Preprints

Integrative Spatial Modelling of Cellular Plasticity using Graph Neural Networks and Geostatistics

Withnell, Celik, Secrier, 2025.

EnrichMap: Spatially informed enrichment analysis for functional interpretation of spatial transcriptomics

Celik, Secrier, 2025.

Balancing tumour proliferation and sustained cell cycle arrest through proteostasis remodelling drives immune niche compartmentalisation in breast cancer

Celik, Withnell, Pan, Chu, Labbadia, Secrier, 2025.

Classifying epithelial-mesenchymal transition states in single cell cancer data using large language models

Pan, Withnell, Secrier, 2024.

A deep learning and graph-based approach to characterise the immunological landscape and spatial architecture of colon cancer tissue

Parreno-Centeno, Tagliazucchi, Withnell, Pan, Secrier, 2021.

2025

TDP-43 loss induces cryptic polyadenylation in ALS/FTD

Bryce-Smith et al, 2025

Nature Neurosci

Decrypting cancer's spatial code: from single cells to tissue niches

Celik, Pan, Withnell, Lam, Secrier, 2025.

Mol Oncol

2024

SpottedPy quantifies relationships between spatial transcriptomic hotspots and uncovers environmental cues of epithelial-mesenchymal plasticity in breast cancer

Withnell, Secrier, 2024.

Genome Biol

2023

Multi-scale characterisation of homologous recombination deficiency in breast cancer

Jacobson, Pan, Fisher, Secrier, 2023.

Genome Med

HistoMIL: A Python package for training multiple instance learning models on histopathology slides

Pan and Secrier, 2023.

iScience

Mutational signature dynamics shaping the evolution of oesophageal adenocarcinoma

Abbas, Pich... Fitzgerald, Secrier, 2023.

Nat Commun

Immune Cell Abundance and T-cell Receptor Landscapes Suggest New Patient Stratification Strategies in Head and Neck Squamous Cell Carcinoma

Secrier, ... Angel, 2023.

Cancer Res Commun

Genomic hallmarks and therapeutic implications of G0 cell cycle arrest in cancer

Wiecek,..., Secrier, 2023.

Genome Biology

Genomic and microenvironmental heterogeneity shaping epithelial-to-mesenchymal trajectories in cancer

Malagoli Tagliazucchi,..., Secrier, 2023.

Nature Commun

2021

Pan-Cancer Survey of Tumor Mass Dormancy and Underlying Mutational Processes

Wiecek*, Jacobson*, Lason, Secrier, 2021.

Front Cell Dev Biol

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

Ococks et al, 2021.

Gastroenterology

NMJ-Analyser identifies subtle early changes in mouse models of neuromuscular disease

Maza et al, 2021.

Sci Rep

2020

A Comparison of Low Read Depth QuantSeq 3' Sequencing to Total RNA-Seq in FUS Mutant Mice

Jarvis et al, 2020.

Front Genet

Endoscopic tumour morphology impacts survival in adenocarcinoma of the oesophagus

Knight et al, 2020.

Eur J Surg Oncol

Truncated stathmin-2 is a marker of TDP-43 pathology in frontotemporal dementia

Prudencio et al, 2020.

J Clin Invest

Identification of Subtypes of Barrett's Esophagus and Esophageal Adenocarcinoma Based on DNA Methylation Profiles and Integration of Transcriptome and Genome Data

Jammula et al, 2020.

Gastroenterology

Genomic Evidence Supports a Clonal Diaspora Model for Metastases of Esophageal Adenocarcinoma

Noorani et al, 2020.

Nat Genetics

2019

Patient-specific Cancer Genes Contribute to Recurrently Perturbed Pathways and Establish Therapeutic Vulnerabilities in Esophageal Adenocarcinoma

Mourikis et al, 2019.

Nat Commun

Transcriptomic Profiling Reveals Three Molecular Phenotypes of Adenocarcinoma at the Gastroesophageal Junction

Bornschein et al, 2019.

Int J Cancer

Immune Activation by DNA Damage Predicts Response to Chemotherapy and Survival in Oesophageal Adenocarcinoma

Turkington et al, 2019.

Gut

The Landscape of Selection in 551 Esophageal Adenocarcinomas Defines Genomic Biomarkers for the Clinic

Frankell et al, 2019.

Nat Genetics

2018

Identification of prognostic phenotypes of esophageal adenocarcinoma in 2 independent cohorts.

Sawas et al, 2018.

Gastroenterology

Organoid cultures recapitulate esophageal adenocarcinoma heterogeneity providing a model for clonality studies and precision therapeutics.

Li, Francies et al, 2018.

Nat Commun

Molecular landscape of esophageal cancer: implications for early detection and personalized therapy.

Talukdar et al. 2018.

Ann N Y Acad Sci

2017

Multicentre cohort study to define and validate pathological assessment of response to neoadjuvant therapy in oesophagogastric adenocarcinoma.

Noble et al. 2017.

Br J Surg

A comparative analysis of whole genome sequencing of esophageal adenocarcinoma pre- and post-chemotherapy.

Noorani et al. 2017.

Genome Res

2016

Mutational signatures in esophageal adenocarcinoma define etiologically distinct subgroups with therapeutic relevance.

Secrier, Li et al. 2016.

Nat Genet

Authentication and characterisation of a new oesophageal adenocarcinoma cell line: MFD-1.

Garcia et al. 2016.

Sci Rep

Whole-genome sequencing of nine esophageal adenocarcinoma cell lines.

Contino et al. 2016.

F1000Res

Signatures of mutational processes and associated risk factors in esophageal squamous cell carcinoma: a geographically independent stratification strategy?

Secrier and Fitzgerald. 2016.

Gastroenterology

2015

Molecular effects of Lapatinib in the treatment of HER2 overexpressing oesophago-gastric adenocarcinoma.

De Silva et al. 2015.

Br J Cancer

Whole-genome sequencing provides new insights into the clonal architecture of Barrett's esophagus and esophageal adenocarcinoma.

Ross-Innes et al. 2015.

Nat Genetics

2014

Ordering of mutations in preinvasive disease stages of esophageal carcinogenesis.

Weaver et al. 2014.

Nat Genetics

Visualizing time-related data in biology, a review.

Secrier and Schneider. 2014.

Brief Bioinform

2013

PhenoTimer: software for the visual mapping of time-resolved phenotypic landscapes.

Secrier and Schneider. 2013.

PLoS One

2012

Arena3D: visualizing time-driven phenotypic differences in biological systems.

Secrier et al 2012.

BMC Bioinformatics

2011

How neurons migrate: a dynamic in-silico model of neuronal migration in the developing cortex.

Setty et al 2011.

BMC Syst Biol

Using graph theory to analyze biological networks.

Pavlopoulos et al 2011.

BioData Min

2009

The ABC of reverse engineering biological signalling systems.

Secrier, Toni and Stumpf. 2009.

Mol Biosyst

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