相关参考文献
注意:仅列出部分参考文献,下载原文获取全部文献信息。On the evolution and development of morphological complexity: A view from gene regulatory networks
Pascal F. Hagolani et al.
PLoS Computational Biology (2021)
Is evolution predictable? Quantitative genetics under complex genotype-phenotype maps
Lisandro Milocco et al.
EVOLUTION (2020)
Deciphering eukaryotic gene-regulatory logic with 100 million random promoters
Carl G. de Boer et al.
NATURE BIOTECHNOLOGY (2020)
Populations of genetic circuits are unable to find the fittest solution in a multilevel genotype-phenotype map
Pablo Catalan et al.
JOURNAL OF THE ROYAL SOCIETY INTERFACE (2020)
Mutation bias interacts with composition bias to influence adaptive evolution
Alejandro V. Cano et al.
PLOS COMPUTATIONAL BIOLOGY (2020)
'IT WILL CHANGE EVERYTHING': DEEPMIND'S AI MAKES GIGANTIC LEAP IN SOLVING PROTEIN STRUCTURES
Ewen Callaway
NATURE (2020)
Nucleic Acid-Barcoding Technologies: Converting DNA Sequencing into a Broad-Spectrum Molecular Counter
Glen Liszczak et al.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2019)
Hachimoji DNA and RNA: A genetic system with eight building blocks
Shuichi Hoshika et al.
SCIENCE (2019)
Large-scale network analysis reveals the sequence space architecture of antibody repertoires
Enkelejda Miho et al.
NATURE COMMUNICATIONS (2019)
The Causes and Consequences of Genetic Interactions (Epistasis)
Júlia Domingo et al.
Annual Review of Genomics and Human Genetics (2019)
Absolute quantification of translational regulation and burden using combined sequencing approaches
Thomas E. Gorochowski et al.
MOLECULAR SYSTEMS BIOLOGY (2019)
Total synthesis of Escherichia coli with a recoded genome
Julius Fredens et al.
NATURE (2019)
Parsimonious Scenario for the Emergence of Viroid-Like Replicons De Novo
Pablo Catalan et al.
VIRUSES-BASEL (2019)
An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape
Victoria O. Pokusaeva et al.
PLOS GENETICS (2019)
Estimating the predictability of cancer evolution
Sayed-Rzgar Hosseini et al.
BIOINFORMATICS (2019)
Biophysics and population size constrains speciation in an evolutionary model of developmental system drift
Bhavin S. Khatri et al.
PLOS COMPUTATIONAL BIOLOGY (2019)
Every which way? On predicting tumor evolution using cancer progression models
Ramon Diaz-Uriarte et al.
PLOS COMPUTATIONAL BIOLOGY (2019)
Recombination and mutational robustness in neutral fitness landscapes
Alexander Klug et al.
PLOS COMPUTATIONAL BIOLOGY (2019)
Model genotype-phenotype mappings and the algorithmic structure of evolution
Daniel Nichol et al.
JOURNAL OF THE ROYAL SOCIETY INTERFACE (2019)
Taming out-of-equilibrium dynamics on interconnected networks
Javier M. Buldu et al.
NATURE COMMUNICATIONS (2019)
Combinatorial Genetics Reveals a Scaling Law for the Effects of Mutations on Splicing
Pablo Baeza-Centurion et al.
CELL (2019)
The causes of evolvability and their evolution
Joshua L. Payne et al.
NATURE REVIEWS GENETICS (2019)
Local Fitness Landscapes Predict Yeast Evolutionary Dynamics in Directionally Changing Environments
Florien A. Gorter et al.
GENETICS (2018)
Faster Evolving Primate Genes Are More Likely to Duplicate
Aine N. O'Toole et al.
MOLECULAR BIOLOGY AND EVOLUTION (2018)
Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families
Ioanna Kalvari et al.
NUCLEIC ACIDS RESEARCH (2018)
Local Fitness Landscapes Predict Yeast Evolutionary Dynamics in Directionally Changing Environments
Florien A. Gorter et al.
GENETICS (2018)
Unraveling the causes of adaptive benefits of synonymous mutations in TEM-1 β-lactamase
Mark P. Zwart et al.
HEREDITY (2018)
Phenotypes can be robust and evolvable if mutations have non-local effects on sequence constraints
Marcel Weiss et al.
JOURNAL OF THE ROYAL SOCIETY INTERFACE (2018)
Evolution on the Biophysical Fitness Landscape of an RNA Virus
Assaf Rotem et al.
MOLECULAR BIOLOGY AND EVOLUTION (2018)
Metagenomic mining of regulatory elements enables programmable species-selective gene expression
Nathan I. Johns et al.
NATURE METHODS (2018)
Darwin Assembly: fast, efficient, multi-site bespoke mutagenesis
Christopher Cozens et al.
NUCLEIC ACIDS RESEARCH (2018)
High-throughput evaluation of T7 promoter variants using biased randomization and DNA barcoding
Ryo Komura et al.
PLOS ONE (2018)
RNA-mediated gene regulation is less evolvable than transcriptional regulation
Joshua L. Payne et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)
Multiplexed gene synthesis in emulsions for exploring protein functional landscapes
Calin Plesa et al.
SCIENCE (2018)
The Third Revolution in Sequencing Technology
Erwin L. van Dijk et al.
