Cell Fate Reprogramming by Control of Intracellular Network Dynamics

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

Is the Voter Model a Model for Voters?

(2014) Juan Fernández-Gracia et al.   PHYSICAL REVIEW LETTERS

An effective network reduction approach to find the dynamical repertoire of discrete dynamic networks

(2013) Jorge G. T. Zañudo et al.   CHAOS

Dynamics and control at feedback vertex sets. II: A faithful monitor to determine the diversity of molecular activities in regulatory networks

(2013) Atsushi Mochizuki et al.   JOURNAL OF THEORETICAL BIOLOGY

The road from systems biology to systems medicine

(2013) Olaf Wolkenhauer et al.   PEDIATRIC RESEARCH

Observability of complex systems

(2013) Y.-Y. Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Duration of T Cell Stimulation Is a Critical Determinant of Cell Fate and Plasticity

(2013) N. Miskov-Zivanov et al.   Science Signaling

Realistic control of network dynamics

(2013) Sean P. Cornelius et al.   Nature Communications

Evolutionary dynamics of cancer in response to targeted combination therapy

(2013) Ivana Bozic et al.   eLife

Integer Programming-Based Approach to Attractor Detection and Control of Boolean Networks

(2012) Tatsuya AKUTSU et al.   IEICE TRANSACTIONS ON INFORMATION AND SYSTEMS

Combinatorial drug therapy for cancer in the post-genomic era

(2012) Bissan Al-Lazikani et al.   NATURE BIOTECHNOLOGY

Boolean modeling in systems biology: an overview of methodology and applications

(2012) Rui-Sheng Wang et al.   PHYSICAL BIOLOGY

Nodal Dynamics, Not Degree Distributions, Determine the Structural Controllability of Complex Networks

(2012) Noah J. Cowan et al.   PLoS One

Comparing Signaling Networks between Normal and Transformed Hepatocytes Using Discrete Logical Models

(2011) J. Saez-Rodriguez et al.   CANCER RESEARCH

Control of the Embryonic Stem Cell State

(2011) Richard A. Young   CELL

Reduction of Boolean network models

(2011) Alan Veliz-Cuba   JOURNAL OF THEORETICAL BIOLOGY

Few inputs can reprogram biological networks

(2011) Franz-Josef Müller et al.   NATURE

Controllability of complex networks

(2011) Yang-Yu Liu et al.   NATURE

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

Logic-Based Models for the Analysis of Cell Signaling Networks

(2010) Melody K. Morris et al.   BIOCHEMISTRY

Odefy -- From discrete to continuous models

(2010) Jan Krumsiek et al.   BMC BIOINFORMATICS

Attractor analysis of asynchronous Boolean models of signal transduction networks

(2010) Assieh Saadatpour et al.   JOURNAL OF THEORETICAL BIOLOGY

Extrinsic regulation of pluripotent stem cells

(2010) Martin F. Pera et al.   NATURE

Network medicine: a network-based approach to human disease

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

A network model for plant-pollinator community assembly

(2010) C. Campbell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dynamically consistent reduction of logical regulatory graphs

(2010) Aurélien Naldi et al.   THEORETICAL COMPUTER SCIENCE

Reliability of Transcriptional Cycles and the Yeast Cell-Cycle Oscillator

(2010) Volkan Sevim et al.   PLoS Computational Biology

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

(2010) Aurélien Naldi et al.   PLoS Computational Biology

Controllability and observability of Boolean control networks

(2009) Daizhan Cheng et al.   AUTOMATICA

Platelet-derived growth factor mediates survival of leukemic large granular lymphocytes via an autocrine regulatory pathway

(2009) J. Yang et al.   BLOOD

Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling

(2009) Dominik M Wittmann et al.   BMC Systems Biology

Statistical physics of social dynamics

(2009) Claudio Castellano et al.   REVIEWS OF MODERN PHYSICS

Cancer attractors: A systems view of tumors from a gene network dynamics and developmental perspective

(2009) Sui Huang et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Systems medicine: the future of medical genomics and healthcare

(2009) Charles Auffray et al.   Genome Medicine

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

(2008) M. V. Shah et al.   BLOOD

Interlinked nonlinear subnetworks underlie the formation of robust cellular patterns in Arabidopsis epidermis: a dynamic spatial model

(2008) Mariana Benítez et al.   BMC Systems Biology

Ablation of PI3K blocks BCR-ABL leukemogenesis in mice, and a dual PI3K/mTOR inhibitor prevents expansion of human BCR-ABL+ leukemia cells

(2008) Michael G. Kharas et al.   JOURNAL OF CLINICAL INVESTIGATION

Global control of cell-cycle transcription by coupled CDK and network oscillators

(2008) David A. Orlando et al.   NATURE

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