Related papers: Shaping Epigenetic Memory via Genomic Bookmarking
We consider a Moran model with recombination in a haploid population of size $N$. At each birth event, with probability $1-\rho_N R$ the offspring copies one parent's chromosome, and with probability $\rho_N R$ she inherits a chromosome…
Epigenetic mechanisms of silencing via heritable chromatin modifications play a major role in gene regulation and cell fate specification. We consider a model of epigenetic chromatin silencing in budding yeast and study the bifurcation…
A Restricted Boltzmann Machine (RBM) is an unsupervised machine-learning bipartite graphical model that jointly learns a probability distribution over data and extracts their relevant statistical features. As such, RBM were recently…
We propose a model for the formation of chromatin loops based on the diffusive sliding of a DNA-bound factor which can dimerise to form a molecular slip-link. Our slip-links mimic the behaviour of cohesin-like molecules, which, along with…
"Epigenetic Tracking" is an evo-devo method to generate arbitrary 2d or 3d shapes; as such, it belongs to the field of "artificial embryology". In silico experiments have proved the effectiveness of the method in devo-evolving shapes of any…
Three-Dimensional (3D) chromatin interactions, such as enhancer-promoter interactions (EPIs), loops, Topologically Associating Domains (TADs), and A/B compartments play critical roles in a wide range of cellular processes by regulating gene…
Fluorescence microscopy reveals that the contents of many (membrane-free) nuclear "bodies" exchange rapidly with the soluble pool whilst the underlying structure persists; such observations await a satisfactory biophysical explanation. To…
Polymers with active segments constitute prospective future materials and are used as a model for some biological systems such as chromatin. The directions of the active forces are typically introduced with temporal or spatial correlations…
Sequencing a genome to determine an individual's DNA produces an enormous number of short nucleotide subsequences known as reads, which must be reassembled to reconstruct the full genome. We present a method for analyzing this type of data…
An In Silico model to relate the properties of proteins to the structure, sequence, function and evolutionary history of proteins is shown. The derived ideal sequences for amino acid residues in proteins can then be considered as attractors…
Low-cost, high-throughput DNA and RNA sequencing (HTS) data is the backbone of the life sciences. Genome sequencing is now becoming a part of Predictive, Preventive, Personalized, and Participatory (termed 'P4') medicine. All genomic data…
Nanoscale chromatin domains, variously termed nucleosome clutches, nanodomains, or packing domains, have emerged as fundamental architectural units of the mammalian genome during interphase and mitosis. Unlike cohesin-dependent loops or…
Statistical analysis of evolutionary-related protein sequences provides insights about their structure, function, and history. We show that Restricted Boltzmann Machines (RBM), designed to learn complex high-dimensional data and their…
The memory of contemporary Large Language Models is bound by a physical paradox: as they learn, they fill up. The linear accumulation (O(N)) of Key-Value states treats context as a warehouse of static artifacts, eventually forcing a…
Recent experimental and theoretical approaches have attempted to quantify the physical organization (compaction and geometry) of the bacterial chromosome with its complement of proteins (the nucleoid). The genomic DNA exists in a complex…
Since the completion of the human genome sequencing project in 2001, significant progress has been made in areas such as gene regulation editing and protein structure prediction. However, given the vast amount of genomic data, the segments…
Molecules in equilibrium follow a Boltzmann distribution, making the underlying energy landscape a physically grounded modeling objective. However, such landscapes are difficult to learn from data and, once learned, hard to sample from.…
In Xenopus early embryos, replication origins neither require specific DNA sequences nor is there an efficient S/M checkpoint, even though the whole genome (3 billion bases) is completely duplicated within 10-20 minutes. This leads to…
Motivated by the problem of domain formation in chromosomes, we studied a co--polymer model where only a subset of the monomers feel attractive interactions. These monomers are displaced randomly from a regularly-spaced pattern, thus…
Abstract: Bionic learning with fused sensing, memory and processing functions outperforms artificial neural networks running on silicon chips in terms of efficiency and footprint. However, digital hardware implementation of bionic learning…