Manifold alignment for heterogeneous single-cell multi-omics data integration using Pamona

Computational methods for single-cell omics across modalities

(2020) Mirjana Efremova et al.   NATURE METHODS

Unsupervised topological alignment for single-cell multi-omics integration

(2020) Kai Cao et al.   BIOINFORMATICS

Poincaré maps for analyzing complex hierarchies in single-cell data

(2020) Anna Klimovskaia et al.   Nature Communications

Integrative single-cell analysis

(2019) Tim Stuart et al.   NATURE REVIEWS GENETICS

Efficient integration of heterogeneous single-cell transcriptomes using Scanorama

(2019) Brian Hie et al.   NATURE BIOTECHNOLOGY

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Single-Cell Multi-omic Integration Compares and Contrasts Features of Brain Cell Identity

(2019) Joshua D. Welch et al.   CELL

Geometric Sketching Compactly Summarizes the Single-Cell Transcriptomic Landscape

(2019) Brian Hie et al.   Cell Systems

Gene expression cartography

(2019) Mor Nitzan et al.   NATURE

High-throughput sequencing of the transcriptome and chromatin accessibility in the same cell

(2019) Song Chen et al.   NATURE BIOTECHNOLOGY

Multi-omics profiling of mouse gastrulation at single-cell resolution

(2019) Ricard Argelaguet et al.   NATURE

Multi‐Omics Factor Analysis—a framework for unsupervised integration of multi‐omics data sets

(2018) Ricard Argelaguet et al.   Molecular Systems Biology

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors

(2018) Laleh Haghverdi et al.   NATURE BIOTECHNOLOGY

Generalizable and Scalable Visualization of Single-Cell Data Using Neural Networks

(2018) Hyunghoon Cho et al.   Cell Systems

Dimensionality reduction for visualizing single-cell data using UMAP

(2018) Etienne Becht et al.   NATURE BIOTECHNOLOGY

Optimal Transport for Domain Adaptation

(2017) Nicolas Courty et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

Integrative clustering of multi-level ‘omic data based on non-negative matrix factorization algorithm

(2017) Prabhakar Chalise et al.   PLoS One

Entropic metric alignment for correspondence problems

(2016) Justin Solomon et al.   ACM TRANSACTIONS ON GRAPHICS

Single-cell multimodal profiling reveals cellular epigenetic heterogeneity

(2016) Lih Feng Cheow et al.   NATURE METHODS

Convolutional wasserstein distances

(2015) Justin Solomon et al.   ACM TRANSACTIONS ON GRAPHICS

Gromov–Wasserstein Distances and the Metric Approach to Object Matching

(2011) Facundo Mémoli   FOUNDATIONS OF COMPUTATIONAL MATHEMATICS

Free boundaries in optimal transport and Monge-Ampère obstacle problems

(2010) Luis Caffarelli et al.   ANNALS OF MATHEMATICS

A Path Following Algorithm for the Graph Matching Problem

(2008) M. Zaslavskiy et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE