Understanding disease mechanisms with models of signaling pathway activities

Inhibition of JAK1, 2/STAT3 Signaling Induces Apoptosis, Cell Cycle Arrest, and Reduces Tumor Cell Invasion in Colorectal Cancer Cells

(2015) Hua Xiong et al.   NEOPLASIA

Genomics and transcriptomics in drug discovery

(2013) Joaquin Dopazo   DRUG DISCOVERY TODAY

Graphite Web: web tool for gene set analysis exploiting pathway topology

(2013) Gabriele Sales et al.   NUCLEIC ACIDS RESEARCH

Inferring the functional effect of gene expression changes in signaling pathways

(2013) Patricia Sebastián-León et al.   NUCLEIC ACIDS RESEARCH

Adiponectin Regulates Vascular Endothelial Growth Factor-C Expression in Macrophages via Syk-ERK Pathway

(2013) Di Hu et al.   PLoS One

A Comparison of Gene Set Analysis Methods in Terms of Sensitivity, Prioritization and Specificity

(2013) Adi L. Tarca et al.   PLoS One

Understanding cellular function and disease with comparative pathway analysis

(2013) Melissa J Davis et al.   Genome Medicine

Differential Expression Analysis for Pathways

(2013) Winston A. Haynes et al.   PLoS Computational Biology

More power via graph-structured tests for differential expression of gene networks

(2012) Laurent Jacob et al.   Annals of Applied Statistics

graphite - a Bioconductor package to convert pathway topology to gene network

(2012) Gabriele Sales et al.   BMC BIOINFORMATICS

Gene interaction enrichment and network analysis to identify dysregulated pathways and their interactions in complex diseases

(2012) Yu Liu et al.   BMC Systems Biology

A Topology-Based Score for Pathway Enrichment

(2012) Maysson Al-Haj Ibrahim et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Preparing for Precision Medicine

(2012) Reza Mirnezami et al.   NEW ENGLAND JOURNAL OF MEDICINE

Along signal paths: an empirical gene set approach exploiting pathway topology

(2012) Paolo Martini et al.   NUCLEIC ACIDS RESEARCH

TEAK: Topology Enrichment Analysis frameworK for detecting activated biological subpathways

(2012) Thair Judeh et al.   NUCLEIC ACIDS RESEARCH

Pathway-Based Evaluation in Early Onset Colorectal Cancer Suggests Focal Adhesion and Immunosuppression along with Epithelial-Mesenchymal Transition

(2012) Seungyoon Nam et al.   PLoS One

Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges

(2012) Purvesh Khatri et al.   PLoS Computational Biology

Jetset: selecting the optimal microarray probe set to represent a gene

(2011) Qiyuan Li et al.   BMC BIOINFORMATICS

Integrating Factor Analysis and a Transgenic Mouse Model to Reveal a Peripheral Blood Predictor of Breast Tumors

(2011) Heather G LaBreche et al.   BMC Medical Genomics

Interactome Networks and Human Disease

(2011) Marc Vidal et al.   CELL

Differential Lipid Partitioning Between Adipocytes and Tissue Macrophages Modulates Macrophage Lipotoxicity and M2/M1 Polarization in Obese Mice

(2011) Xavier Prieur et al.   DIABETES

Differential expression in RNA-seq: A matter of depth

(2011) S. Tarazona et al.   GENOME RESEARCH

Subcutaneous Adipose Tissue Remodeling during the Initial Phase of Weight Gain Induced by Overfeeding in Humans

(2011) M. Alligier et al.   JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Human bone marrow hematopoietic stem cells are increased in frequency and myeloid-biased with age

(2011) W. W. Pang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Systems biology and the future of medicine

(2011) Joseph Loscalzo et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

A sub-pathway-based approach for identifying drug response principal network

(2010) Xiujie Chen et al.   BIOINFORMATICS

Evaluation of gene expression signatures predictive of cytogenetic and molecular subtypes of pediatric acute myeloid leukemia

(2010) B. V. Balgobind et al.   HAEMATOLOGICA

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

(2010)   NATURE BIOTECHNOLOGY

Principles and challenges of genome-wide DNA methylation analysis

(2010) Peter W. Laird   NATURE REVIEWS GENETICS

Network medicine: a network-based approach to human disease

(2010) Albert-László Barabási et al.   NATURE REVIEWS GENETICS

Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling

(2010) Ignacio Medina et al.   NUCLEIC ACIDS RESEARCH

Multidimensional Gene Set Analysis of Genomic Data

(2010) David Montaner et al.   PLoS One

Wnt Fans the Flames in Obesity

(2010) D. Y. Oh et al.   SCIENCE

TLR8-dependent TNF-  overexpression in Fanconi anemia group C cells

(2009) S. M. Vanderwerf et al.   BLOOD

Gene set internal coherence in the context of functional profiling

(2009) David Montaner et al.   BMC GENOMICS

Analysis of Gene Sets Based on the Underlying Regulatory Network

(2009) Ali Shojaie et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Wnt/Planar cell polarity signaling: A new paradigm for cancer therapy

(2009) Y. Wang   MOLECULAR CANCER THERAPEUTICS

Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction

(2009) Julio Saez-Rodriguez et al.   Molecular Systems Biology

Molecular networks as sensors and drivers of common human diseases

(2009) Eric E. Schadt   NATURE

Repeatability of published microarray gene expression analyses

(2009) John P A Ioannidis et al.   NATURE GENETICS

Long-term estrogen exposure promotes carcinogen bioactivation, induces persistent changes in gene expression, and enhances the tumorigenicity of MCF-7 human breast cancer cells

(2009) Barbara C. Spink et al.   TOXICOLOGY AND APPLIED PHARMACOLOGY

The Logic of EGFR/ErbB Signaling: Theoretical Properties and Analysis of High-Throughput Data

(2009) Regina Samaga et al.   PLoS Computational Biology

Identifying Drug Effects via Pathway Alterations using an Integer Linear Programming Optimization Formulation on Phosphoproteomic Data

(2009) Alexander Mitsos et al.   PLoS Computational Biology

Choosing the right path: enhancement of biologically relevant sets of genes or proteins using pathway structure

(2009) Reuben Thomas et al.   GENOME BIOLOGY

Formulating and testing hypotheses in functional genomics

(2008) Joaquin Dopazo   ARTIFICIAL INTELLIGENCE IN MEDICINE

A novel signaling pathway impact analysis

(2008) Adi Laurentiu Tarca et al.   BIOINFORMATICS

Gene-set approach for expression pattern analysis

(2008) D. Nam et al.   BRIEFINGS IN BIOINFORMATICS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH

Superposition of Transcriptional Behaviors Determines Gene State

(2008) Sol Efroni et al.   PLoS One

Network model of survival signaling in large granular lymphocyte leukemia

(2008) R. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Emergent decision-making in biological signal transduction networks

(2008) T. Helikar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Inferring Pathway Activity toward Precise Disease Classification

(2008) Eunjung Lee et al.   PLoS Computational Biology

Identification of genes with abnormal expression changes in acute myeloid leukemia

(2007) Derek L. Stirewalt et al.   GENES CHROMOSOMES & CANCER