Single-cell Long Non-coding RNA Landscape of T Cells in Human Cancer Immunity

Long non-coding RNAs discriminate the stages and gene regulatory states of human humoral immune response

(2019) Xabier Agirre et al.   Nature Communications

Cellular functions of long noncoding RNAs

(2019) Run-Wen Yao et al.   NATURE CELL BIOLOGY

An expanded landscape of human long noncoding RNA

(2019) Shuai Jiang et al.   NUCLEIC ACIDS RESEARCH

Biomarkers for immune checkpoint inhibition in non–small cell lung cancer (NSCLC)

(2019) J. Nicholas Bodor et al.   CANCER

Landscape and Dynamics of Single Immune Cells in Hepatocellular Carcinoma

(2019) Qiming Zhang et al.   CELL

IMPRES does not reproducibly predict response to immune checkpoint blockade therapy in metastatic melanoma

(2019) Jason A. Carter et al.   NATURE MEDICINE

Integrative genome-wide analysis of long noncoding RNAs in diverse immune cell types of melanoma patients

(2018) Lei Wang et al.   CANCER RESEARCH

Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment

(2018) Elham Azizi et al.   CELL

Long noncoding RNAs in the metabolic control of inflammation and immune disorders

(2018) Junfang Xu et al.   Cellular & Molecular Immunology

Long noncoding RNAs in cancer-immunity cycle

(2018) Wei-Di Yu et al.   JOURNAL OF CELLULAR PHYSIOLOGY

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

(2018) Xinyi Guo et al.   NATURE MEDICINE

Single-cell profiling of breast cancer T cells reveals a tissue-resident memory subset associated with improved prognosis

(2018) Peter Savas et al.   NATURE MEDICINE

Towards a complete map of the human long non-coding RNA transcriptome

(2018) Barbara Uszczynska-Ratajczak et al.   NATURE REVIEWS GENETICS

NKILA lncRNA promotes tumor immune evasion by sensitizing T cells to activation-induced cell death

(2018) Di Huang et al.   NATURE IMMUNOLOGY

Robust prediction of response to immune checkpoint blockade therapy in metastatic melanoma

(2018) Noam Auslander et al.   NATURE MEDICINE

Dysfunctional CD8 T Cells Form a Proliferative, Dynamically Regulated Compartment within Human Melanoma

(2018) Hanjie Li et al.   CELL

Lineage tracking reveals dynamic relationships of T cells in colorectal cancer

(2018) Lei Zhang et al.   NATURE

Immune genes are primed for robust transcription by proximal long noncoding RNAs located in nuclear compartments

(2018) Stephanie Fanucchi et al.   NATURE GENETICS

GENCODE reference annotation for the human and mouse genomes

(2018) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

Elements of cancer immunity and the cancer–immune set point

(2017) Daniel S. Chen et al.   NATURE

Normalizing single-cell RNA sequencing data: challenges and opportunities

(2017) Catalina A Vallejos et al.   NATURE METHODS

NONCODEV5: a comprehensive annotation database for long non-coding RNAs

(2017) ShuangSang Fang et al.   NUCLEIC ACIDS RESEARCH

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

(2017) Woosung Chung et al.   Nature Communications

Massively parallel digital transcriptional profiling of single cells

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

Genomic and Transcriptomic Features of Response to Anti-PD-1 Therapy in Metastatic Melanoma

(2016) Willy Hugo et al.   CELL

Biogenesis and Transcriptional Regulation of Long Noncoding RNAs in the Human Immune System

(2016) Charles F. Spurlock et al.   JOURNAL OF IMMUNOLOGY

Potentiating the antitumour response of CD8+ T cells by modulating cholesterol metabolism

(2016) Wei Yang et al.   NATURE

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

The Emerging and Diverse Roles of Src-Like Adaptor Proteins in Health and Disease

(2015) Nikolett Marton et al.   MEDIATORS OF INFLAMMATION

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

The landscape of long noncoding RNAs in the human transcriptome

(2015) Matthew K Iyer et al.   NATURE GENETICS

Computational and analytical challenges in single-cell transcriptomics

(2015) Oliver Stegle et al.   NATURE REVIEWS GENETICS

T-cell-based Immunotherapy: Adoptive Cell Transfer and Checkpoint Inhibition

(2015) R. Houot et al.   Cancer Immunology Research

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

(2014) Simone Picelli et al.   Nature Protocols

lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs

(2014) Xiu Cheng Quek et al.   NUCLEIC ACIDS RESEARCH

The NeST Long ncRNA Controls Microbial Susceptibility and Epigenetic Activation of the Interferon-γ Locus

(2013) J. Antonio Gomez et al.   CELL

Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts

(2013) Liang Sun et al.   NUCLEIC ACIDS RESEARCH

Genome Regulation by Long Noncoding RNAs

(2012) John L. Rinn et al.   Annual Review of Biochemistry

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Large-scale prediction of long non-coding RNA functions in a coding–non-coding gene co-expression network

(2011) Qi Liao et al.   NUCLEIC ACIDS RESEARCH

TM4SF1, a novel primary androgen receptor target gene over-expressed in human prostate cancer and involved in cell migration

(2011) Nathalie Allioli et al.   PROSTATE

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

The tumour-associated antigen L6 (L6-Ag) is recruited to the tetraspanin-enriched microdomains: implication for tumour cell motility

(2008) T. Lekishvili et al.   JOURNAL OF CELL SCIENCE

Mechanism of upregulation of the inhibitory regulator, src-like adaptor protein (SLAP), by glucocorticoids in mast cells

(2008) Seung-Kiel Park et al.   MOLECULAR IMMUNOLOGY