Scientific Publications

Sepehr Golriz Khatami, Christine Robinson, Colin Birkenbihl, Daniel Domingo-Fernández, Charles Tapley Hoyt, Martin Hofmann-Apitius:
Challenges of Integrative Disease Modeling in Alzheimer's Disease

Raza-Ur Rahman, Vikas Bansal, Maksims Fiosins, Anna-Maria Liebhoff, Ashish Rajput, Abdul Sattar, Daniel Sumner Magruder, Sumit Madan, Ting Sun, Abhivyakti Gautam, Sven Heins, Timur Liwinski, Jörn Bethune, Claudia Trenkwalder, Juliane Fluck, Brit Mollenhauer, Stefan Bonn:
SEAweb: The small RNA Expression Atlas web application

Farah Humayun, Daniel Domingo-Fernández, Paul George, Ajay Abisheck, Marie-Thérèse Hopp, Benjamin Syllwasschy, Milena Detzel, Charles Tapley Hoyt, Martin Hofmann-Apitius, Diana Imhof:
A Computational Approach for Mapping Heme Biology in the Context of Hemolytic Disorders

Anne Fröhlich, Sophia Loick, Emma Grace Bawden, Simon Fietz, Jörn Dietrich, Eric Diekmann, Gonzalo Saavedra, Holger Fröhlich, Dennis Niebel, Judith Sirokay, Romina Zarbl, Gerrit H. Gielen, Glen Kristiansen, Friedrich Bootz, Jennifer Landsberg, Dimo Dietrich:
Comprehensive analysis of tumor necrosis factor receptor TNFRSF9 (4-1BB) DNA methylation with regard to molecular and clinicopathological features

Sepehr Golriz Khatami, Sarah Mubeen, Martin Hofmann-Apitius:
Data science in neurodegenerative disease: its capabilities, limitations, and perspectives

Amin Lemsara, Salima Ouadfel, Holger Fröhlich:
PathME: Pathway based Multi-modal Sparse Autoencoders for Clustering of Patient-Level Multi-Omics Data

Luise Gootjes-Dreesbach, Meemansa Sood, Akrishta Sahay, Martin Hofmann-Apitius, Holger Fröhlich:
Variational Autoencoder Modular Bayesian Networks (VAMBN) for Simulation of Heterogeneous Clinical Study Data

Wolfgang Ziegler:
A Landscape Analysis of Standardisation in the Field of Artificial Intelligence

Mohammad Asif Emon; Daniel Domingo-Fernàndez; Martin Hofmann-Apitius:
PS4DR: a multimodal workflow for identification and prioritization of drugs based on pathway signatures

Meemansa Sood, Akrishta Sahay, Reagon Karki, Mohammad Asif Emon, Henri Vrooman, Martin Hofmann-Apitius, Holger Fröhlich:
Realistic Simulation of Virtual Multi-Scale, Multi-Modal Patient Trajectories using Bayesian Networks and Sparse Autoencoders

Colin Birkenbihl, Mohammad Asif Emon, Henri Vrooman, Sarah Westwood, Simon Lovestone, On behalf of the AddNeuroMed Consortium, Martin Hofmann-Apitius, Holger Fröhlich & Alzheimer’s Disease Neuroimaging Initiative:
Differences in cohort study data affect external validation of artificial intelligence models for predictive diagnostics of dementia - lessons for translation into clinical practice

Sara Mora, Sumit Madan, Stephan Gebel, Mauro Giacomini:
Proposal of an Architecture for Terminology Management in a Research Project

Özlem Muslu, Charles Tapley Hoyt, Mauricio Pio De Lacerda, Martin Hofmann-Apitius, Holger Fröhlich:
GuiltyTargets: Prioritization of Novel Therapeutic Targets with Deep Network Representation Learning

Elisha Goldstein, Kristina Yeghiazaryan, Ashar Ahmad, Frank A. Giordano, Holger Fröhlich, Olga Golubnitschaja:
Optimal multiparametric set-up modelled for best survival outcomes in palliative treatment of liver malignancies - Unsupervised machine learning and 3PM recommendations

Reagon Karki, Sumit Madan, Yojana Gadiya, Daniel Domingo-Fernàndez, Alpha Tom Kodamullil, Martin Hofmann-Apitius:
Data-driven modeling of knowledge assemblies in understanding comorbidity between Type 2 Diabetes Mellitus and Alzheimer’s Disease

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

Lisa Langnickel, Roman Baum, Gabriele Wollnik-Korn, Brigitte Fischer-Wagener, Sumit Madan, Juliane Fluck:
The future of German MeSH: a new semi-automatic translation process and new services for search and annotation

Tobias Newmiwaka, Benjamin Engelhardt, Philipp Wendland, Dominik Kahl, Holger Fröhlich, Maik Kschischo:
SEEDS: Data driven inference of structural model errors and unknown inputs for dynamic systems biology

Laurèl Rauschenbach, Anja Wieland, Roman Reinartz, Sied Kebir, Andreas Till, Marvin Darkwah Oppong, Celia Dobersalske, Vivien Ullrich, Ashar Ahmad, Ramazan Jabbarli, Daniela Pierscianek, Holger Fröhlich, Matthias Simon, Oliver Brüstle, Ulrich Sure, Martin Glas, Björn Scheffler:
Drug repositioning of antiretroviral ritonavir for combinatorial therapy in glioblastoma

Colin Birkenbihl, Sarah Westwood, Eric Westman, Liu Shi, Alejo Nevado-Holgado, Simon Lovestone, Martin Hofmann-Apitius:
ANMerge: A comprehensive and accessible Alzheimer's disease patient-level dataset

Mohammad Asif Emon, Ashley Heinson, Ping Wu, Daniel Domingo-Fernandez, Meemansa Sood, Henri Vrooman, Jean-Christophe Corvol, Phil Scordis, Martin Hofmann-Apitius, Holger Fröhlich:
Clustering of Alzheimer’s and Parkinson’s Disease Based on Genetic Burden of Shared Molecular Mechanisms

Lisa Langnickel, Roman Baum, Gabriele Wollnik-Korn, Brigitte Fischer-Wagener, Sumit Madan, Juliane Fluck:
The future of German MeSH: a new semi-automatic translation process and new services for search and annotation

Frederic Brosseron, Carl-Christian Kolbe, Francesco Santarelli, Stephanie Carvalho, Anna Antonell, Sergio Castro-Gomez, Pawel Tacik Aishwarya, Alex Namasivayam, Graziella Mangone, Reinhard Schneider, Eicke Latz, Ullrich Wüllner, Per Svenningsson, Raquel Sánchez-Valle, José Luis Molinuevo, Jean-Christophe Corvol, Michael T.Heneka, on behalf of the AETIONOMY study group (…Martin Hofmann-Apitius (…), Stephan Springstubbe (...), Holger Fröhlich (…)):
Multicenter Alzheimer's and Parkinson's disease immune biomarker verification study Multicenter Alzheimer's and Parkinson's disease immune biomarker verification study

Anatolij Kunin, Nafiseh Sargheini, Colin Birkenbihl, Natalia Moiseeva, Holger Fröhlich, Olga Golubnitschaja:
Voice perturbations under the stress overload in young individuals: phenotyping and suboptimal health as predictors for cascading pathologies

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

Colin Birkenbihl, Yasamin Salimi, Daniel Domingo-Fernandez, Simon Lovestone on behalf of the AddNeuroMed consortium, Holger Fröhlich, Martin Hofmann-Apitius, and the Japanese Alzheimer's Disease Neuroimaging Initiative, and the Alzheimer's Disease Neuroimaging Initiative:
Evaluating the Alzheimer's Disease Data Landscape

Roman Li, Anze Zupanic, Marja Talikka, Vincenzo Belcastro, Sumit Madan, Jens Dörpinghaus, Colette vom Berg, Justyna Szostak, Florian Martin, Manuel C. Peitsch, Julia Hoeng:
Systems toxicology approach for testing chemical cardiotoxicity in larval zebrafish

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

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

Tamás Letoha, Anett Hudák, Erzsébet Kusz, Aladár Pettkó-Szandtner, Ildikó Domonkos, Katalin Jósvay, Martin Hofmann-Apitius & László Szilák:
Contribution of syndecans to cellular internalization and fibrillation of amyloid-β(1–42)

Daniel Domingo-Fernandez, Allison Provost, Alpha Tom Kodamullil, Josep Marin-Llao, Heather Lasseter, Kristophe Diaz, Nikolaos Daskalakis, Lee Lancashire, Martin Hofmann-Apitius, Magali Haas:
PTSD Biomarker Database: Deep Dive Meta-database for PTSD Biomarkers, Visualizations, and Analysis Tools

Daniel Domingo-Fernández, Sarah Mubeen, Josep Marín-Llaó, Charles Tapley Hoyt, Martin Hofmann-Apitius:
PathMe: Merging and exploring mechanistic pathway knowledge

Charles Hoyt, Daniel Domingo-Fernandez, Rana Aldisi, Lingling Xu, Kristian Kolpeja, Sandra Spalek, Esther Wollert, John Bachman, Benjamin Gyori, Patrick Greene, Martin Hofmann-Apitius:
Re-curation and Rational Enrichment of Knowledge Graphs in Biological Expression Language

Sarah Mubeen, Charles Tapley Hoyt, Andre Gemünd, Martin Hofmann-Apitius, Holger Fröhlich, Daniel Domingo-Fernández:
The Impact of Pathway Database Choice on Statistical Enrichment Analysis and Predictive Modeling

Charles Tapley Hoyt, Daniel Domingo-Fernández, Sarah Mubeen, Josep Marin Llaó, Andrej Konotopez, Christian Ebeling, Colin Birkenbihl, Özlem Muslu, Bradley English, Simon Müller, Mauricio Pio de Lacerda, Mehdi Ali, Scott Colby, Dénes Türei, Nicolàs Palacio-Escat, Martin Hofmann-Apitius:
Integration of Structured Biological Data Sources using Biological Expression Language

Reagon Karki, Alpha Tom Kodamullil, Charles Tapley Hoyt, Martin Hofmann-Apitius:
Quantifying mechanisms in neurodegenerative diseases (NDDs) using candidate mechanism perturbation amplitude (CMPA) algorithm

Mehdi Ali, Hajira Jabeen, Charles Tapley Hoyt, Jens Lehmann:
The KEEN Universe: An Ecosystem for Knowledge Graph Embeddings with a Focus on Reproducibility and Transferability

Johann de Jong, Mohammad Asif, Ping Wu, Reagon Karki, Meemansa Sood, Patrice Godard, Ashar Ahmad, Henri Vrooman, Martin Hofmann-Apitius, Holger Fröhlich:
Deep learning for clustering of multivariate clinical patient trajectories with missing values

Sumit Madan, Justyna Szostak, Ravikumar Komandur Elayavilli, Richard Tzong-Han Tsai, Mehdi Ali, Longhua Qian, Majid Rastegar-Mojarad, Julia Hoeng, Juliane Fluck:
The extraction of complex relationships and their conversion to biological expression language (BEL) overview of the BioCreative VI (2017) BEL track

Eduardo Brito, Bogdan Georgiev, Daniel Domingo-Fernández, Charles Tapley Hoyt, Christian Bauckhage:
RatVec: A General Approach for Low-dimensional Distributed Vector Representations via Rational Kernels

Jens Dörpinghaus, Andreas Stefan:
Knowledge Extraction and Applications utilizing Context Data in Knowledge Graphs

Jens Dörpinghaus, Carsten Düing, Vera Weil:
A Minimum Set-Cover Problem with several constraints

Mehdi Ali, Charles Tapley, Hoyt, Daniel Domingo-Fernández, Jens Lehmann:
Predicting Missing Links Using PyKEEN

Wolfgang Ziegler, Ramin Yahyapour, Jens Grabowski, Dieter Kranzlmüller:
A framework for managing quality of service in cloud computing through service level agreements

Daniel Domingo-Fernández, Charles Tapley Hoyt, Carlos Bobis-Álvarez, Josep Marín-Llaó, Martin Hofmann-Apitius:
Publisher Correction: ComPath: an ecosystem for exploring, analyzing, and curating mappings across pathway databases

Charles Tapley Hoyt, Daniel Domingo-Fernández, Rana Aldisi, Lingling Xu, Kristian Kolpeja, Sandra Spalek, Esther Wollert, John Bachman, Benjamin M Gyori, Patrick Greene, Martin Hofmann-Apitius:
Re-curation and rational enrichment of knowledge graphs in Biological Expression Language

Gloria Bahamondez, Holger Fröhlich:
MCMC Techniques for Parameters Estimation of ODE Based Models in Systems Biology

Amit Sharma, Holger Fröhlich, Rong Zhang, Anne-Karoline Ebert, Wolfgang Rösch, Henning Reis, Glen Kristiansen, Jörg Ellinger, Heiko Reutter:
Classic bladder exstrophy and adenocarcinoma of the bladder: methylome analysis provide no evidence for underlying disease-mechanisms of this association

Thorsten Buch, Katharina Moos, Filipa M. Ferreira, Holger Fröhlich, Catherine Gebhar, Achim Tresch:
Benefits of a factorial design focusing on inclusion of female and male animals in one experiment

Bawarjan Schatlo, Oliver P. Gautschi, Christoph M. Friedrich, Christian Ebeling, Max Jägersberg, Zsolt Kulscar, Vitor Mendes Pereira, Karl Schaller, Philippe Bijlenga:
Association of single and multiple aneurysms with tobacco abuse: an @neurIST risk analysis

Gündel, Michaela; Hoyt, Charles Tapley; Hofmann-Apitius, Martin:
BEL2ABM: agent-based simulation of static models in Biological Expression Language

Dörpinghaus, J.; Jacobs, M.; Fluck, J.:
Graph based discovery in biomedical information systems connecting scientific texts with structured expert knowledge

Darms, J.; Dörpinghaus, J.:
Improving document retrieval with a clustering based relevance feedback system

