How to Understand the Cell by Breaking It: Network Analysis of Gene Perturbation Screens

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

A fast and efficient gene-network reconstruction method from multiple over-expression experiments

(2009) Dejan Stokić et al.   BMC BIOINFORMATICS

A network-based integrative approach to prioritize reliable hits from multiple genome-wide RNAi screens in Drosophila

(2009) Li Wang et al.   BMC GENOMICS

Knowledge based identification of essential signaling from genome-scale siRNA experiments

(2009) Armand Bankhead et al.   BMC Systems Biology

Integrating siRNA and protein-protein interaction data to identify an expanded insulin signaling network

(2009) Z. Tu et al.   GENOME RESEARCH

Backup in gene regulatory networks explains differences between binding and knockout results

(2009) Anthony Gitter et al.   Molecular Systems Biology

Elucidating regulatory mechanisms downstream of a signaling pathway using informative experiments

(2009) Ewa Szczurek et al.   Molecular Systems Biology

Systems-level dynamic analyses of fate change in murine embryonic stem cells

(2009) Rong Lu et al.   NATURE

RNAiCut: automated detection of significant genes from functional genomic screens

(2009) Irene M Kaplow et al.   NATURE METHODS

Statistical methods for analysis of high-throughput RNA interference screens

(2009) Amanda Birmingham et al.   NATURE METHODS

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Applying mass spectrometry-based proteomics to genetics, genomics and network biology

(2009) Matthias Gstaiger et al.   NATURE REVIEWS GENETICS

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

Scoring diverse cellular morphologies in image-based screens with iterative feedback and machine learning

(2009) Thouis R. Jones et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A network biology approach to aging in yeast

(2009) D. R. Lorenz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Unbiased Reconstruction of a Mammalian Transcriptional Network Mediating Pathogen Responses

(2009) I. Amit et al.   SCIENCE

Integrative Analysis of Genome-Wide RNA Interference Screens

(2009) J. D. Berndt et al.   Science Signaling

A Factor Graph Nested Effects Model To Identify Networks from Genetic Perturbations

(2009) Charles J. Vaske et al.   PLoS Computational Biology

Analyzing gene perturbation screens with nested effects models in R and bioconductor

(2008) H. Frohlich et al.   BIOINFORMATICS

Identifying functional modules in protein-protein interaction networks: an integrated exact approach

(2008) M. T. Dittrich et al.   BIOINFORMATICS

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

(2008) H. Frohlich et al.   BIOINFORMATICS

Ontologizer 2.0--a multifunctional tool for GO term enrichment analysis and data exploration

(2008) S. Bauer et al.   BIOINFORMATICS

Using iterative cluster merging with improved gap statistics to perform online phenotype discovery in the context of high-throughput RNAi screens

(2008) Zheng Yin et al.   BMC BIOINFORMATICS

Can single knockouts accurately single out gene functions?

(2008) David Deutscher et al.   BMC Systems Biology

Global Analysis of Host-Pathogen Interactions that Regulate Early-Stage HIV-1 Replication

(2008) Renate König et al.   CELL

Learning Causal Bayesian Network Structures From Experimental Data

(2008) Byron Ellis et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

Models from experiments: combinatorial drug perturbations of cancer cells

(2008) Sven Nelander et al.   Molecular Systems Biology

Reverse engineering the genotype–phenotype map with natural genetic variation

(2008) Matthew V. Rockman   NATURE

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

(2008) Manoj N. Krishnan et al.   NATURE

Network-based prediction of human tissue-specific metabolism

(2008) Tomer Shlomi et al.   NATURE BIOTECHNOLOGY

A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology

(2008) Markus J Herrgård et al.   NATURE BIOTECHNOLOGY

A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans

(2008) Insuk Lee et al.   NATURE GENETICS

The art and design of genetic screens: RNA interference

(2008) Michael Boutros et al.   NATURE REVIEWS GENETICS

STRING 8--a global view on proteins and their functional interactions in 630 organisms

(2008) L. J. Jensen et al.   NUCLEIC ACIDS RESEARCH

Highly parallel identification of essential genes in cancer cells

(2008) B. Luo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Genomewide Functional Network for the Laboratory Mouse

(2008) Yuanfang Guan et al.   PLoS Computational Biology

Context-Specific Metabolic Networks Are Consistent with Experiments

(2008) Scott A. Becker et al.   PLoS Computational Biology

Mechanisms of Cell Cycle Control Revealed by a Systematic and Quantitative Overexpression Screen in S. cerevisiae

(2008) Wei Niu et al.   PLoS Genetics