In contrast to population-based Hi-C data, single-cell Hi-C data are zero-inflated and do not indicate the frequency of proximate DNA segments. There are a limited number of computational tools that can model the three-dimensional structures of chromosomes based on single-cell Hi-C data.
We developed SCL (Single-Cell Lattice), a computational method to reconstruct three-dimensional (3D) structures of chromosomes based on single-cell Hi-C data. We designed a loss function and a 2D Gaussian function specifically for the characteristics of single-cell Hi-C data. A chromosome is represented as beads-on-a-string and stored in a 3D cubic lattice. Metropolis-Hastings simulation and simulated annealing are used to simulate the structure and minimize the loss function. We evaluated the SCL-inferred 3D structures (at both 500 kb and 50 kb resolutions) using multiple criteria and compared them with the ones generated by another modeling software program. The results indicate that the 3D structures generated by SCL closely fit single-cell Hi-C data. We also found similar patterns of trans-chromosomal contact beads, Lamin-B1 enriched topological domains, and H3K4me3 enriched domains by mapping data from previous studies onto the SCL-inferred 3D structures.
","abstract_html":"<p>In contrast to population-based Hi-C data, single-cell Hi-C data are zero-inflated and do not indicate the frequency of proximate DNA segments. There are a limited number of computational tools that can model the three-dimensional structures of chromosomes based on single-cell Hi-C data.</p> <p>We developed SCL (Single-Cell Lattice), a computational method to reconstruct three-dimensional (3D) structures of chromosomes based on single-cell Hi-C data. We designed a loss function and a 2D Gaussian function specifically for the characteristics of single-cell Hi-C data. A chromosome is represented as beads-on-a-string and stored in a 3D cubic lattice. Metropolis-Hastings simulation and simulated annealing are used to simulate the structure and minimize the loss function. We evaluated the SCL-inferred 3D structures (at both 500 kb and 50 kb resolutions) using multiple criteria and compared them with the ones generated by another modeling software program. The results indicate that the 3D structures generated by SCL closely fit single-cell Hi-C data. We also found similar patterns of trans-chromosomal contact beads, Lamin-B1 enriched topological domains, and H3K4me3 enriched domains by mapping data from previous studies onto the SCL-inferred 3D structures.</p>","abstract_has_math":false,"creators":["Zhu, Hao"],"institution":null,"degree_name":"Master of Science (MS)","degree_level":"Masters Thesis","degree_discipline":null,"degree_department":null,"school":null,"contributors":["Chaoyang Zhang","Lina Pu","Ras B. Pandey"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2019,"date_issued":"2019-05-01T07:00:00Z","date_published":"2019-05-01T07:00:00Z","updated_at":"2026-07-24T05:45:12Z","subjects":["chromosome","3D modeling","Hi-C technology","single-cell Hi-C data","latice-based","Bioinformatics"],"languages":[],"rights":[],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://aquila.usm.edu/masters_theses/631","outbound_label":"Repository record","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Chaoyang Zhang","Lina Pu","Ras B. Pandey"]},{"key":"dc:creator","label":"Author","values":["Zhu, Hao"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.available","label":"Dc Date Available","values":["2019-03-16T07:00:00Z"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Masters Thesis"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Master of Science (MS)"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["chromosome","3D modeling","Hi-C technology","single-cell Hi-C data","latice-based","Bioinformatics"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["https://aquila.usm.edu/masters_theses/631"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["In contrast to population-based Hi-C data, single-cell Hi-C data are zero-inflated and do not indicate the frequency of proximate DNA segments. There are a limited number of computational tools that can model the three-dimensional structures of chromosomes based on single-cell Hi-C data.
We developed SCL (Single-Cell Lattice), a computational method to reconstruct three-dimensional (3D) structures of chromosomes based on single-cell Hi-C data. We designed a loss function and a 2D Gaussian function specifically for the characteristics of single-cell Hi-C data. A chromosome is represented as beads-on-a-string and stored in a 3D cubic lattice. Metropolis-Hastings simulation and simulated annealing are used to simulate the structure and minimize the loss function. We evaluated the SCL-inferred 3D structures (at both 500 kb and 50 kb resolutions) using multiple criteria and compared them with the ones generated by another modeling software program. The results indicate that the 3D structures generated by SCL closely fit single-cell Hi-C data. We also found similar patterns of trans-chromosomal contact beads, Lamin-B1 enriched topological domains, and H3K4me3 enriched domains by mapping data from previous studies onto the SCL-inferred 3D structures.
"]},{"key":"dc:title","label":"Title","values":["SCL: A Lattice-Based Approach to Infer Three-Dimensional Chromosome Structures from Single-Cell Hi-C Data"]}]}],"canonical_facts":{"dc:contributor":["Chaoyang Zhang","Lina Pu","Ras B. Pandey"],"dc:creator":["Zhu, Hao"],"dc:date.available":["2019-03-16T07:00:00Z"],"dc:description.abstract":["In contrast to population-based Hi-C data, single-cell Hi-C data are zero-inflated and do not indicate the frequency of proximate DNA segments. There are a limited number of computational tools that can model the three-dimensional structures of chromosomes based on single-cell Hi-C data.
We developed SCL (Single-Cell Lattice), a computational method to reconstruct three-dimensional (3D) structures of chromosomes based on single-cell Hi-C data. We designed a loss function and a 2D Gaussian function specifically for the characteristics of single-cell Hi-C data. A chromosome is represented as beads-on-a-string and stored in a 3D cubic lattice. Metropolis-Hastings simulation and simulated annealing are used to simulate the structure and minimize the loss function. We evaluated the SCL-inferred 3D structures (at both 500 kb and 50 kb resolutions) using multiple criteria and compared them with the ones generated by another modeling software program. The results indicate that the 3D structures generated by SCL closely fit single-cell Hi-C data. We also found similar patterns of trans-chromosomal contact beads, Lamin-B1 enriched topological domains, and H3K4me3 enriched domains by mapping data from previous studies onto the SCL-inferred 3D structures.
"],"dc:identifier":["https://aquila.usm.edu/masters_theses/631"],"dc:subject":["chromosome","3D modeling","Hi-C technology","single-cell Hi-C data","latice-based","Bioinformatics"],"dc:title":["SCL: A Lattice-Based Approach to Infer Three-Dimensional Chromosome Structures from Single-Cell Hi-C Data"],"thesis:degree_level":["Masters Thesis"],"thesis:degree_name":["Master of Science (MS)"]},"updated_at":"2026-07-24T05:45:12Z"}