Identification of new marker genes from plant single‐cell RNA‐seq data using interpretable machine learning methods

A single-cell Arabidopsis root atlas reveals developmental trajectories in wild-type and cell identity mutants

(2022) Rachel Shahan et al.   DEVELOPMENTAL CELL

Plant Cell Identity in the Era of Single-Cell Transcriptomics

(2021) Kook Hui Ryu et al.   Annual Review of Genetics

Cell-by-cell dissection of phloem development links a maturation gradient to cell specialization

(2021) Pawel Roszak et al.   SCIENCE

Prediction of condition-specific regulatory genes using machine learning

(2020) Qi Song et al.   NUCLEIC ACIDS RESEARCH

Opening the Black Box: Interpretable Machine Learning for Geneticists

(2020) Christina B. Azodi et al.   TRENDS IN GENETICS

Vascular transcription factors guide plant epidermal responses to limiting phosphate conditions

(2020) Jos R. Wendrich et al.   SCIENCE

Transcriptional landscape of rice roots at the single-cell resolution

(2020) Qing Liu et al.   Molecular Plant

Plant stem-cell organization and differentiation at single-cell resolution

(2020) James W. Satterlee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-cell RNA sequencing resolves molecular relationships among individual plant cells

(2019) Kook Hui Ryu et al.   PLANT PHYSIOLOGY

Dynamics of gene expression in single root cells of A. thaliana

(2019) Ken Jean-Baptiste et al.   PLANT CELL

Spatiotemporal Developmental Trajectories in the Arabidopsis Root Revealed Using High-Throughput Single-Cell RNA Sequencing

(2019) Tom Denyer et al.   DEVELOPMENTAL CELL

A Single-Cell RNA Sequencing Profiles the Developmental Landscape of Arabidopsis Root

(2019) Tian-Qi Zhang et al.   Molecular Plant

Deep learning: new computational modelling techniques for genomics

(2019) Gökcen Eraslan et al.   NATURE REVIEWS GENETICS

High-Throughput Single-Cell Transcriptome Profiling of Plant Cell Types

(2019) Christine N. Shulse et al.   Cell Reports

Scrublet: Computational Identification of Cell Doublets in Single-Cell Transcriptomic Data

(2019) Samuel L. Wolock et al.   Cell Systems

Current best practices in single‐cell RNA‐seq analysis: a tutorial

(2019) Malte D Luecken et al.   Molecular Systems Biology

Molecular Mechanisms Driving Switch Behavior in Xylem Cell Differentiation

(2019) Gina M. Turco et al.   Cell Reports

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

SCMarker: Ab initio marker selection for single cell transcriptome profiling

(2019) Fang Wang et al.   PLoS Computational Biology

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Feature selection in machine learning: A new perspective

(2018) Jie Cai et al.   NEUROCOMPUTING

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

A primer on deep learning in genomics

(2018) James Zou et al.   NATURE GENETICS

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

(2018) Amir Alavi et al.   Nature Communications

Diversification of Root Hair Development Genes in Vascular Plants

(2017) Ling Huang et al.   PLANT PHYSIOLOGY

Massively parallel digital transcriptional profiling of single cells

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

A machine learning approach for the identification of key markers involved in brain development from single-cell transcriptomic data

(2016) Yongli Hu et al.   BMC GENOMICS

High-Resolution Expression Map of the Arabidopsis Root Reveals Alternative Splicing and lincRNA Regulation

(2016) Song Li et al.   DEVELOPMENTAL CELL

Defining cell types and states with single-cell genomics

(2015) Cole Trapnell   GENOME RESEARCH

Advances and Applications of Single-Cell Sequencing Technologies

(2015) Yong Wang et al.   MOLECULAR CELL

Machine learning applications in genetics and genomics

(2015) Maxwell W. Libbrecht et al.   NATURE REVIEWS GENETICS

The circadian clock rephases during lateral root organ initiation in Arabidopsis thaliana

(2015) Ute Voß et al.   Nature Communications

Quantification of cell identity from single-cell gene expression profiles

(2015) Idan Efroni et al.   GENOME BIOLOGY

Unleashing the potential of the root hair cell as a single plant cell type model in root systems biology

(2013) Zhenzhen Qiao et al.   Frontiers in Plant Science

A Gene Regulatory Network for Root Epidermis Cell Differentiation in Arabidopsis

(2012) Angela Bruex et al.   PLoS Genetics

Secondary cell wall patterning during xylem differentiation

(2011) Yoshihisa Oda et al.   CURRENT OPINION IN PLANT BIOLOGY