Identifying 3D Genome Organization in Diploid Organisms via Euclidean Distance Geometry

DOI10.1137/21M1390372zbMath1486.92334arXiv2101.05336OpenAlexW3118387895WikidataQ114074107 ScholiaQ114074107MaRDI QIDQ5065472

Anastasiya Belyaeva, Caroline Uhler, Lawrence J. Sun, Kaie Kubjas

Publication date: 21 March 2022

Published in: SIAM Journal on Mathematics of Data Science (Search for Journal in Brave)

Full work available at URL: https://arxiv.org/abs/2101.05336

zbMATH Keywords

semidefinite programmingsystems of polynomial equationsdiploid organismsEuclidean distance geometryHi-C3D genome organization

Mathematics Subject Classification ID

Semidefinite programming (90C22) Real algebraic sets (14P05) Rigidity and flexibility of structures (aspects of discrete geometry) (52C25) Molecular structure (graph-theoretic methods, methods of differential topology, etc.) (92E10) Genetics and epigenetics (92D10)

Related Items (2)

Algebraic structures in statistical methodology. Abstracts from the workshop held December 4--10, 2022 ⋮ 3D genome reconstruction from partially phased Hi-C data

Uses Software

• CVX
• Mosek

Cites Work

• Sum of squares method for sensor network localization
• Solving Euclidean distance matrix completion problems via semidefinite progrmming
• The convex geometry of linear inverse problems
• Graph Implementations for Nonsmooth Convex Programs
• Euclidean distance matrix completion problems
• Distance Shrinkage and Euclidean Embedding via Regularized Kernel Estimation
• Framework for kernel regularization with application to protein clustering
• Unnamed Item

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