• Extraction of Regulatory Gene Expression Networks from PubMed |accepted to appear in Proceedings of the ACL 2004 Conference, Barcelona, Spain, 2004
  Ulrike Wittig, Andreas Saric, J., Jensen, L. J. , Ouzounova, R. , Rojas, I. and Bork, P.
• Classi?cation of chemical compounds to support complex queries in a pathway Database . |Comp Funct Genom 2004; 5: p 156-162
  Ulrike Wittig, Andreas Weidemann, Renate Kania, Christian Peiss and Isabel Rojas
  

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
  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