Reverse causal reasoning: applying qualitative causal knowledge to the interpretation of high-throughput data

Causal reasoning on biological networks: interpreting transcriptional changes

(2012) Leonid Chindelevitch et al.   BIOINFORMATICS

Assessment of network perturbation amplitudes by applying high-throughput data to causal biological networks

(2012) Florian Martin et al.   BMC Systems Biology

Genes Associated with Intestinal Permeability in Ulcerative Colitis: Changes in Expression Following Infliximab Therapy

(2012) Gary Toedter et al.   INFLAMMATORY BOWEL DISEASES

Comparative Transcriptional Network Modeling of Three PPAR-α/γ Co-Agonists Reveals Distinct Metabolic Gene Signatures in Primary Human Hepatocytes

(2012) Renée Deehan et al.   PLoS One

Active PI3K Pathway Causes an Invasive Phenotype Which Can Be Reversed or Promoted by Blocking the Pathway at Divergent Nodes

(2012) Jeffrey J. Wallin et al.   PLoS One

Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges

(2012) Purvesh Khatri et al.   PLoS Computational Biology

Construction of a computable cell proliferation network focused on non-diseased lung cells

(2011) Jurjen W Westra et al.   BMC Systems Biology

A computable cellular stress network model for non-diseased pulmonary and cardiovascular tissue

(2011) Walter K Schlage et al.   BMC Systems Biology

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

Causal reasoning identifies mechanisms of sensitivity for a novel AKT kinase inhibitor, GSK690693

(2010) Rakesh Kumar et al.   BMC GENOMICS

The PI3K Pathway As Drug Target in Human Cancer

(2010) Kevin D. Courtney et al.   JOURNAL OF CLINICAL ONCOLOGY

Prior biological knowledge-based approaches for the analysis of genome-wide expression profiles using gene sets and pathways

(2010) Michael C Wu et al.   STATISTICAL METHODS IN MEDICAL RESEARCH

Comparative analysis of methods for gene transcription profiling data derived from different microarray technologies in rat and mouse models of diabetes

(2009) Steven P Wilder et al.   BMC GENOMICS

Small molecule activators of SIRT1 replicate signaling pathways triggered by calorie restriction in vivo

(2009) Jesse J Smith et al.   BMC Systems Biology

Nuclear Export-independent Inhibition of Foxa2 by Insulin

(2009) Jessica J. Howell et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

KEGG for representation and analysis of molecular networks involving diseases and drugs

(2009) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

GeneSigDB—a curated database of gene expression signatures

(2009) Aedín C. Culhane et al.   NUCLEIC ACIDS RESEARCH

The Role of Hypoxia in 2-Butoxyethanol–Induced Hemangiosarcoma

(2009) Daphna Laifenfeld et al.   TOXICOLOGICAL SCIENCES

How is mRNA expression predictive for protein expression? A correlation study on human circulating monocytes

(2008) Yanfang Guo et al.   ACTA BIOCHIMICA ET BIOPHYSICA SINICA

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH