Inferring diploid 3D chromatin structures from Hi-C data

Alexandra Gesine Cauer, Gürkan Yardımcı, Jean Philippe Vert, Nelle Varoquaux, William Stafford Noble

Research output: Chapter in Book/Report/Conference proceedingConference contribution

4 Scopus citations


The 3D organization of the genome plays a key role in many cellular processes, such as gene regulation, differentiation, and replication. Assays like Hi-C measure DNA-DNA contacts in a high-throughput 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 Hi-C data is still an open problem. Indeed, the diploid case is very challenging, because Hi-C data typically does not distinguish between homologous chromosomes. We propose a method to infer 3D diploid genomes from Hi-C data. We demonstrate the accuracy 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.

Original languageEnglish (US)
Title of host publication19th International Workshop on Algorithms in Bioinformatics, WABI 2019
EditorsKatharina T. Huber, Dan Gusfield
PublisherSchloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing
ISBN (Electronic)9783959771238
StatePublished - Sep 2019
Externally publishedYes
Event19th International Workshop on Algorithms in Bioinformatics, WABI 2019 - Niagara Falls, United States
Duration: Sep 8 2019Sep 10 2019

Publication series

NameLeibniz International Proceedings in Informatics, LIPIcs
ISSN (Print)1868-8969


Conference19th International Workshop on Algorithms in Bioinformatics, WABI 2019
Country/TerritoryUnited States
CityNiagara Falls


  • 3D modeling
  • Chromatin structure
  • Genome 3D architecture
  • Hi-C

ASJC Scopus subject areas

  • Software


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