Computational methods for single-cell omics across modalities

Lineage Tracing in Humans Enabled by Mitochondrial Mutations and Single-Cell Genomics

(2019) Leif S. Ludwig et al.   CELL

Profiling of Pluripotency Factors in Single Cells and Early Embryos

(2019) Sarah J. Hainer et al.   CELL

Single-cell lineage tracing by endogenous mutations enriched in transposase accessible mitochondrial DNA

(2019) Jin Xu et al.   eLife

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Single-Cell Multi-omic Integration Compares and Contrasts Features of Brain Cell Identity

(2019) Joshua D. Welch et al.   CELL

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

(2019) Urs Mayr et al.   DEVELOPMENT

OUP accepted manuscript

(2018)   BIOINFORMATICS

Single-Cell Transcriptomics Meets Lineage Tracing

(2018) Lennart Kester et al.   Cell Stem Cell

Transcript-indexed ATAC-seq for precision immune profiling

(2018) Ansuman T. Satpathy et al.   NATURE MEDICINE

Single-Cell Multi-omics: An Engine for New Quantitative Models of Gene Regulation

(2018) Jonathan Packer et al.   TRENDS IN GENETICS

Single-cell spatial reconstruction reveals global division of labour in the mammalian liver

(2017) Keren Bahar Halpern et al.   NATURE

Multiplexed quantification of proteins and transcripts in single cells

(2017) Vanessa M Peterson et al.   NATURE BIOTECHNOLOGY

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

TheDrosophilaembryo at single-cell transcriptome resolution

(2017) Nikos Karaiskos et al.   SCIENCE

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin

(2015) Kaia Achim et al.   NATURE BIOTECHNOLOGY

Conditional density-based analysis of T cell signaling in single-cell data

(2014) S. Krishnaswamy et al.   SCIENCE