Associating expression and genomic data using co-occurrence measures

Network-based integration of multi-omics data for prioritizing cancer genes

(2018) Christos Dimitrakopoulos et al.   BIOINFORMATICS

A Comprehensive Pan-Cancer Molecular Study of Gynecologic and Breast Cancers

(2018) Ashton C. Berger et al.   CANCER CELL

Impacts of somatic mutations on gene expression: an association perspective

(2016) Peilin Jia et al.   BRIEFINGS IN BIOINFORMATICS

The BioGRID interaction database: 2017 update

(2016) Andrew Chatr-aryamontri et al.   NUCLEIC ACIDS RESEARCH

Computational approaches for the identification of cancer genes and pathways

(2016) Christos M. Dimitrakopoulos et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

Discovering gene re-ranking efficiency and conserved gene-gene relationships derived from gene co-expression network analysis on breast cancer data

(2016) Marilena M. Bourdakou et al.   Scientific Reports

Discretization of gene expression data revised

(2015) Cristian A. Gallo et al.   BRIEFINGS IN BIOINFORMATICS

Kinome-wide Decoding of Network-Attacking Mutations Rewiring Cancer Signaling

(2015) Pau Creixell et al.   CELL

Pathway and network analysis of cancer genomes

(2015)   NATURE METHODS

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Systematic analysis of somatic mutations impacting gene expression in 12 tumour types

(2015) Jiarui Ding et al.   Nature Communications

Pathway Relevance Ranking for Tumor Samples through Network-Based Data Integration

(2015) Lieven P. C. Verbeke et al.   PLoS One

Mammary Fat of Breast Cancer: Gene Expression Profiling and Functional Characterization

(2014) Fengliang Wang et al.   PLoS One

Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

Systematic Analysis of Challenge-Driven Improvements in Molecular Prognostic Models for Breast Cancer

(2013) A. A. Margolin et al.   Science Translational Medicine

HER-2 gene amplification in human breast cancer without concurrent HER-2 over-expression

(2013) Shiuh-Wen Luoh et al.   SpringerPlus

PARADIGM-SHIFT predicts the function of mutations in multiple cancers using pathway impact analysis

(2012) Sam Ng et al.   BIOINFORMATICS

Network Medicine Strikes a Blow against Breast Cancer

(2012) Janine T. Erler et al.   CELL

Mutant p53 binds to estrogen receptor negative promoter via DNMT1 and HDAC1 in MDA-MB-468 breast cancer cells

(2012) Rita Arabsolghar et al.   MOLECULAR BIOLOGY REPORTS

The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups

(2012) Christina Curtis et al.   NATURE

Wisdom of crowds for robust gene network inference

(2012) Daniel Marbach et al.   NATURE METHODS

Discovering time-lagged rules from microarray data using gene profile classifiers

(2011) Cristian A Gallo et al.   BMC BIOINFORMATICS

Predictive modeling of the hypothalamic-pituitary-adrenal (HPA) axis response to acute and chronic stress

(2011) Vladimir M. Markovic et al.   ENDOCRINE JOURNAL

p53 Binds to Estrogen Receptor 1 Promoter in Human Breast Cancer Cells

(2011) Mozhgan Rasti et al.   PATHOLOGY & ONCOLOGY RESEARCH

GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers

(2011) Craig H Mermel et al.   GENOME BIOLOGY

A similarity measure for indefinite rankings

(2010) William Webber et al.   ACM TRANSACTIONS ON INFORMATION SYSTEMS

Inferring gene regression networks with model trees

(2010) Isabel A Nepomuceno-Chamorro et al.   BMC BIOINFORMATICS

Discretization of Time Series Data

(2010) Elena S. Dimitrova et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Advantages and limitations of current network inference methods

(2010) Riet De Smet et al.   NATURE REVIEWS MICROBIOLOGY

A systems biology view of cancer

(2009) Reinhard Laubenbacher et al.   BIOCHIMICA ET BIOPHYSICA ACTA-REVIEWS ON CANCER

Supervised Risk Predictor of Breast Cancer Based on Intrinsic Subtypes

(2009) Joel S. Parker et al.   JOURNAL OF CLINICAL ONCOLOGY

Prognostic value of matrix Gla protein in breast cancer

(2009) Miki   Molecular Medicine Reports

Aurora-A gene is frequently amplified in basal-like breast cancer

(2009) Staff   ONCOLOGY REPORTS

DISTILLER: a data integration framework to reveal condition dependency of complex regulons in Escherichia coli

(2009) Karen Lemmens et al.   GENOME BIOLOGY

Gene interaction – An evolutionary biclustering approach

(2008) Sushmita Mitra et al.   Information Fusion

Modelling and analysis of gene regulatory networks

(2008) Guy Karlebach et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY