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Treegl specifications

Information


Unique identifier OMICS_25811
Name Treegl
Alternative name Tree-smoothed graphical lasso
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages MATLAB
Computer skills Advanced
Stability Stable
Source code URL http://www.sailing.cs.cmu.edu/main/treegl/treegl_download.zip
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Eric Xing

Publication for Tree-smoothed graphical lasso

Treegl citations

 (4)
library_books

Fused Regression for Multi source Gene Regulatory Network Inference

2016
PLoS Comput Biol
PMCID: 5140053
PMID: 27923054
DOI: 10.1371/journal.pcbi.1005157

[…] s of combining data from multiple experimental platforms and information about operon structure.A number of existing approaches have applied fused regression to related problems in network inference. TreeGL applied fused LASSO to the problem of estimating partial correlations of gene expression in a breast cancer dataset consisting of multiple cell types []. They imposed fusion between the coeffic […]

library_books

Network Analysis of Breast Cancer Progression and Reversal Using a Tree Evolving Network Algorithm

2014
PLoS Comput Biol
PMCID: 4109850
PMID: 25057922
DOI: 10.1371/journal.pcbi.1003713

[…] ted with various reverting agents or vehicle controls as mentioned above. Unfortunately, T4-2 cells reverted by some agents have only one sample per each reversion cell state. Even though our method, Treegl, is designed for small sample size scenarios, having only one sample per state is not enough for network inference — as it is known that it takes at least two samples to measure even a simple q […]

library_books

Summary of talks and papers at ISCB Asia/SCCG 2012

2013
BMC Genomics
PMCID: 3639071
DOI: 10.1186/1471-2164-14-S2-I1

[…] or Biological Sciences) discussed the analysis of expression of the genes in the quiescence signaling pathways of S. cerevisiae. Finally, a keynote by Eric Xing (Carnegie Mellon University) presented TREEGL [], an approach based on ℓ1-penalized linear regression, capable of reconstructing the evolution of a gene network from relatively scarce gene expression data.We close this section by mentionin […]

library_books

Computational biology: plus c'est la même chose, plus ça change

2011
Genome Biol
PMCID: 3245610
PMID: 21861851
DOI: 10.1186/gb-2011-12-8-307

[…] the point of including the session within ISMB itself. Ankur Parikh and Wei Wu, joint recipients of the JBI best translational bioinformatics paper award, reached a further level of specificity with TREEGL, a novel algorithm for reconstruction of human breast cancer cellular lineages from sparse gene expression data. Looking at the earliest stages of translation, my junior faculty keynote at the […]

Citations

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Treegl institution(s)
School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA; Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA; Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA; Joint Carnegie Mellon University-University of Pittsburgh PhD Program in Computational Biology, Pittsburgh, PA, USA
Treegl funding source(s)
Supported by (National Science Foundation DBI-0546594, IIS-0713379); National Institutes of Health (1R01GM093156), and an Alfred P. Sloan Fellowship.

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