Related papers: Domain Boundary Detection in Hi-C Maps: A Probabil…
Stochasticity and spatial heterogeneity are of great interest recently in studying the spread of an infectious disease. The presented method solves an inverse problem to discover the effectively decisive topology of a heterogeneous network…
Involved in mitotic condensation, interaction of transcriptional regulatory elements or isolation of structural domains, understanding loop formation is becoming a paradigm in the deciphering of chromatin architecture and its functional…
In multicellular organisms, cells coordinate their activities through cell-cell communication (CCC), which is crucial for development, tissue homeostasis, and disease progression. Recent advances in single-cell and spatial omics…
Accurately modeling and designing protein complex structures is a central problem in computational structural biology, with broad implications for understanding cellular function and developing therapeutics. This thesis investigates two…
Domain generalization is a technique aimed at enabling models to maintain high accuracy when applied to new environments or datasets (unseen domains) that differ from the datasets used in training. Generally, the accuracy of models trained…
Dynamic graphs are rife with higher-order interactions, such as co-authorship relationships and protein-protein interactions in biological networks, that naturally arise between more than two nodes at once. In spite of the ubiquitous…
Persistent homology is an effective method for extracting topological information, represented as persistent diagrams, of spatial structure data. Hence it is well-suited for the study of protein structures. Attempts to incorporate…
The problem of detecting network structures plays a central role in distributed computing. One of the fundamental problems studied in this area is to determine whether for a given graph $H$, the input network contains a subgraph isomorphic…
A problem of substantial interest is to systematically map variation in chromatin structure to gene expression regulation across conditions, environments, or differentiated cell types. We developed and applied a quantitative framework for…
Large-scale multiple testing tasks often exhibit dependence, and leveraging the dependence between individual tests is still one challenging and important problem in statistics. With recent advances in graphical models, it is feasible to…
Switch-like responses arising from bistability have been linked to cell signaling processes and memory. Revealing the shape and properties of the set of parameters that lead to bistability is necessary to understand the underlying…
We propose a novel method to cluster gene networks. Based on a dissimilarity built using correlation structures, we consider networks that connect all the genes based on the strength of their dissimilarity. The large number of genes require…
Modular and hierarchical community structures are pervasive in real-world complex systems. A great deal of effort has gone into trying to detect and study these structures. Important theoretical advances in the detection of modular have…
Communicating cells can coordinate their gene expressions to form spatial patterns. 'Secrete-and-sense cells' secrete and sense the same molecule to do so and are ubiquitous. Here we address why and how these cells, from disordered…
We consider the problem of inferring the topology of a network using the measurements available at the end nodes, without cooperation from the internal nodes. To this end, we provide a simple method to obtain path interference which…
Embryonic development involves pattern formation characterized by the emergence of spatially localized domains characterized by distinct cell fates resulting from differential gene expression. The boundaries demarcating these domains are…
To separate the overlapped cells, a bottleneck detection approach is proposed in this paper. The cell image is segmented by slope difference distribution (SDD) threshold selection. For each segmented binary clump, its one-dimensional…
In order to cope with the rapidly increasing service demand in cellular networks, more cells are needed with better resource usage efficiency. This poses challenges for the network planning since service demand in practical networks is not…
Exploring the structural topology of genome-based large-scale metabolic network is essential for investigating possible relations between structure and functionality. Visualization would be helpful for obtaining immediate information about…
Most networks found in social and biochemical systems have modular structures. An important question prompted by the modularity of these networks is whether nodes can be said to belong to a single group. If they cannot, we would need to…