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

DeepCAPE: A Deep Convolutional Neural Network for the Accurate Prediction of Enhancers

(2021) Shengquan Chen et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

scGNN is a novel graph neural network framework for single-cell RNA-Seq analyses

(2021) Juexin Wang et al.   Nature Communications

RA3 is a reference-guided approach for epigenetic characterization of single cells

(2021) Shengquan Chen et al.   Nature Communications

A graph neural network model to estimate cell-wise metabolic flux using single-cell RNA-seq data

(2021) Norah Alghamdi et al.   GENOME RESEARCH

netNMF-sc: leveraging gene–gene interactions for imputation and dimensionality reduction in single-cell expression analysis

(2020) Rebecca Elyanow et al.   GENOME RESEARCH

Construction of a human cell landscape at single-cell level

(2020) Xiaoping Han et al.   NATURE

A molecular cell atlas of the human lung from single-cell RNA sequencing

(2020) Kyle J. Travaglini et al.   NATURE

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

(2019) Dvir Aran et al.   NATURE IMMUNOLOGY

DeepTACT: predicting 3D chromatin contacts via bootstrapping deep learning

(2019) Wenran Li et al.   NUCLEIC ACIDS RESEARCH

A comparison of single-cell trajectory inference methods

(2019) Wouter Saelens et al.   NATURE BIOTECHNOLOGY

hicGAN infers super resolution Hi-C data with generative adversarial networks

(2019) Qiao Liu et al.   BIOINFORMATICS

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

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

Metascape provides a biologist-oriented resource for the analysis of systems-level datasets

(2019) Yingyao Zhou et al.   Nature Communications

Supervised classification enables rapid annotation of cell atlases

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

Deep learning for inferring gene relationships from single-cell expression data

(2019) Ye Yuan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Prediction of enhancer-promoter interactions via natural language processing

(2018) Wanwen Zeng et al.   BMC GENOMICS

Mapping gene regulatory networks from single-cell omics data

(2018) Mark W E J Fiers et al.   Briefings in Functional Genomics

Phenotype molding of stromal cells in the lung tumor microenvironment

(2018) Diether Lambrechts et al.   NATURE MEDICINE

Using deep learning to model the hierarchical structure and function of a cell

(2018) Jianzhu Ma et al.   NATURE METHODS

GeneMANIA update 2018

(2018) Max Franz et al.   NUCLEIC ACIDS RESEARCH

High-throughput chromatin accessibility profiling at single-cell resolution

(2018) Anja Mezger et al.   Nature Communications

Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris

(2018) et al.   NATURE

Lineage tracking reveals dynamic relationships of T cells in colorectal cancer

(2018) Lei Zhang et al.   NATURE

Shared and distinct transcriptomic cell types across neocortical areas

(2018) Bosiljka Tasic et al.   NATURE

HumanNet v2: human gene networks for disease research

(2018) Sohyun Hwang et al.   NUCLEIC ACIDS RESEARCH

Multiplexed droplet single-cell RNA-sequencing using natural genetic variation

(2017) Hyun Min Kang et al.   NATURE BIOTECHNOLOGY

FunCoup 4: new species, data, and visualization

(2017) Christoph Ogris et al.   NUCLEIC ACIDS RESEARCH

Single-Cell Multiomics: Multiple Measurements from Single Cells

(2017) Iain C. Macaulay et al.   TRENDS IN GENETICS

Massively parallel digital transcriptional profiling of single cells

(2017) Grace X. Y. Zheng et al.   Nature Communications

A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure

(2016) Maayan Baron et al.   Cell Systems

Walking on multiple disease-gene networks to prioritize candidate genes

(2015) Rui Jiang   Journal of Molecular Cell Biology

STRING v10: protein–protein interaction networks, integrated over the tree of life

(2014) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH