2010

Neil Swainston, Martin Golebiewski, Hanan L. Messiha, Naglis Malys, Renate Kania, Sylvestre Kengne, Olga Krebs, Saqib Mir, Heidrun Sauer-Danzwith, Kieran Smallbone, Andreas Weidemann, Ulrike Wittig, Douglas B. Kell, Pedro Mendes, Wolfgang Müller, Norman W. Paton, and Isabel Rojas (2010).
Enzyme kinetics informatics: from instrument to browser.
FEBS Journal, 277(18):3769-3779, September

Ulrike Wittig, Renate Kania, Isabel Rojas, and Wolfgang Müller (2010).
Herausforderungen bei der extraktion von biochemischen daten aus der literatur.
In Lecture Notes in Informatics (LNI) - Proceedings, Series of the Gesellschaft für Informatik (GI).

2009

Ulrike Wittig, Renate Kania, Martin Golebiewski, Andreas Weidemann, Olga Krebs, Saqib Mir, Henriette Engelken, Heidrun Sauer-Danzwith, Wolfgang Müller, and Isabel Rojas (2009).
Understanding Biochemical Reactions - SABIO-RK: Database for Reaction Kinetics.
BIOforum Europe 6-7:28 and GIT Laboratory Journal Europe 7-8:14.

Wolfgang Müller, Olga Krebs, Isabel Rojas, Katy Wolstencroft, Stuart Owen, Serjgejs Alexejevs, Carole Goble, and Jacky Snoep (2009).
SysMO-DB: Just Enough Exchange for Systems Biology Data and Models.
In Proceedings of Microsoft Research eScience Workshop, Pittsburgh, USA, October 15-17, 2009. link

Henriette Engelken, Martin Golebiewski, Meik Bittkowski, Fritz Hamm, Jasmin Saric, Ulrike Wittig, Wolfgang Müller, Uwe Reyle, and Isabel Rojas (2009).
Flache und semantische Verarbeitung von Namen biochemischer Verbindungen.
In INFORMATIK 2009 - Im Focus das Leben, Beiträge der 39. Jahrestagung der Gesellschaft für Informatik e.V. (GI), Lübeck, Germany, 28.September - 02.Oktober 2009, LNI.

Andreas Dräger, Hannes Planatscher, Dieudonné Motsou Wouamba, Adrian Schröder, Michael Hucka, Lukas Endler, Martin Golebiewski, Wolfgang Müller, and Andreas Zell (2009).
SBML2L^ATEX: Conversion of SBML files into human-readable reports.
Bioinformatics (Advance Access published on April 3, 2009), 25(11):1455-6. DOI link

Saqib Mir, Steffen Staab, and Isabel Rojas (2009).
Site-Wide Wrapper Induction for Life Science Deep Web Databases.
In DILS-2009, Proceedings of the Data Integration in the Life sciences Workshop, Manchester, UK, July 20-22, LNCS, Springer, 2009.

Henriette Engelken (2009).
A System for Semantic Analysis of Chemical Compound Names.
In Proceedings of the ACL-IJCNLP 2009 Student Research Workshop, Singapore, August 2-7, 2009, pages 36-44. Association for Computational Linguistics. PDF

Saqib Mir, Steffen Staab, and Isabel Rojas (2009).
Web-Prospector - An Automatic, Site-Wide Wrapper Induction Approach for Scientific Deep-Web Databases.
In BTW 2009, Datenbanksysteme für Business, Technologie und Web, Tagungsband der 13. BTW-Konferenz (German Database Conference), Münster, Germany, 2.-6.März 2009.

Adrian Hub, Daniel Blank, Andreas Henrich, and Wolfgang Müller (2009).
Picadomo: Faceted Image Browsing for Mobile Devices.
In Seventh International Workshop on Content-Based Multimedia Indexing Chania, Greece, June 03-05, 2009, pages 249-254. IEEE Computer Society. DOI

Ulrike Wittig, Andreas Weidemann, Heidrun Sauer-Danzwith, Sylvestre Kengne, Isabel Rojas, and Wolfgang Müller (2009).
SABIO-RK: Kinetic Data for Reaction Mechanism Steps.
In Proceedings of the 4th International Beilstein Symposium on Experimental Standard Conditions of Enzyme Characterizations, Ruedesheim Rhein, Germany, 2009.

