4.8 Article

Inference of cell state transitions and cell fate plasticity from single-cell with MARGARET

Related references

Note: Only part of the references are listed.
Letter Biotechnology & Applied Microbiology

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

Adam Gayoso et al.

NATURE BIOTECHNOLOGY (2022)

Article Biochemistry & Molecular Biology

Spatiotemporal analysis of human intestinal development at single-cell resolution

David Fawkner-Corbett et al.

Summary: This study uses single-cell RNA sequencing and spatial transcriptomics to investigate human intestinal development, identifying various cell states, developmental programs, and differentiation hierarchies. It provides insights into the formation of different cell types in the gut and offers valuable resources for further research in this field.
Article Multidisciplinary Sciences

Generalized and scalable trajectory inference in single-cell omics data with VIA

Shobana Stassen et al.

Summary: Scalable trajectory inference for multi-omic single cell datasets is challenging due to the complexity of topologies. The VIA method presented in this study overcomes these limitations by using lazy-teleporting random walks to accurately reconstruct complex cellular trajectories.

NATURE COMMUNICATIONS (2021)

Article Biochemical Research Methods

PARC: ultrafast and accurate clustering of phenotypic data of millions of single cells

Shobana V. Stassen et al.

BIOINFORMATICS (2020)

Article Multidisciplinary Sciences

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

Hamim Zafar et al.

NATURE COMMUNICATIONS (2020)

Article Multidisciplinary Sciences

The single-cell transcriptional landscape of mammalian organogenesis

Junyue Cao et al.

NATURE (2019)

Article Multidisciplinary Sciences

Colonic epithelial cell diversity in health and inflammatory bowel disease

Kaushal Parikh et al.

NATURE (2019)

Article Biotechnology & Applied Microbiology

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

Manu Setty et al.

NATURE BIOTECHNOLOGY (2019)

Article Biotechnology & Applied Microbiology

A comparison of single-cell trajectory inference methods

Wouter Saelens et al.

NATURE BIOTECHNOLOGY (2019)

Article Biochemistry & Molecular Biology

g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update)

Uku Raudvere et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Multidisciplinary Sciences

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

Huidong Chen et al.

NATURE COMMUNICATIONS (2019)

Article Multidisciplinary Sciences

A comprehensive single cell transcriptional landscape of human hematopoietic progenitors

Danilo Pellin et al.

NATURE COMMUNICATIONS (2019)

Article Biochemistry & Molecular Biology

Transcriptional Basis of Mouse and Human Dendritic Cell Heterogeneity

Chrysothemis C. Brown et al.

Article Multidisciplinary Sciences

The human body at cellular resolution: the NIH Human Biomolecular Atlas Program

Michael P. Snyder et al.

NATURE (2019)

Article Biotechnology & Applied Microbiology

Visualizing structure and transitions in high-dimensional biological data

Kevin R. Moon et al.

NATURE BIOTECHNOLOGY (2019)

Article Multidisciplinary Sciences

From Louvain to Leiden: guaranteeing well-connected communities

V. A. Traag et al.

SCIENTIFIC REPORTS (2019)

Article Biotechnology & Applied Microbiology

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

Kelly Street et al.

BMC GENOMICS (2018)

Article Biochemistry & Molecular Biology

Recovering Gene Interactions from Single-Cell Data Using Data Diffusion

David van Dijk et al.

Article Biochemistry & Molecular Biology

Mapping the Mouse Cell Atlas by Microwell-Seq

Xiaoping Han et al.

Review Immunology

Human dendritic cell subsets: an update

Matthew Collin et al.

IMMUNOLOGY (2018)

Article Multidisciplinary Sciences

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

Daniel E. Wagner et al.

SCIENCE (2018)

Article Multidisciplinary Sciences

Population snapshots predict early haematopoietic and erythroid hierarchies

Betsabeh Khoramian Tusi et al.

NATURE (2018)

Article Multidisciplinary Sciences

Screening for genes that regulate the differentiation of human megakaryocytic lineage cells

Fangfang Zhu et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)

Article Biochemical Research Methods

Deep generative modeling for single-cell transcriptomics

Romain Lopez et al.

NATURE METHODS (2018)

Article Biotechnology & Applied Microbiology

SCANPY: large-scale single-cell gene expression data analysis

F. Alexander Wolf et al.

GENOME BIOLOGY (2018)

Article Neurosciences

LHX2 Interacts with the NuRD Complex and Regulates Cortical Neuron Subtype Determinants Fezf2 and Sox11

Bhavana Muralidharan et al.

