Related papers: A limiting rule for the variability of coding sequ…
How does the genome encode the form of the organism? What is the nature of this genomic code? Inspired by recent work in machine learning and neuroscience, we propose that the genome encodes a generative model of the organism. In this…
Molecular phenotypes are important links between genomic information and organismic functions, fitness, and evolution. Complex phenotypes, which are also called quantitative traits, often depend on multiple genomic loci. Their evolution…
While measurement advances now allow extensive surveys of gene activity (large numbers of genes across many samples), interpretation of these data is often confounded by noise -- expression counts can differ strongly across samples due to…
Predicting how genetic variation affects phenotypic outcomes at the organismal, cellular, and molecular levels requires deciphering the cis-regulatory code, the sequence rules by which non-coding regions regulate genes. In this perspective,…
It is shown that the density of modes of the vibrational spectrum of globular proteins is universal, i.e., regardless of the protein in question it closely follows one universal curve. The present study, including 135 proteins analyzed with…
Despite major environmental and genetic differences, microbial metabolic networks are known to generate consistent physiological outcomes across vastly different organisms. This remarkable robustness suggests that, at least in bacteria,…
Many of the chemical reactions that take place within a living cell are irreversible. Due to evolutionary pressures, the number of allowable reactions within these systems are highly constrained and thus the resulting metabolic networks…
Single-cell experiments revealed substantial variability in generation times, growth rates but also in birth and division sizes between genetically identical cells. Understanding how these fluctuations determine the fitness of the…
Understanding how genes interact and relate to each other is a fundamental question in biology. However, current practices for describing these relationships, such as drawing diagrams or graphs in a somewhat arbitrary manner, limit our…
A quantitative characterization of the relationship between molecular sequence and structure is essential to improve our understanding of how function emerges. This particular genotype-phenotype map has been often studied in the context of…
Constraints in embryonic development are thought to bias the direction of evolution by making some changes less likely, and others more likely, depending on their consequences on ontogeny. Here, we characterize the constraints acting on…
We model the competition between recombination and point mutation in microbial genomes, and present evidence for two distinct phases, one uniform, the other genetically diverse. Depending on the specifics of homologous recombination, we…
Microbial ecosystems are remarkably diverse, stable, and often consist of a balanced mixture of core and peripheral species. Here we propose a conceptual model exhibiting all these emergent properties in quantitative agreement with real…
Applying machine learning to biological sequences - DNA, RNA and protein - has enormous potential to advance human health, environmental sustainability, and fundamental biological understanding. However, many existing machine learning…
We derive the asymptotic behavior of the total, active and inactive branch lengths of the seed bank coalescent, when the size of the initial sample grows to infinity. Those random variables have important applications for populations…
Spatial fluctuations of guanine and cytosine base content (GC%) are studied by spectral analysis for the complete set of human genomic DNA sequences. We find that (i) the 1/f^alpha decay is universally observed in the power spectra of all…
A general method of coding over expansions is proposed, which allows one to reduce the highly non-trivial problem of coding over continuous channels to a much simpler discrete ones. More specifically, the focus is on the additive…
Protein variability in single cells has been studied extensively in populations, but little is known about temporal protein fluctuations in a single cell over extended times. We present here traces of protein copy number measured in…
Networks describing the interaction of the elements that constitute a complex system grow and develop via a number of different mechanisms, such as the addition and deletion of nodes, the addition and deletion of edges, as well as the…
In this paper, we propose an evolving network model growing fast in units of module, based on the analysis of the evolution characteristics in real complex networks. Each module is a small-world network containing several interconnected…