Manifold learning analysis suggests strategies to align single-cell multimodal data of neuronal electrophysiology and transcriptomics

Benchmarking algorithms for gene regulatory network inference from single-cell transcriptomic data

(2020) Aditya Pratapa et al.   NATURE METHODS

Unsupervised topological alignment for single-cell multi-omics integration

(2020) Kai Cao et al.   BIOINFORMATICS

Deep learning for time series classification: a review

(2019) Hassan Ismail Fawaz et al.   DATA MINING AND KNOWLEDGE DISCOVERY

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Classification of electrophysiological and morphological neuron types in the mouse visual cortex

(2019) Nathan W. Gouwens et al.   NATURE NEUROSCIENCE

Transcriptomic correlates of electrophysiological and morphological diversity within and across excitatory and inhibitory neuron classes

(2019) Claire Bomkamp et al.   PLoS Computational Biology

Layer 4 of mouse neocortex differs in cell types and circuit organization between sensory areas

(2019) Federico Scala et al.   Nature Communications

The art of using t-SNE for single-cell transcriptomics

(2019) Dmitry Kobak et al.   Nature Communications

ManiNetCluster: a novel manifold learning approach to reveal the functional links between gene networks

(2019) Nam D. Nguyen et al.   BMC GENOMICS

Visualizing structure and transitions in high-dimensional biological data

(2019) Kevin R. Moon et al.   NATURE BIOTECHNOLOGY

Unsupervised embedding of single-cell Hi-C data

(2018) Jie Liu et al.   BIOINFORMATICS

Induction of human Somatostatin and Parvalbumin neurons by expressing a single transcription factor LIM Homeobox 6

(2018) Fang Yuan et al.   eLife

Shared and distinct transcriptomic cell types across neocortical areas

(2018) Bosiljka Tasic et al.   NATURE

Dimensionality reduction for visualizing single-cell data using UMAP

(2018) Etienne Becht et al.   NATURE BIOTECHNOLOGY

Development and Functional Diversification of Cortical Interneurons

(2018) Lynette Lim et al.   NEURON

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

Transcriptomic correlates of neuron electrophysiological diversity

(2017) Shreejoy J. Tripathy et al.   PLoS Computational Biology

g:Profiler—a web server for functional interpretation of gene lists (2016 update)

(2016) Jüri Reimand et al.   NUCLEIC ACIDS RESEARCH

Electrophysiological, transcriptomic and morphologic profiling of single neurons using Patch-seq

(2015) Cathryn R Cadwell et al.   NATURE BIOTECHNOLOGY

The promise of single-cell sequencing

(2013) James Eberwine et al.   NATURE METHODS