SigPrimedNet: A Signaling-Informed Neural Network for scRNA-seq Annotation of Known and Unknown Cell Types

Integrating pathway knowledge with deep neural networks to reduce the dimensionality in single-cell RNA-seq data

(2022) Pelin Gundogdu et al.   BioData Mining

Immune-Related Gene SERPINE1 Is a Novel Biomarker for Diffuse Lower-Grade Gliomas via Large-Scale Analysis

(2021) Xiaoming Huang et al.   Frontiers in Oncology

Mapping single-cell data to reference atlases by transfer learning

(2021) Mohammad Lotfollahi et al.   NATURE BIOTECHNOLOGY

A comprehensive comparison of supervised and unsupervised methods for cell type identification in single-cell RNA-seq

(2021) Xiaobo Sun et al.   BRIEFINGS IN BIOINFORMATICS

Biologically informed deep neural network for prostate cancer discovery

(2021) Haitham A. Elmarakeby et al.   NATURE

Efficient and precise single-cell reference atlas mapping with Symphony

(2021) Joyce B. Kang et al.   Nature Communications

SciPy 1.0: fundamental algorithms for scientific computing in Python

(2020) Pauli Virtanen et al.   NATURE METHODS

SciBet as a portable and fast single cell type identifier

(2020) Chenwei Li et al.   Nature Communications

Array programming with NumPy

(2020) Charles R. Harris et al.   NATURE

Single-cell Transcriptomic Landscape of Human Blood Cells

(2020) Xiaowei Xie et al.   National Science Review

Transfer learning efficiently maps bone marrow cell types from mouse to human using single-cell RNA sequencing

(2020) Patrick S. Stumpf et al.   Communications Biology

The Effects of Different Signaling Pathways in Adenylyl Cyclase Stimulation on Red Blood Cells Deformability

(2019) Alexey N. Semenov et al.   Frontiers in Physiology

Fast, sensitive and accurate integration of single-cell data with Harmony

(2019) Ilya Korsunsky et al.   NATURE METHODS

Sphingosine kinase-2 prevents macrophage cholesterol accumulation and atherosclerosis by stimulating autophagic lipid degradation

(2019) Kazuhiro Ishimaru et al.   Scientific Reports

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

(2018) Vladimir Yu Kiselev et al.   NATURE METHODS

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

(2018) Jianzhu Ma et al.   NATURE METHODS

Overfitting remedy by sparsifying regularization on fully-connected layers of CNNs

(2018) Qi Xu et al.   NEUROCOMPUTING

An Introduction to the Analysis of Single-Cell RNA-Sequencing Data

(2018) Aisha A. AlJanahi et al.   Molecular Therapy-Methods & Clinical Development

M3Drop: dropout-based feature selection for scRNASeq

(2018) Tallulah S Andrews et al.   BIOINFORMATICS

Dimensionality reduction for visualizing single-cell data using UMAP

(2018) Etienne Becht et al.   NATURE BIOTECHNOLOGY

Deep generative modeling for single-cell transcriptomics

(2018) Romain Lopez et al.   NATURE METHODS

Antigen-specific CD8 T cells in cell cycle circulate in the blood after vaccination

(2018) Sonia Simonetti et al.   SCANDINAVIAN JOURNAL OF IMMUNOLOGY

A web server for comparative analysis of single-cell RNA-seq data

(2018) Amir Alavi et al.   Nature Communications

Neutrophils as a source of branched-chain, aromatic and positively charged free amino acids

(2018) Svetlana I. Galkina et al.   Cell Adhesion & Migration

Human haematopoietic stem cell lineage commitment is a continuous process

(2017) Lars Velten et al.   NATURE CELL BIOLOGY

Using neural networks for reducing the dimensions of single-cell RNA-Seq data

(2017) Chieh Lin et al.   NUCLEIC ACIDS RESEARCH

Massively parallel digital transcriptional profiling of single cells

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

High throughput estimation of functional cell activities reveals disease mechanisms and predicts relevant clinical outcomes

(2016) Marta R. Hidalgo et al.   Oncotarget

Representation Learning: A Review and New Perspectives

(2013) Y. Bengio et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

Accounting for technical noise in single-cell RNA-seq experiments

(2013) Philip Brennecke et al.   NATURE METHODS

NCBI GEO: archive for functional genomics data sets—update

(2012) Tanya Barrett et al.   NUCLEIC ACIDS RESEARCH

Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples

(2012) Günter P. Wagner et al.   THEORY IN BIOSCIENCES

Counting absolute numbers of molecules using unique molecular identifiers

(2011) Teemu Kivioja et al.   NATURE METHODS

The Pathogenesis of Photoaging: The Role of Neutrophils and Neutrophil-Derived Enzymes

(2009) Feiko Rijken et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY SYMPOSIUM PROCEEDINGS