Spatially resolved transcriptomics and beyond

Genetic and Phenotypic Diversity in Breast Tumor Metastases

(2014) V. Almendro et al.   CANCER RESEARCH

Whole-Brain Imaging with Single-Cell Resolution Using Chemical Cocktails and Computational Analysis

(2014) Etsuo A. Susaki et al.   CELL

Single-Cell Phenotyping within Transparent Intact Tissue through Whole-Body Clearing

(2014) Bin Yang et al.   CELL

Genome-wide RNA Tomography in the Zebrafish Embryo

(2014) Jan Philipp Junker et al.   CELL

Development and Applications of CRISPR-Cas9 for Genome Engineering

(2014) Patrick D. Hsu et al.   CELL

Every Cell Is Special: Genome-wide Studies Add a New Dimension to Single-Cell Biology

(2014) Jan Philipp Junker et al.   CELL

Identification of mRNAs and lincRNAs associated with lung cancer progression using next-generation RNA sequencing from laser micro-dissected archival FFPE tissue specimens

(2014) Matthew L. Morton et al.   LUNG CANCER

Transcriptional landscape of the prenatal human brain

(2014) Jeremy A. Miller et al.   NATURE

Pollination curbs climate risk to cocoa

(2014) Thomas C. Wanger   NATURE

Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq

(2014) Barbara Treutlein et al.   NATURE

Multiplexed ion beam imaging of human breast tumors

(2014) Michael Angelo et al.   NATURE MEDICINE

Next-gen immunohistochemistry

(2014) David L Rimm   NATURE METHODS

Validation of noise models for single-cell transcriptomics

(2014) Dominic Grün et al.   NATURE METHODS

Transcriptome in vivo analysis (TIVA) of spatially defined single cells in live tissue

(2014) Ditte Lovatt et al.   NATURE METHODS

Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry

(2014) Charlotte Giesen et al.   NATURE METHODS

Single-cell in situ RNA profiling by sequential hybridization

(2014) Eric Lubeck et al.   NATURE METHODS

Advanced CLARITY for rapid and high-resolution imaging of intact tissues

(2014) Raju Tomer et al.   Nature Protocols

High-resolution digital profiling of the epigenome

(2014) Gabriel E. Zentner et al.   NATURE REVIEWS GENETICS

Fusion FISH Imaging: Single-Molecule Detection of Gene Fusion Transcripts In Situ

(2014) Fatu Badiane Markey et al.   PLoS One

A Quantitative Comparison of Single-Cell Whole Genome Amplification Methods

(2014) Charles F. A. de Bourcy et al.   PLoS One

Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma

(2014) A. P. Patel et al.   SCIENCE

Intratumor heterogeneity in localized lung adenocarcinomas delineated by multiregion sequencing

(2014) J. Zhang et al.   SCIENCE

Spatial and temporal diversity in genomic instability processes defines lung cancer evolution

(2014) E. C. de Bruin et al.   SCIENCE

Highly Multiplexed Subcellular RNA Sequencing in Situ

(2014) J. H. Lee et al.   SCIENCE

Ten years of next-generation sequencing technology

(2014) Erwin L. van Dijk et al.   TRENDS IN GENETICS

Inference of Tumor Evolution during Chemotherapy by Computational Modeling and In Situ Analysis of Genetic and Phenotypic Cellular Diversity

(2014) Vanessa Almendro et al.   Cell Reports

DNA Dynamics during Early Double-Strand Break Processing Revealed by Non-Intrusive Imaging of Living Cells

(2014) Hicham Saad et al.   PLoS Genetics

The Next-Generation Sequencing Revolution and Its Impact on Genomics

(2013) Daniel C. Koboldt et al.   CELL

Dynamic Imaging of Genomic Loci in Living Human Cells by an Optimized CRISPR/Cas System

(2013) Baohui Chen et al.   CELL

The ventral to dorsal BMP activity gradient in the early zebrafish embryo is determined by graded expression of BMP ligands

(2013) Marie-Christine Ramel et al.   DEVELOPMENTAL BIOLOGY

Structural and molecular interrogation of intact biological systems

(2013) Kwanghun Chung et al.   NATURE

Tumour heterogeneity in the clinic

(2013) Philippe L. Bedard et al.   NATURE

In situ sequencing for RNA analysis in preserved tissue and cells

(2013) Rongqin Ke et al.   NATURE METHODS

Visualizing SNVs to quantify allele-specific expression in single cells

(2013) Marshall J Levesque et al.   NATURE METHODS

Image-based transcriptomics in thousands of single human cells at single-molecule resolution

