Discrete Logic Modelling Optimization to Contextualize Prior Knowledge Networks Using PRUNET

Global DNA methylation and transcriptional analyses of human ESC-derived cardiomyocytes

(2014) Ying Gu et al.   Protein & Cell

Detecting cellular reprogramming determinants by differential stability analysis of gene regulatory networks

(2013) Isaac Crespo et al.   BMC Systems Biology

Reconstruction of Cellular Signal Transduction Networks Using Perturbation Assays and Linear Programming

(2013) Bettina Knapp et al.   PLoS One

A general strategy for cellular reprogramming: The importance of transcription factor cross-repression

(2013) Isaac Crespo et al.   STEM CELLS

Detecting and Removing Inconsistencies between Experimental Data and Signaling Network Topologies Using Integer Linear Programming on Interaction Graphs

(2013) Ioannis N. Melas et al.   PLoS Computational Biology

CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms

(2012) Camille Terfve et al.   BMC Systems Biology

Small Molecule-Mediated TGF-β Type II Receptor Degradation Promotes Cardiomyogenesis in Embryonic Stem Cells

(2012) Erik Willems et al.   Cell Stem Cell

Large-Scale Signaling Network Reconstruction

(2012) Seyedsasan Hashemikhabir et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Predicting missing expression values in gene regulatory networks using a discrete logic modeling optimization guided by network stable states

(2012) Isaac Crespo et al.   NUCLEIC ACIDS RESEARCH

A Novel Network Integrating a miRNA-203/SNAI1 Feedback Loop which Regulates Epithelial to Mesenchymal Transition

(2012) Michèle Moes et al.   PLoS One

Cozzarelli Prize Winner: Robust cardiomyocyte differentiation from human pluripotent stem cells via temporal modulation of canonical Wnt signaling

(2012) X. Lian et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The roles of the reprogramming factors Oct4, Sox2 and Klf4 in resetting the somatic cell epigenome during induced pluripotent stem cell generation

(2012) Ryan Schmidt et al.   GENOME BIOLOGY

ResponseNet: revealing signaling and regulatory networks linking genetic and transcriptomic screening data

(2011) A. Lan et al.   NUCLEIC ACIDS RESEARCH

Systematic Search for Recipes to Generate Induced Pluripotent Stem Cells

(2011) Rui Chang et al.   PLoS Computational Biology

From biological pathways to regulatory networks

(2010) Ritwik K. Layek et al.   Molecular BioSystems

Pathway Commons, a web resource for biological pathway data

(2010) E. G. Cerami et al.   NUCLEIC ACIDS RESEARCH

A robust model to describe the differentiation of T-helper cells

(2010) Luis Mendoza et al.   THEORY IN BIOSCIENCES

Reconstructing signaling pathways from RNAi data using probabilistic Boolean threshold networks

(2009) Lars Kaderali et al.   BIOINFORMATICS

Nested effects models for learning signaling networks from perturbation data

(2009) Holger Fröhlich et al.   BIOMETRICAL JOURNAL

Deterministic Effects Propagation Networks for reconstructing protein signaling networks from multiple interventions

(2009) Holger Fröhlich et al.   BMC BIOINFORMATICS

IRIS: a method for reverse engineering of regulatory relations in gene networks

(2009) Sandro Morganella et al.   BMC BIOINFORMATICS

Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction

(2009) Julio Saez-Rodriguez et al.   Molecular Systems Biology

Estimating large-scale signaling networks through nested effect models with intervention effects from microarray data

(2008) H. Frohlich et al.   BIOINFORMATICS

Synchronous versus asynchronous modeling of gene regulatory networks

(2008) A. Garg et al.   BIOINFORMATICS

Human cardiovascular progenitor cells develop from a KDR+ embryonic-stem-cell-derived population

(2008) Lei Yang et al.   NATURE

MetaReg: A platform for modeling, analysis and visualization of biological systems using large-scale experimental data

(2008) Igor Ulitsky et al.   GENOME BIOLOGY