BioJava:BioJavaInside

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

BioJava: an open-source framework for bioinformatics in 2012
Andreas Prlic; Andrew Yates; Spencer E. Bliven; Peter W. Rose; Julius Jacobsen; Peter V. Troshin; Mark Chapman; Jianjiong Gao; Chuan Hock Koh; Sylvain Foisy; Richard Holland; Gediminas Rimsa; Michael L. Heuer; H. Brandstatter-Muller; Philip E. Bourne; Scooter Willis Bioinformatics 2012;

Contents

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.

R C G Holland, T A Down, M Pocock, A Prlić, D Huen, K James, S Foisy, A Dräger, A Yates, M Heuer, M J Schreiber
BioJava: an open-source framework for bioinformatics.
Bioinformatics: 2008, 24(18);2096-7
[PubMed:18689808] [Worldcat] [EZB] ##EZB_HD## [DOI] (I p)


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

E Hidalgo, V Leautaud, B Demple
The redox-regulated SoxR protein acts from a single DNA site as a repressor and an allosteric activator.
EMBO J.: 1998, 17(9);2629-36
[PubMed:9564045] [Worldcat] [EZB] ##EZB_HD## [DOI] (P p)

G H Jacobs, P A Stockwell, M J Schrieber, W P Tate, C M Brown
Transterm: a database of messenger RNA components and signals.
Nucleic Acids Res.: 2000, 28(1);293-5
[PubMed:10592251] [Worldcat] [EZB] ##EZB_HD## (P p)

Tao Xie, Leroy Hood
ACGT-a comparative genomics tool.
Bioinformatics: 2003, 19(8);1039-40
[PubMed:12761070] [Worldcat] [EZB] ##EZB_HD## (P p)

Mark Schreiber, Chris Brown
Compensation for nucleotide bias in a genome by representation as a discrete channel with noise.
Bioinformatics: 2002, 18(4);507-12
[PubMed:12016048] [Worldcat] [EZB] ##EZB_HD## (P p)

Konrad Büssow, Steve Hoffmann, Volker Sievert
ORFer--retrieval of protein sequences and open reading frames from GenBank and storage into relational databases or text files.
BMC Bioinformatics: 2002, 3();40
[PubMed:12493080] [Worldcat] [EZB] ##EZB_HD## (I p)


2003

Stein Aerts, Gert Thijs, Bert Coessens, Mik Staes, Yves Moreau, Bart De Moor
Toucan: deciphering the cis-regulatory logic of coregulated genes.
Nucleic Acids Res.: 2003, 31(6);1753-64
[PubMed:12626717] [Worldcat] [EZB] ##EZB_HD## (I p)

Diego di Bernardo, Thomas Down, Tim Hubbard
ddbRNA: detection of conserved secondary structures in multiple alignments.
Bioinformatics: 2003, 19(13);1606-11
[PubMed:12967955] [Worldcat] [EZB] ##EZB_HD## (P p)

Chris M Brown, Grant Jacobs, Peter Stockwell, Mark Schreiber
Detection of signals in mRNAs that influence translation.
Appl. Bioinformatics: 2003, 2(3 Suppl);S47-51
[PubMed:15130816] [Worldcat] [EZB] ##EZB_HD## (P p)

A Carbone, A Zinovyev, F Képès
Codon adaptation index as a measure of dominating codon bias.
Bioinformatics: 2003, 19(16);2005-15
[PubMed:14594704] [Worldcat] [EZB] ##EZB_HD## (P p)

Olga L Gurvich, Pavel V Baranov, Jiadong Zhou, Andrew W Hammer, Raymond F Gesteland, John F Atkins
Sequences that direct significant levels of frameshifting are frequent in coding regions of Escherichia coli.
EMBO J.: 2003, 22(21);5941-50
[PubMed:14592990] [Worldcat] [EZB] ##EZB_HD## [DOI] (P p)

Yihua Huang, Tianyun Ni, Lei Zhou, Stanley Su
JXP4BIGI: a generalized, Java XML-based approach for biological information gathering and integration.
Bioinformatics: 2003, 19(18);2351-8
[PubMed:14668218] [Worldcat] [EZB] ##EZB_HD## (P p)

