Related papers: ChromRec: Self-Assembly of Nucleosomes Driven by D…
Deformable image registration across heterogeneous domains remains challenging because coupled appearance variation and geometric misalignment violate the brightness constancy assumption underlying conventional methods. We propose…
The structure of nanoclusters is complex to describe due to their noncrystallinity, even though bonding and packing constraints limit the local atomic arrangements to only a few types. A computational scheme is presented to extract…
Apart from being the gateway for all access to the eukaryotic genome, chromatin has in recent years been identified as carrying an epigenetic code regulating transcriptional activity. The detailed knowledge of this code contrasts the…
Procuring expressive molecular representations underpins AI-driven molecule design and scientific discovery. The research mainly focuses on atom-level homogeneous molecular graphs, ignoring the rich information in subgraphs or motifs.…
In complex multivariate systems, interactions among variables are defined by dependency structures, often encoded as directed acyclic graphs ($\text{DAGs}$). However, dependency structures can vary across subjects, and ignoring this…
We present ChromoSkein, a web-based tool for visualizing three-dimensional chromatin models. The spatial organization of chromatin is essential to its function. Experimental methods, namely Hi-C, reveal the spatial conformation but output a…
Topologies of large deformation Contact-aided Compliant Mechanisms (CCMs), with self and mutual contact, exemplified via path generation applications, are designed using the continuum synthesis approach. Design domains are parameterized…
The specificity and simplicity of the Watson-Crick base pair interactions make DNA one of the most versatile construction materials for creating nanoscale structures and devices. Among several DNA-based approaches, the DNA origami technique…
High-throughput chromatin conformation capture (Hi-C) data provide insights into the 3D structure of chromosomes, with normalization being a crucial pre-processing step. A common technique for normalization is matrix balancing, which…
Unconditional crystal structure generation with diffusion models faces challenges in identifying symmetric crystals as the unit cell size increases. We present the Crystal Host-Guided Generation (CHGGen) framework to address this challenge…
In many biopolymer solutions, attractive interactions that stabilize finite-sized clusters at low concentrations also promote phase separation at high concentrations. Here we study a model biopolymer system that exhibits the opposite…
The metazoan genome is replicated in precise cell lineage specific temporal order. However, the mechanism controlling this orchestrated process is poorly understood as no molecular mechanisms have been identified that actively regulate the…
The integration of multi-omics single-cell data remains challenging due to high-dimensionality and complex inter-modality relationships. To address this, we introduce MoRE-GNN (Multi-omics Relational Edge Graph Neural Network), a…
The recognition of multi-class cell nuclei can significantly facilitate the process of histopathological diagnosis. Numerous pathological datasets are currently available, but their annotations are inconsistent. Most existing methods…
Molecular dynamics simulations are often used to provide feedback in the design workflow of DNA nanostructures. However, even with coarse-grained models, convergence of distributions from unbiased simulation is slow, limiting applications…
Leveraging domain knowledge including fingerprints and functional groups in molecular representation learning is crucial for chemical property prediction and drug discovery. When modeling the relation between graph structure and molecular…
Multi-technique high resolution X-ray mapping enhanced by the recent advent of 4th generation synchrotron facilities can produce colossal datasets, challenging traditional analysis methods. Such difficulty is clearly materialized when…
Domain-generalized nuclei segmentation refers to the generalizability of models to unseen domains based on knowledge learned from source domains and is challenged by various image conditions, cell types, and stain strategies. Recently, the…
Programmable self-assembly enables the construction of complex molecular, supramolecular, and crystalline architectures from well-designed building blocks. We introduce a hypergraph-based formalism, Blocks & Bonds (B&B), that generalizes…
Aqueous solutions of disodium cromoglycate (DSCG), a representative model system for chromonic liquid crystals, exhibit temperature- and concentration-dependent phase behaviors spanning isotropic, nematic, and columnar phases, as well as…