Single‐Cell Multi‐Omics and Its Prospective Application in Cancer Biology

Single-cell microRNA-mRNA co-sequencing reveals non-genetic heterogeneity and mechanisms of microRNA regulation

(2019) Nayi Wang et al.   Nature Communications

Machine Learning and Integrative Analysis of Biomedical Big Data

(2019) Bilal Mirza et al.   Genes

Unravelling Intratumoral Heterogeneity through High-Sensitivity Single-Cell Mutational Analysis and Parallel RNA Sequencing

(2019) Alba Rodriguez-Meira et al.   MOLECULAR CELL

Single-Cell RNA-Seq Reveals AML Hierarchies Relevant to Disease Progression and Immunity

(2019) Peter van Galen et al.   CELL

Spontaneous driving forces give rise to protein−RNA condensates with coexisting phases and complex material properties

(2019) Steven Boeynaems et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Somatic mutations and cell identity linked by Genotyping of Transcriptomes

(2019) Anna S. Nam et al.   NATURE

Simultaneous quantification of protein–DNA contacts and transcriptomes in single cells

(2019) Koos Rooijers et al.   NATURE BIOTECHNOLOGY

Subclonal cooperation drives metastasis by modulating local and systemic immune microenvironments

(2019) Michalina Janiszewska et al.   NATURE CELL BIOLOGY

High-throughput single-cell ChIP-seq identifies heterogeneity of chromatin states in breast cancer

(2019) Kevin Grosselin et al.   NATURE GENETICS

Single-cell Analysis of CAR-T Cell Activation Reveals A Mixed TH1/TH2 Response Independent of Differentiation

(2019) Iva Xhangolli et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

A dream of single-cell proteomics

(2019) Vivien Marx   NATURE METHODS

High-throughput sequencing of the transcriptome and chromatin accessibility in the same cell

(2019) Song Chen et al.   NATURE BIOTECHNOLOGY

Single-cell profiling guided combinatorial immunotherapy for fast-evolving CDK4/6 inhibitor-resistant HER2-positive breast cancer

(2019) Qingfei Wang et al.   Nature Communications

Combined single-cell and spatial transcriptomics reveal the molecular, cellular and spatial bone marrow niche organization

(2019) Chiara Baccin et al.   NATURE CELL BIOLOGY

Multi‐Omics Factor Analysis—a framework for unsupervised integration of multi‐omics data sets

(2018) Ricard Argelaguet et al.   Molecular Systems Biology

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors

(2018) Laleh Haghverdi et al.   NATURE BIOTECHNOLOGY

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

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

High-dimensional single-cell analysis predicts response to anti-PD-1 immunotherapy

(2018) Carsten Krieg et al.   NATURE MEDICINE

scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells

(2018) Stephen J. Clark et al.   Nature Communications

Overcoming Ovarian Cancer Drug Resistance with a Cold Responsive Nanomaterial

(2018) Hai Wang et al.   ACS Central Science

Integrated measurement of intracellular proteins and transcripts in single cells

(2018) Alexander M. Xu et al.   LAB ON A CHIP

Intra-tumour diversification in colorectal cancer at the single-cell level

(2018) Sophie F. Roerink et al.   NATURE

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

(2018) Junyue Cao et al.   SCIENCE

MISC: missing imputation for single-cell RNA sequencing data

(2018) Mary Qu Yang et al.   BMC Systems Biology

Concurrent Single-Cell RNA and Targeted DNA Sequencing on an Automated Platform for Comeasurement of Genomic and Transcriptomic Signatures

(2018) Say Li Kong et al.   CLINICAL CHEMISTRY

Simultaneous multiplexed amplicon sequencing and transcriptome profiling in single cells

(2018) Mridusmita Saikia et al.   NATURE METHODS

Multi-omic tumor data reveal diversity of molecular mechanisms that correlate with survival

(2018) Daniele Ramazzotti et al.   Nature Communications

SIDR: simultaneous isolation and parallel sequencing of genomic DNA and total RNA from single cells

