Gene interaction enrichment and network analysis to identify dysregulated pathways and their interactions in complex diseases

Importance of pre-analytical steps for transcriptome and RT-qPCR analyses in the context of the phase II randomised multicentre trial REMAGUS02 of neoadjuvant chemotherapy in breast cancer patients

(2011) Patricia de Cremoux et al.   BMC CANCER

A CoD-based reduction algorithm for designing stationary control policies on Boolean networks

(2010) Noushin Ghaffari et al.   BIOINFORMATICS

Amplification of LAPTM4B and YWHAZ contributes to chemotherapy resistance and recurrence of breast cancer

(2010) Yang Li et al.   NATURE MEDICINE

Expander: from expression microarrays to networks and functions

(2010) Igor Ulitsky et al.   Nature Protocols

The Genetic Landscape of a Cell

(2010) M. Costanzo et al.   SCIENCE

From ‘differential expression’ to ‘differential networking’ – identification of dysfunctional regulatory networks in diseases

(2010) Alberto de la Fuente   TRENDS IN GENETICS

Identifying Tightly Regulated and Variably Expressed Networks by Differential Rank Conservation (DIRAC)

(2010) James A. Eddy et al.   PLoS Computational Biology

Scara5 Is a Ferritin Receptor Mediating Non-Transferrin Iron Delivery

(2009) Jau Yi Li et al.   DEVELOPMENTAL CELL

Dynamic modularity in protein interaction networks predicts breast cancer outcome

(2009) Ian W Taylor et al.   NATURE BIOTECHNOLOGY

Identifying Gene Interaction Enrichment for Gene Expression Data

(2009) Jigang Zhang et al.   PLoS One

The mitochondrial p53 pathway

(2008) Angelina V. Vaseva et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

Identification of gene interactions associated with disease from gene expression data using synergy networks

(2008) John Watkinson et al.   BMC Systems Biology

Gene Expression Signatures, Clinicopathological Features, and Individualized Therapy in Breast Cancer

(2008) Chaitanya R. Acharya   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Core Signaling Pathways in Human Pancreatic Cancers Revealed by Global Genomic Analyses

(2008) S. Jones et al.   SCIENCE