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DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data

Marcel H Schulz1*, William E Devanny2, Anthony Gitter3, Shan Zhong1, Jason Ernst4 and Ziv Bar-Joseph12*

Author Affiliations

1 Ray and Stephanie Lane Center for Computational Biology, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213 USA

2 Machine Learning Department, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, 15213, PA, USA

3 Computer Science Department, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, 15213, PA, USA

4 Department of Biological Chemistry, University of California Los Angeles, Los Angeles, 90095, CA, USA

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BMC Systems Biology 2012, 6:104  doi:10.1186/1752-0509-6-104

Published: 16 August 2012

Additional files

Additional file 1:

DREM 2.0 Manual. The Manual for using the DREM 2.0 software with details of all parameters and the different dialogs in the GUI.

Format: PDF Size: 3MB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 2:

Supplementary Methods. Additional description for DREM 2.0 for TF expression level scaling, data collection for the protein-DNA binding data sets and the analysis with DECOD on an unannotated split node.

Format: PDF Size: 519KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data