Applications of single-cell sequencing in cancer research: progress and perspectives

Changes in genome architecture and transcriptional dynamics progress independently of sensory experience during post-natal brain development

(2021) Longzhi Tan et al.   CELL

Single-cell lineages reveal the rates, routes, and drivers of metastasis in cancer xenografts

(2021) Jeffrey J. Quinn et al.   SCIENCE

Single-cell analysis reveals the intra-tumor heterogeneity and identifies MLXIPL as a biomarker in the cellular trajectory of hepatocellular carcinoma

(2021) Xiao Dong et al.   Cell Death Discovery

Inhibitory CD161 receptor identified in glioma-infiltrating T cells by single-cell analysis

(2021) Nathan D. Mathewson et al.   CELL

A pan-cancer single-cell transcriptional atlas of tumor infiltrating myeloid cells

(2021) Sijin Cheng et al.   CELL

Identification of leukemic and pre-leukemic stem cells by clonal tracking from single-cell transcriptomics

(2021) Lars Velten et al.   Nature Communications

Direct Comparative Analyses of 10X Genomics Chromium and Smart-seq2

(2021) Xiliang Wang et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

A single‐cell RNA expression atlas of normal, preneoplastic and tumorigenic states in the human breast

(2021) Bhupinder Pal et al.   EMBO JOURNAL

Research Techniques Made Simple: Use of Imaging Mass Cytometry for Dermatological Research and Clinical Applications

(2021) Jesse Veenstra et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY

A unified atlas of CD8 T cell dysfunctional states in cancer and infection

(2021) Yuri Pritykin et al.   MOLECULAR CELL

Cross-tissue organization of the fibroblast lineage

(2021) Matthew B. Buechler et al.   NATURE

Single-cell CUT&Tag profiles histone modifications and transcription factors in complex tissues

(2021) Marek Bartosovic et al.   NATURE BIOTECHNOLOGY

Single-cell profiling of myeloid cells in glioblastoma across species and disease stage reveals macrophage competition and specialization

(2021) Ana Rita Pombo Antunes et al.   NATURE NEUROSCIENCE

Atlas of breast cancer infiltrated B-lymphocytes revealed by paired single-cell RNA-sequencing and antigen receptor profiling

(2021) Qingtao Hu et al.   Nature Communications

Leukocyte Heterogeneity in Pancreatic Ductal Adenocarcinoma: Phenotypic and Spatial Features Associated with Clinical Outcome

(2021) Shannon M. Liudahl et al.   Cancer Discovery

Resolving the spatial and cellular architecture of lung adenocarcinoma by multiregion single-cell sequencing

(2021) Ansam Sinjab et al.   Cancer Discovery

HLA Ligand Atlas: a benign reference of HLA-presented peptides to improve T-cell-based cancer immunotherapy

(2021) Ana Marcu et al.   Journal for ImmunoTherapy of Cancer

The DNA methylation landscape in cancer

(2020) Ksenia Skvortsova et al.   Essays in Biochemistry

Peripheral T cell expansion predicts tumour infiltration and clinical response

(2020) Thomas D. Wu et al.   NATURE

The single-cell pathology landscape of breast cancer

(2020) Hartland W. Jackson et al.   NATURE

Integrating microarray-based spatial transcriptomics and single-cell RNA-seq reveals tissue architecture in pancreatic ductal adenocarcinomas

(2020) Reuben Moncada et al.   NATURE BIOTECHNOLOGY

Transcriptional diversity and bioenergetic shift in human breast cancer metastasis revealed by single-cell RNA sequencing

(2020) Ryan T. Davis et al.   NATURE CELL BIOLOGY

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

(2020) Mirjana Efremova et al.   Nature Protocols

Mutational and transcriptomic landscapes of a rare human prostate basal cell carcinoma

(2020) Xianbin Su et al.   PROSTATE

Liquid Biopsy Based Single‐Cell Transcriptome Profiling Characterizes Heterogeneity of Disseminated Tumor Cells from Lung Adenocarcinoma

