Journal of Integrative Bioinformatics, Volume 4

Volume 4, Number 1, 2007

• Erhard Rahm, Toralf Kirsten, Jörg Lange:
  The GeWare data warehouse platform for the analysisof molecular-biological and clinical data.
  Electronic Edition (link) BibTeX
• Claudia Choi, Richard Münch, Boyke Bunk, Jens Barthelmes, Christian Ebeling, Dietmar Schomburg, Max Schobert, Dieter Jahn:
  Combination of a data warehouse concept with web services for the establishment of the Pseudomonas systems biology database SYSTOMONAS.
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• Olga Krebs, Martin Golebiewski, Renate Kania, Saqib Mir, Jasmin Saric, Andreas Weidemann, Ulrike Wittig, Isabel Rojas:
  SABIO-RK: A data warehouse for biochemical reactions and their kinetics.
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• Peter Walter, Sam Ansari, Volkhard Helms:
  The ABC (Analysing Biomolecular Contacts)-database.
  Electronic Edition (link) BibTeX
• Gautam Chaurasia, Yasir Iqbal, Christian Hänig, Hanspeter Herzel, Erich E. Wanker, Matthias E. Futschik:
  Flexible web-based integration of distributed large-scale human protein interaction maps.
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• Daniela Albrecht, Olaf Kniemeyer, Axel A. Brakhage, Matthias Berth, Reinhard Guthke:
  Integration of Transcriptome and Proteome Data from Human-Pathogenic Fungi by Using a Data Warehouse.
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• Alexander Hinneburg, Björn Egert, Andrea Porzel:
  Duplicate detection of 2D-NMR Spectra.
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• Martin Strauch, Jochen Supper, Christian Spieth, Dierk Wanke, Joachim Kilian, Klaus Harter, Andreas Zell:
  A Two-Step Clustering for 3-D Gene Expression Data Reveals the Main Features of the Arabidopsis Stress Response.
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• Stefan Jablonski, Matthias Färber, Bernhard Volz, Stefanie Genthner:
  Deriving biological applications from domain specific process models.
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• Antje Gaida, Steffen Neumann:
  MetHouse: Raw and Preprocessed Mass Spectrometry Data.
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• Hee-Jeong Jin, Jeong-Won Lee, Hwan-Gue Cho:
  A Reliable and Distributed LIMS for Efficient Management of the Microarray Experiment Environment.
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• Konrad Stark, Johann Eder, Kurt Zatloukal:
  Achieving k-anonymity in DataMarts used for gene expressions exploitation.
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• Christian Kuenne, Ivo Grosse, Inge Matthies, Uwe Scholz, Tatjana Sretenovic-Rajicic, Nils Stein, Andreas Stephanik, Burkhard Steuernagel, Stephan Weise:
  Using Data Warehouse Technology in Crop Plant Bioinformatics.
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Volume 4, Number 2, 2007

• Amitava Karmaker, Kihoon Yoon, Mark Doderer, Russell Kruzelock, Stephen Kwek:
  Identifying Transcription Regulatory Elements in the Human and Mouse Genomes Using Tissue-specific Gene Expression Profiles.
  Electronic Edition (link) BibTeX
• T. Shashi Rekha, Chanchal K. Mitra:
  Frequency Analysis of the Splice Site Regions in Different Organisms.
  Electronic Edition (link) BibTeX

