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

Bayesian Inference of Signaling Network Topology in a Cancer Cell Line

(2012) Steven M. Hill et al.   BIOINFORMATICS

Hub-Centered Gene Network Reconstruction Using Automatic Relevance Determination

(2012) Matthias Böck et al.   PLoS One

Mapping of signaling networks through synthetic genetic interaction analysis by RNAi

(2011) Thomas Horn et al.   NATURE METHODS

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

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

Dynamic deterministic effects propagation networks: learning signalling pathways from longitudinal protein array data

(2010) C. Bender et al.   BIOINFORMATICS

Fast and efficient dynamic nested effects models

(2010) Holger Fröhlich et al.   BIOINFORMATICS

Evidence for a differential modulation of p53-phosphorylating kinases by the cyclin-dependent kinase inhibitor p21WAFI/C1P1

(2010) Denise Neise et al.   CELL CYCLE

High-throughput RNAi screening in mammalian cells with esiRNAs

(2010) Mirko Theis et al.   METHODS

Systems survey of endocytosis by multiparametric image analysis

(2010) Claudio Collinet et al.   NATURE

A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity

(2010) Na-Yu Chia et al.   NATURE

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

(2010) D. Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Reconstructing signaling pathways from RNAi data using probabilistic Boolean threshold networks

(2009) Lars Kaderali et al.   BIOINFORMATICS

RNAither, an automated pipeline for the statistical analysis of high-throughput RNAi screens

(2009) N. Rieber et al.   BIOINFORMATICS

Nested effects models for learning signaling networks from perturbation data

(2009) Holger Fröhlich et al.   BIOMETRICAL JOURNAL

From experimental setup to bioinformatics: An RNAi screening platform to identify host factors involved in HIV-1 replication

(2009) Kathleen Börner et al.   Biotechnology Journal

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

(2009) Holger Fröhlich et al.   BMC BIOINFORMATICS

Reconstructing nonlinear dynamic models of gene regulation using stochastic sampling

(2009) Johanna Mazur et al.   BMC BIOINFORMATICS

Learning Signaling Network Structures with Sparsely Distributed Data

(2009) Karen Sachs et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Complex Systems: From Chemistry to Systems Biology Special Feature: Modeling the temporal interplay of molecular signaling and gene expression by using dynamic nested effects models

(2009) B. Anchang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2008) H. Frohlich et al.   BIOINFORMATICS

Survival of the sparsest: robust gene networks are parsimonious

(2008) Robert D Leclerc   Molecular Systems Biology

RNA interference screen for human genes associated with West Nile virus infection

(2008) Manoj N. Krishnan et al.   NATURE

Identification of Host Proteins Required for HIV Infection Through a Functional Genomic Screen

(2008) Abraham L. Brass et al.   SCIENCE

Structure Learning in Nested Effects Models

(2008) Achim Tresch et al.   Statistical Applications in Genetics and Molecular Biology