Issue October 2011

category image Volume 29
No. 2 (p 251-423)
October 2011
ISSN 0739-1102

Open Access

OnionTree XML: A Format to Exchange Gene-Related Probabilities

Many medical and biological genetics and functional genomics studies include genome-wide analysis. Due to the coordination of cellular functions, the behavior of groups of genes rather than of a single gene can be more informative in these studies. Experimental and technical developments now allow genome-wide measurement of many molecular components of the cell, including mRNA transcripts (1), DNA sequence (2-5) and structure (6-10), DNA binding by transcriptional regulators (11), microRNAs, proteins, and metabolites (12). For each type of data, analysis software has been developed, much of it available within the R/Bioconductor framework (13).

This article can be cited as:
Alexander Favorov, Dmitrijs Lvovs, William Speier, Giovanni Parmigiani, Michael F. Ochs. OnionTree XML: A Format to Exchange Gene-Related Probabilities J. Biomol Struct Dyn 29(2)417-423 (2011).

Alexander Favorov1,2,3
Dmitrijs Lvovs2
William Speier1
Giovanni Parmigiani4
Michael F. Ochs1

1Oncology Biostatistics and Bioinformatics, The Sidney Kimmel Comprehensive Cancer Center 550 North Broadway, Suite 1103, Baltimore, Maryland 21205, US
2Bioinformatics Laboratory, Scientific Center of Russian Federation Research Institute for Genetics and Selection of Industrial Microorganisms, 1 1-st Dorojnyj, Moscow, 117545, RF
3Vavilov Institute of General Genetics of RAS, 3 Gubkina str, Moscow, 119991, RF
4Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, 44 Binney Street CLS 11043 Boston, MA 02115, US

favorov@sensi.org
Open Access Article
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