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Jacob Koehler

This member of staff has left Rothamsted

2007

Hassani-Pak, K. , Hindle, M. , Taubert, J. , Winnenburg, R. , Rawlings, C. , Stoye, J. and Köhler, J. (2007) "Combining Sequence Similarity and Text Mining for Functional Annotation of Genes", 4th Integrative Bioinformatics conference (IB2007)

In Preparation

Köhler, J. , Boeck, L. , Everding, R. , Schiller, R. , Specht, M. and Wolf, O. A. R., A. "Ondex - Ontology Based Text Indexing and Querying, under Review"
Philippi, S. and Köhler, J. "Systems Biology: From Data to Knowledge - Obstacles in Biological Data Integration , under Review"

2008

Pesch, R. , Lysenko, A. , Hindle, M. , Hassani-Pak, K. , Thiele, R. , Rawlings, C. , Koehler, J. and Taubert, J. (2008) "Graph-Based Sequence Annotation Using a Data Integration Approach", J Integrative Bioinformatics, 5
See Paper

2007

Baldwin, T. K. , Winnenburg, R. , Urban, M. , Rawlings, C. , Köhler, J. and Hammond-Kosack, K. E. (2007) "Phi-Base: A Database of Experimentally Verified Pathogenicity, Virulence and Effector Genes in Fungal, Oomycete and Bacterial Pathogens of Animals and Plants.", In Abstracts 13th International Congress on Molecular Plant-Microbe Interactions, Sorrento July 2007
See Paper
Winnenburg, R. , Urban, M. , Beacham, A. , Baldwin, T. K. , Holland, S. , Lindeberg, M. , Hansen, P. D. , Rawlings, C. J. , Hammond-Kosack, K. E. and Koehler, J. (2007) "Phi-Base Update: Additions to the Pathogen-Host Interactions Database", Nucl. Acids Res., In Press
See Paper

2006

Baldwin, T. K., Winnenburg, R., Urban, M., Rawlings, C., Köhler, J. And Hammond-Kosack, K.E. (2006) "Phi-Base Provides Insights into Generic and Novel Themes of Pathogenicity. ", Mol. Plant. Microbe Interact. , 1451-1462
See Paper
Köhler, J. , Munn, K. , Rüegg, A. , Skusa, A. and Smith, B. (2006) "Quality Control for the Gene Ontology: Text- Mining Methodologies and Formal Design Principles - under Review", BMC Bioinformatics, 7
Köhler, J. , Philippi, S. , Specht, M. and Rueegg, A. (2006) "Ontology Based Text Indexing and Querying for the Seamntic Web", Knowledge based systems, 744-754
See Paper
Philippi, S. and Koehler, J. (2006) " Addressing the Problems with Life-Science Databases for Traditional Uses and Systems.", Nature Reviews Genetics, 7, 481-488
See Paper
Philippi, S. and Koehler, J. (2006) " Automated Structure Extraction and Xml Conversion of Life Science Database Flat Files", IEEE Transactions on Information Technology in Biomedicine, 10, 714-721
See Paper

2005

Richter, G. M. , Steuernagel, B. and Köhler, J. (2005) "Modelling Root Activity to Narrow the Gene- Environment Gap", Aspects of Applied Biology, 73, 133-140
Skusa, A. , Ruegg, A. and Köhler, J. (2005) "Extraction of Biological Networks from Scientific Literature", Briefings in Bioinformatics, 6, 263-276
Smith, B. , Ceusters, W. , Klagges, B. , Köhler, J. , Kumar, A. , Lomax, J. , Mungall, C. , Neuhaus, F. , Rector, A. and Rosse, C. (2005) "Relations in Biomedical Ontologies", Genome Biol, 6
See Paper

2004

Köhler, J. (2004) "Integration of Life Science Databases", Drugs Discovery Today: BioSilico, 2, 61-69
See Paper
Köhler, J. , Rawlings, C. , Verrier, P. , Mitchell, R. , Skusa, A. , Ruegg, A. and Philippi, S. (2004) "Linking Experimental Results, Biological Networks and Sequence Analysis Methods Using Ontologies and Generalized Data Structures", In Silico Biology, 5, Manuscript number in online journal: 0005.
Philippi, S. and Köhler, J. (2004) "Using Xml Technology for the Ontology-Based Semantic Integration of Life Science Databases", IEEE Trans Inf Technol Biomed, 8, 154-160

2003

Köhler, J. , Philippi, S. and Lange, M. (2003) "Semeda: Ontology Based Semantic Integration of Biological Databases", Bioinformatics, 19, 2420-2427

2002

Köhler, J. and Schulze-Kremer, S. (2002) "The Semantic Metadatabase (Semeda): Ontology Based Integration of Federated Molecular Biological Data Sources", In Silico Biol, 2, MS number in online journal: 0021

2000

Hills, J. M. , Thomason, J. C. , Davis, H. , Köhler, J. and Millett, E. (2000) "Exploratory Behaviour of Barnacle Larvae in Field Conditions", Biofouling, 16, 171-179
See Paper

1999

Köhler, J. , Hansen, P. D. and Wahl, M. (1999) "Colonization Patterns at the Substratum-Water Interface: How Does Surface Microtopography Influence Recruitment Patterns of Sessile Organisms?", Biofouling, 14, 237-248

2007

Taubert, J. , Hindle, M. , Hoekman, B. , Winnenburg, R. , Weile, J. , Sieren, K. P. , Baumbach, J. , Ernst, S. , Elsner, S. , Hassani-Pak, K. , Lysenko, A. , Philippi, S. , Yates, T. , Verrier, P. , Rawlings, C. and Koehler, J. (2007) "The Ondex Data Integration Framework.", Bioinformatics Open Source Conference (BOSC 2007)

2005

Baldwin, T. K. , Winnenburg, R. , Köhler, J. , Urban, M. and Hammond-Kosack, K. E. (2005) "Bioinformatic and Molecular Genetic Tools for Identifying Genes Involved in the Pathogenicity of Fusarium Graminearum on Wheat Ears", Abstracts ESF-EMBO Symposium on the Comparative Genomics of Eukaryotic Microorganisms,

2004

Rawlings, C. , Verrier, P. and Köhler, J. (2004) "Integration and Exploitation of Data Derived from Post-Genomic Technologies", BBSRC e-science workshop,
Smith, B. , Köhler, J. and Kumar, A. (2004) "On the Application of Formal Principles to Life Science Data: A Case Study in the Gene Ontology", First International Workshop on Data Integration in the Life Sciences (DILS 2004), 2994

2002

Chen, M. , Freier, A. , Köhler, J. and Rüegg, A. (2002) "The Biology Petri Net Markup Language", Promise '2002, 21, 150-161

2000

Köhler, J. , Lange, M. , Hofestädt, R. and Schulze-Kremer, S. (2000) "Logical and Semantic Database Integration", Bioinformatics and Biomedical Engineering, 77-80
See Paper

2009

Taubert, J. , Hindle, M. , Lysenko, A. , Weile, J. , Koehler, J. and Rawlings, C. (2009) "Linking Life Sciences Data Using Graph-Based Mapping", LNBI 5647, 16-30
See Paper