Publications

A decade of the Oesophageal Cancer Clinical and Molecular Stratification Consortium

Authors (23)

CJ Peters
Y Ang
Francesca Ciccarelli
H Coles
HG Coleman
G Contino
[...]
EC Smyth
I Soomro
TJ Underwood
OCCAMS Consortium
RC Fitzgerald

Nature Medicine

Published 1 January 2024

Crick labs

Francesca Ciccarelli

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Rarity: discovering rare cell populations from single-cell imaging data

Authors (6)

Kaspar Märtens
Michele Bortolomeazzi
Lucia Montorsi
Jo Spencer
Francesca Ciccarelli
Christopher Yau

Bioinformatics

Published 1 December 2023

Crick labs

Francesca Ciccarelli

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Understanding the malignant potential of gastric metaplasia of the oesophagus and its relevance to Barrett’s oesophagus surveillance: individual-level data analysis

Authors (12)

Emily L Black
Emma Ococks
Ginny Devonshire
Alvin Wei Tian Ng
Maria O’Donovan
Shalini Malhotra
[...]
Ahmad Miremadi
Adam Freeman
Hannah Coles
Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS) Consortium
Rebecca C Fitzgerald

Gut

Published 21 November 2023

Crick labs

Francesca Ciccarelli

Full details

Apoptosis in mesenchymal stromal cells activates an immunosuppressive secretome predicting clinical response in Crohn's disease

Authors (13)

Tik Shing Cheung
Chiara Giacomini
Matteo Cereda
Alvaro Avivar-Valderas
Daria Capece
Giuliana Minani Bertolino
[...]
Rachele Ciccocioppo
Guido Franzoso
Antonio Galleu
Francesca Ciccarelli
Francesco Dazzi

Molecular Therapy

Published 6 December 2023

Crick labs

Francesca Ciccarelli

Full details

The transcriptional landscape of endogenous retroelements delineates esophageal adenocarcinoma subtypes

Authors (11)

Anastasiya Kazachenka
Jane Loong
Jan Attig
George Young
Piyali Ganguli
Ginny Devonshire
Nicola Grehan
The OCCAMS Consortium
Francesca Ciccarelli
Rebecca C Fitzgerald
George Kassiotis

NAR Cancer

Published 1 September 2023

Crick labs/ facilities

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Mutational signature dynamics shaping the evolution of oesophageal adenocarcinoma

Authors (80)

Sujath Abbas
Oriol Pich
Ginny Devonshire
Shahriar A Zamani
Annalise Katz-Summercorn
Sarah Killcoyne
[...]
Helen Coleman
Russell D Petty
Freddie Bartlett
Rebecca C Fitzgerald
Maria Secrier

Nature Communications

Published 15 July 2023

Crick labs

Francesca Ciccarelli

Full details

Mechanistic insights into the interactions between cancer drivers and the tumour immune microenvironment

Authors (4)

Genome Medicine

Published 5 June 2023

Crick labs

Francesca Ciccarelli

Full details

USP7 inactivation suppresses APC-mutant intestinal hyperproliferation and tumor development

Authors (11)

Stem Cell Reports

Published 14 February 2023

Crick labs/ facilities

Full details

Somatic variation in normal tissues: friend or foe of cancer early detection?

Authors (3)

Annals of Oncology

Published 1 December 2022

Crick labs

Francesca Ciccarelli

Full details

Topoisomerase I poison-triggered immune gene activation is markedly reduced in human small-cell lung cancers by impairment of the cGAS/STING pathway

Authors (7)

Jessica Marinello
Andrea Arleo
Marco Russo
Maria Delcuratolo
Francesca Ciccarelli
Yves Pommier
Giovanni Capranico

British Journal of Cancer

Published 19 October 2022

Crick labs

Francesca Ciccarelli

Full details

Reflected stemness as a potential driver of the tumour microenvironment

Authors (3)

Trends in Cell Biology

Published 1 December 2022

Crick labs

Full details

Exome sequencing of hepatocellular carcinoma in lemurs identifies potential cancer drivers: A pilot study

Authors (14)

Ella F Gunady
Kathryn E Ware
Sarah Hoskinson Plumlee
Nicolas Devos
David Corcoran
Joseph Prinz
[...]
Jeffrey L Thorne
Robert Schopler
Jeffrey I Everitt
William C Eward
Jason A Somarelli

Evolution Medicine and Public Health

Published 10 May 2022

Crick labs

Francesca Ciccarelli

Full details

Genome-protective topoisomerase 2a-dependent G2
arrest requires p53 in hTERT-positive cancer cells

Authors (12)

Nicola Lockwood
Silvia Martini
Ainara Lopez-Pardo
Katharina Deiss
Hendrika A Segeren
Robert K Semple
[...]
Dimitra Repana
Mathias Cobbaut
Tanya Soliman
Francesca Ciccarelli
Peter Parker