Ajay Abisheck Paul George; Heimer, Pascal; Maaß, Astrid; Hamaekers, Jan; Hofmann-Apitius, Martin; Biswas, Arijit; Imhof, Diana:
Insights into the Folding of Disulfide-Rich μ-Conotoxins

Golubnitschaja, O.; Filep, N.; Yeghiazaryan, K.; Blom, H.J.; Hofmann-Apitius, M.; Kuhn, W.:
Multi-omic approach decodes paradoxes of the triple-negative breast cancer: Lessons for predictive, preventive and personalised medicine

Dörpinghaus, Jens; Schrader, R.; Randerat, H.:
Pseudostabile Mengen in Graphen

Hoyt, Charles Tapley; Konotopez, Andrej; Ebeling, Christian:
PyBEL: A computational framework for biological expression language

Dörpinghaus, J.; Klein, J.; Darms, J.; Madan, S.; Jacobs, M.:
SCAIView - A semantic search engine for biomedical research utilizing a microservice architecture

Jacobs, M.; Hodapp, S.; Dörpinghaus, J.:
SDA: Towards a novel knowledge discovery model for information systems

Dörpinghaus, J.; Schaaf, S.; Jacobs, M.:
Soft document clustering using a novel graph covering approach

Hoyt, Charles Tapley; Domingo-Fernandez, Daniel; Balzer, Nora; Güldenpfennig, Anka; Hofmann-Apitius, Martin:
A systematic approach for identifying shared mechanisms in epilepsy and its comorbidities

Khanna, Shashank; Domingo-Fernández, Daniel; Iyappan, Anandhi; Emon, Mohammad Asif; Hofmann-Apitius, Martin; Fröhlich, Holger:
Using Multi-Scale Genetic, Neuroimaging and Clinical Data for Predicting Alzheimer's Disease and Reconstruction of Relevant Biological Mechanisms

Daniel Domingo-Fernández, Charles Tapley Hoyt, Carlos Bobis-Álvarez, Josep Marín-Llaó & Martin Hofmann-Apitius:
ComPath: an ecosystem for exploring, analyzing, and curating mappings across pathway databases

Vincent J. Henry, Ivan Moszer, Olivier Dameron, Marie-Claude Potier, Martin Hofmann-Apitius, Olivier Colliot:
Integrating ontological representation and reasoning into a disease map: application to Alzheimer’s disease

Charles Tapley Hoyt, Daniel Domingo-Fernández, Martin Hofmann-Apitius:
BEL Commons: an environment for exploration and analysis of networks encoded in Biological Expression Language

Henry V., Moszer I., Dameron O., Potier MC., Hofmann-Apitius M., Colliot O.:
Converting Alzheimer’s Disease Map into a Heavyweight Ontology: A Formal Network to Integrate Data

Doubal, F.N., Ali, M., Batty, G.D., Charidimou, A., Eriksdotter, M., Hofmann-Apitius, M., Kim, Y.-H., Levine, D.A., Mead, G., Mucke, H.A.M., Ritchie, C.W., Roberts, C.J., Russ, T.C., Stewart, R., Whiteley, W., Quinn, T.J.:
Big data and data repurposing - using existing data to answer new questions in vascular dementia research

Emon, M.A.E.K., Kodamullil, A.T., Karki, R., Younesi, E., Hofmann-Apitius, M.:
Using Drugs as Molecular Probes: A Computational Chemical Biology Approach in Neurodegenerative Diseases

Fluck, Juliane; Senger, Philipp; Ziegler, Wolfgang; Claus, Steffen; Schwichtenberg, Horst:
The cloud4health Project. Secondary use of clinical data with secure cloud-based text mining services

Geerts, H.; Hofmann-Apitius, M.; Anastasio, T.J.:
Knowledge-driven computational modeling in Alzheimer's disease research: Current state and future trends

Iyappan, A.; Younesi, E.; Redolfi, A.; Vrooman, H.; Khanna, S.; Frisoni, G.B.; Hofmann-Apitius, M.:
Neuroimaging feature terminology: A controlled terminology for the annotation of brain imaging features

Juzenas, S., Venkatesh, G., Hübenthal, M., Hoeppner, M.P., Du, Z.G., Paulsen, M., Rosenstiel, P., Senger, P., Hofmann-Apitius, M., Keller, A., Kupcinskas, L., Franke, A., Hemmrich-Stanisak, G.:
A comprehensive, cell specific microRNA catalogue of human peripheral blood

Karki, R.; Kodamullil, A.T.; Hofmann-Apitius, M.:
Comorbidity analysis between alzheimer's disease and type 2 diabetes mellitus (T2DM) based on shared pathways and the role of T2DM drugs

Kawalia, S.B.; Raschka, T.; Naz, M.; Matos Simoes, R. de; Senger, P.; Hofmann-Apitius, M.:
Analytical strategy to prioritize Alzheimer's disease candidate genes in gene regulatory networks using public expression data

Kodamullil, Alpha & Zekri, Firas & Sood, Meemansa & Hengerer, Bastian & Canard, Luc & McHale, Duncan & Hofmann-Apitius, Martin:
Trial watch: Tracing investment in drug development for Alzheimer disease. Nature Reviews Drug Discovery.

Kodamullil, A.T.; Iyappan, A.; Karki, R.; Madan, S.; Younesi, E.; Hofmann-Apitius, M.:
Of mice and men: Comparative analysis of neuro-inflammatory mechanisms in human and mouse using cause-and-effect models

Langley, G.R., Adcock, I.M., Busquet, F., Crofton, K.M., Csernok, E., Giese, C., Heinonen, T., Herrmann, K., Hofmann-Apitius, M., Landesmann, B., Marshall, L.J., McIvor, E., Muotri, A.R., Noor, F., Schutte, K., Seidle, T., van de Stolpe, A., Van Esch, H., Willett, C., Woszczek, G.:
Towards a 21st-century roadmap for biomedical research and drug discovery: consensus report and recommendations

Akhondi, S.A.; Klenner, A.G.; Tyrchan, C.; Manchala, A.K.; Boppana, K.; Lowe, D.; Zimmermann, M.; Jagarlapudi, S.A.R.P.; Sayle, R.; Kors, J.A.; Muresan, S.:

Annotated chemical patent corpus: A gold standard for text mining
PLoS one. Online journal, Vol.9 (2014), No.9, Art. e107477, 8 pp.
info:doi/10.1371/journal.pone.0107477

Blasi, Lorenzo; Jensen, Jens; Ziegler, Wolfgang:
Expressing quality of service and protection using federation-level service level agreement. (International Conference on Parallel Processing (Euro-Par) <19, 2013, Aachen>)
Euro-Par 2013. Parallel Processing Workshops: BigDataCloud, DIHC, FedICI, HeteroPar, HiBB, LSDVE, MHPC, OMHI, PADABS, PROPER, Resilience, ROME, and UCHPC 2013, Aachen, Germany, August 26-27, 2013; revised selected papers. Berlin: Springer, 2014. (Lecture Notes in Computer Science 8374), pp. 146-156
info:doi/10.1007/978-3-642-54420-0_15

Deyati, A.; Sanam, R.D.; Guggilla, S.R.; Pidugu, V.R.; Novac, N.:
Molecular biomarkers in clinical development: What could we learn from the clinical trial registry?
Personalized medicine, Vol.11 (2014), No.4, pp.381-393
info:doi/10.2217/pme.14.27

Fluck, Juliane; Madan, Sumit; Ansari, Sam; Szostak, Justyna; Hoeng, Julia; Zimmermann, Marc; Hofmann-Apitius, Martin; Peitsch, Manuel C:
BELIEF - a semiautomatic workflow for BEL network creation. (International Symposium on Semantic Mining in Biomedicine (SMBM) <6, 2014, Aveiro>)
Bodenreider, O.: SMBM 2014, 6th International Symposium on Semantic Mining in Biomedicine. Proceedings. Online resource: October 6-7th, 2014, Aveiro, Portugal. Aveiro, 2014, pp. 109-113

Fluck, Juliane; Hofman-Apitius, Martin:
Text mining for systems biology
Drug Discovery Today, Vol.19 (2014), No.2, pp.140-144
info:doi/10.1016/j.drudis.2013.09.012

Holl, S.; Zimmermann, O.; Palmblad, M.; Mohammed, Y.; Hofmann-Apitius, M.:
A new optimization phase for scientific workflow management systems
Future generation computer systems : FGCS, Vol.36 (2014), pp.352-362
info:doi/10.1016/j.future.2013.09.005

Ishitsubo, E.; Hosozawa, T.; Igarashi, M.; Kirshner, K.N.; Sriwilaijaroen, N.; Yokoe, H.; Tubuki, M.; Suzuki, Y.; Tokiwa, H.:
Rational design and development of novel multi-target inhibitors for influenza virus. (Society for Glycobiology; Japanese Society of Carbohydrate Research (SFG & JSCR Joint Annual Meeting) <2014, Honolulu/Hawaii>)
Glycobiology, Vol.24 (2014), No.11, pp.1128

Iyappan, Anandhi; Bagewadi, Shweta; Page, Matthew; Hofmann-Apitius, Martin; Senger, Philipp:
NeuroRDF: Semantic data integration strategies for modeling neurodegenerative diseases. (International Symposium on Semantic Mining in Biomedicine (SMBM) <6, 2014, Aveiro>)
Bodenreider, O.: SMBM 2014, 6th International Symposium on Semantic Mining in Biomedicine. Proceedings. Online resource: October 6-7th, 2014, Aveiro, Portugal. Aveiro, 2014, pp. 11-18

Malhotra, A.; Younesi, E.; Gündel, M.; Müller, B.; Heneka, M.T.; Hofmann-Apitius, M.:
ADO: A disease ontology representing the domain knowledge specific to Alzheimer's disease
Alzheimer's & dementia, Vol.10 (2014), No.2, pp.238-246
info:doi/10.1016/j.jalz.2013.02.009

Malhotra, Ashutosh; Younesi, Erfan; Bagewadi, Shweta; Hofmann-Apitius, Martin:
Linking hypothetical knowledge patterns to disease molecular signatures for biomarker discovery in Alzheimer's disease
Genome medicine, Vol.6 (2014), No.12, Ar. 97, 11 pp.
urn:nbn:de:0011-n-3179045
info:doi/10.1186/s13073-014-0097-z
Volltext

Saeed, A.; Khan, M.S.; Rafique, H.; Shahid, M.; Iqbal, J.:
Design, synthesis, molecular docking studies and in vitro screening of ethyl 4-(3-benzoylthioureido) benzoates as urease inhibitors
Bioorganic chemistry, Vol.52 (2014), pp.1-7
info:doi/10.1016/j.bioorg.2013.10.001

Saeed, A.; Mahesar, P.A.; Zaib, S.; Khan, M.S.; Matin, A.; Shahid, M.; Iqbal, J.:
Synthesis, cytotoxicity and molecular modelling studies of new phenylcinnamide derivatives as potent inhibitors of cholinesterases
European journal of medicinal chemistry, Vol.78 (2014), pp.43-53
info:doi/10.1016/j.ejmech.2014.03.015

Sahadevan, S.; Gunawan, A.; Tholen, E.; Große-Brinkhaus, C.; Tesfaye, D.; Schellander, K.; Hofmann-Apitius, M.; Cinar, M.U.; Uddin, M.J.:
Pathway based analysis of genes and interactions influencing porcine testis samples from boars with divergent androstenone content in back fat
PLoS one. Online journal, Vol.9 (2014), No.3, Art. e91077, 16 pp.
info:doi/10.1371/journal.pone.0091077

Wolf, Antje; Schoof, Sebastian; Baumann, Sascha; Arndt, Hans-Dieter; Kirschner, Karl N.:
Structure-activity relationships of thiostrepton derivatives: implications for rational drug design
Journal of computer aided molecular design, Vol.28 (2014), No.12, pp.1205-1215
info:doi/10.1007/s10822-014-9797-0

Younesi, E.; Ansari, S.; Guendel, M.; Ahmadi, S.; Coggins, C.; Hoeng, J.; Hofmann-Apitius, M.; Peitsch, M.C.:
CSEO - The Cigarette Smoke Exposure Ontology
Journal of biomedical semantics, Vol.5 (2014), Art. 31
info:doi/10.1186/2041-1480-5-31

Zaib, S.; Saeed, A.; Stolte, K.; Flörke, U.; Shahid, M.; Iqbal, J.:
New aminobenzenesulfonamide-thiourea conjugates: Synthesis and carbonic anhydrase inhibition and docking studies
European journal of medicinal chemistry, Vol.78 (2014), pp.140-150
info:doi/10.1016/j.ejmech.2014.03.023

Ziegler, Wolfgang; D'Ippolito, Roberto; D'Auria, Massimo; Berends, Jochem; Nelissen, Maarten; Diaz, Ramon:
Implementing a "one-stop-shop" providing SMEs with integrated HPC simulation resources using Fortissimo resources. (eChallenges Conference <2014, Belfast>)
Cunningham, P.: eChallenges Conference 2014: Belfast, United Kingdom, 29 - 30 October 2014. Piscataway, NJ: IEEE, 2014, pp. 292-302
urn:nbn:de:0011-n-3566448
Volltext

Aisopos, F.; Kardara, M.; Senger, P.; Klinger, R.; Papaoikonomou, A.; Tserpes, K.; Gardner, M.; Varvarigou, T.:
e-Government and Policy Simulation in Intelligent Virtual Environments. (International Conference on Web Information Systems and Technologies (WEBIST) <8, 2012, Porto>)
Krempels, K.-H.: WEBIST 2012, 8th International Conference on Web Information Systems and Technologies. Proceedings: Porto, Portugal, 18 - 21 April, 2012. Setúbal: INSTICC, 2012

