MPI-INF D3 Publications: Journal Article: Rtreemix: an {R} package for estimating evolutionary pathways and genetic progression scores

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Author, Editor(s)

Author(s):

Bogojeska, Jasmina
Alexa, Adrian
Altmann, André
Lengauer, Thomas
Rahnenführer, Jörg

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Not MPG Author(s):

Rahnenführer, Jörg

BibTeX cite key*:

Bogojeska_trees_2008

Title

Title*:

Rtreemix: an R package for estimating evolutionary pathways and genetic progression scores

Journal

Journal Title*:	Bioinformatics	Journal's URL:	http://bioinformatics.oxfordjournals.org/
Download URL for the article:	http://bioinformatics.oxfordjournals.org/cgi/reprint/24/20/2391	Language:	English

Publisher

Publisher's Name:	Oxford University Press	Publisher's URL:
Publisher's Address:	Oxford, UK	ISSN:	1367-4803

Vol, No, pp, Date

Volume*:	24	Number:	20
Publishing Date:	August 2008
Pages*:	2391-2392	Number of VG Pages:
Page Start:		Page End:
Sequence Number:		DOI:	10.1093/bioinformatics/btn410

Note:
(LaTeX) Abstract:	Summary: In genetics, many evolutionary pathways can be modeled by the ordered accumulation of permanent changes. Mixture models of mutagenetic trees have been used to describe disease progression in cancer and in HIV. In cancer, progression is modeled by the accumulation of chromosomal gains and losses in tumor cells; in HIV, the accumulation of drug resistance-associated mutations in the viral genome is known to be associated with disease progression. From such evolutionary models, genetic progression scores can be derived that assign measures for the disease state to single patients. Rtreemix is an R package for estimating mixture models of evolutionary pathways from observed cross-sectional data and for estimating associated genetic progression scores. The package also provides extended functionality for estimating confidence intervals for estimated model parameters and for evaluating the stability of the estimated evolutionary mixture models.
URL for the Abstract:	http://bioinformatics.oxfordjournals.org/cgi/content/abstract/24/20/2391
Categories, Keywords:	Rtreemix, mutagenetic trees, R
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Download Access Level:	Internal

Correlation

MPG Unit:	Max-Planck-Institut für Informatik

MPG Subunit:	Computational Biology and Applied Algorithmics
Appearance:	MPII WWW Server, MPII FTP Server, MPG publications list, university publications list, working group publication list, Fachbeirat, VG Wort

BibTeX Entry:

@ARTICLE{Bogojeska_trees_2008,
AUTHOR = {Bogojeska, Jasmina and Alexa, Adrian and Altmann, Andr{\'e} and Lengauer, Thomas and Rahnenf{\"u}hrer, J{\"o}rg},
TITLE = {Rtreemix: an {R} package for estimating evolutionary pathways and genetic progression scores},
JOURNAL = {Bioinformatics},
PUBLISHER = {Oxford University Press},
YEAR = {2008},
NUMBER = {20},
VOLUME = {24},
PAGES = {2391--2392},
ADDRESS = {Oxford, UK},
MONTH = {August},
ISBN = {1367-4803},
DOI = {10.1093/bioinformatics/btn410},
}

Entry last modified by Ruth Schneppen-Christmann, 04/01/2009

Edit History (please click the blue arrow to see the details)

	Editor(s) Jasmina Bogojeska	Created 12/01/2008 15:38:35
Revisions 2. 1. 0.	Editor(s) Ruth Schneppen-Christmann Ruth Schneppen-Christmann Jasmina Bogojeska	Edit Dates 01.04.2009 09:09:27 22.01.2009 14:43:51 12/01/2008 03:38:35 PM