Rory Johnson
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View article: Robust CRISPR Screens Identify TPL1 as a Novel Long Noncoding RNA Driving Triple-Negative Breast Cancer Hallmarks
Robust CRISPR Screens Identify TPL1 as a Novel Long Noncoding RNA Driving Triple-Negative Breast Cancer Hallmarks Open
Despite the growing catalog of long noncoding RNAs (lncRNAs), the functional roles of their vast majority in cancer remain poorly defined. To systematically explore lncRNA dependencies in triple-negative breast cancer (TNBC), we compiled a…
View article: Pan-cancer immune and stromal deconvolution predicts clinical outcomes and mutation profiles
Pan-cancer immune and stromal deconvolution predicts clinical outcomes and mutation profiles Open
View article: Pan-cancer immune and stromal deconvolution predicts clinical outcomes and mutation profiles
Pan-cancer immune and stromal deconvolution predicts clinical outcomes and mutation profiles Open
Traditional gene expression deconvolution methods assess a limited number of cell types, therefore do not capture the full complexity of the tumor microenvironment (TME). Here, we integrate nine deconvolution tools to assess 79 TME cell ty…
View article: 432 | LOSS OF ENHANCER‐DERIVED lncRNA U47924.31 DECREASES R‐CHOP SENSITIVITY AND IS ASSOCIATED WITH INFERIOR OUTCOME IN DIFFUSE LARGE B CELL LYMPHOMA PATIENTS
432 | LOSS OF ENHANCER‐DERIVED lncRNA U47924.31 DECREASES R‐CHOP SENSITIVITY AND IS ASSOCIATED WITH INFERIOR OUTCOME IN DIFFUSE LARGE B CELL LYMPHOMA PATIENTS Open
View article: 429 | LOSS OF ENHANCER‐DERIVED lncRNA ZMIZ1‐AS1 INCREASES THE SENSITIVITY TO BCL2‐INHIBITOR VENETOCLAX IN MCL IN VITRO MODELS
429 | LOSS OF ENHANCER‐DERIVED lncRNA ZMIZ1‐AS1 INCREASES THE SENSITIVITY TO BCL2‐INHIBITOR VENETOCLAX IN MCL IN VITRO MODELS Open
View article: Classification of non-TCGA cancer samples to TCGA molecular subtypes using compact feature sets
Classification of non-TCGA cancer samples to TCGA molecular subtypes using compact feature sets Open
Molecular subtypes, such as defined by The Cancer Genome Atlas (TCGA), delineate a cancer's underlying biology, bringing hope to inform a patient's prognosis and treatment plan. However, most approaches used in the discovery of subtypes ar…
View article: Enhancer lncRNA LOC730338 limits the innate immune response against lymphoma cells, inhibiting ADAR2-dependent alternative transcription
Enhancer lncRNA LOC730338 limits the innate immune response against lymphoma cells, inhibiting ADAR2-dependent alternative transcription Open
Chronic antigenic stimulation is central to marginal zone lymphoma (MZL) development. While the pharmacological inhibition of the B-cell receptor (BCR) signaling is initially effective, secondary resistance frequently develops. We conducte…
View article: GENCODE 2025: reference gene annotation for human and mouse
GENCODE 2025: reference gene annotation for human and mouse Open
GENCODE produces comprehensive reference gene annotation for human and mouse. Entering its twentieth year, the project remains highly active as new technologies and methodologies allow us to catalog the genome at ever-increasing granularit…
View article: GENCODE: massively expanding the lncRNA catalog through capture long-read RNA sequencing
GENCODE: massively expanding the lncRNA catalog through capture long-read RNA sequencing Open
Accurate and complete gene annotations are indispensable for understanding how genome sequences encode biological functions. For twenty years, the GENCODE consortium has developed reference annotations for the human and mouse genomes, beco…
View article: Single-cell chromatin accessibility reveals malignant regulatory programs in primary human cancers
Single-cell chromatin accessibility reveals malignant regulatory programs in primary human cancers Open
To identify cancer-associated gene regulatory changes, we generated single-cell chromatin accessibility landscapes across eight tumor types as part of The Cancer Genome Atlas. Tumor chromatin accessibility is strongly influenced by copy nu…
View article: Functional identification of <i>cis</i> -regulatory long noncoding RNAs at controlled false discovery rates
Functional identification of <i>cis</i> -regulatory long noncoding RNAs at controlled false discovery rates Open
A key attribute of some long noncoding RNAs (lncRNAs) is their ability to regulate expression of neighbouring genes in cis. However, such ‘cis-lncRNAs’ are presently defined using ad hoc criteria that, we show, are prone to false-positive …
View article: The status of the human gene catalogue
The status of the human gene catalogue Open
View article: Author Correction: Tumour mutations in long noncoding RNAs enhance cell fitness
Author Correction: Tumour mutations in long noncoding RNAs enhance cell fitness Open
View article: Assessment of the Cardiac Noncoding Transcriptome by Single-Cell RNA Sequencing Identifies <i>FIXER</i> , a Conserved Profibrogenic Long Noncoding RNA
Assessment of the Cardiac Noncoding Transcriptome by Single-Cell RNA Sequencing Identifies <i>FIXER</i> , a Conserved Profibrogenic Long Noncoding RNA Open
BACKGROUND: Cardiac fibroblasts have crucial roles in the heart. In particular, fibroblasts differentiate into myofibroblasts in the damaged myocardium, contributing to scar formation and interstitial fibrosis. Fibrosis is associated with …
