Vera Pancaldi

Publications

Article dans une revue (32)

Decoding the Integrated Stress Response of Pancreatic Cancer: Identifying a Serine‐dependent Tumor Subset Under Metabolic Relationships With CAFs. Sauyeun Shin,Mehdi Liauzun,Jacobo Solorzano,Morgane Le Bras,Christine Jeanet al. Advanced Science, 2026, Online ahead of print. ⟨10.1002/advs.202515740⟩ Article dans une revue hal-05548059v1
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 Valdéset al. mSystems, 2025, 10 (7), ⟨10.1128/msystems.00143-25⟩ Article dans une revue hal-05263928v1
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 Dufauet 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
Unraveling the Network Signatures of Oncogenicity in Virus–Human Protein–Protein Interactions Francesco Zambelli,Vera Pancaldi,Manlio de Domenico Entropy, 2025, 27 (12), pp.1248. ⟨10.3390/e27121248⟩ Article dans une revue hal-05558610v1
Unveiling Epigenetic Regulatory Elements Associated with Breast Cancer Development Marta Jardanowska-Kotuniak,Michał Dramiński,Michal Wlasnowolski,Marcin Łapiński,Kaustav Senguptaet al. International Journal of Molecular Sciences, 2025, 26 (14), pp.6558. ⟨10.3390/ijms26146558⟩ Article dans une revue hal-05263929v1
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
Cytidine Deaminase Resolves Replicative Stress and Protects Pancreatic Cancer from DNA-Targeting Drugs Audrey Lumeau,Nicolas Bery,Audrey Francès,Marion Gayral,Guillaume Labrousseet al. Cancer Research, 2024, 84 (7), pp.1013 - 1028. ⟨10.1158/0008-5472.can-22-3219⟩ Article dans une revue hal-04743033v1
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 Xieet al. Frontiers in Immunology, 2024, 15, ⟨10.3389/fimmu.2024.1394965⟩ Article dans une revue hal-04874132v1
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
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 Coullombet 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 Pancaldiet al. Nature Communications, 2023, 14 (1), pp.6678. ⟨10.1038/s41467-023-42485-y⟩ Article dans une revue hal-04881279v1
An agent-based model of monocyte differentiation into tumour-associated macrophages in chronic lymphocytic leukemia Nina Verstraete,Malvina Marku,Marcin Domagala,Hélène Arduin,Julie Bordenaveet al. iScience, 2023, 26 (6), pp.106897. ⟨10.1016/j.isci.2023.106897⟩ Article dans une revue inserm-04777519v1
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
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 Brauseret al. Clinical Epigenetics, 2022, 14 (1), pp.148. ⟨10.1186/s13148-022-01362-z⟩ Article dans une revue hal-04881285v1
The antitumoral activity of TLR7 ligands is corrupted by the microenvironment of pancreatic tumors Marie Rouanet,Naima Hanoun,Cindy Ferreira,Pierre Garcin,Martin Srameket 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-Justelet al. Nucleic Acids Research, 2022, 50 (21), pp.12149-12165. ⟨10.1093/nar/gkac1111⟩ Article dans une revue hal-04881284v1
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 Hucteauet al. Cancers, 2021, 13 (20), pp.5243. ⟨10.3390/cancers13205243⟩ Article dans une revue hal-04415805v1
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 Pauet al. Nucleic Acids Research, 2021, ⟨10.1093/nar/gkab864⟩ Article dans une revue hal-03385084v1
Mitochondrial metabolism supports resistance to IDH mutant inhibitors in acute myeloid leukemia Lucille Stuani,Marie Sabatier,Estelle Saland,Guillaume Cognet,Nathalie Poupinet al. Journal of Experimental Medicine, 2021, 218 (5), pp.e20200924. ⟨10.1084/jem.20200924⟩ Article dans une revue hal-03563454v1
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
Low Replicative Stress Triggers Cell-Type Specific Inheritable Advanced Replication Timing Lilas Courtot,Elodie Bournique,Chrystelle Maric,Laure Guitton-Sert,Miguel Madrid-Mencíaet al. International Journal of Molecular Sciences, 2021, 22 (9), pp.4959. ⟨10.3390/ijms22094959⟩ Article dans une revue hal-03407911v1
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
CovMulNet19, Integrating Proteins, Diseases, Drugs, and Symptoms: A Network Medicine Approach to COVID-19 Nina Verstraete,Giuseppe Jurman,Giulia Bertagnolli,Arsham Ghavasieh,Vera Pancaldiet al. Network and Systems Medicine, 2020, 3 (1), pp.130-141. ⟨10.1089/nsm.2020.0011⟩ Article dans une revue hal-04881288v1
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 Domagalaet al. Cancers, 2020, 12 (12), pp.3664. ⟨10.3390/cancers12123664⟩ Article dans une revue hal-03365450v1
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 Braunet al. Immunity, 2020, 53 (4), pp.824-839.e10. ⟨10.1016/j.immuni.2020.09.006⟩ Article dans une revue hal-03030829v1
Unveiling new disease, pathway, and gene associations via multi-scale neural network Thomas Gaudelet,Noël Malod-Dognin,Jon Sánchez-Valle,Vera Pancaldi,Alfonso Valenciaet al. PLoS ONE, 2020, 15 (4), pp.e0231059. ⟨10.1371/journal.pone.0231059⟩ Article dans une revue inserm-02536487v1
Interpreting molecular similarity between patients as a determinant of disease comorbidity relationships Jon Sánchez-Valle,Hector Tejero,José María Fernández,David Juan,Beatriz Urda-Garcíaet al. Nature Communications, 2020, 11 (1), pp.2854. ⟨10.1038/s41467-020-16540-x⟩ Article dans une revue inserm-02878879v1
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 Barillotet 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. Geschwindet al. Cell, 2016, 167 (5), pp.1145--1149. ⟨10.1016/j.cell.2016.11.007⟩ Article dans une revue hal-01614945v1
Whole-genome fingerprint of the DNA methylome during human B cell differentiation Marta Kulis,Angelika Merkel,Simon Heath,Ana C. Queirós,Ronald P. Schuyleret al. Nature Genetics, 2015, 47 (7), pp.746-756. ⟨10.1038/ng.3291⟩ Article dans une revue hal-01163753v1