(2020) Yu Dong et al.   PROTEOMICS

Clonal kinetics and single-cell transcriptional profiling of CAR-T cells in patients undergoing CD19 CAR-T immunotherapy

(2020) Alyssa Sheih et al.   Nature Communications

Chromatin mapping and single-cell immune profiling define the temporal dynamics of ibrutinib response in CLL

(2020) André F. Rendeiro et al.   Nature Communications

Tracing tumorigenesis in a solid tumor model at single-cell resolution

(2020) Samantha D. Praktiknjo et al.   Nature Communications

Unraveling the Architecture of Classic Hodgkin Lymphoma One Cell at a Time

(2020) Daniel A.C. Fisher et al.   Cancer Discovery

Single Cell Transcriptome in Colorectal Cancer—Current Updates on Its Application in Metastasis, Chemoresistance and the Roles of Circulating Tumor Cells

(2020) Francis Yew Fu Tieng et al.   Frontiers in Pharmacology

Single Eye mRNA-Seq Reveals Normalisation of the Retinal Microglial Transcriptome Following Acute Inflammation

(2020) Oliver H. Bell et al.   Frontiers in Immunology

Single-Nucleus Sequencing of an Entire Mammalian Heart: Cell Type Composition and Velocity

(2020) Markus Wolfien et al.   Cells

Single-Cell Analyses Inform Mechanisms of Myeloid-Targeted Therapies in Colon Cancer

(2020) Lei Zhang et al.   CELL

The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution

(2020) Orit Rozenblatt-Rosen et al.   CELL

Unravelling the heterogeneity and dynamic relationships of tumor‐infiltrating T cells by single‐cell RNA sequencing analysis

(2020) Xin Yu et al.   JOURNAL OF LEUKOCYTE BIOLOGY

Single-Cell Transcriptome Analysis Reveals Intratumoral Heterogeneity in ccRCC, which Results in Different Clinical Outcomes

(2020) Junyi Hu et al.   MOLECULAR THERAPY

Systematic comparison of single-cell and single-nucleus RNA-sequencing methods

(2020) Jiarui Ding et al.   NATURE BIOTECHNOLOGY

A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors

(2020) Michal Slyper et al.   NATURE MEDICINE

Cardelino: computational integration of somatic clonal substructure and single-cell transcriptomes

(2020) Davis J. McCarthy et al.   NATURE METHODS

Simultaneous quantification of protein–DNA interactions and transcriptomes in single cells with scDam&T-seq

(2020) Corina M. Markodimitraki et al.   Nature Protocols

SingleCellSignalR: inference of intercellular networks from single-cell transcriptomics

(2020) Simon Cabello-Aguilar et al.   NUCLEIC ACIDS RESEARCH

Single-cell RNA sequencing demonstrates the molecular and cellular reprogramming of metastatic lung adenocarcinoma

(2020) Nayoung Kim et al.   Nature Communications

Trajectory and Functional Analysis of PD‐1 high CD4 + CD8 + T Cells in Hepatocellular Carcinoma by Single‐Cell Cytometry and Transcriptome Sequencing

(2020) Bo Zheng et al.   Advanced Science

PDIA3 correlates with clinical malignant features and immune signature in human gliomas

(2020) Hao Zhang et al.   Aging-US

Coupled scRNA-Seq and Intracellular Protein Activity Reveal an Immunosuppressive Role of TREM2 in Cancer

(2020) Yonatan Katzenelenbogen et al.   CELL

Dissecting transcriptional heterogeneity in primary gastric adenocarcinoma by single cell RNA sequencing

(2020) Min Zhang et al.   GUT

Principles and innovative technologies for decrypting noncoding RNAs: from discovery and functional prediction to clinical application

(2020) Yu-Meng Sun et al.   Journal of Hematology & Oncology

Robust gene expression programs underlie recurrent cell states and phenotype switching in melanoma