View article: Tumour mutations in long noncoding RNAs enhance cell fitness
Tumour mutations in long noncoding RNAs enhance cell fitness Open
View article: ENHANCER RNAS (ERNAS) PLAY A ROLE IN THE RESPONSE TO SMALL MOLECULES AND IN THE DEVELOPMENT OF ACQUIRED RESISTANCE IN MARGINAL ZONE LYMPHOMA (MZL)
ENHANCER RNAS (ERNAS) PLAY A ROLE IN THE RESPONSE TO SMALL MOLECULES AND IN THE DEVELOPMENT OF ACQUIRED RESISTANCE IN MARGINAL ZONE LYMPHOMA (MZL) Open
Introduction: The therapeutic options for MZL patients with disseminated disease include chemotherapy, rituximab alone or rituximab with chemotherapy but several small molecules are also available. Resistance development is always an issue…
View article: The status of the human gene catalogue
The status of the human gene catalogue Open
Scientists have been trying to identify all of the genes in the human genome since the initial draft of the genome was published in 2001. Over the intervening years, much progress has been made in identifying protein-coding genes, and the …
View article: Author Correction: Analyses of non-coding somatic drivers in 2,658 cancer whole genomes
Author Correction: Analyses of non-coding somatic drivers in 2,658 cancer whole genomes Open
View article: Long non-coding RNAs: definitions, functions, challenges and recommendations
Long non-coding RNAs: definitions, functions, challenges and recommendations Open
View article: A transposable element into the human long noncoding RNA <i>CARMEN</i> is a switch for cardiac precursor cell specification
A transposable element into the human long noncoding RNA <i>CARMEN</i> is a switch for cardiac precursor cell specification Open
Aims The major cardiac cell types composing the adult heart arise from common multipotent precursor cells. Cardiac lineage decisions are guided by extrinsic and cell-autonomous factors, including recently discovered long noncoding RNAs (ln…
View article: Author Correction: Integrative pathway enrichment analysis of multivariate omics data
Author Correction: Integrative pathway enrichment analysis of multivariate omics data Open
In the published version of this paper, the members of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortiumwere listed in the Supplementary Information; however, these members shouldhave been included in themainpaper.The originalArt…
View article: Author Correction: Combined burden and functional impact tests for cancer driver discovery using DriverPower
Author Correction: Combined burden and functional impact tests for cancer driver discovery using DriverPower Open
View article: Author Correction: Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis
Author Correction: Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis Open
View article: Author Correction: Pathway and network analysis of more than 2500 whole cancer genomes
Author Correction: Pathway and network analysis of more than 2500 whole cancer genomes Open
View article: Is Evolutionary Conservation a Useful Predictor for Cancer Long Noncoding RNAs? Insights from the Cancer LncRNA Census 3
Is Evolutionary Conservation a Useful Predictor for Cancer Long Noncoding RNAs? Insights from the Cancer LncRNA Census 3 Open
Evolutionary conservation is a measure of gene functionality that is widely used to prioritise long noncoding RNAs (lncRNA) in cancer research. Intriguingly, while updating our Cancer LncRNA Census (CLC), we observed an inverse relationshi…
View article: Alternative splicing of a transposable element into the human long noncoding RNA CARMEN is a switch for cardiac precursor cell specification
Alternative splicing of a transposable element into the human long noncoding RNA CARMEN is a switch for cardiac precursor cell specification Open
View article: GENCODE: reference annotation for the human and mouse genomes in 2023
GENCODE: reference annotation for the human and mouse genomes in 2023 Open
GENCODE produces high quality gene and transcript annotation for the human and mouse genomes. All GENCODE annotation is supported by experimental data and serves as a reference for genome biology and clinical genomics. The GENCODE consorti…
View article: Functional identification of cis-regulatory long noncoding RNAs at controlled false-discovery rates
Functional identification of cis-regulatory long noncoding RNAs at controlled false-discovery rates Open
A key attribute of some long noncoding RNAs (lncRNAs) is their ability to regulate expression of neighbouring genes in cis. However, such ‘cis-lncRNAs’ are presently defined using ad hoc criteria that, we show, are prone to false-positive …
View article: Is evolutionary conservation a useful predictor for cancer long noncoding RNAs? Insights from the Cancer lncRNA Census 3
Is evolutionary conservation a useful predictor for cancer long noncoding RNAs? Insights from the Cancer lncRNA Census 3 Open
Evolutionary conservation is a measure of gene functionality that is widely used to prioritise long noncoding RNAs (lncRNA) in cancer research. Intriguingly, while updating our Cancer LncRNA Census, we observed an inverse relationship betw…
View article: Multi-hallmark long noncoding RNA maps reveal non-small cell lung cancer vulnerabilities
Multi-hallmark long noncoding RNA maps reveal non-small cell lung cancer vulnerabilities Open