Research

Our lab studies the relationship between patients and cancer, focusing on how the immune system and the tumour interact. Our goal is to understand how variability in the patients, in the tumours, and in their interactions affects the efficacy of cancer therapies throughout computational approaches that include data science, mathematical modeling, network theory and systems biology.

Networks are a useful framework for systems where relationships between objects matter, and what we learn about one network often helps us understand a completely different one. We apply network models to study complex systems as networks of patient–patient similarity, 3D interaction between genes in the nucleus and the interactions between cell types in a tumour.

There are many contexts within the body that are characterised by a heterogeneous mix of cell types. In tissues, complex relationships between cell types establish ‘ecological networks’ whose properties reflect the equilibria that define health against disease. In tumours, cancer cells are surrounded by extremely heterogeneous cell populations, including stromal and immune cells, whose spatial patterns and specific interactions strongly impact response to therapies and patient outcomes. Simulating the complex interactions of these cells in our computers, both at the molecular and intercellular level, offers the possibility to study these systems in a multitude of scenarios. This is an excellent way to formulate new hypotheses and allows better use of our experimental resources.

Overview of the team's research axes: multi-omics data analysis, multiscale dynamical modelling and TAM targeting to control the tumour microenvironment — Our three research axes work together towards controlling the tumour microenvironment.

Characterise

Cell populations and their interactions in the tumour microenvironment (TME) considering cell–cell communication networks and spatial patterns as extracted from transcriptomics (both bulk and single-cell) or spatial omics and imaging produced from patient samples as well as their epigenomic landscape.

Simulate

Dynamic cell processes and inter-cellular interactions in the TME involving cancer, immune and stromal cells, exploiting mathematical models in different scales (molecular, cellular, etc.) of in vitro (2D/3D) and in vivo cancer models.

Control

Develop strategies to reprogram the TME and improve sensitivity of cancer cells to treatments, exploiting an in-house patented monoclonal antibody targeting tumour-associated macrophages, identifying new strategies for TME reprogramming, and expanding our point of view to patient characteristics (immune fitness, microbiome, exposures, etc.)

Projects

Multi-omics descriptions of the tumour microenvironment

Led by Vera Pancaldi

Multiscale dynamical modelling of the tumour microenvironment

Led by Malvina Marku

Experimental studies on cellular interactions in the microenvironment

Led by Mary Poupot

Figure from: CellTFusion: a transcriptional regulatory network framework for the identification of functional multicellular states from bulk RNA-seq data

CellTFusion: a transcriptional regulatory network framework for the identification of functional multicellular states from bulk RNA-seq data

Marcelo Hurtado, Vera Pancaldi

bioRxiv·05 Jul 2026·doi:10.64898/2026.06.30.735682Preprint

Code Documentation

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

Alexis Coullomb, Colas Foulon, Bram van Haastrecht, Paul Monsarrat, Vera Pancaldi

Molecular & Cellular Proteomics·May 2026·doi:10.1016/j.mcpro.2026.101536

Code

Figure from: A new pipeline for cross-validation fold-aware machine learning prediction of clinical outcomes addresses hidden data-leakage in omics based 'predictors'

A new pipeline for cross-validation fold-aware machine learning prediction of clinical outcomes addresses hidden data-leakage in omics based 'predictors'

Marcelo Hurtado, Vera Pancaldi

bioRxiv·16 Mar 2026·doi:10.64898/2026.03.12.711429Preprint

Code Documentation

Figure from: Data driven network inference and longitudinal transcriptomics unveil dynamic regulation in chronic lymphocytic leukaemia models

Data driven network inference and longitudinal transcriptomics unveil dynamic regulation in chronic lymphocytic leukaemia models

Malvina Marku, Hugo Chenel, Julie Bordenave, Marcelo Hurtado, Marcin Domagala, Flavien Raynal, Mary Poupot, Loïc Ysebaert, Andrei Zinovyev, Vera Pancaldi

