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

{{Reference2012}}

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

* [http://www.genostar.com/ Metabolic Pathway Builder]: Software suite dedicated to the exploration of connections among genes, proteins, reactions and metabolic pathways

* [http://www.dengueinfo.org/ DengueInfo]: a Dengue genome information portal that uses BioJava in the middleware and talks to a biosql database.

* [http://www.derkholm.net/thomas/dazzle Dazzle]: A BioJava based DAS server.

* [http://www.idbs.com/InforSenseSuite/BioSense BioSense]: A plugin for the InforSense Suite, an analytics software platform by [http://www.idbs.com/ IDBS] that unitizes BioJava.

* [http://www.bioclipse.net Bioclipse]: A free, open source, workbench for chemo- and bioinformatics with powerful editing and visualization capabilities for molecules, sequences, proteins, spectra etc.

* [http://webclu.bio.wzw.tum.de/prompt PROMPT]: A free, open source framework and application for the comparison and mapping of protein sets. Uses BioJava for handling most input data formats.

* [http://www.cytoscape.org Cytoscape]: An open source bioinformatics software platform for visualizing molecular interaction networks.

* [http://www.bioweka.org BioWeka]: An open source biological data mining application.

* [http://www.biomatters.com Geneious]: A molecular biology toolkit.

* [http://www.ncbi.nlm.nih.gov/staff/slottad/MassSieve/ MassSieve]: An open source application to analyze mass spec proteomics data.

* [http://www.charite.de/bioinf/strap/ Strap]: A tool for multiple sequence alignment and sequence based structure alignment.

* [http://www.jstacs.de Jstacs]: A Java framework for statistical analysis and classification of biological sequences

* [http://www.bioinf.jku.at/software/LSTM_protein/ jLSTM] "Long Short-Term Memory" for protein classification 

* [http://lajolla.sourceforge.net 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.

* [http://www.geneinfinity.org/genbeans/index.html GenBeans]: A rich client platform for bioinformatics primarily focused on molecular biology and sequence analysis.

* [http://bioservices.hs-mittweida.de/equant/ 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 [http://scholar.google.com/scholar?cites=3048631375755320177&as_sdt=2005&sciodt=0,5&hl=en 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>

===2003=== 

<pubmed > 12626717</pubmed>
<pubmed > 12967955 </pubmed>
<pubmed > 15130816 </pubmed>
<pubmed > 14594704 </pubmed>
<pubmed > 14592990 </pubmed>
<pubmed > 14668218</pubmed>
<pubmed > 12824432 </pubmed>
<pubmed > 14583100</pubmed>

=== 2004 ===

<pubmed > 15044242 </pubmed>
<pubmed > 15215471 </pubmed>
<pubmed > 15369604 </pubmed>
<pubmed > 15247332 </pubmed>
<pubmed > 14681429 </pubmed>
<pubmed > 15610565 </pubmed>

=== 2005 ===

<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>

=== 2006 ===

<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>

=== 2007 ===

<pubmed > 17068077</pubmed>
<pubmed > 17288609 </pubmed>
<pubmed > 17238282</pubmed>
<pubmed > 17237069 </pubmed>
<pubmed > 17332025</pubmed>
<pubmed > 17400476</pubmed>
<pubmed > 17537825</pubmed>
<pubmed > 17316423</pubmed>

=== 2008 === 
<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.

=== 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. 
[http://www.mdpi.com/1999-4893/2/2/692 open access full text]

More biojava publications can be found at [http://scholar.google.com/scholar?q=biojava Google Scholar].