If you use BioJava in an application or publication please cite:
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.
In 2008 we published our first Application note. As of Nov. 2014 Google Scholar counts more than 170 citations.
<pubmed name="BioJava2008"> 18689808 </pubmed>
Below a list of publications in which BioJava has been used. If you know of other publications please add them.
<pubmed name="hidalgo1998"> 9564045 </pubmed> <pubmed name="jacobs2000">10592251 </pubmed> <pubmed name="xie2000">12761070</pubmed> <pubmed> 12016048</pubmed> <pubmed> 12493080 </pubmed>
<pubmed> 12626717</pubmed> <pubmed> 12967955 </pubmed> <pubmed> 15130816 </pubmed> <pubmed> 14594704 </pubmed> <pubmed> 14592990 </pubmed> <pubmed> 14668218</pubmed> <pubmed> 12824432 </pubmed> <pubmed> 14583100</pubmed>
<pubmed> 15044242 </pubmed> <pubmed> 15215471 </pubmed> <pubmed> 15369604 </pubmed> <pubmed> 15247332 </pubmed> <pubmed> 14681429 </pubmed> <pubmed> 15610565 </pubmed>
<pubmed> 15537809</pubmed> <pubmed> 15760844</pubmed> <pubmed> 15572471 </pubmed> <pubmed> 15984937 </pubmed> <pubmed> 16083500 </pubmed> <pubmed> 15608201 </pubmed> <pubmed> 15640145 </pubmed> <pubmed> 16204122 </pubmed> <pubmed> 15905283 </pubmed> <pubmed> 16288651 </pubmed>
<pubmed> 16845037 </pubmed> <pubmed> 17002805 </pubmed> <pubmed> 16925840 </pubmed> <pubmed> 16469097</pubmed> <pubmed> 16789813</pubmed> <pubmed> 16990246</pubmed> <pubmed> 16402215</pubmed> <pubmed> 17054788 </pubmed> <pubmed> 16260186 </pubmed> <pubmed> 17000643</pubmed> <pubmed> 16423288</pubmed> <pubmed> 16845480 </pubmed> <pubmed> 16817977 </pubmed> <pubmed> 16845480</pubmed> <pubmed> 16817977</pubmed> <pubmed> 16837528</pubmed> <pubmed> 16872539</pubmed>
<pubmed> 17068077</pubmed> <pubmed> 17288609 </pubmed> <pubmed> 17238282</pubmed> <pubmed> 17237069 </pubmed> <pubmed> 17332025</pubmed> <pubmed> 17400476</pubmed> <pubmed> 17537825</pubmed> <pubmed> 17316423</pubmed>
<pubmed> 18061398</pubmed> <pubmed name="zajac2008">18061398</pubmed> <pubmed name="vernikos2008">18071028</pubmed> <pubmed name="liang2008">17054788</pubmed> <pubmed name="chalk2008">18397893</pubmed> <pubmed name="gront2008">18227118</pubmed>
See above for a link to all recent citations on Google Scholar.
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.