Integrating barcoded neuroanatomy with spatial transcriptional profiling enables identification of gene correlates of projections

BARcode DEmixing through Non-negative Spatial Regression (BarDensr)

(2021) Shuonan Chen et al.   PLoS Computational Biology

Systematic comparison of single-cell and single-nucleus RNA-sequencing methods

(2020) Jiarui Ding et al.   NATURE BIOTECHNOLOGY

BRICseq Bridges Brain-wide Interregional Connectivity to Neural Activity and Gene Expression in Single Animals

(2020) Longwen Huang et al.   CELL

Cellpose: a generalist algorithm for cellular segmentation

(2020) Carsen Stringer et al.   NATURE METHODS

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

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

Reconstruction of 1,000 Projection Neurons Reveals New Cell Types and Organization of Long-Range Connectivity in the Mouse Brain

(2019) Johan Winnubst et al.   CELL

Multimodal Analysis of Cell Types in a Hypothalamic Node Controlling Social Behavior

(2019) Dong-Wook Kim et al.   CELL

High-Throughput Mapping of Long-Range Neuronal Projection Using In Situ Sequencing

(2019) Xiaoyin Chen et al.   CELL

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

(2019) Xiaoyan Qian et al.   NATURE METHODS

Teneurin-3 controls topographic circuit assembly in the hippocampus

(2018) Dominic S. Berns et al.   NATURE

Classes and continua of hippocampal CA1 inhibitory neurons revealed by single-cell transcriptomics

(2018) Kenneth D. Harris et al.   PLOS BIOLOGY

Molecular Architecture of the Mouse Nervous System

(2018) Amit Zeisel et al.   CELL

The logic of single-cell projections from visual cortex

(2018) Yunyun Han et al.   NATURE

Cadherin Combinations Recruit Dendrites of Distinct Retinal Neurons to a Shared Interneuronal Scaffold

(2018) Xin Duan et al.   NEURON

Shared and distinct transcriptomic cell types across neocortical areas

(2018) Bosiljka Tasic et al.   NATURE

Distinct descending motor cortex pathways and their roles in movement

(2018) Michael N. Economo et al.   NATURE

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 Cadherin Superfamily in Neural Circuit Assembly

(2017) James D. Jontes   Cold Spring Harbor Perspectives in Biology

High-Throughput Mapping of Single-Neuron Projections by Sequencing of Barcoded RNA

(2016) Justus M. Kebschull et al.   NEURON

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

(2016) Sheel Shah et al.   NEURON

Alphavirus Infection: Host Cell Shut-Off and Inhibition of Antiviral Responses

(2016) Jelke Fros et al.   Viruses-Basel

An inhibitory corticostriatal pathway

(2016) Crystal Rock et al.   eLife

Guidance for RNA-seq co-expression network construction and analysis: safety in numbers

(2015) S. Ballouz et al.   BIOINFORMATICS

Complex and dynamic expression of cadherins in the embryonic marmoset cerebral cortex

(2015) Eiji Matsunaga et al.   DEVELOPMENT GROWTH & DIFFERENTIATION

The neocortical circuit: themes and variations

(2015) Kenneth D Harris et al.   NATURE NEUROSCIENCE

Spatially resolved, highly multiplexed RNA profiling in single cells

(2015) K. H. Chen et al.   SCIENCE

Type II Cadherins Guide Assembly of a Direction-Selective Retinal Circuit

(2014) Xin Duan et al.   CELL

The role of T-cadherin in axonal pathway formation in neocortical circuits

(2014) Y. Hayano et al.   DEVELOPMENT

Cadherin-8 expression, synaptic localization, and molecular control of neuronal form in prefrontal corticostriatal circuits

(2014) Lauren G. Friedman et al.   JOURNAL OF COMPARATIVE NEUROLOGY

A mesoscale connectome of the mouse brain

(2014) Seung Wook Oh et al.   NATURE

Highly Multiplexed Subcellular RNA Sequencing in Situ

(2014) J. H. Lee et al.   SCIENCE

In situ sequencing for RNA analysis in preserved tissue and cells

(2013) Rongqin Ke et al.   NATURE METHODS

Molecular logic of neocortical projection neuron specification, development and diversity

(2013) Luciano Custo Greig et al.   NATURE REVIEWS NEUROSCIENCE

A Sharp Cadherin-6 Gene Expression Boundary in the Developing Mouse Cortical Plate Demarcates the Future Functional Areal Border

(2012) Youhei W. Terakawa et al.   CEREBRAL CORTEX

Sequencing the Connectome

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

Semaphorin Signaling in Vertebrate Neural Circuit Assembly

(2012) Yutaka Yoshida   Frontiers in Molecular Neuroscience

Parametric Image Alignment Using Enhanced Correlation Coefficient Maximization

(2008) G.D. Evangelidis et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

Imaging individual mRNA molecules using multiple singly labeled probes

(2008) Arjun Raj et al.   NATURE METHODS