Vera Pancaldi

63
Documents

Publications

Publications

Unveiling Epigenetic Regulatory Elements Associated with Breast Cancer Development

Marta Jardanowska-Kotuniak , Michał Dramiński , Michal Wlasnowolski , Marcin Łapiński , Kaustav Sengupta et al.

International Journal of Molecular Sciences, 2025, 26 (14), pp.6558. ⟨10.3390/ijms26146558⟩

Article dans une revue hal-05263929v1

Microbiome gut community structure and functionality are associated with symptom severity in non-responsive celiac disease patients undergoing a gluten-free diet

Laura Judith Marcos-Zambrano , Blanca Lacruz-Pleguezuelos , Elena Aguilar-Aguilar , Helena Marcos-Pasero , Alberto Valdés et al.

mSystems, 2025, 10 (7), ⟨10.1128/msystems.00143-25⟩

Article dans une revue hal-05263928v1
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TNF signature in advanced melanoma patients treated with immune checkpoint inhibitors: Results from the MELANFα clinical study

Mathieu Virazels , Amélie Lusque , Stéphanie Brayer , Matthieu Genais , Carine Dufau et al.

International Journal of Cancer, 2025, ⟨10.1002/ijc.35416⟩

Article dans une revue (data paper) hal-04996473v1

Global chromatin reorganization and regulation of genes with specific evolutionary ages during differentiation and cancer

Flavien Raynal , Kaustav Sengupta , Dariusz Plewczynski , Benoît Aliaga , Vera Pancaldi

Nucleic Acids Research, 2025, 53 (4), ⟨10.1093/nar/gkaf084⟩

Article dans une revue hal-05263926v1
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Cytidine Deaminase Resolves Replicative Stress and Protects Pancreatic Cancer from DNA-Targeting Drugs

Audrey Lumeau , Nicolas Bery , Audrey Francès , Marion Gayral , Guillaume Labrousse et al.

Cancer Research, 2024, 84 (7), pp.1013 - 1028. ⟨10.1158/0008-5472.can-22-3219⟩

Article dans une revue hal-04743033v1
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Transcriptomics profiling of the non-small cell lung cancer microenvironment across disease stages reveals dual immune cell-type behaviors

Marcelo Hurtado , Leila Khajavi , Abdelmounim Essabbar , Michael Kammer , Ting Xie et al.

Frontiers in Immunology, 2024, 15, ⟨10.3389/fimmu.2024.1394965⟩

Article dans une revue hal-04874132v1
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Evidence of Epigenetic Oncogenesis: A Turning Point in Cancer Research

Jean‐pascal Capp , Benoît Aliaga , Vera Pancaldi

BioEssays, 2024, Online ahead of print. ⟨10.1002/bies.202400183⟩

Article dans une revue hal-04840627v1
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An agent-based model of monocyte differentiation into tumour-associated macrophages in chronic lymphocytic leukemia

Nina Verstraete , Malvina Marku , Marcin Domagala , Hélène Arduin , Julie Bordenave et al.

iScience, 2023, 26 (6), pp.106897. ⟨10.1016/j.isci.2023.106897⟩

Article dans une revue inserm-04777519v1
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Integrated Multi-omics Analysis of Early Lung Adenocarcinoma Links Tumor Biological Features with Predicted Indolence or Aggressiveness

Maria-Fernanda Senosain , Yong Zou , Khushbu Patel , Shilin Zhao , Alexis Coullomb et al.

Cancer Research Communications, 2023, 3, pp.1350 - 1365. ⟨10.1158/2767-9764.crc-22-0373⟩

Article dans une revue hal-04874157v1

3D chromatin interactions involving Drosophila insulators are infrequent but preferential and arise before TADs and transcription

Olivier Messina , Flavien Raynal , Julian Gurgo , Jean-Bernard Fiche , Vera Pancaldi et al.

Nature Communications, 2023, 14 (1), pp.6678. ⟨10.1038/s41467-023-42485-y⟩

Article dans une revue hal-04881279v1

From time-series transcriptomics to gene regulatory networks: A review on inference methods

Malvina Marku , Vera Pancaldi

PLoS Computational Biology, 2023, 19 (8), pp.e1011254. ⟨10.1371/journal.pcbi.1011254⟩

Article dans une revue hal-04881280v1
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Network models of chromatin structure

Vera Pancaldi

Current Opinion in Genetics and Development, 2023, 80, pp.102051. ⟨10.1016/j.gde.2023.102051⟩

Article dans une revue hal-04881282v1
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The antitumoral activity of TLR7 ligands is corrupted by the microenvironment of pancreatic tumors

Marie Rouanet , Naima Hanoun , Cindy Ferreira , Pierre Garcin , Martin Sramek et al.

