Single-Cell Genomic Analysis in Plants

Single-cell transcriptomics uncovers distinct molecular signatures of stem cells in chronic myeloid leukemia

(2017) Alice Giustacchini et al.   NATURE MEDICINE

Pooled CRISPR screening with single-cell transcriptome readout

(2017) Paul Datlinger et al.   NATURE METHODS

Visualization and analysis of single-cell RNA-seq data by kernel-based similarity learning

(2017) Bo Wang et al.   NATURE METHODS

Building a lineage from single cells: genetic techniques for cell lineage tracking

(2017) Mollie B. Woodworth et al.   NATURE REVIEWS GENETICS

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

(2017) Chieh Lin et al.   NUCLEIC ACIDS RESEARCH

RNA editing with CRISPR-Cas13

(2017) David B. T. Cox et al.   SCIENCE

Improvements in Genomic Technologies: Application to Crop Genomics

(2017) Yuxuan Yuan et al.   TRENDS IN BIOTECHNOLOGY

Plant hormone-mediated regulation of stress responses

(2016) Vivek Verma et al.   BMC PLANT BIOLOGY

Dissecting Immune Circuits by Linking CRISPR-Pooled Screens with Single-Cell RNA-Seq

(2016) Diego Adhemar Jaitin et al.   CELL

Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens

(2016) Atray Dixit et al.   CELL

Root Regeneration Triggers an Embryo-like Sequence Guided by Hormonal Interactions

(2016) Idan Efroni et al.   CELL

How many ways are there to make a root?

(2016) Kenneth D Birnbaum   CURRENT OPINION IN PLANT BIOLOGY

A Case for Distributed Control of Local Stem Cell Behavior in Plants

(2016) Ramin Rahni et al.   DEVELOPMENTAL CELL

Single-cell analysis at the threshold

(2016) Xi Chen et al.   NATURE BIOTECHNOLOGY

Single-cell genome sequencing: current state of the science

(2016) Charles Gawad et al.   NATURE REVIEWS GENETICS

Advancing Crop Transformation in the Era of Genome Editing

(2016) Fredy Altpeter et al.   PLANT CELL

Transcriptome dynamics of Arabidopsis during sequential biotic and abiotic stresses

(2016) Silvia Coolen et al.   PLANT JOURNAL

How plants handle multiple stresses: hormonal interactions underlying responses to abiotic stress and insect herbivory

(2016) Duy Nguyen et al.   PLANT MOLECULAR BIOLOGY

Rawcopy: Improved copy number analysis with Affymetrix arrays

(2016) Markus Mayrhofer et al.   Scientific Reports

Transcriptome Dynamics of the Stomatal Lineage: Birth, Amplification, and Termination of a Self-Renewing Population

(2015) Jessika Adrian et al.   DEVELOPMENTAL CELL

Single-cell RNA-seq reveals changes in cell cycle and differentiation programs upon aging of hematopoietic stem cells

(2015) Monika S. Kowalczyk et al.   GENOME RESEARCH

Application of single-cell genomics in cancer: promise and challenges

(2015) Quin F. Wills et al.   HUMAN MOLECULAR GENETICS

Abiotic Stresses: Insight into Gene Regulation and Protein Expression in Photosynthetic Pathways of Plants

(2015) Mohammad-Zaman Nouri et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Advances and Applications of Single-Cell Sequencing Technologies

(2015) Yong Wang et al.   MOLECULAR CELL

Bioinformatics approaches to single-cell analysis in developmental biology

(2015) Dicle Yalcin et al.   MOLECULAR HUMAN REPRODUCTION

Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells

(2015) Florian Buettner et al.   NATURE BIOTECHNOLOGY

Copy number variation at the GL7 locus contributes to grain size diversity in rice

(2015) Yuexing Wang et al.   NATURE GENETICS

Computational and analytical challenges in single-cell transcriptomics

(2015) Oliver Stegle et al.   NATURE REVIEWS GENETICS

Identification and characterization of essential genes in the human genome

(2015) T. Wang et al.   SCIENCE

The female gametophyte: an emerging model for cell type-specific systems biology in plant development

(2015) Marc W. Schmid et al.   Frontiers in Plant Science

System approaches to study root hairs as a single cell plant model: current status and future perspectives

(2015) Md Shakhawat Hossain et al.   Frontiers in Plant Science

The Role of Ethylene in Plants Under Salinity Stress

(2015) Jian-Jun Tao et al.   Frontiers in Plant Science

Quantification of cell identity from single-cell gene expression profiles

(2015) Idan Efroni et al.   GENOME BIOLOGY

Development and Applications of CRISPR-Cas9 for Genome Engineering

(2014) Patrick D. Hsu et al.   CELL

Single-Cell Sequencing Technologies: Current and Future

(2014) Jialong Liang et al.   Journal of Genetics and Genomics

Single-cell RNA-seq: advances and future challenges

(2014) Antoine-Emmanuel Saliba et al.   NUCLEIC ACIDS RESEARCH

Interaction between MYC2 and ETHYLENE INSENSITIVE3 Modulates Antagonism between Jasmonate and Ethylene Signaling in Arabidopsis

(2014) S. Song et al.   PLANT CELL

The Root Hair “Infectome” ofMedicago truncatulaUncovers Changes in Cell Cycle Genes and Reveals a Requirement for Auxin Signaling in Rhizobial Infection

