Phenotype Design Space Provides a Mechanistic Framework Relating Molecular Parameters to Phenotype Diversity Available for Selection

The Memory Problem for Neutral Mutational Models of Evolution

(2022) David A. Liberles   JOURNAL OF MOLECULAR EVOLUTION

Constructive Neutral Evolution 20 Years Later

(2021) Sergio A. Muñoz-Gómez et al.   JOURNAL OF MOLECULAR EVOLUTION

Extremely High-Throughput Parallel Microfluidic Vortex-Actuated Cell Sorting

(2021) Alex Zhukov et al.   Micromachines

Damped circadian oscillation in the absence of KaiA in Synechococcus

(2020) Naohiro Kawamoto et al.   Nature Communications

A resurrection study reveals limited evolution of thermal performance in response to recent climate change across the geographic range of the scarlet monkeyflower

(2020) Rachel Wooliver et al.   EVOLUTION

Mechanistic Modeling of Biochemical Systems without A Priori Parameter Values Using the Design Space Toolbox v.3.0

(2020) Miguel Á. Valderrama-Gómez et al.   iScience

‘It will change everything’: DeepMind’s AI makes gigantic leap in solving protein structures

(2020) Ewen Callaway   NATURE

Toward Developing Intuitive Rules for Protein Variant Effect Prediction Using Deep Mutational Scanning Data

(2020) Cheloor Kovilakam Sruthi et al.   ACS Omega

Predicting mutational routes to new adaptive phenotypes

(2019) Peter A Lind et al.   eLife

Circadian Rhythms in Plants

(2019) Nicky Creux et al.   Cold Spring Harbor Perspectives in Biology

Cryptic genetic variation accelerates evolution by opening access to diverse adaptive peaks

(2019) Jia Zheng et al.   SCIENCE

Distribution of fitness effects of mutations obtained from a simple genetic regulatory network model

(2019) R. G. Brajesh et al.   Scientific Reports

Inferring the distribution of fitness effects of spontaneous mutations in Chlamydomonas reinhardtii

(2019) Katharina B. Böndel et al.   PLOS BIOLOGY

The distribution of fitness effects among synonymous mutations in a gene under directional selection

(2019) Eleonore Lebeuf-Taylor et al.   eLife

Phenotype-centric modeling for elucidation of biological design principles

(2018) Miguel A. Valderrama-Gómez et al.   JOURNAL OF THEORETICAL BIOLOGY

Sign of selection on mutation rate modifiers depends on population size

(2018) Yevgeniy Raynes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mutation dynamics and fitness effects followed in single cells

(2018) Lydia Robert et al.   SCIENCE

Temperature drives diversification in a model adaptive radiation

(2018) Quan-Guo Zhang et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Inference of Distribution of Fitness Effects and Proportion of Adaptive Substitutions from Polymorphism Data

(2017) Paula Tataru et al.   GENETICS

Why Phenotype Robustness Promotes Phenotype Evolvability

(2017) Xinzhu Wei et al.   Genome Biology and Evolution

Environment determines evolutionary trajectory in a constrained phenotypic space

(2017) David T Fraebel et al.   eLife

Inference of Distribution of Fitness Effects and Proportion of Adaptive Substitutions from Polymorphism Data

(2017) Paula Tataru et al.   GENETICS

Selection on metabolic pathway function in the presence of mutation-selection-drift balance leads to rate-limiting steps that are not evolutionarily stable

(2016) Alena Orlenko et al.   Biology Direct

Flux Control in Glycolysis Varies Across the Tree of Life

(2016) Alena Orlenko et al.   JOURNAL OF MOLECULAR EVOLUTION

Genetic and epigenomic mechanisms of mammalian circadian transcription

(2016) Romeo Papazyan et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Molecular mechanisms at the core of the plant circadian oscillator

(2016) Maria A Nohales et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Genetic and epigenomic mechanisms of mammalian circadian transcription

(2016) Romeo Papazyan et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Molecular mechanisms at the core of the plant circadian oscillator

