Concepts and limitations for learning developmental trajectories from single cell genomics

Single-cell RNA-seq denoising using a deep count autoencoder

(2019) Gökcen Eraslan et al.   Nature Communications

Integrative single-cell analysis

(2019) Tim Stuart et al.   NATURE REVIEWS GENETICS

Characterization of cell fate probabilities in single-cell data with Palantir

(2019) Manu Setty et al.   NATURE BIOTECHNOLOGY

A single-cell molecular map of mouse gastrulation and early organogenesis

(2019) Blanca Pijuan-Sala et al.   NATURE

The single-cell transcriptional landscape of mammalian organogenesis

(2019) Junyue Cao et al.   NATURE

Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming

(2019) Geoffrey Schiebinger et al.   CELL

A comparison of single-cell trajectory inference methods

(2019) Wouter Saelens et al.   NATURE BIOTECHNOLOGY

Inferring population dynamics from single-cell RNA-sequencing time series data

(2019) David S. Fischer et al.   NATURE BIOTECHNOLOGY

Exploring single cells in space and time during tissue development, homeostasis and regeneration

(2019) Urs Mayr et al.   DEVELOPMENT

Mapping chromatin modifications at the single cell level

(2019) Connor H. Ludwig et al.   DEVELOPMENT

Recording development with single cell dynamic lineage tracing

(2019) Aaron McKenna et al.   DEVELOPMENT

GrandPrix: Scaling up the Bayesian GPLVM for single-cell data

(2018) Sumon Ahmed et al.   BIOINFORMATICS

Evaluating methods of inferring gene regulatory networks highlights their lack of performance for single cell gene expression data

(2018) Shuonan Chen et al.   BMC BIOINFORMATICS

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics

(2018) Kelly Street et al.   BMC GENOMICS

Single-Cell Transcriptomics Meets Lineage Tracing

(2018) Lennart Kester et al.   Cell Stem Cell

Using single‐cell genomics to understand developmental processes and cell fate decisions

(2018) Jonathan A Griffiths et al.   Molecular Systems Biology

Whole-organism clone tracing using single-cell sequencing

(2018) Anna Alemany et al.   NATURE

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors

(2018) Laleh Haghverdi et al.   NATURE BIOTECHNOLOGY

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

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain

(2018) Bushra Raj et al.   NATURE BIOTECHNOLOGY

Simultaneous lineage tracing and cell-type identification using CRISPR–Cas9-induced genetic scars

(2018) Bastiaan Spanjaard et al.   NATURE BIOTECHNOLOGY

Defining murine organogenesis at single-cell resolution reveals a role for the leukotriene pathway in regulating blood progenitor formation

(2018) Ximena Ibarra-Soria et al.   NATURE CELL BIOLOGY

On the design of CRISPR-based single-cell molecular screens

(2018) Andrew J Hill et al.   NATURE METHODS

Alignment of single-cell trajectories to compare cellular expression dynamics

(2018) Ayelet Alpert et al.   NATURE METHODS

Single-cell transcriptional profiling: a window into embryonic cell-type specification

(2018) Blanca Pijuan-Sala et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Frequent sgRNA-barcode recombination in single-cell perturbation assays

(2018) Shiqi Xie et al.   PLoS One

Fundamental limits on dynamic inference from single-cell snapshots

(2018) Caleb Weinreb et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cell type atlas and lineage tree of a whole complex animal by single-cell transcriptomics

(2018) Mireya Plass et al.   SCIENCE

Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis

(2018) Jeffrey A. Farrell et al.   SCIENCE

Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo

(2018) Daniel E. Wagner et al.   SCIENCE

Interpretable dimensionality reduction of single cell transcriptome data with deep generative models

(2018) Jiarui Ding et al.   Nature Communications

scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells

(2018) Stephen J. Clark et al.   Nature Communications

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

Joint profiling of chromatin accessibility and gene expression in thousands of single cells