(2020) Jasper Wouters et al.   NATURE CELL BIOLOGY

Dissecting intratumour heterogeneity of nodal B-cell lymphomas at the transcriptional, genetic and drug-response levels

(2020) Tobias Roider et al.   NATURE CELL BIOLOGY

Multidimensional study of the heterogeneity of leukemia cells in t(8;21) acute myelogenous leukemia identifies the subtype with poor outcome

(2020) Lu Jiang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic and epigenetic regulation of cancer coagulome – lessons from heterogeneity of cancer cell populations

(2020) Nadim Tawil et al.   THROMBOSIS RESEARCH

Single-cell RNA-seq reveals that glioblastoma recapitulates a normal neurodevelopmental hierarchy

(2020) Charles P. Couturier et al.   Nature Communications

A single-cell survey of cellular hierarchy in acute myeloid leukemia

(2020) Junqing Wu et al.   Journal of Hematology & Oncology

Analysis of circulating breast cancer cell heterogeneity and interactions with peripheral blood mononuclear cells

(2020) Heather M. Brechbuhl et al.   MOLECULAR CARCINOGENESIS

Integrated RNA Sequencing and Single-Cell Mass Cytometry Reveal a Novel Role of LncRNA HOXA-AS2 in Tumorigenesis and Stemness of Hepatocellular Carcinoma

(2020) Qinchen Lu et al.   OncoTargets and Therapy

Single-cell transcriptomes of pancreatic preinvasive lesions and cancer reveal acinar metaplastic cells’ heterogeneity

(2020) Yehuda Schlesinger et al.   Nature Communications

Characterization of BRCA1-deficient premalignant tissues and cancers identifies Plekha5 as a tumor metastasis suppressor

(2020) Jianlin Liu et al.   Nature Communications

Single-cell RNA sequencing highlights the role of inflammatory cancer-associated fibroblasts in bladder urothelial carcinoma

(2020) Zhaohui Chen et al.   Nature Communications

Single-cell transcriptome atlas of lung adenocarcinoma featured with ground glass nodules

(2020) Tao Lu et al.   Cell Discovery

Stromal Cells Exhibit Prevalent Genetic Aberrations in Colorectal Cancer

(2020) Kathleen M. McAndrews et al.   CANCER CELL

Single-cell landscape of the ecosystem in early-relapse hepatocellular carcinoma

(2020) Yunfan Sun et al.   CELL

Cadherin 11 Promotes Immunosuppression and Extracellular Matrix Deposition to Support Growth of Pancreatic Tumors and Resistance to Gemcitabine in Mice

(2020) Ivana Peran et al.   GASTROENTEROLOGY

LncRNA MIAT correlates with immune infiltrates and drug reactions in hepatocellular carcinoma

(2020) Lirong Peng et al.   INTERNATIONAL IMMUNOPHARMACOLOGY

RNA sequencing: new technologies and applications in cancer research

(2020) Mingye Hong et al.   Journal of Hematology & Oncology

Circulating tumor cell detection and single‐cell analysis using an integrated workflow based on ChimeraX ® ‐i120 Platform: A prospective study

(2020) Peng‐Xiang Wang et al.   Molecular Oncology

A single cell atlas of the human liver tumor microenvironment

(2020) Hassan Massalha et al.   Molecular Systems Biology

Defining the carrier proteome limit for single-cell proteomics

(2020) Tommy K. Cheung et al.   NATURE METHODS

Applying high-dimensional single-cell technologies to the analysis of cancer immunotherapy

(2020) Satyen H. Gohil et al.   Nature Reviews Clinical Oncology

Single-cell RNA landscape of intratumoral heterogeneity and immunosuppressive microenvironment in advanced osteosarcoma

(2020) Yan Zhou et al.   Nature Communications

Immune suppressive landscape in the human esophageal squamous cell carcinoma microenvironment

(2020) Yingxia Zheng et al.   Nature Communications

CRISPR Screening of CAR T Cells and Cancer Stem Cells Reveals Critical Dependencies for Cell-Based Therapies

