Evaluation of the EVA Descriptor for QSAR Studies: 3. The use of a Genetic Algorithm to Search for Models with Enhanced Predictive Properties (EVA_GA) [PDF]
, 2000 The EVA structural descriptor, based upon calculated fundamental molecular vibrational frequencies, has proved to be an effective descriptor for both QSAR and database similarity calculations.
Turner, D.B., Willett, P.
core +1 more source
Identification of Structural Variation in Chimpanzees Using Optical Mapping and Nanopore Sequencing. [PDF]
, 2020 Recent efforts to comprehensively characterize great ape genetic diversity using short-read sequencing and single-nucleotide variants have led to important discoveries related to selection within species, demographic history, and lineage-specific traits.
Andrés, Aida M +7 more
core +3 more sources
Integrating transposable elements in the 3D genome [PDF]
, 2019 Chromosome organisation is increasingly recognised as an essential component of genome regulation, cell fate and cell health. Within the realm of transposable elements (TEs) however, the spatial information of how genomes are folded is still only rarely ...
A Bousios +105 more
core +5 more sources
GIVE: portable genome browsers for personal websites. [PDF]
, 2018 Growing popularity and diversity of genomic data demand portable and versatile genome browsers. Here, we present an open source programming library called GIVE that facilitates the creation of personalized genome browsers without requiring a system ...
Alvin Zheng +31 more
core +2 more sources
Imaging plant germline differentiation within Arabidopsis flowers by light sheet microscopy [PDF]
, 2020 In higher plants, germline differentiation occurs during a relatively short period within developing flowers. Understanding of the mechanisms that govern germline differentiation lags behind other plant developmental processes.
Bainar, Petr +8 more
core +1 more source
3D chromosome structure reconstruction using graph convolutional neural networks
, 2022 Chromosome conformation capture (3C) is a method of measuring chromosome topology in terms of loci interaction. The Hi-C method is a derivative of 3C that allows for genome-wide quantification of chromosome interaction. From such interaction data, it is possible to infer the three-dimensional (3D) structure of the underlying ...
Van Hovenga, +2 more
openaire +1 more source
Network concepts for analyzing 3D genome structure from chromosomal contact maps [PDF]
EPJ Nonlinear Biomedical Physics, 2016 The recent experimental technique of chromosome conformational capture gives an in-vivo access to pairwise contact frequencies between genomic loci. We present how network analysis can be exploited to extract information from genome-wide contact maps. We recently proposed to use graph distance for deriving a complete distance matrix from sparse contact
Morlot, Jean-Baptiste +2 more
openaire +2 more sources
RNA surveillance controls 3D genome structure via stable cohesin-chromosome interaction [PDF]
, 2021 Summary The 3D architecture that the genome is folded into is regulated by CTCF, which determines domain borders, and cohesin, which generates interactions within domains. However, organisms lacking CTCF have been reported to still have cohesin-mediated 3D structures with strong borders.
Yujin Chun +4 more
openaire +1 more source
Inferential Structure Determination of Chromosomes from Single-Cell Hi-C Data. [PDF]
PLoS Computational Biology, 2016 Chromosome conformation capture (3C) techniques have revealed many fascinating insights into the spatial organization of genomes. 3C methods typically provide information about chromosomal contacts in a large population of cells, which makes it difficult
Simeon Carstens +2 more
doaj +1 more source
Diversity and complexity in neural organoids
FEBS Letters, EarlyView.Neural organoid research aims to expand genetic diversity on one side and increase tissue complexity on the other. Chimeroids integrate multiple donor genomes within single organoids. Self‐organising multi‐identity organoids, exogenous cell seeding, or enforced assembly of region‐specific organoids contribute to tissue complexity.
Ilaria Chiaradia, Madeline A. Lancaster
wiley +1 more source