Ali, S.; Saeed, A.; Abbas, N.; Shahid, M.; Bolte, M.; Iqbal, J.:
Design, synthesis and molecular modelling of novel methyl[4-oxo-2-(aroylimino)-3-(substituted phenyl)thiazolidin-5-ylidene]acetates as potent and selective aldose reductase inhibitors
Medicinal chemistry communications : MedChemComm, Vol.3 (2012), No.11, pp.1428-1434
info:doi/10.1039/c2md20228j

Cacciari, Claudio; Mallmann, Daniel; D'Andria, Francesco; Hagemeier, Björn; Rumpl, Angela; Ziegler, Wolfgang; Zsigri, Csilla; Martrat, Josep:
SLA-based management of software licenses as web service resources in distributed computing infrastructures
Future generation computer systems : FGCS, Vol.28 (2012), No.8, pp.1340-1349
info:doi/10.1016/j.future.2011.11.005

Danelutto, M.; Desprez, F.; Getov, V.; Ziegler, W.:
CoreGRID/ERCIM workshop on grids, clouds and P2P computing - CGWS2011. Introduction. (International Conference on Parallel Processing (Euro-Par) <17, 2011, Bordeaux>)
Alexander, M.: Euro-Par 2011 Parallel processing workshops. CCPI, CGWS, HeteroPar, HiBB, HPCVirt, HPPC, HPSS, MDGS, ProPer, Resilience, UCHPC, VHPC. Part 1: Bordeaux, France, August 29-September 2, 2011. Revised selected papers. Heidelberg: Springer, 2012. (Lecture notes in computer science 7155), pp. 113-114
info:doi/10.1007/978-3-642-29737-3_13

Gurulingappa, Harsha; Rajput, Abdul-Mateen; Roberts, Angus; Fluck, Juliane; Hofmann-Apitius, Martin; Toldo, Luca:
Development of a benchmark corpus to support the automatic extraction of drug-related adverse effects from medical case reports
Journal of biomedical informatics : JBI, Vol.45 (2012), No.5, pp.885-892
info:doi/10.1016/j.jbi.2012.04.008

Holl, S.; Zimmermann, O.; Hofmann-Apitius, M.:
A new optimization phase for scientific workflow management systems. (International Conference on E-Science (e-Science) <8, 2012, Chicago/Ill.>)
Institute of Electrical and Electronics Engineers -IEEE-: IEEE 8th International Conference on E-Science 2012: Chicago, Illinois, 8 - 12 October 2012. Piscataway: IEEE, 2012, 8 pp.
info:doi/10.1109/eScience.2012.6404479

Holl, S.; Zimmermann, O.; Demuth, B.; Schuller, B.; Hofmann-Apitius, M.:
Secure multi-level parallel execution of scientific workflows on HPC grid resources by combining taverna and UNICORE services. (UNICORE Summit <8, 2012, Dresden>)
Huber, V.: UNICORE Summit 2012. Proceedings: 30 - 31 May 2012, Dresden, Germany. Jülich: Forschungszentrum Jülich, 2012. (Schriften des Forschungszentrums Jülich, IAS Series 15), pp. 27-34

Juan Ferrer, A.; Hernández, F.; Tordsson, J.; Elmroth, E.; Ali-Eldin, A.; Zsigri, C.; Sirvent, R.; Guitart, J.; Badia, R.M.; Djemame, K.; Ziegler, W.; Dimitrakos, T.; Nair, S.K.; Kousiouris, G.; Konstanteli, K.; Varvarigou, T.; Hudzia, B.; Kipp, A.; Wesner, S.; Corrales, M.; Forgo, N.; Sharif, T.; Sheridan, C.:
OPTIMIS: A holistic approach to cloud service provisioning
Future generation computer systems : FGCS, Vol.28 (2012), No.1, pp.66-77
info:doi/10.1016/j.future.2011.05.022

Klinger, R.; Senger, P.; Madan, S.; Jacovi, M.:
Online communities support policy-making: The need for data analysis. (International Conference on Electronic Participation (ePart) <4, 2012, Kristiansand>)
Tambouris, E.: Electronic participation. 4th IFIP WG 8.5 international conference, ePart 2012: Kristiansand, Norway, September 3 - 5, 2012. Proceedings. Berlin: Springer, 2012. (Lecture Notes in Computer Science 7444), pp. 132-143
info:doi/10.1007/978-3-642-33250-0_12

Rasheed, Hassan; Rumpl, Angela; Wäldrich, Oliver; Ziegler, Wolfgang:
A standards-based approach for negotiating service QoS with cloud infrastructure providers. (eChallenges Conference <22, 2012, Lisbon>)
Cunningham, P.: eChallenges e-2012. Conference Proceedings. CD-ROM: 17-19 October 2012, Lisbon, Portugal. Dublin: IIMC, 2012, 9 pp.
urn:nbn:de:0011-n-2255882
Volltext

Sahadevan, S.; Hofmann-Apitius, M.; Schellander, K.; Tesfaye, D.; Fluck, J.; Friedrich, C.M.:
Text mining in livestock animal science: Introducing the potential of text mining to animal sciences
Journal of animal science, Vol.90 (2012), No.10, pp.3666-3676
info:doi/10.2527/jas.2011-4841

Temelso B.; Morrell, T.E.; Shields, R.M.; Allodi, M.A.; Wood, E. K.; Kirschner, K.N.; Castonguay, T.C.; Archer, K.A.; Shields, G.C.:
Quantum mechanical study of sulfuric acid hydration: Atmospheric implications
Journal of physical chemistry. A, Vol.116 (2012), No.9, pp.2209-2224
info:doi/10.1021/jp2119026

Tordsson, Johan; Djemame, Karim; Espling, Daniel; Katsaros, Gregory; Ziegler, Wolfgang; Wäldrich, Oliver; Konstanteli, Kleopatra; Sajjad, Ali; Rajarajan, Muttukrishnan; Gallizo, Georgina; Nair, Srijith:
Towards holistic cloud management
Petcu, D.: European research activities in cloud computing. Newcastle: Cambridge Scholars Publishing, 2012, pp. 122-150

Wolf, A.; Baumann, S.; Arndt, H.D.; Kirschner, K.N.:
Influence of thiostrepton binding on the ribosomal GTPase associated region characterized by molecular dynamics simulation
Bioorganic & medicinal chemistry, Vol.20 (2012), No.24, pp.7194-7205
info:doi/10.1016/j.bmc.2012.09.025

Younesi, Erfan; Toldo, Luca; Müller, Bernd; Friedrich, Christoph M.; Novac, Natalia; Scheer, Alexander; Hofmann-Apitius, Martin; Fluck, Juliane:
Mining biomarker information in biomedical literature
BMC medical informatics and decision making. Online journal, Vol.12 (2012), Art. 148, 13 pp.
urn:nbn:de:0011-n-2281049
info:doi/10.1186/1472-6947-12-148
Volltext

Ziegler, Wolfgang:
SLAs for energy-efficient data centres: The standards-based approach of the OPTIMIS project. (International Workshop on Energy-Efficient Data Centers (E2DC) <1, 2012, Madrid>)
Huusko, J.: Energy Efficient Data Centers: First International Workshop, E2DC 2012, Madrid, Spain, Mai 8, 2012, Revised Selected Papers. Berlin: Springer, 2012. (Lecture Notes in Computer Science 7396), pp. 37-46
info:doi/10.1007/978-3-642-33645-4_4

Armstrong, Django; Djemame, Karim; Nair, Srijith; Tordsson, Johan; Ziegler, Wolfgang:
Towards a contextualization solution for cloud platform services. (International Conference on Cloud Computing Technology and Science (CloudCom) <3, 2011, Athens>)
Institute of Electrical and Electronics Engineers -IEEE-: Third IEEE International Conference on Cloud Computing Technology and Science, CloudCom 2011: Athens, Greece, Nov 29 - Dec 1, 2011. New York, NY: IEEE, 2011, pp. 328-331

Aslam, M.A.S.; Mahmood, S.-U.; Shahid, M.; Saeed, A.; Iqbal, J.:
Synthesis, biological assay in vitro and molecular docking studies of new Schiff base derivatives as potential urease inhibitors
European journal of medicinal chemistry, Vol.46 (2011), No.11, pp.5473-5479
info:doi/10.1016/j.ejmech.2011.09.009

Badia, R.M.; Corrales, M.; Dimitrakos, T.; Djemame, K.; Elmroth, E.; Juan Ferrer, A.; Forgo, N.; Guitart, J.; Hernández, F.; Hudzia, B.; Kipp, A.; Konstanteli, K.; Kousiouris, G.; Nair, S.K.; Sharif, T.; Sheridan, C.; Sirvent, R.; Tordsson, J.; Varvarigou, T.; Wesner, S.; Ziegler, W.; Zsigri, C.:
Demonstration of the OPTIMIS toolkit for cloud service provisioning. (European Conference ServiceWave <4, 2011, Poznan>)
Abramowicz, W.: Towards a service-based internet. 4th European conference, ServiceWave 2011: Poznan, Poland, October 26 - 28, 2011; Proceedings. Berlin: Springer, 2011. (Lecture Notes in Computer Science 6994), pp. 331-333
info:doi/10.1007/978-3-642-24755-2_40

Barnitzke, Benno; Ziegler, Wolfgang; Vafiadis, George; Nair, Srijith; Kousiouris, George; Corrales, Marcelo; Wäldrich, Oliver; Forgó, Nikolaus; Varvarigou, Theodora:
Legal restraints and security requirements on personal data and their technical implementation in clouds. (eChallenges Conference <2011, Florence>)
Cunningham, P.: eChallenges e-2011. Proceedings. CD-ROM: Conference & Exhibition, 26-28 October 2011 Florence, Italy. Dublin: IIMC, 2011

Birkenheuer, G.; Brinkmann, A.; Högqvist, M.; Papaspyrou, A.; Schott, B.; Sommerfeld, D.; Ziegler, W.:
Infrastructure federation through virtualized delegation of resources and services: DGSI: Adding interoperability to DCI meta schedulers
Journal of grid computing, Vol.9 (2011), No.3, pp.355-377
info:doi/10.1007/s10723-011-9192-1

Cacciari, C.; Mallmann, D.; Zsigri, C.; D'Andria, F.; Hagemeier, B.; García Peréz, D.; Rumpl, A.; Ziegler, W.; Gozalo, M.; Martrat, J.:
Software licenses as mobile objects in distributed computing environments. (Parallel Processing Workshops <2010, Ischia>)
Guarracino, M.R.: Euro-Par 2010 Parallel Processing Workshops: HeteroPAR, HPCC, HiBB, CoreGrid, UCHPC, HPCF, PROPER, CCPI, VHPC; Ischia, Italy, August 31 - September 3, 2010; revised selected papers. Heidelberg: Springer, 2011. (Lecture Notes in Computer Science 6586), pp. 279-286
info:doi/10.1007/978-3-642-21878-1_35

Djemame, K.; Lawrence, A.; Wäldrich, O.; Ziegler, W.; Zsigri, C.:
Using service level agreements for optimising cloud infrastructure. (International Conference ServiceWave <2010, Ghent>)
Cezon, M.: Towards a service-based internet: ServiceWave 2010 workshops, international workshops OCS, EMSOA, SMART, and EDBPM 2010, Ghent, Belgium, December 13 - 15, 2010; revised selected papers. Berlin: Springer, 2011. (Lecture Notes in Computer Science 6569), pp. 38-49
info:doi/10.1007/978-3-642-22760-8_4

Gurulingappa, Harsha; Fluck, Juliane; Hofmann-Apitius, Martin; Toldo, Luca:
Identification of adverse drug event assertive sentences in medical case reports. (International Workshop on Knowledge Discovery in Health Care and Medicine (KDHCM) <1, 2011, Athen>)
Rangwala, H.: The first International Workshop on Knowledge Discovery in Health Care and Medicine, KDHCM'11. Online prodeedings: September 9, 2011, Athens, Greece. Athen, 2011, 12 pp.

Gurulingappa, Harsha; Müller, Bernd; Hofmann-Apitius, Martin; Fluck, Juliane:
Information retrieval framework for technology survey in biomedical and chemistry literature. (Text REtrieval Conference (TREC) <20, 2011, Gaithersburg/Md.>)
Voorhees, E.M.: The Twentieth Text REtrieval Conference, TREC 2011. Proceedings: November 2011, Gaithersburg, Maryland, USA. Gaithersburg, MD: NIST, 2011. (NIST special publication 500-295), 4 pp.

Gurulingappa, Harsha; Müller, Bernd; Hofmann-Apitius, Martin; Fluck, Juliane:
A semantic platform for information retrieval from e-health records. (Text REtrieval Conference (TREC) <20, 2011, Gaithersburg/Md.>)
Voorhees, E.M.: The Twentieth Text REtrieval Conference, TREC 2011. Proceedings: November 2011, Gaithersburg, Maryland, USA. Gaithersburg, MD: NIST, 2011. (NIST special publication 500-295), 9 pp.

