Expansion sequencing: Spatially precise in situ transcriptomics in intact biological systems

Excised linear introns regulate growth in yeast

(2019) Jeffrey T. Morgan et al.   NATURE

Microtubule-Driven Stress Granule Dynamics Regulate Inhibitory Immune Checkpoint Expression in T Cells

(2019) Don-Marc Franchini et al.   Cell Reports

Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution

(2019) Samuel G. Rodriques et al.   SCIENCE

Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+

(2019) Chee-Huat Linus Eng et al.   NATURE

HIF-1 transcription activity: HIF1A driven response in normoxia and in hypoxia

(2019) Flora Cimmino et al.   BMC Medical Genetics

Comprehensive catalog of dendritically localized mRNA isoforms from sub-cellular sequencing of single mouse neurons

(2019) Sarah A. Middleton et al.   BMC BIOLOGY

Local protein synthesis is a ubiquitous feature of neuronal pre- and postsynaptic compartments

(2019) Anne-Sophie Hafner et al.   SCIENCE

FOXP2 exhibits neuron class specific expression, but is not required for multiple aspects of cortical histogenesis

(2019) Ryan J Kast et al.   eLife

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Local translation in neurons: visualization and function

(2019) Christine E. Holt et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Immunofibroblasts are pivotal drivers of tertiary lymphoid structure formation and local pathology

(2019) Saba Nayar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multiplexed detection of RNA using MERFISH and branched DNA amplification

(2019) Chenglong Xia et al.   Scientific Reports

High-definition spatial transcriptomics for in situ tissue profiling

(2019) Sanja Vickovic et al.   NATURE METHODS

Generation of in situ sequencing based OncoMaps to spatially resolve gene expression profiles of diagnostic and prognostic markers in breast cancer

(2019) Jessica Svedlund et al.   EBioMedicine

Probabilistic cell typing enables fine mapping of closely related cell types in situ

(2019) Xiaoyan Qian et al.   NATURE METHODS

Free circular introns with an unusual branchpoint in neuronal projections

(2019) Harleen Saini et al.   eLife

A Suite of Transgenic Driver and Reporter Mouse Lines with Enhanced Brain-Cell-Type Targeting and Functionality

(2018) Tanya L. Daigle et al.   CELL

Third-generationin situhybridization chain reaction: multiplexed, quantitative, sensitive, versatile, robust

(2018) Harry M. T. Choi et al.   DEVELOPMENT

Expansion microscopy: enabling single cell analysis in intact biological systems

(2018) Shahar Alon et al.   FEBS Journal

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

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Three-dimensional intact-tissue sequencing of single-cell transcriptional states

(2018) Xiao Wang et al.   SCIENCE

Protein S100-A8: A potential metastasis-associated protein for breast cancer determined via iTRAQ quantitative proteomic and clinicopathological analysis

(2018) Jing‑Min Zhong et al.   Oncology Letters

Multiplexed imaging of high-density libraries of RNAs with MERFISH and expansion microscopy

(2018) Guiping Wang et al.   Scientific Reports

Rare Cell Detection by Single-Cell RNA Sequencing as Guided by Single-Molecule RNA FISH

(2018) Eduardo Torre et al.   Cell Systems

A Structured Tumor-Immune Microenvironment in Triple Negative Breast Cancer Revealed by Multiplexed Ion Beam Imaging

(2018) Leeat Keren et al.   CELL

Developmental barcoding of whole mouse via homing CRISPR

(2018) Reza Kalhor et al.   SCIENCE

Shared and distinct transcriptomic cell types across neocortical areas

(2018) Bosiljka Tasic et al.   NATURE

ClampFISH detects individual nucleic acid molecules using click chemistry–based amplification

(2018) Sara H Rouhanifard et al.   NATURE BIOTECHNOLOGY

Spatial organization of the somatosensory cortex revealed by osmFISH

(2018) Simone Codeluppi et al.   NATURE METHODS

Expansion microscopy: principles and uses in biological research

(2018) Asmamaw T. Wassie et al.   NATURE METHODS

Molecular, spatial, and functional single-cell profiling of the hypothalamic preoptic region

(2018) Jeffrey R. Moffitt et al.   SCIENCE

VAST (Volume Annotation and Segmentation Tool): Efficient Manual and Semi-Automatic Labeling of Large 3D Image Stacks

(2018) Daniel R. Berger et al.   Frontiers in Neural Circuits

Spatially and functionally distinct subclasses of breast cancer-associated fibroblasts revealed by single cell RNA sequencing