Volume 4, Number 3, 2007

• Richard Banks, L. Jason Steggles:
  A High-Level Petri Net Framework for Genetic Regulatory Networks.
  Electronic Edition (link) BibTeX
• A. Yartseva, R. Devillers, H. Klaudel, François Képès:
  From MIN model to ordinary differential equations.
  Electronic Edition (link) BibTeX
• Jan Taubert, Klaus Peter Sieren, Matthew Hindle, Berend Hoekman, Rainer Winnenburg, Stephan Philippi, Christopher J. Rawlings, Jacob Köhler:
  The OXL format for the exchange of integrated datasets.
  Electronic Edition (link) BibTeX
• Sridhar Hariharaputran, Thoralf Töpel, Björn Brockschmidt, Ralf Hofestädt:
  VINEdb: a data warehouse for integration and interactive exploration of life science data.
  Electronic Edition (link) BibTeX
• Ela Hunt, Joanna Jakubowska, Caroline Bösinger, Moira C. Norrie:
  Defining Mapping Mashups with BioXMash.
  Electronic Edition (link) BibTeX
• Mounia Belmamoune, Fons J. Verbeek:
  Developmental Anatomy Ontology of Zebrafish: an Integrative semantic framework.
  Electronic Edition (link) BibTeX
• Bashar Ibrahim, Peter Dittrich, Stephan Diekmann, Eberhard Schmitt:
  Stochastic effects in a compartmental model for mitotic checkpoint regulation.
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• Jian Zhang, Zhiyuan Zhao, Jennifer Evershed, Guoying Li:
  Monophyletic clustering and characterization of protein families.
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• Matthias Lange, Axel Himmelbach, Patrick Schweizer, Uwe Scholz:
  Data Linkage Graph: computation, querying and knowledge discovery of life science database networks.
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• Intikhab Alam, Mike Cornell, Darren M. Soanes, Cornelia Hedeler, Han Min Wong, Magnus Rattray, Simon J. Hubbard, Nicholas J. Talbot, Stephen G. Oliver, Norman W. Paton:
  A Methodology for Comparative Functional Genomics.
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• Reza Samavi, Mariano P. Consens, Shahan Khatchadourian, Thodoros Topaloglou:
  Exploring PSI-MI XML Collections Using DescribeX.
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• Michael Telgkamp, Dirk Koschützki, Henning Schwöbbermeyer, Falk Schreiber:
  Community-based Linking of Biological Network Resources: Databases, Formats and Tools.
  Electronic Edition (link) BibTeX
• Matthias Oesterheld, Hans-Werner Mewes, Volker Stümpflen:
  Analysis of integrated biomolecular networks using a generic network analysis suite.
  Electronic Edition (link) BibTeX
• E. L. Souche, B. Hellemans, J. K. J. Van Houdt, A. Canario, S. Klages, R. Reinhardt, F. A. M. Volckaert:
  Mining for Single Nucleotide Polymorphisms in Expressed Sequence Tags.
  Electronic Edition (link) BibTeX
• Samantha Riccadonna, Giuseppe Jurman, Stefano Merler, Silvano Paoli, A. Quattrone, Cesare Furlanello:
  Supervised classification of combined copy number and gene expression data.
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• Jan Baumbach, Alexander Bunkowski, Sita Lange, Timm Oberwahrenbrock, Nils Kleinbölting, Sven Rahmann, Jörg Ingo Baumbach:
  IMS2 - An integrated medical software system for early lung cancer detection using ion mobility spectrometry data of human breath.
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• Matthias E. Futschik, Gautam Chaurasia, Anna Tschaut, Jenny Russ, M. Madan Babu, Hanspeter Herzel:
  Functional and Transcriptional Coherency of Modules in the Human Protein Interaction Network .
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• José A. Reyes, David Gilbert:
  Prediction of protein-protein interactions using one-class classification methods and integrating diverse biological data.
  Electronic Edition (link) BibTeX
• Sabah Khalid, Mohsin Khan, Alistair Symonds, Karl Fraser, Ping Wang, Xiaohui Liu, Suling Li:
  CIDA: An integrated software for the design, characterisation and global comparison of microarrays.
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• Anaïs Mottaz, Yum Lina Yip, Patrick Ruch, Anne-Lise Veuthey:
  Mapping protein information to disease terminologies.
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• Allyson L. Lister, Matthew R. Pocock, Anil Wipat:
  Integration of constraints documented in SBML, SBO, and the SBML Manual facilitates validation of biological models.
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• Joel Arrais, Bruno Santos, João Fernandes, Laura Carreto, Manuel A. S. Santos, José Luís Oliveira:
  GeneBrowser: an approach for integration and functional classification of genomics data.
  Electronic Edition (link) BibTeX
• Vaida Jakoniene, Patrick Lambrix:
  A Tool for Evaluating Strategies for Grouping of Biological Data.
  Electronic Edition (link) BibTeX
• Bernard de Bono, Imre Vastrik, Peter D'Eustachio, Esther Schmidt, Gopal Gopinath, David Croft, Marc Gillespie, Bijay Jassal, Suzanna Lewis, Lisa Matthews, Guanming Wu, Ewan Birney, Lincoln Stein:
  Reactome: An integrated expert model of human molecular processes and access toolkit.
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