H Sugawara, S Miyazaki
Biological SOAP servers and web services provided by the public sequence data bank.
Nucleic Acids Res.: 2003, 31(13);3836-9
[PubMed:12824432] [Worldcat] [EZB] ##EZB_HD## (I p)

Scott D Zuyderduyn, Steven J M Jones
A knowledge discovery object model API for Java.
BMC Bioinformatics: 2003, 4();51
[PubMed:14583100] [Worldcat] [EZB] ##EZB_HD## [DOI] (I e)


2004

Stein Aerts, Peter Van Loo, Yves Moreau, Bart De Moor
A genetic algorithm for the detection of new cis-regulatory modules in sets of coregulated genes.
Bioinformatics: 2004, 20(12);1974-6
[PubMed:15044242] [Worldcat] [EZB] ##EZB_HD## [DOI] (P p)

Xiaoli Dong, Paul Stothard, Ian J Forsythe, David S Wishart
PlasMapper: a web server for drawing and auto-annotating plasmid maps.
Nucleic Acids Res.: 2004, 32(Web Server issue);W660-4
[PubMed:15215471] [Worldcat] [EZB] ##EZB_HD## [DOI] (I p)

Thomas A Down, Tim J P Hubbard
What can we learn from noncoding regions of similarity between genomes?
BMC Bioinformatics: 2004, 5();131
[PubMed:15369604] [Worldcat] [EZB] ##EZB_HD## [DOI] (I e)

Ashwin Hajarnavis, Ian Korf, Richard Durbin
A probabilistic model of 3' end formation in Caenorhabditis elegans.
Nucleic Acids Res.: 2004, 32(11);3392-9
[PubMed:15247332] [Worldcat] [EZB] ##EZB_HD## [DOI] (I e)

Christiane Hertz-Fowler, Chris S Peacock, Valerie Wood, Martin Aslett, Arnaud Kerhornou, Paul Mooney, Adrian Tivey, Matthew Berriman, Neil Hall, Kim Rutherford, Julian Parkhill, Alasdair C Ivens, Marie-Adele Rajandream, Bart Barrell
GeneDB: a resource for prokaryotic and eukaryotic organisms.
Nucleic Acids Res.: 2004, 32(Database issue);D339-43
[PubMed:14681429] [Worldcat] [EZB] ##EZB_HD## [DOI] (I p)

Hyeong Jun An, Doheon Lee, Kwang Hyung Lee, Jonghwa Bhak
The association of Alu repeats with the generation of potential AU-rich elements (ARE) at 3' untranslated regions.
BMC Genomics: 2004, 5(1);97
[PubMed:15610565] [Worldcat] [EZB] ##EZB_HD## [DOI] (I e)


2005

A Carbone, F Képès, A Zinovyev
Codon bias signatures, organization of microorganisms in codon space, and lifestyle.
Mol. Biol. Evol.: 2005, 22(3);547-61
[PubMed:15537809] [Worldcat] [EZB] ##EZB_HD## [DOI] (P p)

Thomas A Down, Tim J P Hubbard
NestedMICA: sensitive inference of over-represented motifs in nucleic acid sequence.
Nucleic Acids Res.: 2005, 33(5);1445-53
[PubMed:15760844] [Worldcat] [EZB] ##EZB_HD## [DOI] (I e)

G Finak, N Godin, M Hallett, F Pepin, Z Rajabi, V Srivastava, Z Tang
BIAS: Bioinformatics Integrated Application Software.
Bioinformatics: 2005, 21(8);1745-6
[PubMed:15572471] [Worldcat] [EZB] ##EZB_HD## [DOI] (P p)

Alexander N Gorban, Tatyana G Popova, Andrei Y Zinovyev
Four basic symmetry types in the universal 7-cluster structure of microbial genomic sequences.
In Silico Biol. (Gedrukt): 2005, 5(3);265-82
[PubMed:15984937] [Worldcat] [EZB] ##EZB_HD## (P p)