(2020) Dongrui Wang et al.   Cancer Discovery

Redox Regulator GLRX Is Associated With Tumor Immunity in Glioma

(2020) Yuanhao Chang et al.   Frontiers in Immunology

Mechanisms Generating Cancer Genome Complexity: Back to the Future

(2020) Franck Toledo   Cancers

Global immune characterization of HBV/HCV-related hepatocellular carcinoma identifies macrophage and T-cell subsets associated with disease progression

(2020) Guohe Song et al.   Cell Discovery

Discovery and Validation of a Metastasis-Related Prognostic and Diagnostic Biomarker for Melanoma Based on Single Cell and Gene Expression Datasets

(2020) Qi Wan et al.   Frontiers in Oncology

Single-cell analysis supports a luminal-neuroendocrine transdifferentiation in human prostate cancer

(2020) Baijun Dong et al.   Communications Biology

Single-Nucleus and In Situ RNA–Sequencing Reveal Cell Topographies in the Human Pancreas

(2020) Luca Tosti et al.   GASTROENTEROLOGY

Molecular signatures of multiple myeloma progression through single cell RNA-Seq

(2019) Jin Sung Jang et al.   Blood Cancer Journal

Ex vivo Dynamics of Human Glioblastoma Cells in a Microvasculature-on-a-Chip System Correlates with Tumor Heterogeneity and Subtypes

(2019) Yang Xiao et al.   Advanced Science

Pancreatic adenocarcinomas with mature blood vessels have better overall survival

(2019) Eriko Katsuta et al.   Scientific Reports

Liquid Biopsies in Cancer Diagnosis, Monitoring, and Prognosis

(2019) Gabriele De Rubis et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Lenvatinib plus anti-PD-1 antibody combination treatment activates CD8+ T cells through reduction of tumor-associated macrophage and activation of the interferon pathway

(2019) Yu Kato et al.   PLoS One

SuperCT: a supervised-learning framework for enhanced characterization of single-cell transcriptomic profiles

(2019) Peng Xie et al.   NUCLEIC ACIDS RESEARCH

Neutrophils escort circulating tumour cells to enable cell cycle progression

(2019) Barbara Maria Szczerba et al.   NATURE

De novo gene signature identification from single‐cell RNA‐seq with hierarchical Poisson factorization

(2019) Hanna Mendes Levitin et al.   Molecular Systems Biology

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

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

Single-Cell Genomics

(2019) Carmela Paolillo et al.   CLINICAL CHEMISTRY

Single-cell profiling of cutaneous T-cell lymphoma reveals underlying heterogeneity associated with disease progression

(2019) Nicholas Borcherding et al.   CLINICAL CANCER RESEARCH

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

(2019) Peter van Galen et al.   CELL

Intraclonal Plasticity in Mammary Tumors Revealed through Large-Scale Single-Cell Resolution 3D Imaging

(2019) Anne C. Rios et al.   CANCER CELL

A Single-Cell Atlas of the Tumor and Immune Ecosystem of Human Breast Cancer

(2019) Johanna Wagner et al.   CELL

Single-Cell Transcriptomics Uncovers Glial Progenitor Diversity and Cell Fate Determinants during Development and Gliomagenesis

(2019) Qinjie Weng et al.   Cell Stem Cell

Single-Cell Lymphocyte Heterogeneity in Advanced Cutaneous T-cell Lymphoma Skin Tumors

(2019) Alyxzandria M. Gaydosik et al.   CLINICAL CANCER RESEARCH

Single-Cell Transcriptomics of Human and Mouse Lung Cancers Reveals Conserved Myeloid Populations across Individuals and Species

(2019) Rapolas Zilionis et al.   IMMUNITY

Childhood cerebellar tumours mirror conserved fetal transcriptional programs

(2019) Maria C. Vladoiu et al.   NATURE

Single‑cell intratumoral stemness analysis reveals the involvement of cell cycle and DNA damage repair in two different types of esophageal cancer

