Software

GitHub repository: sysbiolux

rFASTCORMICS (RNASeq): Identifying and targeting cancer-specific metabolism using network-based drug target prediction

Maria Pires Pacheco, Tamara Bintener, Dominik Ternes, Dagmar Kulms, Serge Haan, Elisabeth Letellier and Thomas Sauter

EBioMedicine. 2019 May;43:98-106.

DOWNLOAD: via GitHub repository: sysbiolux-rFASTCORMICS

FASTCORE: Fast Reconstruction of Compact Context-Specific Metabolic Network Models

Nikos Vlassis 1, Maria Pires Pacheco 2, and Thomas Sauter 2

1 Luxembourg Centre for Systems Biomedicine, University of Luxembourg
2 Life Sciences Research Unit, University of Luxembourg

PLoS Comput Biol. 2014 Jan;10(1):e1003424.

DOWNLOAD: via GitHub repository: sysbiolux-FASTCORE

FASTCORMICS: Integrated metabolic modelling reveals cell-type specific epigenetic control points of the macrophage metabolic network

Maria Pires Pacheco, Elisabeth John, Tony Kaoma, Merja Heinäniemi, Nathalie Nicot, Laurent Vallar, Jean-Luc Bueb, Lasse Sinkkonen and Thomas Sauter

BMC Genomics. 2015 Oct 19;16(1):809.

DOWNLOAD: via GitHub repository: sysbiolux-FASTCORMICS

IDARE: Integrated analysis of transcript-level regulation of metabolism reveals disease-relevant nodes of the human metabolic network

Galhardo M, Sinkkonen L, Berninger P, Lin J, Sauter T, Heinäniemi M.

Nucleic Acids Res. 2014 Feb;42(3):1474-96.

LINK to IDARE webpage:

https://code.google.com/p/adipoflux/

Model: Identification of New IkappaBalpha Complexes by an Iterative Experimental and Mathematical Modeling Approach

Fabian Konrath, Johannes Witt, Thomas Sauter, Dagmar Kulms

PLoS Comput Biol. 2014 Mar 27;10(3):e1003528.

DOWNLOAD Final Model M3:

DyGloSA: Matlab-based tool for Dynamical Global parameter Sensitivity Analysis of ODE models of biological systems

Baumuratova T.; Dobre S., Bastogne T., Sauter T.

PLoS One. 2013 Dec 18;8(12):e82973.

DOWNLOAD:

• DyGloSA_Toolbox_package

DIAMOND

DIAMOND : an automatic pipeline for metabolic model comparison

Nicolas Beaume, Maria Pires Pacheco and Thomas Sauter

Life Science Research Unit, University of Luxembourg, Belvaux, L-4367, Luxembourg

DOWNLOAD: