HiCLift: a fast and efficient tool for converting chromatin interaction data between genome assemblies

Article Multidisciplinary Sciences

The complete sequence of a human genome

Sergey Nurk et al.

Summary: The Telomere-to-Telomere (T2T) Consortium has presented a complete sequence of a human genome, T2T-CHM13, which covers the whole genome except for the Y chromosome. This new sequence includes gapless assemblies, error corrections in previous references, and nearly 200 million base pairs of additional sequence with gene predictions, including protein coding genes. The completion of important regions allows for further studies on genetic variations and functions.

SCIENCE (2022)

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Article Multidisciplinary Sciences

The 4D Nucleome Data Portal as a resource for searching and visualizing curated nucleomics data

Sarah B. Reiff et al.

Summary: The 4D Nucleome (4DN) Network aims to study the complex structure and organization of chromosomes in the nucleus and their impact on disease biology. The 4DN Data Portal is a repository for datasets generated in the network, providing a primary resource for chromosome contact and nuclear architecture data.

NATURE COMMUNICATIONS (2022)

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Article Multidisciplinary Sciences

EagleC: A deep-learning framework for detecting a full range of structural variations from bulk and single-cell contact maps

Xiaotao Wang et al.

Summary: The Hi-C technique is promising for detecting structural variations in human genomes, but lacks algorithms for full-range SV detection. EagleC combines deep-learning and ensemble-learning strategies to predict a full range of SVs at high resolution, uniquely capturing a set of fusion genes. EagleC also effectively captures SVs in other chromatin interaction platforms.

SCIENCE ADVANCES (2022)

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Article Genetics & Heredity

Long-range phasing of dynamic, tissue-specific and allele-specific regulatory elements

Sofia Battaglia et al.

Summary: The use of targeted nanopore sequencing allowed researchers to analyze chromatin accessibility and DNA methylation on contiguous DNA molecules, leading to the identification of gene regulatory elements such as promoters, enhancers, insulators, and transcription factor binding sites. They also inferred relationships among dynamic elements within immune loci and determined the order of remodeling events during T cell stimulation. Additionally, they phased primary sequences and regulatory elements across the H19/IGF2 locus, revealing primate-specific features and a mechanism that overrides IGF2 imprinting in human cells.

NATURE GENETICS (2022)

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Article Multidisciplinary Sciences