Molecular Therapy, 2022, 30 (4), pp.1553-1563. ⟨10.1016/j.ymthe.2022.01.018⟩

Article dans une revue hal-04577745v1

3D chromatin connectivity underlies replication origin efficiency in mouse embryonic stem cells

Karolina Jodkowska , Vera Pancaldi , Maria Rigau , Ricardo Almeida , José M Fernández-Justel et al.

Nucleic Acids Research, 2022, 50 (21), pp.12149-12165. ⟨10.1093/nar/gkac1111⟩

Article dans une revue hal-04881284v1

Epigenome-wide analysis of T-cell large granular lymphocytic leukemia identifies BCL11B as a potential biomarker

Patricia Johansson , Teresa Laguna , Julio Ossowski , Vera Pancaldi , Martina Brauser et al.

Clinical Epigenetics, 2022, 14 (1), pp.148. ⟨10.1186/s13148-022-01362-z⟩

Article dans une revue hal-04881285v1

Activation of Vitamin D Receptor Pathway Enhances Differentiating Capacity in Acute Myeloid Leukemia with Isocitrate Dehydrogenase Mutations

Marie Sabatier , Emeline Boet , Sonia Zaghdoudi , Nathan Guiraud , Alexis Hucteau et al.

Cancers, 2021, 13 (20), pp.5243. ⟨10.3390/cancers13205243⟩

Article dans une revue hal-04415805v1
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Mitochondrial metabolism supports resistance to IDH mutant inhibitors in acute myeloid leukemia

Lucille Stuani , Marie Sabatier , Estelle Saland , Guillaume Cognet , Nathalie Poupin et al.

Journal of Experimental Medicine, 2021, 218 (5), pp.e20200924. ⟨10.1084/jem.20200924⟩

Article dans une revue hal-03563454v1
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STAG2 loss-of-function affects short-range genomic contacts and modulates the basal-luminal transcriptional program of bladder cancer cells

Laia Richart , Eleonora Lapi , Vera Pancaldi , Mirabai Cuenca-Ardura , Enrique Carrillo-De-Santa Pau et al.

Nucleic Acids Research, 2021, ⟨10.1093/nar/gkab864⟩

Article dans une revue hal-03385084v1
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Tysserand—fast and accurate reconstruction of spatial networks from bioimages

Alexis Coullomb , Vera Pancaldi

Bioinformatics, 2021, 37 (21), pp.3989-3991. ⟨10.1093/bioinformatics/btab490⟩

Article dans une revue hal-04875000v1

Chromatin Network Analyses: Towards Structure-Function Relationships in Epigenomics

Vera Pancaldi

Frontiers in Bioinformatics, 2021, 1, ⟨10.3389/fbinf.2021.742216⟩

Article dans une revue hal-04881286v1
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Low Replicative Stress Triggers Cell-Type Specific Inheritable Advanced Replication Timing

Lilas Courtot , Elodie Bournique , Chrystelle Maric , Laure Guitton-Sert , Miguel Madrid-Mencía et al.

International Journal of Molecular Sciences, 2021, 22 (9), pp.4959. ⟨10.3390/ijms22094959⟩

Article dans une revue hal-03407911v1
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Interpreting molecular similarity between patients as a determinant of disease comorbidity relationships

Jon Sánchez-Valle , Hector Tejero , José María Fernández , David Juan , Beatriz Urda-García et al.

Nature Communications, 2020, 11 (1), pp.2854. ⟨10.1038/s41467-020-16540-x⟩

Article dans une revue inserm-02878879v1

CovMulNet19, Integrating Proteins, Diseases, Drugs, and Symptoms: A Network Medicine Approach to COVID-19

Nina Verstraete , Giuseppe Jurman , Giulia Bertagnolli , Arsham Ghavasieh , Vera Pancaldi et al.

Network and Systems Medicine, 2020, 3 (1), pp.130-141. ⟨10.1089/nsm.2020.0011⟩

Article dans une revue hal-04881288v1
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Eomes-Dependent Loss of the Co-activating Receptor CD226 Restrains CD8+ T Cell Anti-tumor Functions and Limits the Efficacy of Cancer Immunotherapy

Marianne Weulersse , Assia Asrir , Andrea C Pichler , Lea Lemaitre , Matthias Braun et al.