JOURNAL OF NEUROSCIENCE (2017)

Review Multidisciplinary Sciences

Scaling single-cell genomics from phenomenology to mechanism

Amos Tanay et al.

NATURE (2017)

Article Multidisciplinary Sciences

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

Keren Bahar Halpern et al.

NATURE (2017)

Article Multidisciplinary Sciences

Massively parallel digital transcriptional profiling of single cells

Grace X. Y. Zheng et al.

NATURE COMMUNICATIONS (2017)

Article Biology

The Human Cell Atlas

Aviv Regev et al.

ELIFE (2017)

Article Biotechnology & Applied Microbiology

SiFit: inferring tumor trees from single-cell sequencing data under finite-sites models

Hamim Zafar et al.

GENOME BIOLOGY (2017)

Article Biotechnology & Applied Microbiology

Wishbone identifies bifurcating developmental trajectories from single-cell data

Manu Setty et al.

NATURE BIOTECHNOLOGY (2016)

Review Neurosciences

Disentangling neural cell diversity using single-cell transcriptomics

Jean-Francois Poulin et al.

NATURE NEUROSCIENCE (2016)

Article Multidisciplinary Sciences

Oligodendrocyte heterogeneity in the mouse juvenile and adult central nervous system

Sueli Marques et al.

SCIENCE (2016)

Article Biochemistry & Molecular Biology

Transcriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors

Franziska Paul et al.

Article Biochemistry & Molecular Biology

MYB controls erythroid versus megakaryocyte lineage fate decision through the miR-486-3p-mediated downregulation of MAF

E. Bianchi et al.

CELL DEATH AND DIFFERENTIATION (2015)

Review Immunology

New developments in goblet cell mucus secretion and function

G. M. H. Birchenough et al.

MUCOSAL IMMUNOLOGY (2015)

Article Biotechnology & Applied Microbiology

Spatial reconstruction of single-cell gene expression data

Rahul Satija et al.

NATURE BIOTECHNOLOGY (2015)

Review Cell & Tissue Engineering

Quantitative Single-Cell Approaches to Stem Cell Research

Martin Etzrodt et al.

CELL STEM CELL (2014)

Review Immunology

Plasmacytoid Dendritic Cells: Recent Progress and Open Questions

Boris Reizis et al.

ANNUAL REVIEW OF IMMUNOLOGY, VOL 29 (2011)

Review Hematology

The multifunctional role of EKLF/KLF1 during erythropoiesis

Miroslawa Siatecka et al.

BLOOD (2011)

Article Multidisciplinary Sciences

The two mucus layers of colon are organized by the MUC2 mucin, whereas the outer layer is a legislator of host-microbial interactions

Malin E. V. Johansson et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

Article Physics, Multidisciplinary

Link prediction based on local random walk

Weiping Liu et al.

Review Biochemistry & Molecular Biology

Hematopoiesis: An evolving paradigm for stem cell biology

Stuart H. Orkin et al.

Article Biochemistry & Molecular Biology

CLEC9A is a novel activation C-type lectin-like receptor expressed on BDCA3+ dendritic cells and a subset of monocytes

Cristal Huysamen et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2008)

Review Cell Biology

Nanog and transcriptional networks in embryonic stem cell pluripotency

Guangjin Pan et al.

CELL RESEARCH (2007)

Article Developmental Biology

A direct role for Sox10 in specification of neural crest-derived sensory neurons

Thomas J. Carney et al.

DEVELOPMENT (2006)

Article Nutrition & Dietetics

Aquaporin-8 is involved in water transport in isolated superficial colonocytes from rat proximal colon

Umberto Laforenza et al.

JOURNAL OF NUTRITION (2005)

Review Biochemistry & Molecular Biology

GATA1 function, a paradigm for transcription factors in hematopoiesis

R Ferreira et al.

MOLECULAR AND CELLULAR BIOLOGY (2005)

Article Developmental Biology

Neural crest development is regulated by the transcription factor Sox9

M Cheung et al.

DEVELOPMENT (2003)

Article Physics, Fluids & Plasmas

Evolutionary reconstruction of networks

M Ipsen et al.

PHYSICAL REVIEW E (2002)

Article Biochemistry & Molecular Biology

E2F repression by C/EBPα is required for adipogenesis and granulopoiesis in vivo

BT Porse et al.

Article Multidisciplinary Sciences

A global geometric framework for nonlinear dimensionality reduction

JB Tenenbaum et al.

SCIENCE (2000)

Article Multidisciplinary Sciences

A clonogenic common myeloid progenitor that gives rise to all myeloid lineages

K Akashi et al.

NATURE (2000)