TRENDS IN GENETICS (2018)
Rapid host strain improvement by in vivo rearrangement of a synthetic yeast chromosome
B. A. Blount et al.
NATURE COMMUNICATIONS (2018)
On the networked architecture of genotype spaces and its critical effects on molecular evolution
Jacobo Aguirre et al.
OPEN BIOLOGY (2018)
On the role of sparseness in the evolution of modularity in gene regulatory networks
Carlos Espinosa-Soto
PLOS COMPUTATIONAL BIOLOGY (2018)
Multi-environment fitness landscapes of a tRNA gene
Chuan Li et al.
NATURE ECOLOGY & EVOLUTION (2018)
Synthetic circuits reveal how mechanisms of gene regulatory networks constrain evolution
Yolanda Schaerli et al.
MOLECULAR SYSTEMS BIOLOGY (2018)
Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in Escherichia coli
Guillaume Cambray et al.
NATURE BIOTECHNOLOGY (2018)
Deep generative models of genetic variation capture the effects of mutations
Adam J. Riesselman et al.
NATURE METHODS (2018)
Inferring the shape of global epistasis
Jakub Otwinowski et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)
Degeneracy and genetic assimilation in RNA evolution
Reza Rezazadegan et al.
BMC BIOINFORMATICS (2018)
Deep scanning lysine metabolism in Escherichia coli
Marcelo C. Bassalo et al.
MOLECULAR SYSTEMS BIOLOGY (2018)
Designing efficient translation
Thomas E. Gorochowski et al.
NATURE BIOTECHNOLOGY (2018)
Cancer progression models and fitness landscapes: a many-to-many relationship
Ramon Diaz-Uriarte
BIOINFORMATICS (2018)
Statistical theory of phenotype abundance distributions: A test through exact enumeration of genotype spaces
Juan Antonio Garcia-Martin et al.
EPL (2018)
An Efficient Dual Sampling Algorithm with Hamming Distance Filtration
Christopher Barrett et al.
JOURNAL OF COMPUTATIONAL BIOLOGY (2018)
DNAplotlib: Programmable Visualization of Genetic Designs and Associated Data
Bryan S. Der et al.
ACS SYNTHETIC BIOLOGY (2017)
Genotypic Complexity of Fisher's Geometric Model
Sungmin Hwang et al.
GENETICS (2017)
Deep learning of the regulatory grammar of yeast 5′ untranslated regions from 500,000 random sequences
Josh T. Cuperus et al.
GENOME RESEARCH (2017)
Structural properties of genotype-phenotype maps
S. E. Ahnert
JOURNAL OF THE ROYAL SOCIETY INTERFACE (2017)
Distribution of genotype network sizes in sequence-to-structure genotype - phenotype maps
Susanna Manrubia et al.
JOURNAL OF THE ROYAL SOCIETY INTERFACE (2017)
Enumerating secondary structures and structural moieties for circular RNAs
Jose A. Cuesta et al.
JOURNAL OF THEORETICAL BIOLOGY (2017)
Mutational Biases Influence Parallel Adaptation
Arlin Stoltzfus et al.
MOLECULAR BIOLOGY AND EVOLUTION (2017)
Genetic circuit characterization and debugging using RNA-seq
Thomas E. Gorochowski et al.
MOLECULAR SYSTEMS BIOLOGY (2017)
A semi-synthetic organism that stores and retrieves increased genetic information
Yorke Zhang et al.
NATURE (2017)
Beyond editing to writing large genomes
Raj Chari et al.
NATURE REVIEWS GENETICS (2017)
The infinitesimal model: Definition, derivation, and implications
N. H. Barton et al.
THEORETICAL POPULATION BIOLOGY (2017)
Synthetic DNA Synthesis and Assembly: Putting the Synthetic in Synthetic Biology
Randall A. Hughes et al.
COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY (2017)
Design Automation in Synthetic Biology
Evan Appleton et al.
COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY (2017)
A reporter system coupled with high-throughput sequencing unveils key bacterial transcription and translation determinants
Eva Yus et al.
NATURE COMMUNICATIONS (2017)
The origin of a primordial genome through spontaneous symmetry breaking
Nobuto Takeuchi et al.
NATURE COMMUNICATIONS (2017)
Single molecule multiplexed nanopore protein screening in human serum using aptamer modified DNA carriers
Jasmine Y. Y. Sze et al.
NATURE COMMUNICATIONS (2017)
The genotype-phenotype map of an evolving digital organism
Miguel A. Fortuna et al.
PLOS COMPUTATIONAL BIOLOGY (2017)
Genotypic Complexity of Fisher's Geometric Model
Sungmin Hwang et al.
GENETICS (2017)
A thousand empirical adaptive landscapes and their navigability
Jose Aguilar-Rodriguez et al.
NATURE ECOLOGY & EVOLUTION (2017)
The space of genotypes is a network of networks: implications for evolutionary and extinction dynamics
Pablo Yubero et al.
SCIENTIFIC REPORTS (2017)
Evolutionary Conflict Leads to Innovation: Symmetry Breaking in a Spatial Model of RNA-Like Replicators
Samuel H. A. von der Dunk et al.
LIFE-BASEL (2017)
Expression properties exhibit correlated patterns with the fate of duplicated genes, their divergence, and transcriptional plasticity in Saccharomycotina
Florian Mattenberger et al.
DNA RESEARCH (2017)
The Damaging Effect of Passenger Mutations on Cancer Progression
Christopher D. McFarland et al.
CANCER RESEARCH (2017)
Intrinsic protein disorder reduces small-scale gene duplicability
Sanghita Banerjee et al.
