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Cancer is a number of related yet highly heterogeneous diseases. Correct identification of cancer subtypes is critical for clinical decisions. The advance in sequencing technologies has made it possible to study cancer based on abundant…
Understanding how cellular morphology, gene expression, and spatial context jointly shape tissue function is a central challenge in biology. Image-based spatial transcriptomics technologies now provide high-resolution measurements of cell…
We use Topological Data Analysis tools for studying the inner organization of cells in segmented images of epithelial tissues. More specifically, for each segmented image, we compute different persistence barcodes, which codify lifetime of…
Sequence data, such as DNA, RNA, and protein sequences, exhibit intricate, multi-scale structures that pose significant challenges for conventional analysis methods, particularly those relying on alignment or purely statistical…
Graphs are naturally used to describe the structures of various real-world systems in biology, society, computer science etc., where subgraphs or motifs as basic blocks play an important role in function expression and information…
Accurately modeling multi-class cell topology is crucial in digital pathology, as it provides critical insights into tissue structure and pathology. The synthetic generation of cell topology enables realistic simulations of complex tissue…
Structural equation modeling (SEM) is a popular tool in the social and behavioural sciences, where it is being applied to ever more complex data types. The high-dimensional data produced by modern sensors, brain images, or (epi)genetic…
Gene regulatory networks are powerful tools for modeling interactions among genes to regulate their expression for homeostasis and differentiation. Single-cell sequencing offers a unique opportunity to build these networks with…
Gene regulatory networks (GRNs) define the regulatory relationships among molecules such as transcription factors, chromatin remodelers, and target genes. GRNs play a critical role in diverse biological processes, including development,…
Single-cell proteomics (SCP) is transforming our understanding of biological complexity by shifting from bulk proteomics, where signals are averaged over thousands of cells, to the proteome analysis of individual cells. This granular…
Due to the sequential sample arrival, changing experiment conditions, and evolution of knowledge, the demand to continually visualize evolving structures of sequential and diverse single-cell RNA-sequencing (scRNA-seq) data becomes…
Recent advances in high-resolution sequencing have paved the way for population-scale analysis in single-cell RNA-sequencing (scRNA-seq) data. scRNA-seq data, in particular, have proven to be extremely powerful in profiling a variety of…
Large language models excel at interpreting complex natural language instructions, enabling them to perform a wide range of tasks. In the life sciences, single-cell RNA sequencing (scRNA-seq) data serves as the "language of cellular…
Spatial transcriptomics clustering is pivotal for identifying cell subpopulations by leveraging spatial location information. While recent graph-based methods modeling cell-cell interactions have improved clustering accuracy, they remain…
Understanding how the spatial structure of blood vessel networks relates to their function in healthy and abnormal biological tissues could improve diagnosis and treatment for diseases such as cancer. New imaging techniques can generate…
The rise of single-cell sequencing technologies has revolutionized the exploration of drug resistance, revealing the crucial role of cellular heterogeneity in advancing precision medicine. By building computational models from existing…
The rapid emergence of single-cell data has facilitated the study of many different biological conditions at the cellular level. Cluster analysis has been widely applied to identify cell types, capturing the essential patterns of the…
Influenced by breakthroughs in LLMs, single-cell foundation models are emerging. While these models show successful performance in cell type clustering, phenotype classification, and gene perturbation response prediction, it remains to be…
The analysis of differential gene expression from RNA-Seq data has become a standard for several research areas mainly involving bioinformatics. The steps for the computational analysis of these data include many data types and file…
Single-cell RNA sequencing (scRNA-seq) and spatially-resolved imaging/sequencing technologies have revolutionized biomedical research. On one hand, scRNA-seq provides information about a large portion of the transcriptome for individual…