2009

Corinna Kolářik, Roman Klinger, and Martin Hofmann-Apitius, Identification of Histone Modifications in Biomedical Text for Supporting Epigenomic Research. Supplement Issue of BMC Bioinformatics to appear

2008

Corinna Kolářik, Hofmann-Apitius, Martin, Linking Chemical and Biological Information with Natural Language Processing. Book chapter in: Chemical Information Mining: Facilitating Literature-Based Discovery, 2008, Editor: Debra L. Banville, ISBN: 9781420076493, ISBN 10: 1420076493

Oster, Marius, Using Latent Semantic Indexing for the Disambiguation of Global Abbreviations in Biomedical Literature.
Sankt Augustin, 2008, Sankt Augustin, Fachhochschule Bonn-Rhein-Sieg, Diplomarbeit, 2008

Furlong, Laura I.; Dach, Holger; Hofmann-Apitius, Martin; Sanz, Ferran, OSIRISv1.2 : a named entity recognition system for sequence variants of genes in biomedical literature. BMC bioinformatics 9, Art. 84 (2008)

Breton, Vincent; Jacq, Nicolas; Kasam, Vinod; Hofmann-Apitius, Martin, Grid-added value to address malaria. IEEE transactions on information technology in biomedicine 12 (2008), 2, S. 173-181,  link

David Ruau, Corinna Kolářik, Theodor Heinz Mevissen, Emmanuel Muller, Ira Assent, Ralph Krieger, Thomas Seidl, Martin Hofmann-Apitius and Martin Zenke, Public microarray repository semantic annotation with ontologies using text mining and expression profile correlation. Poster at 4th ISCB Student Council Symposium, Toronto, accepted

Faroughi, A.; Faroughi, R.; Wieder, P.; Ziegler, W.
Attributes and VOs: Extending the UNICORE authorisation capabilities. 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), ISBN: 978-3-540-78472-2, ISBN: 3-540-78472-1, S.121-130

Talia, D.; Yahyapour, R.; Ziegler, W., Grid middleware and services; Challenges and solutions.
Berlin: Springer US, 2008, XX, 420 S., CoreGrid series, 8, Workshop on Using Service Level Agreements in Grids (Grid) 2007, Austin/Tex., ISBN: 978-0-387-78445-8, ISBN: 0-387-78445-4

Bouge, L.; Forsell, M.; Larsson Träff, J.; Streit, A.; Ziegler, W.; Alexander, M.; Childs, S.
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, XVII, 236 S., Lecture Notes in Computer Science, 4854, International Workshop on Highly Parallel Processing on a Chip (HPPC) 2007, Rennes, UNICORE Summit Workshop 2007, Rennes, International Workshop on Visualization/Xen in High-Performance Cluster and Grid Computing (VHPC) 2007, Rennes, ISBN: 978-3-540-78472-2, ISBN: 3-540-78472-1

Seidel, J.; Wäldrich, O.; Wieder, P.; Yahyapour, R.; Ziegler, W.
Using SLA for resource management and scheduling - a survey. Workshop on Using Service Level Agreements in Grids (Grid) , Grid middleware and services : Challenges and solutions, Berlin: Springer US, 2008 (CoreGrid series 8), ISBN: 978-0-387-78445-8, ISBN: 0-387-78445-4

Rajasekaran, H.; , Iacono, L. 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 Manag-ment through Integration of Heterogeneous Data, Computing, and Complex Processing Services. Proceedings of the 21st IEEE International Symposium on computer-based medical systems, 2008

Hofmann-Apitius, M.; Fluck, J. ; Furlong, L. I.; Fornes, O.; Kolářik, C. ; Hanser, S.; Boeker, M.; Schulz, S.; Sanz, F.; Klinger, R.; Mevissen, H.; Gattermayer, T. ; Oliva, B.; Friedrich, C. M. Knowledge Environments Representing Molecular Entities for the Virtual Physiological Human. Philosophical Transactions of the Royal Society A, 2008, DOI:10.1098/rsta.2008.0099

