Zixuan Cang

A mathematical method and software for spatially mapping intercellular communication

Cang, Z., & Nie, Q. (2023, January 24). NATURE METHODS, Vol. 1.

AVIDA: An alternating method for visualizing and integrating data

JOURNAL OF COMPUTATIONAL SCIENCE, 68, 101998.

Screening cell-cell communication in spatial transcriptomics via collective optimal transport

Cang, Z., Zhao, Y., Almet, A. A. A., Stabell, A., Ramos, R., Plikus, M. V. V., … Nie, Q. (2023, January 23). NATURE METHODS, Vol. 1.

Deciphering tissue structure and function using spatial transcriptomics

Communications Biology.

Identifying multicellular spatiotemporal organization of cells with SpaceFlow

NATURE COMMUNICATIONS, 13(1).

Screening cell-cell communication in spatial transcriptomics via collective optimal transport

Cang, Z., Zhao, Y., Almet, A. A., Stabell, A., Ramos, R., Plikus, M., … Nie, Q. (2022, August 26).

A multiscale model via single-cell transcriptomics reveals robust patterning mechanisms during early mammalian embryo development

PLOS Computational Biology, 17(3), e1008571.

Charge substitutions at the voltage-sensing module of domain III enhance actions of site-3 and site-4 toxins on an insect sodium channel

Insect Biochemistry and Molecular Biology, 137, 103625.

DEEPsc: A Deep Learning-Based Map Connecting Single-Cell Transcriptomics and Spatial Imaging Data

Frontiers in Genetics, 12.

Single-cell transcriptomic analysis of zebrafish cranial neural crest reveals spatiotemporal regulation of lineage decisions during development

Cell Reports.

The landscape of cell–cell communication through single-cell transcriptomics

Current Opinion in Systems Biology.

A review of mathematical representations of biomolecular data

Physical Chemistry Chemical Physics.

A topology-based network tree for the prediction of protein–protein binding affinity changes following mutation

Nature Machine Intelligence.

Defining Epidermal Basal Cell States during Skin Homeostasis and Wound Healing Using Single-Cell Transcriptomics

Cell Reports, 30(11), 3932–3947.e6.

Evolutionary homology on coupled dynamical systems with applications to protein flexibility analysis

Journal of Applied and Computational Topology, 4(4), 481–507.

Inferring spatial and signaling relationships between cells from single cell transcriptomic data

Nature Communications.

Persistent Cohomology for Data With Multicomponent Heterogeneous Information

SIAM Journal on Mathematics of Data Science, 2(2), 396–418.

Structural cavities are critical to balancing stability and activity of a membrane-integral enzyme

Proceedings of the National Academy of Sciences, 117(36), 22146–22156.

Mathematical deep learning for pose and binding affinity prediction and ranking in D3R Grand Challenges

Journal of Computer-Aided Molecular Design, 33(1), 71–82.

Integration of element specific persistent homology and machine learning for protein‐ligand binding affinity prediction

International Journal for Numerical Methods in Biomedical Engineering, 34(2).

Protein pocket detection via convex hull surface evolution and associated Reeb graph

Bioinformatics, 34(17), i830–i837.

Representability of algebraic topology for biomolecules in machine learning based scoring and virtual screening

PLOS Computational Biology, 14(1), e1005929.

Analysis and prediction of protein folding energy changes upon mutation by element specific persistent homology

Bioinformatics, 7.

TopologyNet: Topology based deep convolutional and multi-task neural networks for biomolecular property predictions

PLOS Computational Biology, 13(7), e1005690.

A topological approach for protein classification

Computational and Mathematical Biophysics, 3(1).