Adapting machine-learning algorithms to design gene circuits

Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks

(2017) Fabian Fröhlich et al.   PLoS Computational Biology

Incoherent Inputs Enhance the Robustness of Biological Oscillators

(2017) Zhengda Li et al.   Cell Systems

Optimal Regulatory Circuit Topologies for Fold-Change Detection

(2017) Miri Adler et al.   Cell Systems

Dynamic Gene Regulatory Networks Drive Hematopoietic Specification and Differentiation

(2016) Debbie K. Goode et al.   DEVELOPMENTAL CELL

Discovering governing equations from data by sparse identification of nonlinear dynamical systems

(2016) Steven L. Brunton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Continuous genetic recording with self-targeting CRISPR-Cas in human cells

(2016) S. D. Perli et al.   SCIENCE

Data-driven modelling of a gene regulatory network for cell fate decisions in the growing limb bud

(2015) M. Uzkudun et al.   Molecular Systems Biology

Deep learning

(2015) Yann LeCun et al.   NATURE

Synthetic biology devices for in vitro and in vivo diagnostics

(2015) Shimyn Slomovic et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolving Robust Gene Regulatory Networks

(2015) Nasimul Noman et al.   PLoS One

CellNet: Network Biology Applied to Stem Cell Engineering

(2014) Patrick Cahan et al.   CELL

A framework for parameter estimation and model selection from experimental data in systems biology using approximate Bayesian computation

(2014) Juliane Liepe et al.   Nature Protocols

Evolving phenotypic networks in silico

(2014) Paul François   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Transcription Factor Networks in Drosophila melanogaster

(2014) David Y. Rhee et al.   Cell Reports

Perturbation Biology: Inferring Signaling Networks in Cellular Systems

(2013) Evan J. Molinelli et al.   PLoS Computational Biology

Designing Synthetic Regulatory Networks Capable of Self-Organizing Cell Polarization

(2012) Angela H. Chau et al.   CELL

Deciphering a global network of functionally associated post-translational modifications

(2012) Pablo Minguez et al.   Molecular Systems Biology

Efficient Reverse-Engineering of a Developmental Gene Regulatory Network

(2012) Anton Crombach et al.   PLoS Computational Biology

Synthetic conversion of a graded receptor signal into a tunable, reversible switch

(2011) S. Palani et al.   Molecular Systems Biology

Progress in understanding reprogramming to the induced pluripotent state

(2011) Kathrin Plath et al.   NATURE REVIEWS GENETICS

Sequential Establishment of Stripe Patterns in an Expanding Cell Population

(2011) C. Liu et al.   SCIENCE

An atlas of gene regulatory networks reveals multiple three-gene mechanisms for interpreting morphogen gradients

(2010) James Cotterell et al.   Molecular Systems Biology

Emerging properties of animal gene regulatory networks

(2010) Eric H. Davidson   NATURE

Fundamental limits on the suppression of molecular fluctuations

(2010) Ioannis Lestas et al.   NATURE

Synthetic biology: applications come of age

(2010) Ahmad S. Khalil et al.   NATURE REVIEWS GENETICS

Defining Network Topologies that Can Achieve Biochemical Adaptation

(2009) Wenzhe Ma et al.   CELL

Synthetic biology: understanding biological design from synthetic circuits

(2009) Shankar Mukherji et al.   NATURE REVIEWS GENETICS

Synthetic Gene Networks That Count

(2009) A. E. Friedland et al.   SCIENCE

Canalization of Gene Expression in the Drosophila Blastoderm by Gap Gene Cross Regulation

(2009) Manu et al.   PLOS BIOLOGY

Canalization of Gene Expression and Domain Shifts in the Drosophila Blastoderm by Dynamical Attractors

(2009) Manu et al.   PLoS Computational Biology

A Quantitative Spatiotemporal Atlas of Gene Expression in the Drosophila Blastoderm

(2008) Charless C. Fowlkes et al.   CELL

A fast, robust and tunable synthetic gene oscillator

(2008) Jesse Stricker et al.   NATURE

Scaling of the BMP activation gradient in Xenopus embryos

(2008) Danny Ben-Zvi et al.   NATURE

Tuning gene expression to changing environments: from rapid responses to evolutionary adaptation

(2008) Luis López-Maury et al.   NATURE REVIEWS GENETICS

Design principles of biochemical oscillators

(2008) Béla Novák et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY