
Harsha Gurulingappa, Abdul Mateen Rajput, Angus Roberts, Juliane Fluck, Martin Hofmann-Apitius, Luca Toldo
Development of a benchmark corpus to support the automatic extraction of drug-related adverse effects from medical case reports. J. Biomed. Informatics 45 (5) (2012)
Olga Ivchenko, Erfan Younesi, Mohammad Shahid, Antje Wolf, Bernd Müller, Martin Hofmann-Apitius
PLIO: an ontology for formal description of protein-ligand interactions. Bioinform. 27 (12) (2011)
Harsha Gurulingappa, Bernd Müller, Martin Hofmann-Apitius, Juliane Fluck
Information Retrieval Framework for Technology Survey in Biomedical and Chemistry Literature. TREC (2011)
Harsha Gurulingappa, Bernd Müller, Martin Hofmann-Apitius, Juliane Fluck
A Semantic Platform for Information Retrieval from E-Health Records. TREC (2011)
Philippe E. Thomas, Roman Klinger, Laura Inés Furlong, Martin Hofmann-Apitius, Christoph M. Friedrich
Challenges in the association of human single nucleotide polymorphism mentions with unique database identifiers. BMC Bioinform. 12 (S-4) (2011)
Sonja Holl, Olav Zimmermann, Martin Hofmann-Apitius
A UNICORE Plugin for HPC-Enabled Scientific Workflows in Taverna 2.2. SERVICES (2011)
Harsha Gurulingappa, Bernd Müller, Roman Klinger, Heinz-Theodor Mevissen, Martin Hofmann-Apitius, Christoph M. Friedrich, Juliane Fluck
Prior Art Search in Chemistry Patents Based On Semantic Concepts and Co-Citation Analysis. TREC (2010)
Nabeel Azam, Moustafa Ghanem, Dimitrios Kalaitzopoulos, Antje Wolf, Vinod Kasam, Yongjian Wang, Martin Hofmann-Apitius
DockFlow: Achieving interoperability of protein docking tools across heterogeneous Grid middleware. Int. J. Ad Hoc Ubiquitous Comput. 6 (4) (2010)
Bernd Müller, Roman Klinger, Harsha Gurulingappa, Heinz-Theodor Mevissen, Martin Hofmann-Apitius, Juliane Fluck, Christoph M. Friedrich
Abstracts versus Full Texts and Patents: A Quantitative Analysis of Biomedical Entities. IRFC (2010)
Antje Wolf, Martin Hofmann-Apitius, Moustafa Ghanem, Nabeel Azam, Dimitrios Kalaitzopoulos, Kunqian Yu, Vinod Kasam
DockFlow - a prototypic PharmaGrid for Virtual Screening Integrating Four Different Docking Tools. HealthGrid (2009)
Corinna Kolárik, Roman Klinger, Martin Hofmann-Apitius
Identification of histone modifications in biomedical text for supporting epigenomic research. BMC Bioinform. 10 (S-1) (2009)
Martin Hofmann-Apitius, Erfan Younesi, Vinod Kasam
Direct use of information extraction from scientific text for modeling and simulation in the life sciences. Libr. Hi Tech 27 (4) (2009)
Harsha Gurulingappa, Corinna Kolárik, Martin Hofmann-Apitius, Juliane Fluck
Concept-Based Semi-Automatic Classification of Drugs. J. Chem. Inf. Model. 49 (8) (2009)
Mohammad Shahid, Martin Hofmann-Apitius, Oliver Wäldrich, Wolfgang Ziegler
A Robust Framework for Rapid Deployment of a Virtual Screening Laboratory. HealthGrid (2009)
Harsha Gurulingappa, Bernd Müller, Roman Klinger, Heinz-Theodor Mevissen, Martin Hofmann-Apitius, Juliane Fluck, Christoph M. Friedrich
Patent Retrieval in Chemistry Based on Semantically Tagged Named Entities. TREC (2009)
Jimison Iavindrasana, Luigi Lo Iacono, Henning Müller, Ivan Periz, Paul E. Summers, Jessica Wright, Christoph M. Friedrich, Holger Dach, Tobias Gattermayer, Gerhard Engelbrecht, Siegfried Benkner, Martin Hofmann-Apitius, Robert Dunlop, Antonio Arbona, Hariharan Rajasekaran, Jochen Fingberg, Alessandro Chiarini, Bob Moore, Philippe Bijlenga, Rod D. Hose, Alejandro F. Frangi
The @neurIST project. HealthGrid (2008)
