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Many life-history traits, like the age at maturity or adult longevity, are important determinants of the generation time. For instance, semelparous species whose adults reproduce once and die have shorter generation times than iteroparous…
We give a non-technical introduction to convergence-divergence models, a new modeling approach for phylogenetic data that allows for the usual divergence of species post speciation but also allows for species to converge, i.e. become more…
In environments that vary frequently and unpredictably, bet-hedgers can overtake the population. Diversifying bet-hedgers have a diverse set of offspring so that, no matter the conditions they find themselves in, at least some offspring…
Very low levels of genetic diversity have been reported in vertebrates with large genomes, notably salamanders and lungfish [1-3]. Interpreting differences in heterozygosity, which reflects genetic diversity in a population, is complicated…
The modeling of time series is becoming increasingly critical in a wide variety of applications. Overall, data evolves by following different patterns, which are generally caused by different user behaviors. Given a time series, we define…
The antibody repertoire of each individual is continuously updated by the evolutionary process of B cell receptor mutation and selection. It has recently become possible to gain detailed information concerning this process through…
The solution of high-dimensional inference and prediction problems in computational biology is almost always a compromise between mathematical theory and practical constraints such as limited computational resources. As time progresses,…
Evolution has fascinated quantitative and physical scientists for decades: how can the random process of mutation, recombination, and duplication of genetic information generate the diversity of life? What determines the rate of evolution?…
This paper studies identification and inference in transformation models with endogenous censoring. Many kinds of duration models, such as the accelerated failure time model, proportional hazard model, and mixed proportional hazard model,…
Several biomarkers are hypothesized to indicate early stages of Alzheimer's disease, well before the cognitive symptoms manifest. Their precise relations to the disease progression, however, is poorly understood. This lack of understanding…
Diversity is an important factor in evolutionary algorithms to prevent premature convergence towards a single local optimum. In order to maintain diversity throughout the process of evolution, various means exist in literature. We analyze…
Across metazoans, early embryos exhibit a strikingly conserved slowing down of their cell duplication speed, despite widely varying developmental paces and underlying molecular mechanisms. Here we show that this common behavior arises…
Developing reliable mechanisms for continuous local learning is a central challenge faced by biological and artificial systems. Yet, how the environmental factors and structural constraints on the learning network influence the optimal…
The dynamics of cellular pattern formation is crucial for understanding embryonic development and tissue morphogenesis. Recent studies have shown that human dermal fibroblasts cultured on liquid crystal elastomers can exhibit an increase in…
We represent a process of learning by using bit strings, where 1-bits represent the knowledge acquired by individuals. Two ways of learning are considered: individual learning by trial-and-error; and social learning by copying knowledge…
Bow-tie or hourglass structure is a common architectural feature found in biological and technological networks. A bow-tie in a multi-layered structure occurs when intermediate layers have much fewer components than the input and output…
Constraints on changes in expression levels across all cell components imposed by the steady growth of cells have recently been discussed both experimentally and theoretically. By assuming a small environmental perturbation and considering…
Biological genotypes do not code directly for phenotypes; developmental physiology is the control layer that separates genomes from capacities ascertained by selection. A key aspect is competency, as cells are not a passive material but…
Epigenetics is the study of how people's behavior and environments influence the way their genes are expressed, even though their DNA sequence is itself unchanged. By aggregating age-related epigenetic markers, epigenetic 'clocks' have…
Sex chromosomes have evolved repeatedly across the Tree of Life, yet their evolutionary fates differ strikingly. In sharp contrast to mammals and birds with degenerated, stable Y/W chromosomes, in most amphibians, teleosts, non avian…