Network‐based prediction of protein function

R Sharan, I Ulitsky, R Shamir - Molecular systems biology, 2007 - embopress.org
Functional annotation of proteins is a fundamental problem in the post‐genomic era. The
recent availability of protein interaction networks for many model species has spurred on the …

[HTML][HTML] Identification and validation of oncogenes in liver cancer using an integrative oncogenomic approach

L Zender, MS Spector, W Xue, P Flemming… - Cell, 2006 - cell.com
The heterogeneity and instability of human tumors hamper straightforward identification of
cancer-causing mutations through genomic approaches alone. Herein we describe a mouse …

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

A de la Fuente - Trends in genetics, 2010 - cell.com
Understanding diseases requires identifying the differences between healthy and affected
tissues. Gene expression data have revolutionized the study of diseases by making it …

Decoding global gene expression programs in liver cancer by noninvasive imaging

E Segal, CB Sirlin, C Ooi, AS Adler, J Gollub… - Nature …, 2007 - nature.com
Paralleling the diversity of genetic and protein activities, pathologic human tissues also
exhibit diverse radiographic features. Here we show that dynamic imaging traits in non …

[HTML][HTML] A modular analysis framework for blood genomics studies: application to systemic lupus erythematosus

D Chaussabel, C Quinn, J Shen, P Patel, C Glaser… - Immunity, 2008 - cell.com
The analysis of patient blood transcriptional profiles offers a means to investigate the
immunological mechanisms relevant to human diseases on a genome-wide scale. In …

[HTML][HTML] MMP1 and MMP7 as potential peripheral blood biomarkers in idiopathic pulmonary fibrosis

IO Rosas, TJ Richards, K Konishi, Y Zhang… - PLoS …, 2008 - journals.plos.org
Background Idiopathic pulmonary fibrosis (IPF) is a chronic progressive fibrotic lung disease
associated with substantial morbidity and mortality. The objective of this study was to …

Motif module map reveals enforcement of aging by continual NF-κB activity

AS Adler, S Sinha, TLA Kawahara… - Genes & …, 2007 - genesdev.cshlp.org
Aging is characterized by specific alterations in gene expression, but their underlying
mechanisms and functional consequences are not well understood. Here we develop a …

Genomics and signaling pathways in hepatocellular carcinoma

A Villanueva, P Newell, DY Chiang… - Seminars in liver …, 2007 - thieme-connect.com
Hepatocellular carcinoma (HCC) is a leading cause of death among cirrhotic patients and
has become a major health problem in developed countries. There is an elemental …

Natural history and evolutionary principles of gene duplication in fungi

I Wapinski, A Pfeffer, N Friedman, A Regev - Nature, 2007 - nature.com
Gene duplication and loss is a powerful source of functional innovation. However, the
general principles that govern this process are still largely unknown. With the growing …

Radiogenomics: creating a link between molecular diagnostics and diagnostic imaging

AM Rutman, MD Kuo - European journal of radiology, 2009 - Elsevier
Studies employing high-throughput biological techniques have recently contributed to an
improved characterization of human cancers, allowing for novel sub-classification, better …