Barcoded oligonucleotides ligated on RNA amplified for multiplexed and parallel in situ analyses

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

(2021) Shahar Alon et al.   SCIENCE

SCRINSHOT enables spatial mapping of cell states in tissue sections with single-cell resolution

(2020) Alexandros Sountoulidis et al.   PLOS BIOLOGY

REST and Neural Gene Network Dysregulation in iPSC Models of Alzheimer’s Disease

(2019) Katharina Meyer 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

Single-cell transcriptomic analysis of Alzheimer’s disease

(2019) Hansruedi Mathys et al.   NATURE

High-definition spatial transcriptomics for in situ tissue profiling

(2019) Sanja Vickovic et al.   NATURE METHODS

Optical Pooled Screens in Human Cells

(2019) David Feldman et al.   CELL

A Combination of Ontogeny and CNS Environment Establishes Microglial Identity

(2018) F. Chris Bennett et al.   NEURON

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

(2018) Xiao Wang et al.   SCIENCE

DNA-Sequence-Encoded Rolling Circle Amplicon for Single-Cell RNA Imaging

(2018) Ruijie Deng et al.   Chem

GENCODE reference annotation for the human and mouse genomes

(2018) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

Microglia emerge as central players in brain disease

(2017) Michael W Salter et al.   NATURE MEDICINE

An interactive framework for whole-brain maps at cellular resolution

(2017) Daniel Fürth et al.   NATURE NEUROSCIENCE

Targeted DNA sequencing and in situ mutation analysis using mobile phone microscopy

(2017) Malte Kühnemund et al.   Nature Communications

Patient-specific models of microglia-mediated engulfment of synapses and neural progenitors

(2016) C M Sellgren et al.   MOLECULAR PSYCHIATRY

Nanoscale imaging of RNA with expansion microscopy

(2016) Fei Chen et al.   NATURE METHODS

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

(2016) Sheel Shah et al.   NEURON

Sensitive and specific miRNA detection method using SplintR Ligase

(2016) Jingmin Jin et al.   NUCLEIC ACIDS RESEARCH

High-performance multiplexed fluorescence in situ hybridization in culture and tissue with matrix imprinting and clearing

(2016) Jeffrey R. Moffitt 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

Quantitative approaches for investigating the spatial context of gene expression

(2016) Je H. Lee   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

Co-expression networks in generation of induced pluripotent stem cells

(2016) Sharan Paul et al.   Biology Open

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

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

(2015) Je Hyuk Lee et al.   Nature Protocols

Expansion microscopy

(2015) F. Chen et al.   SCIENCE

Rapid neurogenesis through transcriptional activation in human stem cells

(2014) V. Busskamp et al.   Molecular Systems Biology

Generation of cerebral organoids from human pluripotent stem cells

(2014) Madeline A Lancaster et al.   Nature Protocols

Highly Multiplexed Subcellular RNA Sequencing in Situ

(2014) J. H. Lee et al.   SCIENCE

Levenshtein error-correcting barcodes for multiplexed DNA sequencing

(2013) Tilo Buschmann et al.   BMC BIOINFORMATICS

MALAT-1 interacts with hnRNP C in cell cycle regulation

(2013) Feng Yang et al.   FEBS LETTERS

In situ sequencing for RNA analysis in preserved tissue and cells

(2013) Rongqin Ke et al.   NATURE METHODS

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

(2013) Nico Battich et al.   NATURE METHODS

Cellular-resolution connectomics: challenges of dense neural circuit reconstruction

(2013) Moritz Helmstaedter   NATURE METHODS

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

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

Consistent Errors in First Strand cDNA Due to Random Hexamer Mispriming

(2013) Thomas P. van Gurp et al.   PLoS One

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

APCluster: an R package for affinity propagation clustering

(2011) U. Bodenhofer et al.   BIOINFORMATICS

The Nuclear-Retained Noncoding RNA MALAT1 Regulates Alternative Splicing by Modulating SR Splicing Factor Phosphorylation

(2010) Vidisha Tripathi et al.   MOLECULAR CELL

In situ detection and genotyping of individual mRNA molecules

(2010) Chatarina Larsson et al.   NATURE METHODS

Multiplex padlock targeted sequencing reveals human hypermutable CpG variations

(2009) J. B. Li et al.   GENOME RESEARCH

miRNA in situ hybridization in formaldehyde and EDC–fixed tissues

(2009) John T G Pena et al.   NATURE METHODS