Philippe Gouret, Vérane Vitiello, Nathalie Balandraud, André Gilles, Pierre Pontarotti, Etienne G J Danchin
FIGENIX: intelligent automation of genomic annotation: expertise integration in a new software platform.
BMC Bioinformatics: 2005, 6();198
[PubMed:16083500] [Worldcat] [EZB] ##EZB_HD## [DOI] (I e)

Paul Kersey, Lawrence Bower, Lorna Morris, Alan Horne, Robert Petryszak, Carola Kanz, Alexander Kanapin, Ujjwal Das, Karine Michoud, Isabelle Phan, Alexandre Gattiker, Tamara Kulikova, Nadeem Faruque, Karyn Duggan, Peter Mclaren, Britt Reimholz, Laurent Duret, Simon Penel, Ingmar Reuter, Rolf Apweiler
Integr8 and Genome Reviews: integrated views of complete genomes and proteomes.
Nucleic Acids Res.: 2005, 33(Database issue);D297-302
[PubMed:15608201] [Worldcat] [EZB] ##EZB_HD## [DOI] (I p)

Debleena Pain, Gung-Wei Chirn, Christopher Strassel, Daniel M Kemp
Multiple retropseudogenes from pluripotent cell-specific gene expression indicates a potential signature for novel gene identification.
J. Biol. Chem.: 2005, 280(8);6265-8
[PubMed:15640145] [Worldcat] [EZB] ##EZB_HD## [DOI] (P p)

Andreas Prlić, Thomas A Down, Tim J P Hubbard
Adding some SPICE to DAS.
Bioinformatics: 2005, 21 Suppl 2();ii40-1
[PubMed:16204122] [Worldcat] [EZB] ##EZB_HD## [DOI] (I p)

Rainer Pudimat, Ernst-Günter Schukat-Talamazzini, Rolf Backofen
A multiple-feature framework for modelling and predicting transcription factor binding sites.
Bioinformatics: 2005, 21(14);3082-8
[PubMed:15905283] [Worldcat] [EZB] ##EZB_HD## [DOI] (P p)

Eliot R Spindel, Mark A Pauley, Yibing Jia, Courtney Gravett, Shaun L Thompson, Nicholas F Boyle, Sergio R Ojeda, Robert B Norgren
Leveraging human genomic information to identify nonhuman primate sequences for expression array development.
BMC Genomics: 2005, 6();160
[PubMed:16288651] [Worldcat] [EZB] ##EZB_HD## [DOI] (I e)


2006

Eckart Bindewald, Thomas D Schneider, Bruce A Shapiro
CorreLogo: an online server for 3D sequence logos of RNA and DNA alignments.
Nucleic Acids Res.: 2006, 34(Web Server issue);W405-11
[PubMed:16845037] [Worldcat] [EZB] ##EZB_HD## [DOI] (I p)

Thomas Down, Bernard Leong, Tim J P Hubbard
A machine learning strategy to identify candidate binding sites in human protein-coding sequence.
BMC Bioinformatics: 2006, 7();419
[PubMed:17002805] [Worldcat] [EZB] ##EZB_HD## [DOI] (I e)

David Carter, Richard Durbin
Vertebrate gene finding from multiple-species alignments using a two-level strategy.
Genome Biol.: 2006, 7 Suppl 1();S6.1-12
[PubMed:16925840] [Worldcat] [EZB] ##EZB_HD## [DOI] (I p)

Christoph Gille, Peter N Robinson
HotSwap for bioinformatics: a STRAP tutorial.
BMC Bioinformatics: 2006, 7();64
[PubMed:16469097] [Worldcat] [EZB] ##EZB_HD## [DOI] (I e)

Samiul Hasan, Sabine Daugelat, P S Srinivasa Rao, Mark Schreiber
Prioritizing genomic drug targets in pathogens: application to Mycobacterium tuberculosis.
PLoS Comput. Biol.: 2006, 2(6);e61
[PubMed:16789813] [Worldcat] [EZB] ##EZB_HD## [DOI] (I p)

Samiul Hasan, Mark Schreiber
Recovering motifs from biased genomes: application of signal correction.
Nucleic Acids Res.: 2006, 34(18);5124-32
[PubMed:16990246] [Worldcat] [EZB] ##EZB_HD## [DOI] (I p)

