Network information improves cancer outcome prediction

Google Goes Cancer: Improving Outcome Prediction for Cancer Patients by Network-Based Ranking of Marker Genes

(2012) Christof Winter et al.   PLoS Computational Biology

Identifying cancer biomarkers by network-constrained support vector machines

(2011) Li Chen et al.   BMC Systems Biology

Boosting Signal-to-Noise in Complex Biology: Prior Knowledge Is Power

(2011) Trey Ideker et al.   CELL

Integrative computational biology for cancer research

(2011) Kristen Fortney et al.   HUMAN GENETICS

Subnetwork State Functions Define Dysregulated Subnetworks in Cancer

(2011) Salim A. Chowdhury et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

A Network-Based Approach to Prioritize Results from Genome-Wide Association Studies

(2011) Nirmala Akula et al.   PLoS One

Most Random Gene Expression Signatures Are Significantly Associated with Breast Cancer Outcome

(2011) David Venet et al.   PLoS Computational Biology

Protein Networks as Logic Functions in Development and Cancer

(2011) Janusz Dutkowski et al.   PLoS Computational Biology

Inferring cancer subnetwork markers using density-constrained biclustering

(2010) Phuong Dao et al.   BIOINFORMATICS

Integration of pathway knowledge into a reweighted recursive feature elimination approach for risk stratification of cancer patients

(2010) Marc Johannes et al.   BIOINFORMATICS

Genomic and Gene Expression Profiling Defines Indolent Forms of Mantle Cell Lymphoma

(2010) V. Fernandez et al.   CANCER RESEARCH

Surfing a genetic association interaction network to identify modulators of antibody response to smallpox vaccine

(2010) N A Davis et al.   GENES AND IMMUNITY

Expression Signature of E2F1 and Its Associated Genes Predict Superficial to Invasive Progression of Bladder Tumors

(2010) Ju-Seog Lee et al.   JOURNAL OF CLINICAL ONCOLOGY

Prognostic and Predictive Gene Signature for Adjuvant Chemotherapy in Resected Non–Small-Cell Lung Cancer

(2010) Chang-Qi Zhu et al.   JOURNAL OF CLINICAL ONCOLOGY

Tumor-Associated Macrophages and Survival in Classic Hodgkin's Lymphoma

(2010) Christian Steidl et al.   NEW ENGLAND JOURNAL OF MEDICINE

DEGAS: De Novo Discovery of Dysregulated Pathways in Human Diseases

(2010) Igor Ulitsky et al.   PLoS One

An Integrative -omics Approach to Identify Functional Sub-Networks in Human Colorectal Cancer

(2010) Rod K. Nibbe et al.   PLoS Computational Biology

Inferring the functions of longevity genes with modular subnetwork biomarkers of Caenorhabditis elegans aging

(2010) Kristen Fortney et al.   GENOME BIOLOGY

Molecular signatures to improve diagnosis in peripheral T-cell lymphoma and prognostication in angioimmunoblastic T-cell lymphoma

(2009) J. Iqbal et al.   BLOOD

A Gene Signature Predictive for Outcome in Advanced Ovarian Cancer Identifies a Survival Factor: Microfibril-Associated Glycoprotein 2

(2009) Samuel C. Mok et al.   CANCER CELL

A Genomic Approach to Improve Prognosis and Predict Therapeutic Response in Chronic Lymphocytic Leukemia

(2009) D. R. Friedman et al.   CLINICAL CANCER RESEARCH

Experimentally Derived Metastasis Gene Expression Profile Predicts Recurrence and Death in Patients With Colon Cancer

(2009) J. Joshua Smith et al.   GASTROENTEROLOGY

Identification and Validation of a Gene Expression Signature That Predicts Outcome in Adult Men With Germ Cell Tumors

(2009) James E. Korkola et al.   JOURNAL OF CLINICAL ONCOLOGY

Immune profile and mitotic index of metastatic melanoma lesions enhance clinical staging in predicting patient survival

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

A novel signaling pathway impact analysis

(2008) Adi Laurentiu Tarca et al.   BIOINFORMATICS

Facts from text: can text mining help to scale-up high-quality manual curation of gene products with ontologies?

(2008) R. Winnenburg et al.   BRIEFINGS IN BIOINFORMATICS

A Six-Gene Signature Predicting Breast Cancer Lung Metastasis

(2008) T. Landemaine et al.   CANCER RESEARCH

Stem Cell–Related “Self-Renewal” Signature and High Epidermal Growth Factor Receptor Expression Associated With Resistance to Concomitant Chemoradiotherapy in Glioblastoma

(2008) Anastasia Murat et al.   JOURNAL OF CLINICAL ONCOLOGY

Gene Expression Signatures Predictive of Early Response and Outcome in High-Risk Childhood Acute Lymphoblastic Leukemia: A Children's Oncology Group Study

(2008) Deepa Bhojwani et al.   JOURNAL OF CLINICAL ONCOLOGY

An empirical framework for binary interactome mapping

(2008) Kavitha Venkatesan et al.   NATURE METHODS

Stromal Gene Signatures in Large-B-Cell Lymphomas

(2008) G. Lenz et al.   NEW ENGLAND JOURNAL OF MEDICINE

Human Protein Reference Database--2009 update

(2008) T. S. Keshava Prasad et al.   NUCLEIC ACIDS RESEARCH

Estimating the size of the human interactome

(2008) M. P. H. Stumpf et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA