Publications
Listed in reverse chronological order by year, and categorized by publication type.
Preprints
[64] Misrepresenting biases in arrival
Refereed Journal Publications
[63] Robust genetic codes enhance protein evolvability
[62] Alphabet cardinality and adaptive evolution
Special issue on Random Landscapes in Evolution, Ecology, & Beyond
[61] Developmental selection and the perception of mutation bias
[60] Environment-dependent epistasis increases phenotypic diversity in gene regulatory networks
[59] Mutation and selection induce correlations between selection coefficients and mutation rates
[58] Interdisciplinary approaches to predicting evolutionary biology
Introduction to special issue on predicting evolution.
[57] Mutation bias and the predictability of evolution
[56] On the incongruence of genotype-phenotype and fitness landscapes
[55] The adaptive potential of non-heritable somatic mutations
[54] Mutation bias shapes the spectrum of adaptive substitutions
[53] Little evidence the standard genetic code is optimized for resource conservation
See commentary by Ornob Alam in Nature Ecology & Evolution.
[52] From genotypes to organisms: State-of-the-art and perspectives of a cornerstone in evolutionary dynamics
[51] Mutation bias interacts with composition bias to influence adaptive evolution
[50] Enhancers facilitate the birth of de novo genes and gene integration into regulatory networks
[49] Transition bias influences the evolution of antibiotic resistance in Mycobacterium tuberculosis
[48] Cryptic genetic variation accelerates evolution by opening access to diverse adaptive peaks
See commentary by Lee & Marx (2019) “Tales from the crypt(ic).” Science, 365, 318-319. [pdf]
[47] The causes of evolvability and their evolution
[46] The architecture of an empirical genotype-phenotype map
[45] RNA-mediated gene regulation is less evolvable than transcriptional regulation
This paper received a rating of “very good” by the Faculty of 1000. [link]
[44] A thousand empirical adaptive landscapes and their navigability
José Aguilar-Rodríguez received the SIB Best Swiss Bioinformatics Graduate Paper Award for this manuscript.
[43] Genonets Server - A web server for the construction, analysis, and visualization of genotype networks
[42] No tradeoff between versatility and robustness in gene circuit motifs
[41] The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases
[40] Mechanisms of mutational robustness in transcriptional regulation
[39] Function does not follow form in gene regulatory circuits
[38] Phenotypic robustness and the assortativity signature of human transcription factor networks
[37] Latent phenotypes pervade gene regulatory circuits
[36] The robustness and evolvability of transcription factor binding sites
[35] Robustness, evolvability, and the logic of genetic regulation
[34] Constraint and contingency in multifunctional gene regulatory circuits
[33] The influence of assortativity on the robustness and evolvability of gene regulatory networks upon gene birth
[32] Complex and dynamic population structures: Synthesis, open questions, and future directions
[31] Evolutionary dynamics on multiple scales: A quantitative analysis of the interplay between genotype, phenotype, and fitness in linear genetic programming
[30] The influence of assortativity on the robustness of signal-integration logic in gene regulatory networks
[29] Exact solutions for social and biological contagion models on mixed directed and undirected, degree-correlated random networks
[28] Direct, physically motivated derivation of the contagion condition for spreading processes on generalized random networks
[27] The evolution of conditional dispersal and reproductive isolation along environmental gradients
[26] Exploiting graphics processing units for computational biology and bioinformatics
[25] Information cascades on degree-correlated random networks
[24] Evolutionary dynamics on scale-free interaction networks
[23] Pair approximations of takeover dynamics in regular population structures
[22] Underdominance, multiscale interactions, and self-organizing barriers to gene flow
[21] Analysis of a threshold model of social contagion on degree-correlated networks
[20] Genomic mining for complex disease traits with 'Random Chemistry’
Refereed Conference Publications
[19] An alternative route to robustness: The relationship between assortativity, in-components, and characteristic path length in gene regulatory networks
[18] Robustness, evolvability, and accessibility in the signal-integration space of gene regulatory circuits
Best paper award
[17] The influence of whole genome duplication and subsequent diversification on environmental robustness and evolutionary innovation in gene regulatory networks
[16] Robustness, evolvability, and accessibility in linear genetic programming
Nominated for a best paper award
[15] Sexual recombination in self-organizing interaction networks
[14] The influence of scaling and assortativity on takeover times in scale-free topologies
Nominated for a best paper award
[13] Parameterizing pair approximations for takeover dynamics
[12] Takeover times on scale-free topologies
[11] Sensitivity of self-organized speciation to long-distance dispersal
Best student paper award
[10] Using pair approximations to predict takeover dynamics in spatially structured populations
[9] Emergent mating topologies in spatially structured genetic algorithms
[8] Hill climbing through 'Random Chemistry' for detecting epistasis
[7] Speciation by self-organizing barriers to gene flow in simulated populations with localized mating
[6] A hybrid genetic algorithm with pattern search for finding heavy atoms in protein crystals
Nominated for a best paper award
Refereed Book Chapters
[5] The robustness and evolvability of transcriptional regulation
[4] Robustness and evolvability in molecular evolution
[3] Pair approximations
[2] Exploiting expert knowledge of protein-protein interactions in a computational evolution system for detecting epistasis
[1] Sensible initialization of a computational evolution system using expert knowledge for epistasis analysis in human genetics
Dissertations
Mutation-biased adaptation
Regulatory and developmental novelties and their implications for evolutionary trajectories
Interaction topologies and information flow