Here is a list of articles citing Bioclipse. If you know more papers that should be listed here, please send an email to the mailing-list bioclipse-devel! 

Gupta RR, Gifford EM, Liston T, Waller CL, Hohman M, Bunin BA, Ekins S.: Using open source computational tools for predicting human metabolic stability and additional absorption, distribution, metabolism, excretion, and toxicity properties. Drug Metab Dispos. 2010 Nov;38(11):2083-90. doi: 10.1124/dmd.110.034918

Winschel V, Kratzig M: JBendge: An Object-Oriented System for Solving, Estimating and Selecting Nonlinear Dynamic Models. SFB 649 Discussion Papers SFB649DP2008-034, Sonderforschungsbereich 649, Humboldt University, Berlin, Germany 2008Willighagen EL,

Alvarsson J, Andersson A, Eklund M, Lampa S, Lapins M, Spjuth O, Wikberg JES: Linking the Resource Description Framework to Cheminformatics and Proteochemometrics. Accepted in Journal of Biomedical Semantics

Willighagen EL, et al.: Userscripts for the life sciences. BMC BIOINFORMATICS 2007, 8:487.Wagener J, Spjuth O, Willighagen EL, Wikberg JES: XMPP for cloud computing in bioinformatics supporting discovery and invocation of asynchronous Web services. BMC Bioinformatics 2009, 10(279).

Thielen B, Heinen S, Schomburg D: mSpecs: a software tool for the administration and editing of mass spectral libraries in the field of metabolomics. BMC Bioinformatics 2009, 10:229.

Spjuth O, Willighagen EL, Guha R, Wikberg JES: Towards interoperable and reproducible QSAR analyses: Exchange of data sets. Journal of Cheminformatics 2010, 2:5.

Carlsson L,Spjuth O, Adams S, Glen R. C, and Boyer S: Use of historic metabolic biotransformation data as a means of anticipating metabolic sites using MetaPrint2D and Bioclipse BMC Bioinformatics 2010, 11:362

Spjuth O, Carlsson L, Eklund M, Boyer S: Integrated decision support for chemical liability. Submitted.

Spjuth O: Bioclipse: Integration of Data and Software in the Life Sciences. PhD thesis, Uppsala University 2009.

Spjuth O, Alvarsson J: Bioclipse 2: Towards integrated biocheminformatics. EMBnet news 2009.

Smith JC, Lambert JP, Elisma F, Figeys D: Proteomics in 2005/2006: Developments, applications and challenges. ANALYTICAL CHEMISTRY 2007, 79(12):4325–4343.

Munteanu CR, Magalhaes AL: Prot-2S; a new python web tool for protein secondary structure studies. Int. J. Bioinformatics Res. Appl. 2009, 5(4):402–416.

Mrozek D, Mastej A, Malysiak B: Protein Molecular Viewer for Visualizing Structures Stored in the PDBML Format. In Information Technologies in Biomedicine 2008:377–386.

Lapins M, Wikberg JES: Proteochemometric Modeling of Drug Resistance over the Mutational Space for Multiple HIV Protease Variants and Multiple Protease Inhibitors. JOURNAL OF CHEMICAL INFORMATION AND MODELING 2009, 49(5):1202– 1210.

Kuhn T, Zielesny A, Steinbeck C: Creating chemo- and bioinformatics workflows, further developments within the CDK-Taverna Pro ject. Chemistry Central Journal 2009, 3(Suppl 1):P42,

Kuhn S, Torrance G, Steinbeck C: Components for computer-assisted structure elucidation 2009,

Kuhn S, et al.: Chemical markup, XML, and the world wide web. 7. CMLSpect, an XML vocabulary for spectral data. JOURNAL OF CHEMICAL INFORMATION AND MODELING 2007, 47(6):2015–2034.

Kind T, Leamy T, Leary JA, Fiehn O: Software platform virtualization in chemistry research and university teaching. J Cheminform 2009, 1:18.

Kahlem P, et al.: ENFIN - A European network for integrative systems biology. COMPTES RENDUS BIOLOGIES 2009, 332(11):1050–1058.

Guha R, et al.: Advances in Cheminformatics Methodologies and Infrastructure to Support the Data Mining of Large, Heterogeneous Chemical Datasets. CURRENT COMPUTER-AIDED DRUG DESIGN 2010, 6:50–67.

Guha R, et al.: Improving Usability and Accessibility of Cheminformatics Tools for Chemists through Cyberinfrastructure and Education 2007

Eklund M, Spjuth O, Wikberg JES: An eScience-Bayes strategy for analyzing omics data. Submitted.

Eklund M, Spjuth O, Wikberg JES: The (CC2)-C-1: A framework for simultaneous model selection and assessment. BMC BIOINFORMATICS 2008, 9:360.

Wikberg JES, Spjuth O, Eklund M and Lapins M. Chemoinformatics taking Biology into Account: Proteochemometrics. In: Computational Approaches in Cheminformatics and Bioinformatics (Eds R. Guha and A. Bender . Wiley, 2010). ISBN: 978-0-470-38441-1