DNA RESEARCH (2017)
An Expanded View of Complex Traits: From Polygenic to Omnigenic
Evan A. Boyle et al.
CELL (2017)
Evolution of evolvability and phenotypic plasticity in virtual cells
Thomas D. Cuypers et al.
BMC EVOLUTIONARY BIOLOGY (2017)
Adaptive multiscapes: an up-to-date metaphor to visualize molecular adaptation
Pablo Catalan et al.
BIOLOGY DIRECT (2017)
Bridging the physical scales in evolutionary biology: from protein sequence space to fitness of organisms and populations
Shimon Bershtein et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2017)
Large-scale inference of conjunctive Bayesian networks
Hesam Montazeri et al.
BIOINFORMATICS (2016)
RNAiFold2T: Constraint Programming design of thermo-IRES switches
Juan Antonio Garcia-Martin et al.
BIOINFORMATICS (2016)
RNAdualPF: software to compute the dual partition function with sample applications in molecular evolution theory
Juan Antonio Garcia-Martin et al.
BMC BIOINFORMATICS (2016)
Epistasis and the Structure of Fitness Landscapes: Are Experimental Fitness Landscapes Compatible with Fisher's Geometric Model?
Francois Blanquart et al.
GENETICS (2016)
Effect of Host Species on Topography of the Fitness Landscape for a Plant RNA Virus
Hector Cervera et al.
JOURNAL OF VIROLOGY (2016)
How Good Are Statistical Models at Approximating Complex Fitness Landscapes?
Louis du Plessis et al.
MOLECULAR BIOLOGY AND EVOLUTION (2016)
Local fitness landscape of the green fluorescent protein
Karen S. Sarkisyan et al.
NATURE (2016)
The power of multiplexed functional analysis of genetic variants
Molly Gasperini et al.
NATURE PROTOCOLS (2016)
Gene Duplicability of Core Genes Is Highly Consistent across All Angiosperms
Zhen Li et al.
PLANT CELL (2016)
Algorithmic methods to infer the evolutionary trajectories in cancer progression
Giulio Caravagna et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)
Network of epistatic interactions within a yeast snoRNA
Olga Puchta et al.
SCIENCE (2016)
The fitness landscape of a tRNA gene
Chuan Li et al.
SCIENCE (2016)
The complete local genotype-phenotype landscape for the alternative splicing of a human exon
Philippe Julien et al.
NATURE COMMUNICATIONS (2016)
Competition among networks highlights the power of the weak
Jaime Iranzo et al.
NATURE COMMUNICATIONS (2016)
Computational Cancer Biology: An Evolutionary Perspective
Niko Beerenwinkel et al.
PLOS COMPUTATIONAL BIOLOGY (2016)
Genetic Correlations Greatly Increase Mutational Robustness and Can Both Reduce and Enhance Evolvability
Sam F. Greenbury et al.
PLOS COMPUTATIONAL BIOLOGY (2016)
Epistasis and the Structure of Fitness Landscapes: Are Experimental Fitness Landscapes Compatible with Fisher's Geometric Model?
Francois Blanquart et al.
GENETICS (2016)
Environmental changes bridge evolutionary valleys
Barrett Steinberg et al.
SCIENCE ADVANCES (2016)
CAPRI: efficient inference of cancer progression models from cross-sectional data
Daniele Ramazzotti et al.
BIOINFORMATICS (2015)
Identifying restrictions in the order of accumulation of mutations during tumor progression: effects of passengers, evolutionary models, and sampling
Ramon Diaz-Uriarte
BMC BIOINFORMATICS (2015)
The pathogenicity of splicing defects: mechanistic insights into pre-mRNA processing inform novel therapeutic approaches
Elisabeth Daguenet et al.
EMBO REPORTS (2015)
Simple Biophysical Model Predicts Faster Accumulation of Hybrid Incompatibilities in Small Populations Under Stabilizing Selection
Bhavin S. Khatri et al.
GENETICS (2015)
The impact of high-order epistasis in the within-host fitness of a positive-sense plant RNA virus
J. Lalic et al.
JOURNAL OF EVOLUTIONARY BIOLOGY (2015)
The organization of biological sequences into constrained and unconstrained parts determines fundamental properties of genotype-phenotype maps
S. F. Greenbury et al.
JOURNAL OF THE ROYAL SOCIETY INTERFACE (2015)
A coarse-grained biophysical model of sequence evolution and the population size dependence of the speciation rate
Bhavin S. Khatri et al.
JOURNAL OF THEORETICAL BIOLOGY (2015)
Protein folding and binding can emerge as evolutionary spandrels through structural coupling
Michael Manhart et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)
Breaking evolutionary constraint with a tradeoff ratchet
Marjon G. J. de Vos et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)
Are there ergodic limits to evolution? Ergodic exploration of genome space and convergence
Tom C. B. McLeish
INTERFACE FOCUS (2015)
The structure of the genotype - phenotype map strongly constrains the evolution of non-coding RNA
Kamaludin Dingle et al.
INTERFACE FOCUS (2015)
Tipping points and early warning signals in the genomic composition of populations induced by environmental changes
Jacobo Aguirre et al.
SCIENTIFIC REPORTS (2015)
Emerging viruses: why they are not jacks of all trades?
Stephanie Bedhomme et al.