NPJ Systems Biology and Applications·15 Jan 2026·doi:10.1038/s41540-025-00645-4

Code

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

Marcelo Hurtado, Abdelmounim Essabbar, Leila Khajavi, Vera Pancaldi

bioRxiv·03 May 2025·doi:10.1101/2025.04.29.651220Preprint

Code Documentation

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·08 Feb 2025·doi:10.1093/nar/gkaf084

Code

Figure from: Transcriptomics profiling of the non-small cell lung cancer microenvironment across disease stages reveals dual immune cell-type behaviors

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, Alexis Coullomb, Anne Pradines, Anne Casanova, Anna Kruczynski, Sandrine Gouin, Estelle Clermont, Léa Boutillet, Maria Fernanda Senosain, Yong Zou, Shillin Zhao, Prosper Burq, Abderrahim Mahfoudi, Jerome Besse, Pierre Launay, Alexandre Passioukov, Eric Chetaille, Gilles Favre, Fabien Maldonado, Francisco Cruzalegui, Olivier Delfour, Julien Mazières, Vera Pancaldi

Frontiers in Immunology·31 Oct 2024·doi:10.3389/fimmu.2024.1394965

Code

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, Jean-Jacques Fournié, Loïc Ysebaert, Mary Poupot, Vera Pancaldi

iScience·Jun 2023·doi:10.1016/j.isci.2023.106897

Code

Tysserand — fast and accurate reconstruction of spatial networks from bioimages

Alexis Coullomb, Vera Pancaldi

Bioinformatics·05 Nov 2021·doi:10.1093/bioinformatics/btab490

Code

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·07 May 2020·doi:10.1093/nar/gkaa159

Code Documentation

All publications

2026

Correction: γδ T cells in immunotherapies for B-cell malignancies

Léa Rimailho, Carla Faria, Marcin Domagala, Camille Laurent, Christine Bezombes, Mary Poupot

Frontiers in Immunology·17 Aug 2026·doi:10.3389/fimmu.2026.1933915

CellTFusion: a transcriptional regulatory network framework for the identification of functional multicellular states from bulk RNA-seq data

Marcelo Hurtado, Vera Pancaldi

bioRxiv·05 Jul 2026·doi:10.64898/2026.06.30.735682Preprint

Code Documentation

Specific dendritic cells spatial organization is associated to ICB Response in Non–Small-Cell Lung Cancer

Elisa Gobbini, Pierre Duplouye, Marcelo Hurtado, Anne-Claire Doffin, Alexia Gazeu, Léo Hermet, Martial Scavino, Justine Berthet, Leo Laoubi, Sylvie Lantuejoul, Nicolas Gadot, Bertrand Dubois, Audrey Page, Eleonora Sosa Cuevas, Marie-Cécile Michallet, Laurent Greillier, Lionel Falchero, Jean Bernard Auliac, Marie Bernardi, Sophie Bayle, Marie Marcq, Julian Pinsolle, Stéphane Hominal, Olivier Bylicki, Sabine Vieillot, Fabrice Barlesi, Frédérique Penault-Llorca, Emmanuel Barillot, Stephane Depil, Margaux Hubert, Christophe Caux, Nicolas Girard, Vera Pancaldi, Jenny Valladeau-Guilemond

bioRxiv·07 May 2026·doi:10.64898/2026.05.04.720587Preprint

Code

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

Alexis Coullomb, Colas Foulon, Bram van Haastrecht, Paul Monsarrat, Vera Pancaldi

Molecular & Cellular Proteomics·May 2026·doi:10.1016/j.mcpro.2026.101536

Code

A new pipeline for cross-validation fold-aware machine learning prediction of clinical outcomes addresses hidden data-leakage in omics based 'predictors'

