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Martin Hofmann-Apitius

Martin Hofmann 0009

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affiliation: Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Sankt Augustin, Germany
affiliation: University of Bonn, Bonn-Aachen International Center for IT (B-IT), Germany

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2024
[j51]
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  - journals/data/KhatamiSRDZKSMG24
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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): 25 (2024)
2023
[j50]
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  - journals/biodb/ZhangLWSGJKHK23
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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)
[j49]
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Yojana Gadiya, Andrea Zaliani, Philip Gribbon, Martin Hofmann-Apitius:
PEMT: a patent enrichment tool for drug discovery. Bioinform. 39(1) (2023)
2022
[j48]
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  - journals/bib/MubeenKHD22
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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)
[j47]
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  - journals/bioinformatics/BalabinHBGBKPHD22
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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): 1648-1656 (2022)
[j46]
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  - journals/bioinformatics/WegnerSUDSGSBSK22
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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): 3850-3852 (2022)
[j45]
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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): 5466-5468 (2022)
[j44]
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  - journals/bmcbi/FigueiredoSRHKM22
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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): 231 (2022)
[j43]
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  - journals/ijmi/MadanZBSFFNMHS22
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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: 104724 (2022)
[j42]
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  - journals/patterns/Lage-RupprechtS22
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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): 100433 (2022)
[j41]
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  - journals/tcbb/MusluHLHF22
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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): 491-500 (2022)
2021
[j40]
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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): 5703-5705 (2021)
[j39]
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  - journals/bioinformatics/Marin-LlaoMPHPD21
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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): 137-139 (2021)
[j38]
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  - journals/bioinformatics/Domingo-Fernandez21
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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): 1332-1334 (2021)
[j37]
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  - journals/bioinformatics/BharadhwajABMLH21
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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): 3311-3318 (2021)
[j36]
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  - journals/fini/StefanovskiMPTL21
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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: 630172 (2021)
2020
[j35]
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  - journals/bmcbi/EmonDHH20
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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): 231 (2020)
[j34]
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  - journals/fdata/Gootjes-Dreesbach20
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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: 16 (2020)
[j33]
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  - journals/ploscb/Rivas-BarraganM20
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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)
2019
[j32]
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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: baz068 (2019)
[j31]
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  - journals/biodb/Domingo-Fernandez19
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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: baz081 (2019)
[j30]
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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): 243:1-243:12 (2019)
[j29]
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  - journals/bmcbi/KarkiKHH19
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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): 494:1-494:8 (2019)
2018
[j28]
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  - journals/biodb/HoytDBGH18
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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: bay050 (2018)
[j27]
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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: bay126 (2018)
[j26]
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  - journals/bioinformatics/GundelHH18
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Michaela Gündel, Charles Tapley Hoyt, Martin Hofmann-Apitius:
BEL2ABM: agent-based simulation of static models in Biological Expression Language. Bioinform. 34(13): 2316-2318 (2018)
2017
[j25]
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  - journals/bioinformatics/Domingo-Fernandez17
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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): 3679-3681 (2017)
2016
[j24]
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  - journals/bib/NazKH16
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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): 505-516 (2016)
[j23]
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  - journals/biomedsem/IyappanKRHS16
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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: 45 (2016)
2015
[j22]
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Shweta Bagewadi Kawalia, Subash Adhikari, Anjani Dhrangadhariya, Afroza Khanam Irin, Christian Ebeling, Aishwarya Alex Namasivayam, Matthew Page, Martin Hofmann-Apitius, Philipp Senger:
NeuroTransDB: highly curated and structured transcriptomic metadata for neurodegenerative diseases. Database J. Biol. Databases Curation 2015 (2015)
[j21]
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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)
2014
[j20]
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  - journals/biomedsem/YounesiAGACHHP14
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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: 31 (2014)
[j19]
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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: 352-362 (2014)
2013
[j18]
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  - journals/biomedsem/GundelYMWLZBMH13
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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: 35 (2013)
[j17]
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  - journals/ploscb/MalhotraYGH13
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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)
2012
[j16]
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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): 885-892 (2012)
[j15]
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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: 148 (2012)
2011
[j14]
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  - journals/bioinformatics/IvchenkoYSWMH11
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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): 1684-1690 (2011)
[j13]
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  - journals/bmcbi/ThomasKFHF11
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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): S4 (2011)
2010
[j12]
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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): 235-251 (2010)
2009
[j11]
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  - journals/bmcbi/KolarikKH09
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Corinna Kolárik, Roman Klinger, Martin Hofmann-Apitius:
Identification of histone modifications in biomedical text for supporting epigenomic research. BMC Bioinform. 10(S-1) (2009)
[j10]
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  - journals/jcisd/GurulingappaKHF09
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Harsha Gurulingappa, Corinna Kolárik, Martin Hofmann-Apitius, Juliane Fluck:
Concept-Based Semi-Automatic Classification of Drugs. J. Chem. Inf. Model. 49(8): 1986-1992 (2009)
[j9]
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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): 505-519 (2009)
2008
[j8]
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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)
[j7]
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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)
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Nicolas Jacq, Jean Salzemann, Florence Jacq, Yannick Legré, Emmanuel Medernach, Johan Montagnat, Astrid Maaß, Matthieu Reichstadt, Horst Schwichtenberg, Mahendrakar Sridhar, Vinod Kasam, Marc Zimmermann, Martin Hofmann, Vincent Breton:
Grid-enabled Virtual Screening Against Malaria. J. Grid Comput. 6(1): 29-43 (2008)
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Vincent Breton, Nicolas Jacq, Vinod Kasam, Martin Hofmann-Apitius:
Grid-Added Value to Address Malaria. IEEE Trans. Inf. Technol. Biomed. 12(2): 173-181 (2008)
2007
[j4]
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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): 1277-1296 (2007)
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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): 1036-1044 (2007)
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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): 1818-1828 (2007)
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Nicolas Jacq, Vincent Breton, Hsin-Yen Chen, Li-Yung Ho, Martin Hofmann, Vinod Kasam, Hurng-Chun Lee, Yannick Legré, Simon C. Lin, Astrid Maaß:
Virtual screening on large scale grids. Parallel Comput. 33(4-5): 289-301 (2007)

