Single-Cell Transcriptome Analysis in Plants: Advances and Challenges
Published 2020 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Single-Cell Transcriptome Analysis in Plants: Advances and Challenges
Authors
Keywords
-
Journal
Molecular Plant
Volume 14, Issue 1, Pages 115-126
Publisher
Elsevier BV
Online
2020-11-03
DOI
10.1016/j.molp.2020.10.012
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- Integrating microarray-based spatial transcriptomics and single-cell RNA-seq reveals tissue architecture in pancreatic ductal adenocarcinomas
- (2020) Reuben Moncada et al. NATURE BIOTECHNOLOGY
- Computational methods for single-cell omics across modalities
- (2020) Mirjana Efremova et al. NATURE METHODS
- Single-cell transcriptional diversity is a hallmark of developmental potential
- (2020) Gunsagar S. Gulati et al. SCIENCE
- Computational methods for the integrative analysis of single-cell data
- (2020) Mattia Forcato et al. BRIEFINGS IN BIOINFORMATICS
- The promise of single-cell genomics in plants
- (2020) José L McFaline-Figueroa et al. CURRENT OPINION IN PLANT BIOLOGY
- Benchmarking single-cell RNA-sequencing protocols for cell atlas projects
- (2020) Elisabetta Mereu et al. NATURE BIOTECHNOLOGY
- A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors
- (2020) Michal Slyper et al. NATURE MEDICINE
- Tools for the analysis of high-dimensional single-cell RNA sequencing data
- (2020) Yan Wu et al. Nature Reviews Nephrology
- Single-nucleus RNA sequencing of mouse auditory cortex reveals critical period triggers and brakes
- (2020) Brian T. Kalish et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Integrative Methods and Practical Challenges for Single-Cell Multi-omics
- (2020) Anjun Ma et al. TRENDS IN BIOTECHNOLOGY
- Global Dynamic Molecular Profiling of Stomatal Lineage Cell Development by Single-Cell RNA Sequencing
- (2020) Zhixin Liu et al. Molecular Plant
- Transcriptional output, cell types densities and normalization in spatial transcriptomics
- (2020) Manuel Saiselet et al. Journal of Molecular Cell Biology
- Vascular transcription factors guide plant epidermal responses to limiting phosphate conditions
- (2020) Jos R. Wendrich et al. SCIENCE
- Single-cell transcriptomic analysis of mouse neocortical development
- (2019) Lipin Loo et al. Nature Communications
- Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution
- (2019) Samuel G. Rodriques et al. SCIENCE
- 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
- The single-cell transcriptional landscape of mammalian organogenesis
- (2019) Junyue Cao et al. NATURE
- Complementary Roles for Single-Nucleus and Single-Cell RNA Sequencing in Kidney Disease Research
- (2019) Eoin D. O’Sullivan et al. JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY
- Spatiotemporal Developmental Trajectories in the Arabidopsis Root Revealed Using High-Throughput Single-Cell RNA Sequencing
- (2019) Tom Denyer et al. DEVELOPMENTAL CELL
- Single cell RNA sequencing and its promise in reconstructing plant vascular cell lineages
- (2019) Antia Rodriguez-Villalon et al. CURRENT OPINION IN PLANT BIOLOGY
- A Single-Cell RNA Sequencing Profiles the Developmental Landscape of Arabidopsis Root
- (2019) Tian-Qi Zhang et al. Molecular Plant
- A comparison of single-cell trajectory inference methods
- (2019) Wouter Saelens et al. NATURE BIOTECHNOLOGY
- Defining the developmental program leading to meiosis in maize
- (2019) Brad Nelms et al. SCIENCE
- 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
- DoubletFinder: Doublet Detection in Single-Cell RNA Sequencing Data Using Artificial Nearest Neighbors
- (2019) Christopher S. McGinnis et al. Cell Systems
- Comprehensive Integration of Single-Cell Data
- (2019) Tim Stuart et al. CELL
- Single-Cell Multi-omic Integration Compares and Contrasts Features of Brain Cell Identity
- (2019) Joshua D. Welch et al. CELL
- Single-Cell RNA Sequencing in Cancer: Lessons Learned and Emerging Challenges
- (2019) Mario L. Suvà et al. MOLECULAR CELL
- Current best practices in single‐cell RNA‐seq analysis: a tutorial
- (2019) Malte D Luecken et al. Molecular Systems Biology
- Joint analysis of heterogeneous single-cell RNA-seq dataset collections
- (2019) Nikolas Barkas et al. NATURE METHODS