Marcelo Hurtado, Vera Pancaldi

bioRxiv·16 Mar 2026·doi:10.64898/2026.03.12.711429Preprint

Code Documentation

Figure from: Decoding the integrated stress response of pancreatic cancer: identifying a serine-dependent tumor subset under metabolic relationships with CAFs

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 Jean, Benjamin Fourneaux, Margaux Dore, Lea Fevrier, Ismahane Belhabib, Alexia Brunel, Cindy Neuzillet, Marion Larroque, Carine Joffre, Stephane Rocchi, Nicolas Fraunhoffer, Aurelie Perraud, Muriel Mathonnet, Vera Pancaldi, Laetitia Linares, Juan Iovanna, Nelson Dusetti, Ola Larsson, Remy Nicolle, Stephane Pyronnet, Corinne Bousquet, Yvan Martineau

Advanced Science·Mar 2026·doi:10.1002/advs.202515740

Data driven network inference and longitudinal transcriptomics unveil dynamic regulation in chronic lymphocytic leukaemia models

Malvina Marku, Hugo Chenel, Julie Bordenave, Marcelo Hurtado, Marcin Domagala, Flavien Raynal, Mary Poupot, Loïc Ysebaert, Andrei Zinovyev, Vera Pancaldi

NPJ Systems Biology and Applications·15 Jan 2026·doi:10.1038/s41540-025-00645-4

Code

2025

Unraveling the network signatures of oncogenicity in virus-human protein-protein interactions

Francesco Zambelli, Vera Pancaldi, Manlio De Domenico

Entropy·11 Dec 2025·doi:10.3390/e27121248

Figure from: PhysiGym: bridging the gap between the Gymnasium reinforcement learning application interface and the PhysiCell agent-based model software

PhysiGym: bridging the gap between the Gymnasium reinforcement learning application interface and the PhysiCell agent-based model software

Alexandre Bertin, Elmar Bucher, Owen Griere, Marcelo Hurtado, Heber Rocha, Randy Heiland, Aneequa Sundus, Paul Macklin, Vincent François-Lavet, Emmanuel Rachelson, Vera Pancaldi

bioRxiv·24 Sep 2025·doi:10.1101/2025.09.18.677030Preprint

Code

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, Jean Milhès, Thomas Filleron, Cécile Pagès, Vincent Sibaud, Laurent Mortier, Olivier Dereure, Maha Ayyoub, Amandine Fabre, Nathalie Andrieu‐Abadie, Vera Pancaldi, Céline Colacios, Nicolas Meyer, Bruno Ségui, Anne Montfort

International Journal of Cancer·Aug 2025·doi:10.1002/ijc.35416

Figure from: Microbiome gut community structure and functionality are associated with symptom severity in non-responsive celiac disease patients

Microbiome gut community structure and functionality are associated with symptom severity in non-responsive celiac disease patients

Laura Judith Marcos-Zambrano, Blanca Lacruz-Pleguezuelos, Elena Aguilar-Aguilar, Helena Marcos-Pasero, Alberto Valdés, Viviana Loria-Kohen, Alejandro Cifuentes, Ana Ramirez de Molina, Alberto Diaz-Ruiz, Vera Pancaldi, Enrique Carrillo de Santa Pau

mSystems·22 Jul 2025·doi:10.1128/msystems.00143-25

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

Marcelo Hurtado, Abdelmounim Essabbar, Leila Khajavi, Vera Pancaldi

bioRxiv·03 May 2025·doi:10.1101/2025.04.29.651220Preprint

Code Documentation

Evidence of epigenetic oncogenesis: a turning point in cancer research

Jean‐Pascal Capp, Benoît Aliaga, Vera Pancaldi

BioEssays·Mar 2025·doi:10.1002/bies.202400183

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·08 Feb 2025·doi:10.1093/nar/gkaf084

Code

2024

Transcriptomics profiling of the non-small cell lung cancer microenvironment across disease stages reveals dual immune cell-type behaviors