(2017) Kyung Yeon Han et al.   GENOME RESEARCH

Multiplexed quantification of proteins and transcripts in single cells

(2017) Vanessa M Peterson et al.   NATURE BIOTECHNOLOGY

Simultaneous epitope and transcriptome measurement in single cells

(2017) Marlon Stoeckius et al.   NATURE METHODS

Power analysis of single-cell RNA-sequencing experiments

(2017) Valentine Svensson et al.   NATURE METHODS

Genome-wide mapping of DNase I hypersensitive sites in rare cell populations using single-cell DNase sequencing

(2017) James Cooper et al.   Nature Protocols

Tumour heterogeneity and resistance to cancer therapies

(2017) Ibiayi Dagogo-Jack et al.   Nature Reviews Clinical Oncology

Spatial reconstruction of immune niches by combining photoactivatable reporters and scRNA-seq

(2017) Chiara Medaglia et al.   SCIENCE

Combating subclonal evolution of resistant cancer phenotypes

(2017) Samuel W. Brady et al.   Nature Communications

Single-cell RNA-seq enables comprehensive tumour and immune cell profiling in primary breast cancer

(2017) Woosung Chung et al.   Nature Communications

Abseq: Ultrahigh-throughput single cell protein profiling with droplet microfluidic barcoding

(2017) Payam Shahi et al.   Scientific Reports

ISMB 2016 Proceedings

(2016) Pierre Baldi et al.   BIOINFORMATICS

Genome, transcriptome and proteome: the rise of omics data and their integration in biomedical sciences

(2016) Claudia Manzoni et al.   BRIEFINGS IN BIOINFORMATICS

Interaction of MSC with tumor cells

(2016) Catharina Melzer et al.   Cell Communication and Signaling

Single-cell triple omics sequencing reveals genetic, epigenetic and transcriptomic heterogeneity in hepatocellular carcinomas

(2016) Yu Hou et al.   CELL RESEARCH

Assessment of megabase-scale somatic copy number variation using single-cell sequencing

(2016) Kristin A. Knouse et al.   GENOME RESEARCH

Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution

(2016) M Ryan Corces et al.   NATURE GENETICS

Highly multiplexed simultaneous detection of RNAs and proteins in single cells

(2016) Andreas P Frei et al.   NATURE METHODS

Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity

(2016) Christof Angermueller et al.   NATURE METHODS

Laser capture microscopy coupled with Smart-seq2 for precise spatial transcriptomic profiling

(2016) Susanne Nichterwitz et al.   Nature Communications

Simultaneous Multiplexed Measurement of RNA and Proteins in Single Cells

(2016) Spyros Darmanis et al.   Cell Reports

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

Integrated genome and transcriptome sequencing of the same cell

(2015) Siddharth S Dey et al.   NATURE BIOTECHNOLOGY

G&T-seq: parallel sequencing of single-cell genomes and transcriptomes

(2015) Iain C Macaulay et al.   NATURE METHODS

Profiling DNA methylome landscapes of mammalian cells with single-cell reduced-representation bisulfite sequencing

(2015) Hongshan Guo et al.   Nature Protocols

Single-cell analysis of lung adenocarcinoma cell lines reveals diverse expression patterns of individual cells invoked by a molecular target drug treatment

(2015) Ayako Suzuki et al.   GENOME BIOLOGY

Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity

(2014) Sébastien A Smallwood et al.   NATURE METHODS

Full-length RNA-seq from single cells using Smart-seq2

(2014) Simone Picelli et al.   Nature Protocols

Co-detection and sequencing of genes and transcripts from the same single cells facilitated by a microfluidics platform

(2014) Lin Han et al.   Scientific Reports

Single-Cell DNA-Methylation Analysis Reveals Epigenetic Chimerism in Preimplantation Embryos

(2013) C. Lorthongpanich et al.   SCIENCE

Tumour evolution inferred by single-cell sequencing

(2011) Nicholas Navin et al.   NATURE

Single-Cell Mass Cytometry of Differential Immune and Drug Responses Across a Human Hematopoietic Continuum

(2011) S. C. Bendall et al.   SCIENCE

Tumor heterogeneity: Causes and consequences

(2009) Andriy Marusyk et al.   BIOCHIMICA ET BIOPHYSICA ACTA-REVIEWS ON CANCER