Related papers: Zygotic combinatorial process in plants
Mixture models provide a flexible representation of heterogeneity in a finite number of latent classes. From the Bayesian point of view, Markov Chain Monte Carlo methods provide a way to draw inferences from these models. In particular,…
In higher organisms, all cells share the same genome, but every cell expresses only a limited and specific set of genes that defines the cell type. During cell division, not only the genome, but also the cell type is inherited by the…
Obtaining rigorous statistical guarantees for generalization under distribution shift remains an open and active research area. We study a setting we call combinatorial distribution shift, where (a) under the test- and…
Spatial systems with heterogeneities are ubiquitous in nature, from precipitation, temperature and soil gradients controlling vegetation growth to morphogen gradients controlling gene expression in embryos. Such systems, generally described…
Motivated by recent findings, we discuss the existence of a direct and robust mechanism providing discontinuous absorbing transitions in short range systems with single species, with no extra symmetries or conservation laws. We consider…
To tackle the challenge of producing tractable phylogenetic trees in contexts where complete information is available, we introduce APOGeT: an online, pluggable, clustering algorithm for a stream of genomes. It is designed to run alongside…
The purpose of this paper is to present a model of a phenomenon of plant stem morphogenesis observed by Cesar Gomez-Campo in 1970. We consider a simplified model of auxin dynamics in plant stems, showing that, after creation of the original…
The presence of phenomena analogous to phase transition in Statistical Mechanics, has been suggested in the evolution of a polygenic trait under stabilizing selection, mutation and genetic drift. By using numerical simulations of a model…
We study the thermodynamic phase transition of a spin Hamiltonian comprising two 3D magnetic sublattices. Each sublattice contains XY spins coupled by the usual bilinear exchange, while spins in different sublattices only interact via…
Beyond the genetic code, there is another layer of information encoded as chemical modifications on histone proteins positioned along the DNA. Maintaining these modifications is crucial for survival and identity of cells. How the…
Cells receive a wide variety of cellular and environmental signals, which must be processed combinatorially to generate specific and timely genetic responses. We present here a theoretical study on the combinatorial control and integration…
It has recently been shown that the NP-hard problem of calculating the minimum number of hybridization events that is needed to explain a set of rooted binary phylogenetic trees by means of a hybridization network is fixed-parameter…
Gene activation in eukaryotes involves the concerted action of histone tail modifiers, chromatin remodellers and transcription factors, whose precise coordination is currently unknown. We demonstrate that the experimentally observed…
A number field $K$ is called \emph{monogenic} if its ring of integers $\mathbb{Z}_K$ can be expressed as a simple ring extension $\mathbb{Z}[\alpha]$ for some $\alpha \in \mathbb{Z}_K$. A monic irreducible polynomial $f(x)\in\mathbb{Z}[x]$…
We performed "weighted ensemble" path-sampling simulations of adenylate kinase, using several semi-atomistic protein models. Our study investigated both the biophysics of conformational transitions as well as the possibility of increasing…
We present a combinatorial procedure (based on the W-graph of the Coxeter group) which shows that the characters of many intersection cohomology complexes on low rank complex flag varieties with coefficients in an arbitrary field are given…
We study the equilibrium properties of a model of magnetic diblock copolymer where each monomer is decorated with an Ising-like spin. Spins interact ferromagnetically within each block and antiferromagnetically across blocks, generating…
Identifiability of phylogenetic models is a necessary condition to ensure that the model parameters can be uniquely determined from data. Mixture models are phylogenetic models where the probability distributions in the model are convex…
This paper presents a new type of hybrid model for Bayesian optimization (BO) adept at managing mixed variables, encompassing both quantitative (continuous and integer) and qualitative (categorical) types. Our proposed new hybrid models…
The coupling of a mesoscopic system with its environment usually causes total decoherence: at long times the reduced density matrix of the system evolves in time to a limit which is independent of its initial value, losing all the quantum…