Related papers: Nucleosome shape dictates chromatin-fiber structur…
The epigenome, i.e. the whole of chromatin modifications, is transferred from mother to daughter cells during cell differentiation. When de novo chromatin modifications (establishment or erasure of, respectively, new or pre-existing DNA…
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…
Chromatin loop extrusion by Structural Maintenance of Chromosome (SMC) complexes is thought to underlie intermediate-scale chromatin organization inside cells. Motivated by a number of experiments suggesting that nucleosomes may block loop…
It has been reported that the number of transcription factors encoded in prokaryotic genomes scales approximately quadratically with their total number of genes. We propose a conceptual explanation of this finding and illustrate it using a…
The three-dimensional organisation of chromosomes can be probed using methods such as Capture-C. However it is unclear how such population level data relates to the organisation within a single cell, and the mechanisms leading to the…
An active loop-extrusion mechanism is regarded as the main out--of--equilibrium mechanism responsible for the structuring of megabase-sized domains in chromosomes. We developed a model to study the dynamics of the chromosome fibre by…
The relationship between microscopic observations and macroscopic behavior is a fundamental open question in biophysical systems. Here, we develop a unified approach that---in contrast with existing methods---predicts cell type from…
In solid tumors, cells constantly interact with the surrounding extracellular matrix. In particular cancer-associated fibroblasts modulate the architecture of the matrix by exerting forces and contracting collagen fibres, creating paths…
Epigenetics plays a key role in cellular differentiation and maintaining cell identity, enabling cells to regulate their genetic activity without altering the DNA sequence. Epigenetic regulation occurs within the context of hierarchically…
Protein chains of the (FG)$_n$ ($n \simeq$ 300) type cap the cytoplasmatic side of the nucleopore complex, which connects the nucleus to the remainder of an eukaryotic cell. We study the properties of three fundamental polymer models that…
The architecture of the eukaryotic genome is characterized by a high degree of spatial organization. Chromosomes occupy preferred territories correlated to their state of activity and, yet, displace their genes to interact with remote sites…
Structural quantities such as order parameters and correlation functions are often employed to gain insight into the physical behavior and properties of condensed matter systems. While standard quantities for characterizing structure exist,…
A comparative classification scheme provides a good basis for several approaches to understand proteins, including prediction of relations between their structure and biological function. But it remains a challenge to combine a…
How genes affect tissue scale organization remains a longstanding biological puzzle. As experimental efforts aim to quantify gene expression, chromatin organization, cellular structure, and tissue structure, computational modeling lags…
The properties of polycrystalline materials are often dominated by the size of their grains and by the atomic structure of their grain boundaries. These effects should be especially pronounced in 2D materials, where even a line defect can…
Proteins control many vital functions in living cells, such as cell growth and cell division. Reliable coordination of these functions requires the spatial and temporal organizaton of proteins inside cells, which encodes information about…
The intricate three-dimensional geometries of protein tertiary structures underlie protein function and emerge through a folding process from one-dimensional chains of amino acids. The exact spatial sequence and configuration of amino…
In nature the three-dimensional structure of a protein is encoded in the corresponding gene. In this paper we describe a new method for encoding the three-dimensional structure of a protein into a binary sequence. The feature of the method…
Cellular functions crucially depend on the precise execution of complex biochemical reactions taking place on the chromatin fiber in the tightly packed environment of the cell nucleus. Despite the availability of large data sets probing…
Protein structure prediction models are now capable of generating accurate 3D structural hypotheses from sequence alone. However, they routinely fail to capture the conformational diversity of dynamic biomolecular complexes, often requiring…