(2018) Michael Bartoschek et al.   Nature Communications

Clinical Significance of Elevated S100A8 Expression in Breast Cancer Patients

(2018) Dujuan Wang et al.   Frontiers in Oncology

Prothymosin alpha-deficiency enhances anxiety-like behaviors and impairs learning/memory functions and neurogenesis

(2017) Hiroshi Ueda et al.   JOURNAL OF NEUROCHEMISTRY

Elements of cancer immunity and the cancer–immune set point

(2017) Daniel S. Chen et al.   NATURE

Single-cell spatial reconstruction reveals global division of labour in the mammalian liver

(2017) Keren Bahar Halpern et al.   NATURE

Hypoxia in the glioblastoma microenvironment: shaping the phenotype of cancer stem-like cells

(2017) Nicole Colwell et al.   NEURO-ONCOLOGY

Using high-throughput barcode sequencing to efficiently map connectomes

(2017) Ian D. Peikon et al.   NUCLEIC ACIDS RESEARCH

Efficient in situ barcode sequencing using padlock probe-based BaristaSeq

(2017) Xiaoyin Chen et al.   NUCLEIC ACIDS RESEARCH

The long noncoding RNA Malat1: Its physiological and pathophysiological functions

(2017) Xuejing Zhang et al.   RNA Biology

Global mRNA polarization regulates translation efficiency in the intestinal epithelium

(2017) Andreas E. Moor et al.   SCIENCE

The promise of spatial transcriptomics for neuroscience in the era of molecular cell typing

(2017) Ed Lein et al.   SCIENCE

Highly specific imaging of mRNA in single cells by target RNA-initiated rolling circle amplification

(2017) Ruijie Deng et al.   Chemical Science

The Human Cell Atlas

(2017) Aviv Regev et al.   eLife

Bacterial Stress Responses during Host Infection

(2016) Ferric C. Fang et al.   Cell Host & Microbe

Protein-retention expansion microscopy of cells and tissues labeled using standard fluorescent proteins and antibodies

(2016) Paul W Tillberg et al.   NATURE BIOTECHNOLOGY

Nanoscale imaging of RNA with expansion microscopy

(2016) Fei Chen et al.   NATURE METHODS

Adult mouse cortical cell taxonomy revealed by single cell transcriptomics

(2016) Bosiljka Tasic et al.   NATURE NEUROSCIENCE

Life at Low Copy Number: How Dendrites Manage with So Few mRNAs

(2016) Kenneth S. Kosik   NEURON

In Situ Transcription Profiling of Single Cells Reveals Spatial Organization of Cells in the Mouse Hippocampus

(2016) Sheel Shah et al.   NEURON

Glutamate-induced RNA localization and translation in neurons

(2016) Young J. Yoon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-throughput single-cell gene-expression profiling with multiplexed error-robust fluorescence in situ hybridization

(2016) Jeffrey R. Moffitt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Efficient in situ detection of mRNAs using the Chlorella virus DNA ligase for padlock probe ligation

(2016) Nils Schneider et al.   RNA

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics

(2016) P. L. Stahl et al.   SCIENCE

Simple, Scalable Proteomic Imaging for High-Dimensional Profiling of Intact Systems

(2015) Evan Murray et al.   CELL

Fezf2expression in layer 5 projection neurons of mature mouse motor cortex

(2015) Malinda L.S. Tantirigama et al.   JOURNAL OF COMPARATIVE NEUROLOGY

Organocatalytic removal of formaldehyde adducts from RNA and DNA bases

(2015) Saswata Karmakar et al.   Nature Chemistry

Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues

(2015) Je Hyuk Lee et al.   Nature Protocols

Mechanisms of Long Non-coding RNAs in Mammalian Nervous System Development, Plasticity, Disease, and Evolution

(2015) James A. Briggs et al.   NEURON

Foxg1 localizes to mitochondria and coordinates cell differentiation and bioenergetics

(2015) Laura Pancrazi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Expansion microscopy

(2015) F. Chen et al.   SCIENCE

Simulate_PCR for amplicon prediction and annotation from multiplex, degenerate primers and probes

(2014) Shea N Gardner et al.   BMC BIOINFORMATICS

Independent optical excitation of distinct neural populations

(2014) Nathan C Klapoetke et al.   NATURE METHODS

Spatially resolved transcriptomics and beyond

(2014) Nicola Crosetto et al.   NATURE REVIEWS GENETICS

Highly Multiplexed Subcellular RNA Sequencing in Situ

(2014) J. H. Lee et al.   SCIENCE

The embryo as a laboratory: quantifying transcription in Drosophila

(2014) Thomas Gregor et al.   TRENDS IN GENETICS

PEAR: a fast and accurate Illumina Paired-End reAd mergeR

(2013) J. Zhang et al.   BIOINFORMATICS

From single-cell to cell-pool transcriptomes: Stochasticity in gene expression and RNA splicing

