Works (25)

Updated: May 19th, 2023 05:01

2023 article

A mathematical method and software for spatially mapping intercellular communication

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

By: Z. Cang & Q. Nie

Sources: Web Of Science, ORCID
Added: February 20, 2023

2023 journal article

AVIDA: An alternating method for visualizing and integrating data

JOURNAL OF COMPUTATIONAL SCIENCE, 68, 101998.

By: K. Dover, Z. Cang, A. Ma, Q. Nie & R. Vershynin

author keywords: Dimension reduction; Data integration; Multi-omics data
Sources: Web Of Science, ORCID
Added: May 15, 2023

2023 article

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.

By: Z. Cang, Y. Zhao, A. Almet, A. Stabell, R. Ramos, M. Plikus, S. Atwood, Q. Nie

Sources: Web Of Science, ORCID
Added: March 13, 2023

2022 journal article

Deciphering tissue structure and function using spatial transcriptomics

Communications Biology.

By: B. Walker*, Z. Cang, H. Ren*, E. Bourgain-Chang* & Q. Nie*

Source: ORCID
Added: March 11, 2022

2022 journal article

Identifying multicellular spatiotemporal organization of cells with SpaceFlow

NATURE COMMUNICATIONS, 13(1).

By: H. Ren*, B. Walker*, Z. Cang & Q. Nie*

Sources: Web Of Science, ORCID
Added: July 26, 2022

2022 article

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).

By: Z. Cang, Y. Zhao*, A. Almet*, A. Stabell*, R. Ramos*, M. Plikus*, S. Atwood*, Q. Nie*

Source: ORCID
Added: May 18, 2023

2021 journal article

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

PLOS Computational Biology, 17(3), e1008571.

By: Z. Cang, Y. Wang*, Q. Wang, K. Cho*, W. Holmes* & Q. Nie*

Ed(s): D. Umulis

Source: ORCID
Added: August 22, 2021

2021 journal article

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.

By: Q. Zhu*, Y. Du*, Y. Nomura*, R. Gao*, Z. Cang, G. Wei*, D. Gordon*, M. Gurevitz*, J. Groome*, K. Dong*

author keywords: Insect sodium channel; Scorpion alpha-toxin; Scorpion beta-toxin; Homology modeling; Mutagenesis; Electrophysiology
Source: ORCID
Added: August 22, 2021

2021 journal article

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

Frontiers in Genetics, 12.

By: F. Maseda*, Z. Cang & Q. Nie*

author keywords: spatial gene expression atlas; scRNA-seq data; spatial information imputation; deep learning; metric learning; comprehensive evaluation metric
Source: ORCID
Added: August 22, 2021

2021 journal article

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

Cell Reports.

By: D. Tatarakis*, Z. Cang, X. Wu*, P. Sharma*, M. Karikomi*, A. MacLean, Q. Nie*, T. Schilling*

Source: ORCID
Added: December 22, 2021

2021 journal article

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

Current Opinion in Systems Biology.

By: A. Almet*, Z. Cang, S. Jin & Q. Nie*

author keywords: Cell-cell interactions; Cell signaling; Inference; Intercellular communi- cation; Ligand-receptor interactions; Signaling networks; Single-cell RNA-Seq; Spatial transcriptomics
Source: ORCID
Added: August 22, 2021

2020 journal article

A review of mathematical representations of biomolecular data

Physical Chemistry Chemical Physics.

By: D. Nguyen*, Z. Cang & G. Wei*

Source: ORCID
Added: August 22, 2021

2020 journal article

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

Nature Machine Intelligence.

By: M. Wang*, Z. Cang & G. Wei*

Source: ORCID
Added: August 22, 2021

2020 journal article

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

Cell Reports, 30(11), 3932–3947.e6.

By: D. Haensel*, S. Jin, P. Sun*, R. Cinco*, M. Dragan*, Q. Nguyen*, Z. Cang, Y. Gong* ...

Source: ORCID
Added: August 22, 2021

2020 journal article

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

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

By: Z. Cang, E. Munch* & G. Wei*

Source: ORCID
Added: August 22, 2021

2020 journal article

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

Nature Communications.

By: Z. Cang & Q. Nie*

Source: ORCID
Added: August 22, 2021

2020 journal article

Persistent Cohomology for Data With Multicomponent Heterogeneous Information

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

By: Z. Cang & G. Wei

author keywords: topological data analysis; machine learning; biophysics; drug design
Source: ORCID
Added: August 22, 2021

2020 journal article

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.

By: R. Guo*, Z. Cang, J. Yao*, M. Kim*, E. Deans*, G. Wei*, S. Kang*, H. Hong*

author keywords: membrane protein stability; cavity; packing; GIpG; steric trapping
Source: ORCID
Added: August 22, 2021

2019 journal article

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.

By: D. Nguyen*, Z. Cang, K. Wu*, M. Wang*, Y. Cao* & G. Wei*

author keywords: Drug design; Pose prediction; Binding affinity; Machine learning; Algebraic topology; Graph theory
Source: ORCID
Added: August 22, 2021

2018 journal article

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).

By: Z. Cang & G. Wei*

author keywords: protein-ligand binding affinity; machine learning; topology
Source: ORCID
Added: August 22, 2021

2018 journal article

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

Bioinformatics, 34(17), i830–i837.

By: R. Zhao*, Z. Cang, Y. Tong* & G. Wei*

Source: ORCID
Added: August 22, 2021

2018 journal article

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

PLOS Computational Biology, 14(1), e1005929.

By: Z. Cang, L. Mu* & G. Wei*

Ed(s): J. Peng

Source: ORCID
Added: August 22, 2021

2017 journal article

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

Bioinformatics, 7.

By: Z. Cang & G. Wei*

Source: ORCID
Added: August 22, 2021

2017 journal article

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

PLOS Computational Biology, 13(7), e1005690.

By: Z. Cang & G. Wei*

Ed(s): R. Dunbrack

Source: ORCID
Added: August 22, 2021

2015 journal article

A topological approach for protein classification

Computational and Mathematical Biophysics, 3(1).

By: Z. Cang, L. Mu*, K. Wu*, K. Opron*, K. Xia* & G. Wei*

Source: ORCID
Added: August 22, 2021