361 citations · 786 across the 19 of their papers we have counts for
9 papers · 1 filter
RAFT-UP: Robust Alignment for Spatial Transcriptomics with Explicit Control of Spatial Distortion
Yaqi Wu, Jingfeng Wang, Xin Maizie Zhou +2
Spatial transcriptomics (ST) profiles gene expression across a tissue section while preserving the spatial coordinates. Because current ST technologies typically profile two-dimens…
PHD-MS: Multiscale Domain Identification for Spatial Transcriptomics via Persistent Homology
Perry Beamer, Zixuan Cang
Spatial transcriptomics (ST) measures gene expression at a set of spatial locations in a tissue. Communities of nearby cells that express similar genes form \textit{spatial domains…
Topological and geometric analysis of cell states in single-cell transcriptomic data
Tram Huynh, Zixuan Cang
Single-cell RNA sequencing (scRNA-seq) enables dissecting cellular heterogeneity in tissues, resulting in numerous biological discoveries. Various computational methods have been d…
AVIDA: Alternating method for Visualizing and Integrating Data
Kathryn Dover, Zixuan Cang, Anna Ma +2
High-dimensional multimodal data arises in many scientific fields. The integration of multimodal data becomes challenging when there is no known correspondence between the samples…
Persistent cohomology for data with multicomponent heterogeneous information
Zixuan Cang, Guo-Wei Wei
Persistent homology is a powerful tool for characterizing the topology of a data set at various geometric scales. When applied to the description of molecular structures, persisten…
Representability of algebraic topology for biomolecules in machine learning based scoring and virtual screening
Zixuan Cang, Lin Mu, Guowei Wei
This work introduces a number of algebraic topology approaches, such as multicomponent persistent homology, multi-level persistent homology and electrostatic persistence for the re…
TopologyNet: Topology based deep convolutional neural networks for biomolecular property predictions
Zixuan Cang, Guo-Wei Wei
Although deep learning approaches have had tremendous success in image, video and audio processing, computer vision, and speech recognition, their applications to three-dimensional…
Topological fingerprints reveal protein-ligand binding mechanism
Zixuan Cang, Guo-Wei Wei
Protein-ligand binding is a fundamental biological process that is paramount to many other biological processes, such as signal transduction, metabolic pathways, enzyme constructio…
Analysis and prediction of protein folding energy changes upon mutation by element specific persistent homology
Zixuan Cang, Guo-Wei Wei
Motivation: Site directed mutagenesis is widely used to understand the structure and function of biomolecules. Computational prediction of protein mutation impacts offers a fast, e…