Frontiers in Immunology·31 Oct 2024·doi:10.3389/fimmu.2024.1394965

Code

Editorial: New insights into innate immune cell-based immunotherapies in cancer

Anne Caignard, Mary Poupot-Marsan, Virginie Lafont, Daniela Wesch, Chiara Porta

Frontiers in Immunology·09 Apr 2024·doi:10.3389/fimmu.2024.1401665

Cytidine deaminase resolves replicative stress and protects pancreatic cancer from DNA-targeting drugs

Audrey Lumeau, Nicolas Bery, Audrey Francès, Marion Gayral, Guillaume Labrousse, Cyril Ribeyre, Charlene Lopez, Adele Nevot, Abdessamad El Kaoutari, Naima Hanoun, Emeline Sarot, Marion Perrier, Frederic Pont, Juan-Pablo Cerapio, Jean-Jacques Fournié, Frederic Lopez, Miguel Madrid-Mencia, Vera Pancaldi, Marie-Jeanne Pillaire, Valerie Bergoglio, Jerome Torrisani, Nelson Dusetti, Jean-Sebastien Hoffmann, Louis Buscail, Malik Lutzmann, Pierre Cordelier

Cancer Research·01 Apr 2024·doi:10.1158/0008-5472.CAN-22-3219

2023

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

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, Marcelo Nollmann

Nature Communications·21 Oct 2023·doi:10.1038/s41467-023-42485-y

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

Malvina Marku, Vera Pancaldi

PLoS Computational Biology·10 Aug 2023·doi:10.1371/journal.pcbi.1011254

Code

Figure from: Integrated multi-omics analysis of early lung adenocarcinoma links tumor biological features with predicted indolence or aggressiveness

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, Dianna J. Rowe, Jonathan M. Lehman, Jonathan M. Irish, Fabien Maldonado, Michael N. Kammer, Vera Pancaldi, Carlos F. Lopez

Cancer Research Communications·26 Jul 2023·doi:10.1158/2767-9764.CRC-22-0373

γδ T cells in immunotherapies for B-cell malignancies

Léa Rimailho, Carla Faria, Marcin Domagala, Camille Laurent, Christine Bezombes, Mary Poupot

Frontiers in Immunology·22 Jun 2023·doi:10.3389/fimmu.2023.1200003

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, Jean-Jacques Fournié, Loïc Ysebaert, Mary Poupot, Vera Pancaldi

iScience·Jun 2023·doi:10.1016/j.isci.2023.106897

Code

Network models of chromatin structure

Vera Pancaldi

Current Opinion in Genetics & Development·Jun 2023·doi:10.1016/j.gde.2023.102051

Dissecting cellular phenotypes in the tumour microenvironment through gene regulatory networks: inference, analysis and dynamical modelling

Marku M, Chenel H, Pancaldi V

Immunology and Cancer Biology (book chapter)·2023

A practical introduction to single-cell RNA-seq in immuno-oncology

Aliaga B, Genais M, Pancaldi V

Immunology and Cancer Biology (book chapter)·2023

2022

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, Ulrich Dührsen, Lara Keuneke, Ana Queiros, Julia Richter, José I. Martín-Subero, Reiner Siebert, Brigitte Schlegelberger, Ralf Küppers, Jan Dürig, Eva M. Murga Penas, Enrique Carillo-de Santa Pau, Anke K. Bergmann

Clinical Epigenetics·Dec 2022·doi:10.1186/s13148-022-01362-z

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

Karolina Jodkowska, Vera Pancaldi, Maria Rigau, Ricardo Almeida, José M Fernández-Justel, Osvaldo Graña-Castro, Sara Rodríguez-Acebes, Miriam Rubio-Camarillo, Enrique Carrillo-de Santa Pau, David Pisano, Fátima Al-Shahrour, Alfonso Valencia, María Gómez, Juan Méndez

Nucleic Acids Research·28 Nov 2022·doi:10.1093/nar/gkac1111

The antitumoral activity of TLR7 ligands is corrupted by the microenvironment of pancreatic tumors