CURRENT OPINION IN VIROLOGY (2015)
Exhaustive Analysis of a Genotype Space Comprising 1015 Central Carbon Metabolisms Reveals an Organization Conducive to Metabolic Innovation
Sayed-Rzgar Hosseini et al.
PLOS COMPUTATIONAL BIOLOGY (2015)
Quantitative System Drift Compensates for Altered Maternal Inputs to the Gap Gene Network of the Scuttle Fly Megaselia abdita
Karl R. Wotton et al.
ELIFE (2015)
Experimental evolution reveals hidden diversity in evolutionary pathways
Peter A. Lind et al.
ELIFE (2015)
The differential view of genotype-phenotype relationships
Virginie Orgogozo et al.
FRONTIERS IN GENETICS (2015)
Evolution on neutral networks accelerates the ticking rate of the molecular clock
Susanna Manrubia et al.
JOURNAL OF THE ROYAL SOCIETY INTERFACE (2015)
Cancer Evolution: Mathematical Models and Computational Inference
Niko Beerenwinkel et al.
SYSTEMATIC BIOLOGY (2015)
The Utility of Fisher's Geometric Model in Evolutionary Genetics
O. Tenaillon
ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS, VOL 45 (2014)
The Effects of Recombination on Phenotypic Exploration and Robustness in Evolution
Ting Hu et al.
ARTIFICIAL LIFE (2014)
Robustness, Evolvability, and the Logic of Genetic Regulation
Joshua L. Payne et al.
ARTIFICIAL LIFE (2014)
Mutational Robustness Accelerates the Origin of Novel RNA Phenotypes through Phenotypic Plasticity
Andreas Wagner
BIOPHYSICAL JOURNAL (2014)
Latent phenotypes pervade gene regulatory circuits
Joshua L. Payne et al.
BMC SYSTEMS BIOLOGY (2014)
A Comprehensive Biophysical Description of Pairwise Epistasis throughout an Entire Protein Domain
C. Anders Olson et al.
CURRENT BIOLOGY (2014)
Merging molecular mechanism and evolution: theory and computation at the interface of biophysics and evolutionary population genetics
Adrian W. R. Serohijos et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2014)
Properties of selected mutations and genotypic landscapes under Fisher's geometric model
Francois Blanquart et al.
EVOLUTION (2014)
Hybrid Incompatibility Arises in a Sequence-Based Bioenergetic Model of Transcription Factor Binding
Alexander Y. Tulchinsky et al.
GENETICS (2014)
Evolution of Functional Diversification within Quasispecies
Enrico Sandro Colizzi et al.
GENOME BIOLOGY AND EVOLUTION (2014)
Fitness valleys constrain HIV-1's adaptation to its secondary chemokine coreceptor
J. da Silva et al.
JOURNAL OF EVOLUTIONARY BIOLOGY (2014)
Mutation Rates and Evolution of Multiple Coding in RNA-based Protocells
Folkert K. de Boer et al.
JOURNAL OF MOLECULAR EVOLUTION (2014)
A tractable genotype-phenotype map modelling the self-assembly of protein quaternary structure
Sam F. Greenbury et al.
JOURNAL OF THE ROYAL SOCIETY INTERFACE (2014)
Mutational and fitness landscapes of an RNA virus revealed through population sequencing
Ashley Acevedo et al.
NATURE (2014)
Does evolutionary theory need a rethink? - POINT Yes, urgently
Kevin Laland et al.
NATURE (2014)
Large-scale de novo DNA synthesis: technologies and applications
Sriram Kosuri et al.
NATURE METHODS (2014)
Deep mutational scanning: a new style of protein science
Douglas M. Fowler et al.
NATURE METHODS (2014)
Principles of genetic circuit design
Jennifer A. N. Brophy et al.
NATURE METHODS (2014)
Empirical fitness landscapes and the predictability of evolution
J. Arjan G. M. de Visser et al.
NATURE REVIEWS GENETICS (2014)
Complete RNA inverse folding: computational design of functional hammerhead ribozymes
Ivan Dotu et al.
NUCLEIC ACIDS RESEARCH (2014)
Synchronization of Interconnected Networks: The Role of Connector Nodes
J. Aguirre et al.
PHYSICAL REVIEW LETTERS (2014)
The Arrival of the Frequent: How Bias in Genotype-Phenotype Maps Can Steer Populations to Local Optima
Steffen Schaper et al.
PLOS ONE (2014)
Defining functional DNA elements in the human genome
Manolis Kellis et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)
Inferring fitness landscapes by regression produces biased estimates of epistasis
Jakub Otwinowski et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)
MODELING EVOLUTION USING THE PROBABILITY OF FIXATION: HISTORY AND IMPLICATIONS
David M. McCandlish et al.
QUARTERLY REVIEW OF BIOLOGY (2014)
The Robustness and Evolvability of Transcription Factor Binding Sites
Joshua L. Payne et al.
SCIENCE (2014)
A unified design space of synthetic stripe-forming networks
Yolanda Schaerli et al.
NATURE COMMUNICATIONS (2014)
toyLIFE: a computational framework to study the multi-level organisation of the genotype-phenotype map
Clemente F. Arias et al.
SCIENTIFIC REPORTS (2014)
Dissecting the Human Protein-Protein Interaction Network via Phylogenetic Decomposition
Cho-Yi Chen et al.
SCIENTIFIC REPORTS (2014)
Using Synthetic Biological Parts and Microbioreactors to Explore the Protein Expression Characteristics of Escherichia coli
Thomas E. Gorochowski et al.
