相关论文: Phylogenetic Analysis of Cell Types using Histone …
Cell heterogeneity and the inherent complexity due to the interplay of multiple molecular processes within the cell pose difficult challenges for current single-cell biology. We introduce an approach that identifies a disease phenotype from…
Background Analyzing images to accurately estimate the number of different cell types in the brain using automatic methods is a major objective in neuroscience. The automatic and selective detection and segmentation of neurons would be an…
Haplotypes, the global patterns of DNA sequence variation, have important implications for identifying complex traits. Recently, blocks of limited haplotype diversity have been discovered in human chromosomes, intensifying the research on…
High-dimensional single-cell data poses significant challenges in identifying underlying biological patterns due to the complexity and heterogeneity of cellular states. We propose a comprehensive gene-cell dependency visualization via…
Biological tree (BioTree) analysis is a foundational tool in biology, enabling the exploration of evolutionary and differentiation relationships among organisms, genes, and cells. Traditional tree construction methods, while instrumental in…
The problem of unicellular-multicellular transition is one of the main issues that is discussing in evolutionary biology. In [1] the fitness of a colony of cells is considered in terms of its two basic components, viability and fecundity.…
The rapid development of digital pathology and modern deep learning has facilitated the emergence of pathology foundation models that are expected to solve general pathology problems under various disease conditions in one unified model,…
Molecular phylogeny has focused mainly on improving models for the reconstruction of gene trees based on sequence alignments. Yet, most phylogeneticists seek to reveal the history of species. Although the histories of genes and species are…
Identifying cell types and subtypes in routine histopathology is fundamental for understanding disease. Existing tile-based models capture nuclear detail but miss the broader tissue context that influences cell identity. Current human…
Essential life processes take place across multiple space and time scales in living organisms but understanding their mechanistic interactions remains an ongoing challenge. Advanced multiscale modeling techniques are providing new…
Many cellular processes involve information processing and decision making. We can probe these processes at increasing molecular detail. The analysis of heterogeneous data remains a challenge that requires new ways of thinking about cells…
The way to infer well-supported phylogenetic trees that precisely reflect the evolutionary process is a challenging task that completely depends on the way the related core genes have been found. In previous computational biology studies,…
The cell cycle duration is a variable cellular phenotype that underlies long-term population growth and age structures. By analyzing the stationary solutions of a branching process with heritable cell division times, we demonstrate…
With ongoing developments and innovations in single-cell RNA sequencing methods, advancements in sequencing performance could empower significant discoveries as well as new emerging possibilities to address biological and medical…
Single-cell RNA sequencing (scRNA-seq) is powerful technology that allows researchers to understand gene expression patterns at the single-cell level. However, analysing scRNA-seq data is challenging due to issues and biases in data…
RNA-Seq technology allows for studying the transcriptional state of the cell at an unprecedented level of detail. Beyond quantification of whole-gene expression, it is now possible to disentangle the abundance of individual alternatively…
Reticulate evolutionary processes result in phylogenetic histories that cannot be modeled using a tree topology. Here, we apply methods from topological data analysis to molecular sequence data with reticulations. Using a simple example, we…
Trajectory inference is a critical problem in single-cell transcriptomics, which aims to reconstruct the dynamic process underlying a population of cells from sequencing data. Of particular interest is the reconstruction of differentiation…
Stem cell heterogeneity is essential for the homeostasis in tissue development. This paper established a general formulation for understanding the dynamics of stem cell regeneration with cell heterogeneity and random transitions of…
Migration of cells can be characterized by two, prototypical types of motion: individual and collective migration. We propose a statistical-inference approach designed to detect the presence of cell-cell interactions that give rise to…