(2014) Andrew Breakspear et al.   PLANT CELL

Plant single-cell and single-cell-type metabolomics

(2014) Biswapriya B. Misra et al.   TRENDS IN PLANT SCIENCE

Current Challenges in the Bioinformatics of Single Cell Genomics

(2014) Luwen Ning et al.   Frontiers in Oncology

FishingCNV: a graphical software package for detecting rare copy number variations in exome-sequencing data

(2013) Yuhao Shi et al.   BIOINFORMATICS

Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives

(2013) Min Zhao et al.   BMC BIOINFORMATICS

Massively parallel polymerase cloning and genome sequencing of single cells using nanoliter microwells

(2013) Jeff Gole et al.   NATURE BIOTECHNOLOGY

Characterization of transcriptional networks in blood stem and progenitor cells using high-throughput single-cell gene expression analysis

(2013) Victoria Moignard et al.   NATURE CELL BIOLOGY

Quantitative single-cell RNA-seq with unique molecular identifiers

(2013) Saiful Islam et al.   NATURE METHODS

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

(2013) Philip Brennecke et al.   NATURE METHODS

Smart-seq2 for sensitive full-length transcriptome profiling in single cells

(2013) Simone Picelli et al.   NATURE METHODS

The promise of single-cell sequencing

(2013) James Eberwine et al.   NATURE METHODS

Single-cell sequencing-based technologies will revolutionize whole-organism science

(2013) Ehud Shapiro et al.   NATURE REVIEWS GENETICS

Alternative Splicing at the Intersection of Biological Timing, Development, and Stress Responses

(2013) D. Staiger et al.   PLANT CELL

Transcriptome Responses to Combinations of Stresses in Arabidopsis

(2013) S. Rasmussen et al.   PLANT PHYSIOLOGY

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

Genome-wide Single-Cell Analysis of Recombination Activity and De Novo Mutation Rates in Human Sperm

(2012) Jianbin Wang et al.   CELL

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Genome-wide copy number analysis of single cells

(2012) Timour Baslan et al.   Nature Protocols

Evolution of the cancer genome

(2012) Lucy R. Yates et al.   NATURE REVIEWS GENETICS

Positional cloning and characterization reveal the molecular basis for soybean maturity locus E1 that regulates photoperiodic flowering

(2012) Z. Xia et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-Wide Detection of Single-Nucleotide and Copy-Number Variations of a Single Human Cell

(2012) C. Zong et al.   SCIENCE

Probing Meiotic Recombination and Aneuploidy of Single Sperm Cells by Whole-Genome Sequencing

(2012) S. Lu et al.   SCIENCE

CEL-Seq: Single-Cell RNA-Seq by Multiplexed Linear Amplification

(2012) Tamar Hashimshony et al.   Cell Reports

V(D)J Recombination: Mechanisms of Initiation

(2011) David G. Schatz et al.   Annual Review of Genetics

Cell Identity Regulators Link Development and Stress Responses in the Arabidopsis Root

(2011) Anjali S. Iyer-Pascuzzi et al.   DEVELOPMENTAL CELL

Tumour evolution inferred by single-cell sequencing

(2011) Nicholas Navin et al.   NATURE

Regeneration in plants and animals: dedifferentiation, transdifferentiation, or just differentiation?

(2011) Kaoru Sugimoto et al.   TRENDS IN CELL BIOLOGY

Future medical applications of single-cell sequencing in cancer

(2011) Nicholas Navin et al.   Genome Medicine

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Phylogenetically Distinct Cellulose Synthase Genes Support Secondary Wall Thickening in Arabidopsis Shoot Trichomes and Cotton Fiber

(2010) Lissete Betancur et al.   Journal of Integrative Plant Biology

Global analysis of the root hair morphogenesis transcriptome reveals new candidate genes involved in root hair formation in barley

(2010) Miroslaw Kwasniewski et al.   JOURNAL OF PLANT PHYSIOLOGY

Overview of single-cell analyses: microdevices and applications

(2010) Sara Lindström et al.   LAB ON A CHIP

RNA-Seq analysis to capture the transcriptome landscape of a single cell

(2010) Fuchou Tang et al.   Nature Protocols

Tissue-Adapted Invasion Strategies of the Rice Blast FungusMagnaporthe oryzae

(2010) Sylvain Marcel et al.   PLANT CELL

Genome-wide mapping of alternative splicing in Arabidopsis thaliana

(2009) S. A. Filichkin et al.   GENOME RESEARCH

Cells keep a memory of their tissue origin during axolotl limb regeneration

(2009) Martin Kragl et al.   NATURE

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS

Stress-induced changes in theArabidopsis thalianatranscriptome analyzed using whole-genome tiling arrays

(2009) Georg Zeller et al.   PLANT JOURNAL

Antagonism between abscisic acid and ethylene in Arabidopsis acts in parallel with the reciprocal regulation of their metabolism and signaling pathways

(2009) Wan-Hsing Cheng et al.   PLANT MOLECULAR BIOLOGY

Complete Transcriptome of the Soybean Root Hair Cell, a Single-Cell Model, and Its Alteration in Response to Bradyrhizobium japonicum Infection

(2009) M. Libault et al.   PLANT PHYSIOLOGY

Gene expression map of the Arabidopsis shoot apical meristem stem cell niche

(2009) R. K. Yadav et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Plant cell types: reporting and sampling with new technologies

(2008) Timothy Nelson et al.   CURRENT OPINION IN PLANT BIOLOGY

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

Gene expression profiling of single epidermal, basal and trichome cells of Arabidopsis thaliana

(2007) Elke Lieckfeldt et al.   JOURNAL OF PLANT PHYSIOLOGY