ACS SYNTHETIC BIOLOGY (2014)
A Synergism between Adaptive Effects and Evolvability Drives Whole Genome Duplication to Fixation
Thomas D. Cuypers et al.
PLOS COMPUTATIONAL BIOLOGY (2014)
Biophysical Fitness Landscapes for Transcription Factor Binding Sites
Allan Haldane et al.
PLOS COMPUTATIONAL BIOLOGY (2014)
Comparative RNAi Screens in C. elegans and C. briggsae Reveal the Impact of Developmental System Drift on Gene Function
Adrian J. Verster et al.
PLOS GENETICS (2014)
The Same but Different: Worms Reveal the Pervasiveness of Developmental System Drift
Eric S. Haag
PLOS GENETICS (2014)
Epistasis between mutations is host-dependent for an RNA virus
Jasna Lalic et al.
BIOLOGY LETTERS (2013)
Highly Abundant Proteins Favor More Stable 3D Structures in Yeast
Adrian W. R. Serohijos et al.
BIOPHYSICAL JOURNAL (2013)
Should evolutionary geneticists worry about higher-order epistasis?
Daniel M. Weinreich et al.
CURRENT OPINION IN GENETICS & DEVELOPMENT (2013)
FISHER'S GEOMETRIC MODEL OF ADAPTATION MEETS THE FUNCTIONAL SYNTHESIS: DATA ON PAIRWISE EPISTASIS FOR FITNESS YIELDS INSIGHTS INTO THE SHAPE AND SIZE OF PHENOTYPE SPACE
Daniel M. Weinreich et al.
EVOLUTION (2013)
On the Immortality of Television Sets: Function in the Human Genome According to the Evolution-Free Gospel of ENCODE
Dan Graur et al.
GENOME BIOLOGY AND EVOLUTION (2013)
Evolution of molecular phenotypes under stabilizing selection
Armita Nourmohammad et al.
JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT (2013)
The peaks and geometry of fitness landscapes
Kristina Crona et al.
JOURNAL OF THEORETICAL BIOLOGY (2013)
Patterns of Epistasis between Beneficial Mutations in an Antibiotic Resistance Gene
Martijn F. Schenk et al.
MOLECULAR BIOLOGY AND EVOLUTION (2013)
Adaptive dynamics under development-based genotype-phenotype maps
Isaac Salazar-Ciudad et al.
NATURE (2013)
Accelerated gene evolution through replication-transcription conflicts
Sandip Paul et al.
NATURE (2013)
A latent capacity for evolutionary innovation through exaptation in metabolic systems
Aditya Barve et al.
NATURE (2013)
Successful strategies for competing networks
J. Aguirre et al.
NATURE PHYSICS (2013)
Massive functional mapping of a 5'-UTR by saturation mutagenesis, phenotypic sorting and deep sequencing
Erik Holmqvist et al.
NUCLEIC ACIDS RESEARCH (2013)
Comprehensive experimental fitness landscape and evolutionary network for small RNA
Jose I. Jimenez et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)
Composability of regulatory sequences controlling transcription and translation in Escherichia coli
Sriram Kosuri et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)
Does the terrestrial biosphere have planetary tipping points?
Barry W. Brook et al.
TRENDS IN ECOLOGY & EVOLUTION (2013)
Visualization of Evolutionary Stability Dynamics and Competitive Fitness of Escherichia coli Engineered with Randomized Multigene Circuits
Sean C. Sleight et al.
ACS SYNTHETIC BIOLOGY (2013)
RNAiFOLD: A CONSTRAINT PROGRAMMING ALGORITHM FOR RNA INVERSE FOLDING AND MOLECULAR DESIGN
Juan Antonio Garcia-Martin et al.
JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY (2013)
A Comparison of Genotype-Phenotype Maps for RNA and Proteins
Evandro Ferrada et al.
BIOPHYSICAL JOURNAL (2012)
Evolutionary dynamics on multiple scales: a quantitative analysis of the interplay between genotype, phenotype, and fitness in linear genetic programming
Ting Hu et al.
GENETIC PROGRAMMING AND EVOLVABLE MACHINES (2012)
Virtual Genomes in Flux: An Interplay of Neutrality and Adaptability Explains Genome Expansion and Streamlining
Thomas D. Cuypers et al.
GENOME BIOLOGY AND EVOLUTION (2012)
Magnitude and sign epistasis among deleterious mutations in a positive-sense plant RNA virus
J. Lalic et al.
HEREDITY (2012)
Approaching a state shift in Earth's biosphere
Anthony D. Barnosky et al.
NATURE (2012)
Evolutionary paths to antibiotic resistance under dynamically sustained drug selection
Erdal Toprak et al.
NATURE GENETICS (2012)
Less Can Be More: RNA-Adapters May Enhance Coding Capacity of Replicators
Folkert K. de Boer et al.
PLOS ONE (2012)
Chromosomal duplication is a transient evolutionary solution to stress
Avihu H. Yona et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)
Generic Indicators for Loss of Resilience Before a Tipping Point Leading to Population Collapse
Lei Dai et al.
SCIENCE (2012)
Anticipating Critical Transitions
Marten Scheffer et al.
SCIENCE (2012)
Evolution of Cooperation in Multiplex Networks
Jesus Gomez-Gardenes et al.
SCIENTIFIC REPORTS (2012)
Protein Biophysics Explains Why Highly Abundant Proteins Evolve Slowly
Adrian W. R. Serohijos et al.