(2013) Nico Battich et al.   NATURE METHODS

Allele-specific detection of single mRNA molecules in situ

(2013) Clinton H Hansen et al.   NATURE METHODS

Quantitative assessment of single-cell RNA-sequencing methods

(2013) Angela R Wu et al.   NATURE METHODS

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

(2013) Simone Picelli et al.   NATURE METHODS

Single-molecule mRNA detection and counting in mammalian tissue

(2013) Anna Lyubimova et al.   Nature Protocols

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

(2013) Ehud Shapiro et al.   NATURE REVIEWS GENETICS

Turbo FISH: A Method for Rapid Single Molecule RNA FISH

(2013) Sydney M. Shaffer et al.   PLoS One

Sequencing mRNA from Cryo-Sliced Drosophila Embryos to Determine Genome-Wide Spatial Patterns of Gene Expression

(2013) Peter A. Combs et al.   PLoS One

Live-Cell Visualization of Pre-mRNA Splicing with Single-Molecule Sensitivity

(2013) Robert M. Martin et al.   Cell Reports

Dorsal-Ventral Gene Expression in the Drosophila Embryo Reflects the Dynamics and Precision of the Dorsal Nuclear Gradient

(2012) Gregory T. Reeves et al.   DEVELOPMENTAL CELL

Image analysis and empirical modeling of gene and protein expression

(2012) Nathanie Trisnadi et al.   METHODS

An anatomically comprehensive atlas of the adult human brain transcriptome

(2012) Michael J. Hawrylycz et al.   NATURE

A versatile genome-scale PCR-based pipeline for high-definition DNA FISH

(2012) Magda Bienko et al.   NATURE METHODS

Single-cell systems biology by super-resolution imaging and combinatorial labeling

(2012) Eric Lubeck et al.   NATURE METHODS

Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing

(2012) Marco Gerlinger et al.   NEW ENGLAND JOURNAL OF MEDICINE

Transcriptome Tomography for Brain Analysis in the Web-Accessible Anatomical Space

(2012) Yuko Okamura-Oho et al.   PLoS One

Versatile design and synthesis platform for visualizing genomes with Oligopaint FISH probes

(2012) B. J. Beliveau 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

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

(2012) Tamar Hashimshony et al.   Cell Reports

Fluorescence in situ hybridization with high-complexity repeat-free oligonucleotide probes generated by massively parallel synthesis

(2011) Shelagh Boyle et al.   CHROMOSOME RESEARCH

Image analysis for understanding embryo development: a bridge from microscopy to biological insights

(2011) MA Luengo-Oroz et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq

(2011) S. Islam et al.   GENOME RESEARCH

Cell-to-cell variability of alternative RNA splicing

(2011) Z. Waks et al.   Molecular Systems Biology

Tumour evolution inferred by single-cell sequencing

(2011) Nicholas Navin et al.   NATURE

Single-molecule transcript counting of stem-cell markers in the mouse intestine

(2011) Shalev Itzkovitz et al.   NATURE CELL BIOLOGY

Single-tube linear DNA amplification (LinDA) for robust ChIP-seq

(2011) Pattabhiraman Shankaranarayanan et al.   NATURE METHODS

Can some patients avoid adjuvant chemotherapy for early-stage breast cancer?

(2011) Philippe L. Bedard et al.   Nature Reviews Clinical Oncology

Next-generation transcriptome assembly

(2011) Jeffrey A. Martin et al.   NATURE REVIEWS GENETICS

Single-Cell Mass Cytometry of Differential Immune and Drug Responses Across a Human Hematopoietic Continuum

(2011) S. C. Bendall et al.   SCIENCE

Dynamics of single mRNP nucleocytoplasmic transport and export through the nuclear pore in living cells

(2010) Amir Mor et al.   NATURE CELL BIOLOGY

In situ detection and genotyping of individual mRNA molecules

(2010) Chatarina Larsson et al.   NATURE METHODS

Chromosome Territories

(2010) T. Cremer et al.   Cold Spring Harbor Perspectives in Biology

Imaging individual mRNA molecules using multiple singly labeled probes

(2008) Arjun Raj et al.   NATURE METHODS

Ligation-based molecular tools for lab-on-a-chip devices

(2008) Jonas Melin et al.   New Biotechnology