Clonal phylogenies inferred from bulk, single cell, and spatial transcriptomic analysis of epithelial cancers

Clonal phylogenies inferred from bulk, single cell, and spatial transcriptomic analysis of epithelial cancers

Epithelial cancers are typically heterogeneous with primary prostate cancer being a typical example of histological and genomic variation. Prior studies of primary prostate cancer tumour genetics revealed extensive inter and intra-patient genomic tumour heterogeneity. Recent advances in machine lear...

Disgrifiad llawn

Manylion Llyfryddiaeth
Prif Awduron:	Erickson, A, Figiel, S, Rajakumar, T, Rao, S, Yin, W, Doultsinos, D, Magnussen, A, Singh, R, Poulose, N, Bryant, RJ, Cussenot, O, Hamdy, FC, Woodcock, D, Mills, IG, Lamb, AD
Fformat:	Journal article
Iaith:	English
Cyhoeddwyd:	Public Library of Science 2025

Eitemau Tebyg

Clonal phylogenies inferred from bulk, single cell, and spatial transcriptomic analysis of epithelial cancers.
gan: Andrew Erickson, et al.
Cyhoeddwyd: (2025-01-01)

A systematic review of prostate cancer heterogeneity: understanding the clonal ancestry of multifocal disease
gan: Erickson, A, et al.
Cyhoeddwyd: (2021)

Spatial transcriptomic analysis of virtual prostate biopsy reveals confounding effect of tissue heterogeneity on genomic signatures
gan: Figiel, S, et al.
Cyhoeddwyd: (2023)

Spatially resolved clonal copy number alterations in benign and malignant tissue
gan: Erickson, A, et al.
Cyhoeddwyd: (2022)

Spatial transcriptomic analysis of virtual prostate biopsy reveals confounding effect of tissue heterogeneity on genomic signatures
gan: Sandy Figiel, et al.
Cyhoeddwyd: (2023-10-01)

Derivation and application of molecular signatures to prostate cancer: Opportunities and challenges
gan: Doultsinos, D, et al.
Cyhoeddwyd: (2021)

Harnessing the power of RNA in determining the origin of lethal micro-metastatic prostate cancer
gan: A.M. Erickson, et al.
Cyhoeddwyd: (2020-07-01)

Genomic evolution and transcriptional changes in the evolution of prostate cancer into neuroendocrine and ductal carcinoma types
gan: Rao, SR, et al.
Cyhoeddwyd: (2023)

Molecular analysis of archival diagnostic prostate cancer biopsies identifies genomic similarities in cases with progression post-radiotherapy, and those with de novo metastatic disease
gan: Charlton, P, et al.
Cyhoeddwyd: (2023)

Ductal adenocarcinoma of the prostate: A systematic review and meta‐analysis of incidence, presentation, prognosis, and management
gan: Ranasinha, N, et al.
Cyhoeddwyd: (2021)

Molecular analysis of archival diagnostic prostate cancer biopsies identifies genomic similarities in cases with progression post-radiotherapy, and those with de novo metastatic disease
gan: Charlton, PV, et al.
Cyhoeddwyd: (2024)

The role of the androgen receptor as a driver and mitigator of cellular stress
gan: Doultsinos, D, et al.
Cyhoeddwyd: (2020)

Molecular Anatomy of Prostate Cancer and Its Implications in Active Surveillance and Early Intervention Strategies
gan: Sandy Figiel, et al.
Cyhoeddwyd: (2023-10-01)

Vascular normalisation as the stepping stone into tumour microenvironment transformation
gan: Magnussen, AL, et al.
Cyhoeddwyd: (2021)

Investigating tumour immune microenvironment effects of hypofractionated radiotherapy +/- immune checkpoint blockade in immunocompetent pre-clinical prostate cancer models
gan: Y Philippou, et al.
Cyhoeddwyd: (2020-07-01)

Inhibition of CDK9 activity compromises global splicing in prostate cancer cells
gan: Hu, Q, et al.
Cyhoeddwyd: (2021)