Shahid, M.; Ziegler, W.; Kasam, V.; Zimmermann, M.; and Hofmann-Apitius, M. , Virtual High Throughput Screening (vHTS) on an Optical High Speed Testbed. Proceedings of the HealthGrid 2008, IOS Press, 125-134, ISBN 978-1-58603-874-8

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.; Frangi, A. F. The @neurIST project. Proceedings of the HealthGrid 2008, IOS Press, 161-164, ISBN 978-1-58603-874-8

Hanser, S.; Fluck, J. ; Furlong, L. I.; Friedrich, C. M.; Hofmann-Apitius, M.; Stenzhorn, H.; Boeker, M. Knowledge Structuring and Retrieval for Intracranial Aneurysm Research. Proceedings of the HealthGrid 2008, 2008. accepted.

Friedrich, C. M.; Dach, H.; Gattermayer, T.; Engelbrecht, G.; Benkner, S.; Hofmann-Apitius, M. @neuLink: A Service-oriented Application for Biomedical Knowledge Discovery. Proceedings of the HealthGrid 2008, IOS Press, 165-172, ISBN 978-1-58603-874-8

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. F. @neurIST -- Chronic Disease Management through Integration of Heterogeneous Data and Computer-interpretable Guideline-Services. Proceedings of the HealthGrid 2008, IOS Press, 173-177, ISBN 978-1-58603-874-8

Roman Klinger, Corinna Kolářik, Juliane Fluck, Martin Hofmann-Apitius, and Christoph M. Friedrich. Detection of IUPAC and IUPAC-like Chemical Names. Bioinformatics, 2008. Proceedings of the International Conference Intelligent Systems for Molecular Biology (ISMB). Vol. 24, 268-276, DOI:10.1093/bioinformatics/btn181

Corinna Kolářik, Roman Klinger, Christoph M. Friedrich, Martin Hofmann-Apitius, and Juliane Fluck. Chemical Names: Terminological Resources and Corpora Annotation. In Workshop on Building and evaluating resources for biomedical text mining (6th edition of the Language Resources and Evaluation Conference), Marrakech, Morocco, 2008. 51-58

A. Arbona, S. Benkner, G. Engelbrecht, J. Fingberg, M. Hofmann, K. Kumpf, G. Lonsdale, A. Woehrer. A service-oriented grid infrastructure for biomedical data and com-pute services. IEEE Trans Nanobioscience. 2007 Jun;6(2):136-41.

Friedrich Christoph M.; Hofmann-Apitius, Martin; Dunlop, Robert; Chronakis, Ioannis; Sturkenboom, Miriam C.J.M.; Risselada, Roelof; Oliva, Baldo; Sanz, Ferran. Initial Results on Knowledge Discovery and Desicion Support for Intracranial Aneurysms. Proceedings of HEALTHINF 2008, 265--272, INSTICC,  HEALTHINF Madeira/Portugal

Breton, V., Jacq, N., Kasam, V., Hofmann-Apitius, M. Grid Added Value to Address Malaria. IEEE Trans Inf Technol Biomed. 2008 Mar;12(2):173-81

Nicolas Jacq, Jean Salzemann, Yannick Legré, Emmanuel Medernach, Johan Montagnat, Astrid Maaß, Matthieu Reichstadt, Horst Schwichtenberg, Mahendrakar Sridhar, Vinod Kasam, Marc Zimmermann, M. Hofmann, Vincent Breton: Grid-enabled Virtual Screening Against Malaria. J. Grid Comput. 6(1): 29-43 (2008)