Holl, S.; Zimmermann, O.; Hofmann-Apitius, M.:
A UNICORE plugin for HPC-enabled scientific workflows in Taverna 2.2. (World Congress on Services (SERVICES) <7, 2011, Washington/DC>)
Institute of Electrical and Electronics Engineers -IEEE-: 2011 IEEE World Congress on Services, SERVICES 2011. Proceedings: Washington, DC, USA, 4 - 9 July 2011. Piscataway, NJ: IEEE, 2011, pp. 220-223
info:doi/10.1109/SERVICES.2011.46

Ivchenko, O.; Younesi, E.; Shahid, M.; Wolf, A.; Müller, B.; Hofmann-Apitius, M.:
PLIO: An ontology for formal description of protein-ligand interactions
Bioinformatics, Vol.27 (2011), No.12, pp.1684-1690
info:doi/10.1093/bioinformatics/btr256

Jonker, H.R.A.; Baumann, S.; Wolf, A.; Schoof, S.; Hiller, F.; Schulte, K.W.; Kirschner, K.N.; Schwalbe, H.; Arndt, H.-D.:
NMR structures of thiostrepton derivatives for characterization of the ribosomal binding site
Angewandte Chemie. International edition, Vol.50 (2011), No.14, pp.3308-3312
info:doi/10.1002/anie.201003582

Klinger, R.:
Automatically Selected Skip Edges in Conditional Random Fields for Named Entity Recognition. (Workshop on Biomedical Natural Language Procession (BiomedNLP) <2011, Hissar/Bulgaria>)
Savova, G.: Proceedings of the Workshop on Biomedical Natural Language Processing, BiomedNLP 2011: 15 September, 2011, Hissar, Bulgaria : held in conjunction with the 8th International Conference Recent Advances in Natural Language Processing, RANLP 2011. Shoumen: INCOMA, 2011, pp. 580-585

Klinger, Roman:
Automatically Selected Skip Edges in Conditional Random Fields for Named Entity Recognition. (International Conference "Recent Advances in Natural Language Processing" (RANLP) <2011, Hissar/Bulgaria>)
Angelova, G.: Recent Advances in Natural Language Processing, RANLP 2011: 12-14 September, 2011, Hissar, Bulgaria. Hissar, Bulgaria, 2011, pp. 580-585

Lupu, Mihai; Jiashu, Zhao; Huang, Jimmy; Gurulingappa, Harsha; Fluck, Juliane; Zimmermann, Marc; Filippov, Igor; Tait, John:
Overview of the TREC 2011 Chemical IR Track. (Text REtrieval Conference (TREC) <20, 2011, Gaithersburg/Md.>)
Voorhees, E.M.: The Twentieth Text REtrieval Conference, TREC 2011. Proceedings: November 2011, Gaithersburg, Maryland, USA. Gaithersburg, MD: NIST, 2011. (NIST special publication 500-295), 11 pp.

Ngo, Canh; Laat, Cees de; Demchenko, Yuri; Rong, Chunmin; Wlodarczyk, Tomasz Wiktor; Ziegler, Wolfgang:
Security infrastructure for on-demand provisioned cloud infrastructure services. (International Conference on Cloud Computing Technology and Science (CloudCom) <3, 2011, Athens>)
Institute of Electrical and Electronics Engineers -IEEE-: Third IEEE International Conference on Cloud Computing Technology and Science, CloudCom 2011: Athens, Greece, Nov 29 - Dec 1, 2011. New York, NY: IEEE, 2011, pp. 255-263
info:doi/10.1109/CloudCom.2011.42

Randrianarivony, M.:
Adaptive discontinuous Galerkin B-splines on parametric geometries. (International Conference on Computational Science and Its Applications (ICCSA) <11, 2011, Santander>)
Murgante, B.: Computational science and its applications - ICCSA 2011. Proceedings Pt.4: International conference, Santander, Spain, June 20-23, 2011. Berlin: Springer, 2011. (Lecture Notes in Computer Science 6785), pp. 59-74
info:doi/10.1007/978-3-642-21898-9_6

Randrianarivony, M.:
On transfinite interpolations with respect to convex domains
Computer aided geometric design : CAGD, Vol.28 (2011), No.2, pp.135-149
info:doi/10.1016/j.cagd.2010.10.003

Thomas, P.; Solt, I.; Klinger, R.; Leser, U.:
Learning Protein Protein Interaction Extraction using Distant Supervision. (Workshop on Robust Unsupervised and Semisupervised Methods in Natural Language Processing (ROBUS) <2011, Hissar/Bulgaria>)
Biemann, C.: Proceedings of Workshop on Robust Unsupervised and Semisupervised Methods in Natural Language Processing, ROBUS 2011: At RANLP 2011, 15 September, 2011, Hissar, Bulgaria. Shoumen: INCOMA, 2011, pp. 34-41

Thomas, P.E.; Klinger, R.; Furlong, L.I.; Hofmann-Apitius, M.; Friedrich, C.M.:
Challenges in the association of human single nucleotide polymorphism mentions with unique database identifiers
BMC bioinformatics. Online journal, Vol.12 (2011), Suppl.4, Art. S4
info:doi/10.1186/1471-2105-12-S4-S4

Zimmermann, M.:
Chemical structure reconstruction with chemoCR. (Text REtrieval Conference (TREC) <20, 2011, Gaithersburg/Md.>)
Voorhees, E.M.: The Twentieth Text REtrieval Conference, TREC 2011. Proceedings: November 2011, Gaithersburg, Maryland, USA. Gaithersburg, MD: NIST, 2011. (NIST special publication 500-295)

Azam, N.; Ghanem, M.; Kalaitzopoulos, D.; Wolf, A.; Kasam, V.; Wang, Y.; Hofmann-Apitius, M.:
DockFlow: Achieving interoperability of protein docking tools across heterogeneous grid middleware
International journal of ad hoc and ubiquitous computing : IJAHUC, Vol.6 (2010), No.4, pp.235-251
info:doi/10.1504/IJAHUC.2010.035535

Battré, D.; Hovestadt, M.; Wäldrich, O.:
Lessons learned from implementing WS-agreement. (Workshop on Service Level Agreements in Grids <2, 2009, Banff>)
Wieder, P. et al.: Grids and service-oriented architectures for service level agreements: This book contains the proceedings of the 2nd Workshop on Service Level Agreements in Grids, which was held in conjunction with the IEEE GRID 2009 Conference on October 13, 2009, and the proceedings of the Dagstuhl seminar Service Level Agreements in Grids organized in March 2009. Berlin: Springer US, 2010. (CoreGrid series 13), pp. 23-34
info:doi/10.1007/978-1-4419-7320-7_3

Battré, D.; Brazier, F.M.; Clark, K.P.; Oey, M.; Papaspyrou, A.; Wäldrich, O.; Wieder, P.; Ziegler, W.:
A proposal for WS-agreement negotiation. (International Conference on Grid Computing (Grid) <11, 2010, Brussels>)
Association for Computing Machinery -ACM-: 11th IEEE/ACM International Conference on Grid Computing 2010. Proceedings: 25-29 October 2010 in Brussels, Belgium. New York, NY: IEEE, 2010, pp. 233-241
info:doi/10.1109/GRID.2010.5697976

Benkner, S.; Arbona, A.; Berti, G.; Chiarini, A.; Dunlop, R.; Engelbrecht, G.; Frangi, A.F.; Friedrich, C.M.; Hanser, S.; Hasselmeyer, P.; Hose, R.D.; Iavindrasana, J.; Köhler, M.; Lo Iacono, L.; Lonsdale, G.; Meyer, R.; Moore, B.; Rajasekaran, H.; Summers, P.E.; Wöhrer, A.; Wood, S.:
@neurIST: Infrastructure for advanced disease management through integration of heterogeneous data, computing, and complex processing services
IEEE transactions on information technology in biomedicine, Vol.14 (2010), No.6, pp.1365-1377
info:doi/10.1109/TITB.2010.2049268

Birkenheuer, G.; Carlson, A.; Fölling, A.; Högqvist, M.; Hoheisel, A.; Papaspyrou, A.; Rieger, K.; Schott, B.; Ziegler, W.:
Connecting communities on the meta-scheduling level: The DGSI approach. (Cracow Grid Workshop (CGW) <2009, Krakow>)
Bubak, M.: Cracow Grid Workshop 2009. Proceedings: October 12 - 14, 2009, Cracow, Poland. Krakow: Academic Computer Centre CYFRONET, 2010, pp. 96-103

Cacciari, C.; D'Andria, F.; Hagemeier, B.; Mallmann, D.; Martrat, J.; García Peréz, D.; Rumpl, A.; Ziegler, W.; Zsigri, C.:
elasticLM - Software license management for distributed computing infrastructures
ERCIM News, (2010), No.83, pp.43

Cacciari, C.; D'Andria, F.; Gozalo, M.; Hagemeier, B.; Mallmann, D.; Martrat, J.; García Peréz, D.; Rumpl, A.; Ziegler, W.; Zsigri, C.:
elasticLM: A novel approach for software licensing in distributed computing infrastructures. (International Conference on Cloud Computing Technology and Science (CloudCom) <2, 2010, Indianapolis/Ind.>)
Qiu, J.: IEEE 2nd International Conference on Cloud Computing Technology and Science, CloudCom 2010: 30 November-3 December 2010, Indianapolis, Indiana, USA; proceedings. Los Alamitos, Calif.: IEEE Computer Society Press, 2010, pp. 67-74
info:doi/10.1109/CloudCom.2010.19

Cacciari, C.; Mallmann, D.; Zsigri, C.; D'Andria, F.; Hagemeier, B.; Rumpl, A.; Ziegler, W.; Martrat, J.:
SLA-based management of software licenses as web service resources in distributed environments. (International Workshop on Grid Economics and Business Models (GECON) <7, 2010, Ischia>)
Altmann, J.: Economics of grids, clouds, systems, and services. 7th international workshop, GECON 2010: Ischia, Italy, August 31, 2010; Proceedings. Berlin: Springer, 2010. (Lecture Notes in Computer Science 6296), pp. 78-92
info:doi/10.1007/978-3-642-15681-6_6

Cai, Y.; He, Z.; Shi, X.; Kong, X.; Gu, L.; Xie, L.:
A novel sequence-based method of predicting protein DNA-binding residues, using a machine learning approach
Molecules and cells : MaC, Vol.30 (2010), No.2, pp.99-105
info:doi/10.1007/s10059-010-0093-0

Friedrich, C.M.; Ebeling, C.; Manset, D.:
Ceoss-project uptake of biomedical text mining results for candidate gene searchers
ERCIM News, (2010), No.82, pp.45-46

Friedrich, C.M.; et al.:
Genome-wide association study of intracranial aneurysm identifies three new risk loci
Nature Genetics, Vol.42 (2010), No.5, pp.420-425
info:doi/10.1038/ng.563

Gurulingappa, H.; Hofmann-Apitius, M.; Fluck, J.:
Concept identification and assertion classification in patient health records. (Workshop Challenges in Natural Language Processing for Clinical Data <4, 2010, Washington/DC>)
Fourth i2b2/VA Shared-Task and Workshop Challenges in Natural Language Processing for Clinical Data 2010: Washington, DC, November 12-13, 2010. Albany/NY: State University of New York, 2010, 5 pp.
urn:nbn:de:0011-n-1518436
Volltext

Gurulingappa, H.; Klinger, R.; Hofmann-Apitius, M.; Fluck, J.:
An empirical evaluation of resources for the identification of diseases and adverse effects in biomedical literature. (Workshop on Building and Evaluating Resources for Biomedical Text Mining (BioTxtM) <2, 2010, Valletta>)
Ananiadou, S.: 2nd Workshop on Building and Evaluating Resources for Biomedical Text Mining, BioTxtM 2010: Tuesday, 18th March 2010 Valletta, Malta, LREC 2010. Valletta, 2010, pp. 15-22

Gurulingappa, H.; Müller, B.; Klinger, R.; Mevissen, H.-T.; Hofmann-Apitius, M.; Friedrich, C.M.; Fluck, J.:
Prior art search in chemistry patents based on semantic concepts and co-citation analysis. (Text REtrieval Conference (TREC) <19, 2010, Gaithersburg/Md.>)
National Institute of Standards and Technology -NIST-: Nineteenth Text REtrieval Conference, TREC 2010. Proceedings: Gaithersburg, Maryland, USA, November 16-19, 2010. Washington, DC: NIST, 2010, 9 pp.

Hagemeier, B.; Mallmann, D.; Ziegler, W.:
Securing software licenses in a location independent manner. (Cracow Grid Workshop (CGW) <2009, Krakow>)
Bubak, M.: Cracow Grid Workshop 2009. Proceedings: October 12 - 14, 2009, Cracow, Poland. Krakow: Academic Computer Centre CYFRONET, 2010, pp. 112-119

Klatt, T.; Rasheed, H.; Shahid, M.; Wäldrich, O.; Ziegler, W.:
SCAI-VHTS - a fully automated virtual high throughput screening framework
ERCIM News, (2010), No.82, pp.23-24

Kuebert, R.; Tenschert, A.; Wäldrich, O.; Ziegler, W.; Battre, D.:
A service level agreement layer for the D-Grid infrastructure. (eChallenges Conference <2010, Warsaw>)
Cunningham, M.: eChallenges 2010. CD-ROM: e-2010, 27-29 October 2010, Warsaw, Poland. Dublin: IIMC, 2010

Lu, J.; Zhu, Y.B.; Li, Y.J.; Lu, W.C.; Hu, L.L.; Niu, B.; Qing, P.F.; Gu, L.:
Prediction of interaction between enzymes and small molecules in metabolic pathways through integrating multiple classifiers
Protein and peptide letters, Vol.17 (2010), No.12, pp.1536-1541

Müller, B.; Klinger, R.; Gurulingappa, H.; Mevissen, H.-T.; Hofmann-Apitius, M.; Fluck, J.; Friedrich, C.M.:
Abstracts versus full texts and patents: A quantitative analysis of biomedical entities. (Information Retrieval Facility Conference (IRFC) <1, 2010, Vienna>)
Cunningham, H.: Advances in multidisciplinary retrieval. First Information Retrieval Facility Conference, IRFC 2010: Vienna, Austria, May 31, 2010; Proceedings. Berlin: Springer, 2010. (Lecture Notes in Computer Science 6107), pp. 152-165
info:doi/10.1007/978-3-642-13084-7_12

Rana, O.; Ziegler, W.:
Research challenges in managing and using Service Level Agreements. (Workshop on Grids, P2P and Service Computing <2009, Delft>)
Desprez, F.: Grids, P2P and Services Computing: Based on the CoreGrid ERCIM Working Group Workshop on Grids, P2P and Service Computing in Conjunction with EuroPar 2009, August 24th, 2009 in Delft, The Netherlands. New York: Springer Science+Business Meda, 2010. (CoreGrid series 12), pp. 187-200
info:doi/10.1007/978-1-4419-6794-7_15

