If you use BioJava in an application or publication please cite:

Projects

The following projects make use of BioJava. If you know of other projects please add them to the list.

• Metabolic Pathway Builder: Software suite dedicated to the exploration of connections among genes, proteins, reactions and metabolic pathways

• DengueInfo: a Dengue genome information portal that uses BioJava in the middleware and talks to a biosql database.

• Dazzle: A BioJava based DAS server.

• BioSense: A plugin for the InforSense Suite, an analytics software platform by IDBS that unitizes BioJava.

• Bioclipse: A free, open source, workbench for chemo- and bioinformatics with powerful editing and visualization capabilities for molecules, sequences, proteins, spectra etc.

• PROMPT: A free, open source framework and application for the comparison and mapping of protein sets. Uses BioJava for handling most input data formats.

• Cytoscape: An open source bioinformatics software platform for visualizing molecular interaction networks.

• BioWeka: An open source biological data mining application.

• Geneious: A molecular biology toolkit.

• MassSieve: An open source application to analyze mass spec proteomics data.

• Strap: A tool for multiple sequence alignment and sequence based structure alignment.

• Jstacs: A Java framework for statistical analysis and classification of biological sequences

• jLSTM “Long Short-Term Memory” for protein classification

• LaJolla Structural alignment of RNA and proteins using an index structure for fast alignment of thousands of structures. Including an easy to use command line interface. Open source at Sourceforge.

• GenBeans: A rich client platform for bioinformatics primarily focused on molecular biology and sequence analysis.

• eQuant: A model quality assessment server to state the reliability of protein structures.

Publications

In 2008 we published our first Application note. As of Nov. 2014 Google Scholar counts more than 170 citations.

18689808

Below a list of publications in which BioJava has been used. If you know of other publications please add them.

9564045 10592251 12761070 12016048 12493080

2003

12626717 12967955 15130816 14594704 14592990 14668218 12824432 14583100

2004

15044242 15215471 15369604 15247332 14681429 15610565

2005

15537809 15760844 15572471 15984937 16083500 15608201 15640145 16204122 15905283 16288651

2006

16845037 17002805 16925840 16469097 16789813 16990246 16402215 17054788 16260186 17000643 16423288 16845480 16817977 16845480 16817977 16837528 16872539

2007

17068077 17288609 17238282 17237069 17332025 17400476 17537825 17316423

2008

18061398 18061398 18071028 17054788 18397893 18227118

See above for a link to all recent citations on Google Scholar.

2009

Bauer, R.; Rother, K.; Moor, P.; Reinert, K.; Steinke, T.; Bujnicki, J. M.; Preissner, R. Fast Structural Alignment of Biomolecules Using a Hash Table, N-Grams and String Descriptors. Algorithms 2009, 2, 692-709. open access full text

More biojava publications can be found at Google Scholar.