Deep generative modeling of transcriptional dynamics for RNA velocity analysis in single cells

Unsupervised removal of systematic background noise from droplet-based single-cell experiments using CellBender

(2023) Stephen J. Fleming et al.   NATURE METHODS

A Python library for probabilistic analysis of single-cell omics data

(2022) Adam Gayoso et al.   NATURE BIOTECHNOLOGY

CellRank for directed single-cell fate mapping

(2022) Marius Lange et al.   NATURE METHODS

Alevin-fry unlocks rapid, accurate and memory-frugal quantification of single-cell RNA-seq data

(2022) Dongze He et al.   NATURE METHODS

High-throughput total RNA sequencing in single cells using VASA-seq

(2022) Fredrik Salmen et al.   NATURE BIOTECHNOLOGY

RNA velocity unraveled

(2022) Gennady Gorin et al.   PLoS Computational Biology

Towards reliable quantification of cell state velocities

(2022) Valérie Marot-Lassauzaie et al.   PLoS Computational Biology

Preprocessing choices affect RNA velocity results for droplet scRNA-seq data

(2021) Charlotte Soneson et al.   PLoS Computational Biology

Spatiotemporal dissection of the cell cycle with single-cell proteogenomics

(2021) Diana Mahdessian et al.   NATURE

Joint probabilistic modeling of single-cell multi-omic data with totalVI

(2021) Adam Gayoso et al.   NATURE METHODS

Modular, efficient and constant-memory single-cell RNA-seq preprocessing

(2021) Páll Melsted et al.   NATURE BIOTECHNOLOGY

Simultaneous trimodal single-cell measurement of transcripts, epitopes, and chromatin accessibility using TEA-seq

(2021) Elliott Swanson et al.   eLife

VeloViz: RNA velocity informed embeddings for visualizing cellular trajectories

(2021) Lyla Atta et al.   BIOINFORMATICS

RNA velocity—current challenges and future perspectives

(2021) Volker Bergen et al.   Molecular Systems Biology

Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells

(2021) Eleni P. Mimitou et al.   NATURE BIOTECHNOLOGY

Sequencing metabolically labeled transcripts in single cells reveals mRNA turnover strategies

(2020) Nico Battich et al.   SCIENCE

Generalizing RNA velocity to transient cell states through dynamical modeling

(2020) Volker Bergen et al.   NATURE BIOTECHNOLOGY

Enhancing scientific discoveries in molecular biology with deep generative models

(2020) Romain Lopez et al.   Molecular Systems Biology

Conditional out-of-distribution generation for unpaired data using transfer VAE

(2020) Mohammad Lotfollahi et al.   BIOINFORMATICS

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

(2019) Manu Setty et al.   NATURE BIOTECHNOLOGY

The barcode, UMI, set format and BUStools

(2019) Páll Melsted et al.   BIOINFORMATICS

Single-Cell RNA-Seq Analysis of Retinal Development Identifies NFI Factors as Regulating Mitotic Exit and Late-Born Cell Specification

(2019) Brian S. Clark et al.   NEURON

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Comprehensive single cell mRNA profiling reveals a detailed roadmap for pancreatic endocrinogenesis

(2019) Aimée Bastidas-Ponce et al.   DEVELOPMENT

scGen predicts single-cell perturbation responses

(2019) Mohammad Lotfollahi et al.   NATURE METHODS

Single-cell transcriptional logic of cell-fate specification and axon guidance in early-born retinal neurons

(2019) Quentin Lo Giudice et al.   DEVELOPMENT

Single-cell transcriptomic profiling of the aging mouse brain

(2019) Methodios Ximerakis et al.   NATURE NEUROSCIENCE

Cell type-specific transcriptional programs in mouse prefrontal cortex during adolescence and addiction

(2019) Aritra Bhattacherjee et al.   Nature Communications

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

(2018) Kelly Street et al.   BMC GENOMICS

Integrated Single-Cell Analysis Maps the Continuous Regulatory Landscape of Human Hematopoietic Differentiation

(2018) Jason D. Buenrostro et al.   CELL

Conserved properties of dentate gyrus neurogenesis across postnatal development revealed by single-cell RNA sequencing

(2018) Hannah Hochgerner et al.   NATURE NEUROSCIENCE

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

The Mammalian Spermatogenesis Single-Cell Transcriptome, from Spermatogonial Stem Cells to Spermatids

(2018) Brian P. Hermann et al.   Cell Reports

Variational Inference: A Review for Statisticians

(2017) David M. Blei et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

Scaling single-cell genomics from phenomenology to mechanism

(2017) Amos Tanay et al.   NATURE

Revealing the vectors of cellular identity with single-cell genomics

(2016) Allon Wagner et al.   NATURE BIOTECHNOLOGY

Diffusion pseudotime robustly reconstructs lineage branching

(2016) Laleh Haghverdi et al.   NATURE METHODS

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

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Coupled pre-mRNA and mRNA dynamics unveil operational strategies underlying transcriptional responses to stimuli

(2011) A. Zeisel et al.   Molecular Systems Biology