Cancer subtype classification and modeling by pathway attention and propagation

Predictive modelling using pathway scores: robustness and significance of pathway collections

(2019) Marcelo P. Segura-Lepe et al.   BMC BIOINFORMATICS

A graph-embedded deep feedforward network for disease outcome classification and feature selection using gene expression data

(2018) Yunchuan Kong et al.   BIOINFORMATICS

Modeling polypharmacy side effects with graph convolutional networks

(2018) Marinka Zitnik et al.   BIOINFORMATICS

Classifying tumors by supervised network propagation

(2018) Wei Zhang et al.   BIOINFORMATICS

The Human Transcription Factors

(2018) Samuel A. Lambert et al.   CELL

A Comprehensive Immunologic Portrait of Triple-Negative Breast Cancer

(2018) Zhixian Liu et al.   Translational Oncology

The Interleukin-17 Family of Cytokines in Breast Cancer

(2018) Joseph Fabre et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Network propagation: a universal amplifier of genetic associations

(2017) Lenore Cowen et al.   NATURE REVIEWS GENETICS

TRRUST v2: an expanded reference database of human and mouse transcriptional regulatory interactions

(2017) Heonjong Han et al.   NUCLEIC ACIDS RESEARCH

De novo pathway-based biomarker identification

(2017) Nicolas Alcaraz et al.   NUCLEIC ACIDS RESEARCH

Influence maximization in time bounded network identifies transcription factors regulating perturbed pathways

(2016) Kyuri Jo et al.   BIOINFORMATICS

Protein interaction network (PIN)-based breast cancer subsystem identification and activation measurement for prognostic modeling

(2016) S. Lim et al.   METHODS

Can we open the black box of AI?

(2016) Davide Castelvecchi   NATURE

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

(2016) Maxim V. Kuleshov et al.   NUCLEIC ACIDS RESEARCH

InteractiVenn: a web-based tool for the analysis of sets through Venn diagrams

(2015) Henry Heberle et al.   BMC BIOINFORMATICS

The Role of Cytokines in Breast Cancer Development and Progression

(2015) Marcela Esquivel-Velázquez et al.   JOURNAL OF INTERFERON AND CYTOKINE RESEARCH

Can Breast Cancer Molecular Subtype Help to Select Patients for Preoperative MR Imaging?

(2015) Lars J. Grimm et al.   RADIOLOGY

Pan-cancer network analysis identifies combinations of rare somatic mutations across pathways and protein complexes

(2014) Mark D M Leiserson et al.   NATURE GENETICS

SOCS3-mediated regulation of inflammatory cytokines in PTEN and p53 inactivated triple negative breast cancer model

(2014) G Kim et al.   ONCOGENE

The PI3K/AKT/mTOR pathway in breast cancer: targets, trials and biomarkers

(2014) Elisavet Paplomata et al.   Therapeutic Advances in Medical Oncology

Growth of Triple-Negative Breast Cancer Cells Relies upon Coordinate Autocrine Expression of the Proinflammatory Cytokines IL-6 and IL-8

(2013) Z. C. Hartman et al.   CANCER RESEARCH

Network-based stratification of tumor mutations

(2013) Matan Hofree et al.   NATURE METHODS

Pathway-based classification of cancer subtypes

(2012) Shinuk Kim et al.   Biology Direct

A comprehensive morphological study for basal-like breast carcinomas with comparison to nonbasal-like carcinomas

(2012) Asli Cakir et al.   Diagnostic Pathology

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

Wavelets on graphs via spectral graph theory

(2010) David K. Hammond et al.   APPLIED AND COMPUTATIONAL HARMONIC ANALYSIS

A pathway-based classification of human breast cancer

(2010) M. L. Gatza et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

KEGGgraph: a graph approach to KEGG PATHWAY in R and bioconductor

(2009) Jitao David Zhang et al.   BIOINFORMATICS

Supervised Risk Predictor of Breast Cancer Based on Intrinsic Subtypes

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

Accurate and Reliable Cancer Classification Based on Probabilistic Inference of Pathway Activity

(2009) Junjie Su et al.   PLoS One

Walking the Interactome for Prioritization of Candidate Disease Genes

(2008) Sebastian Köhler et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Getting Started in Biological Pathway Construction and Analysis

(2008) Ganesh A Viswanathan et al.   PLoS Computational Biology