2007

Larry Smith, Lorraine K. Tanabe, Rie Johnson nee Ando, Cheng-Ju Juo, I-Fang Chung, Chun-Nan Hsu, Yu-Shi Lin, Roman Klinger, Christoph M. Friedrich, Kuzman Ganchev, Manabu Torii, Hongfang Liu, Barry Haddow, Craig A. Struble, Richard J. Povinelli, Andreas Vlachos, William A. Baumgartner Jr., Lawrence Hunter, Bob Carpenter, Richard Tzong-Han Tsai, Hong jie Dai, Feng Liu, Yifei Chen, Chengjie Sun, Sophia Katrenko, Pieter Adriaans, Christian Blaschke, Rafel Torres Perez, Mariana Neves, Preslav Nakov, Anna Divoli, Manuel Mana, Jacinto Mata-Vazquez, and W. John Wilbur. Overview of BioCreative II Gene Mention Recognition. Genome Biology, 2007. in print

Roman Klinger and Katrin Tomanek. Classical Probabilistic Models and Conditional Random Fields. Algorithm Engineering Report TR07-2-013, Department of Computer Science, Dortmund University of Technology, December 2007. ISSN 1864-4503. Link

Klinger, Roman; Furlong, Laura I.; Friedrich, Christoph M.; Mevissen, Heinz Theodor; Fluck, Juliane; Sanz, Ferran, and Hofmann-Apitius, Martin Identifying Gene Specific Variants in Biomedical Text. Journal of Bioinformatics and Computational Biology, 2007, 5, 1277-1296, to appear   Link

Hülsmann, Marco and Friedrich, Christoph M. Comparison of a Novel Combined ECOC Strategy with Different Multiclass Algorithms Together with Parameter Optimization Methods. Proceedings of the International Conference on Machine Learning and Data Mining MLDM´2007, Springer Verlag, 17--31,  DOI:10.1007/978-3-540-73499-4_3

Algorri, Maria-Elena; Zimmermann, Marc; Friedrich, Christoph M; Akle, Santiago, and Hofmann-Apitius, Martin
Reconstruction of Chemical Molecules from Images. Proceedings of the 29th Annual International Conference of the IEEE Engineering in Medicine and Biology Society EMBC 2007, 4609 - 4612,  DOI:10.1109/IEMBS.2007.4353366

Fluck, Juliane; Mevissen, Heinz Theodor; Dach, Holger; Oster, Marius, and Hofmann-Apitius, Martin
ProMiner: Recognition of Human Gene and Protein Names using regularly updated Dictionaries. Proceedings of the Second BioCreative Challenge Evaluation Workshop, 2007, 149--151  Download PDF, 154 KB

Antje Wolf, Marc Zimmermann, and Martin Hofmann-Apitius. Alternative to Consensus Scoring-A New Approach Toward the Qualitative Combination of Docking Algorithms. J. Chem. Inf. Model.; 2007; 47(3) pp 1036 - 1044; (Article)   DOI: 10.1021/ci6004965

Christoph Barz, Thomas Eickermann, Markus Pilz, Oliver Wäldrich, Lidia Westphal, Wolfgang Ziegler: Co-Allocating Compute and Network Resources- Bandwidth on Demand in the VIOLA Testbed. CoreGRID Symposium, Rennes, France, August 2007, to appear.

J. Biskup, C. Tsatedem, L. Wiese: Secure mediation of join queries by processing ciphertexts. In: Proceedings of the First International Workshop on Security Technologies for Next Generation Collaborative Business Applications (SECOBAP'07), to appear.

Nicolas Jacq, Henning Müller, Ignacio Blanquer, Yannick Legré, Vincent Breton, Dominique Hausser, Vicente Hernández, Tony Solomonides, Martin Hofmann-Apitius. From Genes to Personalized HealthCare: Grid Solutions for the Life Sciences - Proceedings of HealthGrid 2007. Studies in Health Technology and Informatics, Volume 126, 2007, (ISBN 978-1-58603-738-3)

Corinna Kolářik, Martin Hofmann-Apitius, Marc Zimmermann and Juliane Fluck. Identification of New Drug Classification Terms in Textual Resources. Bioinformatics 2007 23: i264-i272 (ISMB/ECCB 2007 Conference Proceedings)
 Link


Roman Klinger, Christoph M. Friedrich, Juliane Fluck and Martin Hofmann-Apitius. Named Entity Recognition with Combinations of Conditional Random Fields. Proceedings of the Second BioCreative Challenge Evaluation Workshop, Madrid, Spain, April 2007, 89-91. Link

Thomas Eickermann, Wolfgang Frings, Oliver Wäldrich, Philipp Wieder, Wolfgang Ziegler: Co-allocation of MPI Jobs with the VIOLA Grid MetaScheduling Framework. Proccedings of the German eScience Conference GES2007, Baden Baden, Mai 2007,  Link.

Kai Kumpf, Theo Mevissen, Oliver Wäldrich, Thomas Weuffel, Wolfgang Ziegler: Multi-Cluster Text Mining on the Grid using the D-Grid UNICORE environment. Proccedings of the German eScience Conference GES2007, Baden Baden, Mai 2007,  Link.

2006

Christoph Barz; Thomas Eickermann; Lidia Kirtchakova; Markus Pilz; Oliver Wäldrich; Wolfgang Ziegler: Co-Allocation of Compute and Network Resources in the VIOLA Testbed. TERENA Networking Conference 2006, Catania, Italy, to appear

Ralf Gruber; Vincent Keller; Pierre Manneback; Michela Thiémard; Oliver Wäldrich; Philipp Wieder; Wolfgang Ziegler: Integration of Grid Cost Model into ISS/VIOLA Meta-Scheduler Environment. UNICORE Summit in conjunction with Euro-Par 2006, UNICORE Summit 2006, Springer LNCS 4375, P. 215 - 224

Han, B., Friedrich, C.M., Manthey, R. and Hofmann-Apitius, M., Bayesian Network Modelling for the Prodiction of Treatment Outcomes of Intracranial aneurysms" In D. Huson, O Kohlbacher, A. Lupas, K. Nieselt and A. Zell, editors; Short Papers and Poster Abstracts of the German Conference on Bioinformatics (GCB 2006), Page 122, 2006.

Friedrich, C.M., Zimmermann, M. and Hofmann-Apitius, M., "Grid Computing - An Opportunity for Biomedical and Statistical Computing"; Talk at Statistical Computing 2006; Abstracts of the Statistical Computing 2006; Page 5; Schloss Reisenburg; Germany 2006.

Ananiadou S. and Fluck J.Introduction: Proceedings of the Second International Symposium for Semantic Mining in Biomedicine. 2006. BMC Bioinformatics 2006, 7(Suppl 3):S1. www.biomedcentral.com/1471-2105/7

L.I. Furlong, H. Dach, M. Hofmann-Apitius, F. Sanz. Towards a development of a text-mining system for genes, sequence variants and phenotypes: integration of OSIRIS with ProMiner. Spanish Symposium on Bioinformatics and Computational Biology, 2006

Karopka T, Fluck J, Mevissen HT, Glass A.
The Autoimmune Disease Database: a dynamically compiled literature-derived database.
BMC Bioinformatics. 2006 Jun 27;7:325.
www.biomedcentral.com/1471-2105/7/325

Friedrich, C.M., Revillion, T., Hofmann, M., Fluck, J.
Biomedical and Chemical Named Entity Recognition with Conditional Random Fields: The Advantage of Dictionary Features. Proceedings of the Second International Symposium on Semantic Mining in Biomedicine, Jena, April 9-12, 2006. Edited by Sophia Ananiadou and Juliane Fluck
CEUR-WS.org/Vol-177/

Lyn-Marie Birkholtz, Olivier Bastien, Gordon Wells, Delphine Grando, Fourie Joubert, Vinod Kasam, Marc Zimmermann, Philippe Ortet, Nicolas Jacq, Nadia Saidani, Sylvaine Roy, Martin Hofmann-Apitius, Vincent Breton, Abraham I Louw and Eric Marechal, Integration and mining of malaria molecular, functional and pharmacological data: how far are we from a chemogenomic knowledge space? Malaria Journal 2006, 5:110 (17 Nov 2006)

Vinod Kasam, Marc Zimmermann, Astrid Maaß, Horst Schwichtenberg, Antje Wolf, Nicolas Jacq, Vincent Breton, Martin Hofmann. Design of New Plasmepsin Inhibitors: A Virtual High Throughput Screening Approach On The EGEE Grid. submitted to Journal of Chemical Information and Modeling (JCIM)

Vincent Breton, Nicolas Jacq and Martin Hofmann, Grid added value to address malaria, Biogrid Workshop, May 2006, Singapore

Nicolas Jacq, Jean Salzemann, Yannick Legré, Matthieu Reichstadt, Florence Jacq, Marc Zimmermann, Astrid Maass, Mahendrakar Sridhar, Kasam Vinod-Kusam, Horst Schwichtenberg, Martin Hofmann and Vincent Breton, Demonstration of In Silico Docking at a Large Scale on Grid Infrastructure in: Challenges and Opportunities of HealthGrids; Proceedings of HealthGrid 2006; Part III: Bioinformatics on the Grid [2006]

A. Arbona, S. Benkner, J. Fingberg, A.F. Frangi, M. Hofmann, D.R. Hose, G. Lonsdale, D. Ruefenacht and M. Viceconti
Outlook for Grid Service Technologies Within the @neurIST eHealth Environment in: Challenges and Opportunities of HealthGrids; Proceedings of HealthGrid 2006; Part VI: Posters and Short Contributions [2006]

Ralf Gruber; Vincent Keller; Pierre Manneback; Michela Thiémard; Oliver Wäldrich; Philipp Wieder; Wolfgang Ziegler: Integration of Grid Cost Model into ISS/VIOLA Meta-Scheduler Environment. Euro-Par 2006, UNICORE Summit, Springer LNCS, to appear

Philipp Wieder; Oliver Wäldrich; Wolfgang Ziegler: Advanced Techniques for Scheduling, Reservation, and Access Management for Remote Laboratories. Proceedings of the e-Science 2006, Amsterdam, to appear

Philipp Wieder; Oliver Wäldrich; Ramin Yahyapour; Wolfgang Ziegler: Improving Workflow execution through SLA-based Advance Reservation Inregrated Research in Grid Computing, S. 333-344, CoreGRID Integration Workshop 2006, Krakow, Poland, ISBN: 83-915141-6-1

Paolo Missier; Philipp Wieder; Wolfgang Ziegler: Semantic support for meta-scheduling in Grids. CoreGRID Institute on Knowledge and Data Management, Poznan Workshop, September 2005, Springer 2006, CoreGRID Series, Knowledge and Data Management in GRIDs, S. 169 - 183

Lyn-Marie Birkholtz, Olivier Bastien, Gordon Wells, Delphine Grando, Fourie Joubert, Vinod Kasam, Marc Zimmermann, Philippe Ortet, Nicolas Jacq, Nadia Saïdani, Sylvaine Roy, Martin Hofmann-Apitius, Vincent Breton, Abraham I Louw and Eric Maréchal:
Integration and mining of malaria molecular, functional and pharmacological data: how far are we from a chemogenomic knowledge space?
 www.malariajournal.com/content/5/1/110

Boris Bierbaum; Carsten Clauss; Thomas Eickermann; Lidia Kirtchakova; Arnold Krechel; Stephan Springstubbe; Oliver Wäldrich; Wolfgang Ziegler: Reliable Orchestration of distributed MPI-Applications in a UNICORE-based Grid with MetaMPICH and MetaScheduling. EuroPVM/MPI 2006, Bonn, Germany, September 2006, Springer LNCS 4192, S. 174 - 183

Heiko Ludwig; Toshiyuki Nakata; Oliver Wäldrich; Philipp Wieder; Wolfgang Ziegler: Reliable Orchestration of Resources using WS-Agreement. The 2006 International Conference on High Performance Computing and Communications , (HPCC06), Munich Germany, September 2006, Springer LNCS 4208, S. 753 - 762

Christoph Barz; Thomas Eickermann; Lidia Kirtchakova; Markus Pilz; Oliver Wäldrich; Wolfgang Ziegler: Co-Allocation of Compute and Network Resources in the VIOLA Testbed. TERENA Networking Conference 2006, Catania, Italy, to appear

Jens-Michael Milke; Michael Schiffers; Wolfgang Ziegler: Virtuelle Organisationen in Grids. Charakterisierung und Management. PIK - Praxis der Informationsverarbeitung und Kommunikation, 2006, Jahrgang 29, Heft 3, S. 166 - 171

2005

Zimmermann, M., Friedrich, C.M. and Algorri, M.E., "Combating Illiteracy in Chemistry: Towards Computer-Based Chemical Structure Reconstruction" 1st German Conference on Chemoinfromatics, 2005 Goslar.

Revillion, T., Friedrich, C.M., Fluck, J. and Hofmann, M., "Biological and Chemical Entity Recognition from text using Conditional Random Fields", German Conference on Bioinformatics (GCB 2005), 2005 Hamburg.

Wang, Y., Bui Thi, L.T., Friedrich, C.M., Zimmermann, M., Algorri, M.E., Noltemeier, H. and Hofmann, M., "CSR - Chemical Structure Recognition from Images", German Conference on Bioinformatics ( GCB 2005), 2005 Hamburg.

Friedrich, C.M., "Kombination evolutionär optimierter Klassifikatoren", PhD Thesis, University of Witten/Herdecke, Faculty of Life Sciences, 2005, Fraunhofer Information and Communication Series, Shaker Verlag.

Martin Hofmann und Eva Eggeling (eds.), Grid Strategien in der Wirtschaft
Positionspapier für das Bundesministerium für Bildung und Forschung (BMBF), Oktober, 2005

Orian-Rousseau, V.; Mink, S.; Mengwasser, J.; HogenEsch, H.; Guo, F.; Thies, W. G.; Hofmann, M.; Herrlich, P. and Ponta, H.: Genes upregulated in a metastasizing human colon carcinoma cell line. Int J Cancer. 2005 Feb 20; 113(5): 699-705

Holger Dach, Kai Kumpf, Martin Hofmann, Rainer Manthey, Juliane Fluck
A new information system to maintain and analyse biochemical interaction networks.
German Conference on Bioinformatics (GCB 2005), 2005 Hamburg. Poster

Sabine Trochim, Holger Dach
Extracting Pathways from Huge Literature Networks. German Conference on Bioinformatics (GCB 2005), 2005 Hamburg. Poster

Holger Dach, Juliane Fluck, Kai Kumpf, Rainer Manthey
A new Information System to manage and analyse information on biochemical interactions
Poster at the FEBS SysBio 2005: Advanced Lecture Course on Systems Biology, Gosau.

Zimmermann, Marc; Bui Thi, Le Thuy and Hofmann, Martin: Combating Illiteracy in Chemistry: Towards Computer-Based Chemical Structure Reconstruction. ERCIM News No. 60, January 2005

Fluck, J.; Hofmann, M.; Hahn, U.; Wermter J. und Schulz, S.: Text mining in den Life Sciences: Perspektiven der automatischen Informationsextraktion aus biomedizinischen Fachtexten (in German). DZKF, 5/6 p20-26

Fluck, Juliane; Stitt, Marc; Selbig, Joachim; Hofmann, Martin and Thimm, Oliver: Using named entity recognition for ontology annotation. An experimental approach for Arabidopsis functional genome annotation. Proceedings of the 4th European Conference on Computational Biology, ECCB 2005

Achim Streit, Philipp Wieder, Oliver Wäldrich, Wolfgang Ziegler: On Scheduling in UNICORE - Extending the Web Services Agreement based Resource Management Framework.In Parallel Computing: Current & Future Issues of High-End Computing, Proc. of Parallel Computing 2005 (ParCo 2005), G.R. Joubert, W.E. Nagel, F.J. Peters, O. Plata, P. Tirado, E. Zapata (eds.), pp.57-64, John von Neumann Institute for Computing (NIC), Malaga, ES, September 13-16, 2005. ISBN: 3-00-017352-8.