CELL REPORTS (2012)
Nonheritable Cellular Variability Accelerates the Evolutionary Processes of Cancer
Steven A. Frank et al.
PLOS BIOLOGY (2012)
Exploring the Complexity of the HIV-1 Fitness Landscape
Roger D. Kouyos et al.
PLOS GENETICS (2012)
ViennaRNA Package 2.0
Ronny Lorenz et al.
ALGORITHMS FOR MOLECULAR BIOLOGY (2011)
Phenotypic plasticity can facilitate adaptive evolution in gene regulatory circuits
Carlos Espinosa-Soto et al.
BMC EVOLUTIONARY BIOLOGY (2011)
Robust Design of Biological Circuits: Evolutionary Systems Biology Approach
Bor-Sen Chen et al.
JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY (2011)
Mutation-induced fold switching among lattice proteins
Christian Holzgrafe et al.
JOURNAL OF CHEMICAL PHYSICS (2011)
The evolvability of programmable hardware
Karthik Raman et al.
JOURNAL OF THE ROYAL SOCIETY INTERFACE (2011)
Motif frequency and evolutionary search times in RNA populations
Michael Stich et al.
JOURNAL OF THEORETICAL BIOLOGY (2011)
Reciprocal sign epistasis is a necessary condition for multi-peaked fitness landscapes
Frank J. Poelwijk et al.
JOURNAL OF THEORETICAL BIOLOGY (2011)
A systems analysis of mutational effects in HIV-1 protease and reverse transcriptase
Trevor Hinkley et al.
NATURE GENETICS (2011)
The pleiotropic structure of the genotype-phenotype map: the evolvability of complex organisms
Guenter P. Wagner et al.
NATURE REVIEWS GENETICS (2011)
Evolutionary dynamics in a simple model of self-assembly
Iain G. Johnston et al.
PHYSICAL REVIEW E (2011)
Robustness of a Network of Networks
Jianxi Gao et al.
PHYSICAL REVIEW LETTERS (2011)
Correction: Topological Structure of the Space of Phenotypes: The Case of RNA Neutral Networks
Jacobo Aguirre et al.
PLoS One (2011)
The Temporal Order of Genetic and Pathway Alterations in Tumorigenesis
Moritz Gerstung et al.
PLOS ONE (2011)
Topology of protein interaction network shapes protein abundances and strengths of their functional and nonspecific interactions
Muyoung Heo et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)
A biophysical protein folding model accounts for most mutational fitness effects in viruses
C. Scott Wylie et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)
The evolution and evolutionary consequences of marginal thermostability in proteins
Richard A. Goldstein
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2011)
Negative Epistasis Between Beneficial Mutations in an Evolving Bacterial Population
Aisha I. Khan et al.
SCIENCE (2011)
Diminishing Returns Epistasis Among Beneficial Mutations Decelerates Adaptation
Hsin-Hung Chou et al.
SCIENCE (2011)
Epistasis between Beneficial Mutations and the Phenotype-to-Fitness Map for a ssDNA Virus
Darin R. Rokyta et al.
PLOS GENETICS (2011)
Genotype networks in metabolic reaction spaces
Areejit Samal et al.
BMC SYSTEMS BIOLOGY (2010)
Multiple peaks and reciprocal sign epistasis in an empirically determined genotype-phenotype landscape
Alexandre Dawid et al.
CHAOS (2010)
INTRINSIC REPRODUCTIVE ISOLATION BETWEEN TWO SISTER SPECIES OF DROSOPHILA
Daniel R. Matute et al.
EVOLUTION (2010)
THE ACCUMULATION OF REPRODUCTIVE INCOMPATIBILITIES IN AFRICAN CICHLID FISH
Rike B. Stelkens et al.
EVOLUTION (2010)
Fitness Epistasis and Constraints on Adaptation in a Human Immunodeficiency Virus Type 1 Protein Region
Jack da Silva et al.
GENETICS (2010)
Fitness Epistasis among 6 Biosynthetic Loci in the Budding Yeast Saccharomyces cerevisiae
David W. Hall et al.
JOURNAL OF HEREDITY (2010)
Analysis of a complete DNA-protein affinity landscape
William Rowe et al.
JOURNAL OF THE ROYAL SOCIETY INTERFACE (2010)
Degeneracy: A design principle for achieving robustness and evolvability
James Whitacre et al.
JOURNAL OF THEORETICAL BIOLOGY (2010)
A computational model of teeth and the developmental origins of morphological variation
Isaac Salazar-Ciudad et al.
NATURE (2010)
Mutational robustness can facilitate adaptation
Jeremy A. Draghi et al.
NATURE (2010)
Catastrophic cascade of failures in interdependent networks
Sergey V. Buldyrev et al.
NATURE (2010)
Evolutionary Innovations and the Organization of Protein Functions in Genotype Space
Evandro Ferrada et al.
PLOS ONE (2010)
Sex, mixability, and modularity
Adi Livnat et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)
Rapid Construction of Empirical RNA Fitness Landscapes
Jason N. Pitt et al.
SCIENCE (2010)
Robustness and Evolvability
Joanna Masel et al.
TRENDS IN GENETICS (2010)
Exploring the Effect of Sex on Empirical Fitness Landscapes
J. Arjan G. M. de Visser et al.
AMERICAN NATURALIST (2009)
Quantifying cancer progression with conjunctive Bayesian networks
Moritz Gerstung et al.
