Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition
Chromatin is reprogrammed after fertilization to produce a totipotent zygote with the potential
to generate a new organism. The maternal genome inherited from the oocyte and the …
to generate a new organism. The maternal genome inherited from the oocyte and the …
Structural variants drive context-dependent oncogene activation in cancer
Higher-order chromatin structure is important for the regulation of genes by distal regulatory
sequences,. Structural variants (SVs) that alter three-dimensional (3D) genome organization …
sequences,. Structural variants (SVs) that alter three-dimensional (3D) genome organization …
Integrative detection and analysis of structural variation in cancer genomes
Structural variants (SVs) can contribute to oncogenesis through a variety of mechanisms.
Despite their importance, the identification of SVs in cancer genomes remains challenging …
Despite their importance, the identification of SVs in cancer genomes remains challenging …
The embryonic stress response to in vitro culture: insight from genomic analysis
Recent genomic studies have shed light on the impact of in vitro culture (IVC) on embryonic
homeostasis and the differential gene expression profiles associated with lower …
homeostasis and the differential gene expression profiles associated with lower …
Novel insights into chromosomal conformations in cancer
Exploring gene function is critical for understanding the complexity of life. DNA sequences
and the three-dimensional organization of chromatin (chromosomal interactions) are …
and the three-dimensional organization of chromatin (chromosomal interactions) are …
Predicting DNA methylation state of CpG dinucleotide using genome topological features and deep networks
The hypo-or hyper-methylation of the human genome is one of the epigenetic features of
leukemia. However, experimental approaches have only determined the methylation state of …
leukemia. However, experimental approaches have only determined the methylation state of …
Integrated protein function prediction by mining function associations, sequences, and protein–protein and gene–gene interaction networks
Motivations Protein function prediction is an important and challenging problem in
bioinformatics and computational biology. Functionally relevant biological information such …
bioinformatics and computational biology. Functionally relevant biological information such …
A graph neural network-based interpretable framework reveals a novel DNA fragility–associated chromatin structural unit
Y Sun, X Xu, L Lin, K Xu, Y Zheng, C Ren, H Tao… - Genome Biology, 2023 - Springer
Background DNA double-strand breaks (DSBs) are among the most deleterious DNA
lesions, and they can cause cancer if improperly repaired. Recent chromosome …
lesions, and they can cause cancer if improperly repaired. Recent chromosome …
Large-scale reconstruction of 3D structures of human chromosomes from chromosomal contact data
Chromosomes are not positioned randomly within a nucleus, but instead, they adopt
preferred spatial conformations to facilitate necessary long-range gene–gene interactions …
preferred spatial conformations to facilitate necessary long-range gene–gene interactions …
A maximum likelihood algorithm for reconstructing 3D structures of human chromosomes from chromosomal contact data
O Oluwadare, Y Zhang, J Cheng - BMC genomics, 2018 - Springer
Background The development of chromosomal conformation capture techniques,
particularly, the Hi-C technique, has made the analysis and study of the spatial conformation …
particularly, the Hi-C technique, has made the analysis and study of the spatial conformation …