2008

Ulrike Wittig, Renate Kania, Martin Golebiewski, Olga Krebs, Saqib Mir, Andreas Weidemann, Henriette Engelken, and Isabel Rojas (2008).
Integration and Annotation of Kinetic Data of Biochemical Reactions in SABIO-RK.
In Proceedings of the 3rd International Beilstein Workshop on "Experimental Standard Conditions of Enzyme Characterizations", Ruedesheim am Rhein, Germany, 2007. PDF

Doug Howe, Maria Costanzo, Petra Fey, Takashi Gojobori, Linda Hannick, Winston Hide, David P. Hill, Renate Kania, Mary Schaeffer, Susan St. Pierre, Simon Twigger, Owen White, and Seung Yon Rhee Yon (2008).
Big data: The future of biocuration.
Nature, (455):47-50. DOI link

Andreas Weidemann, Stefan Richter, Matthias Stein, Sven Sahle, Ralph Gauges, Razif Gabdoulline, Irina Surovtsova, Nils Semmelrock, Bruno Besson, Isabel Rojas, Rebecca Wade, and Ursula Kummer (2008).
SYCAMORE - A SYstems biology Computational and Analysis MOdeling Research Environment.
Bioinformatics, 24(12):1463-1464. DOI link

Jasmin Saric, Henriette Engelken, and Uwe Reyle (2008).
Discovering biomedical knowledge from Literature.
In J. D. Thompson, C. Schaeffer-Reiss, and M. Ueffing, editors, Functional Proteomics (Methods in Molecular Biology). Humana Press.

2007

Ulrike Wittig, Renate Kania, Martin Golebiewski, Olga Krebs, Saqib Mir, Andreas Weidemann, Henriette Engelken, and Isabel Rojas (2007).
SABIO-RK: Database for biochemical reactions and their kinetics.
Journal of Inherited Metabolic Diseases, 30(6):997.

Olga Krebs, Martin Golebiewski, Renate Kania, Saqib Mir, Jasmin Saric, Andreas Weidemann, Ulrike Wittig, and Isabel Rojas (2007).
SABIO-RK: A data warehouse for biochemical reactions and their kinetics.
Journal of Integrative Bioinformatics. PDF

Isabel Rojas, Martin Golebiewski, Renate Kania, Olga Krebs, Saqib Mir, Andreas Weidemann, and Ulrike Wittig (2007).
SABIO-RK: A database for biochemical reactions and their kinetics.
BMC Systems Biology, 1 (Suppl 1):S6. link

Martin Golebiewski, Saqib Mir, Renate Kania, Olga Krebs, Andreas Weidemann, Ulrike Wittig, and Isabel Rojas (2007).
Integration of SABIO-RK in workbenches for kinetic model design.
BMC Systems Biology, 1 (Suppl 1):P4. link

Massimiliano Ciaramita, Aldo Gangemi, Esther Ratsch, Jasmin Saric, and Isabel Rojas (2007).
Bridging the Gap between Text and Knowledge - Selected Contributions to Ontology Learning and Population from Text, chapter Unsupervised Learning of Semantic Relations for Molecular Biology Ontologies.
IOS Press.

Isabel Rojas-Muijca, Martin Golebiewski, Renate Kania, Olga Krebs, Saqib Mir, Andreas Weidemann, and Ulrike Wittig (2007).
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, 2006. PDF

Isabel Rojas, Martin Golebiewski, Renate Kania, Olga Krebs, Saqib Mir, Andreas Weidemann, and Ulrike Wittig (2007).
Storing and annotating of kinetic data.
In Silico Biol., 7 (Suppl 2)(17822389):37-44. link

2006

Renate Kania, Ulrike Wittig, Martin Golebiewski, Olga Krebs, Andreas Weidemann, Saqib Mir, and Isabel Rojas (2006).
A Curated Database for Reaction Kinetics.
In Proceedings of the 1st International Symposium on Systems Biology (From genome to In Silico and back), Murcia, Spain, June 2006.

Lars J. Jensen, Jasmin Saric, and Peer Bork (2006).
Literature mining for the biologist: from information retrieval to biological discovery.
Nat. Rev. Genet., 7(2):119-29.

