Metabolic Constraint-Based Refinement of Transcriptional Regulatory Networks

A Whole-Cell Computational Model Predicts Phenotype from Genotype

(2012) Jonathan R. Karr et al.   CELL

Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks

(2012) D. Marbach et al.   GENOME RESEARCH

Wisdom of crowds for robust gene network inference

(2012) Daniel Marbach et al.   NATURE METHODS

Gis1 and Rph1 Regulate Glycerol and Acetate Metabolism in Glucose Depleted Yeast Cells

(2012) Jakub Orzechowski Westholm et al.   PLoS One

GeneNetWeaver: in silico benchmark generation and performance profiling of network inference methods

(2011) Thomas Schaffter et al.   BIOINFORMATICS

Improving the iMM904 S. cerevisiae metabolic model using essentiality and synthetic lethality data

(2011) Ali R Zomorrodi et al.   BMC Systems Biology

Behavior-specific changes in transcriptional modules lead to distinct and predictable neurogenomic states

(2011) S. Chandrasekaran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Computationally efficient flux variability analysis

(2010) Steinn Gudmundsson et al.   BMC BIOINFORMATICS

Transcriptional regulation of respiration in yeast metabolizing differently repressive carbon substrates

(2010) Sarah-Maria Fendt et al.   BMC Systems Biology

Unraveling condition-dependent networks of transcription factors that control metabolic pathway activity in yeast

(2010) Sarah-Maria Fendt et al.   Molecular Systems Biology

High-throughput generation, optimization and analysis of genome-scale metabolic models

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

Comprehensive reanalysis of transcription factor knockout expression data in Saccharomyces cerevisiae reveals many new targets

(2010) Jüri Reimand et al.   NUCLEIC ACIDS RESEARCH

YEASTRACT: providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface

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

Probabilistic integrative modeling of genome-scale metabolic and regulatory networks inEscherichia coliandMycobacterium tuberculosis

(2010) Sriram Chandrasekaran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

(2010) et al.   SCIENCE

An Automated Phenotype-Driven Approach (GeneForce) for Refining Metabolic and Regulatory Models

(2010) Dipak Barua et al.   PLoS Computational Biology

Connecting extracellular metabolomic measurements to intracellular flux states in yeast

(2009) Monica L Mo et al.   BMC Systems Biology

High-resolution DNA-binding specificity analysis of yeast transcription factors

(2009) C. Zhu et al.   GENOME RESEARCH

Sequences and consequences

(2009) S. Brenner   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

GrowMatch: An Automated Method for Reconciling In Silico/In Vivo Growth Predictions

(2009) Vinay Satish Kumar et al.   PLoS Computational Biology

Network-based prediction of human tissue-specific metabolism

(2008) Tomer Shlomi et al.   NATURE BIOTECHNOLOGY

Learning biological networks: from modules to dynamics

(2008) Richard Bonneau   Nature Chemical Biology

Functional organization of the transcriptome in human brain

(2008) Michael C Oldham et al.   NATURE NEUROSCIENCE

Reconstruction of biochemical networks in microorganisms

(2008) Adam M. Feist et al.   NATURE REVIEWS MICROBIOLOGY

Dynamic Analysis of Integrated Signaling, Metabolic, and Regulatory Networks

(2008) Jong Min Lee et al.   PLoS Computational Biology