Improving Breast Cancer Survival Analysis through Competition-Based Multidimensional Modeling

Prize-based contests can provide solutions to computational biology problems

(2013) Karim R Lakhani et al.   NATURE BIOTECHNOLOGY

A large-scale evaluation of computational protein function prediction

(2013) Predrag Radivojac et al.   NATURE METHODS

Industrial methodology for process verification in research (IMPROVER): toward systems biology verification

(2012) P. Meyer et al.   BIOINFORMATICS

Developing predictive molecular maps of human disease through community-based modeling

(2012) Jonathan M J Derry et al.   NATURE GENETICS

Wisdom of crowds for robust gene network inference

(2012) Daniel Marbach et al.   NATURE METHODS

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

(2011) Trey Ideker et al.   CELL

Assemblathon 1: A competitive assessment of de novo short read assembly methods

(2011) D. Earl et al.   GENOME RESEARCH

The self-assessment trap: can we all be better than average?

(2011) R. Norel et al.   Molecular Systems Biology

Verification of systems biology research in the age of collaborative competition

(2011) Pablo Meyer et al.   NATURE BIOTECHNOLOGY

miRNA-mRNA Integrated Analysis Reveals Roles for miRNAs in Primary Breast Tumors

(2011) Espen Enerly et al.   PLoS One

Integrated molecular profiles of invasive breast tumors and ductal carcinoma in situ (DCIS) reveal differential vascular and interleukin signaling

(2011) V. N. Kristensen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Crowdsourcing Network Inference: The DREAM Predictive Signaling Network Challenge

(2011) R. J. Prill et al.   Science Signaling

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

(2011) David Venet et al.   PLoS Computational Biology

Supervised normalization of microarrays

(2010) Brigham H. Mecham et al.   BIOINFORMATICS

A multilevel model to address batch effects in copy number estimation using SNP arrays

(2010) R. B. Scharpf et al.   BIOSTATISTICS

Erratum: Large meta-analysis of multiple cancers reveals a common, compact and highly prognostic hypoxia metagene

(2010) F M Buffa et al.   BRITISH JOURNAL OF CANCER

An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man

(2010) Timothy Ravasi et al.   CELL

Genomic instability in breast cancer: Pathogenesis and clinical implications

(2010) Kevin A. Kwei et al.   Molecular Oncology

The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models

(2010)   NATURE BIOTECHNOLOGY

Towards a Rigorous Assessment of Systems Biology Models: The DREAM3 Challenges

(2010) Robert J. Prill et al.   PLoS One

Core epithelial-to-mesenchymal transition interactome gene-expression signature is associated with claudin-low and metaplastic breast cancer subtypes

(2010) J. H. Taube et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Revealing strengths and weaknesses of methods for gene network inference

(2010) D. Marbach et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RETRACTED: A Pleiotropically Acting MicroRNA, miR-31, Inhibits Breast Cancer Metastasis

(2009) Scott Valastyan et al.   CELL

Current molecular diagnostics of breast cancer and the potential incorporation of microRNA

(2009) Christine K Zoon et al.   EXPERT REVIEW OF MOLECULAR DIAGNOSTICS

Gene-Expression Signatures in Breast Cancer

(2009) Christos Sotiriou et al.   NEW ENGLAND JOURNAL OF MEDICINE

Assessment of CASP8 structure predictions for template free targets

(2009) Moshe Ben-David et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Clinical Application of the 70-Gene Profile: The MINDACT Trial

(2008) Fatima Cardoso et al.   JOURNAL OF CLINICAL ONCOLOGY

An embryonic stem cell–like gene expression signature in poorly differentiated aggressive human tumors

(2008) Ittai Ben-Porath et al.   NATURE GENETICS