DeepDRIM: a deep neural network to reconstruct cell-type-specific gene regulatory network using single-cell RNA-seq data

Benchmarking algorithms for gene regulatory network inference from single-cell transcriptomic data

(2020) Aditya Pratapa et al.   NATURE METHODS

COVID-19: towards understanding of pathogenesis

(2020) Wei Cao et al.   CELL RESEARCH

Exploring Diseases/Traits and Blood Proteins Causally Related to Expression of ACE2, the Putative Receptor of SARS-CoV-2: A Mendelian Randomization Analysis Highlights Tentative Relevance of Diabetes-Related Traits

(2020) Shitao Rao et al.   DIABETES CARE

Current Status of Cell-Based Therapies for Respiratory Virus Infections: Applicability to COVID-19

(2020) Maroun Khoury et al.   EUROPEAN RESPIRATORY JOURNAL

Why COVID-19 Silent Hypoxemia Is Baffling to Physicians

(2020) Martin J. Tobin et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Epigenetic dysregulation of ACE2 and interferon-regulated genes might suggest increased COVID-19 susceptibility and severity in lupus patients

(2020) Amr H. Sawalha et al.   CLINICAL IMMUNOLOGY

COVID-19/SARS-CoV-2 Infection: Lysosomes and Lysosomotropism Implicate New Treatment Strategies and Personal Risks

(2020) Markus Blaess et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Systems biological assessment of immunity to mild versus severe COVID-19 infection in humans

(2020) Prabhu S. Arunachalam et al.   SCIENCE

Stem cell differentiation trajectories in Hydra resolved at single-cell resolution

(2019) Stefan Siebert et al.   SCIENCE

A single-cell atlas of entorhinal cortex from individuals with Alzheimer’s disease reveals cell-type-specific gene expression regulation

(2019) Alexandra Grubman et al.   NATURE NEUROSCIENCE

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

JRmGRN: joint reconstruction of multiple gene regulatory networks with common hub genes using data from multiple tissues or conditions

(2018) Wenping Deng et al.   BIOINFORMATICS

Evaluating methods of inferring gene regulatory networks highlights their lack of performance for single cell gene expression data

(2018) Shuonan Chen et al.   BMC BIOINFORMATICS

Distinct tissue-specific transcriptional regulation revealed by gene regulatory networks in maize

(2018) Ji Huang et al.   BMC PLANT BIOLOGY

Recovering Gene Interactions from Single-Cell Data Using Data Diffusion

(2018) David van Dijk et al.   CELL

Single-cell full-length total RNA sequencing uncovers dynamics of recursive splicing and enhancer RNAs

(2018) Tetsutaro Hayashi et al.   Nature Communications

An accurate and robust imputation method scImpute for single-cell RNA-seq data

(2018) Wei Vivian Li et al.   Nature Communications

Co-expression in Single-Cell Analysis: Saving Grace or Original Sin?

(2018) Megan Crow et al.   TRENDS IN GENETICS

Computational methods for Gene Regulatory Networks reconstruction and analysis: A review

(2018) Fernando M. Delgado et al.   ARTIFICIAL INTELLIGENCE IN MEDICINE

GRNBoost2 and Arboreto: efficient and scalable inference of gene regulatory networks

(2018) Thomas Moerman et al.   BIOINFORMATICS

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

(2018) Amir Alavi et al.   Nature Communications

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

SC3: consensus clustering of single-cell RNA-seq data

(2017) Vladimir Yu Kiselev et al.   NATURE METHODS

Gene Regulatory Network Inference from Single-Cell Data Using Multivariate Information Measures

(2017) Thalia E. Chan et al.   Cell Systems

Cross-Tissue Regulatory Gene Networks in Coronary Artery Disease

(2016) Husain A. Talukdar et al.   Cell Systems

Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells

(2015) Allon M. Klein et al.   CELL

Reconstructing gene regulatory networks from knock-out data using Gaussian Noise Model and Pearson Correlation Coefficient

(2015) Faridah Hani Mohamed Salleh et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

Bayesian approach to single-cell differential expression analysis

(2014) Peter V Kharchenko et al.   NATURE METHODS

Conditional mutual inclusive information enables accurate quantification of associations in gene regulatory networks

(2014) Xiujun Zhang et al.   NUCLEIC ACIDS RESEARCH

The joint graphical lasso for inverse covariance estimation across multiple classes

(2013) Patrick Danaher et al.   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY

Inferring gene regulatory networks by ANOVA

(2012) Robert Küffner et al.   BIOINFORMATICS

TIGRESS: Trustful Inference of Gene REgulation using Stability Selection

(2012) Anne-Claire Haury et al.   BMC Systems Biology

Wisdom of crowds for robust gene network inference

(2012) Daniel Marbach et al.   NATURE METHODS

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Using Gene Expression Noise to Understand Gene Regulation

(2012) B. Munsky et al.   SCIENCE

Inferring gene regulatory networks from gene expression data by path consistency algorithm based on conditional mutual information

(2011) Xiujun Zhang et al.   BIOINFORMATICS

From RNA-seq reads to differential expression results

(2011) Alicia Oshlack et al.   GENOME BIOLOGY

Breast Tissue Composition and Susceptibility to Breast Cancer

(2010) N. F. Boyd et al.   JNCI-Journal of the National Cancer Institute

DREAM4: Combining Genetic and Dynamic Information to Identify Biological Networks and Dynamical Models

(2010) Alex Greenfield et al.   PLoS One

ChIP–seq: advantages and challenges of a maturing technology

(2009) Peter J. Park   NATURE REVIEWS GENETICS