2007 -- now

2006:

Literature mining for the biologist: from information retrieval to biological discovery |  Nat. Rev. Genet. 2006 Feb;7(2):119-29.
L.J. Jensen, J. Saric and P. Bork

SABIO-RK (System for the Analysis of Biochemical Pathways Reaction Kinetics)  |  In proceedings of the 2nd International Symposium on "Experimental Standard Conditions of Enzyme Characterizations". Ruedesheim am Rhein, Germany, March 2006. (To appear)
Rojas-Muijca, I., Golebiewski, M., Kania R., Krebs, O., Mir, S., Weidemann, A. and Wittig, U.

SABIO-RK: integration and curation of reaction kinetics data  |  Lecture Notes in Computer Science, 4075: 94-103
Wittig U, Golebiewski M, Kania R, Krebs O, Mir S, Weidemann A, Anstein S, Saric J, Rojas I.

A Curated Database for Reaction Kinetics |  In proceeding of the 1st International Symposium on Systems Biology (From genome to In Silico and back). June 1-2, 2006. Murcia, Spain (to appear)
Kania, R., Wittig, U., Golebiewski, M., Krebs, O., Weidemann, A., Mir, S. and Rojas, I.

2005:

SABIO-RK - a reaction kinetics database |  Proceedings of the 4th Workshop on Computation of Biochemical Partways and Genetic Networks, BioSim, September 12-13, Heidelberg, Germany,  pp. 63-67 (2005)
Rojas, I., Kania, R., Wittig, U., Weidemann, A., Golebiewski, M., and Krebs, O.

Unsupervised Learning of Semantic Relations between Concepts of a Molecular Biology Ontology | In proceedings of the Nineteenth International Joint Conference on Artificial Intelligence, Edinburgh, UK, July 30th - August 5th.  (2005)
Ciaramita, M., Gangemi, A., Ratsch, E., Saric, J. and Rojas, I.

SABIO-RK - a reaction kinetics database. | Poster at the Sixth International Conference on Systems Biology  (ICSB 2005). October 19-24, Boston, Massachusetts, USA. (2005)
Andreas Weidemann, Renate Kania, Ulrike Wittig, Martin Golebiewski, Olga Krebs and Isabel Rojas.

Global gene expression profiling and cluster analysis in Xenopus laevis. | Mechanism of  Development,  Mar;122(3): 441-75  (2005)
Baldessari D, Shin Y, Krebs O, Konig R, Koide T, Vinayagam A, Fenger U, Mochii M, Terasaka C, Kitayama A, Peiffer D, Ueno N, Eils R, Cho KW, Niehrs C.

Extraction of regulatory gene/protein networks from Medline |   Bioinformatics, PMID: 16046493 (2005)
J. Saric , L. J. Jensen, R. Ouzounova, I. Rojas and P. Bork

SABIO-RK: a reaction kinetics database. | Poster and Talk at the First International Biocurators Meeting, December 8-11,  Asilomar Conference Center, Pacific Grove, CA (2005)
Renate Kania, Ulrike Wittig, Martin Golebiewski, Andreas Weidemann, Olga Krebs, Isabel Rojas. 


2004:

Classification of chemical compounds to support complex queries in a pathway database. | In: Comparative and Functional Genomics, v.5,  pp.156-162 (2004)
Wittig U, Weidemann A, Kania R, Peiss C, Rojas I .

Extraction of Regulatory Gene Expression Networks from PubMed |  Proceedings of the ACL 2004 Conference, Barcelona, Spain, July 21-26, (2004)
Jasmin Saric, Lars J. Jensen, Rosita Ouzounova, Isabel Rojas and Peer Bork

Modelling gene expression. |  Proceedings of the 4th International Workshop on Network Tools and Application is Biology (Nettab), Camerino, Italy, September 5-7.(2004)
Jasmin Saric, Isabel Rojas, Esther Ratsch, Renate Kania, Ulrike Wittig and Aldo Gangemi

Web-based visualisation of the transcriptional control network of Escheriachia Coli |   In Silico Biol 4,0042 (2004)
Nestor, Sosa, Andreas Kremling, Esther Ratsch and Isabel Rojas

The Mycoplasma pneumoniae Database.  |  15th IOM (International Organisation for Mycoplasmology ) Congress, Athens, GA, US. July 11-16, 2004    Isabel Rojas, Ulrike Wittig, Renate Kania, Esther Ratsch, Andreas Weidemann and Olga Krebs

SABIO: A system to query and analyse biochemical pathways  |Poster at the 5th International Conference on Systems Biology (ICSB), Heidelberg, Germany, October 9-13, 2004.
Rojas, I., Krebs, O., Wittig, U., Kania, R., Weidemann, A.

