Publications

2015

Natalie J. Stanford, Katherine Wolstencroft, Martin Golebiewski, Renate Kania, Nick Juty, Christopher Tomlinson, Stuart Owen, Sarah Butcher, Henning Hermjakob, Nicolas Le Novère, Wolfgang Mueller, Jacky Snoep, Carole Goble (2015)
The evolution of standards and data management practices in systems biology
Molecular Systems Biology, doi: 10.15252/msb.20156053/ link

Falk Schreiber, Gary D. Bader, Martin Golebiewski, Michael Hucka, Benjamin Kormeier, Nicolas Le Novère, Chris Myers, David Nickerson, Björn Sommer, Dagmar Waltemath and Stephan Weise (2015)
Specifications of Standards in Systems and Synthetic Biology
Journal of Integrative Bioinformatics, doi: 10.2390/biecoll-jib-2015-258 PDF

Michael Hucka, David P. Nickerson, Gary D. Bader , Frank T. Bergmann, Jonathan Cooper, Emek Demir, Alan Garny, Martin Golebiewski, Chris J. Myers, Falk Schreiber, Dagmar Waltemath and Nicolas Le Novère (2015)
Promoting coordinated development of community-based information standards for modeling in biology: the COMBINE initiative
Frontiers in Bioengeneering and Biotechnologydoi: 10.3389/fbioe.2015.00019

Wolstencroft K, Owen S, Krebs O, Nguyen Q, Stanford NJ, Golebiewski M, Weidemann A, Bittkowski M, An L, Shockley D, Snoep JL, Mueller W, Goble C (2015)
SEEK: a systems biology data and model management platform
BMC Systems Biology, 9:33. doi: 10.1186/s12918-015-0174-y PDF

2014

Frank T. Bergmann, Richard Adams, Stuart Moodie, Jonathan Cooper, Mihai Glont, Martin Golebiewski, Michael Hucka, Camille Laibe, Andrew K. Miller, David P. Nickerson, Brett G. Olivier, Nicolas Rodriguez, Herbert M. Sauro, Martin Scharm, Stian Soiland-Reyes, Dagmar Waltemath, Florent Yvon, Nicolas Le Novère (2014)
COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project
BMC Bioinformatics, 15:369

Dagmar Waltemath, Frank T Bergmann, Claudine Chaouiya, Tobias Czauderna, Padraig Gleeson, Carole Goble, Martin Golebiewski, Michael Hucka, Nick Juty, Olga Krebs, Nicolas Le Novère, Huaiyu Mi, Ion I Moraru, Chris J Myers, David Nickerson, Brett G Olivier, Nicolas Rodriguez, Falk Schreiber, Lucian Smith, Fengkai Zhang, Eric Bonnet (2014)
Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE)
Standards in Genomic Sciences, 9:1285-1301

Ulrike Wittig, Maja Rey, Renate Kania, Meik Bittkowski, Lei Shi, Martin Golebiewski, Andreas Weidemann, Wolfgang Müller, and Isabel Rojas (2014)
Challenges for an enzymatic reaction kinetics database
FEBS Journal, 281(2):572-582 PDF

Ulrike Wittig, Renate Kania, Meik Bittkowski, Elina Wetsch, Lei Shi, Lenneke Jong, Martin Golebiewski, Maja Rey, Andreas Weidemann, Isabel Rojas, Wolfgang Müller (2014).
Data extraction for the reaction kinetics database SABIO-RK.
Perspectives in Science 1, 33–40

2013

Katherine Wolstencroft, Stuart Owen, Olga Krebs, Wolfgang Müller, Quyen Nguyen, Jacky L. Snoep, and Carole Goble (2013)
Semantic Data and Models Sharing in Systems Biology: The Just Enough Results Model and the SEEK Platform
The Semantic Web-ISWC 2013, 8219:212-227, January

Lei Shi, Lenneke Jong, Ulrike Wittg, Philippe Lucarelli, Markus Stepath, Stephanie Mueller, Lorenza Alice D`Alessandro, Klingmüller Ursula, and Müller Wolfgang (2013)
Excemplify: A Flexible Template Based Solution, Parsing and Managing Data in Spreadsheets for Experimentalists
Journal of Integrative Bioinformatics, 10(2):220, April

Finja Büchel, Nicolas Rodriguez, Neil Swainston, Clemens Wrzodek, Tobias Czauderna, Roland Keller, Florian Mittag, Michael Schubert, Mihai Glont, Martin Golebiewski, Martijn van Iersel, Sarah Keating, Matthias Rall, Michael Wybrow, Henning Hermjakob, Michael Hucka, Douglas. B. Kell, Wolfgang Müller, Pedro Mendes, ANdreas Zell, Claudine Chaouiya, Julio Saez-Rodriguez, Falk Schreiber, Camille Laibe, Andreas Dräger, and Nicolas Le Novère (2013)
Path2Models: large-scale generation of computational models from biochemical pathway maps
BMC Systems Biology, 7(1):116, November

2012

Ulrike Wittig, Renate Kania, Martin Golebiewski, Maja Rey, Lei Shi, Lenneke Jong, Enkhjargal Algaa, Andreas Weidemann, Heidrun Sauer-Danzwith, Saqib Mir, Olga Krebs, Meik Bittkowski, Elina Wetsch, Isabel Rojas, and Wolfgang Müller (2012)
SABIO-RK – database for biochemical reaction kinetics
Nucleic Acids Res, 40(D1):D790-6 PDF

2011

Mélanie Courtot, Nick Juty, Christian Knüpfer, Dagmar Waltemath, Anna Zhukova, Andreas Dräger, Michel Dumontier, Andrew Finney, Martin Golebiewski, Janna Hastings, Stefan Hoops, Sarah Keating, Douglas B Kell, Samuel Kerrien, James Lawson, Allyson Lister, James Lu, Rainer Machne, Pedro Mendes, Matthew Pocock, Nicolas Rodriguez, Alice Villeger, Darren J Wilkinson, Sarala Wimalaratne, Camille Laibe, Michael Hucka, and Nicolas Le Novère (2011)
Controlled vocabularies and semantics in systems biology
Molecular Systems Biology, 7:543, October

Wolfgang Müller, Isabel Rojas, Andreas Eberhart, Peter Haase, and Michael Schmidt (2011)
A-R-E: The Author-Review-Execute Environment
Procedia CS, 4:627-636

Lei Shi, Lenneke Jong, Wolfgang Müller, and Enkhjargal Algaa (2011)
50x Faster: Speeding up an SQL-based legacy system with few changes
In Lecture Notes in Informatics (LNI) – Proceedings, Series of the Gesellschaft für Informatik (GI), volume P-192

2010

Olga Krebs, Martin Golebiewski, Renate Kania, Andreas Weidemann, Ulrike Wittig, Isabel Rojas, and Wolfgang Müller (2010)
SabioRK-A Relational Database for Biochemical reactions and their Kinetics
In Computational Systems Biology, pages 51-57. Shaker Verlag,
ISBN 978-3-8322-9695-7

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)
SBML2LATEX: 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 Link

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 LINK

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. LINK

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.