C E H Lee, B Gaëta, H R Malming, M E Bain, W A Sewell, A M Collins
Reconsidering the human immunoglobulin heavy-chain locus: 1. An evaluation of the expressed human IGHD gene repertoire.
Immunogenetics: 2006, 57(12);917-25
[PubMed:16402215] [Worldcat] [EZB] ##EZB_HD## [DOI] (P p)

Chunguang Liang, Thomas Dandekar
inGeno--an integrated genome and ortholog viewer for improved genome to genome comparisons.
BMC Bioinformatics: 2006, 7();461
[PubMed:17054788] [Worldcat] [EZB] ##EZB_HD## [DOI] (I e)

Qiang Lu, Pei Hao, Vasa Curcin, Weizhong He, Yuan-Yuan Li, Qing-Ming Luo, Yi-Ke Guo, Yi-Xue Li
KDE Bioscience: platform for bioinformatics analysis workflows.
J Biomed Inform: 2006, 39(4);440-50
[PubMed:16260186] [Worldcat] [EZB] ##EZB_HD## [DOI] (I p)

Todd McDonald, Simon Sheng, Brian Stanley, Dawn Chen, Young Ko, Robert N Cole, Peter Pedersen, Jennifer E Van Eyk
Expanding the subproteome of the inner mitochondria using protein separation technologies: one- and two-dimensional liquid chromatography and two-dimensional gel electrophoresis.
Mol. Cell Proteomics: 2006, 5(12);2392-411
[PubMed:17000643] [Worldcat] [EZB] ##EZB_HD## [DOI] (P p)

Bradford C Powell, Clyde A Hutchison
Similarity-based gene detection: using COGs to find evolutionarily-conserved ORFs.
BMC Bioinformatics: 2006, 7();31
[PubMed:16423288] [Worldcat] [EZB] ##EZB_HD## [DOI] (I e)

Christian Ross, Qingxi J Shen
Computational prediction and experimental verification of HVA1-like abscisic acid responsive promoters in rice (Oryza sativa).
Plant Mol. Biol.: 2006, 62(1-2);233-46
[PubMed:16845480] [Worldcat] [EZB] ##EZB_HD## [DOI] (P p)

Thorsten Schmidt, Dmitrij Frishman
PROMPT: a protein mapping and comparison tool.
BMC Bioinformatics: 2006, 7();331
[PubMed:16817977] [Worldcat] [EZB] ##EZB_HD## [DOI] (I e)

Christian Ross, Qingxi J Shen
Computational prediction and experimental verification of HVA1-like abscisic acid responsive promoters in rice (Oryza sativa).
Plant Mol. Biol.: 2006, 62(1-2);233-46
[PubMed:16845480] [Worldcat] [EZB] ##EZB_HD## [DOI] (P p)

Thorsten Schmidt, Dmitrij Frishman
PROMPT: a protein mapping and comparison tool.
BMC Bioinformatics: 2006, 7();331
[PubMed:16817977] [Worldcat] [EZB] ##EZB_HD## [DOI] (I e)

Georgios S Vernikos, Julian Parkhill
Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands.
Bioinformatics: 2006, 22(18);2196-203
[PubMed:16837528] [Worldcat] [EZB] ##EZB_HD## [DOI] (I p)

Juan Antonio Vizcaíno, Francisco Javier González, M Belén Suárez, José Redondo, Julian Heinrich, Jesús Delgado-Jarana, Rosa Hermosa, Santiago Gutiérrez, Enrique Monte, Antonio Llobell, Manuel Rey
Generation, annotation and analysis of ESTs from Trichoderma harzianum CECT 2413.
BMC Genomics: 2006, 7();193
[PubMed:16872539] [Worldcat] [EZB] ##EZB_HD## [DOI] (I e)


2007

Antonina Andreeva, Andreas Prlić, Tim J P Hubbard, Alexey G Murzin
SISYPHUS--structural alignments for proteins with non-trivial relationships.
Nucleic Acids Res.: 2007, 35(Database issue);D253-9
[PubMed:17068077] [Worldcat] [EZB] ##EZB_HD## [DOI] (I p)

Huynh-Hoa Bui, Jason Botten, Nicolas Fusseder, Valerie Pasquetto, Bianca Mothe, Michael J Buchmeier, Alessandro Sette
Protein sequence database for pathogenic arenaviruses.
Immunome Res: 2007, 3();1
[PubMed:17288609] [Worldcat] [EZB] ##EZB_HD## [DOI] (I e)

Thomas A Down, Casey M Bergman, Jing Su, Tim J P Hubbard
Large-scale discovery of promoter motifs in Drosophila melanogaster.
PLoS Comput. Biol.: 2007, 3(1);e7
[PubMed:17238282] [Worldcat] [EZB] ##EZB_HD## [DOI] (I p)

Jan E Gewehr, Martin Szugat, Ralf Zimmer
BioWeka--extending the Weka framework for bioinformatics.
Bioinformatics: 2007, 23(5);651-3
[PubMed:17237069] [Worldcat] [EZB] ##EZB_HD## [DOI] (I p)

Kristian Hanekamp, Uta Bohnebeck, Bánk Beszteri, Klaus Valentin
PhyloGena--a user-friendly system for automated phylogenetic annotation of unknown sequences.
Bioinformatics: 2007, 23(7);793-801
[PubMed:17332025] [Worldcat] [EZB] ##EZB_HD## [DOI] (I p)

J R Macías, N Jiménez-Lozano, J M Carazo
Integrating electron microscopy information into existing Distributed Annotation Systems.
J. Struct. Biol.: 2007, 158(2);205-13
[PubMed:17400476] [Worldcat] [EZB] ##EZB_HD## [DOI] (P p)

Swetlana Nikolajewa, Rainer Pudimat, Michael Hiller, Matthias Platzer, Rolf Backofen
BioBayesNet: a web server for feature extraction and Bayesian network modeling of biological sequence data.
Nucleic Acids Res.: 2007, 35(Web Server issue);W688-93
[PubMed:17537825] [Worldcat] [EZB] ##EZB_HD## [DOI] (I p)

Ola Spjuth, Tobias Helmus, Egon L Willighagen, Stefan Kuhn, Martin Eklund, Johannes Wagener, Peter Murray-Rust, Christoph Steinbeck, Jarl E S Wikberg
Bioclipse: an open source workbench for chemo- and bioinformatics.
BMC Bioinformatics: 2007, 8();59
[PubMed:17316423] [Worldcat] [EZB] ##EZB_HD## [DOI] (I e)


2008

Pawel Zajac, Erik Pettersson, Marcus Gry, Joakim Lundeberg, Afshin Ahmadian
Expression profiling of signature gene sets with trinucleotide threading.
Genomics: 2008, 91(2);209-17
[PubMed:18061398] [Worldcat] [EZB] ##EZB_HD## [DOI] (I p)

Pawel Zajac, Erik Pettersson, Marcus Gry, Joakim Lundeberg, Afshin Ahmadian
Expression profiling of signature gene sets with trinucleotide threading.
Genomics: 2008, 91(2);209-17
[PubMed:18061398] [Worldcat] [EZB] ##EZB_HD## [DOI] (I p)

Georgios S Vernikos, Julian Parkhill
Resolving the structural features of genomic islands: a machine learning approach.
Genome Res.: 2008, 18(2);331-42
[PubMed:18071028] [Worldcat] [EZB] ##EZB_HD## [DOI] (P p)

Chunguang Liang, Thomas Dandekar
inGeno--an integrated genome and ortholog viewer for improved genome to genome comparisons.
BMC Bioinformatics: 2006, 7();461
[PubMed:17054788] [Worldcat] [EZB] ##EZB_HD## [DOI] (I e)

Alistair M Chalk, Erik L L Sonnhammer
siRNA specificity searching incorporating mismatch tolerance data.
Bioinformatics: 2008, 24(10);1316-7
[PubMed:18397893] [Worldcat] [EZB] ##EZB_HD## [DOI] (I p)

Dominik Gront, Andrzej Kolinski
Utility library for structural bioinformatics.
Bioinformatics: 2008, 24(4);584-5
[PubMed:18227118] [Worldcat] [EZB] ##EZB_HD## [DOI] (I p)


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.

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