(2019) Hongjin Wu et al.   ONCOLOGY REPORTS

Single-cell genomics identifies cell type–specific molecular changes in autism

(2019) Dmitry Velmeshev et al.   SCIENCE

Notch Signaling Mediates Secondary Senescence

(2019) Yee Voan Teo et al.   Cell Reports

Dissecting the Single-Cell Transcriptome Network Underlying Gastric Premalignant Lesions and Early Gastric Cancer

(2019) Peng Zhang et al.   Cell Reports

Ovarian cancer and the evolution of subtype classifications using transcriptional profiling†

(2019) David P Cook et al.   BIOLOGY OF REPRODUCTION

Single-cell RNA-seq highlights intra-tumoral heterogeneity and malignant progression in pancreatic ductal adenocarcinoma

(2019) Junya Peng et al.   CELL RESEARCH

Single-cell RNA sequencing reveals novel gene expression signatures of trastuzumab treatment in HER2+ breast cancer

(2019) Jun Wang et al.   MEDICINE

Hydro-Seq enables contamination-free high-throughput single-cell RNA-sequencing for circulating tumor cells

(2019) Yu-Heng Cheng et al.   Nature Communications

Intrinsic Resistance to Immune Checkpoint Blockade in a Mismatch Repair–Deficient Colorectal Cancer

(2019) Carino Gurjao et al.   Cancer Immunology Research

Recharacterizing Tumor-Infiltrating Lymphocytes by Single-Cell RNA Sequencing

(2019) Lei Zhang et al.   Cancer Immunology Research

Human Tumor-Infiltrating Dendritic Cells: From in Situ Visualization to High-Dimensional Analyses

(2019) Hubert et al.   Cancers

Single-cell RNA-seq reveals RAD51AP1 as a potent mediator of EGFRvIII in human glioblastomas

(2019) Qixue Wang et al.   Aging-US

Single-cell RNA-seq of esophageal squamous cell carcinoma cell line with fractionated irradiation reveals radioresistant gene expression patterns

(2019) Ling Yang et al.   BMC GENOMICS

Single-Cell Transcriptomics in Medulloblastoma Reveals Tumor-Initiating Progenitors and Oncogenic Cascades during Tumorigenesis and Relapse

(2019) Liguo Zhang et al.   CANCER CELL

Single-cell transcriptomics reveals the landscape of intra-tumoral heterogeneity and stemness-related subpopulations in liver cancer

(2019) Daniel Wai-Hung Ho et al.   CANCER LETTERS

Acquired Resistance Mutations to ALK Inhibitors Identified by Single Circulating Tumor Cell Sequencing in ALK-Rearranged Non–Small-Cell Lung Cancer

(2019) Emma Pailler et al.   CLINICAL CANCER RESEARCH

Alterations in the transcriptional programs of myeloma cells and the microenvironment during extramedullary progression affect proliferation and immune evasion

(2019) Daeun Ryu et al.   CLINICAL CANCER RESEARCH

Altered Gene Expression along the Glycolysis–Cholesterol Synthesis Axis Is Associated with Outcome in Pancreatic Cancer

(2019) Joanna M. Karasinska et al.   CLINICAL CANCER RESEARCH

Single‐cell RNA sequencing reveals chemokine self‐feeding of myeloma cells promotes extramedullary metastasis

(2019) Shuang Geng et al.   FEBS LETTERS

Tracing Tumor Evolution in Sarcoma Reveals Clonal Origin of Advanced Metastasis

(2019) Yuning J. Tang et al.   Cell Reports

Comprehensive intra-individual genomic and transcriptional heterogeneity: Evidence-based Colorectal Cancer Precision Medicine

(2019) Ioannis D. Kyrochristos et al.   CANCER TREATMENT REVIEWS

Landscape and Dynamics of Single Immune Cells in Hepatocellular Carcinoma

(2019) Qiming Zhang et al.   CELL

Genomic and transcriptomic profiling of carcinogenesis in patients with familial adenomatous polyposis

