About Us

AltAnalyze is an open-source software project principally run by developers in the Bruce Conklin laboratory at the J. David Gladstone Institutes and the University of California San Francisco. The goal of this project is to provide easy to use applications for biologists with little computational training as well as computational biologists for the analysis of microarray and ultimately RNA sequencing datasets. AltAnalyze is funded by an NIH RO1 grant (ARRA Suppl. GM080223-06S1).

Our hope, is that AltAnalyze and associated tools will help researchers to provide greater biological insight and uncover new mechanisms that regulate cellular biology. Thus, much of the focus of AltAnalyze is on functional interpretation of results rather than the development of new statistical methods. Examples include protein domain, microRNA binding site and pathway analysis. An ongoing goal of ours is to transition AltAnalyze to the Cytoscape environment, providing new tools for RNA sequencing and alternative splicing microarray analysis, sequence motif analysis, discovery of novel alternative exons and transcripts and associated data visualization. As a part of Cytoscape, AltAnalyze will be able to utilize many of the powerful tools built for this environment (e.g., expression clustering, visualization of multiple data types and complex network analyses).

If you would like to contribute to AltAnalyze development or to the documentation on this site, we welcome your contributions.

Citing AltAnalyze

The following citations are most relevant:

AltAnalyze and DomainGraph: analyzing and visualizing exon expression data. Emig D, Salomonis N, Baumbach J, Lengauer T, Conklin BR, Albrecht M. Nucleic Acids Res. 2010 Jul 1;38 Suppl:W755-62. Epub 2010 May 31.

Alternative splicing regulates mouse embryonic stem cell pluripotency and differentiation. Salomonis N, Schlieve CR, Pereira L, Wahlquist C, Colas A, Zambon AC, Vranizan K, Spindler MJ, Pico AR, Cline MS, Clark TA, Williams A, Blume JE, Samal E, Mercola M, Merrill BJ, Conklin BR. Proc Natl Acad Sci U S A. 2010 Jun 8;107(23):10514-9. Epub 2010 May 24.

Alternative splicing in the differentiation of human embryonic stem cells into cardiac precursors. Salomonis N, Nelson B, Vranizan K, Pico AR, Hanspers K, Kuchinsky A, Ta L, Mercola M, Conklin BR. PLoS Comput Biol. 2009 Nov;5(11):e1000553. Epub 2009 Nov 6.

Other Articles

Canadian Bioinformatics News letter feature

Articles Citing AltAnalyze

Development Team