Results 31 to 40 of about 8,821,447 (199)

Bayesian inference of spatial organizations of chromosomes. [PDF]

PLoS Computational Biology, 2013
Knowledge of spatial chromosomal organizations is critical for the study of transcriptional regulation and other nuclear processes in the cell. Recently, chromosome conformation capture (3C) based technologies, such as Hi-C and TCC, have been developed ...
Ming Hu, Ke Deng, Zhaohui Qin, Jesse Dixon, Siddarth Selvaraj, Jennifer Fang, Bing Ren, Jun S Liu   +7 more
doaj   +1 more source

Large-scale reconstruction of 3D structures of human chromosomes from chromosomal contact data

Nucleic Acids Research, 2014
Abstract Chromosomes are not positioned randomly within a nucleus, but instead, they adopt preferred spatial conformations to facilitate necessary long-range gene–gene interactions and regulations. Thus, obtaining the 3D shape of chromosomes of a genome is critical for understanding how the genome folds, functions and how its genes ...
Trieu, Tuan, Cheng, Jianlin
openaire   +2 more sources

Manifold Based Optimization for Single-Cell 3D Genome Reconstruction. [PDF]

PLoS Computational Biology, 2015
The three-dimensional (3D) structure of the genome is important for orchestration of gene expression and cell differentiation. While mapping genomes in 3D has for a long time been elusive, recent adaptations of high-throughput sequencing to chromosome ...
Jonas Paulsen, Odin Gramstad, Philippe Collas   +2 more
doaj   +1 more source

Dynamic interplay between structural variations and 3D chromosome organization in pancreatic cancer [PDF]

, 2021
Summary Structural variations (SVs) are the greatest source of variation in the genome and can lead to oncogenesis. However, the identification and interpretation of SVs in human pancreatic cancer remain largely undefined due to technological limitations.
Yongxing Du, Zongting Gu, Zongze Li, Zan Yuan, Yue Zhao, Xiaohao Zheng, Xiaochen Bo, Hebing Chen, Chengfeng Wang   +8 more
openaire   +1 more source

Characterizing the 3D structure and dynamics of chromosomes and proteins in a common contact matrix framework [PDF]

Nucleic Acids Research, 2018
Abstract Any conformational ensemble of biopolymers, whether they are proteins or chromosomes, can be described using contact matrices derived from experimental or computational studies. One powerful approach to extract meaningful information from these contact matrices is to perform principal component analysis (PCA) on the covariance ...
Lindsay, Richard J., Pham, Bill, Shen, Tongye, McCord, Rachel Patton   +3 more
openaire   +2 more sources

Inter- and intra-specific gene-density-correlated radial chromosome territory arrangements are conserved in Old World monkeys [PDF]

, 2005
Recently it has been shown that the gene-density correlated radial distribution of human 18 and 19 homologous chromosome territories (CTs) is conserved in higher primates in spite of chromosomal rearrangements that occurred during evolution.
Ishida, T., KüPPER, Katrin, Kupper, K., 田辺　, 秀之, Neusser, M., NEUSSER, Michaela, Mizusawa, H., TANABE, Hideyuki, Tanabe, H., ISHIDA, Takafumi, MIZUSAWA, Hiroshi   +10 more
core   +1 more source

Large-scale 3D chromatin reconstruction from chromosomal contacts

BMC Genomics, 2019
Background Recent advances in genome analysis have established that chromatin has preferred 3D conformations, which bring distant loci into contact. Identifying these contacts is important for us to understand possible interactions between these loci ...
Yanlin Zhang, Weiwei Liu, Yu Lin, Yen Kaow Ng, Shuaicheng Li   +4 more
doaj   +1 more source

Applications of image analysis in plant chromosome and chromatin structure study

Quantitative Biology, 2022
Background The use of image analysis to understand the structure of chromosome and chromatin is critical to the study of genetic evolution and diversification.
Nobuko Ohmido, Astari Dwiranti, Seiji Kato, Kiichi Fukui   +3 more
doaj   +1 more source

Structure of the hDmc1-ssDNA filament reveals the principles of its architecture [PDF]

, 2010
In eukaryotes, meiotic recombination is a major source of genetic diversity, but its defects in humans lead to abnormalities such as Down's, Klinefelter's and other syndromes.
Dmitry V Bugreev, Julie Hodgkinson, Yuriy L Chaban, Bugreev, DV, Orlova, Elena, Orlova, EV, Hodgkinson, J.L., Orlova Elena V., Chaban, Y.L., Bugreev, D.V., Andrei L Okorokov, Chaban Yuriy L., Okorokov, AL, Elena V Orlova, Okorokov, A.L., Hodgkinson, J, Bugreev Dmitry V., Chaban, YL, Okorokov Andrei L., Mazin, AV, Hodgkinson Julie, Mazin, A.V., Alexander V Mazin, Mazin Alexander V.   +23 more
core   +2 more sources

Inference of chromosome 3D structures from GAM data by a physics computational approach

Methods, 2020
The combination of modelling and experimental advances can provide deep insights for understanding chromatin 3D organization and ultimately its underlying mechanisms. In particular, models of polymer physics can help comprehend the complexity of genomic contact maps, as those emerging from technologies such as Hi-C, GAM or SPRITE.
Fiorillo L., Bianco S., Chiariello A. M., Barbieri M., Esposito A., Annunziatella C., Conte M., Corrado A., Prisco A., Pombo A., Nicodemi M.   +10 more
openaire   +5 more sources