Marie Rouanet, Naima Hanoun, Hubert Lulka, Cindy Ferreira, Pierre Garcin, Martin Sramek, Godefroy Jacquemin, Agnès Coste, Delphine Pagan, Carine Valle, Emeline Sarot, Vera Pancaldi, Frédéric Lopez, Louis Buscail, Pierre Cordelier

Molecular Therapy·Apr 2022·doi:10.1016/j.ymthe.2022.01.018

2021

Community-wide hackathons to identify central themes in single-cell multi-omics

Kim-Anh Lê Cao, Al J. Abadi, Emily F. Davis-Marcisak, Lauren Hsu, Arshi Arora, Alexis Coullomb, Atul Deshpande, Yuzhou Feng, Pratheepa Jeganathan, Melanie Loth, Chen Meng, Wancen Mu, Vera Pancaldi, Kris Sankaran, Dario Righelli, Amrit Singh, Joshua S. Sodicoff, Genevieve L. Stein-O’Brien, Ayshwarya Subramanian, Joshua D. Welch, Yue You, Ricard Argelaguet, Vincent J. Carey, Ruben Dries, Casey S. Greene, Susan Holmes, Michael I. Love, Matthew E. Ritchie, Guo-Cheng Yuan, Aedin C. Culhane, Elana Fertig

Genome Biology·Dec 2021·doi:10.1186/s13059-021-02433-9

Figure from: STAG2 loss-of-function affects short-range genomic contacts and modulates the basal-luminal transcriptional program of bladder cancer cells

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, Miguel Madrid-Mencía, Hélène Neyret-Kahn, François Radvanyi, Juan Antonio Rodríguez, Yasmina Cuartero, François Serra, François Le Dily, Alfonso Valencia, Marc A Marti-Renom, Francisco X Real

Nucleic Acids Research·08 Nov 2021·doi:10.1093/nar/gkab864

Tysserand — fast and accurate reconstruction of spatial networks from bioimages

Alexis Coullomb, Vera Pancaldi

Bioinformatics·05 Nov 2021·doi:10.1093/bioinformatics/btab490

Code

Chromatin network analyses: towards structure-function relationships in epigenomics

Vera Pancaldi

Frontiers in Bioinformatics·27 Oct 2021·doi:10.3389/fbinf.2021.742216

Figure from: Activation of vitamin D receptor pathway enhances differentiating capacity in acute myeloid leukemia with isocitrate dehydrogenase mutations

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, Nathaniel Polley, Guillaume Cognet, Estelle Saland, Laura Lauture, Thomas Farge, Ambrine Sahal, Vera Pancaldi, Emeline Chu-Van, Florence Castelli, Sarah Bertoli, Pierre Bories, Christian Récher, Héléna Boutzen, Véronique Mansat-De Mas, Lucille Stuani, Jean-Emmanuel Sarry

Cancers·19 Oct 2021·doi:10.3390/cancers13205243

Low replicative stress triggers cell-type specific inheritable advanced replication timing

Lilas Courtot, Elodie Bournique, Chrystelle Maric, Laure Guitton-Sert, Miguel Madrid-Mencía, Vera Pancaldi, Jean-Charles Cadoret, Jean-Sébastien Hoffmann, Valérie Bergoglio

International Journal of Molecular Sciences·07 May 2021·doi:10.3390/ijms22094959

Mitochondrial metabolism supports resistance to IDH mutant inhibitors in acute myeloid leukemia