BIOINFORMATICS (2009)
Statistical Mechanics and the Evolution of Polygenic Quantitative Traits
N. H. Barton et al.
GENETICS (2009)
Lethal Mutagenesis in Viruses and Bacteria
Peiqiu Chen et al.
GENETICS (2009)
On the application of statistical physics to evolutionary biology
N. H. Barton et al.
JOURNAL OF THEORETICAL BIOLOGY (2009)
Congruent Evolution of Genetic and Environmental Robustness in Micro-RNA
Gergely J. Szoellosi et al.
MOLECULAR BIOLOGY AND EVOLUTION (2009)
Early-warning signals for critical transitions
Marten Scheffer et al.
NATURE (2009)
High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis
Rupali P. Patwardhan et al.
NATURE BIOTECHNOLOGY (2009)
Evolutionary dynamics on networks of selectively neutral genotypes: Effects of topology and sequence stability
Jacobo Aguirre et al.
PHYSICAL REVIEW E (2009)
Emergence of species in evolutionary simulated annealing''
Muyoung Heo et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)
Statistical mechanics of convergent evolution in spatial patterning
Bhavin S. Khatri et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)
Stepwise acquisition of pyrimethamine resistance in the malaria parasite
Elena R. Lozovsky et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)
The dawn of the RNA World: Toward functional complexity through ligation of random RNA oligomers
Carlos Briones et al.
RNA (2009)
From fitness landscapes to seascapes: non-equilibrium dynamics of selection and adaptation
Ville Mustonen et al.
TRENDS IN GENETICS (2009)
Evolutionary Constraints to Viroid Evolution
Santiago F. Elena et al.
VIRUSES-BASEL (2009)
Evolutionary Plasticity and Innovations in Complex Metabolic Reaction Networks
Joao F. Matias Rodrigues et al.
PLOS COMPUTATIONAL BIOLOGY (2009)
Multilevel Selection in Models of Prebiotic Evolution II: A Direct Comparison of Compartmentalization and Spatial Self-Organization
Nobuto Takeuchi et al.
PLOS COMPUTATIONAL BIOLOGY (2009)
Robustness and epistasis in mutation-selection models
Andrea Wolff et al.
PHYSICAL BIOLOGY (2009)
Protein folding: Then and now
Yiwen Chen et al.
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS (2008)
Evolution of complexity in RNA-like replicator systems
Nobuto Takeuchi et al.
BIOLOGY DIRECT (2008)
Neutral network sizes of biological RNA molecules can be computed and are not atypically small
Thomas Jorg et al.
BMC BIOINFORMATICS (2008)
Evolution of evolvability in a developmental model
Jeremy Draghi et al.
EVOLUTION (2008)
On the structural repertoire of pools of short, random RNA sequences
Michael Stich et al.
JOURNAL OF THEORETICAL BIOLOGY (2008)
Survival of the sparsest: robust gene networks are parsimonious
Robert D. Leclerc
MOLECULAR SYSTEMS BIOLOGY (2008)
The effect of recombination on the neutral evolution of genetic robustness
Gergely J. Szollosi et al.
MATHEMATICAL BIOSCIENCES (2008)
Virus Adaptation by Manipulation of Host's Gene Expression
Patricia Agudelo-Romero et al.
PLOS ONE (2008)
Energy-dependent fitness:: A quantitative model for the evolution of yeast transcription factor binding sites
Ville Mustonen et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)
A mixability theory for the role of sex in evolution
Adi Livnat et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)
An End to Endless Forms: Epistasis, Phenotype Distribution Bias, and Nonuniform Evolution
Elhanan Borenstein et al.
PLOS COMPUTATIONAL BIOLOGY (2008)
The Ascent of the Abundant: How Mutational Networks Constrain Evolution
Matthew C. Cowperthwaite et al.
PLOS COMPUTATIONAL BIOLOGY (2008)
Evolution of Evolvability in Gene Regulatory Networks
Anton Crombach et al.
PLOS COMPUTATIONAL BIOLOGY (2008)
Distribution of fitness and virulence effects caused by single-nucleotide substitutions in tobacco etch virus
Purificacion Carrasco et al.
JOURNAL OF VIROLOGY (2007)
Protein stability imposes limits on organism complexity and speed of molecular evolution
Konstantin B. Zeldovich et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)
Innovation and robustness in complex regulatory gene networks
S. Ciliberti et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)
The Biological Big Bang model for the major transitions in evolution
Eugene V. Koonin
BIOLOGY DIRECT (2007)
The distribution of fitness effects of new mutations
Adam Eyre-Walker et al.
NATURE REVIEWS GENETICS (2007)
A first-principles model of early evolution: Emergence of gene families, species, and preferred protein folds
Konstantin B. Zeldovich et al.
PLOS COMPUTATIONAL BIOLOGY (2007)
Chromosome rearrangements and the evolution of genome structuring and adaptability
Anton Crombach et al.
MOLECULAR BIOLOGY AND EVOLUTION (2007)
Distributions of epistasis in microbes fit predictions from a fitness landscape model
Guillaume Martin et al.
NATURE GENETICS (2007)
Phenotypic complexity and local variations in neutral degree
Per Kristian Lehre et al.
BIOSYSTEMS (2007)
Robustness can evolve gradually in complex regulatory gene networks with varying topology
Stefano Ciliberti et al.