Conference and Workshop Papers

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2023
[c29]
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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: 124-125
2022
[c28]
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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: 103-107
2020
[c27]
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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: 1-12
2018
[c26]
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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: 207-215
2013
[c25]
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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: 80-88
[c24]
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Tamara Bobic, Juliane Fluck, Martin Hofmann-Apitius:
SCAI: Extracting drug-drug interactions using a rich feature vector. SemEval@NAACL-HLT 2013: 675-683
2012
[c23]
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  - conf/eScience/HollZH12
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Sonja Holl, Olav Zimmermann, Martin Hofmann-Apitius:
A new optimization phase for scientific workflow management systems. eScience 2012: 1-8
[c22]
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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
2011
[c21]
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Sonja Holl, Olav Zimmermann, Martin Hofmann-Apitius:
A UNICORE Plugin for HPC-Enabled Scientific Workflows in Taverna 2.2. SERVICES 2011: 220-223
[c20]
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Harsha Gurulingappa, Bernd Müller, Martin Hofmann-Apitius, Juliane Fluck:
Information Retrieval Framework for Technology Survey in Biomedical and Chemistry Literature. TREC 2011
[c19]
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Harsha Gurulingappa, Bernd Müller, Martin Hofmann-Apitius, Juliane Fluck:
A Semantic Platform for Information Retrieval from E-Health Records. TREC 2011
2010
[c18]
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  - conf/irfc/MullerKGMHFF10
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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: 152-165
[c17]
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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
2009
[c16]
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  - conf/healthgrid/WolfHGAKYK09
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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: 3-12
[c15]
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  - conf/healthgrid/ShahidHWZ09
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Mohammad Shahid, Martin Hofmann-Apitius, Oliver Wäldrich, Wolfgang Ziegler:
A Robust Framework for Rapid Deployment of a Virtual Screening Laboratory. HealthGrid 2009: 212-221
[c14]
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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
2008
[c13]
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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: 265-272
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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: 361-366
[c11]
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Mohammad Shahid, Wolfgang Ziegler, Vinod Kasam, Marc Zimmermann, Martin Hofmann-Apitius:
Virtual High Throughput Screening (vHTS) on an Optical High Speed Testbed. HealthGrid 2008: 125-134
[c10]
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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: 161-164
[c9]
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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: 165-172
[c8]
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Roman Klinger, Corinna Kolárik, Juliane Fluck, Martin Hofmann-Apitius, Christoph M. Friedrich:
Detection of IUPAC and IUPAC-like chemical names. ISMB 2008: 268-276
2007
[c7]
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María-Elena Algorri, Marc Zimmermann, Martin Hofmann-Apitius:
Automatic Recognition of Chemical Images. ENC 2007: 41-46
[c6]
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Corinna Kolárik, Martin Hofmann-Apitius, Marc Zimmermann, Juliane Fluck:
Identification of new drug classification terms in textual resources. ISMB/ECCB (Supplement of Bioinformatics) 2007: 264-272
2006
[c5]
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Vincent Breton, Nicolas Jacq, Martin Hofmann:
Grid Added Value to Address Malaria. CCGRID 2006: 40
[c4]
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Nicolas Jacq, Vincent Breton, Hsin-Yen Chen, Li-Yung Ho, Martin Hofmann, Hurng-Chun Lee, Yannick Legré, Simon C. Lin, Astrid Maaß, Emmanuel Medernach, Ivan Merelli, Luciano Milanesi, Giulio Rastelli, Matthieu Reichstadt, Jean Salzemann, Horst Schwichtenberg, Mahendrakar Sridhar, Vinod Kasam, Ying-Ta Wu, Marc Zimmermann:
Grid-Enabled High Throughput Virtual Screening. GCCB 2006: 45-59
[c3]
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Nicolas Jacq, Jean Salzemann, Yannick Legré, Matthieu Reichstadt, Florence Jacq, Marc Zimmermann, Astrid Maaß, Mahendrakar Sridhar, Kasam Vinod-Kusam, Horst Schwichtenberg, Martin Hofmann, Vincent Breton:
Demonstration of In Silico Docking at a Large Scale on Grid Infrastructure. HealthGrid 2006: 155-157
[c2]
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Christoph M. Friedrich, Thomas Revillion, Martin Hofmann, Juliane Fluck:
Biomedical and Chemical Named Entity Recognition with Conditional Random Fields: The Advantage of Dictionary Features. SMBM 2006
2005
[c1]
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  - conf/gi/HofmannB05
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Martin Hofmann, Uta Bohnebeck:
GRID Computing. GI Jahrestagung (2) 2005: 716-717