Cancer Research

Published 1 March 2022

Crick labs/ facilities

Full details

A SIMPLI (Single-cell Identification from MultiPLexed Images) approach for spatially-resolved tissue phenotyping at single-cell resolution

Authors (11)

Michele Bortolomeazzi
Lucia Montorsi
Damjan Temelkovski
Mohamed Reda Keddar
Amelia Acha
Michael J Pitcher
Gianluca Basso
Luigi Laghi
Manuel Rodriguez-Justo
Jo Spencer
Francesca Ciccarelli

Nature Communications

Published 9 February 2022

Crick labs

Francesca Ciccarelli

Full details

Comparative assessment of genes driving cancer and somatic evolution in non-cancer tissues: an update of the Network of Cancer Genes (NCG) resource

Authors (16)

Genome Biology

Published 26 January 2022

Crick labs/ facilities

Full details

Clone competition as a mechanism to reduce tumor formation

Authors (3)

Developmental Cell

Published 20 December 2021

Crick labs

Full details

Serial circulating tumor DNA detection using a personalized, tumor-informed assay in esophageal adenocarcinoma patients following resection

Authors (82)

Emma Ococks
Shruti Sharma
Alvin Wei Tian Ng
OCCAMS Consortium
Alexey Aleshin
Rebecca C Fitzgerald
[...]
Anna Grabowska
Richard Turkington
Damian McManus
Helen Coleman
Russell D Petty

Gastroenterology

Published 1 November 2021

Crick labs

Francesca Ciccarelli

Full details

Immunogenomics of colorectal cancer response to checkpoint blockade: analysis of the KEYNOTE 177 trial and validation cohorts

Authors (29)

Michele Bortolomeazzi
Mohamed Reda Keddar
Lucia Montorsi
Amelia Acha
Lorena Benedetti
Damjan Temelkovski
[...]
Peter Parker
Manuel Rodriguez-Justo
Kai-Keen Shiu
Jo Spencer
Francesca Ciccarelli

Gastroenterology

Published 1 October 2021

Crick labs/ facilities

Full details

ImmunoCluster provides a computational framework for the nonspecialist to profile high-dimensional cytometry data

Authors (18)

James W Opzoomer
Jessica A Timms
Kevin Blighe
Thanos P Mourikis
Nicolas Chapuis
Richard Bekoe
[...]
Peter Parker
Michaela Fontenay
Paul R Barber
James N Arnold
Shahram Kordasti

eLife

Published 30 April 2021

Crick labs

Full details

Pan-cancer detection of driver genes at the single-patient resolution

Authors (4)

Genome Medicine: medicine in the post-genomic era

Published 1 February 2021

Crick labs

Francesca Ciccarelli

Full details

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Postdoctoral clinical fellows

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: Publications

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Pubications

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Journal

A decade of the Oesophageal Cancer Clinical and Molecular Stratification Consortium

Rarity: discovering rare cell populations from single-cell imaging data

Understanding the malignant potential of gastric metaplasia of the oesophagus and its relevance to Barrett’s oesophagus surveillance: individual-level data analysis

Apoptosis in mesenchymal stromal cells activates an immunosuppressive secretome predicting clinical response in Crohn's disease

The transcriptional landscape of endogenous retroelements delineates esophageal adenocarcinoma subtypes

Mutational signature dynamics shaping the evolution of oesophageal adenocarcinoma

Mechanistic insights into the interactions between cancer drivers and the tumour immune microenvironment

USP7 inactivation suppresses APC-mutant intestinal hyperproliferation and tumor development

Somatic variation in normal tissues: friend or foe of cancer early detection?

Topoisomerase I poison-triggered immune gene activation is markedly reduced in human small-cell lung cancers by impairment of the cGAS/STING pathway

Reflected stemness as a potential driver of the tumour microenvironment

Exome sequencing of hepatocellular carcinoma in lemurs identifies potential cancer drivers: A pilot study

Genome-protective topoisomerase 2a-dependent G2
arrest requires p53 in hTERT-positive cancer cells

A SIMPLI (Single-cell Identification from MultiPLexed Images) approach for spatially-resolved tissue phenotyping at single-cell resolution

Comparative assessment of genes driving cancer and somatic evolution in non-cancer tissues: an update of the Network of Cancer Genes (NCG) resource

Clone competition as a mechanism to reduce tumor formation

Serial circulating tumor DNA detection using a personalized, tumor-informed assay in esophageal adenocarcinoma patients following resection

Immunogenomics of colorectal cancer response to checkpoint blockade: analysis of the KEYNOTE 177 trial and validation cohorts

ImmunoCluster provides a computational framework for the nonspecialist to profile high-dimensional cytometry data

Pan-cancer detection of driver genes at the single-patient resolution

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