Rasheed, H.; Rumpl, A.; Ziegler, W.; Gozalo, M.:
Demonstration of the SmartLM license management technology for distributed computing infrastructures. (European Conference ServiceWave <3, 2010, Ghent>)
Nitto, E. di: Towards a service-based internet. Third European conference, ServiceWave 2010: Ghent, Belgium, December 13-15, 2010 ; proceedings. Berlin: Springer, 2010. (Lecture Notes in Computer Science 6481), pp. 190-192
info:doi/10.1007/978-3-642-17694-4_18

Rasheed, H.; Rumpl, A.; Ziegler, W.; Hagemeier, B.; Mallmann, D.; Eickenbusch, H.:
Running license protected applications with SmartLM and UNICORE. (UNICORE Summit <6, 2010, Jülich>)
Streit, A. et al.: UNICORE Summit 2010, Proceedings: 18 – 19 May 2010, Jülich. (Schriften des Forschungszentrums Jülich, IAS Series), pp. 69-74

Risselada, R.; Lingsma, H.F.; Bauer-Mehre, A.; Friedrich, C.M.; Molyneux, A.J.; Kerr, R.S.; Yarnold, J.; Sneade, M.; Steyerberg, E.W.; Sturkenboom, M.C.:
Prediction of 60 day case-fatality after aneurysmal subarachnoid haemorrhage: Results from the International Subarachnoid Aneurysm Trial (ISAT)
European journal of epidemiology, Vol.25 (2010), No.4, pp.261-266
urn:nbn:de:0011-n-1187102
info:doi/10.1007/s10654-010-9432-x
Volltext

Rumpl, A.; Wäldrich, O.; Ziegler, W.:
Extending WS-AGREEMENT with multi-round negotiation capability. (Workshop on Service Level Agreements in Grids <2, 2009, Banff>)
Wieder, P. et al.: Grids and service-oriented architectures for service level agreements: This book contains the proceedings of the 2nd Workshop on Service Level Agreements in Grids, which was held in conjunction with the IEEE GRID 2009 Conference on October 13, 2009, and the proceedings of the Dagstuhl seminar Service Level Agreements in Grids organized in March 2009. Berlin: Springer US, 2010. (CoreGrid series 13), pp. 89-103
info:doi/10.1007/978-1-4419-7320-7_9

Shahid, M.; Kasam, V.; Hofmann-Apitius, M.:
An improved weighted-residue profile based method of using protein-ligand interaction information in increasing hits selection from virtual screening: A study on virtual screening of human GPCR A2A receptor antagonists
Molecular informatics, Vol.29 (2010), No.11, pp.781-791
info:doi/10.1002/minf.201000068

Streit, A.; Bala, P.; Beck-Ratzka, A.; Benedyczak, K.; Bergmann, S.; Breu, R.; Daivandy, J.M.; Demuth, B.; Eifer, A.; Giesler, A.; Hagemeier, B.; Holl, S.; Huber, V.; Lamla, N.; Mallmann, D.; Memon, A.S.; Memon, M.S.; Rambadt, M.; Riedel, M.; Romberg, M.; Schuller, B.; Schlauch, T.; Schreiber, A.; Soddemann, T.; Ziegler, W.:
UNICORE 6 - recent and future advancements
Annales des telecommunications, Vol.65 (2010), No.11-12, pp.757-762
info:doi/10.1007/s12243-010-0195-x

Wolf, A.; Shahid, M.; Kasam, V.; Ziegler, W.; Hofmann-Apitius, M.:
In silico drug discovery approaches on grid computing infrastructures
Current clinical pharmacology, Vol.5 (2010), No.1, pp.37-46
info:doi/10.2174/157488410790410560

Yilmaz, S.; Bijlenga, P.; Rashid, M.; Collot-Teixeira, S.; Brocheton, J.; Proust, C.; Rotival, M.; Risselada, R.; Summers, P.; Blasco, J.; Singh, J.; Waterworth, A.; Ebeling, C.; Friedrich, C.M.; Frangi, A.F.; Macho, J.J.; Byrne, J.; Sturkenboom, M.C.; Schaller, K.; Cambien, F.; Gunel, M.; McGregor, J.L.:
Gene expression signature in peripheral blood cells detects intracranial aneurysm
Neurosurgery, Vol.67 (2010), No.2, pp.540
info:doi/10.1227/01.NEU.0000386985.32689.26

Yuan, Y.; Shi, X.; Li, X.; Lu, W.; Cai, Y.; Gu, L.; Liu, L.; Li, M.; Kong, X.; Xing, M.:
Prediction of interactiveness of proteins and nucleic acids based on feature selections
Molecular Diversity, Vol.14 (2010), No.4, pp.627-633
info:doi/10.1007/s11030-009-9198-9

Degliesposti, G.; Kasam, V.; Da Costa, A.; Kang, H.-K.; Kim, N.; Kim, D.-W.; Breton, V.; Kim, D.; Rastelli, G.:
Design and discovery of plasmepsin II inhibitors using an automated workflow on large-scale grids
ChemMedChem, Vol.4 (2009), No.7, pp.1164-1173
info:doi/10.1002/cmdc.200900111

Friedrich, C.M.; Gündel, M.:
Combining text mining and microarray analysis. (R User Conference (useR!) <2009, Rennes>)
R Foundation for Statistical Computing: UseR!, the R User Conference 2009: July 8-10, Agrocampus-Ouest, Rennes, France. Rennes, 2009, pp. 63
urn:nbn:de:0011-n-1021426
Volltext

Friedrich, C.M.; Klinger, R.:
rSMILE, an interface to the Bayesian network package GeNIe/SMILE. (R User Conference (useR!) <2009, Rennes>)
R Foundation for Statistical Computing: UseR!, the R User Conference 2009: July 8-10, Agrocampus-Ouest, Rennes, France. Rennes, 2009, pp. 104
urn:nbn:de:0011-n-1035369
Volltext

Friedrich, C.M.:
The @neuLink approach to literature. (European Society of Minimally Invasive Neurological Therapy (ESMINT Teaching Course) <2, 2009, Barcelona>)
European Society of Minimally Invasive Neurological Therapy -ESMINT-: ESMINT Teaching Course Journal 2009: 2nd Teaching Course of the European Society of Minimally Invasive Neurological Therapy, Barcelona, Spain, December 13-18, 2009. Tutorial. Barcelona: ESMINT, 2009, pp. 62-67

Groeper, R.; Grimm, C.; Makedanz, S.; Pfeiffenberger, H.; Ziegler, W.; Gietz, P.; Schiffers, M.:
A concept for attribute-based authorization on D-Grid resources
Future generation computer systems : FGCS, Vol.25 (2009), No.3, pp.275-280
info:doi/10.1016/j.future.2008.05.008

Guitart, J.; Mac¡as, M.; Rana, O.; Wieder, P.; Yahyapour, R.; Ziegler, W.:
SLA-based resource management and allocation
Buyya, R.: Market-oriented grid and utility computing. Hoboken/N.J.: Wiley & Sons, 2009, pp. 261-284

Gurulingappa, H.; Kolarik, C.; Hofmann-Apitius, M.; Fluck, J.:
Concept-based semi-automatic classification of drugs
Journal of chemical information and modeling, Vol.49 (2009), No.8, pp.1986-1992
info:doi/10.1021/ci9000844

Gurulingappa, H.; Müller, B.; Klinger, R.; Mevissen, H.-T.; Hofmann-Apitius, M.; Fluck, J.; Friedrich, C.M.:
Patent retrieval in chemistry based on semantically tagged named entities. (Text REtrieval Conference (TREC '09) <18, 2009, Gaithersburg/Md.>)
National Institute of Standards and Technology -NIST-: Eighteenth Text REtrieval Conference, TREC 2009. Proceedings: November 16-17, 2009, Gaithersburg, Maryland. Washington, DC: NIST, 2009, 9 pp.
urn:nbn:de:0011-n-1186068
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Hofmann-Apitius, M.; Younesi, E.; Kasam, V.:
Direct use of information extraction from scientific text for modeling and simulation in the life sciences. (International Bielefeld Conference <9, 2009, Bielefeld>)
Höppner, M.: "Upgrading the eLibrary: Enhanced information services driven by technology and economics": Proceedings of the 9th International Bielefeld Conference, Bielefeld, Germany, 3 - 5 February 2009. Bingley: Emerald, 2009. (Library hi tech 27.2009, Nr.4), pp. 505-519
info:doi/10.1108/07378830911007637

Holi, S.; Riedel, M.; Demuth, B.; Romberg, M.; Streit, A.; Kasam, V.:
Life science application support in an interoperable E-Science environment. (IEEE International Symposium on Computer-Based Medical Systems (CBMS) <22, 2009, Albuquerque>)
IEEE Computer Society, Technical Committee on Computational Medicine: 22nd IEEE International Symposium on Computer-Based Medical Systems, CBMS 2009. Piscataway: IEEE, 2009, Art. 5255322
info:doi/10.1109/CBMS.2009.5255322

Joosten, R.P.; Salzemann, J.; Bloch, V.; Stockinger, H.; Berglund, A.-C.; Blanchet, C.; Bongcam-Rudloff, E.; Combet, C.; Da Costa, A.L.; Deleage, G.; Diarena, M.; Fabbretti, R.; Fettahi, G.; Flegel, V.; Gisel, A.; Kasam, V.; Kervinen, T.; Korpelainen, E.; Mattila, K.; Pagni, M.; Reichstadt, M.; Breton, V.; Tickle, I.J.; Vriend, G.:
PDB REDO: Automated re-refinement of X-ray structure models in the PDB
Journal of Applied Crystallography, Vol.42 (2009), No.3, pp.376-384
info:doi/10.1107/S0021889809008784

Joseph, L.C.; Bennett, J.A.; Kirschner, K.N.; Shields, G.C.; Hughes, J.; Lostritto, N.; Jacobson, H.I.; Andersen, T.T.:
Antiestrogenic and anticancer activities of peptides derived from the active site of alpha-fetoprotein
Journal of peptide science, Vol.15 (2009), No.4, pp.319-325
info:doi/10.1002/psc.1119

Kasam, V.; Salzemann, J.; Botha, M.; Dacosta, A.; Degliesposti, G.; Isea, R.; Kim, D.; Maaß, A.; Kenyon, C.; Rastelli, G.; Hofmann-Apitius, M.; Breton, V.:
WISDOM-II: Screening against multiple targets implicated in malaria using computational grid infrastructures
Malaria journal. Online journal, Vol.8 (2009), Art. 88, 16 pp.
urn:nbn:de:0011-n-1017390
info:doi/10.1186/1475-2875-8-88
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Keller, V.; Rasheed, H.; Wäldrich, O.; Ziegler, W.; Gruber, R.; Sawley, M.-C.; Wieder, P.:
Models and internals of the IANOS resource broker
Computer science, research + development, Vol.23 (2009), No.3-4, pp.259-266
urn:nbn:de:0011-n-970718
info:doi/10.1007/s00450-009-0074-8
Volltext

Keller, V.; Ziegler, W.:
ÏANOS: How to do more science with less energy
ERCIM News, (2009), No.79, pp.26-27

Klinger, R.; Pesch, R.; Mevissen, T.; Fluck, J.:
Text mining in full text articles- methodical and representation issues: 3rd International Biocuration Conference, Berlin, 16.-19.4. 2009. (International Biocuration Conference <3, 2009, Berlin>)
Nature precedings. Online preprint server, (2009), 22. April, 1 pp.
urn:nbn:de:0011-n-936860
info:doi/10.1038/npre.2009.3141.1
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Klinger, R.; Friedrich, C.M.:
Feature subset selection in conditional random fields for named entity. (International Conference Recent Advances in Natural Language Processing (RANLP) <2009, Borovets>)
Angelova, G..: Proceedings of the International Conference Recent Advances in Natural Language Processing, RANLP 2009: 14-16 September 2009, Borovets, Bulgaria. Borovets, 2009, pp. 185-191

Klinger, R.; Friedrich, C.M.:
User's choice of precision and recall in named entity recognition. (International Conference Recent Advances in Natural Language Processing (RANLP) <2009, Borovets>)
Angelova, G..: Proceedings of the International Conference Recent Advances in Natural Language Processing, RANLP 2009: 14-16 September 2009, Borovets, Bulgaria. Borovets, 2009, pp. 192-196

Kolarik, C.; Klinger, R.; Hofmann-Apitius, M.:
Identification of histone modifications in biomedical text for supporting epigenomic research. (Asia-Pacific Bioinformatics Conference (APBC) <7, 2009, Beijing>)
BMC bioinformatics. Online journal, Vol.10 (2009), Supplement 1, S28
urn:nbn:de:0011-n-906382
info:doi/10.1186/1471-2105-10-S1-S28
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Kolarik, C.; Hofmann-Apitius, M.:
Linking chemical and biological information with natural language processing
Banville, D.L.: Chemical information mining: Facilitating literature-based discovery. Boca Raton, Fla.: CRC Press, 2009, pp. 123-150

Pichot, A.; Wieder, P.; Wäldrich, O.; Ziegler, W.:
Towards dynamic service level agreement negotiation: An approach based on WS-agreement. (International Conference on Web Information Systems and Technologies (WEBIST) <4, 2008, Funchal>)
Cordeiro, J.: Web information systems and technologies: 4th international conference; Revised selected papers / WEBIST 2008, Funchal, Madeira, Portugal, May 4 - 7, 2008. Berlin: Springer, 2009. (Lecture Notes in Business Information Processing 18), pp. 107-119
urn:nbn:de:0011-n-941998
info:doi/10.1007/978-3-642-01344-7 9
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Risselada, R.; Friedrich, C.M.; Ebeling, C.; Klinger, R.; Bauer-Mehren, A.; Pastor, M.; Cruz Villa, M.; Pozo, J.M.; Frangi, A.F.; Hofmann-Apitius, M.:
Workflows for data mining in integrated multi-modal data of intracranial aneurysms using KNIME. (R User Conference (useR!) <2009, Rennes>)
R Foundation for Statistical Computing: UseR!, the R User Conference 2009: July 8-10, Agrocampus-Ouest, Rennes, France. Rennes, 2009, pp. 166
urn:nbn:de:0011-n-1035334
Volltext