Editorship

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2009
[e2]
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Tony Solomonides, Martin Hofmann-Apitius, Mathias Freudigmann, Sebastian Claudius Semler, Yannick Legré, Mary Kratz:
Healthgrid Research, Innovation and Business Case - Proceedings of HealthGrid 2009, Berlin, Germany, 29 June - 1 July 2009. Studies in Health Technology and Informatics 147, IOS Press 2009, ISBN 978-1-60750-027-8 [contents]
2007
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Nicolas Jacq, Henning Müller, Ignacio Blanquer, Yannick Legré, Vincent Breton, Dominique Hausser, Vicente Hernández, Tony Solomonides, Martin Hofmann-Apitius:
From Genes to Personalized HealthCare: Grid Solutions for the Life Sciences - Proceedings of HealthGrid 2007, Geneva, Switzerland, April 24-27, 2007. Studies in Health Technology and Informatics 126, IOS Press 2007, ISBN 978-1-58603-738-3 [contents]

Informal and Other Publications

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2014
[i6]
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  - journals/f1000research/KawaliaBHFK14
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Shweta Bagewadi Kawalia, Tamara Bobic, Martin Hofmann-Apitius, Juliane Fluck, Roman Klinger:
Detecting miRNA Mentions and Relations in Biomedical Literature. F1000Research 3: 205 (2014)
2007
[i5]
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Alejandro F. Frangi, Aurelio Ruiz, Martin Hofmann-Apitius:
Understanding Cerebral Aneurysms - The @neurIST Project. ERCIM News 2007(69) (2007)
2006
[i4]
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  - journals/corr/abs-cs-0611084
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Nicolas Jacq, Vincent Breton, Hsin-Yen Chen, Li-Yung Ho, Martin Hofmann, Hurng-Chun Lee, Yannick Legré, Simon C. Lin, Astrid Maaß, Emmanuel Medernach, Ivan Merelli, Luciano Milanesi, Giulio Rastelli, Matthieu Reichstadt, Jean Salzemann, Horst Schwichtenberg, Mahendrakar Sridhar, Vinod Kasam, Ying-Ta Wu, Marc Zimmermann:
Large Scale In Silico Screening on Grid Infrastructures. CoRR abs/cs/0611084 (2006)
[i3]
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  - journals/corr/abs-q-bio-0611052
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Vincent Breton, Nicolas Jacq, Martin Hofmann:
Grid Added Value to Address Malaria. CoRR abs/q-bio/0611052 (2006)
[i2]
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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 abs/q-bio/0611053 (2006)
[i1]
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Nicolas Jacq, Jean Salzemann, Florence Jacq, Yannick Legré, Emmanuel Medernach, Johan Montagnat, Astrid Maaß, Matthieu Reichstadt, Horst Schwichtenberg, Mahendrakar Sridhar, Vinod Kasam, Marc Zimmermann, Martin Hofmann, Vincent Breton:
Grid enabled virtual screening against malaria. CoRR abs/q-bio/0611054 (2006)

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