Lucille Stuani, Marie Sabatier, Estelle Saland, Guillaume Cognet, Nathalie Poupin, Claudie Bosc, Florence A. Castelli, Lara Gales, Evgenia Turtoi, Camille Montersino, Thomas Farge, Emeline Boet, Nicolas Broin, Clément Larrue, Natalia Baran, Madi Y. Cissé, Marc Conti, Sylvain Loric, Tony Kaoma, Alexis Hucteau, Aliki Zavoriti, Ambrine Sahal, Pierre-Luc Mouchel, Mathilde Gotanègre, Cédric Cassan, Laurent Fernando, Feng Wang, Mohsen Hosseini, Emeline Chu-Van, Laurent Le Cam, Martin Carroll, Mary A. Selak, Norbert Vey, Rémy Castellano, François Fenaille, Andrei Turtoi, Guillaume Cazals, Pierre Bories, Yves Gibon, Brandon Nicolay, Sébastien Ronseaux, Joseph R. Marszalek, Koichi Takahashi, Courtney D. DiNardo, Marina Konopleva, Véra Pancaldi, Yves Collette, Floriant Bellvert, Fabien Jourdan, Laetitia K. Linares, Christian Récher, Jean-Charles Portais, Jean-Emmanuel Sarry

Journal of Experimental Medicine·03 May 2021·doi:10.1084/jem.20200924

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

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, Mei-Shiue Kuo, Alexis Hucteau, Alexis Coullomb, Nina Verstraete, Olivier Delfour, Francisco Cruzalegui, Vera Pancaldi

bioRxiv·11 Apr 2021·doi:10.1101/2021.04.09.439207Preprint

Code

2020

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, Jean-Jacques Fournié, Loïc Ysebaert, Mary Poupot, Vera Pancaldi

Cancers·07 Dec 2020·doi:10.3390/cancers12123664

Code

Supporting clinical decision-making during the SARS-CoV-2 pandemic through a global research commitment: the TERAVOLT experience

Annalisa Trama, Claudia Proto, Jennifer G. Whisenant, Valter Torri, Alessio Cortellini, Olivier Michielin, Fabrice Barlesi, Anne-Marie C. Dingemans, Jan Van Meerbeeck, Vera Pancaldi, Julien Mazieres, Ross A. Soo, Natasha B. Leighl, Solange Peters, Heather Wakelee, Leora Horn, Matthew Hellmann, Selina K. Wong, Marina Chiara Garassino, Javier Baena

Cancer Cell·Nov 2020·doi:10.1016/j.ccell.2020.10.002

CovMulNet19, integrating proteins, diseases, drugs, and symptoms: a network medicine approach to COVID-19

Nina Verstraete, Giuseppe Jurman, Giulia Bertagnolli, Arsham Ghavasieh, Vera Pancaldi, Manlio De Domenico

Network and Systems Medicine·01 Nov 2020·doi:10.1089/nsm.2020.0011

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, Nadège Carrié, Marie-Véronique Joubert, Marie Le Moine, Laura Do Souto, Guillaume Gaud, Indrajit Das, Elisa Brauns, Clara M. Scarlata, Elena Morandi, Ashmitha Sundarrajan, Marine Cuisinier, Laure Buisson, Sabrina Maheo, Sahar Kassem, Arantxa Agesta, Michaël Pérès, Els Verhoeyen, Alejandra Martinez, Julien Mazieres, Loïc Dupré, Thomas Gossye, Vera Pancaldi, Camille Guillerey, Maha Ayyoub, Anne S. Dejean, Abdelhadi Saoudi, Stanislas Goriely, Hervé Avet-Loiseau, Tobias Bald, Mark J. Smyth, Ludovic Martinet

Immunity·Oct 2020·doi:10.1016/j.immuni.2020.09.006

Chromatin network markers of leukemia

N Malod-Dognin, V Pancaldi, A Valencia, N Pržulj

Bioinformatics·01 Jul 2020·doi:10.1093/bioinformatics/btaa445

COVID-19 in patients with thoracic malignancies (TERAVOLT): first results of an international, registry-based, cohort study

