New avenues for systematically inferring cell-cell communication: through single-cell transcriptomics data

Single-cell multimodal omics: the power of many

(2020) Chenxu Zhu et al.   NATURE METHODS

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

(2020) Mirjana Efremova et al.   Nature Protocols

N 6 ‐methyladenosine Reader Protein Ythdc2 Suppresses Liver Steatosis via Regulation of mRNA Stability of Lipogenic Genes

(2020) Bing Zhou et al.   HEPATOLOGY

Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage

(2019) Dvir Aran et al.   NATURE IMMUNOLOGY

A miRNA-HERC4 pathway promotes breast tumorigenesis by inactivating tumor suppressor LATS1

(2019) Youqin Xu et al.   Protein & Cell

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

(2019) Samuel G. Rodriques et al.   SCIENCE

Cell lineage and communication network inference via optimization for single-cell transcriptomics

(2019) Shuxiong Wang et al.   NUCLEIC ACIDS RESEARCH

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

Neutrophils escort circulating tumour cells to enable cell cycle progression

(2019) Barbara Maria Szczerba et al.   NATURE

Dissecting the transcriptome landscape of the human fetal neural retina and retinal pigment epithelium by single-cell RNA-seq analysis

(2019) Yuqiong Hu et al.   PLOS BIOLOGY

Single-Cell Analysis of Crohn’s Disease Lesions Identifies a Pathogenic Cellular Module Associated with Resistance to Anti-TNF Therapy

(2019) Jerome C. Martin et al.   CELL

Landscape of Intercellular Crosstalk in Healthy and NASH Liver Revealed by Single-Cell Secretome Gene Analysis

(2019) Xuelian Xiong et al.   MOLECULAR CELL

A dream of single-cell proteomics

(2019) Vivien Marx   NATURE METHODS

Copy number variation is highly correlated with differential gene expression: a pan-cancer study

(2019) Xin Shao et al.   BMC Medical Genetics

Gene expression cartography

(2019) Mor Nitzan et al.   NATURE

Single-cell immune landscape of human atherosclerotic plaques

(2019) Dawn M. Fernandez et al.   NATURE MEDICINE

Single cell analysis reveals immune cell–adipocyte crosstalk regulating the transcription of thermogenic adipocytes

(2019) Prashant Rajbhandari et al.   eLife

Prediction of Adverse Drug Reactions by Combining Biomedical Tripartite Network and Graph Representation Model

(2019) Rui Xue et al.   CHEMICAL RESEARCH IN TOXICOLOGY

Single-Cell Mass Spectrometry Approaches to Explore Cellular Heterogeneity

(2018) Linwen Zhang et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Recent advances in microfluidic technologies for cell-to-cell interaction studies

(2018) Mario Rothbauer et al.   LAB ON A CHIP

Hormone-dependent medial preoptic/lumbar spinal cord/autonomic coordination supporting male sexual behaviors

(2018) Donald W. Pfaff et al.   MOLECULAR AND CELLULAR ENDOCRINOLOGY

Tracing the temporal-spatial transcriptome landscapes of the human fetal digestive tract using single-cell RNA-sequencing

(2018) Shuai Gao et al.   NATURE CELL BIOLOGY

scmap: projection of single-cell RNA-seq data across data sets

(2018) Vladimir Yu Kiselev et al.   NATURE METHODS

Mapping the physical network of cellular interactions

(2018) Jean-Charles Boisset et al.   NATURE METHODS

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

(2018) Xiao Wang et al.   SCIENCE

Single-Cell Transcriptional Profiling Reveals Cellular Diversity and Intercommunication in the Mouse Heart

(2018) Daniel A. Skelly et al.   Cell Reports

TMEM43-S358L mutation enhances NF-κB-TGFβ signal cascade in arrhythmogenic right ventricular dysplasia/cardiomyopathy

(2018) Guoxing Zheng et al.   Protein & Cell

Sensory Neuron Diversity in the Inner Ear Is Shaped by Activity

(2018) Brikha R. Shrestha et al.   CELL

Network pharmacology study reveals energy metabolism and apoptosis pathways-mediated cardioprotective effects of Shenqi Fuzheng

(2018) Jie Liao et al.   JOURNAL OF ETHNOPHARMACOLOGY

PDGFRβ Cells Rapidly Relay Inflammatory Signal from the Circulatory System to Neurons via Chemokine CCL2

(2018) Lihui Duan et al.   NEURON

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

Joint profiling of chromatin accessibility and gene expression in thousands of single cells

(2018) Junyue Cao et al.   SCIENCE

Tissue Unit-ed: Lung Cells Team up to Drive Alveolar Macrophage Development

(2018) Charlotte L. Scott et al.   CELL

Lung Single-Cell Signaling Interaction Map Reveals Basophil Role in Macrophage Imprinting

(2018) Merav Cohen et al.   CELL

Transcriptome Landscape of Human Folliculogenesis Reveals Oocyte and Granulosa Cell Interactions

(2018) Yaoyao Zhang et al.   MOLECULAR CELL

Single-cell reconstruction of the early maternal–fetal interface in humans

(2018) Roser Vento-Tormo et al.   NATURE

Proteomics goes parallel

(2018) Ben C Collins et al.   NATURE BIOTECHNOLOGY

Highly parallel single-molecule identification of proteins in zeptomole-scale mixtures

(2018) Jagannath Swaminathan et al.   NATURE BIOTECHNOLOGY

Analysis of Single-Cell RNA-Seq Identifies Cell-Cell Communication Associated with Tumor Characteristics

(2018) Manu P. Kumar et al.   Cell Reports

Multilineage communication regulates human liver bud development from pluripotency

(2017) J. Gray Camp et al.   NATURE

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

Unraveling cell-to-cell signaling networks with chemical biology

(2017) Zev J Gartner et al.   Nature Chemical Biology

Simultaneous epitope and transcriptome measurement in single cells

(2017) Marlon Stoeckius et al.   NATURE METHODS

Sequencing thousands of single-cell genomes with combinatorial indexing

(2017) Sarah A Vitak et al.   NATURE METHODS

Comprehensive single-cell transcriptional profiling of a multicellular organism

(2017) Junyue Cao et al.   SCIENCE

Massively parallel digital transcriptional profiling of single cells

(2017) Grace X. Y. Zheng et al.   Nature Communications

A single-cell resolution map of mouse hematopoietic stem and progenitor cell differentiation

(2016) S. Nestorowa et al.   BLOOD

Single-cell multimodal profiling reveals cellular epigenetic heterogeneity

(2016) Lih Feng Cheow et al.   NATURE METHODS

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

(2016) I. Tirosh et al.   SCIENCE

Exploring the interaction between Salvia miltiorrhiza and human serum albumin: Insights from herb–drug interaction reports, computational analysis and experimental studies

(2016) Xin Shao et al.   SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY

Cell communication across gap junctions: a historical perspective and current developments

(2015) W. Howard Evans   BIOCHEMICAL SOCIETY TRANSACTIONS

Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells

(2015) Allon M. Klein et al.   CELL

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

Single-cell messenger RNA sequencing reveals rare intestinal cell types

(2015) Dominic Grün et al.   NATURE

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

A draft network of ligand–receptor-mediated multicellular signalling in human

(2015) Jordan A. Ramilowski et al.   Nature Communications

Single-cell RNA-Seq resolves cellular complexity in sensory organs from the neonatal inner ear

(2015) Joseph C. Burns et al.   Nature Communications

Single-cell RNA-seq reveals dynamic paracrine control of cellular variation

(2014) Alex K. Shalek et al.   NATURE

Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types

(2014) D. A. Jaitin et al.   SCIENCE

The osteogenic differentiation of mesenchymal stem cells by controlled cell-cell interaction on micropatterned surfaces

(2013) Xinlong Wang et al.   JOURNAL OF BIOMEDICAL MATERIALS RESEARCH PART A

Macrophages support pathological erythropoiesis in polycythemia vera and β-thalassemia

(2013) Pedro Ramos et al.   NATURE MEDICINE

Smart-seq2 for sensitive full-length transcriptome profiling in single cells

(2013) Simone Picelli et al.   NATURE METHODS

Insights into the regulation of protein abundance from proteomic and transcriptomic analyses

(2012) Christine Vogel et al.   NATURE REVIEWS GENETICS

CEL-Seq: Single-Cell RNA-Seq by Multiplexed Linear Amplification

(2012) Tamar Hashimshony et al.   Cell Reports

Mass Cytometry: Technique for Real Time Single Cell Multitarget Immunoassay Based on Inductively Coupled Plasma Time-of-Flight Mass Spectrometry

(2009) Dmitry R. Bandura et al.   ANALYTICAL CHEMISTRY

Cell–cell interaction networks regulate blood stem and progenitor cell fate

(2009) Daniel C Kirouac et al.   Molecular Systems Biology