About Us

AltAnalyze is an open-source software project principally run by developers in the Nathan Salomonis laboratory at Cincinnati Children's Hosptial Medical Center and the University of Cincinnati. This project began in the laboratory of Bruce Conklin at the Gladstone Institutes. 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, bulk and single-cell RNA sequencing datasets.

AltAnalyze and its associated tools have provided a broad range novel biological insights across distinct domains of biology (see Citations below). A significnat focus of AltAnalyze is on the functional interpretation of results (alternative splicing, single-cell, gene regulatory mechanisms).

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. co-first author

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.

Single-cell analysis of mixed-lineage states leading to a binary cell fate choice. Olsson A, Venkatasubramanian M, Chaudhri VK, Aronow BJ, Salomonis N, Singh H, Grimes HL. Nature. 2016 Aug 31;537(7622):698-702. co-corresponding*

Articles Citing AltAnalyze

Development Team

Name Role Affiliation
Nathan Salomonis Principle Investigator CCHMC
Kenneth Eaton Senior Application Developer CCHMC
Stuart Hay Application Developer CCHMC
Meenakshi Venkatasubramanian PhD Candidate University of Cincinnati
Krithika Ramasamy Subramanian PhD Candidate University of Cincinnati
Dorothea Emig Software Design Max Planck Institute
Mario Albrecht Software Design Max Planck Institute
Jared Churko Software Design Stanford University
Kristina Hanspers Software Design Gladstone Institutes
Lee Grimes Advisory Board CCHMC
Harinder Singh Advisory Board CCHMC
Alex Pico Advisory Board Gladstone Institutes
Bruce Conklin Advisory Board Gladstone Institutes