Marina Chiara Garassino, Jennifer G Whisenant, Li-Ching Huang, Annalisa Trama, Valter Torri, Francesco Agustoni, Javier Baena, Giuseppe Banna, Rossana Berardi, Anna Cecilia Bettini, Emilio Bria, Matteo Brighenti, Jacques Cadranel, Alessandro De Toma, Claudio Chini, Alessio Cortellini, Enriqueta Felip, Giovanna Finocchiaro, Pilar Garrido, Carlo Genova, Raffaele Giusti, Vanesa Gregorc, Francesco Grossi, Federica Grosso, Salvatore Intagliata, Nicla La Verde, Stephen V Liu, Julien Mazieres, Edoardo Mercadante, Olivier Michielin, Gabriele Minuti, Denis Moro-Sibilot, Giulia Pasello, Antonio Passaro, Vieri Scotti, Piergiorgio Solli, Elisa Stroppa, Marcello Tiseo, Giuseppe Viscardi, Luca Voltolini, Yi-Long Wu, Silvia Zai, Vera Pancaldi, Anne-Marie Dingemans, Jan Van Meerbeeck, Fabrice Barlesi, Heather Wakelee, Solange Peters, Leora Horn

The Lancet Oncology·Jul 2020·doi:10.1016/S1470-2045(20)30314-4

Interpreting molecular similarity between patients as a determinant of disease comorbidity relationships

Jon Sánchez-Valle, Héctor Tejero, José María Fernández, David Juan, Beatriz Urda-García, Salvador Capella-Gutiérrez, Fátima Al-Shahrour, Rafael Tabarés-Seisdedos, Anaïs Baudot, Vera Pancaldi, Alfonso Valencia

Nature Communications·05 Jun 2020·doi:10.1038/s41467-020-16540-x

TERAVOLT: Thoracic Cancers International COVID-19 Collaboration

Jennifer G. Whisenant, Annalisa Trama, Valter Torri, Alessandro De Toma, Giuseppe Viscardi, Alessio Cortellini, Olivier Michielin, Fabrice Barlesi, Anne-Marie C. Dingemans, Jan Van Meerbeeck, Vera Pancaldi, Ross A. Soo, Natasha B. Leighl, Solange Peters, Heather Wakelee, Marina Chiara Garassino, Leora Horn

Cancer Cell·Jun 2020·doi:10.1016/j.ccell.2020.05.008

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·07 May 2020·doi:10.1093/nar/gkaa159

Code Documentation

Unveiling new disease, pathway, and gene associations via multi-scale neural network

Thomas Gaudelet, Noël Malod-Dognin, Jon Sánchez-Valle, Vera Pancaldi, Alfonso Valencia, Nataša Pržulj

PLoS One·06 Apr 2020·doi:10.1371/journal.pone.0231059

2019

ChiCMaxima: a robust and simple pipeline for detection and visualization of chromatin looping in Capture Hi-C

Yousra Ben Zouari, Anne M. Molitor, Natalia Sikorska, Vera Pancaldi, Tom Sexton

Genome Biology·Dec 2019·doi:10.1186/s13059-019-1706-3

Figure from: Transcriptomic metaanalyses of autistic brains reveals shared gene expression and biological pathway abnormalities with cancer

Transcriptomic metaanalyses of autistic brains reveals shared gene expression and biological pathway abnormalities with cancer

Jaume Forés-Martos, Ferrán Catalá-López, Jon Sánchez-Valle, Kristina Ibáñez, Héctor Tejero, Helena Palma-Gudiel, Joan Climent, Vera Pancaldi, Lourdes Fañanás, Celso Arango, Mara Parellada, Anaïs Baudot, Daniel Vogt, John L. Rubenstein, Alfonso Valencia, Rafael Tabarés-Seisdedos

Molecular Autism·Dec 2019·doi:10.1186/s13229-019-0262-8

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, Michele Caselle, Alfonso Valencia, Andrei Zinovyev, Laura Cantini

International Journal of Molecular Sciences·26 Jun 2019·doi:10.3390/ijms20133114