Immunity, 2020, 53 (4), pp.824-839.e10. ⟨10.1016/j.immuni.2020.09.006⟩

Article dans une revue hal-03030829v1

Insights on TAM Formation from a Boolean Model of Macrophage Polarization Based on In Vitro Studies

Malvina Marku , Nina Verstraete , Flavien Raynal , Miguel Madrid-Mencía , Marcin Domagala et al.

Cancers, 2020, 12 (12), pp.3664. ⟨10.3390/cancers12123664⟩

Article dans une revue hal-03365450v1
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Unveiling new disease, pathway, and gene associations via multi-scale neural network

Thomas Gaudelet , Noël Malod-Dognin , Jon Sánchez-Valle , Vera Pancaldi , Alfonso Valencia et al.

PLoS ONE, 2020, 15 (4), pp.e0231059. ⟨10.1371/journal.pone.0231059⟩

Article dans une revue inserm-02536487v1

Using GARDEN-NET and ChAseR to explore human haematopoietic 3D chromatin interaction networks

Miguel Madrid-Mencía , Emanuele Raineri , Tran Bich Ngoc Cao , Vera Pancaldi

Nucleic Acids Research, 2020, 48 (8), pp.4066-4080. ⟨10.1093/nar/gkaa159⟩

Article dans une revue hal-04881287v1
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Molecular Inverse Comorbidity between Alzheimer’s Disease and Lung Cancer: New Insights from Matrix Factorization

Alessandro Greco , Jon Sanchez Valle , Vera Pancaldi , Anaïs Baudot , Emmanuel Barillot et al.

International Journal of Molecular Sciences, 2019, 20 (13), pp.3114. ⟨10.3390/ijms20133114⟩

Article dans une revue hal-02277045v2

The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery

Eileen Furlong , Sitanshu Gakkhar , Nina Gasparoni , Gilles Gasparoni , Daniel H. Geschwind et al.

Cell, 2016, 167 (5), pp.1145--1149. ⟨10.1016/j.cell.2016.11.007⟩

Article dans une revue hal-01614945v1
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Whole-genome fingerprint of the DNA methylome during human B cell differentiation

Marta Kulis , Angelika Merkel , Simon Heath , Ana C. Queirós , Ronald P. Schuyler et al.

Nature Genetics, 2015, 47 (7), pp.746-756. ⟨10.1038/ng.3291⟩

Article dans une revue hal-01163753v1

multideconv - an integrative pipeline for efficiently combining first and second generation cell type deconvolution results

Marcelo Hurtado , Abdelmounim Essabbar , Leila Khajavi , Vera Pancaldi

2025

Pré-publication, Document de travail hal-05263946v1

FOLR2 transfer by trogocytosis from nurse-like cells to CLL cells is linked to their activation and proliferation

Marcin Domagala , Chloe Bazile , Bastien Gerby , Loïc Ysebaert , Vera Pancaldi et al.

2025

Pré-publication, Document de travail hal-05263935v1

Gut microbial ecosystems differ across metabolic and obesity phenotypes

Blanca Lacruz-Pleguezuelos , Guadalupe Bazán , Sergio Romero-Tapiador , Gala Freixer , Jorge Fernández-Cabezas et al.

2025

Pré-publication, Document de travail hal-05263936v1

Time-series RNA-Seq and data-driven network inference unveil dynamics of cell activation, survival and crosstalk in Chronic Lymphocytic Leukaemia in vitro models

Malvina Marku , Hugo Chenel , Julie Bordenave , Marcelo Hurtado , Marcin Domagala et al.

2025

Pré-publication, Document de travail (preprint/prepublication) hal-05263934v1

Multilayer network approaches to omics data integration in Digital Twins for cancer research

Hugo Chenel , Malvina Marku , Tim James , Andrei Zinovyev , Vera Pancaldi

2025

Pré-publication, Document de travail hal-05263933v1

mosna reveals different types of cellular interactions predictive of response to immunotherapies and survival in cancer

Alexis Coullomb , Paul Monsarrat , Vera Pancaldi

2025

Pré-publication, Document de travail hal-05263931v1

GEM-DeCan: Improved tumor immune microenvironment profiling through novel gene expression and DNA methylation signatures predicts immunotherapy response

Ting Xie , Jacobo Solórzano , Miguel Madrid-Mencía , Abdelmounim Essabbar , Julien Pernet et al.