- A single-nucleus RNA-sequencing pipeline to decipher the molecular anatomy and pathophysiology of human kidneys
- (2019) Blue B. Lake et al. Nature Communications
- Genetic mapping of cell type specificity for complex traits
- (2019) Kyoko Watanabe et al. Nature Communications
- Molecular Mechanisms Driving Switch Behavior in Xylem Cell Differentiation
- (2019) Gina M. Turco et al. Cell Reports
- SingleCellNet: A Computational Tool to Classify Single Cell RNA-Seq Data Across Platforms and Across Species
- (2019) Yuqi Tan et al. Cell Systems
- Cell Size Control in Plants
- (2019) Marco D'Ario et al. Annual Review of Genetics
- Beyond bulk: a review of single cell transcriptomics methodologies and applications
- (2019) Ashwinikumar Kulkarni et al. CURRENT OPINION IN BIOTECHNOLOGY
- GPU accelerated t-distributed stochastic neighbor embedding
- (2019) David M. Chan et al. JOURNAL OF PARALLEL AND DISTRIBUTED COMPUTING
- Supervised classification enables rapid annotation of cell atlases
- (2019) Hannah A. Pliner et al. NATURE METHODS
- High-definition spatial transcriptomics for in situ tissue profiling
- (2019) Sanja Vickovic et al. NATURE METHODS
- Spatial transcriptomics: putting genome-wide expression on the map
- (2019) K. R. Maynard et al. NEUROPSYCHOPHARMACOLOGY
- cellHarmony: cell-level matching and holistic comparison of single-cell transcriptomes
- (2019) Erica A K DePasquale et al. NUCLEIC ACIDS RESEARCH
- Fast, sensitive and accurate integration of single-cell data with Harmony
- (2019) Ilya Korsunsky et al. NATURE METHODS
- Cell-type–specific transcriptome and histone modification dynamics during cellular reprogramming in the Arabidopsis stomatal lineage
- (2019) Laura R. Lee et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Single-Cell Transcriptomics: A High-Resolution Avenue for Plant Functional Genomics
- (2019) Charlotte Rich-Griffin et al. TRENDS IN PLANT SCIENCE
- The art of using t-SNE for single-cell transcriptomics
- (2019) Dmitry Kobak et al. Nature Communications
- DoubletDecon: Deconvoluting Doublets from Single-Cell RNA-Sequencing Data
- (2019) Erica A.K. DePasquale et al. Cell Reports
- Single-nuclei RNA-seq on human retinal tissue provides improved transcriptome profiling
- (2019) Qingnan Liang et al. Nature Communications
- Evaluation of tools for highly variable gene discovery from single-cell RNA-seq data
- (2018) Shun H Yip et al. BRIEFINGS IN BIOINFORMATICS
- Platforms for Single-Cell Collection and Analysis
- (2018) Lukas Valihrach et al. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
- Integrating single-cell transcriptomic data across different conditions, technologies, and species
- (2018) Andrew Butler et al. NATURE BIOTECHNOLOGY
- Transcriptome profiling of sorted endoreduplicated nuclei from tomato fruits: how the global shift in expression ascribed to DNA ploidy influences RNA-Seq data normalization and interpretation
- (2018) Julien Pirrello et al. PLANT JOURNAL
- Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database
- (2018) Luke Zappia et al. PLoS Computational Biology
- RNA velocity of single cells
- (2018) Gioele La Manno et al. NATURE
- Single-Cell RNA Sequencing of Microglia throughout the Mouse Lifespan and in the Injured Brain Reveals Complex Cell-State Changes
- (2018) Timothy R. Hammond et al. IMMUNITY
- Dimensionality reduction for visualizing single-cell data using UMAP
- (2018) Etienne Becht et al. NATURE BIOTECHNOLOGY
- Single-nucleus and single-cell transcriptomes compared in matched cortical cell types
- (2018) Trygve E. Bakken et al. PLoS One
- Adapting INTACT to analyse cell-type-specific transcriptomes and nucleocytoplasmic mRNA dynamics in the Arabidopsis embryo
- (2018) Joakim Palovaara et al. Plant Reproduction
- Reversed graph embedding resolves complex single-cell trajectories
- (2017) Xiaojie Qiu et al. NATURE METHODS
- Gramene 2018: unifying comparative genomics and pathway resources for plant research
- (2017) Marcela K Tello-Ruiz et al. NUCLEIC ACIDS RESEARCH
- Changes in Gene Expression in Space and Time Orchestrate Environmentally Mediated Shaping of Root Architecture
- (2017) Liam Walker et al. PLANT CELL
- Framework for gradual progression of cell ontogeny in theArabidopsisroot meristem