Large-scale extraction of gene regulation for model organisms in an ontological context |  In In Silico Biology 5, 0004 (2004)
Jasmin Saric, Lars J. Jensen and Isabel Rojas

SABIO: a System to Support the Analysis of Biochemical Pathways. |   Poster at the 12th International Conference on Intelligent Systems for Molecular Biology (ISMB); 3rd European Conference on Computational Biology (ECCB), Glasgow, UK July 31-August 4 2004
Isabel Rojas, Ulrike Wittig, Renate Kania, Esther Ratsch, Andreas Eberhart and Olga Krebs

2003:

Notes on the use of ontologies in the biochemical domain |In Silico Biol. 4, 0009 (2003).
Isabel Rojas, Esther Ratsch, Jasmin Saric and Ulrike Wittig   

Web-based exchange of biochemical information |Bioinformatics. 2003 Sep 1;19(13):1730-1
Guler S, Eberhart A, Rojas I  

Developing a protein-interactions ontology |Comparative and Functional Genomics Feb. 2003. 4(1):85-89
Esther Ratch, Jörg Schultz, Jasmin Saric, Philipp Cimiano Lavin, Ulrike Wittig, Uwe Reyle and Isabel Rojas  


2002:

A database system for the analysis of biochemical pathways | In Silico Biol 2,0007 (2002)
Isabel Rojas I, Bernardi L, Ratsch E, Kania R, Wittig U, Saric J  

Interdisciplinary Work: The Key to a Functional Genomics | IEEE Intelligent Systems, May/June 2002 (under Mining Information for functional genomics), p 66-68.
Luca Bernardi, Esther Ratsch, Renate Kania, Jasmin Saric and Isabel Rojas   

Corpus Driven Information Extraction | Proccedings of the EFMI Workshop on Natural Languages Processing in Biomedical Applications, 87-91
Reyle, Uwe and Saric, Jasmin   

Integration and Visualisation of Experimental Data (Poster) | European Conference on Computational Biology, Saarbrücken, Germany, October 6-9, 2002
Hella Knäble, Esther Ratsch, Renate Kania, Ulrike Wittig, Isabel Rojas   


2001:

Ontology Driven Information Extraction | Proceedings of the nineteenth Twente Workshop on Language Technology, University of Twente, Enschede, Netherlands, 2001
Reyle, Uwe and Saric, Jasmin   

Analysis and comparison of metabolic pathway databases | Briefings in Bioinformatics , 2, 126-142
Ulrike Wittig, De Beuckelaer, Ann  

Meeting the Spirit of History | In Proceedings of the International Symposium on Virtual Reality, Archaeology and Cultural Heritage, VAST 2001, Glyfada, Nr Athens, Greece. 28-30 November 2001
Ursula Kretschmer, Volker Coors, Ulrike Spierling, Dieter Grasbon, Rainer Malaka, Isabel Rojas  

A graph layout algorithm for drawing metabolic pathways | Bioinformatics, 17, 461-467
Moritz Y. Becker, Isabel Rojas  


2000:

Integrating Biomolecular Databases - XML and ORB approaches | In Proceedings of the 1st Workshop on XML and Object Technology of the 14th European Conference on Object-Oriented Programming, Sophia Antipolis, France, June 12, 2000
Michael Baumhackl, Isabel Rojas and Thomas Mueck   

Modellierung und Visualisierung von biochemischen Stoffwechselwegen | Bioinformatik-Industrietag, Bielefeld, February 2, 2000
Isabel Rojas, Ulrike Wittig, Andreas Kohlbecker, Michael Baumhackl   

A database system for biochemical pathway analysis | German Conference on Bioinformatics - GCB 2000, Heidelberg, October 5-7, 2000
Andreas Kohlbecker, Ulrike Wittig, Ralph Gauges, Moritz Becker, Michael Baumhackl, Ann De Beuckelaer, Erich Bornberg-Bauer, Isabel Rojas   


1999:

A Comprehensible Database Model for the Computation of Biochemical Pathways | In Proceedings of the Workshop on Computation of Biochemical Pathways and Genetic Networks (Bornberg-Bauer, DeBeuckelaer, Kummer, Rost, eds.), Logos, Berlin, 97-103
Isabel Rojas, Erich Bornberg-Bauer