Publications

Peer-reviewed research articles and reviews

* denotes equal contribution · Highlighted papers indicate first/corresponding author work

2025

Standardized metrics for assessment and reproducibility of imaging-based spatial transcriptomics datasets

Plummer JT*, Dezem FS*, Cook DP*, Park J*, ... Wrana JL, ... Martelotto LG

Nature Biotechnology Link ↗
Loss of LATS1 and LATS2 promotes ovarian tumor formation by enhancing AKT activity and PD-L1 expression

Zhu Y, Abedini A, ... Cook DP, Vanderhyden BC

Oncogene Link ↗
Inherent inter- and intratumoral heterogeneity drives phenotypic plasticity and treatment response of pancreatic cancer organoids

Papargyriou A, Najajreh M, Cook DP, ... Rad R, Reichert M

Nature Biomedical Engineering Link ↗
LAG3 marks activated but hyporesponsive NK cells

Vasilyeva V, Makinson O, ... Cook DP, ... Ardolino M, Marotel M

European Journal of Immunology Link ↗
Transglutaminase 2 regulates ovarian cancer metastasis by modulating the immune microenvironment

Ibrahim D, Grondin M, ... Cook DP, Keillor JW, Vanderhyden BC

Frontiers in Immunology Link ↗
A human single-nuclei atlas reveals novel cell states during the pseudoglandular-to-canalicular transition

Renesme L, Lesage F, Cook DP, ... Mižík I, Thébaud B

American Journal of Respiratory Cell and Molecular Biology Link ↗
Mapping disease-specific vascular cell populations responsible for obliterative arterial remodelling during the development of pulmonary arterial hypertension

Cober ND, McCourt E, Godoy RS, ... Bonnet S, Stewart DJ

Cardiovascular Research Link ↗

2024

PD-L1 promotes oncolytic virus infection via a metabolic shift that inhibits the type I IFN pathway

Hodgins JJ, Abou-Hamad J, ... Cook DP, Ardolino M

Journal of Experimental Medicine Link ↗
Single-cell RNA sequencing reveals repair features of human umbilical cord mesenchymal stromal cells

Cyr-Depauw C, Cook DP, Mižík I, ... Vanderhyden BC, ... Thébaud B

American Journal of Respiratory and Critical Care Medicine Link ↗
Transcriptional regulation of the postnatal cardiac conduction system heterogeneity

Oh Y, Abid R, Dababneh S, Cook DP, ... Vanderhyden BC, ... Kim KH

Nature Communications Link ↗
PTEN loss shapes macrophage dynamics in high-grade serous ovarian carcinoma

Spear S, Le Saux O, ... Cook DP, Vanderhyden BC, ... McNeish IA

Cancer Research Link ↗
The Drosophila adult midgut progenitor cells arise from asymmetric divisions in neuroblast-like cells

Plygawko AT, Attolini CSO, Pitsidianaki I, Cook DP, Darby AC, Campbell K

Developmental Cell Link ↗
LINE1 and PRC2 control nucleolar organization and repression of the 8C state in human ESCs

Zhang J, Ataei L, ... Cook DP, ... Wrana JL, ... Ramalho-Santos M

Developmental Cell Link ↗
Chromatin remodelling in damaged intestinal crypts orchestrates redundant TGFβ and Hippo signaling to drive regeneration

Fink M, Njah K, Patel SJ, Cook DP, ... Wrana JL

Nature Cell Biology Link ↗
FGL2 promotes tumour growth and attenuates infiltration of activated immune cells in melanoma and ovarian cancer models

Galpin KJC, Rodriguez GM, Maranda V, Cook DP, ... Ardolino M, Vanderhyden BC

Scientific Reports Link ↗

2023

Comparative analysis of syngeneic mouse models of high-grade serous ovarian cancer

Cook DP, Galpin K, Rodriguez G, ... Koti M, Vanderhyden BC

Communications Biology Link ↗
Single cell analysis predicts CD8 T cell exhaustion through the LGALS3-LAG3 axis by mesenchymal cancer cells in ovarian tumours

Yakubovich E, Cook DP, Rodriguez GM, Vanderhyden BC

npj Systems Biology and Applications Link ↗
Single cell transcriptomic atlas of lung microvascular regeneration after targeted endothelial cell ablation

Godoy RS, Cober ND, Cook DP, ... Stewart DJ

eLife Link ↗
Prenatal low-dose methylmercury exposure causes CREB-dependent premature neuronal differentiation and autism-like behaviours in a rodent model

Loan AC, Leung JW, Cook DP, Ko C, Vanderhyden BC, Wang J, Chan HM

iScience Link ↗
Absolute scaling of single-cell transcriptomes identifies pervasive hypertranscription in adult stem and progenitor cells