Philipp Wieder, Oliver Wäldrich, Wolfgang Ziegler: A Meta-Scheduling Service for Co-allocating Arbitrary Types of Resources. Grid Resource Management Workshop 2005, PPAM Conference, Poznan, Poland, September 2005, Springer LNCS 3911, p. 782 - 791

Vincent Keller, Kevin Cristiano, Ralf Gruber, Pierre Kuonen, Sergio Maffioletti, Nello Nellari, Marie-Christine Sawley, Trach-Minh Tran, Oliver Wäldrich, Philipp Wieder, Wolfgang Ziegler: Integration of ISS into the VIOLA Meta-scheduling Environment. CoreGRID Integration Workshop 2005, Pisa, November 2005, to appear 2006 in Springer LNCS

van der Vet, Paul; Huibers, Theo; Binz, Pierre-Alain and Hofmann, Martin: ESF Workshop Sustainability and Governance of Web and GRID Resources in Functional Genomics. Comparative and Functional Genomics, accepted for publication

Zimmermann, Marc; Fluck, Juliane; Bui Thi, Le Thuy; Kolarik, Corinna; Kumpf, Kai; and Hofmann, Martin: Information Extraction in the Life Sciences: Perspectives for Medicinal Chemistry, Pharmacology and Toxicology. Current Topics in Medicinal Chemistry (CTMC), 2005; 5(8):785-96.

Fluck, Juliane; Zimmermann, Marc; Kurapkat, Günther and Hofmann, Martin: Information Extraction Technologies for the Life Science Industry. Drug Discovery Today – Technologies (DDT-T), accepted for publication

Daniel Hanisch, Katrin Fundel, Heinz-Theodor Mevissen, Ralf Zimmer and Juliane Fluck (2005). ProMiner: Rule based protein and gene entity recognition BMC: 2005, 6(Suppl 1):S14

J. Fluck, H. Deneke & C. Gieger (2005) Text mining in life sciences. Text Mining and its Applications to Intelligence, CRM and Knowledge Management; WIT press

J. Wermter, Juliane Fluck, Jannik Stroetgen, Stefan Geißler and Udo Hahn (2005) Recognizing noun phrases in biomedical text: An evaluation of lab prototypes and commercial chunker First International Symposium on Semantic Mining in Biomedicine (SMBM) - 10th -13th April, 2005

2004

Jones, C.; Bilofsky, H.; Ziegler, R., Hofmann, M. and Breton, V.: Grid enabled pharmaceutical R&D: PharmaGrids. White Paper of the European HealthGRID Organisation, August 2004 www.healthgrid.org

Solomonides, T. and Hofmann, M.: GRIDs for Epidemiological Studies. White Paper of the European HealthGRID Organisation, August 2004
www.healthgrid.org

Kumpf, K. and Hofmann, M.: Bioinformatics and the Semantic GRID. ERCIM News No. 59, October 2004

Philipp Wieder; Wolfgang Ziegler: Bringing Knowledge to Middleware – Grid Scheduling Ontology. CoreGRID Integration Workshop 2004, Dagstuhl, November 2004, Springer, 2006, CoreGRID Series, Future Generation Grids, p. 47 - 59

M. Zimmermann, A. Tresch, A. Maass and M. Hofmann. Drilling into a HTS data set of e. coli. Poster: 15th European Symposium on Quantitative Structure-Activity Relationships, Proceeding of the Euro-QSAR2004 Conference (2004).

