TripletCell: a deep metric learning framework for accurate annotation of cell types at the single-cell level

scGraph: a graph neural network-based approach to automatically identify cell types

(2022) Qijin Yin et al.   BIOINFORMATICS

Cross-tissue immune cell analysis reveals tissue-specific features in humans

(2022) C. Domínguez Conde et al.   SCIENCE

Automatic Cell Type Annotation Using Marker Genes for Single-Cell RNA Sequencing Data

(2022) Yu Chen et al.   Biomolecules

Automated methods for cell type annotation on scRNA-seq data

(2021) Giovanni Pasquini et al.   Computational and Structural Biotechnology Journal

Why can deep convolutional neural networks improve protein fold recognition? A visual explanation by interpretation

(2021) Yan Liu et al.   BRIEFINGS IN BIOINFORMATICS

Improving protein fold recognition using triplet network and ensemble deep learning

(2021) Yan Liu et al.   BRIEFINGS IN BIOINFORMATICS

Tutorial: guidelines for annotating single-cell transcriptomic maps using automated and manual methods

(2021) Zoe A. Clarke et al.   Nature Protocols

scDeepSort: a pre-trained cell-type annotation method for single-cell transcriptomics using deep learning with a weighted graph neural network

(2021) Xin Shao et al.   NUCLEIC ACIDS RESEARCH

MACA: marker-based automatic cell-type annotation for single-cell expression data

(2021) Yang Xu et al.   BIOINFORMATICS

A robust and scalable graph neural network for accurate single-cell classification

(2021) Yuansong Zeng et al.   BRIEFINGS IN BIOINFORMATICS

scMRMA: single cell multiresolution marker-based annotation

(2021) Jia Li et al.   NUCLEIC ACIDS RESEARCH

Systematic comparison of single-cell and single-nucleus RNA-sequencing methods

(2020) Jiarui Ding et al.   NATURE BIOTECHNOLOGY

SCSA: A Cell Type Annotation Tool for Single-Cell RNA-seq Data

(2020) Yinghao Cao et al.   Frontiers in Genetics

Searching large-scale scRNA-seq databases via unbiased cell embedding with Cell BLAST

(2020) Zhi-Jie Cao et al.   Nature Communications

A spectral clustering with self-weighted multiple kernel learning method for single-cell RNA-seq data

(2020) Ren Qi et al.   BRIEFINGS IN BIOINFORMATICS

Therapy-Induced Evolution of Human Lung Cancer Revealed by Single-Cell RNA Sequencing

(2020) Ashley Maynard et al.   CELL

Graph Convolutional Networks for Hyperspectral Image Classification

(2020) Danfeng Hong et al.   IEEE TRANSACTIONS ON GEOSCIENCE AND REMOTE SENSING

Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage

(2019) Dvir Aran et al.   NATURE IMMUNOLOGY

Challenges in unsupervised clustering of single-cell RNA-seq data

(2019) Vladimir Yu Kiselev et al.   NATURE REVIEWS GENETICS

Single-cell RNA-seq denoising using a deep count autoencoder

(2019) Gökcen Eraslan et al.   Nature Communications

LAmbDA: Label Ambiguous Domain Adaptation Dataset Integration Reduces Batch Effects and Improves Subtype Detection

(2019) Travis S Johnson et al.   BIOINFORMATICS

Polled Digital Cell Sorter (p-DCS): Automatic identification of hematological cell types from single cell RNA-sequencing clusters

(2019) Sergii Domanskyi et al.   BMC BIOINFORMATICS

CHETAH: a selective, hierarchical cell type identification method for single-cell RNA sequencing

(2019) Jurrian K de Kanter et al.   NUCLEIC ACIDS RESEARCH

SCINA: Semi-Supervised Analysis of Single Cells in Silico

(2019) Zhang et al.   Genes

Conserved cell types with divergent features in human versus mouse cortex

(2019) Rebecca D. Hodge et al.   NATURE

Supervised classification enables rapid annotation of cell atlases

(2019) Hannah A. Pliner et al.   NATURE METHODS

Probabilistic cell-type assignment of single-cell RNA-seq for tumor microenvironment profiling

(2019) Allen W. Zhang et al.   NATURE METHODS

scmap: projection of single-cell RNA-seq data across data sets

(2018) Vladimir Yu Kiselev et al.   NATURE METHODS

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

Shared and distinct transcriptomic cell types across neocortical areas

(2018) Bosiljka Tasic et al.   NATURE

Bayesian deep learning for single-cell analysis

(2018) Gregory P. Way et al.   NATURE METHODS

Why Does Deep and Cheap Learning Work So Well?

(2017) Henry W. Lin et al.   JOURNAL OF STATISTICAL PHYSICS

Single-cell RNA-seq enables comprehensive tumour and immune cell profiling in primary breast cancer

(2017) Woosung Chung et al.   Nature Communications

Uniform algebras and approximation on manifolds

(2011) Håkan Samuelsson et al.   INVENTIONES MATHEMATICAE