---
title: BioJava:BioJavaInside
permalink: wiki/BioJava%3ABioJavaInside
---
**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](http://www.genostar.com/): Software
suite dedicated to the exploration of connections among genes,
proteins, reactions and metabolic pathways
- [DengueInfo](http://www.dengueinfo.org/): a Dengue genome
information portal that uses BioJava in the middleware and talks to
a biosql database.
- [Dazzle](http://www.derkholm.net/thomas/dazzle): A BioJava based DAS
server.
- [BioSense](http://www.idbs.com/InforSenseSuite/BioSense): A plugin
for the InforSense Suite, an analytics software platform by
[IDBS](http://www.idbs.com/) that unitizes BioJava.
- [Bioclipse](http://www.bioclipse.net): A free, open source,
workbench for chemo- and bioinformatics with powerful editing and
visualization capabilities for molecules, sequences, proteins,
spectra etc.
- [PROMPT](http://webclu.bio.wzw.tum.de/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](http://www.cytoscape.org): An open source bioinformatics
software platform for visualizing molecular interaction networks.
- [BioWeka](http://www.bioweka.org): An open source biological data
mining application.
- [Geneious](http://www.biomatters.com): A molecular biology toolkit.
- [MassSieve](http://www.ncbi.nlm.nih.gov/staff/slottad/MassSieve/):
An open source application to analyze mass spec proteomics data.
- [Strap](http://www.charite.de/bioinf/strap/): A tool for multiple
sequence alignment and sequence based structure alignment.
- [Jstacs](http://www.jstacs.de): A Java framework for statistical
analysis and classification of biological sequences
- [jLSTM](http://www.bioinf.jku.at/software/LSTM_protein/) "Long
Short-Term Memory" for protein classification
- [LaJolla](http://lajolla.sourceforge.net) 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](http://www.geneinfinity.org/genbeans/index.html): A rich
client platform for bioinformatics primarily focused on molecular
biology and sequence analysis.
- [eQuant](http://bioservices.hs-mittweida.de/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](http://scholar.google.com/scholar?cites=3048631375755320177&as_sdt=2005&sciodt=0,5&hl=en).
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](http://www.mdpi.com/1999-4893/2/2/692)
More biojava publications can be found at [Google
Scholar](http://scholar.google.com/scholar?q=biojava).