C. Gieger, D. Hanisch, J. Fluck,  H.-T. Mevissen, A. Tresch, H. Deneke:
Using Text Mining Networks for the Context Specific Interpretation of Gene Expression Data
Biometrical Journal, Vol. 46, Supplement Abstracts of the Joint Meeting of the IBS-DR and the DAE, 2004, p.56

D. Hanisch, K. Fundel, H.-T. Mevissen, R. Zimmer, J. Fluck:
ProMiner: Organism specific protein name detection using approximate string matching
Embo Workshop A critical assessment of text mining methods in molecular biology Granada, Spain, March 28 -March 31, 2004

M. Zimmermann:
Rechnerunterstützte Analyse von HTS-Daten
 Shaker Verlag, 2004, ISBN: 3-8322-2703-2

T. Lengauer, C. Lemmen, M. Rarey, M. Zimmermann:
Novel technologies for virtual screening
Drug Discovery Today, vol. 9, iss. 1, pp. 27-34

2003

van der Vet, P.E.; Hofmann, M.; Huibers, T.W.C.; Roosendaal, H.E.: Managing a portal of digital web resources by content syndication. P.M.E. De Bra (ed.), Proceedings Informatiewetenschap 2003, Computer Science Report 03-11, Technische Universiteit Eindhoven, 2003, pp. 99—105

M. Zimmermann, M. Rarey, T. Naumann, H. Matter, G. Hessler, T. Lengauer:
Extracting Knowledge from High-Throughput Screening Data: Towards the Generation of Biophore Models
Proceedings of the 14th European Symposium on Quantitative Structure-Activity Relationships, to appear (2003)

C. Gieger, H. Deneke, J. Fluck:
The Future of Text Mining in Genome-based Clinical Research
BIOSILICO: Vol. 1, pp. 97-102

N. von Öhsen, I. Sommer, R. Zimmer:
Profile-Profile Alignment: A Powerful Tool For Protein Structure Prediction
Proc. PSB '03, pp. 252-263

A. Zien, J. Fluck, R. Zimmer, Th. Lengauer:
Microarrays: How Many Do You Need?
Journal of Computational Biology, vol. 10, pp. 653-667

D. Hanisch, J. Fluck, H.-T. Mevissen, R. Zimmer:
Playing Biology's Name Game: Identifying Protein Names in Scientific Texts
Proc. PSB '03, pp. 403-414

2002

I. Sommer, A. Zien, N. von Öhsen, R. Zimmer, T. Lengauer:
Confidence Measures for Protein Fold Recognition
Bioinformatics 18 (6), pp. 802-812

A. Zien, J. Fluck, R. Zimmer, T. Lengauer:
Microarrays: How Many Do You Need?
Proc. RECOMB '02, pp. 321-330

2001

S. Niland, A. Cremer, J. Fluck, J. A. Eble, T. Krieg, S. Sollberg:
Contraction-dependent apoptosis of normal dermal fibroblasts
J. Invest Dermatol. 116 (5), pp. 686-692

I. Sommer, N. von Öhsen, A. Zien, R. Zimmer, Th. Lengauer:
Confidence Measures for Fold Recognition
Proc. GCB '01, pp. 26-33

N. von Öhsen, R. Zimmer:
Improving profile-profile alignments via log average scoring
in: O. Gascuel, B.M. E. Moret (eds.): Algorithms in Informatics: Proc. WABI 2001, Springer Verlag Berlin Heidelberg, (Lecture notes in computer science ; Vol. 2149), pp. 11-26

R. Grübel, N. von Öhsen:
Tail expansions for random record distributions
Math. Proc. Camb. Phil. Soc. 130, pp. 365-382

2000

A. Zien, R. Küffner, T. Mevissen, R. Zimmer, T. Lengauer:
Identification of Drug Target Proteins
ERCIM News 43, pp. 16-17

C. Lemmen, M. Zimmermann, T. Lengauer:
Molecular Superpositioning as an Tool for Virtual Database Screening
Perspectives in Drug Discovery and Design 20, pp.43-6