(2019) Jingyun Li et al.   GUT

Population and single‑cell transcriptome analyses reveal diverse transcriptional changes associated with radioresistance in esophageal squamous cell carcinoma

(2019) Hongjin Wu et al.   INTERNATIONAL JOURNAL OF ONCOLOGY

CoBATCH for High-Throughput Single-Cell Epigenomic Profiling

(2019) Qianhao Wang et al.   MOLECULAR CELL

Tumor mutation burden, immune checkpoint crosstalk and radiosensitivity in single-cell RNA sequencing data of breast cancer

(2019) Bum-Sup Jang et al.   RADIOTHERAPY AND ONCOLOGY

Single-cell transcriptomics reveals multi-step adaptations to endocrine therapy

(2019) Sung Pil Hong et al.   Nature Communications

Non-Genetic Intra-Tumor Heterogeneity Is a Major Predictor of Phenotypic Heterogeneity and Ongoing Evolutionary Dynamics in Lung Tumors

(2019) Anchal Sharma et al.   Cell Reports

Glioblastoma extracellular vesicles induce the tumour-promoting transformation of neural stem cells

(2019) Jian Wang et al.   CANCER LETTERS

Single-cell transcriptome analysis reveals tumor immune microenvironment heterogenicity and granulocytes enrichment in colorectal cancer liver metastases

(2019) Yunbin Zhang et al.   CANCER LETTERS

Immune profiling of human tumors identifies CD73 as a combinatorial target in glioblastoma

(2019) Sangeeta Goswami et al.   NATURE MEDICINE

Massively multiplex chemical transcriptomics at single-cell resolution

(2019) Sanjay R. Srivatsan et al.   SCIENCE

Tracking the important role of JUNB in hepatocellular carcinoma by single‑cell sequencing analysis

(2019) Peng Yan et al.   Oncology Letters

Single-Cell Transcriptome Analysis Reveals Disease-Defining T-cell Subsets in the Tumor Microenvironment of Classic Hodgkin Lymphoma

(2019) Tomohiro Aoki et al.   Cancer Discovery

Single-Cell Profiling Defines Transcriptomic Signatures Specific to Tumor-Reactive versus Virus-Responsive CD4+ T Cells

(2019) Assaf Magen et al.   Cell Reports

Mapping the Mouse Cell Atlas by Microwell-Seq

(2018) Xiaoping Han et al.   CELL

Simultaneous lineage tracing and cell-type identification using CRISPR–Cas9-induced genetic scars

(2018) Bastiaan Spanjaard et al.   NATURE BIOTECHNOLOGY

Global characterization of T cells in non-small-cell lung cancer by single-cell sequencing

(2018) Xinyi Guo et al.   NATURE MEDICINE

Transcript-indexed ATAC-seq for precision immune profiling

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

A receptor tyrosine kinase ROR1 inhibitor (KAN0439834) induced significant apoptosis of pancreatic cells which was enhanced by erlotinib and ibrutinib

(2018) Amir Hossein Daneshmanesh et al.   PLoS One

Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding

(2018) Alexander B. Rosenberg et al.   SCIENCE

A comparative analysis of library prep approaches for sequencing low input translatome samples

(2018) Yang Song et al.   BMC GENOMICS

Human germinal center transcriptional programs are de-synchronized in B cell lymphoma

(2018) Pierre Milpied et al.   NATURE IMMUNOLOGY

Single-cell RNA-Seq of lymphoma cancers reveals malignant B cell types and co-expression of T cell immune checkpoints

(2018) Noemi Andor et al.   BLOOD

KDM5 Histone Demethylase Activity Links Cellular Transcriptomic Heterogeneity to Therapeutic Resistance

(2018) Kunihiko Hinohara et al.   CANCER CELL

A Cancer Cell Program Promotes T Cell Exclusion and Resistance to Checkpoint Blockade

