Inferring diploid 3D chromatin structures from HiC data The 3D organization of the genome plays a key role in many cellular processes, such as gene regulation, differentiation, and replication. Assays like HiC measure DNADNA contacts in a highthroughput fashion, and inferring accurate 3D models of chromosomes can yield insights hidden in the raw data. For example, structural inference can account for noise in the data, disambiguate the distinct structures of homologous chromosomes, orient genomic regions relative to nuclear landmarks, and serve as a framework for integrating other data types. Although many methods exist to infer the 3D structure of haploid genomes, inferring a diploid structure from HiC data is still an open problem. Indeed, the diploid case is very challenging, because HiC data typically does not distinguish between homologous chromosomes. We propose a method to infer 3D diploid genomes from HiC data. We demonstrate the accuarcy of the method on simulated data, and we also use the method to infer 3D structures for mouse chromosome X, confirming that the active homolog exhibits a bipartite structure, whereas the active homolog does not.

shinyChromosome: An RShiny Application for Interactive Creation of Noncircular Plots of Whole Genomes Abstract   Noncircular plots of whole genomes are natural representations of genomic data aligned along all chromosomes. Currently, there is no specialized graphical user interface (GUI) designed to produce noncircular whole genome diagrams, and the use of existing tools requires considerable coding effort from users. Moreover, such tools also require improvement, including the addition of new functionalities. To address these issues, we developed a new RShiny application, named shinyChromosome, as a GUI for the interactive creation of noncircular whole genome diagrams. shinyChromosome can be easily installed on personal computers for own use as well as on local or public servers for community use. Publicationquality images can be readily generated and annotated from user input using diverse widgets. shinyChromosome is deployed at  http:150.109.59.144:3838shinyChromosome ,  http:shinyChromosome.ncpgr.cn , and  https:yimingyu.shinyapps.ioshinyChromosome  for online use. The source code and manual of shinyChromosome are freely available at  https:github.comvenyaoshinyChromosome .