(2013) G. K. Marinov et al.   GENOME RESEARCH

In situ sequencing for RNA analysis in preserved tissue and cells

(2013) Rongqin Ke et al.   NATURE METHODS

Molecular mechanisms of dendrite stability

(2013) Anthony J. Koleske   NATURE REVIEWS NEUROSCIENCE

Patterns of mRNA and protein expression for 12 GABAA receptor subunits in the mouse brain

(2013) H. Hörtnagl et al.   NEUROSCIENCE

Efficient DNA ligation in DNA–RNA hybrid helices by Chlorella virus DNA ligase

(2013) Gregory J. S. Lohman et al.   NUCLEIC ACIDS RESEARCH

Subcellular RNA Sequencing Reveals Broad Presence of Cytoplasmic Intron-Sequence Retaining Transcripts in Mouse and Rat Neurons

(2013) Mugdha Khaladkar et al.   PLoS One

Role of epidermal growth factor receptor in breast cancer

(2012) Hiroko Masuda et al.   BREAST CANCER RESEARCH AND TREATMENT

Large-Scale Cellular-Resolution Gene Profiling in Human Neocortex Reveals Species-Specific Molecular Signatures

(2012) Hongkui Zeng et al.   CELL

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The Local Transcriptome in the Synaptic Neuropil Revealed by Deep Sequencing and High-Resolution Imaging

(2012) Iván J. Cajigas et al.   NEURON

Sequencing the Connectome

(2012) Anthony M. Zador et al.   PLOS BIOLOGY

Multiobjective evolutionary algorithms to identify highly autocorrelated areas: the case of spatial distribution in financially compromised farms

(2011) Carlos R. García-Alonso et al.   ANNALS OF OPERATIONS RESEARCH

Addressing challenges in the production and analysis of illumina sequencing data

(2011) Martin Kircher et al.   BMC GENOMICS

Cytoplasmic Intron Sequence-Retaining Transcripts Can Be Dendritically Targeted via ID Element Retrotransposons

(2011) Peter T. Buckley et al.   NEURON

Up-regulation of Nob1 in the rat auditory system with noise-induced hearing loss

(2011) Yu Han et al.   NEUROSCIENCE LETTERS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Three groups of interneurons account for nearly 100% of neocortical GABAergic neurons

(2010) Bernardo Rudy et al.   Developmental Neurobiology

Molecular mechanisms of micronucleus, nucleoplasmic bridge and nuclear bud formation in mammalian and human cells

(2010) M. Fenech et al.   MUTAGENESIS

High-performance genetically targetable optical neural silencing by light-driven proton pumps

(2010) Brian Y. Chow et al.   NATURE

Cux1 and Cux2 Regulate Dendritic Branching, Spine Morphology, and Synapses of the Upper Layer Neurons of the Cortex

(2010) Beatriz Cubelos et al.   NEURON

Molecular Motors in Neurons: Transport Mechanisms and Roles in Brain Function, Development, and Disease

(2010) Nobutaka Hirokawa et al.   NEURON

Aldehyde Dehydrogenase Activity of Breast Cancer Stem Cells Is Primarily Due To Isoform ALDH1A3 and Its Expression Is Predictive of Metastasis

(2010) Paola Marcato et al.   STEM CELLS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Polysomes, P bodies and stress granules: states and fates of eukaryotic mRNAs

(2009) Vidya Balagopal et al.   CURRENT OPINION IN CELL BIOLOGY

Regulation of Synaptic Structure by Ubiquitin C-Terminal Hydrolase L1

(2009) A. E. Cartier et al.   JOURNAL OF NEUROSCIENCE

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Design of 240,000 orthogonal 25mer DNA barcode probes

(2009) Q. Xu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Efficient mapping of Applied Biosystems SOLiD sequence data to a reference genome for functional genomic applications

(2008) Brian D. Ondov et al.   BIOINFORMATICS

Mechanisms and cellular roles of local protein synthesis in mammalian cells

(2008) Alexis J Rodriguez et al.   CURRENT OPINION IN CELL BIOLOGY

Smaller Dendritic Spines, Weaker Synaptic Transmission, but Enhanced Spatial Learning in Mice Lacking Shank1

(2008) A. Y. Hung et al.   JOURNAL OF NEUROSCIENCE

Imaging individual mRNA molecules using multiple singly labeled probes

(2008) Arjun Raj et al.   NATURE METHODS