Edge-based sensitivity analysis of signaling networks by using Boolean dynamics

Dynamical Robustness against Multiple Mutations in Signaling Networks

(2016) Yung-Keun Kwon et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Tumor suppressive functions of ceramide: evidence and mechanisms

(2015) Sehamuddin Galadari et al.   APOPTOSIS

Effective Boolean dynamics analysis to identify functionally important genes in large-scale signaling networks

(2015) Hung-Cuong Trinh et al.   BIOSYSTEMS

Targeting the MDM2/MDM4 Interaction Interface as a Promising Approach for p53 Reactivation Therapy

(2015) Marsha Pellegrino et al.   CANCER RESEARCH

Widespread Macromolecular Interaction Perturbations in Human Genetic Disorders

(2015) Nidhi Sahni et al.   CELL

Exploring the relationship between hub proteins and drug targets based on GO and intrinsic disorder

(2015) Yuanyuan Fu et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

Revisiting the sphingolipid rheostat: Evolving concepts in cancer therapy

(2015) Jason Newton et al.   EXPERIMENTAL CELL RESEARCH

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

SIGNOR: a database of causal relationships between biological entities

(2015) Livia Perfetto et al.   NUCLEIC ACIDS RESEARCH

The Reactome pathway Knowledgebase

(2015) Antonio Fabregat et al.   NUCLEIC ACIDS RESEARCH

Targeting RING domains of Mdm2–MdmX E3 complex activates apoptotic arm of the p53 pathway in leukemia/lymphoma cells

(2015) W Wu et al.   Cell Death & Disease

Inference of Network Dynamics and Metabolic Interactions in the Gut Microbiome

(2015) Steven N. Steinway et al.   PLoS Computational Biology

Analysis of Individual Protein Regions Provides Novel Insights on Cancer Pharmacogenomics

(2015) Eduard Porta Pardo et al.   PLoS Computational Biology

Robustness of Oscillatory Behavior in Correlated Networks

(2015) Takeyuki Sasai et al.   PLoS One

Global dynamic optimization approach to predict activation in metabolic pathways

(2014) Gundián M de Hijas-Liste et al.   BMC Systems Biology

Comprehensive analysis of microRNA-regulated protein interaction network reveals the tumor suppressive role of microRNA-149 in human hepatocellular carcinoma via targeting AKT-mTOR pathway

(2014) Yanqiong Zhang et al.   Molecular Cancer

Graph analysis of functional brain networks: practical issues in translational neuroscience

(2014) F. De Vico Fallani et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

PANET: A GPU-Based Tool for Fast Parallel Analysis of Robustness Dynamics and Feed-Forward/Feedback Loop Structures in Large-Scale Biological Networks

(2014) Hung-Cuong Trinh et al.   PLoS One

Construction and Analysis of the Protein-Protein Interaction Networks Based on Gene Expression Profiles of Parkinson's Disease

(2014) Hindol Rakshit et al.   PLoS One

Positive Feedback Promotes Oscillations in Negative Feedback Loops

(2014) Bharath Ananthasubramaniam et al.   PLoS One

Hot spots in protein–protein interfaces: Towards drug discovery

(2014) Engin Cukuroglu et al.   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

A Network Characteristic That Correlates Environmental and Genetic Robustness

(2014) Zeina Shreif et al.   PLoS Computational Biology

Robustness and Evolvability of the Human Signaling Network

(2014) Junil Kim et al.   PLoS Computational Biology

NOA: a cytoscape plugin for network ontology analysis

(2013) Chao Zhang et al.   BIOINFORMATICS

DrugBank 4.0: shedding new light on drug metabolism

(2013) Vivian Law et al.   NUCLEIC ACIDS RESEARCH

Mutations that disrupt PHOXB interaction with the neuronal calcium sensor HPCAL1 impede cellular differentiation in neuroblastoma

(2013) W Wang et al.   ONCOGENE

Three-dimensional reconstruction of protein networks provides insight into human genetic disease

(2012) Xiujuan Wang et al.   NATURE BIOTECHNOLOGY

The effects of feedback loops on disease comorbidity in human signaling networks

(2011) Duc-Hau Le et al.   BIOINFORMATICS

NOA: a novel Network Ontology Analysis method

(2011) Jiguang Wang et al.   NUCLEIC ACIDS RESEARCH

The p53 inhibitors MDM2/MDMX complex is required for control of p53 activity in vivo

(2011) L. Huang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reduction of Complex Signaling Networks to a Representative Kernel

(2011) J.-R. Kim et al.   Science Signaling

Dynamical and Structural Analysis of a T Cell Survival Network Identifies Novel Candidate Therapeutic Targets for Large Granular Lymphocyte Leukemia

(2011) Assieh Saadatpour et al.   PLoS Computational Biology

Integrated Genome-Scale Prediction of Detrimental Mutations in Transcription Networks

(2011) Mirko Francesconi et al.   PLoS Genetics

Identification of potential targets in biological signalling systems through network perturbation analysis

(2010) Francisco Azuaje et al.   BIOSYSTEMS

Diversity and Plasticity of Th Cell Types Predicted from Regulatory Network Modelling

(2010) Aurélien Naldi et al.   PLoS Computational Biology

Protein evolution on a human signaling network

(2009) Qinghua Cui et al.   BMC Systems Biology

Coherent coupling of feedback loops: a design principle of cell signaling networks

(2008) Yung-Keun Kwon et al.   BIOINFORMATICS

Quantitative analysis of robustness and fragility in biological networks based on feedback dynamics

(2008) Yung-Keun Kwon et al.   BIOINFORMATICS

Molecular profiling of LGL leukemia reveals role of sphingolipid signaling in survival of cytotoxic lymphocytes

(2008) M. V. Shah et al.   BLOOD