(2018) Livnat Jerby-Arnon et al.   CELL

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

Hypermutagenesis in untreated adult gliomas due to inherited mismatch mutations

(2018) Jason K. Sa et al.   INTERNATIONAL JOURNAL OF CANCER

Advantages of Single-Nucleus over Single-Cell RNA Sequencing of Adult Kidney: Rare Cell Types and Novel Cell States Revealed in Fibrosis

(2018) Haojia Wu et al.   JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY

Comparative Analysis of Droplet-Based Ultra-High-Throughput Single-Cell RNA-Seq Systems

(2018) Xiannian Zhang et al.   MOLECULAR CELL

Time to abandon single-site irradiation for inducing abscopal effects

(2018) Eric D. Brooks et al.   Nature Reviews Clinical Oncology

CancerSEA: a cancer single-cell state atlas

(2018) Huating Yuan et al.   NUCLEIC ACIDS RESEARCH

Single-cell RNA-seq analysis reveals the platinum resistance gene COX7B and the surrogate marker CD63

(2018) Nobuyuki Tanaka et al.   Cancer Medicine

Ibrutinib treatment improves T cell number and function in CLL patients

(2017) Meixiao Long et al.   JOURNAL OF CLINICAL INVESTIGATION

Distinct populations of inflammatory fibroblasts and myofibroblasts in pancreatic cancer

(2017) Daniel Öhlund et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Bevacizumab for advanced cervical cancer: final overall survival and adverse event analysis of a randomised, controlled, open-label, phase 3 trial (Gynecologic Oncology Group 240)

(2017) Krishnansu S Tewari et al.   LANCET

Comparative Analysis of Single-Cell RNA Sequencing Methods

(2017) Christoph Ziegenhain et al.   MOLECULAR CELL

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

Sequencing thousands of single-cell genomes with combinatorial indexing

(2017) Sarah A Vitak et al.   NATURE METHODS

Massively parallel single-nucleus RNA-seq with DroNc-seq

(2017) Naomi Habib et al.   NATURE METHODS

Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput

(2017) Todd M Gierahn et al.   NATURE METHODS

Decoupling genetics, lineages, and microenvironment in IDH-mutant gliomas by single-cell RNA-seq

(2017) Andrew S. Venteicher et al.   SCIENCE

Collagen-derived proline promotes pancreatic ductal adenocarcinoma cell survival under nutrient limited conditions

(2017) Orianne Olivares et al.   Nature Communications

Matrix stiffness induces epithelial–mesenchymal transition and promotes chemoresistance in pancreatic cancer cells

(2017) A J Rice et al.   Oncogenesis

Immune escape to PD-L1/PD-1 blockade: seven steps to success (or failure)

(2016) J. M. Kim et al.   ANNALS OF ONCOLOGY

Dissecting Immune Circuits by Linking CRISPR-Pooled Screens with Single-Cell RNA-Seq

(2016) Diego Adhemar Jaitin et al.   CELL

Genomic analyses identify molecular subtypes of pancreatic cancer

(2016) Peter Bailey et al.   NATURE

Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma

(2016) Itay Tirosh et al.   NATURE

The heterogeneity of human CD127+ innate lymphoid cells revealed by single-cell RNA sequencing

(2016) Åsa K Björklund et al.   NATURE IMMUNOLOGY

Genotype tunes pancreatic ductal adenocarcinoma tissue tension to induce matricellular fibrosis and tumor progression

(2016) Hanane Laklai et al.   NATURE MEDICINE

Monovar: single-nucleotide variant detection in single cells

(2016) Hamim Zafar et al.   NATURE METHODS

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics

(2016) P. L. Stahl et al.   SCIENCE

Neuronal subtypes and diversity revealed by single-nucleus RNA sequencing of the human brain

(2016) B. B. Lake et al.   SCIENCE

Div-Seq: Single-nucleus RNA-Seq reveals dynamics of rare adult newborn neurons

(2016) Naomi Habib et al.   SCIENCE

Nuclear RNA-seq of single neurons reveals molecular signatures of activation

(2016) Benjamin Lacar et al.   Nature Communications

Downregulation of 26S proteasome catalytic activity promotes epithelial-mesenchymal transition

