Unraveling a tumor type-specific regulatory core underlying E2F1-mediated epithelial-mesenchymal transition to predict receptor protein signatures

Functional characterization of somatic mutations in cancer using network-based inference of protein activity

(2016) Mariano J Alvarez et al.   NATURE GENETICS

The FGFR Landscape in Cancer: Analysis of 4,853 Tumors by Next-Generation Sequencing

(2015) T. Helsten et al.   CLINICAL CANCER RESEARCH

The Role of EGFR Family Inhibitors in Muscle Invasive Bladder Cancer: A Review of Clinical Data and Molecular Evidence

(2015) Benjamin A. Mooso et al.   JOURNAL OF UROLOGY

The Cancer Cell Map Initiative: Defining the Hallmark Networks of Cancer

(2015) Nevan J. Krogan et al.   MOLECULAR CELL

Network modelling reveals the mechanism underlying colitis-associated colon cancer and identifies novel combinatorial anti-cancer targets

(2015) Junyan Lu et al.   Scientific Reports

Network Modeling of TGF  Signaling in Hepatocellular Carcinoma Epithelial-to-Mesenchymal Transition Reveals Joint Sonic Hedgehog and Wnt Pathway Activation

(2014) S. N. Steinway et al.   CANCER RESEARCH

E2F1 induces miR-224/452 expression to drive EMT through TXNIP downregulation

(2014) S. Knoll et al.   EMBO REPORTS

Association of RHAMM with E2F1 promotes tumour cell extravasation by transcriptional up-regulation of fibronectin

(2014) Claudia Meier et al.   JOURNAL OF PATHOLOGY

A comprehensive transcriptional portrait of human cancer cell lines

(2014) Christiaan Klijn et al.   NATURE BIOTECHNOLOGY

Molecular mechanisms of epithelial–mesenchymal transition

(2014) Samy Lamouille et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Identification of Important Nodes in Directed Biological Networks: A Network Motif Approach

(2014) Pei Wang et al.   PLoS One

Mammalian Lysine Histone Demethylase KDM2A Regulates E2F1-Mediated Gene Transcription in Breast Cancer Cells

(2014) Wasia Rizwani et al.   PLoS One

Hybrid modeling of the crosstalk between signaling and transcriptional networks using ordinary differential equations and multi-valued logic

(2013) Faiz M. Khan et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps

(2013) Inna Kuperstein et al.   BMC Systems Biology

A comprehensive map of the influenza A virus replication cycle

(2013) Yukiko Matsuoka et al.   BMC Systems Biology

Kinetic Modeling-Based Detection of Genetic Signatures That Provide Chemoresistance via the E2F1-p73/DNp73-miR-205 Network

(2013) J. Vera et al.   CANCER RESEARCH

FGF Receptors: Cancer Biology and Therapeutics

(2013) Masaru Katoh et al.   MEDICINAL RESEARCH REVIEWS

Network-based stratification of tumor mutations

(2013) Matan Hofree et al.   NATURE METHODS

HER2/Neu tumorigenesis and metastasis is regulated by E2F activator transcription factors

(2013) E R Andrechek   ONCOGENE

E2F1 promotes angiogenesis through the VEGF-C/VEGFR-3 axis in a feedback loop for cooperative induction of PDGF-B

(2013) David Engelmann et al.   Journal of Molecular Cell Biology

CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms

(2012) Camille Terfve et al.   BMC Systems Biology

The Dark Side of E2F1: In Transit beyond Apoptosis

(2012) D. Engelmann et al.   CANCER RESEARCH

E2F1 confers anticancer drug resistance by targeting ABC transporter family members and Bcl-2 via the p73/DNp73-miR-205 circuitry

(2012) Vijay Alla et al.   CELL CYCLE

GPEC: A Cytoscape plug-in for random walk-based gene prioritization and biomedical evidence collection

(2012) Duc-Hau Le et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

High epidermal growth factor receptor immunohistochemical expression in urothelial carcinoma of the bladder is not associated with EGFR mutations in exons 19 and 21: a study using formalin-fixed, paraffin-embedded archival tissues

(2012) Alcides Chaux et al.   HUMAN PATHOLOGY

Analysis of cell adhesion during early stages of colon cancer based on an extended multi-valued logic approach

(2012) Daniel V. Guebel et al.   Molecular BioSystems

STRING v9.1: protein-protein interaction networks, with increased coverage and integration

(2012) Andrea Franceschini et al.   NUCLEIC ACIDS RESEARCH

FGFR1-Induced Epithelial to Mesenchymal Transition through MAPK/PLCγ/COX-2-Mediated Mechanisms

(2012) Darren C. Tomlinson et al.   PLoS One

FGFR Genetic Alterations Predict for Sensitivity to NVP-BGJ398, a Selective Pan-FGFR Inhibitor

(2012) V. Guagnano et al.   Cancer Discovery

NetDS: a Cytoscape plugin to analyze the robustness of dynamics and feedforward/feedback loop structures of biological networks

(2011) Duc-Hau Le et al.   BIOINFORMATICS

PSICQUIC and PSISCORE: accessing and scoring molecular interactions

(2011) Bruno Aranda et al.   NATURE METHODS

The Transcription Factors Snail and Slug Activate the Transforming Growth Factor-Beta Signaling Pathway in Breast Cancer

(2011) Archana Dhasarathy et al.   PLoS One

Functional Motifs in Biochemical Reaction Networks

(2010) John J. Tyson et al.   Annual Review of Physical Chemistry

Predicting and preventing melanoma invasiveness: advances in clarifying E2F1 function

(2010) Brigitte M Pützer et al.   Expert Review of Anticancer Therapy

The retinoblastoma tumor suppressor controls androgen signaling and human prostate cancer progression

(2010) Ankur Sharma et al.   JOURNAL OF CLINICAL INVESTIGATION

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

miRTarBase: a database curates experimentally validated microRNA–target interactions

(2010) Sheng-Da Hsu et al.   NUCLEIC ACIDS RESEARCH

A Comprehensive Molecular Interaction Map for Rheumatoid Arthritis

(2010) Gang Wu et al.   PLoS One

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Cancer systems biology: a network modeling perspective

(2009) P. K. Kreeger et al.   CARCINOGENESIS

Optimization of biochemical systems through mathematical programming: Methods and applications

(2009) Julio Vera et al.   COMPUTERS & OPERATIONS RESEARCH

E2F1 in Melanoma Progression and Metastasis

(2009) Vijay Alla et al.   JNCI-Journal of the National Cancer Institute

The Systems Biology Graphical Notation

(2009) Nicolas Le Novère et al.   NATURE BIOTECHNOLOGY

TransmiR: a transcription factor–microRNA regulation database

(2009) Juan Wang et al.   NUCLEIC ACIDS RESEARCH

Topological properties of protein interaction networks from a structural perspective

(2008) Attila Gursoy et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

A comprehensive modular map of molecular interactions in RB/E2F pathway

(2008) Laurence Calzone et al.   Molecular Systems Biology

The miR-200 family and miR-205 regulate epithelial to mesenchymal transition by targeting ZEB1 and SIP1

(2008) Philip A. Gregory et al.   NATURE CELL BIOLOGY

Human Protein Reference Database--2009 update

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

E2F – at the crossroads of life and death

(2008) Shirley Polager et al.   TRENDS IN CELL BIOLOGY