(2018) Junyue Cao et al.   SCIENCE

Endocrine lineage biases arise in temporally distinct endocrine progenitors during pancreatic morphogenesis

(2018) Marissa A. Scavuzzo et al.   Nature Communications

Lineage dynamics of murine pancreatic development at single-cell resolution

(2018) Lauren E. Byrnes et al.   Nature Communications

Aligning Single-Cell Developmental and Reprogramming Trajectories Identifies Molecular Determinants of Myogenic Reprogramming Outcome

(2018) Davide Cacchiarelli et al.   Cell Systems

Single-cell reconstruction of the early maternal–fetal interface in humans

(2018) Roser Vento-Tormo et al.   NATURE

Dimensionality reduction for visualizing single-cell data using UMAP

(2018) Etienne Becht et al.   NATURE BIOTECHNOLOGY

Deep generative modeling for single-cell transcriptomics

(2018) Romain Lopez et al.   NATURE METHODS

A test metric for assessing single-cell RNA-seq batch correction

(2018) Maren Büttner et al.   NATURE METHODS

Barcoded solid-phase RNA capture for Spatial Transcriptomics profiling in mammalian tissue sections

(2018) Fredrik Salmén et al.   Nature Protocols

Synthetic recording and in situ readout of lineage information in single cells

(2017) Kirsten L. Frieda et al.   NATURE

Scaling single-cell genomics from phenomenology to mechanism

(2017) Amos Tanay et al.   NATURE

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

Simultaneous epitope and transcriptome measurement in single cells

(2017) Marlon Stoeckius et al.   NATURE METHODS

histoCAT: analysis of cell phenotypes and interactions in multiplex image cytometry data

(2017) Denis Schapiro et al.   NATURE METHODS

Pooled CRISPR screening with single-cell transcriptome readout

(2017) Paul Datlinger et al.   NATURE METHODS

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

Reconstructing blood stem cell regulatory network models from single-cell molecular profiles

(2017) Fiona K. Hamey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2017) Ed Lein et al.   SCIENCE

The Human Cell Atlas

(2017) Aviv Regev et al.   eLife

Gene Regulatory Network Inference from Single-Cell Data Using Multivariate Information Measures

(2017) Thalia E. Chan et al.   Cell Systems

Dissecting Immune Circuits by Linking CRISPR-Pooled Screens with Single-Cell RNA-Seq

(2016) Diego Adhemar Jaitin et al.   CELL

Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens

(2016) Atray Dixit et al.   CELL

A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response

(2016) Britt Adamson et al.   CELL

Resolving early mesoderm diversification through single-cell expression profiling

(2016) Antonio Scialdone et al.   NATURE

Wishbone identifies bifurcating developmental trajectories from single-cell data

(2016) Manu Setty et al.   NATURE BIOTECHNOLOGY

Diffusion pseudotime robustly reconstructs lineage branching

(2016) Laleh Haghverdi et al.   NATURE METHODS

Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis

(2016) Jean Fan et al.   NATURE METHODS

Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells

(2015) Florian Buettner et al.   NATURE BIOTECHNOLOGY

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

Spatially resolved, highly multiplexed RNA profiling in single cells

(2015) K. H. Chen et al.   SCIENCE

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Cell-Cycle Control of Developmentally Regulated Transcription Factors Accounts for Heterogeneity in Human Pluripotent Cells

(2014) Amar M. Singh et al.   Stem Cell Reports

Characterization of transcriptional networks in blood stem and progenitor cells using high-throughput single-cell gene expression analysis

(2013) Victoria Moignard et al.   NATURE CELL BIOLOGY

A novel approach for resolving differences in single-cell gene expression patterns from zygote to blastocyst

(2012) F. Buettner et al.   BIOINFORMATICS

Transcriptional regulation of α-cell differentiation

(2011) N. C. Bramswig et al.   DIABETES OBESITY & METABOLISM

Mechanisms of Asymmetric Stem Cell Division

(2008) Juergen A. Knoblich   CELL