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Bias in the arrival of variation can dominate over natural selection in Richard Dawkins’s biomorphs

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Fast free-energy-based neutral set size estimates for the RNA genotype–phenotype map

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A complex network perspective on brain disease

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Statistical mechanics of phenotypic eco-evolution: From adaptive dynamics to complex diversification

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Dynamical theory for adaptive systems

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A Family of Fitness Landscapes Modeled through Gene Regulatory Networks

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Distribution of the number of fitness maxima in Fisher's geometric model

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Life finds a way

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Self-empowerment of life through RNA networks, cells and viruses

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Random and Natural Non-Coding RNA Have Similar Structural Motif Patterns but Differ in Bulge, Loop, and Bond Counts

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Robustness and stability of spin-glass ground states to perturbed interactions

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Learning the Shape of Evolutionary Landscapes: Geometric Deep Learning Reveals Hidden Structure in Phenotype-to-Fitness Maps

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Genotype-to-Protein Map and Collective Adaptation in a Viral Population

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Predicting the topography of fitness landscapes from the structure of genotype–phenotype maps

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Information-theoretic characterization of the complete genotype-phenotype map of a complex pre-biotic world

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Virus-host protein co-expression networks reveal temporal organization and strategies of viral infection

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Non-Poissonian Bursts in the Arrival of Phenotypic Variation Can Strongly Affect the Dynamics of Adaptation

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The interplay of tissue mechanics and gene regulatory networks in the evolution of morphogenesis

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Bounding phenotype transition probabilities via conditional complexity

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Entropic contribution to phenotype fitness

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Reducing Epistasis and Pleiotropy Can Avoid the Survival of the Flattest Tragedy

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What Can We Know About That Which We Cannot Even Imagine?

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Complexity and accessibility of random landscapes

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Mapping life’s disparity and evolutionary constraints in a geometric complexity space

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Hierarchical genotype networks and incipient ecological speciation in Qβ phage quasispecies

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Did organs precede organisms in the origin of life?

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Conflicting effects of recombination on the evolvability and robustness in neutrally evolving populations

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DNA Damage, Genome Stability, and Adaptation: A Question of Chance or Necessity?

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Evolving Complexity is Hard

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RNA plasticity emerges as an evolutionary response to fluctuating environmentsPreprint

García-Galindo, P., & Ahnert, S. E. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.10.02.614758 · Cited by 3 · see citing works

Modeling Evolutionary Accessibility in Phenotype space

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The Genomic Kaleidoscope: On the Hidden Dimensions of Within-Species Genomic Diversity

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Genotype networks drive oscillating endemicity and epidemic trajectories in viral evolution

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Descent from a common ancestor restricts exploration of protein sequence space

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Uncovering Evolutionary Adaptations in Common Warthogs through Genomic Analyses

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Eco-Evolutionary Constraints for the Endemicity of Rapidly Evolving Viruses

Soriano‐Paños, D. (2025) · PRX Life · doi:10.1103/43bd-hxhl · Cited by 2 · see citing works

Genotype-phenotype maps and the predictability of evolution

de Visser, J. A. G. M. (2021) · Physics of Life Reviews · doi:10.1016/j.plrev.2021.08.003 · Cited by 2 · see citing works

Redundancy-selection trade-off in phenotype-structured populations

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Physics of diffusion in viral genome evolution

Manrubia, S. C., & Cuesta, J. A. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2310999120 · Cited by 2 · see citing works

Design principles of multi-map variation in biological systems

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Random and natural non-coding RNA have similar structural motif patterns but can be distinguished by bulge, loop, and bond countsPreprint

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Functional bottlenecks can emerge from non-epistatic underlying traitsPreprint

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Natural protein structures have evolved exceptional robustness to mutationsPreprint

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Phenotypic cliffs in the RNA genotype–phenotype map

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A mathematical framework for the quantitative analysis of genetic buffering

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Modeling Complex Biological Systems: Tackling the Parameter Curse Through Evolution

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The search for universality in evolutionary landscapes

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Bias in the arrival of variation can dominate over natural selection in Richard Dawkins’ biomorphsPreprint

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The long and winding road to understanding organismal construction

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On the misuse of evolutionary theory to bolster the ‘scientific’ case for intelligent design: A cautionary note

Traulsen, A., Rasmussen, M. N., Krug, J., & Beyer, A. (2024) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2024.111985

High fitness paths can connect proteins with low sequence overlapPreprint

Kantroo, P., Wagner, G. P., & Machta, B. B. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.11.13.623265

Modeling the Biologically Possible

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A simple model captures key characteristics of biological non-deterministic genotype-phenotype maps

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Protein functional domain analysis enhances genotype–phenotype associations in comparative genomic studies of Pseudomonas aeruginosa

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Functional bottlenecks can emerge from non-epistatic underlying traits

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Toward a systems view of life’s origins: Modeling the emergence of complexity across chemical, informational and ecological levels

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Predicting the response of the oceanic carbon cycle to climate change : eco-evolutionary modeling of the microbial loop and the role of viruses

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The Challenge of Scale in Molecular Adaptation: Local Searches in Astronomical Genotype Networks

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