An engineering design approach to systems biology

Exploiting Temporal Collateral Sensitivity in Tumor Clonal Evolution

(2016) Boyang Zhao et al.   CELL

Modeling Development and Disease with Organoids

(2016) Hans Clevers   CELL

Antisense transcription as a tool to tune gene expression

(2016) J. A. Brophy et al.   Molecular Systems Biology

Constraints on Fluctuations in Sparsely Characterized Biological Systems

(2016) Andreas Hilfinger et al.   PHYSICAL REVIEW LETTERS

Limits to the precision of gradient sensing with spatial communication and temporal integration

(2016) Andrew Mugler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Early signaling dynamics of the epidermal growth factor receptor

(2016) Raven J. Reddy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A global genetic interaction network maps a wiring diagram of cellular function

(2016) M. Costanzo et al.   SCIENCE

Learning (from) the errors of a systems biology model

(2016) Benjamin Engelhardt et al.   Scientific Reports

Agent-based computational model investigates muscle-specific responses to disuse-induced atrophy

(2015) Kyle S. Martin et al.   JOURNAL OF APPLIED PHYSIOLOGY

Do genome-scale models need exact solvers or clearer standards?

(2015) A. Ebrahim et al.   Molecular Systems Biology

An analysis of critical factors for quantitative immunoblotting

(2015) Kevin A. Janes   Science Signaling

IκBβ enhances the generation of the low-affinity NFκB/RelA homodimer

(2015) Rachel Tsui et al.   Nature Communications

Multiscale models of skeletal muscle reveal the complex effects of muscular dystrophy on tissue mechanics and damage susceptibility

(2015) Kelley M. Virgilio et al.   Interface Focus

Inference of Network Dynamics and Metabolic Interactions in the Gut Microbiome

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

An analysis of critical factors for quantitative immunoblotting

(2015) Kevin A. Janes   Science Signaling

Identification of Causal Genetic Drivers of Human Disease through Systems-Level Analysis of Regulatory Networks

(2014) James C. Chen et al.   CELL

Molecular Mechanisms Underlying Bacterial Persisters

(2014) Etienne Maisonneuve et al.   CELL

Integrating Biological Redesign: Where Synthetic Biology Came From and Where It Needs to Go

(2014) Jeffrey C. Way et al.   CELL

Multiplatform Analysis of 12 Cancer Types Reveals Molecular Classification within and across Tissues of Origin

(2014) Katherine A. Hoadley et al.   CELL

The National Institutes of Health's Big Data to Knowledge (BD2K) initiative: capitalizing on biomedical big data

(2014) Ronald Margolis et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Discovery and saturation analysis of cancer genes across 21 tumour types

(2014) Michael S. Lawrence et al.   NATURE

A time- and matrix-dependent TGFBR3–JUND–KRT5 regulatory circuit in single breast epithelial cells and basal-like premalignancies

(2014) Chun-Chao Wang et al.   NATURE CELL BIOLOGY

Conditional density-based analysis of T cell signaling in single-cell data

(2014) S. Krishnaswamy et al.   SCIENCE

Multiscale Computational Models of Complex Biological Systems

(2013) Joseph Walpole et al.   Annual Review of Biomedical Engineering

Models of signalling networks - what cell biologists can gain from them and give to them

(2013) K. A. Janes et al.   JOURNAL OF CELL SCIENCE

Systems genetics approaches to understand complex traits

(2013) Mete Civelek et al.   NATURE REVIEWS GENETICS

How Cells Know Where They Are

(2013) A. D. Lander   SCIENCE

Computational Analysis of the Regulation of EGFR by Protein Tyrosine Phosphatases

(2012) Calixte S. Monast et al.   BIOPHYSICAL JOURNAL

Mechanical regulation of fibroblast migration and collagen remodelling in healing myocardial infarcts

(2012) Andrew D. Rouillard et al.   JOURNAL OF PHYSIOLOGY-LONDON

Erratum: Integrated genomic analyses of ovarian carcinoma

(2012) The Cancer Genome Atlas Research Network   NATURE

Regulation of nuclear PKA revealed by spatiotemporal manipulation of cyclic AMP

(2012) Vedangi Sample et al.   Nature Chemical Biology

Negative Feedback and Adaptive Resistance to the Targeted Therapy of Cancer

(2012) Sarat Chandarlapaty   Cancer Discovery

Ensuring Congruency in Multiscale Modeling: Towards Linking Agent Based and Continuum Biomechanical Models of Arterial Adaptation

(2011) Heather N. Hayenga et al.   ANNALS OF BIOMEDICAL ENGINEERING

Robustness portraits of diverse biological networks conserved despite order-of-magnitude parameter uncertainty

(2011) Anthony R. Soltis et al.   BIOINFORMATICS

Network News: Innovations in 21st Century Systems Biology

(2011) Adam P. Arkin et al.   CELL

The multiple dimensions of Integrative Biology

(2011)   Integrative Biology

What's wrong with correlative experiments?

(2011) Marco Vilela et al.   NATURE CELL BIOLOGY

The productivity crisis in pharmaceutical R&D

(2011) Fabio Pammolli et al.   NATURE REVIEWS DRUG DISCOVERY

Integrating Multiple Types of Data for Signaling Research: Challenges and Opportunities

(2011) H. S. Wiley   Science Signaling

To Explain or to Predict?

(2011) Galit Shmueli   STATISTICAL SCIENCE

Systems Analysis of Small Signaling Modules Relevant to Eight Human Diseases

(2010) Kelly F. Benedict et al.   ANNALS OF BIOMEDICAL ENGINEERING

A synchronized quorum of genetic clocks

(2010) Tal Danino et al.   NATURE

Pairwise network mechanisms in the host signaling response to coxsackievirus B3 infection

(2010) F. S. Garmaroudi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Upscaling microbial chemotaxis in porous media

(2009) Francisco J. Valdés-Parada et al.   ADVANCES IN WATER RESOURCES

The Allen Brain Atlas: 5 years and beyond

(2009) Allan R. Jones et al.   NATURE REVIEWS NEUROSCIENCE

Therapeutically Targeting ErbB3: A Key Node in Ligand-Induced Activation of the ErbB Receptor-PI3K Axis

(2009) B. Schoeberl et al.   Science Signaling

Cytokine-Induced Signaling Networks Prioritize Dynamic Range over Signal Strength

(2008) Kevin A. Janes et al.   CELL

Frequency-modulated nuclear localization bursts coordinate gene regulation

(2008) Long Cai et al.   NATURE

Breakdown of Fourier’s Law in Nanotube Thermal Conductors

(2008) C. W. Chang et al.   PHYSICAL REVIEW LETTERS

Fault Diagnosis Engineering of Digital Circuits Can Identify Vulnerable Molecules in Complex Cellular Pathways

(2008) A. Abdi et al.   Science Signaling

Modeling a Snap-Action, Variable-Delay Switch Controlling Extrinsic Cell Death

(2008) John G Albeck et al.   PLOS BIOLOGY