3D structures of individual mammalian genomes studied by single-cell Hi-C

Comparison of the 3D organization of sperm and fibroblast genomes using the Hi-C approach

I-42: Origins and Differentiation of Somatic Progenitors of The Mammalian Gonad Revealed by Single Cell RNA-Seq

Background - MaterialsAndMethods N;Results N;Conclusion N;

Cell biochemistry studied by single-molecule imaging.

Over the last decade, there have been remarkable developments in live-cell imaging. We can now readily observe individual protein molecules within living cells and this should contribute to a systems level understanding of biological pathways. Direct observation of single fluorophores enables several types of molecular information to be gathered. Temporal and spatial trajectories enable diffusi...

3D chromosome rendering from Hi-C data using virtual reality

Most genome browsers display DNA linearly, using single-dimensional depictions that are useful to examine certain epigenetic mechanisms such as DNA methylation. However, these representations are insufficient to visualize intrachromosomal interactions and relationships between distal genome features. Relationships between DNA regions may be difficult to decipher or missed entirely if those regi...

miniMDS: 3D structural inference from high-resolution Hi-C data

Motivation Recent experiments have provided Hi-C data at resolution as high as 1 kbp. However, 3D structural inference from high-resolution Hi-C datasets is often computationally unfeasible using existing methods. Results We have developed miniMDS, an approximation of multidimensional scaling (MDS) that partitions a Hi-C dataset, performs high-resolution MDS separately on each partition, and ...