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

Nature communications, 2020-04, Vol.11 (1), p.2084-2084, Article 2084

2020

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

PLoS computational biology, 2017-07, Vol.13 (7), p.e1005690-e1005690

2017

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

PLoS computational biology, 2018-01, Vol.14 (1), p.e1005929-e1005929

2018

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A review of mathematical representations of biomolecular data

Physical chemistry chemical physics : PCCP, 2020-02, Vol.22 (8), p.4343-4367

2020

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Identifying multicellular spatiotemporal organization of cells with SpaceFlow

Nature communications, 2022-07, Vol.13 (1), p.4076-4076, Article 4076

2022

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

Cell reports (Cambridge), 2020-03, Vol.30 (11), p.3932-3947.e6

2020

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

Frontiers in genetics, 2021-03, Vol.12, p.636743-636743

2021

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Deciphering tissue structure and function using spatial transcriptomics

Communications biology, 2022-03, Vol.5 (1), p.220-220, Article 220

2022

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

PLoS computational biology, 2021-03, Vol.17 (3), p.e1008571-e1008571

2021

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

Cell reports (Cambridge), 2021-12, Vol.37 (12), p.110140-110140, Article 110140

2021

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A Study of Gene Expression, Structure, and Contractility of iPSC-Derived Cardiac Myocytes from a Family with Heart Disease due to LMNA Mutation

Annals of biomedical engineering, 2021-12, Vol.49 (12), p.3524-3539

2021

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A mathematical method and software for spatially mapping intercellular communication

Nature methods, 2023-02, Vol.20 (2), p.185

2023

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Topological and geometric analysis of cell states in single-cell transcriptomic data

Briefings in bioinformatics, 2024-03, Vol.25 (3)

2024

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

Bioinformatics, 2017-11, Vol.33 (22), p.3549

2017

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

International journal for numerical methods in biomedical engineering, 2018-02, Vol.34 (2), p.n/a

2018

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Supervised Optimal Transport

SIAM journal on applied mathematics, 2022-01, Vol.82 (5), p.1851-1877

2022

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

Current opinion in systems biology, 2021-06, Vol.26, p.12-23

2021

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Poisson-Boltzmann-based machine learning model for electrostatic analysis

Biophysical journal, 2024-02

2024

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

Bioinformatics, 2018-09, Vol.34 (17), p.i830-i837

2018

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

Nature methods, 2023-02, Vol.20 (2), p.218

2023

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

Proceedings of the National Academy of Sciences - PNAS, 2020-09, Vol.117 (36), p.22146-22156

2020

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

Journal of computer-aided molecular design, 2019-01, Vol.33 (1), p.71-82

2019

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AVIDA: An alternating method for visualizing and integrating data

Journal of computational science, 2023-04, Vol.68, p.101998, Article 101998

2023

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The Role of Packing Defects in the Stability and Function of the Intramembrane Protease GlpG

Biophysical journal, 2017-02, Vol.112 (3), p.86a-86a

2017

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

Journal of applied and computational topology, 2020-12, Vol.4 (4), p.481-507

2020

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

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

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

A review of mathematical representations of biomolecular data

Identifying multicellular spatiotemporal organization of cells with SpaceFlow

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

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

Deciphering tissue structure and function using spatial transcriptomics

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

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

A Study of Gene Expression, Structure, and Contractility of iPSC-Derived Cardiac Myocytes from a Family with Heart Disease due to LMNA Mutation

A mathematical method and software for spatially mapping intercellular communication

Topological and geometric analysis of cell states in single-cell transcriptomic data

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

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

Supervised Optimal Transport

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

Poisson-Boltzmann-based machine learning model for electrostatic analysis

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

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

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

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

AVIDA: An alternating method for visualizing and integrating data

The Role of Packing Defects in the Stability and Function of the Intramembrane Protease GlpG

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

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