Model genotype–phenotype mappings and the algorithmic structure of evolution

Antibiotic collateral sensitivity is contingent on the repeatability of evolution

(2019) Daniel Nichol et al.   Nature Communications

The architecture of an empirical genotype-phenotype map

(2018) José Aguilar-Rodríguez et al.   EVOLUTION

The Influence of Higher-Order Epistasis on Biological Fitness Landscape Topography

(2018) Daniel M. Weinreich et al.   JOURNAL OF STATISTICAL PHYSICS

Phenotypes can be robust and evolvable if mutations have non-local effects on sequence constraints

(2018) Marcel Weiß et al.   Journal of the Royal Society Interface

Adding levels of complexity enhances robustness and evolvability in a multilevel genotype–phenotype map

(2018) Pablo Catalán et al.   Journal of the Royal Society Interface

The effects of antibiotic cycling and mixing on antibiotic resistance in intensive care units: a cluster-randomised crossover trial

(2018) Pleun Joppe van Duijn et al.   LANCET INFECTIOUS DISEASES

Mapping the malaria parasite druggable genome by using in vitro evolution and chemogenomics

(2018) Annie N. Cowell et al.   SCIENCE

Structural properties of genotype–phenotype maps

(2017) S. E. Ahnert   Journal of the Royal Society Interface

Competing memories of mitogen and p53 signalling control cell-cycle entry

(2017) Hee Won Yang et al.   NATURE

Integrating evolutionary dynamics into treatment of metastatic castrate-resistant prostate cancer

(2017) Jingsong Zhang et al.   Nature Communications

How evolution learns to generalise: Using the principles of learning theory to understand the evolution of developmental organisation

(2017) Kostas Kouvaris et al.   PLoS Computational Biology

A thousand empirical adaptive landscapes and their navigability

(2017) José Aguilar-Rodríguez et al.   Nature Ecology & Evolution

Collateral sensitivity networks reveal evolutionary instability and novel treatment strategies in ALK mutated non-small cell lung cancer

(2017) Andrew Dhawan et al.   Scientific Reports

Stochasticity in the Genotype-Phenotype Map: Implications for the Robustness and Persistence of Bet-Hedging

(2016) Daniel Nichol et al.   GENETICS

Innovation in the pharmaceutical industry: New estimates of R&D costs

(2016) Joseph A. DiMasi et al.   JOURNAL OF HEALTH ECONOMICS

New paradigms in clonal evolution: punctuated equilibrium in cancer

(2016) William CH Cross et al.   JOURNAL OF PATHOLOGY

Identification of neutral tumor evolution across cancer types

(2016) Marc J Williams et al.   NATURE GENETICS

Tumor cells can follow distinct evolutionary paths to become resistant to epidermal growth factor receptor inhibition

(2016) Aaron N Hata et al.   NATURE MEDICINE

Exploiting evolutionary principles to prolong tumor control in preclinical models of breast cancer

(2016) Pedro M. Enriquez-Navas et al.   Science Translational Medicine

Adaptive Landscape by Environment Interactions Dictate Evolutionary Dynamics in Models of Drug Resistance

(2016) C. Brandon Ogbunugafor et al.   PLoS Computational Biology

Stochasticity in the Genotype-Phenotype Map: Implications for the Robustness and Persistence of Bet-Hedging

(2016) Daniel Nichol et al.   GENETICS

Non-genetic cancer cell plasticity and therapy-induced stemness in tumour relapse: ‘What does not kill me strengthens me’

(2015) A O Pisco et al.   BRITISH JOURNAL OF CANCER

The organization of biological sequences into constrained and unconstrained parts determines fundamental properties of genotype–phenotype maps

(2015) S. F. Greenbury et al.   Journal of the Royal Society Interface

Big Bang and context-driven collapse

(2015) Mark Robertson-Tessi et al.   NATURE GENETICS

A Big Bang model of human colorectal tumor growth

(2015) Andrea Sottoriva et al.   NATURE GENETICS

Rational Design of Antibiotic Treatment Plans: A Treatment Strategy for Managing Evolution and Reversing Resistance