Pré-publication, Document de travail (10)

Network analysis to understand gene regulation: across spatial scales and towards multi-level models Vera Pancaldi 2026 Pré-publication, Document de travail hal-05558709v1
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 Domagalaet al. 2025 Pré-publication, Document de travail (preprint/prepublication) hal-05263934v1
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 Pancaldiet 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-Cabezaset al. 2025 Pré-publication, Document de travail hal-05263936v1
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 Pernetet al. 2025 Pré-publication, Document de travail (preprint/prepublication) hal-05263930v1
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 Ribeyreet al. 2021 Pré-publication, Document de travail hal-03409378v1
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-Mencíaet al. 2020 Pré-publication, Document de travail hal-03006823v1

Poster de conférence (7)

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 Espagnolleet al. 10th Annual ICSA Conference, Sep 2025, Rome, Italy. Poster de conférence hal-05273625v1
P3.18.60 The COALA (Cure Oncogene-Addicted Lung Adenocarcinoma) research network: a nationwide consortium dedicated to improving lung cancer outcomes J. Mazières,V. Albinet,O Calvayrac,M. Alifano,Sébastien Benzekryet al. WCLC 2025 - IASLC World Conference on Lung Cancer, Sep 2025, Barcelone, Spain. Journal of Thoracic Oncology, 20 (10, Supplement 1), pp.S570-S571, 2025, ⟨10.1016/j.jtho.2025.09.1075⟩ Poster de conférence hal-05559320v1
Dissecting cellular communication in the tumour microenvironment through multiscale dynamical modelling Malvina Marku,Hugo Chenel,Julie Bordenave,Loic Ysebaert,Mary Poupotet 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 Labrousseet 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

Communication dans un congrès (18)

P2.06.43 Estimating Tumour Microenvironment Cellular States From Bulk RNAseq Produces Biomarkers of Clinical Outcome Across Stages M. Hurtado,E. Gobbini,Laurent Greillier,L. Khajavi,A. Essabbaret al. 2025 IASLC World Conference on Lung Cancer, Sep 2025, Barcelone, Spain. pp.S308-S309, ⟨10.1016/j.jtho.2025.09.577⟩ Communication dans un congrès hal-05559337v1
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
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
Time series analysis of cellular interactions through gene regulatory network inference Hugo Chenel,Malvina Marku,Julie Bordenave,Marcin Jakub Domagala,Mary Poupotet al. Computational Systems Biology of Cancer, Curie Institute, Sep 2024, Paris, France Communication dans un congrès hal-04988661v1
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 Junget al. FEBS Sphingolipid biology, Oct 2023, Funchal (Madeira Island), Portugal Communication dans un congrès hal-04974669v1
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 Jeanet al. Translacore MC & WG meeting 2024, Apr 2024, Prague (CZ), Czech Republic Communication dans un congrès hal-04872956v1
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
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
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 Junget 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 Jeanet al. Pancreatic Cancer Symposium 2023, Oct 2023, Bordeaux, France Communication dans un congrès hal-04872923v1
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
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

Thèse (1)

Impact of TNF on ceramide metabolism and on the inflammatory and differentiation status of melanoma : from basic mechanisms to the clinic and back Bruno Ségui,Matthieu Genais,Vera Pancaldi Life Sciences [q-bio]. Université Paul Sabatier - Toulouse III, 2023. English. ⟨NNT : 2023TOU30348⟩ Thèse tel-05002536v1