Christoph M. Friedrich, Martin Hofmann-Apitius, Robert Dunlop, Ioannis Chronakis, Miriam C. J. M. Sturkenboom, Roelof Risselada, Baldo Oliva, Ferran Sanz
Initial Results on Knowledge Discovery and Decision Support for Intracranial Aneurysms. HEALTHINF (1) (2008)
Roman Klinger, Corinna Kolárik, Juliane Fluck, Martin Hofmann-Apitius, Christoph M. Friedrich
Detection of IUPAC and IUPAC-like chemical names. ISMB (2008)
David Ruau, Corinna Kolárik, Heinz-Theodor Mevissen, Emmanuel Müller, Ira Assent, Ralph Krieger, Thomas Seidl, Martin Hofmann-Apitius, Martin Zenke
Public microarray repository semantic annotation with ontologies employing text mining and expression profile correlation. BMC Bioinform. 9 (S-10) (2008)
Vincent Breton, Nicolas Jacq, Vinod Kasam, Martin Hofmann-Apitius
Grid-Added Value to Address Malaria. IEEE Trans. Inf. Technol. Biomed. 12 (2) (2008)
Hariharan Rajasekaran, Luigi Lo Iacono, Peer Hasselmeyer, Jochen Fingberg, Paul E. Summers, Siegfried Benkner, Gerhard Engelbrecht, Antonio Arbona, Alessandro Chiarini, Christoph M. Friedrich, Martin Hofmann-Apitius, Kai Kumpf, Bob Moore, Philippe Bijlenga, Jimison Iavindrasana, Henning Müller, Rod D. Hose, Robert Dunlop, Alejandro F. Frangi
@neurIST - Towards a System Architecture for Advanced Disease Management through Integration of Heterogeneous Data, Computing, and Complex Processing Services. CBMS (2008)
Mohammad Shahid, Wolfgang Ziegler, Vinod Kasam, Marc Zimmermann, Martin Hofmann-Apitius
Virtual High Throughput Screening (vHTS) on an Optical High Speed Testbed. HealthGrid (2008)
Christoph M. Friedrich, Holger Dach, Tobias Gattermayer, Gerhard Engelbrecht, Siegfried Benkner, Martin Hofmann-Apitius
@neuLink: A Service-oriented Application for Biomedical Knowledge Discovery. HealthGrid (2008)
Laura Inés Furlong, Holger Dach, Martin Hofmann-Apitius, Ferran Sanz
OSIRISv1.2: A named entity recognition system for sequence variants of genes in biomedical literature. BMC Bioinform. 9 (2008)
María-Elena Algorri, Marc Zimmermann, Martin Hofmann-Apitius
Automatic Recognition of Chemical Images. ENC (2007)
Alejandro F. Frangi, Aurelio Ruiz, Martin Hofmann-Apitius
Understanding Cerebral Aneurysms - The @neurIST Project. ERCIM News 2007 (69) (2007)
Vinod Kasam, Marc Zimmermann, Astrid Maaß, Horst Schwichtenberg, Antje Wolf, Nicolas Jacq, Vincent Breton, Martin Hofmann-Apitius
Design of New Plasmepsin Inhibitors: A Virtual High Throughput Screening Approach on the EGEE Grid. J. Chem. Inf. Model. 47 (5) (2007)
Antje Wolf, Marc Zimmermann, Martin Hofmann-Apitius
Alternative to Consensus ScoringA New Approach Toward the Qualitative Combination of Docking Algorithms. J. Chem. Inf. Model. 47 (3) (2007)
Corinna Kolárik, Martin Hofmann-Apitius, Marc Zimmermann, Juliane Fluck
Identification of new drug classification terms in textual resources. ISMB/ECCB (Supplement of Bioinformatics) (2007)
Roman Klinger, Christoph M. Friedrich, Heinz-Theodor Mevissen, Juliane Fluck, Martin Hofmann-Apitius, Laura Inés Furlong, Ferran Sanz
Identifying gene-Specific Variations in Biomedical Text. J. Bioinform. Comput. Biol. 5 (6) (2007)
L.-M. Birkholtz, Olivier Bastien, Gordon Wells, D. Grando, F. Joubert, Vinod Kasam, Marc Zimmermann, Philippe Ortet, Nicolas Jacq, Sylvaine Roy, Martin Hofmann-Apitius, Vincent Breton, A. I. Louw, Eric Maréchal
Integration and mining of malaria molecular, functional and pharmacological data: how far are we from a chemogenomic knowledge space? CoRR (2006)