2025

Pré-publication, Document de travail (preprint/prepublication) hal-05263930v1
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Cytidine deaminase protects pancreatic cancer cells from replicative stress and drives resistance to DNA-targeting drugs

A. Lumeau , N. Bery , A. Francès , M. Gayral , Cyril Ribeyre et al.

2021

Pré-publication, Document de travail hal-03409378v1
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Low replication stress leads to specific replication timing advances associated to chromatin remodelling in cancer cells

Lilas Courtot , Elodie Bournique , Chrystelle Maric , Laure Guitton-Sert , Miguel Madrid-Mencía et al.

2020

Pré-publication, Document de travail hal-03006823v1
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Modulation of the osteogenic potential of bone-marrow mesenchymal stromal cells (BM-MSCs) in 3D-spheroids in the context of aging

Sara Gouarderes , Benoît Aliaga , Paul Bensadoun , Victorien Arnaud , Nicolas Espagnolle et al.

10th Annual ICSA Conference, Sep 2025, Rome, Italy.

Poster de conférence hal-05273625v1
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Dissecting cellular communication in the tumour microenvironment through multiscale dynamical modelling

Malvina Marku , Hugo Chenel , Julie Bordenave , Loic Ysebaert , Mary Poupot et al.

PerMedCoE (Personalised Medicine Center of Excellence) training school and online seminar, Jun 2023, Sant Feliu de Guixols, Spain

Poster de conférence hal-04988682v1

Integrating transcriptomics, imaging and genetic mutations reveals biomarkers potentially associated to immunotherapy response in lung cancer

Leila Khajavi-Ettouati , Abdelmounim Essabbar , Marcelo Hurtado , Julien Mazieres , Vera Pancaldi

Annual EACR Congress: Innovative Cancer Science Europe, Jun 2023, Torino, Italy

Poster de conférence hal-04988648v1

Preclinical and patient transcriptomics RNA-seq highlight the impact of TNF blockade on the inflammatory status of melanoma tumours.

Matthieu Genais , Mathieu Virazels , Anne Montfort , Vera Pancaldi , Bruno Ségui

EACR conferences: Defence is the Best Attack: Immuno-Oncology Breakthroughs, May 2023, Barcelona (ES), Spain

Poster de conférence hal-04991620v1

Network approaches to dissect the epigenome-phenotype connection in immune cells Vera Pancaldi

Vera Pancaldi

Physics of Living Systems: From molecules to systems, Jun 2021, Dresde ( Virtual event ), Germany

Poster de conférence hal-04988686v1

Cytidine deaminase protects pancreatic cancer cells from replicative stress and drive response to DNA-targeting drugs

Audrey Lumeau , Nicolas Béry , Cyril Ribeyre , Abdessamad Elkaoutari , Guillaume Labrousse et al.

AACR Virtual Special Conference: Pancreatic Cancer, Sep 2021, En ligne, United States. American Association for Cancer Research (AACR), Cancer Research, 81 (22 Suppl.), pp.PO-043, 2021, Abstracts: AACR Virtual Special Conference: Pancreatic Cancer; September 29-30, 2021

Poster de conférence hal-05523885v1

One Digital Twin fits all? Building Digital Twins from heterogeneous datasets

Hugo Chenel , Malvina Marku , Vera Pancaldi , Mary Poupot

JOBIM, Apr 2024, Toulouse, France

Communication dans un congrès hal-05026951v1

One Digital Twin fits all? Building Digital Twins from heterogeneous datasets

Malvina Marku , Vera Pancaldi , Mary Poupot

JOBIM, Jun 2024, Toulouse, France

Communication dans un congrès hal-05026942v1

Time series analysis of cellular interactions through gene regulatory network inference

Hugo Chenel , Malvina Marku , Julie Bordenave , Marcin Jakub Domagala , Mary Poupot et al.

Computational Systems Biology of Cancer, Curie Institute, Sep 2024, Paris, France

Communication dans un congrès hal-04988661v1
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Exploring the relation between evolutionary gene age, gene expression and chromatin 3D structure in cancer

Flavien Raynal , Benoît Aliaga , Kaustav Sengupta , Dariusz Plewczynski , Vera Pancaldi

ISMB/ECCB 2023, Jul 2023, Lyon, France

Communication dans un congrès hal-04987967v1

An Agent-Based Model of Monocyte Differentiation into Tumor-Associated Macrophages in Chronic Lymphocytic Leukemia

Nina Verstraete , Marcin Jakub Domagala , Mary Poupot , Vera Pancaldi

JOBIM, Jun 2023, Toulouse, France

Communication dans un congrès hal-05026957v1

Abstract: Tools for analysing spatial data in the context of immuno-oncology

Abdelmounim Essabbar , Alexis Coullomb , Marcelo Hurtado , Leila Khajavi , Vera Pancaldi

Journées de la Cancéropôle Grand Sud Ouest, Cancéropôle Grand Sud Ouest, Nov 2023, Arcachon, France. ⟨10.1101/2023.03.16.532947)⟩

Communication dans un congrès hal-04988666v1

A Comprehensive Study of a Pancreatic Cancer Subtype: The Interplay between Translation and Transcription in the Tumor Microenvironment.

Jacobo Solorzano , Mehdi Liauzun , Sauyeun Shin , Alexia Brunel , Christine Jean et al.

Translacore MC & WG meeting 2024, Apr 2024, Prague (CZ), Czech Republic

Communication dans un congrès hal-04872956v1

Deciphering cellular interactions through gene regulatory network inference

Hugo Chenel , Malvina Marku , Vera Pancaldi , Mary Poupot , Marcin Jakub Domagala

EMBO Workshop, Nov 2023, Sant Feliu de Guíxols, Spain

Communication dans un congrès hal-05026975v1

From gene regulatory network inference to dynamical modeling: revealing cell behavior through network modeling in Chronic Lymphocytic Leukemia

Malvina Marku , Mary Poupot , Vera Pancaldi , Marcin Jakub Domagala , Hugo Chenel

19th Annual Meeting of the Canceropole GSO, Nov 2023, Arcachon, France

Communication dans un congrès hal-05026969v1

Ceramide metabolism alterations contribute to Tumor Necrosis Factor-induced melanoma dedifferentiation.

Bruno Ségui , Carine Dufau , Matthieu Genais , Elodie Mucher , Benjamin Jung et al.

International Ceramide Conference, Apr 2023, Charleston, South Carolina, United States

Communication dans un congrès hal-04974508v1

A Comprehensive Study of a Pancreatic Cancer Subtype: The Interplay between Translation and Transcription in the Tumor Microenvironment

Jacobo Solorzano , Mehdi Liauzun , Sauyeun Shin , Alexia Brunel , Christine Jean et al.

Pancreatic Cancer Symposium 2023, Oct 2023, Bordeaux, France

Communication dans un congrès hal-04872923v1
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Exploring the relation between evolutionary gene age, gene expression variability and chromatin 3D structure in cancer

Flavien Raynal , Kaustav Sengupta , Benoît Aliaga , Dariusz Plewczynski , Vera Pancaldi

4DGenomics2023: Investigating, modelling and understanding the genome in space and time, INC COST, May 2023, Milan (Italie), Italy

Communication dans un congrès hal-04987992v1

A transcriptional regulatory network approach to unravel cell states from immune cell type deconvolution and cell niches potentially predictive of cancer progression

Marcelo Hurtado , Abdelmounim Essabbar , Leila Khajavi-Ettouati , Vera Pancaldi

Journées de la Cancéropôle Grand Sud Ouest, Cancéropôle Grand Sud Ouest, Nov 2023, Arcachon, France

Communication dans un congrès hal-04988676v1

Ceramide metabolism alterations contribute to Tumor Necrosis Factor-induced melanoma dedifferentiation: from basic research to immunotherapy in advanced melanoma patients.

Bruno Ségui , Carine Dufau , Matthieu Genais , Elodie Mucher , Benjamin Jung et al.

FEBS Sphingolipid biology, Oct 2023, Funchal (Madeira Island), Portugal

Communication dans un congrès hal-04974669v1

An Agent-Based Model of Tumor-Associated Macrophage Differentiation in Chronic Lymphocytic Leukaemia

Nina Verstraete , Marcin Jakub Domagala , Mary Poupot , Vera Pancaldi

ESCS 2022 7th European Student Council Symposium, Sep 2022, Barcelone, Spain

Communication dans un congrès hal-05026991v1

An agent-based model of tumour-associated macrophage differentiation in chronic lymphocytic leukaemia

Nina Verstraete , Vera Pancaldi , Marcin Jakub Domagala , Mary Poupot

SysMod COSI: Computational Modeling of Biological Systems, Jul 2021, Toulouse, France

Communication dans un congrès hal-05026995v1

Combining imaging and gene expression data in mathematical models for immuno-oncology

Vera Pancaldi

JOINT 12th EBSA congress and 10th ICBP – IUPAP congress, July 20-24, 2019, Jul 2019, Madrid, Spain

Communication dans un congrès hal-04988030v1