Temporal modelling using single-cell transcriptomics

Single-cell lineages reveal the rates, routes, and drivers of metastasis in cancer xenografts

(2021) Jeffrey J. Quinn et al.   SCIENCE

Optimal marker gene selection for cell type discrimination in single cell analyses

(2021) Bianca Dumitrascu et al.   Nature Communications

LineageOT is a unified framework for lineage tracing and trajectory inference

(2021) Aden Forrow et al.   Nature Communications

Reconstructed Single-Cell Fate Trajectories Define Lineage Plasticity Windows during Differentiation of Human PSC-Derived Distal Lung Progenitors

(2020) Killian Hurley et al.   Cell Stem Cell

CellPhoneDB: inferring cell–cell communication from combined expression of multi-subunit ligand–receptor complexes

(2020) Mirjana Efremova et al.   Nature Protocols

Lineage tracing on transcriptional landscapes links state to fate during differentiation

(2020) Caleb Weinreb et al.   SCIENCE

Determining sequencing depth in a single-cell RNA-seq experiment

(2020) Martin Jinye Zhang et al.   Nature Communications

Inferring TF activation order in time series scRNA-Seq studies

(2020) Chieh Lin et al.   PLoS Computational Biology

The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution

(2020) Orit Rozenblatt-Rosen et al.   CELL

An Engineered CRISPR-Cas9 Mouse Line for Simultaneous Readout of Lineage Histories and Gene Expression Profiles in Single Cells

(2020) Sarah Bowling et al.   CELL

Time course regulatory analysis based on paired expression and chromatin accessibility data

(2020) Zhana Duren et al.   GENOME RESEARCH

Sci-fate characterizes the dynamics of gene expression in single cells

(2020) Junyue Cao et al.   NATURE BIOTECHNOLOGY

Predicting cell lineages using autoencoders and optimal transport

(2020) Karren Dai Yang et al.   PLoS Computational Biology

Seamless integration of image and molecular analysis for spatial transcriptomics workflows

(2020) Joseph Bergenstråhle et al.   BMC GENOMICS

Generalizing RNA velocity to transient cell states through dynamical modeling

(2020) Volker Bergen et al.   NATURE BIOTECHNOLOGY

Single-cell lineage tracing by integrating CRISPR-Cas9 mutations with transcriptomic data

(2020) Hamim Zafar et al.   Nature Communications

A comprehensive survey of regulatory network inference methods using single cell RNA sequencing data

(2020) Hung Nguyen et al.   BRIEFINGS IN BIOINFORMATICS

Massively parallel and time-resolved RNA sequencing in single cells with scNT-seq

(2020) Qi Qiu et al.   NATURE METHODS

A Single-Cell Transcriptomic Atlas of Human Skin Aging

(2020) Zhiran Zou et al.   DEVELOPMENTAL CELL

Lineage tracing using a Cas9-deaminase barcoding system targeting endogenous L1 elements

(2019) Byungjin Hwang et al.   Nature Communications

Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution

(2019) Samuel G. Rodriques et al.   SCIENCE

Integrative single-cell analysis

(2019) Tim Stuart et al.   NATURE REVIEWS GENETICS

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

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

The single-cell transcriptional landscape of mammalian organogenesis

(2019) Junyue Cao et al.   NATURE

Single cell transcriptomics reveals spatial and temporal dynamics of gene expression in the developing mouse spinal cord

(2019) Julien Delile et al.   DEVELOPMENT

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

(2019) Geoffrey Schiebinger et al.   CELL

Identification of Enteroendocrine Regulators by Real-Time Single-Cell Differentiation Mapping

(2019) Helmuth Gehart et al.   CELL

The Human Lung Cell Atlas - A high-resolution reference map of the human lung in health and disease

(2019) Herbert B Schiller et al.   AMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY

Continuous-state HMMs for modeling time-series single-cell RNA-Seq data

(2019) Chieh Lin et al.   BIOINFORMATICS

Single-cell virus sequencing of influenza infections that trigger innate immunity

(2019) Alistair B. Russell et al.   JOURNAL OF VIROLOGY

Molecular recording of mammalian embryogenesis

(2019) Michelle M. Chan et al.   NATURE

A comparison of single-cell trajectory inference methods

(2019) Wouter Saelens et al.   NATURE BIOTECHNOLOGY

Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis

(2019) Silas Maniatis et al.   SCIENCE

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Concepts and limitations for learning developmental trajectories from single cell genomics

(2019) Sophie Tritschler et al.   DEVELOPMENT

Understanding the kidney one cell at a time

(2019) Jihwan Park et al.   KIDNEY INTERNATIONAL

scSLAM-seq reveals core features of transcription dynamics in single cells

(2019) Florian Erhard et al.   NATURE

Single-cell trajectories reconstruction, exploration and mapping of omics data with STREAM

(2019) Huidong Chen et al.   Nature Communications

NASC-seq monitors RNA synthesis in single cells

(2019) Gert-Jan Hendriks et al.   Nature Communications

Epigenomics and Single-cell Sequencing Define a Developmental Hierarchy in Langerhans Cell Histiocytosis

