LISA2: Learning Complex Single-Cell Trajectory and Expression Trends

Lineage tracing meets single-cell omics: opportunities and challenges

(2020) Daniel E. Wagner et al.   NATURE REVIEWS GENETICS

Pinpointing Cell Identity in Time and Space

(2020) Anca F. Savulescu et al.   Frontiers in Molecular Biosciences

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

(2019) Manu Setty et al.   NATURE BIOTECHNOLOGY

The single-cell transcriptional landscape of mammalian organogenesis

(2019) Junyue Cao et al.   NATURE

Single-Cell Proteomics Reveal that Quantitative Changes in Co-expressed Lineage-Specific Transcription Factors Determine Cell Fate

(2019) Carmen G. Palii et al.   Cell Stem Cell

PROSSTT: probabilistic simulation of single-cell RNA-seq data for complex differentiation processes

(2019) Nikolaos Papadopoulos et al.   BIOINFORMATICS

The accessible chromatin landscape of the murine hippocampus at single-cell resolution

(2019) John R. Sinnamon et al.   GENOME RESEARCH

Epigenetic evolution and lineage histories of chronic lymphocytic leukaemia

(2019) Federico Gaiti et al.   NATURE

A comparison of single-cell trajectory inference methods

(2019) Wouter Saelens et al.   NATURE BIOTECHNOLOGY

Transcription Factors Sp8 and Sp9 Regulate Medial Ganglionic Eminence-Derived Cortical Interneuron Migration

(2019) Guangxu Tao et al.   Frontiers in Molecular Neuroscience

Concepts and limitations for learning developmental trajectories from single cell genomics

(2019) Sophie Tritschler et al.   DEVELOPMENT

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

(2019) Urs Mayr et al.   DEVELOPMENT

Current best practices in single‐cell RNA‐seq analysis: a tutorial

(2019) Malte D Luecken et al.   Molecular Systems Biology

Beyond bulk: a review of single cell transcriptomics methodologies and applications

(2019) Ashwinikumar Kulkarni et al.   CURRENT OPINION IN BIOTECHNOLOGY

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

(2018) Kelly Street et al.   BMC GENOMICS

bigSCale: an analytical framework for big-scale single-cell data

(2018) Giovanni Iacono et al.   GENOME RESEARCH

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

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

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

(2018) Hannah Hochgerner et al.   NATURE NEUROSCIENCE

Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis

(2018) Jeffrey A. Farrell et al.   SCIENCE

The dynamics of gene expression in vertebrate embryogenesis at single-cell resolution

(2018) James A. Briggs et al.   SCIENCE

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

(2018) Daniel E. Wagner et al.   SCIENCE

Reconstruction of complex single-cell trajectories using CellRouter

(2018) Edroaldo Lummertz da Rocha 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

DensityPath: an algorithm to visualize and reconstruct cell state-transition path on density landscape for single-cell RNA sequencing data

(2018) Ziwei Chen et al.   BIOINFORMATICS

Integrative single-cell analysis of transcriptome, DNA methylome and chromatin accessibility in mouse oocytes

(2018) Chan Gu et al.   CELL RESEARCH

Single-cell multiomics sequencing and analyses of human colorectal cancer

(2018) Shuhui Bian et al.   SCIENCE

chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data

(2017) Alicia N Schep et al.   NATURE METHODS

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

Simultaneous measurement of chromatin accessibility, DNA methylation, and nucleosome phasing in single cells

(2017) Sebastian Pott   eLife

De Novo Prediction of Stem Cell Identity using Single-Cell Transcriptome Data

(2016) Dominic Grün et al.   Cell Stem Cell

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

(2016) Zhicheng Ji et al.   NUCLEIC ACIDS RESEARCH

Molecular Identity of Human Outer Radial Glia during Cortical Development

(2015) Alex A. Pollen et al.   CELL

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state

(2015) Assaf Rotem et al.   NATURE BIOTECHNOLOGY

Lung regeneration: mechanisms, applications and emerging stem cell populations

(2014) Darrell N Kotton et al.   NATURE MEDICINE

Principal trend analysis for time-course data with applications in genomic medicine

(2013) Yuping Zhang et al.   Annals of Applied Statistics

The habenula: from stress evasion to value-based decision-making

(2010) Okihide Hikosaka   NATURE REVIEWS NEUROSCIENCE

A Novel Role for Dbx1-Derived Cajal-Retzius Cells in Early Regionalization of the Cerebral Cortical Neuroepithelium

(2010) Amélie Griveau et al.   PLOS BIOLOGY

Fast unfolding of communities in large networks

(2008) Vincent D Blondel et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT