Works (25)

Updated: July 8th, 2023 21:17

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

MeSH headings : Cell Communication; Software
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 n, 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.

MeSH headings : Humans; Transcriptome; Cell Communication / genetics; Gene Expression Profiling; Signal Transduction; Computer Simulation; Single-Cell Analysis
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*

MeSH headings : Transcriptome
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 n & Q. Nie*

MeSH headings : Humans; Transcriptome / genetics
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).

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

MeSH headings : Animals; Embryo, Mammalian / cytology; Embryo, Mammalian / metabolism; Embryo, Mammalian / physiology; Embryonic Development / genetics; Germ Layers / cytology; Germ Layers / metabolism; Germ Layers / physiology; Mice; Models, Biological; Single-Cell Analysis; Transcriptome / genetics
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
MeSH headings : Animals; Cnidarian Venoms / pharmacology; Drosophila melanogaster / drug effects; Drosophila melanogaster / genetics; Drosophila melanogaster / metabolism; Insect Proteins / genetics; Insect Proteins / metabolism; Oocytes / drug effects; Oocytes / metabolism; Scorpion Venoms / pharmacology; Sodium Channels / genetics; Sodium Channels / metabolism
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.

MeSH headings : Animals; Animals, Genetically Modified; Branchial Region / metabolism; Cell Communication; Cell Differentiation; Cell Lineage; Cell Movement; Cranial Nerves / metabolism; Embryo, Nonmammalian / metabolism; Gene Expression Profiling / methods; Gene Expression Regulation, Developmental; Neural Crest / metabolism; RNA-Seq; Signal Transduction; Single-Cell Analysis; Wnt Proteins / metabolism; Zebrafish / genetics; Zebrafish / metabolism; Zebrafish Proteins / genetics; Zebrafish Proteins / metabolism
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* ...

MeSH headings : Animals; Cell Movement / genetics; Epidermis / metabolism; Epidermis / pathology; Female; Gene Expression Profiling; Homeostasis / genetics; Inflammation / genetics; Inflammation / pathology; Mice, Inbred C57BL; Mice, Transgenic; Single-Cell Analysis; Up-Regulation / genetics; Wound Healing / genetics
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*

MeSH headings : Animals; Cell Communication; Cluster Analysis; Databases, Genetic; Drosophila / embryology; Drosophila / genetics; Gene Expression Regulation, Developmental; Reproducibility of Results; Sequence Analysis, RNA; Signal Transduction / genetics; Single-Cell Analysis; Transcriptome / genetics; Visual Cortex / metabolism; Zebrafish / embryology; Zebrafish / genetics
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
MeSH headings : Catalytic Domain; DNA-Binding Proteins / chemistry; DNA-Binding Proteins / metabolism; Endopeptidases / chemistry; Endopeptidases / metabolism; Escherichia coli Proteins / chemistry; Escherichia coli Proteins / metabolism; Humans; Membrane Proteins / chemistry; Membrane Proteins / metabolism; Models, Molecular; Molecular Dynamics Simulation; Mutation; Protein Conformation; Protein Folding; Protein Stability; Serine Endopeptidases / chemistry
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
MeSH headings : Binding Sites; Cathepsins / chemistry; Computer-Aided Design; Crystallography, X-Ray; Databases, Protein; Deep Learning; Drug Design; Ligands; Molecular Docking Simulation / methods; Protein Binding; Protein Conformation; Protein Kinases / chemistry; Receptors, Cytoplasmic and Nuclear / chemistry; Thermodynamics
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
MeSH headings : Databases, Protein; Hydrogen Bonding; Ligands; Machine Learning; Protein Binding; Proteins / chemistry; Proteins / metabolism
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*

MeSH headings : Algorithms; Binding Sites; Ligands; Protein Binding; Protein Conformation; Proteins / chemistry; Software
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

MeSH headings : Algorithms; Area Under Curve; Computational Biology / methods; Databases, Protein; Humans; Ligands; Machine Learning; Models, Neurological; Molecular Dynamics Simulation; Neural Networks, Computer; Nucleic Acids / chemistry; Protein Binding; Protein Interaction Mapping; Proteins / chemistry; Static Electricity
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*

MeSH headings : Algorithms; Computational Biology / methods; Mutagenesis; Mutation / physiology; Protein Folding; Protein Stability; Proteins / chemistry; Proteins / genetics; Proteins / metabolism; Software; Structural Homology, Protein; Thermodynamics
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

MeSH headings : Computational Biology / methods; Image Processing, Computer-Assisted; Machine Learning; Membrane Proteins / chemistry; Membrane Proteins / metabolism; Membrane Proteins / physiology; Models, Statistical; Molecular Dynamics Simulation; Neural Networks, Computer; Protein Binding; Protein Folding
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