Shahid, M.; Hofmann-Apitius, M.; Wäldrich, O.; Ziegler, W.:
A robust framework for rapid deployment of a virtual screening laboratory. (HealthGrid Conference <7, 2009, Berlin>)
Solomonides, T. et al.: Healthgrid research, innovation and business case: Proceedings of HealthGrid 2009, 29 June - 1 July, Berlin. Amsterdam: IOS Press, 2009. (Studies in health technology and informatics 147), pp. 212-221

Wolf, A.; Hofmann-Apitius, M.; Ghanem, M.; Azam, N.; Kalaitzopoulos, D.; Yu, K.; Kasam, V.:
DockFlow - a prototypic PharmaGrid for virtual screening integrating four different docking tools. (HealthGrid Conference <7, 2009, Berlin>)
Solomonides, T. et al.: Healthgrid research, innovation and business case: Proceedings of HealthGrid 2009, 29 June - 1 July, Berlin. Amsterdam: IOS Press, 2009. (Studies in health technology and informatics 147), pp. 3-12
info:doi/10.3233/978-1-60750-027-8-3

Akle, S.; Algorri, M.-E.; Zimmermann, M.:
Framework for extracting rotation invariant features for image classification and an application using haar wavelets. (International Conference on Artificial Intelligence, Knowledge Engineering and Data Bases (AIKED) <7, 2008, Cambridge>)
World Scientific and Engineering Academy and Society -WSEAS-: Advances on artificial intelligence, knowledge engineering and data bases: Proceedings of the 7th WSEAS International Conference on Artificial intelligence, knowledge engineering and data bases (AIKED 2008), University of Cambridge, Cambridge, UK, February 20-22, 2008. Montclair/NJ: WSEAS, 2008. (Artificial intelligence series), pp. 89-94

Breton, V.; Jacq, N.; Kasam, V.; Hofmann-Apitius, M.:
Grid-added value to address malaria
IEEE transactions on information technology in biomedicine, Vol.12 (2008), No.2, pp.173-181
info:doi/10.1109/TITB.2007.895930

Dunlop, R.; Arbona, T.; Rajasekaran, H.; Lo Iacono, L.; Fingberg, J.; Summers, P.; Benkner, S.; Engelbrecht, S.; Chiarini, A.; Friedrich, C.; Moore, B.; Bijlenga, P.; Iavindrasana, J.; Hose, R.D.; Frangi, A.:
@neurIST - chronic disease management through integration of heterogeneous data and computer-interpretable guideline services. (HealthGrid Conference <6, 2008, Chicago/Ill.>)
Solomonides, T.: Global healthgrid : e-science meets biomedical informatics. Proceedings of HealthGrid 2008. Amsterdam: IOS Press, 2008. (Studies in health technology and informatics 138), pp. 173-177

Faroughi, A.; Faroughi, R.; Wieder, P.; Ziegler, W.:
Attributes and VOs: Extending the UNICORE authorisation capabilities. (International Workshop on Highly Parallel Processing on a Chip (HPPC) <2007, Rennes>)
Bouge, L. et al.: Parallel Processing - Euro-Par 2007 Workshops: HPPC 2007, UNICORE Summit 2007, and VHPC 2007, Rennes, France, August 28-31, 2007, Revised Selected Paper. Berlin: Springer, 2008. (Lecture Notes in Computer Science 4854), pp. 121-130
urn:nbn:de:0011-n-701220
info:doi/10.1007/978-3-540-78474-6 16
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Friedrich, C.M.; Dach, H.; Gattermayer, T.; Engelbrecht, G.; Benkner, S.; Hofmann-Apitius, M.:
@neuLink: A service-oriented application for biomedical knowledge discovery. (HealthGrid Conference <6, 2008, Chicago/Ill.>)
Solomonides, T.: Global healthgrid : e-science meets biomedical informatics. Proceedings of HealthGrid 2008. Amsterdam: IOS Press, 2008. (Studies in health technology and informatics 138), pp. 165-172

Friedrich, C.M.; Hofmann-Apitius, M.; Dunlop, R.; Chronakis, I.; Sturkenboom, M.C.; Risselada, R.; Oliva, B.; Sanz, F.:
Initial results on knowledge discovery and decision support for intracranial aneurysms. (International Conference on Health Informatics (HEALTHINF) <1, 2008, Funchal>)
Azevedo, L.: Proceedings of the First International Conference on Health Informatics: Part of BIOSTEC, International Joint Conference on Biomedical Engineering Systems and Technologies. Funchal, Madeira, Portugal, January 28 - 31, 2008. Setúbal: INSTICC Press, 2008. (Proceedings of the first International Conference on Health Informatics 1), pp. 265-272

Furlong, L.I.; Dach, H.; Hofmann-Apitius, M.; Sanz, F.:
OSIRISv1.2: A named entity recognition system for sequence variants of genes in biomedical literature
BMC bioinformatics. Online journal, Vol.9 (2008), Art. 84
info:doi/10.1186/1471-2105-9-84

Grimme, C.; Lepping, J.; Papaspyrou, A.; Wieder, P.; Yahyapour, R.; Oleksiak, A.; Wäldrich, O.; Ziegler, W.:
Towards a standards-based grid scheduling architecture. (CoreGRID Integration Workshop (CGIW) <2008, Hersonissos/Crete>)
Gorlatch, S.: Grid computing. Achievements and prospects: Selection of best papers presented at the CoreGRID Integration Workshop 2008 (CGIW'2008), which took place on 2 - 4 April 2008 in Hersonissos, Crete, Greece. New York/NY: Springer, 2008. (CoreGrid series 9), pp. 147-158
urn:nbn:de:0011-n-941976
info:doi/10.1007/978-0-387-09457-1 13
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Hofmann-Apitius, M.; Fluck, J.; Furlong, L.I.; Fornes, O.; Kolarik, C.; Hanser, S.; Boeker, M.; Schulz, S.; Sanz, F.; Klinger, R.; Mevissen, T.; Gattermayer, T.; Oliva, B.; Friedrich, C.M.:
Knowledge environments representing molecular entities for the virtual physiological human
Philosophical Transactions of the Royal Society of London. Series A, Vol.366 (2008), No.1878, pp.3091-3110
info:doi/10.1098/rsta.2008.0099

Iavindrasana, J.; Lo Iacono, L.; Müller, H.; Periz, I.; Summers, P.; Wright, J.; Friedrich, C.M.; Dach, H.; Gattermayer, T.; Engelbrecht, G.; Benkner, S.; Hofmann-Apitius, M.; Dunlop, R.; Arbona, A.; Rajasekaran, H.; Fingberg, J.; Chiarini, A.; Moore, B.; Bijlenga, P.; Hose, R.D.; Frangi, A.:
The @neurIST project. (HealthGrid Conference <6, 2008, Chicago/Ill.>)
Solomonides, T.: Global healthgrid : e-science meets biomedical informatics. Proceedings of HealthGrid 2008. Amsterdam: IOS Press, 2008. (Studies in health technology and informatics 138), pp. 161-164

Jacq, N.; Salzemann, J.; Legré, Y.; Medernach, E.; Montagnat, J.; Maaß, A.; Reichstadt, M.; Schwichtenberg, H.; Sridhar, M.; Kasam, V.; Zimmermann, M.; Hofmann, M.; Breton, V.:
Grid-enabled virtual screening against malaria
Journal of grid computing, Vol.6 (2008), No.1, pp.29-43
info:doi/10.1007/s10723-007-9085-5

Klinger, R.; Kolarik, C.; Fluck, J.; Hofmann-Apitius, M.; Friedrich, C.M.:
Detection of IUPAC and IUPAC-like chemical names
Bioinformatics, Vol.24 (2008), No.13, pp.i268-i276
info:doi/10.1093/bioinformatics/btn181

Kolarik, C.; Klinger, R.; Friedrich, C.M.; Hofmann-Apitius, M.; Fluck, J.:
Chemical names: Terminological resources and corpora annotation. (International Conference on Language Resources and Evaluation (LREC) <6, 2008, Marrakech>)
European Language Resources Association -ELRA-, Paris: LREC 2008, Sixth International Language Resources and Evaluation. Proceedings. CD-ROM: May 26-June 1, 2008, Marrakech, Marokko. Paris: ELRA, 2008, pp. 51-58

Li, J.; Wäldrich, O.; Ziegler, W.:
Towards SLA-based software licenses. (CoreGRID Symposium <2008, Las Palmas>)
Priol, T.: From grids to service and pervasive computing: Based on the 2008 CoreGRID Symposium, held August 25 - 26 in the Canary Islands, Spain. New York/NY: Springer, 2008. (CoreGrid series 10), pp. 139-152
urn:nbn:de:0011-n-941969
info:doi/10.1007/978-0-387-09455-7 10
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Morgan, A.A.; Lu, Z.; Wang, X.; Cohen, A.M.; Fluck, J.; Ruch, P.; Divoli, A.; Fundel, K.; Leaman, R.; Hakenberg, J.; Sun, C.; Liu, H.-h.; Rorres, R.; Krauthammer, M.; Lau, W.W.; Liu, H.; Hsu, C.-N.; Schuemie, M.; Cohen, K.B.; Hirschman, L.:
Overview of BioCreative II gene normalization. (Conference "The BioCreative II - Critical Assessment for Information Extraction in Biology Challenge" <2007, Madrid>)
Genome biology, Vol.9 (2008), Supplement 2, Art. S3, 19 pp.
urn:nbn:de:0011-n-1024605
info:doi/10.1186/gb-2008-9-s2-s3
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Pichot, A.; Wieder, P.; Wäldrich, O.; Ziegler, W.:
Dynamic SLA negotiation based on WS-agreement. (International Conference on Web Information Systems and Technologies (WEBIST) <4, 2008, Funchal>)
Cordeiro, J.: WEBIST 2008, 4th International Conference on Web Information Systems and Technologies. Proceedings: 4 - 7 May, 2008, Funchal, Madeira - Portugal. Setúbal: INSTICC, 2008

Rajasekaran, H.; Lo Iacono, L.; Hasselmeyer, P.; Fingberg, J.; Summers, P.; Benkner, S.; Engelbrecht, G.; Arbona, A.; Chiarini, A.; Friedrich, C.M.; Hofmann-Apitius, M.; Kumpf, K.; Moore, B.; Bijlenga, P.; Iavindrasana, J.; Mueller, H.; Hose, R.D.; Dunlop, R.; Frangi, A.: 
@neurIST - Towards a system architecture for advanced disease management through integration of heterogeneous data, computing, and complex processing services. (International Symposium on Computer-Based Medical Systems (CBMS) <21, 2008, Jyväskylä>)
Puuronen, S.: Proceedings of the 21st IEEE International Symposium on Computer-Based Medical Systems: June 17 - 19, 2008, Jyväskylä, Finland. Los Alamitos, Calif.: IEEE Computer Society, 2008, pp. 361-366
info:doi/10.1109/CBMS.2008.42

Rasheed, H.; Gruber, R.; Keller, V.; Ziegler, W.; Wäldrich, O.; Kuonen, P.; Wieder, P.:
IANOS: An intelligent application oriented scheduling framework for an HPCN grid. (CoreGRID Integration Workshop (CGIW) <2008, Hersonissos/Crete>)
Gorlatch, S.: Grid computing. Achievements and prospects: Selection of best papers presented at the CoreGRID Integration Workshop 2008 (CGIW'2008), which took place on 2 - 4 April 2008 in Hersonissos, Crete, Greece. New York/NY: Springer, 2008. (CoreGrid series 9), pp. 237-248
urn:nbn:de:0011-n-941983
info:doi/10.1007/978-0-387-09457-1 20
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Ruau, D.; Kolarik, C.; Mevissen, H.-T.; Müller, E.; Assent, I.; Krieger, R.; Seidl, T.; Hofmann-Apitius, M.; Zenke, M.:
Public microarray repository semantic annotation with ontologies employing text mining and expression profile correlation. (International Society for Computational Biology (Student Council Symposium) <4, 2008, Toronto>)
BMC bioinformatics. Online journal, Vol.9 (2008), Supplement 10, Art. 05
info:doi/10.1186/1471-2105-9-S10-O5

Scholz, J.; Toska, K.; Luborzewski, A.; Maaß, A.; Schünemann, V.; Haavik, J.; Moser, A.:
Endogenous tetrahydroisoquinolines associated with Parkinson's disease mimic the feedback inhibition of tyrosine hydroxylase by catecholamines
FEBS journal, Vol.275 (2008), No.9, pp.2109-2121
info:doi/10.1111/j.1742-4658.2008.06365.x

Shahid, M.; Ziegler, W.; Kasam, V.; Zimmermann, M.; Hofmann-Apitius, M.:
Virtual high throughput screening (vHTS) on an optical high speed testbed. (HealthGrid Conference <6, 2008, Chicago/Ill.>)
Solomonides, T.: Global healthgrid : e-science meets biomedical informatics. Proceedings of HealthGrid 2008. Amsterdam: IOS Press, 2008. (Studies in health technology and informatics 138), pp. 125-134