(2016) Maria A Nohales et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Genetic Correlations Greatly Increase Mutational Robustness and Can Both Reduce and Enhance Evolvability

(2016) Sam F. Greenbury et al.   PLoS Computational Biology

Design Space Toolbox V2: Automated Software Enabling a Novel Phenotype-Centric Modeling Strategy for Natural and Synthetic Biological Systems

(2016) Jason G. Lomnitz et al.   Frontiers in Genetics

Rapid Discrimination Among Putative Mechanistic Models of Biochemical Systems

(2016) Jason G. Lomnitz et al.   Scientific Reports

Evolvability as a Function of Purifying Selection in TEM-1 β-Lactamase

(2015) Michael A. Stiffler et al.   CELL

Circadian Rhythms in Cyanobacteria

(2015) Susan E. Cohen et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Determinants of spontaneous mutation in the bacteriumEscherichia colias revealed by whole-genome sequencing

(2015) Patricia L. Foster et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Experimental evolution reveals hidden diversity in evolutionary pathways

(2015) Peter A Lind et al.   eLife

Effects of new mutations on fitness: insights from models and data

(2014) Thomas Bataillon et al.   Annals of the New York Academy of Sciences

FISHER'S GEOMETRIC MODEL WITH A MOVING OPTIMUM

(2014) Sebastian Matuszewski et al.   EVOLUTION

Cryptic genetic variation: evolution's hidden substrate

(2014) Annalise B. Paaby et al.   NATURE REVIEWS GENETICS

The Robustness and Evolvability of Transcription Factor Binding Sites

(2014) J. L. Payne et al.   SCIENCE

Strategy Revealing Phenotypic Differences among Synthetic Oscillator Designs

(2014) Jason G. Lomnitz et al.   ACS Synthetic Biology

Three dimensional microfluidics with embedded microball lenses for parallel and high throughput multicolor fluorescence detection

(2013) Y. J. Fan et al.   Biomicrofluidics

Phenotypic deconstruction of gene circuitry

(2013) Jason G. Lomnitz et al.   CHAOS

Genome dynamics during experimental evolution

(2013) Jeffrey E. Barrick et al.   NATURE REVIEWS GENETICS

The essential role of cAMP/Ca2+signalling in mammalian circadian timekeeping

(2012) John S. O'Neill et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

The Molecular Diversity of Adaptive Convergence

(2012) O. Tenaillon et al.   SCIENCE

Measuring Selection Coefficients Below 10−3: Method, Questions, and Prospects

(2011) Romain Gallet et al.   GENETICS

Duplication Frequency in a Population of Salmonella enterica Rapidly Approaches Steady State With or Without Recombination

(2010) A. B. Reams et al.   GENETICS

Mutational robustness can facilitate adaptation

(2010) Jeremy A. Draghi et al.   NATURE

Evolution of the mutation rate

(2010) Michael Lynch   TRENDS IN GENETICS

Qualitatively distinct phenotypes in the design space of biochemical systems

(2009) Michael A. Savageau et al.   FEBS LETTERS

Adaptive Divergence in Experimental Populations of Pseudomonas fluorescens. IV. Genetic Constraints Guide Evolutionary Trajectories in a Parallel Adaptive Radiation

(2009) M. J. McDonald et al.   GENETICS

A tunable synthetic mammalian oscillator

(2009) Marcel Tigges et al.   NATURE

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

Phenotypes and tolerances in the design space of biochemical systems

(2009) M. A. Savageau et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome Streamlining Results in Loss of Robustness of the Circadian Clock in the Marine Cyanobacterium Prochlorococcus marinus PCC 9511

(2008) Julia Holtzendorff et al.   JOURNAL OF BIOLOGICAL RHYTHMS

A fast, robust and tunable synthetic gene oscillator

(2008) Jesse Stricker et al.   NATURE

Genome-wide association studies for complex traits: consensus, uncertainty and challenges

(2008) Mark I. McCarthy et al.   NATURE REVIEWS GENETICS