Kim YK, Cho B, Cook DP, Trcka D, Wrana JL, Ramalho-Santos M

Cell Reports Link ↗

2022

A specialist-generalist framework for epithelial-mesenchymal plasticity in cancer

Cook DP, Wrana JL

Trends in Cancer Link ↗
Transcriptional census of epithelial-mesenchymal plasticity in cancer

Cook DP, Vanderhyden BC

Science Advances Link ↗
Metformin prevents age-associated ovarian fibrosis by modulating the immune landscape in female mice

Landry DA, Yakubovich E, Cook DP, Fasih S, Upham J, Vanderhyden BC

Science Advances Link ↗
When killers become thieves: trogocytosed PD-1 inhibits NK cells in cancer

Hasim MS, Vulpis E, ... Cook DP, ... Ardolino M

Science Advances Link ↗
The tumor immune profile of murine ovarian cancer models: an essential tool for ovarian cancer immunotherapy research

Rodriguez G, Galpin K, Cook DP, ... Vanderhyden BC

Cancer Research Communications Link ↗
VIVA1: A more invasive subclone of MDA-MB-134VI invasive lobular carcinoma cells with increased metastatic potential in xenograft models

Allen V, Coulombe J, ... Cook DP, ... Addison C

British Journal of Cancer Link ↗
Single-cell transcriptomic analysis of chemosensory neuroepithelial cells from the gills of zebrafish

Pan W, Godoy RS, Cook DP, Scott AL, Nurse CA, Jonz MG

Scientific Reports Link ↗
Single-cell RNA sequencing-based characterization of resident lung mesenchymal stromal cells in bronchopulmonary dysplasia

Mižíková I, Lesage F, Cyr-Depauw C, Cook DP, ... Vanderhyden BC, Thébaud B

Stem Cells Link ↗
Preventing surgery-induced NK cell dysfunction using anti-TGFβ immunotherapeutics

Market M, Tennakoon G, Scaffidi M, Cook DP, ... Vanderhyden BC, Auer RC

International Journal of Molecular Sciences Link ↗

2021

Transcriptional heterogeneity of stemness phenotypes in the ovarian epithelium

Carter LE*, Cook DP*, McCloskey CW, ... Vanderhyden BC

Communications Biology Link ↗
Single-cell transcriptomic analysis of murine lung development on hyperoxia-induced damage

Hurskainen KM, Mižíková I, Cook DP, ... Vanderhyden BC, Thébaud B

Nature Communications Link ↗
Identification of novel lipid droplet factors that regulate lipophagy and cholesterol efflux in macrophage foam cells

Robichaud S, Fairman G, ... Cook DP, ... Ouimet M

Autophagy Link ↗
Identification of Rac guanine nucleotide exchange factors promoting Lgl1 phosphorylation in glioblastoma

Lavictoire SJ, Jomaa D, Gont A, Jardine K, Cook DP, Lorimer IAJ

Journal of Biological Chemistry Link ↗
Periostin gene expression in Neu-positive breast cancer cells is regulated by a FGFR signaling cross talk with TGFβ/PI3K/AKT pathways

Labreche C, Cook DP, Abou-Hamad J, ... Sabourin L

Breast Cancer Research Link ↗

2020

Context specificity of the EMT transcriptional response

Cook DP, Vanderhyden BC

Nature Communications Link ↗
RIPK1 gene variants associate with obesity in humans and can be therapeutically silenced to reduce obesity in mice

Karunakaran D, Turner AW, ... Cook DP, ... Rayner KJ

Nature Metabolism Link ↗
Loss of the Ste20-like kinase induces a basal/stem-like phenotype in HER2-positive breast cancers

Al-Zahrani K, Abou-Hamad J, Cook DP, ... Vanderhyden BC, Sabourin LA

Oncogene Link ↗
Science outreach: Six examples of programs that enrich the learning environments of students and educators

Cook DP, Steed K, Read C, ... Carnegie J

HAPS Educator Link ↗

2019

Ovarian cancer and the evolution of subtype classifications using transcriptional profiling

Cook DP, Vanderhyden BC

Biology of Reproduction Link ↗
Metformin abrogates age-associated ovarian fibrosis

McCloskey CW, Cook DP, Kelly BS, ... Vanderhyden BC

Clinical Cancer Research Link ↗
COX2 is induced in the ovarian epithelium during ovulatory wound repair and promotes cell survival

Carter LE, Cook DP, Collins O, ... Vanderhyden BC

Biology of Reproduction Link ↗

2018

Single-cell RNA sequencing reveals transcriptional dynamics of estrogen-induced dysplasia in the ovarian surface epithelium

Vuong NH*, Cook DP*, Forrest LA, ... Vanderhyden BC

PLoS Genetics Link ↗
Assessing the efficacy of androgen receptor and Sox10 as independent markers of the triple-negative breast cancer subtype by transcriptome profiling

Al-Zahrani K, Cook DP, Vanderhyden BC, Sabourin LA

Oncotarget Link ↗

2017

The evolution and functional diversification of the deubiquitinating enzyme superfamily

Vlasschaert C, Cook DP, Xia X, Gray D

Genome Biology and Evolution Link ↗

2025

Standardized metrics for assessment and reproducibility of imaging-based spatial transcriptomics datasets

Loss of LATS1 and LATS2 promotes ovarian tumor formation by enhancing AKT activity and PD-L1 expression

Inherent inter- and intratumoral heterogeneity drives phenotypic plasticity and treatment response of pancreatic cancer organoids

LAG3 marks activated but hyporesponsive NK cells

Transglutaminase 2 regulates ovarian cancer metastasis by modulating the immune microenvironment

A human single-nuclei atlas reveals novel cell states during the pseudoglandular-to-canalicular transition

Mapping disease-specific vascular cell populations responsible for obliterative arterial remodelling during the development of pulmonary arterial hypertension

2024

PD-L1 promotes oncolytic virus infection via a metabolic shift that inhibits the type I IFN pathway

Single-cell RNA sequencing reveals repair features of human umbilical cord mesenchymal stromal cells

Transcriptional regulation of the postnatal cardiac conduction system heterogeneity

PTEN loss shapes macrophage dynamics in high-grade serous ovarian carcinoma

The Drosophila adult midgut progenitor cells arise from asymmetric divisions in neuroblast-like cells

LINE1 and PRC2 control nucleolar organization and repression of the 8C state in human ESCs

Chromatin remodelling in damaged intestinal crypts orchestrates redundant TGFβ and Hippo signaling to drive regeneration

FGL2 promotes tumour growth and attenuates infiltration of activated immune cells in melanoma and ovarian cancer models

2023

Comparative analysis of syngeneic mouse models of high-grade serous ovarian cancer

Single cell analysis predicts CD8 T cell exhaustion through the LGALS3-LAG3 axis by mesenchymal cancer cells in ovarian tumours

Single cell transcriptomic atlas of lung microvascular regeneration after targeted endothelial cell ablation

Prenatal low-dose methylmercury exposure causes CREB-dependent premature neuronal differentiation and autism-like behaviours in a rodent model

Absolute scaling of single-cell transcriptomes identifies pervasive hypertranscription in adult stem and progenitor cells

2022

A specialist-generalist framework for epithelial-mesenchymal plasticity in cancer

Transcriptional census of epithelial-mesenchymal plasticity in cancer

Metformin prevents age-associated ovarian fibrosis by modulating the immune landscape in female mice

When killers become thieves: trogocytosed PD-1 inhibits NK cells in cancer

The tumor immune profile of murine ovarian cancer models: an essential tool for ovarian cancer immunotherapy research

VIVA1: A more invasive subclone of MDA-MB-134VI invasive lobular carcinoma cells with increased metastatic potential in xenograft models

Single-cell transcriptomic analysis of chemosensory neuroepithelial cells from the gills of zebrafish

Single-cell RNA sequencing-based characterization of resident lung mesenchymal stromal cells in bronchopulmonary dysplasia

Preventing surgery-induced NK cell dysfunction using anti-TGFβ immunotherapeutics

2021

Transcriptional heterogeneity of stemness phenotypes in the ovarian epithelium

Single-cell transcriptomic analysis of murine lung development on hyperoxia-induced damage

Identification of novel lipid droplet factors that regulate lipophagy and cholesterol efflux in macrophage foam cells

Identification of Rac guanine nucleotide exchange factors promoting Lgl1 phosphorylation in glioblastoma

Periostin gene expression in Neu-positive breast cancer cells is regulated by a FGFR signaling cross talk with TGFβ/PI3K/AKT pathways

2020

Context specificity of the EMT transcriptional response

RIPK1 gene variants associate with obesity in humans and can be therapeutically silenced to reduce obesity in mice

Loss of the Ste20-like kinase induces a basal/stem-like phenotype in HER2-positive breast cancers

Science outreach: Six examples of programs that enrich the learning environments of students and educators

2019

Ovarian cancer and the evolution of subtype classifications using transcriptional profiling

Metformin abrogates age-associated ovarian fibrosis

COX2 is induced in the ovarian epithelium during ovulatory wound repair and promotes cell survival

2018

Single-cell RNA sequencing reveals transcriptional dynamics of estrogen-induced dysplasia in the ovarian surface epithelium

Assessing the efficacy of androgen receptor and Sox10 as independent markers of the triple-negative breast cancer subtype by transcriptome profiling

2017

The evolution and functional diversification of the deubiquitinating enzyme superfamily