Impacts of combining anti-PD-L1 immunotherapy and radiotherapy on the tumour immune microenvironment in a murine prostate cancer model
gan: Philippou, Y, et al.
Cyhoeddwyd: (2020)

First report of prostate-specific membrane antigen-targeted immunotherapy in prostate cancer: the future is bright
gan: Lamb, A, et al.
Cyhoeddwyd: (2018)

Clonal approaches to immune regulation by lymphocytes.
gan: Feldmann, M, et al.
Cyhoeddwyd: (1984)

Bulk solids handling : an introduction to the practice and technology/
gan: Woodcock, C. R., et al.
Cyhoeddwyd: (1987)

O-GlcNAc transferase maintains metabolic homeostasis in response to CDK9 inhibition
gan: Gondane, A, et al.
Cyhoeddwyd: (2022)

Computational validation of clonal and subclonal copy number alterations from bulk tumor sequencing using CNAqc
gan: Alice Antonello, et al.
Cyhoeddwyd: (2024-01-01)

Implications of celebrity endorsement of prostate cancer awareness in a tertiary referral unit – the ‘Fry‐Turnbull’ effect
gan: Lovegrove, CE, et al.
Cyhoeddwyd: (2020)

Bulk T-cell receptor sequencing confirms clonality in obstetric antiphospholipid syndrome and may as a potential biomarker
gan: Qi Liu, et al.
Cyhoeddwyd: (2024-12-01)

Evaluating statistical approaches to define clonal origin of tumours using bulk DNA sequencing: context is everything
gan: Tanjina Kader, et al.
Cyhoeddwyd: (2022-02-01)

Failure of phylogeny inferred from multilocus sequence typing to represent bacterial phylogeny
gan: Alan K. L. Tsang, et al.
Cyhoeddwyd: (2017-07-01)

Harnessing the potential of multimodal radiotherapy in prostate cancer
gan: Philippou, Y, et al.
Cyhoeddwyd: (2020)

Perspectives on technology - prostate cancer: is local anaesthetic transperineal prostate biopsy really better than transrectal biopsy?
gan: Berridge, C, et al.
Cyhoeddwyd: (2024)

CDK9 inhibition activates innate immune response through viral mimicry
gan: Yalala, S, et al.
Cyhoeddwyd: (2024)

Comparative phylogenies of yellow fever isolates from Peru and Brazil.
gan: Bryant, J, et al.
Cyhoeddwyd: (2003)

The architecture of clonal expansions in morphologically normal tissue from cancerous and non-cancerous prostates
gan: Buhigas, C, et al.
Cyhoeddwyd: (2022)

Anti-tumor memory CD4 and CD8 T-cells quantified by bulk T-cell receptor (TCR) clonal analysis
gan: Yanhua Gao, et al.
Cyhoeddwyd: (2023-03-01)

ClonalFrameML: efficient inference of recombination in whole bacterial genomes
gan: Didelot, X, et al.
Cyhoeddwyd: (2015)

Diagnostic pathways for screen-detected prostate cancer: The plot thickens
gan: Hamdy, F, et al.
Cyhoeddwyd: (2017)

Inferring phylogenies from RAD sequence data.
gan: Benjamin E R Rubin, et al.
Cyhoeddwyd: (2012-01-01)

Bootstrapping phylogenies inferred from rearrangement data
gan: Lin Yu, et al.
Cyhoeddwyd: (2012-08-01)

Statistical analysis plan for the TRANSLATE (TRANSrectal biopsy versus Local Anaesthetic Transperineal biopsy Evaluation of potentially clinically significant prostate cancer) multicentre randomised controlled trial
gan: Marian, IR, et al.
Cyhoeddwyd: (2024)

The dissociation of interleukin-2 production and antigen-specific helper activity by clonal analysis.
gan: Lamb, JR, et al.
Cyhoeddwyd: (1983)

Systematic evaluation of B-cell clonal family inference approaches
gan: Daria Balashova, et al.
Cyhoeddwyd: (2024-02-01)

Likelihood-Based Inference of B Cell Clonal Families.
gan: Duncan K Ralph, et al.
Cyhoeddwyd: (2016-10-01)