PLOS COMPUTATIONAL BIOLOGY (2007)
Empirical fitness landscapes reveal accessible evolutionary paths
Frank J. Poelwijk et al.
NATURE (2007)
Thermodynamics of neutral protein evolution
Jesse D. Bloom et al.
GENETICS (2007)
fRNAdb: a platform for mining/annotating functional RNA candidates from non-coding RNA sequences
Taishin Kin et al.
NUCLEIC ACIDS RESEARCH (2007)
Epochal evolution shapes the phylodynamics of interpandemic influenza A (H3N2) in humans
Katia Koelle et al.
SCIENCE (2006)
In silico predicted robustness of viroid RNA secondary structures.: II.: Interaction between mutation pairs
Rafael Sanjuan et al.
MOLECULAR BIOLOGY AND EVOLUTION (2006)
In silico predicted robustness of viroids RNA secondary structures.: I.: The effect of single mutations
Rafael Sanjuan et al.
MOLECULAR BIOLOGY AND EVOLUTION (2006)
Quantifying antagonistic epistasis in a multifunctional RNA secondary structure of the Rous sarcoma virus
Rafael Sanjuan
JOURNAL OF GENERAL VIROLOGY (2006)
Protein folding thermodynamics and dynamics: Where physics, chemistry, and biology meet
Eugene Shakhnovich
CHEMICAL REVIEWS (2006)
Prediction of RNA secondary structures: from theory to models and real molecules
Peter Schuster
REPORTS ON PROGRESS IN PHYSICS (2006)
Direct evolution of genetic robustness in microRNA
E Borenstein et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)
Darwinian evolution can follow only very few mutational paths to fitter proteins
DM Weinreich et al.
SCIENCE (2006)
Sexual reproduction selects for robustness and negative epistasis in artificial gene networks
RBR Azevedo et al.
NATURE (2006)
Natural selection is not required to explain universal compositional patterns in rRNA secondary structure categories
S Smit et al.
RNA (2006)
Compact and ordered collapse of randomly generated RNA sequences
EA Schultes et al.
NATURE STRUCTURAL & MOLECULAR BIOLOGY (2005)
Evolutionary population genetics of promoters:: Predicting binding sites and functional phylogenies
V Mustonen et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)
The biochemical architecture of an ancient adaptive landscape
M Lunzer et al.
SCIENCE (2005)
Spontaneous evolution of modularity and network motifs
N Kashtan et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)
Evolution of genetic potential
LA Meyers et al.
PLOS COMPUTATIONAL BIOLOGY (2005)
The application of statistical physics to evolutionary biology
G Sella et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)
An empirical test of the mutational landscape model of adaptation using a single-stranded DNA virus
DR Rokyta et al.
NATURE GENETICS (2005)
The 'evolvability' of promiscuous protein functions
A Aharoni et al.
NATURE GENETICS (2005)
Avida: A software platform for research in computational evolutionary biology
C Ofria et al.
ARTIFICIAL LIFE (2004)
Evidence for positive epistasis in HIV-1
S Bonhoeffer et al.
SCIENCE (2004)
Adaptive evolution of transcription factor binding sites -: art. no. 42
J Berg et al.
BMC EVOLUTIONARY BIOLOGY (2004)
The contribution of epistasis to the architecture of fitness in an RNA virus
R Sanjuán et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2004)
Organismal complexity, protein complexity, and gene duplicability
J Yang et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2003)
Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes
WJ Kent et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2003)
Structural determinant of protein designability
JL England et al.
PHYSICAL REVIEW LETTERS (2003)
Transcription-associated mutational asymmetry in mammalian evolution
P Green et al.
NATURE GENETICS (2003)
How the global structure of protein interaction networks evolves
A Wagner
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2003)
Designability of protein structures: A lattice-model study using the Miyazawa-Jernigan matrix
H Li et al.
PROTEINS-STRUCTURE FUNCTION AND GENETICS (2002)
Roles of mutation and recombination in the evolution of protein thermodynamics
Y Xia et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)
Gene location and bacterial sequence divergence
A Mira et al.
MOLECULAR BIOLOGY AND EVOLUTION (2002)
Enumerating designing sequences in the HP model
A Irback et al.
JOURNAL OF BIOLOGICAL PHYSICS (2002)
Why are proteins marginally stable?
DM Taverna et al.
PROTEINS-STRUCTURE FUNCTION AND GENETICS (2002)
Toward a new synthesis: population genetics and evolutionary developmental biology
NA Johnson et al.
GENETICA (2001)
Multidimensional epistasis and the disadvantage of sex
FA Kondrashov et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2001)
Evolution of digital organisms at high mutation rates leads to survival of the flattest
CO Wilke et al.
NATURE (2001)
Adaptive evolution on neutral networks
CO Wilke
BULLETIN OF MATHEMATICAL BIOLOGY (2001)
Phylogenetics and speciation
TG Barraclough et al.
TRENDS IN ECOLOGY & EVOLUTION (2001)
Developmental system drift and flexibility in evolutionary trajectories
JR True et al.
EVOLUTION & DEVELOPMENT (2001)
Replication and mutation on neutral networks
C Reidys et al.
BULLETIN OF MATHEMATICAL BIOLOGY (2001)
Rapid speciation via parallel, directional selection on regulatory genetic pathways
NA Johnson et al.
JOURNAL OF THEORETICAL BIOLOGY (2000)
One sequence, two ribozymes: Implications for the emergence of new ribozyme folds
EA Schultes et al.
SCIENCE (2000)