Related papers: 3D genome reconstruction from partially phased Hi-…
This article considers the problem of 3-dimensional genome reconstruction for single-cell data, and the uniqueness of such reconstructions in the setting of haploid organisms. We consider multiple graph models as representations of this…
The spatial organization of the DNA in the cell nucleus plays an important role for gene regulation, DNA replication, and genomic integrity. Through the development of chromosome conformation capture experiments (such as 3C, 4C, Hi-C) it is…
We present a minimal computational model, which allows very fast, on-the-fly construction of three dimensional haploid interphase genomes from single cell Hi-C contact maps using the HOOMD-blue molecular dynamics package on graphics…
Understanding the three-dimensional (3D) structure of the genome is essential for elucidating vital biological processes and their links to human disease. To determine how the genome folds within the nucleus, chromosome conformation capture…
It is widely believed that the folding of the chromosome in the nucleus has a major effect on genetic expression. For example co-regulated genes in several species have been shown to colocalize in space despite being far away on the DNA…
Modern technology for producing extremely bright and coherent X-ray laser pulses provides the possibility to acquire a large number of diffraction patterns from individual biological nanoparticles, including proteins, viruses, and DNA.…
In this study, we present a conditional diffusion-transformer framework for generating ensembles of three-dimensional Escherichia coli genome conformations guided by Hi-C contact maps. Instead of producing a single deterministic structure,…
Coherent diffraction imaging (CDI) allows the retrieval of the structure of an isolated object, such as a macromolecule, from its diffraction pattern. CDI requires the fulfilment of two conditions: the imaging radiation must be coherent and…
Analysis of microscopy images can provide insight into many biological processes. One particularly challenging problem is cell nuclear segmentation in highly anisotropic and noisy 3D image data. Manually localizing and segmenting each and…
The 3D organisation of the genome in interphase cells is not a randomly folded polymer. Rather, experiments show that chromosomes arrange into a network of 3D compartments that correlate with biological processes, such as transcription,…
Cryogenic electron microscopy (cryo-EM) has transformed structural biology by allowing to reconstruct 3D biomolecular structures up to near-atomic resolution. However, the 3D reconstruction process remains challenging, as the 3D structures…
Electron tomography is a technique used in both materials science and structural biology to image features well below optical resolution limit. In this work, we present a new algorithm for reconstructing the three-dimensional(3D)…
In this article we show that the reconstructions of semiconductor surfaces can be determined using a genetic procedure. Coupled with highly optimized interatomic potentials, the present approach represents an efficient tool for finding and…
Recovering the 3D geometric structure of a face from a single input image is a challenging active research area in computer vision. In this paper, we present a novel method for reconstructing 3D heads from a single or multiple image(s)…
We introduce a Bayesian genetic algorithm for reconstructing atomic models of nanoparticles from a single projection using Z-contrast imaging. The number of atoms in a projected atomic column obtained from annular dark field scanning…
In 3-D reconstruction problems, the image data obtained from cryo electron microscopy is the projection of many heterogeneous instances of the object under study (e.g., a virus). When the object is heterogeneous but has an overall symmetry,…
Fast and robust three-dimensional reconstruction of facial geometric structure from a single image is a challenging task with numerous applications. Here, we introduce a learning-based approach for reconstructing a three-dimensional face…
3D dense reconstruction refers to the process of obtaining the complete shape and texture features of 3D objects from 2D planar images. 3D reconstruction is an important and extensively studied problem, but it is far from being solved. This…
The probability of two loci, separated by a certain genome length, being in contact can be inferred using the Chromosome Conformation Capture (3C) method and related Hi-C experiments. How to go from the contact map, a matrix listing the…
A software for processing sets of full-color images of biological tissue histological sections is developed. We used histological sections obtained by the method of high-precision layer-by-layer grinding of frozen biological tissues. The…