(2016) Asoka Banno et al.   Oncotarget

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

The Technology and Biology of Single-Cell RNA Sequencing

(2015) Aleksandra A. Kolodziejczyk et al.   MOLECULAR CELL

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

Virtual microdissection identifies distinct tumor- and stroma-specific subtypes of pancreatic ductal adenocarcinoma

(2015) Richard A Moffitt et al.   NATURE GENETICS

Immunological landscape and immunotherapy of hepatocellular carcinoma

(2015) Jesús Prieto et al.   Nature Reviews Gastroenterology & Hepatology

PD-1 Blockade in Tumors with Mismatch-Repair Deficiency

(2015) Dung T. Le et al.   NEW ENGLAND JOURNAL OF MEDICINE

Single cell-derived clonal analysis of human glioblastoma links functional and genomic heterogeneity

(2015) Mona Meyer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Anti-angiogenic therapy for cancer: current progress, unresolved questions and future directions

(2014) Naveen S. Vasudev et al.   ANGIOGENESIS

Ibrutinib inhibits BCR and NF- B signaling and reduces tumor proliferation in tissue-resident cells of patients with CLL

(2014) S. E. M. Herman et al.   BLOOD

Circulating Tumor Cell Clusters Are Oligoclonal Precursors of Breast Cancer Metastasis

(2014) Nicola Aceto et al.   CELL

Vitamin D Receptor-Mediated Stromal Reprogramming Suppresses Pancreatitis and Enhances Pancreatic Cancer Therapy

(2014) Mara H. Sherman et al.   CELL

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

(2014) D. A. Jaitin et al.   SCIENCE

Interleukin-6 Is Required for Pancreatic Cancer Progression by Promoting MAPK Signaling Activation and Oxidative Stress Resistance

(2013) Y. Zhang et al.   CANCER RESEARCH

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

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

(2013) Simone Picelli et al.   NATURE METHODS

RNA-sequencing from single nuclei

(2013) R. V. Grindberg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Targeting CXCL12 from FAP-expressing carcinoma-associated fibroblasts synergizes with anti-PD-L1 immunotherapy in pancreatic cancer

(2013) C. Feig et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Circulating Breast Tumor Cells Exhibit Dynamic Changes in Epithelial and Mesenchymal Composition

(2013) M. Yu et al.   SCIENCE

The RNA-Binding Protein Musashi-1 Regulates Proteasome Subunit Expression in Breast Cancer- and Glioma-Initiating Cells

(2013) Chann Lagadec et al.   STEM CELLS

Enzymatic Targeting of the Stroma Ablates Physical Barriers to Treatment of Pancreatic Ductal Adenocarcinoma

(2012) Paolo P. Provenzano et al.   CANCER CELL

Hyaluronan impairs vascular function and drug delivery in a mouse model of pancreatic cancer

(2012) Michael A Jacobetz et al.   GUT

A restricted cell population propagates glioblastoma growth after chemotherapy

(2012) Jian Chen et al.   NATURE

Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells

(2012) Daniel Ramsköld et al.   NATURE BIOTECHNOLOGY

Transcriptional burst frequency and burst size are equally modulated across the human genome

(2012) R. D. Dar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Desmoplastic Stroma Plays an Essential Role in the Accumulation and Modulation of Infiltrated Immune Cells in Pancreatic Adenocarcinoma

(2011) Vegard Tjomsland et al.   Clinical & Developmental Immunology

Tumour evolution inferred by single-cell sequencing

(2011) Nicholas Navin et al.   NATURE

Subtypes of pancreatic ductal adenocarcinoma and their differing responses to therapy

(2011) Eric A Collisson et al.   NATURE MEDICINE

Cancer-Associated Fibroblasts Are Activated in Incipient Neoplasia to Orchestrate Tumor-Promoting Inflammation in an NF-κB-Dependent Manner

(2010) Neta Erez et al.   CANCER CELL

Distant metastasis occurs late during the genetic evolution of pancreatic cancer

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