Vera Pancaldi

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Publications

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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-04996473 v1
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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-04743033 v1
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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-04874132 v1
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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-04840627 v1

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-04881280 v1

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-04881279 v1

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-04777519 v1
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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-04874157 v1

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-04881282 v1
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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-04577745 v1

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-04881284 v1

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-04881285 v1

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-04415805 v1
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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-03385084 v1
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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-03563454 v1

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-04881286 v1
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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-04875000 v1
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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-03407911 v1
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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-02878879 v1
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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-02536487 v1

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-03365450 v1
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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-03030829 v1

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 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-05036253 v1

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-04881288 v1

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-04881287 v1
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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-02277045 v2

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-01614945 v1
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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-01163753 v1

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-05026951 v1

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-05026942 v1

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-04988661 v1

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-05026957 v1
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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-04987967 v1

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-04988666 v1

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-04872956 v1

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-05026975 v1

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-05026969 v1

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-04974508 v1

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-04872923 v1
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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-04987992 v1

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-04988676 v1

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-04974669 v1

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-05026991 v1

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-05026995 v1

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-04988030 v1
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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-04988682 v1

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-04988648 v1

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-04991620 v1

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-04988686 v1