Related papers: Local stability and evolution of the genetic code
Mutation testing has been demonstrated to be one of the most powerful fault-revealing tools in the tester's tool kit. Much previous work implicitly assumed it to be sufficient to re-compute mutant suites per release. Sadly, this makes…
Genetic drift is stochastic fluctuations of alleles frequencies in a population due to sampling effects. We consider a model of drift in an equilibrium population, with high mutation rates: few functional mutations per generation. Such…
Predicting the impact of single-point amino acid mutations on protein stability is essential for understanding disease mechanisms and advancing drug development. Protein stability, quantified by changes in Gibbs free energy ($\Delta\Delta…
The aim of this work is to elucidate how physical principles of protein design are reflected in natural sequences that evolved in response to the thermal conditions of the environment. Using an exactly solvable lattice model, we design…
For cellular biochemical reaction systems where the numbers of molecules is small, significant noise is associated with chemical reaction events. This molecular noise can give rise to behavior that is very different from the predictions of…
Diverse biological networks exhibit universal features distinguished from those of random networks, calling much attention to their origins and implications. Here we propose a minimal evolution model of Boolean regulatory networks, which…
Modular and well-written software is an ideal that programmers strive to achieve. However, real-world project constraints limit the amount of reusable and modular code that programmers can produce. Many techniques exist that refactor code…
We discuss recently developed methods that quantify the stability and generalizability of statistical findings under distributional changes. In many practical problems, the data is not drawn i.i.d. from the target population. For example,…
Benchmark rankings are routinely used to justify scientific claims about method quality in gene regulatory network (GRN) inference, yet the stability of these rankings under plausible evaluation protocol choices is rarely examined. We…
Deep neural networks such as AlphaFold and RoseTTAFold predict remarkably accurate structures of proteins compared to other algorithmic approaches. It is known that biologically small perturbations in the protein sequence do not lead to…
Random linear codes are a workhorse in coding theory, and are used to show the existence of codes with the best known or even near-optimal trade-offs in many noise models. However, they have little structure besides linearity, and are not…
The structure of the genetic code is discussed in formal terms. A rectangular table of the code ("the code matrix"), whose properties reveal its arithmetical content tagged with the information symbols in several notations. New parameters…
Essential genes constitute the core of genes which cannot be mutated too much nor lost along the evolutionary history of a species. Natural selection is expected to be stricter on essential genes and on conserved (highly shared) genes, than…
Models of codon evolution are commonly used to identify positive selection. Positive selection is typically a heterogeneous process, i.e., it acts on some branches of the evolutionary tree and not others. Previous work on DNA models showed…
Explaining to what extent the real power of genetic algorithms lies in the ability of crossover to recombine individuals into higher quality solutions is an important problem in evolutionary computation. In this paper we show how the…
This paper explores the design of convolutional codes for varying constraint lengths, focusing on their role in error correction in digital communication systems. Convolutional codes are essential in achieving reliable data transmission…
Stochastic gradient descent (SGD) and adaptive gradient methods, such as Adam and RMSProp, have been widely used in training deep neural networks. We empirically show that while the difference between the standard generalization performance…
We construct and investigate Boolean networks that follow a given reliable trajectory in state space, which is insensitive to fluctuations in the updating schedule, and which is also robust against noise. Robustness is quantified as the…
BACKGROUND: Many of the mutations accumulated by naturally evolving proteins are neutral in the sense that they do not significantly alter a protein's ability to perform its primary biological function. However, new protein functions evolve…
Motivated by recent experiments on an antibiotic resistance gene, we investigate genetic interactions between synonymous mutations in the framework of exclusion models of translation. We show that the range of possible interactions is…