Smith, L.; Tanabe, L.K.; Johnson nee Ando, R.; Juo, C.-J.; Chung, I.-F.; Hsu, C.-N.; Lin, Y.-S.; Klinger, R.; Friedrich, C.M.; Ganchev, K.; Torii, M.; Liu, H.; Haddow, B.; Struble, C.A.; Povinelli, R.J.; Vlachos, A.; Baumgartner, W.A.; Hunter, L.; Carpenter, B.; Tsai, R.T.; Dai, H.J.; Liu, F.; Chen, Y.; Sun, C.; Katrenko, S.; Adriaans, P.; Blaschke, C.; Torres Perez, R.; Neves, M.; Nakov, P.; Divoli, A.; Mana, M.; Mata-Vazquez, J.; Wilbur, J.:
Overview of BioCreative II gene mention recognition. (Conference "The BioCreative II - Critical Assessment for Information Extraction in Biology Challenge" <2007, Madrid>)
Genome biology, Vol.9 (2008), Supplement 2, 19 pp.
urn:nbn:de:0011-n-941249
info:doi/10.1186/gb-2008-9-s2-s2
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Wieder, P.; Seidel, J.; Wäldrich, O.; Ziegler, W.; Yahyapour, R.:
Using SLA for resource management and scheduling - a survey. (Workshop on Using Service Level Agreements in Grids (Grid) <2007, Austin/Tex.>)
Talia, D. et al.: Grid middleware and services: Challenges and solutions. Berlin: Springer US, 2008. (CoreGrid series 8), pp. 335-347
urn:nbn:de:0011-n-703340
info:doi/10.1007/978-0-387-78446-5 22
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Wieder, P.; Ziegler, W.; Keller, V.:
IANOS - efficient use of HPC grid resources
ERCIM News, (2008), No.74, pp.27-29

Algorri, M.-E.; Zimmermann, M.; Friedrich, C.M.; Akle, S.; Hofmann-Apitius, M.:
Reconstruction of chemical molecules from images. (IEEE Engineering in Medicine and Biology Society (Annual International Conference EMBS) <29, 2007, Lyon>)
IEEE Engineering in Medicine and Biology Society -EMBS-: 29th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS 2007: August 23-26, 2007, Cité Internationale, Lyon, France, in conjunction with the biennial conference of the Société Française de Génie Biologique et Médical (SFGBM). New York, NY: IEEE, 2007, pp. 4609-4612
info:doi/10.1109/IEMBS.2007.4353366

Algorri, M.-E.; Zimmermann, M.; Hofmann-Apitius, M.:
Automatic recognition of chemical images. (Mexican International Conference on Current Trends in Computer Science (ENC) <8, 2007, Morelia>)
Farach-Colton, M.: Eighth Mexican International Conference on Current Trends in Computer Science. Proceedings: 24 - 28 September 2007, Morelia, Michoacan, Mexico. Piscataway, NJ: IEEE, 2007, pp. 41-46
info:doi/10.1109/ENC.2007.25

Arbona, A.; Benkner, S.; Engelbrecht, G.; Fingberg, J.; Hofmann, M.; Kumpf, K.; Lonsdale, G.; Woehrer, A.:
A service-oriented grid infrastructure for biomedical data and compute services
IEEE transactions on nanobioscience, Vol.6 (2007), No.2, pp.136-141
info:doi/10.1109/TNB.2007.897438

Barz, C.; Eickermann, T.; Pilz, M.; Wäldrich, O.; Westphal, L.; Ziegler, W.:
Co-allocating compute and network resources - bandwidth on demand in the VIOLA testbed. (CoreGRID Symposium <2007, Rennes>)
Priol, T.: Towards next generation Grid. Proceedings of the CoreGRID Symposium 2007: August 27-28, Rennes, France. New York, NY: Springer, 2007, pp. 193-202
urn:nbn:de:0011-n-655736
info:doi/10.1007/978-0-387-72498-0 18
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Biskup, J.; Tsatedem, C.; Wiese, L.:
Secure mediation of join queries by processing ciphertexts. (International Conference on Data Engineering (ICDE) <23, 2007, Istanbul>)
Institute of Electrical and Electronics Engineers -IEEE-: 2007 IEEE 23rd International Conference on Data Engineering. Workshops proceedings. Vol.2: 17 - 20 April, 2007, Istanbul, Turkey. Piscataway, NJ: IEEE, 2007, pp. 715-724
info:doi/10.1109/ICDEW.2007.4401059

Eickermann, T.; Frings, W.; Wäldrich, O.; Wieder, P.; Ziegler, W.:
Co-allocation of MPI jobs with the VIOLA grid MetaScheduling framework. (German e-Science Conference (GES) <2007, Baden-Baden>)
Helmholtz-Gemeinschaft: German e-Science Conference 2007. Proceedings: 2. - 4. Mai 2007 in Baden-Baden. Baden-Baden, 2007, 10 pp.
urn:nbn:de:0011-n-665101
Volltext

Figuerola, S.; Ciulli, N.; Leenheer, M. de; Demchenko, Y.; Ziegler, W.; Binczewski, A.:
PHOSPHORUS: Single-step on-demand services across multi-domain networks for e-science. (Asia-Pacific Optical Communications Conference (APOC) <2007, Wuhan>)
Wang, J.: Network Architectures, Management, and Applications V: SPIE Asia-Pacific Optical Communications (APOC), Wuhan, China, Nov. 1-5, 2007; Proceedings. Bellingham, WA: SPIE, 2007. (SPIE Proceedings Series 6784), Paper 67842X
urn:nbn:de:0011-n-682713
info:doi/10.1117/12.746371
Volltext

Fluck, J.; Mevissen, T.H.; Dach, H.; Oster, M.; Hofmann-Apitius, M.:
ProMiner: Recognition of human gene and protein names using regularly updated dictionaries. (BioCreative Challenge Evaluation Workshop <2, 2007, Madrid>)
Valencia, A.: Second BioCreative Challenge Evaluation Workshop 2007. Proceedings: Critical Assessment of Information Extraction in Molecular Biology, April 23-25 2007, Madrid, Spain. Madrid, 2007, pp. 149-151
urn:nbn:de:0011-n-574930
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Frangi, A.F.; Ruiz, A.; Hofmann-Apitius, M.:
Understanding cerebral aneurysms - the @neurIST project
ERCIM News, (2007), No.69, pp.16-17

Grimm, C.; Groeper, R.; Gietz, P.; Haase, M.; Makedanz, S.; Pfeiffenberger, H.; Schiffers, M.; Ziegler, W.:
Trust issues in shibboleth-enabled federated grid authentication and authorization infrastructures supporting multiple grid middlewares. (International Conference on e-Science and Grid Computing (e-Science) <3, 2007, Bangalore>)
Fox, G.C.: E-science 2007, 3rd IEEE International Conference on e-Science and Grid Computing: 10 - 13 December 2007, Bangalore, India ; proceedings; including workshop papers. New York, NY: IEEE, 2007, pp. 569-576
info:doi/10.1109/E-SCIENCE.2007.80

Gruber, R.; Keller, V.; Thiémard, M.; Wäldrich, O.; Wieder, P.; Ziegler, W.; Manneback, P.:
Integration of grid cost model into ISS/VIOLA meta-scheduler environment. (CoreGRID Workshop on Grid Middleware <2006, Dresden>)
Lehner, W.: Euro-Par 2006 workshops. Parallel processing. CoreGRID 2006, UNICORE Summit 2006, petascale computational biology and bioinformatics: Dresden, Germany, August 29-September 1, 2006; revised selected papers. Berlin: Springer, 2007. (Lecture Notes in Computer Science 4375), pp. 215-224
urn:nbn:de:0011-n-587252
info:doi/10.1007/978-3-540-72337-0 21
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Jacq, N.; Breton, V.; Chen, H.-Y.; Ho, L.-Y.; Hofmann, M.; Lee, H.-C.; Legré, Y.; Lin, S.C.; Maaß, A.; Medernach, E.; Merelli, I.; Milanesi, L.; Rastelli, G.; Reichstadt, M.; Salzemann, J.; Schwichtenberg, H.; Sridhar, M.; Kasam, V.; Wu, Y.-T.; Zimmermann, M.:
Grid-enabled high throughput virtual screening. (International Workshop on Distributed, High-Performance and Grid Computing in Computational Biology (GCCB) <2007, Eilat>)
Dubitzky, W.: Distributed, high-performance and Grid computing in computational biology. International workshop, GCCB 2006: Eilat, Israel, January 21, 2007; Proceedings. Berlin: Springer, 2007. (Lecture notes in bioinformatics 4360), pp. 45-59
info:doi/10.1007/978-3-540-69968-2 5

Jacq, N.; Breton, V.; Chen, H.-Y.; Ho, L.-Y.; Hofmann, M.; Kasam, V.; Lee, H.-C.; Legré, Y.; Lin, S.C.; Maaß, A.; Medernach, E.; Merelli, I.; Milanesi, L.; Rastelli, G.; Reichstadt, M.; Salzemann, J.; Schwichtenberg, H.; Wu, Y.-T.; Zimmermann, M.:
Virtual screening on large scale grids. (GRIDs@Large Workshop <2005, Lisboa>)
Cérin, C.: Large scale grids: Grid@Large, co-located with Europar 2005 in Lisboa. Amsterdam: Elsevier, 2007. (Parallel computing 33.2007, Nr.4/5), pp. 289-301
info:doi/10.1016/j.parco.2007.02.010

Kasam, V.; Zimmermann, M.; Maaß, A.; Schwichtenberg, H.; Wolf, A.; Jacq, N.; Breton, V.; Hofmann-Apitius, M.:
Design of new plasmepsin inhibitors: A virtual high throughput screening approach on the EGEE grid
Journal of chemical information and modeling, Vol.47 (2007), No.5, pp.1818-1828
info:doi/10.1021/ci600451t

Kasam, V.; Salzemann, J.; Jacq, N.; Mass, A.; Breton, V.:
Large scale deployment of molecular docking application on computational grid infrastructures for combating malaria. (IEEE International Symposium on Cluster Computing and the Grid (CCGrid) <7, 2007, Rio de Janeiro>)
Schulze, B.: Seventh IEEE International Symposium on Cluster Computing and the Grid, CCGRID 2007. Piscataway: IEEE Computer Society, 2007, pp. 691-696
info:doi/10.1109/CCGRID.2007.66

Klinger, R.; Rudolph, G.:
Automatic composition of music with methods of computational intelligence
WSEAS transactions on information science and applications, Vol.4 (2007), No.3, pp.508-515
urn:nbn:de:0011-n-545240
Volltext

Klinger, R.; Friedrich, C.M.; Fluck, J.; Hofmann-Apitius, M.:
Named entity recognition with combinations of conditional random fields. (BioCreative Challenge Evaluation Workshop <2, 2007, Madrid>)
Valencia, A.: Second BioCreative Challenge Evaluation Workshop 2007. Proceedings: Critical Assessment of Information Extraction in Molecular Biology, April 23-25 2007, Madrid, Spain. Madrid, 2007, pp. 89-91
urn:nbn:de:0011-n-574949
Volltext

Klinger, R.; Furlong, L.I.; Friedrich, C.M.; Mevissen, H.-T.; Fluck, J.; Sanz, F.; Hofmann-Apitius, M.:
Identifying gene specific variants in biomedical text
Journal of bioinformatics and computational biology, Vol.5 (2007), No.6, pp.1277-1296
urn:nbn:de:0011-n-704383
info:doi/10.1142/S0219720007003156
Volltext

Kolarik, C.; Hofmann-Apitius, M.; Zimmermann, M.; Fluck, J.:
Identification of new drug classification terms in textual resources
Bioinformatics, Vol.23 (2007), No.13, pp.I264-I272
info:doi/10.1093/bioinformatics/btm196

Kumpf, K.; Mevissen, T.; Wäldrich, O.; Ziegler, W.; Ginzel, S.; Weuffel, T.:
Multi-cluster text mining on the grid using the d-grid UNICORE environment. (German e-Science Conference (GES) <2007, Baden-Baden>)
Helmholtz-Gemeinschaft: German e-Science Conference 2007. Proceedings: 2. - 4. Mai 2007 in Baden-Baden. Baden-Baden, 2007, 11 pp.
urn:nbn:de:0011-n-655813
Volltext

Missier, P.; Wieder, P.; Ziegler, W.:
Semantic support for meta-scheduling in grids
Talia, D.: Knowledge and data management in GRIDs. New York/NY: Springer, 2007. (CoreGrid series 3), pp. 169-183
urn:nbn:de:0011-n-574620
info:doi/10.1007/978-0-387-37831-2 11
Volltext

Wieder, P.; Wäldrich, O.; Yahyapour, R.; Ziegler, W.:
Improving workflow execution through SLA-based advance reservation. (CoreGRID Integration Workshop <2006, Krakow>)
Gorlatch, S.: Achievements in European research on grid systems: CoreGRID Integration Workshop 2006 (selected papers); October 19-20, Krakow, Poland. New York/NY: Springer Science+Business Media, 2007. (CoreGrid series 6), pp. 207-221
info:doi/10.1007/978-0-387-72812-4 16

Wolf, A.; Zimmermann, M.; Hofmann-Apitius, M.:
Alternative to consensus scoring - A new approach toward the qualitative combination of docking algorithms
Journal of chemical information and modeling, Vol.47 (2007), No.3, pp.1036-1044
info:doi/10.1021/ci6004965

Zimmermann, M.:
Über die Kunst, dem Rechner das Lesen beizubringen
Nachrichten aus der Chemie, Vol.55 (2007), No.10, pp.997-999

Ananiadou, S.; Fluck, J.:
Proceedings of the Second International Symposium for Semantic Mining in Biomedicine. Introduction. (International Symposium on Semantic Mining in Biomedicine (SMBM) <2, 2006, Jena>)
Ananiadou, S. et al.: Second International Symposium on Semantic Mining in Biomedicine, SMBM 2006. Proceedings: Jena, April 9-12, 2006. Aachen: RWTH, 2006. (BMC Bioinformatics 7, Suppl. 3), pp. S1
info:doi/10.1186/1471-2105-7-S3-S1

Arbona, A.; Benkner, S.; Fingberg, J.; Frangi, A.F.; Hofmann, M.; Hose, D.R.; Lonsdale, G.; Ruefenacht, D.; Viceconti, M.:
Outlook for grid service technologies within the @neurIST eHealth environment. (HealthGrid Conference <4, 2006, Valencia>)
Hernández, V.: Challenges and opportunities of healthgrids. Proceedings of Healthgrid 2006. Amsterdam: IOS Press, 2006. (Studies in health technology and informatics 120), pp. 401-404

Barz, C.; Eickermann, T.; Kirtchakova, L.; Pilz, M.; Wäldrich, O.; Ziegler, W.:
Co-allocation of compute and network resources in the VIOLA-testbed. (TERENA Networking Conference <2006, Catania>)
Melve, I.: TERENA Networking Conference 2006: 15. - 18.05.2006 in Catania. Bradford, West Yorkshire: Emerald, 2006. (Campus-wide information systems 23.2006,4), 12 pp.