(2015) Portia M. Mira et al.   PLoS One

Bridging scales in cancer progression: Mapping genotype to phenotype using neural networks

(2015) Philip Gerlee et al.   SEMINARS IN CANCER BIOLOGY

The structure of the genotype–phenotype map strongly constrains the evolution of non-coding RNA

(2015) Kamaludin Dingle et al.   Interface Focus

Steering Evolution with Sequential Therapy to Prevent the Emergence of Bacterial Antibiotic Resistance

(2015) Daniel Nichol et al.   PLoS Computational Biology

A tractable genotype-phenotype map modelling the self-assembly of protein quaternary structure

(2014) S. F. Greenbury et al.   Journal of the Royal Society Interface

Drug resistance to targeted therapies: Déjà vu all over again

(2014) Floris H. Groenendijk et al.   Molecular Oncology

Empirical fitness landscapes and the predictability of evolution

(2014) J. Arjan G.M. de Visser et al.   NATURE REVIEWS GENETICS

Who will develop new antibacterial agents?

(2014) S. T. Cole   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Coherent feedforward transcriptional regulatory motifs enhance drug resistance

(2014) Daniel A. Charlebois et al.   PHYSICAL REVIEW E

The Arrival of the Frequent: How Bias in Genotype-Phenotype Maps Can Steer Populations to Local Optima

(2014) Steffen Schaper et al.   PLoS One

The Robustness and Evolvability of Transcription Factor Binding Sites

(2014) J. L. Payne et al.   SCIENCE

toyLIFE: a computational framework to study the multi-level organisation of the genotype-phenotype map

(2014) Clemente F. Arias et al.   Scientific Reports

Robustness, Evolvability, and the Logic of Genetic Regulation

(2013) Joshua L. Payne et al.   ARTIFICIAL LIFE

Should evolutionary geneticists worry about higher-order epistasis?

(2013) Daniel M Weinreich et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Quantitative analyses of empirical fitness landscapes

(2013) Ivan G Szendro et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

Bet-hedging in stochastically switching environments

(2013) J. Müller et al.   JOURNAL OF THEORETICAL BIOLOGY

Patterns of Epistasis between Beneficial Mutations in an Antibiotic Resistance Gene

(2013) Martijn F. Schenk et al.   MOLECULAR BIOLOGY AND EVOLUTION

Designing Antibiotic Cycling Strategies by Determining and Understanding Local Adaptive Landscapes

(2013) Christiane P. Goulart et al.   PLoS One

Phase i trialist

(2012) Jacob Scott   LANCET ONCOLOGY

Clonal evolution in cancer

(2012) Mel Greaves et al.   NATURE

Intratumor Heterogeneity: Seeing the Wood for the Trees

(2012) T. A. Yap et al.   Science Translational Medicine

Exploring the Complexity of the HIV-1 Fitness Landscape

(2012) Roger D. Kouyos et al.   PLoS Genetics

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

Bet hedging or not? A guide to proper classification of microbial survival strategies

(2011) Imke G. de Jong et al.   BIOESSAYS

The molecular and mathematical basis of Waddington's epigenetic landscape: A framework for post-Darwinian biology?

(2011) Sui Huang   BIOESSAYS

Stochastic State Transitions Give Rise to Phenotypic Equilibrium in Populations of Cancer Cells

(2011) Piyush B. Gupta et al.   CELL

A systems analysis of mutational effects in HIV-1 protease and reverse transcriptase

(2011) Trevor Hinkley et al.   NATURE GENETICS

The pleiotropic structure of the genotype–phenotype map: the evolvability of complex organisms

(2011) Günter P. Wagner et al.   NATURE REVIEWS GENETICS

Gene Expression Noise Facilitates Adaptation and Drug Resistance Independently of Mutation

(2011) Daniel A. Charlebois et al.   PHYSICAL REVIEW LETTERS

Hidden Randomness between Fitness Landscapes Limits Reverse Evolution

(2011) Longzhi Tan et al.   PHYSICAL REVIEW LETTERS

Negative Epistasis Between Beneficial Mutations in an Evolving Bacterial Population

