Newest papers

MultiPASE: Shape-Aware Comparative 3D Genome Analysis

N. Nipu, G. Johnson, C. Roth, D. Rogers, S. R. Starkenburg, C. R. Steadman, G. E. Marai · 2026 · arXiv (Cornell University)

DOI: 10.48550/arxiv.2610.22786 · cited by 0 works (OpenAlex) · open-access PDF

Chinese

3D 基因组验证结构结构是由 Hi-C 数据重建的,对基因组组织提供有价值的见解,但在条件和时间点之间比较它们仍然是困难的,因为噪音,变量和任意导向。最先进的结构比较方法往往依赖于基于接触矩阵的概述,这些概述不保留重建基因组结构的空间地理学,并使基因表达和染色素可访问性难以整合。因此,需要强大的结构调整和空间抽象方法,这些方法支持条件和时间点的综合分析。我们提供 MultiPASE,一个用于重建 3D 基因组结构的比较分析的计算管道,以基因级空间点云为代表。APASE 将云调配成一个共享的协调框架,即我们使用基于 PCA 进行实验的

Machine translation (Meta M2M100); the English original follows.

Abstract

3D genome structures reconstructed from Hi-C data provide valuable insights into chromatin organization, but comparing them across conditions and time points remains challenging because of noise, variability, and arbitrary orientation. State-of-the-art comparison approaches often rely on contact-matrix-based summaries, which do not preserve the spatial geometry of the reconstructed structures and make integration with gene expression and chromatin accessibility difficult. There is therefore a need for robust structural alignment and spatial abstraction methods that support integrated analysis across conditions and time points. We present MultiPASE, a computational pipeline for comparative analysis of reconstructed 3D genome structures represented as gene-level spatial point clouds. MultiPASE aligns point clouds into a shared coordinate frame using coarse-to-fine rigid registration with PCA-based axis disambiguation and robust ICP refinement, then summarizes spatial organization using two complementary shape abstraction methods that produce stable, nested, multi-scale representations from dense core regions to broader structural extent. Using Hi-C-derived reconstructions from viral infection experiments, we show how the approach reveals condition-dependent structural changes that are difficult to interpret from raw 3D structures alone. By integrating spatial structure with gene expression and chromatin accessibility, MultiPASE supports interactive analysis of spatial organization and gene relocation patterns. A quantitative validation, reported in the Supplementary Materials, shows that the proposed shape abstractions preserve non-convex features, remain stable across samples, and that the alignment pipeline is necessary for meaningful comparison. A usage case and a usability evaluation with eight participants demonstrate the pipeline's effectiveness for comparative structural analysis.

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Topics: Computer science, Chromatin, Abstraction, Pipeline (software), Point cloud, Computational biology

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