(2019) Florian Halbritter et al.   Cancer Discovery

Integrating multi-omics longitudinal data to reconstruct networks underlying lung development

(2019) Jun Ding et al.   AMERICAN JOURNAL OF PHYSIOLOGY-LUNG CELLULAR AND MOLECULAR PHYSIOLOGY

SCOPIT: sample size calculations for single-cell sequencing experiments

(2019) Alexander Davis et al.   BMC BIOINFORMATICS

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

(2018) Kelly Street et al.   BMC GENOMICS

SLAM-ITseq: sequencing cell type-specific transcriptomes without cell sorting

(2018) Wayo Matsushima et al.   DEVELOPMENT

Reconstructing differentiation networks and their regulation from time series single-cell expression data

(2018) Jun Ding et al.   GENOME RESEARCH

Whole-organism clone tracing using single-cell sequencing

(2018) Anna Alemany et al.   NATURE

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

TimeLapse-seq: adding a temporal dimension to RNA sequencing through nucleoside recoding

(2018) Jeremy A Schofield et al.   NATURE METHODS

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

(2018) Xiao Wang et al.   SCIENCE

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

(2018) Daniel E. Wagner et al.   SCIENCE

Uncovering pseudotemporal trajectories with covariates from single cell and bulk expression data

(2018) Kieran R Campbell et al.   Nature Communications

iDREM: Interactive visualization of dynamic regulatory networks

(2018) Jun Ding et al.   PLoS Computational Biology

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

Lineage dynamics of murine pancreatic development at single-cell resolution

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

Single-Cell Transcriptomic Analysis of Cardiac Differentiation from Human PSCs Reveals HOPX-Dependent Cardiomyocyte Maturation

(2018) Clayton E. Friedman et al.   Cell Stem Cell

Expanding the Nucleoside Recoding Toolkit: Revealing RNA Population Dynamics with 6-Thioguanosine

(2018) Lea Kiefer et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris

(2018) et al.   NATURE

Dimensionality reduction for visualizing single-cell data using UMAP

(2018) Etienne Becht et al.   NATURE BIOTECHNOLOGY

Spatial organization of the somatosensory cortex revealed by osmFISH

(2018) Simone Codeluppi et al.   NATURE METHODS

Spatiotemporal transcriptomic divergence across human and macaque brain development

(2018) Ying Zhu et al.   SCIENCE

A web server for comparative analysis of single-cell RNA-seq data

(2018) Amir Alavi et al.   Nature Communications

Assessing the reliability of spike-in normalization for analyses of single-cell RNA sequencing data

(2017) Aaron T.L. Lun et al.   GENOME RESEARCH

Multiplexed droplet single-cell RNA-sequencing using natural genetic variation

(2017) Hyun Min Kang et al.   NATURE BIOTECHNOLOGY

Thiol-linked alkylation of RNA to assess expression dynamics

(2017) Veronika A Herzog et al.   NATURE METHODS

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

Using neural networks for reducing the dimensions of single-cell RNA-Seq data

(2017) Chieh Lin et al.   NUCLEIC ACIDS RESEARCH

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

Single-cell analysis resolves the cell state transition and signaling dynamics associated with melanoma drug-induced resistance

(2017) Yapeng Su et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications

(2017) Ashraful Haque et al.   Genome Medicine

Single-cell RNA sequencing reveals intrinsic and extrinsic regulatory heterogeneity in yeast responding to stress

(2017) Audrey P. Gasch et al.   PLOS BIOLOGY

Selecting the most appropriate time points to profile in high-throughput studies

(2017) Michael Kleyman et al.   eLife

Dissecting direct reprogramming from fibroblast to neuron using single-cell RNA-seq

(2016) Barbara Treutlein et al.   NATURE

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

(2016) Sheel Shah et al.   NEURON

TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis

(2016) Zhicheng Ji et al.   NUCLEIC ACIDS RESEARCH

Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction

(2016) Florian Schmidt et al.   NUCLEIC ACIDS RESEARCH

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

Whole-organism lineage tracing by combinatorial and cumulative genome editing

(2016) Aaron McKenna et al.   SCIENCE

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Spatially resolved, highly multiplexed RNA profiling in single cells

(2015) K. H. Chen et al.   SCIENCE

Single-Cell Trajectory Detection Uncovers Progression and Regulatory Coordination in Human B Cell Development

(2014) Sean C. Bendall et al.   CELL

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

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape

(2014) Eugenio Marco et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Linking the signaling cascades and dynamic regulatory networks controlling stress responses

(2012) A. Gitter et al.   GENOME RESEARCH

Studying and modelling dynamic biological processes using time-series gene expression data

(2012) Ziv Bar-Joseph et al.   NATURE REVIEWS GENETICS

Colon Stem Cell and Crypt Dynamics Exposed by Cell Lineage Reconstruction

(2011) Yitzhak Reizel et al.   PLoS Genetics