Beibei, H.; Friedrich, C.M.; Manthey, R.; Hofmann-Apitius, M.:
Bayesian network modeling for the prediction of treatment outcomes of intracranial aneurysms. (German Conference on Bioinformatics (GCB) <2006, Tübingen>)
Huson, D. et al.: German Conference on Bioinformatics 2006. Short papers and poster abstracts: GCB 2006, 19.9.2006-22.9.2006 in Tübingen, Germany. Tübingen, 2006, pp. 122

Bierbaum, B.; Clauss, C.; Eickermann, T.; Kirtchakova, L.; Krechel, A.; Springstubbe, S.; Wäldrich, O.; Ziegler, W.:
Reliable orchestration of distributed MPI-applications in a UNICORE-based grid with MetaMPICH and MetaScheduling. (European PVM/MPI Users' Group Meeting <13, 2006, Bonn>)
Mohr, B.: Recent advances in parallel virtual machine and message passing interface: 13th European PVM, MPI User's Group Meeting, Bonn, Germany, September 17-20, 2006; Proceedings. Berlin: Springer, 2006. (Lecture Notes in Computer Science 4192), pp. 174-183
info:doi/10.1007/11846802 29

Birkholtz, L.-M.; Bastien, O.; Wells, G.; Grando, D.; Joubert, F.; Kasam, V.; Zimmermann, M.; Ortet, P.; Jacq, N.; Saïdani, N.; Roy, S.; Hofmann-Apitius, M.; Breton, V.; Louw, A.I.; Maréchal, E.:
Integration and mining of malaria molecular, functional and pharmacological data: How far are we from a chemogenomic knowledge space?
Malaria journal. Online journal, Vol.5 (2006), Art. 110, 24 pp.
urn:nbn:de:0011-n-574927
info:doi/10.1186/1475-2875-5-110
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Breton, V.; Jacq, N.; Hofmann, M.:
Grid added value to address malaria. (International Symposium on Cluster Computing and the Grid (CCGrid) <6, 2006, Singapore>)
Institute of Electrical and Electronics Engineers -IEEE-: Sixth International Symposium on Cluster Computing and the Grid, CCGrid 2006. Proceedings: 16-19 May, 2006, Singapore. Los Alamitos/Calif.: IEEE, 2006, pp. 40
info:doi/10.1109/CCGRID.2006.139

Friedrich, C.M.; Zimmermann, M.; Hofmann, M.:
Grid computing - an opportunity for biomedical and statistical computing: Talk at Statistical Computing 2006. (Arbeitstagung über Methoden und Werkzeuge der Informatik für die Statistik (Statistical Computing) <38, 2006, Reisensburg/Günzburg>)
Statistical Computing 2006. Abstracts: 38. Arbeitstagung über Methoden und Werkzeuge der Informatik für die Statistik, 25. - 28.06.2006, Schloss Reisensburg (Günzburg). Günzburg, 2006, pp. 5

Jacq, N.; Salzemann, J.; Legré, Y.; Reichstadt, M.; Jacq, F.; Zimmermann, M.; Maaß, A.; Sridhar, M.; Vinod-Kusam, K.; Schwichtenberg, H.; Hofmann, M.; Breton, V.:
Demonstration of in silico docking at a large scale on grid infrastructure. (HealthGrid Conference <4, 2006, Valencia>)
Hernández, V.: Challenges and opportunities of healthgrids. Proceedings of Healthgrid 2006. Amsterdam: IOS Press, 2006. (Studies in health technology and informatics 120), pp. 155-157

Karopka, T.; Fluck, J.; Mevissen, H.-T.; Glass, Ä.:
The autoimmune disease database. A dynamically compiled literature-derived database
BMC bioinformatics. Online journal, Vol.7 (2006), pp.325
info:doi/10.1186/1471-2105-7-325

Keller, V.; Gruber, R.; Spada, M.; Tran, T.-M.; Cristiano, K.; Kuonen, P.; Wieder, P.; Ziegler, W.; Wäldrich, O.; Maffioletti, S.; Sawley, M.-C.; Nellari, N.:
Integration of the ISS into the VIOLA meta-scheduling. (Workshop "Integrated Research in Grid Computing" <2005, Pisa>)
Gorlatch, S.: Integrated research in GRID computing: CoreGRID Integration Workshop 2005, selected papers, November 28-30, Pisa, Ialy. Berlin: Springer US, 2006, pp. 203-214
info:doi/10.1007/978-0-387-47658-2 15

Klinger, R.; Rudolph, G.:
Evolutionary composition of music with learned melody evaluation. (International Conference on Computational Intelligence, Man-Machine Systems and Cybernetics (CIMMACS) <5, 2006, Venice>)
Mastorakis, N. et al.: 5th WSEAS International Conference on Computational Intelligence, Man-Machine Systems and Cybernetics, CIMMACS '06. Proceedings: Venice, Italy, November 20-22, 2006. Venice, 2006, pp. 234-239
urn:nbn:de:0011-n-545258
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Kumpf, K.; Mevissen, T.; Wäldrich, O.; Weuffel, T.; Ziegler, W.:
Text mining on the grid. (Workshop on Grid Technologies for Knowledge-based Industries and Businesses <2006, Helsinki>)
Grid Technologies for Knowledge-based Industries and Businesses: Helsinki, Finland, November 21-23, 2006; Proceedings. Helsinki, 2006, 4 pp.

Ludwig, H.; Nakata, T.; Wäldrich, O.; Wieder, P.; Ziegler, W.:
Reliable orchestration of resources using WS-agreement. (International Conference on High Performance Computing and Communications (HPCC) <2, 2006, München>)
Gerndt, M.: High performance computing and communications. Second international conference, HPCC 2006: Munich, Germany, September 13-15, 2006; Proceedings. Berlin: Springer, 2006. (Lecture Notes in Computer Science 4208), pp. 753-762

Milke, J.-M.; Schiffers, M.; Ziegler, W.:
Virtuelle Organisationen in Grids: Charakterisierung und Management
Praxis der Informationsverarbeitung und Kommunikation : PIK, Vol.29 (2006), No.3, pp.166-171
info:doi/10.1515/PIKO.2006.165

Springstubbe, S.; Ziegler, W.:
CoreGRID summer school 2006: First steps in next generation grid technologies
ERCIM News, (2006), No.67, pp.4

Streit, A.; Wäldrich, O.; Wieder, P.; Ziegler, W.:
On scheduling in UNICORE - extending the web services agreement based resource management framework. (International Conference on Parallel Computing (ParCo) <2005, Malaga>)
Joubert, G.R.: Parallel computing. Current and futures issues of high end computing: Proceedings of the International Conference ParCo 2005, Central Institute for Applied Mathematics. Jülich: NIC, 2006. (NIC Series 33), pp. 57-64

Wäldrich, O.; Wieder, P.; Ziegler, W.:
A meta-scheduling service for co-allocating arbitrary types of resources. (International Conference on Parallel Processing and Applied Mathematics (PPAM) <6, 2005, Poznan>)
Wyrzykowski, R.: Parallel processing and applied mathematics. 6th international conference, PPAM 2005: Poznan', Poland, September 11-14, 2005. Revised selected papers. Berlin: Springer, 2006. (Lecture Notes in Computer Science 3911), pp. 782-791
info:doi/10.1007/11752578 94

Wieder, P.; Wäldrich, O.; Ziegler, W.:
Advanced techniques for scheduling, reservation, and access management for remote laboratories. (International Conference on e-Science and Grid Computing (e-Science) <2, 2006, Amsterdam>)
Institute of Electrical and Electronics Engineers -IEEE-: Second IEEE International Conference on e-Science and Grid Computing, e-Science 2006: The meeting was held on Dec. 4-6, 2006, Amsterdam, Netherlands. Los Alamitos, Calif.: IEEE Computer Society, 2006, pp. 128
info:doi/10.1109/E-SCIENCE.2006.261061

Wieder, P.; Wäldrich, O.; Yahyapour, R.; Ziegler, W.:
Improving workflow execution through SLA-based advance reservation. (CoreGRID Integration Workshop <2006, Krakow>)
Integrated Research in Grid Computing: CoreGRID Integration Workshop, Krakow, October 19-20, 2006. Krakow, 2006, pp. 333-344

Ziegler, W.; Wieder, P.:
Bringing knowledge to middleware - grid scheduling ontology. (Workshop on Future Generation Grids <2004, Dagstuhl>)
Getov, V.: Future generation grids: Proceedings of the Workshop on Future Generation Grids, November 1 - 5, 2004, Dagstuhl, Germany. New York, NY: Springer, 2006, pp. 47-59

Cristiano, K.; Gruber, R.; Keller, V.; Kuonnen, P.; Maffioletti, S.; Nellari, N.; Sawley, M.-C.; Spada, M.; Tran, T.-M.; Wieder, P.; Wäldrich, O.; Ziegler, W.:  

Integration of ISS into the VIOLA meta-scheduling environment. (Workshop "Integrated Research in Grid Computing" <2005, Pisa>)
Gorlach, S.: CoreGRID Workshop on Integrated Research in Grid Computing. Proceedings: Pisa, IT, 20.-28. November 2005. Pisa: Università di Pisa, 2005, pp. 357-366

Fluck, J.; Hofmann, M.; Hahn, U.; Wermter, J.; Schulz, S.:
Text mining in den Life Sciences: Perspektiven der automatischen Informationsextraktion aus biomedizinischen Fachtexten
Deutsche Zeitschrift für klinische Forschung, (2005), No.5/6, pp.20-26

Fluck, J.; Zimmermann, M.; Kurapkat, G.; Hofmann, M.:
Information extraction technologies for the life science industry
Drug Discovery Today, Vol.2 (2005), No.3, pp.217-224
info:doi/10.1016/j.ddtec.2005.08.013

Fluck, J.; Deneke, H.; Gieger, C.:
Text mining in life sciences
Zanasi, A.: Text mining and its applications to intelligence, CRM and knowledge management. Southampton: WIT Press, 2005. (Advances in Management Information Systems 2), pp. 279-284
info:doi/10.2495/978-1-85312-995-7/17

Fluck, J.; Stitt, M.; Selbig, J.; Hofmann, M.; Thimm, O.:
Using named entity recognition for ontology annotation: An experimental approach for Arabidopsis functional genome annotation. (European Conference on Computational Biology (ECCB) <4, 2005, Madrid>)
Bioinformatics National Institute -INB-: ECCB 2005, Workshop on Biomedical Ontologies and Text Processing: 28 September, 2005 Madrid, Spain, the workshop is part of the 4th European Conference on Computational Biology (ECCB). Madrid, 2005

Hanisch, D.; Fundel, K.; Mevissen, H.-T.; Zimmer, R.; Fluck, J.:
ProMiner: Rule-based protein and gene entity recognition
BMC bioinformatics. Online journal, Vol.6 (2005), No.1, pp.14
info:doi/10.1186/1471-2105-6-S1-S14

Hessler, G.; Zimmermann, M.; Matter, H.; Evers, A.; Naumann, T.; Lengauer, T.; Rarey, M.:
Multiple-ligand-based virtual screening: Methods and applications of the MTree approach
Journal of medicinal chemistry, Vol.48 (2005), No.21, pp.6575-6584
info:doi/10.1021/jm050078w

Orian-Rousseau, V.; Mink, S.; Mengwasser, J.; HogenEsch, H.; Guo, F.; Thies, W.-G.; Hoffmann, M.; Herrlich, P.; Ponta, H.:
Genes upregulated in a metastasizing human colon carcinoma cell line
International journal of cancer, Vol.113 (2005), No.5, pp.699-705
info:doi/10.1002/ijc.20644

Reinhardt, S.; Marian, C.M.:
Carboborosilazane ceramics: Initial reactions between TSDE and methylamine - A combined quantum chemical and first principles molecular dynamics study. (International Conference on Non-Crystalline Materials (CONCIM) <2005>)
Journal of non-crystalline solids, Vol.351 (2005), No.12-13, pp.1113-1120
info:doi/10.1016/j.jnoncrysol.2005.01.025

Vet, P. van der; Huibers, T.; Binz, P.-A.; Hofmann, M.:
ESF workshop on 'sustainability and governance of web and GRID resources in functional genomics'
Comparative and functional genomics, Vol.6 (2005), No.5-6, pp.307-310
info:doi/10.1002/cfg.488

Wermter, J.; Fluck, J.; Strötgen, J.; Geißler, S.; Hahn, U.:
Recognizing noun phrases in biomedical text: An evaluation of lab prototypes and commercial chunkers. (International Symposium on Semantic Mining in Biomedicine (SMBM) <1, 2005, Hinxton>)
Hahn, U.: SMBM 2005: First International Symposium on Semantic Mining in Biomedicine (SMBM). EBI, Hinxton, UK, 10-12 April 2005. Aachen: Rheinisch-Westfälische Technische Hochschule Aachen, 2005. (CEUR Workshop Proceedings 148), 9 pp.

Zimmermann, M.; Thi, L.T.B.; Hofmann, M.:
Combating illiteracy in chemistry: Towards computer-based chemical structure reconstruction
ERCIM News, (2005), No.60, pp.40-41

Zimmermann, M.; Fluck, J.; Thi, L.T.B.; Kolarik, C.; Kumpf, K.; Hofmann, M.:
Information extraction in the life sciences: Perspectives for medicinal chemistry, pharmacology and toxicology
Current topics in medicinal chemistry, Vol.5 (2005), No.8, pp.785-796
info:doi/10.2174/1568026054637692