Gerhard Kremer, Stefanie Anstein, and Uwe Reyle (2006).
Analysing and Classifying Names of Chemical Compounds with CHEMorph.
In Sophia Ananiadou and Juliane Fluck, editors, Proceedings of the Second International Symposium on Semantic Mining in Biomedicine, Friedrich-Schiller-Universität Jena, Germany, 2006, pages 37-43. PDF

Ulrike Wittig, Martin Golebiewski, Renate Kania, Olga Krebs, Saqib Mir, Andreas Weidemann, Stefanie Anstein, Jasmin Saric, and Isabel Rojas (2006).
SABIO-RK: integration and curation of reaction kinetics data.
Lecture Notes in Computer Science, (4075):94-103.

2005

Isabel Rojas, Renate Kania, Ulrike Wittig, Andreas Weidemann, Martin Golebiewski, and Olga Krebs (2005).
SABIO-RK - a reaction kinetics database.
In Proceedings of the 4th Workshop on Computation of Biochemical Pathways and Genetic Networks, BioSim, Heidelberg, Germany, September 2005, pages 63-67.

Massimiliano Ciaramita, Aldo Gangemi, Esther Ratsch, Jasmin Saric, and Isabel Rojas (2005).
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-August 2005.

Danila Baldessari, Yongchol Shin, Olga Krebs, Rainer König, Tetsuya Koide, Arunachalam Vinayagam, Ursula Fenger, Makoto Mochii, Chie Terasaka, Atsushi Kitayama, Daniel Peiffer, Naoto Ueno, Roland Eils, Ken W. Cho, and Christoph Niehrs (2005).
Global gene expression profiling and cluster analysis in Xenopus laevis.
Mechanism of Development, 122(3):441-75.

Jasmin Saric, Lars J. Jensen, Rosita Ouzounova, Isabel Rojas, and Peer Bork (2005).
Extraction of regulatory gene/protein networks from Medline.
Bioinformatics, (16046493).

2004

Ulrike Wittig, Andreas Weidemann, Renate Kania, Christian Peiss, and Isabel Rojas (2004).
Classification of chemical compounds to support complex queries in a pathway database.
In Comparative and Functional Genomics, 5:156-162,

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

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

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

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

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

2003

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

Sinan Güler, Andreas Eberhart, and Isabel Rojas (2003).
Web-based exchange of biochemical information.
Bioinformatics, 19(13):1730-1.

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

2002

Isabel Rojas, Luca Bernardi, Esther Ratsch, Renate Kania, Ulrike Wittig, and Jasmin Saric (2002).
A database system for the analysis of biochemical pathways.
In Silico Biol, 2(0007).

Luca Bernardi, Esther Ratsch, Renate Kania, Jasmin Saric, and Isabel Rojas (2002).
Interdisciplinary Work: The Key to a Functional Genomics.
IEEE Intelligent Systems.

Uwe Reyle and Jasmin Saric (2002).
Corpus driven information extraction.
In Proceedings of the EFMI Workshop on Natural Language Processing in Biomedical Applications, pages 87-91.

2001

Uwe Reyle and Jasmin Saric (2001).
Ontology Driven Information Extraction.
In Proceedings of the 19th Twente Workshop on Language Technology, University of Twente, Enschede, Netherlands, 2001.

Ulrike Wittig and Ann De Beuckelaer (2001).
Analysis and comparison of metabolic pathway databases.
Briefings in Bioinformatics , 2, pages 126-142.

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

Moritz Y. Becker and Isabel Rojas (2001).
A graph layout algorithm for drawing metabolic pathways.
Bioinformatics, 17:461-467.

2000

Michael Baumhackl, Isabel Rojas, and Thomas Mueck (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 2000.

Andreas Kohlbecker, Ulrike Wittig, Ralph Gauges, Moritz Becker, Michael Baumhackl, Ann De Beuckelaer, Erich Bornberg-Bauer, and Isabel Rojas (2000).
A database system for biochemical pathway analysis.
In German Conference on Bioinformatics, Heidelberg, October 2000.

1999

Isabel Rojas and Erich Bornberg-Bauer (1999).
A Comprehensible Database Model for the Computation of Biochemical Pathways.
In Erich Bornberg-Bauer, Ann DeBeuckelaer, Ursula Kummer, and Ursula Rost, editors, Proceedings of the Workshop on Computation of Biochemical Pathways and Genetic Networks, Berlin, Germany, 1999. pages 97-103.