- (2017) Jos R. Wendrich et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Plant Systems Biology at the Single-Cell Level
- (2017) Marc Libault et al. TRENDS IN PLANT SCIENCE
- A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications
- (2017) Ashraful Haque et al. Genome Medicine
- Single-Cell (Multi)omics Technologies
- (2016) Lia Chappell et al. Annual Review of Genomics and Human Genetics
- Co-evolution of Hormone Metabolism and Signaling Networks Expands Plant Adaptive Plasticity
- (2016) Jing-Ke Weng et al. CELL
- Root Regeneration Triggers an Embryo-like Sequence Guided by Hormonal Interactions
- (2016) Idan Efroni et al. CELL
- Single-cell states versus single-cell atlases — two classes of heterogeneity that differ in meaning and method
- (2016) Kevin A Janes CURRENT OPINION IN BIOTECHNOLOGY
- High-Resolution Expression Map of the Arabidopsis Root Reveals Alternative Splicing and lincRNA Regulation
- (2016) Song Li et al. DEVELOPMENTAL CELL
- The contribution of cell cycle to heterogeneity in single-cell RNA-seq data
- (2016) Andrew McDavid et al. NATURE BIOTECHNOLOGY
- The origin and evolution of cell types
- (2016) Detlev Arendt et al. NATURE REVIEWS GENETICS
- Visualization and analysis of gene expression in tissue sections by spatial transcriptomics
- (2016) P. L. Stahl et al. SCIENCE
- Genetic regulation of salt stress tolerance revealed by RNA-Seq in cotton diploid wild species, Gossypium davidsonii
- (2016) Feng Zhang et al. Scientific Reports
- Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells
- (2015) Allon M. Klein et al. CELL
- Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets
- (2015) Evan Z. Macosko et al. CELL
- Genes and networks regulating root anatomy and architecture
- (2015) Guy Wachsman et al. NEW PHYTOLOGIST
- Quantification of cell identity from single-cell gene expression profiles
- (2015) Idan Efroni et al. GENOME BIOLOGY
- Comparative transcriptome analysis of RNA-seq data for cold-tolerant and cold-sensitive rice genotypes under cold stress
- (2014) Chunxiu Shen et al. JOURNAL OF PLANT BIOLOGY
- The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells
- (2014) Cole Trapnell et al. NATURE BIOTECHNOLOGY
- Spatially resolved transcriptomics and beyond
- (2014) Nicola Crosetto et al. NATURE REVIEWS GENETICS
- The use of fluorescence-activated cell sorting in studying plant development and environmental responses
- (2013) Anthony D. Carter et al. INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY
- In situ sequencing for RNA analysis in preserved tissue and cells
- (2013) Rongqin Ke et al. NATURE METHODS
- Accounting for technical noise in single-cell RNA-seq experiments
- (2013) Philip Brennecke et al. NATURE METHODS
- STAR: ultrafast universal RNA-seq aligner
- (2012) Alexander Dobin et al. BIOINFORMATICS
- Effects of Drought on Gene Expression in Maize Reproductive and Leaf Meristem Tissue Revealed by RNA-Seq
- (2012) A. Kakumanu et al. PLANT PHYSIOLOGY
- Counting absolute numbers of molecules using unique molecular identifiers
- (2011) Teemu Kivioja et al. NATURE METHODS
- Next-generation transcriptome assembly
- (2011) Jeffrey A. Martin et al. NATURE REVIEWS GENETICS
- The INTACT method for cell type–specific gene expression and chromatin profiling in Arabidopsis thaliana
- (2010) Roger B Deal et al. Nature Protocols
- Control of Transcription by Cell Size
- (2010) Chia-Yung Wu et al. PLOS BIOLOGY
- Reconstructing spatiotemporal gene expression data from partial observations
- (2009) D. A. Cartwright et al. BIOINFORMATICS
- Fast unfolding of communities in large networks
- (2008) Vincent D Blondel et al. JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT
- Cell-specific nitrogen responses mediate developmental plasticity
- (2008) M. L. Gifford et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Cell Identity Mediates the Response of Arabidopsis Roots to Abiotic Stress
- (2008) J. R. Dinneny et al. SCIENCE
Find Funding. Review Successful Grants.
Explore over 25,000 new funding opportunities and over 6,000,000 successful grants.
ExploreAsk a Question. Answer a Question.
Quickly pose questions to the entire community. Debate answers and get clarity on the most important issues facing researchers.
Get Started