(2011) A. I. Khan et al.   SCIENCE

Diminishing Returns Epistasis Among Beneficial Mutations Decelerates Adaptation

(2011) H.-H. Chou et al.   SCIENCE

Using graph theory to analyze biological networks

(2011) Georgios A Pavlopoulos et al.   BioData Mining

The Systems Biology Approach to Drug Development: Application to Toxicity Assessment of Cardiac Drugs

(2010) B Rodriguez et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

Fitness Epistasis and Constraints on Adaptation in a Human Immunodeficiency Virus Type 1 Protein Region

(2010) J. da Silva et al.   GENETICS

Fitness Epistasis among 6 Biosynthetic Loci in the Budding Yeast Saccharomyces cerevisiae

(2010) D. W. Hall et al.   JOURNAL OF HEREDITY

Reciprocal sign epistasis is a necessary condition for multi-peaked fitness landscapes

(2010) Frank J. Poelwijk et al.   JOURNAL OF THEORETICAL BIOLOGY

Compensatory Mutations Restore Fitness during the Evolution of Dihydrofolate Reductase

(2010) K. M. Brown et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genotype-phenotype mapping and the end of the 'genes as blueprint' metaphor

(2010) M. Pigliucci   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Beneficial mutations and the dynamics of adaptation in asexual populations

(2010) P. D. Sniegowski et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Phenotypic plasticity in development and evolution: facts and concepts

(2010) G. Fusco et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Adaptive Therapy

(2009) R. A. Gatenby et al.   CANCER RESEARCH

Cancer systems biology: a network modeling perspective

(2009) P. K. Kreeger et al.   CARCINOGENESIS

Non-genetic heterogeneity of cells in development: more than just noise

(2009) S. Huang   DEVELOPMENT

Non-genetic heterogeneity — a mutation-independent driving force for the somatic evolution of tumours

(2009) Amy Brock et al.   NATURE REVIEWS GENETICS

Quantitative approaches in developmental biology

(2009) Andrew C. Oates et al.   NATURE REVIEWS GENETICS

Fitness and its role in evolutionary genetics

(2009) H. Allen Orr   NATURE REVIEWS GENETICS

Stepwise acquisition of pyrimethamine resistance in the malaria parasite

(2009) E. R. Lozovsky et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Is Genetic Evolution Predictable?

(2009) D. L. Stern et al.   SCIENCE

Hidden Reaction Norms, Cryptic Genetic Variation, and Evolvability

(2008) Carl D. Schlichting   Annals of the New York Academy of Sciences

Bistability, Epigenetics, and Bet-Hedging in Bacteria

(2008) Jan-Willem Veening et al.   Annual Review of Microbiology

Modelling evolutionary cell behaviour using neural networks: Application to tumour growth

(2008) P. Gerlee et al.   BIOSYSTEMS

Bad Bugs, No Drugs: No ESKAPE! An Update from the Infectious Diseases Society of America

(2008) Helen W. Boucher et al.   CLINICAL INFECTIOUS DISEASES

Ascidians and the Plasticity of the Chordate Developmental Program

(2008) Patrick Lemaire et al.   CURRENT BIOLOGY

A hybrid cellular automaton model of clonal evolution in cancer: The emergence of the glycolytic phenotype

(2008) P. Gerlee et al.   JOURNAL OF THEORETICAL BIOLOGY

Darwin 200: Beneath the surface

(2008) Tanguy Chouard   NATURE

Pleiotropic scaling of gene effects and the ‘cost of complexity’

(2008) Günter P. Wagner et al.   NATURE

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

(2008) David A. Orlando et al.   NATURE

Epistasis — the essential role of gene interactions in the structure and evolution of genetic systems

(2008) Patrick C. Phillips   NATURE REVIEWS GENETICS

Gene Regulation by Transcription Factors and MicroRNAs

(2008) O. Hobert   SCIENCE

Evolution of Evolvability in Gene Regulatory Networks

(2008) Anton Crombach et al.   PLoS Computational Biology

Robustness and evolvability: a paradox resolved

(2007) A. Wagner   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The role of hybridization in evolution

(2003) N. H. Barton   MOLECULAR ECOLOGY