Search Results - "Pancaldi, Véra"

Chromatin Network Analyses: Towards Structure-Function Relationships in Epigenomics by Pancaldi, Vera

“…Recent technological advances have allowed us to map chromatin conformation and uncover the genome's spatial organization of the genome inside the nucleus…”
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From time-series transcriptomics to gene regulatory networks: A review on inference methods by Marku, Malvina, Pancaldi, Vera

“…Inference of gene regulatory networks has been an active area of research for around 20 years, leading to the development of sophisticated inference algorithms…”
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In silico characterization and prediction of global protein-mRNA interactions in yeast by Pancaldi, Vera, Bähler, Jürg

“…Post-transcriptional gene regulation is mediated through complex networks of protein-RNA interactions. The targets of only a few RNA binding proteins (RBPs)…”
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ChiCMaxima: a robust and simple pipeline for detection and visualization of chromatin looping in Capture Hi-C by Ben Zouari, Yousra, Molitor, Anne M, Sikorska, Natalia, Pancaldi, Vera, Sexton, Tom

“…Capture Hi-C (CHi-C) is a new technique for assessing genome organization based on chromosome conformation capture coupled to oligonucleotide capture of…”
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Whole-genome fingerprint of the DNA methylome during human B cell differentiation by Kulis, Marta, Merkel, Angelika, Heath, Simon, Queirós, Ana C, Schuyler, Ronald P, Castellano, Giancarlo, Beekman, Renée, Raineri, Emanuele, Esteve, Anna, Clot, Guillem, Verdaguer-Dot, Néria, Duran-Ferrer, Martí, Russiñol, Nuria, Vilarrasa-Blasi, Roser, Ecker, Simone, Pancaldi, Vera, Rico, Daniel, Agueda, Lidia, Blanc, Julie, Richardson, David, Clarke, Laura, Datta, Avik, Pascual, Marien, Agirre, Xabier, Prosper, Felipe, Alignani, Diego, Paiva, Bruno, Caron, Gersende, Fest, Thierry, Muench, Marcus O, Fomin, Marina E, Lee, Seung-Tae, Wiemels, Joseph L, Valencia, Alfonso, Gut, Marta, Flicek, Paul, Stunnenberg, Hendrik G, Siebert, Reiner, Küppers, Ralf, Gut, Ivo G, Campo, Elías, Martín-Subero, José I

“…José Martín-Subero and colleagues report the whole-genome bisulfite sequencing of ten blood cell subpopulations representing the cellular stages during B cell…”
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3D chromatin interactions involving Drosophila insulators are infrequent but preferential and arise before TADs and transcription by Messina, Olivier, Raynal, Flavien, Gurgo, Julian, Fiche, Jean-Bernard, Pancaldi, Vera, Nollmann, Marcelo

“…In mammals, insulators contribute to the regulation of loop extrusion to organize chromatin into topologically associating domains. In Drosophila the role of…”
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Interpreting molecular similarity between patients as a determinant of disease comorbidity relationships by Sánchez-Valle, Jon, Tejero, Héctor, Fernández, José María, Juan, David, Urda-García, Beatriz, Capella-Gutiérrez, Salvador, Al-Shahrour, Fátima, Tabarés-Seisdedos, Rafael, Baudot, Anaïs, Pancaldi, Vera, Valencia, Alfonso

“…Comorbidity is a medical condition attracting increasing attention in healthcare and biomedical research. Little is known about the involvement of potential…”
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Unveiling new disease, pathway, and gene associations via multi-scale neural network by Gaudelet, Thomas, Malod-Dognin, Noël, Sánchez-Valle, Jon, Pancaldi, Vera, Valencia, Alfonso, Pržulj, Nataša

“…Diseases involve complex modifications to the cellular machinery. The gene expression profile of the affected cells contains characteristic patterns linked to…”
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Genome-wide analysis of differential transcriptional and epigenetic variability across human immune cell types by Ecker, Simone, Chen, Lu, Pancaldi, Vera, Bagger, Frederik O, Fernández, José María, Carrillo de Santa Pau, Enrique, Juan, David, Mann, Alice L, Watt, Stephen, Casale, Francesco Paolo, Sidiropoulos, Nikos, Rapin, Nicolas, Merkel, Angelika, Stunnenberg, Hendrik G, Stegle, Oliver, Frontini, Mattia, Downes, Kate, Pastinen, Tomi, Kuijpers, Taco W, Rico, Daniel, Valencia, Alfonso, Beck, Stephan, Soranzo, Nicole, Paul, Dirk S

“…A healthy immune system requires immune cells that adapt rapidly to environmental challenges. This phenotypic plasticity can be mediated by transcriptional and…”
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Ceramide metabolism alterations contribute to Tumor Necrosis Factor-induced melanoma dedifferentiation and predict resistance to immune checkpoint inhibitors in advanced melanoma patients by Dufau, Carine, Genais, Matthieu, Mucher, Elodie, Jung, Benjamin, Garcia, Virginie, Montfort, Anne, Tosolini, Marie, Clarke, Christopher J, Medin, Jeffrey A, Levade, Thierry, Delord, Jean-Pierre, Meyer, Nicolas, Pancaldi, Vera, Andrieu-Abadie, Nathalie, Ségui, Bruno

“…Advanced cutaneous melanoma is a skin cancer characterized by a poor prognosis and high metastatic potential. During metastatic spread, melanoma cells often…”
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Transcriptomic metaanalyses of autistic brains reveals shared gene expression and biological pathway abnormalities with cancer by Forés-Martos, Jaume, Catalá-López, Ferrán, Sánchez-Valle, Jon, Ibáñez, Kristina, Tejero, Héctor, Palma-Gudiel, Helena, Climent, Joan, Pancaldi, Vera, Fañanás, Lourdes, Arango, Celso, Parellada, Mara, Baudot, Anaïs, Vogt, Daniel, Rubenstein, John L, Valencia, Alfonso, Tabarés-Seisdedos, Rafael

“…Epidemiological and clinical evidence points to cancer as a comorbidity in people with autism spectrum disorders (ASD). A significant overlap of genes and…”
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Transcriptomics profiling of the non-small cell lung cancer microenvironment across disease stages reveals dual immune cell-type behaviors by Hurtado, Marcelo, Khajavi, Leila, Essabbar, Abdelmounim, Kammer, Michael, Xie, Ting, Coullomb, Alexis, Pradines, Anne, Casanova, Anne, Kruczynski, Anna, Gouin, Sandrine, Clermont, Estelle, Boutillet, Léa, Senosain, Maria Fernanda, Zou, Yong, Zhao, Shillin, Burq, Prosper, Mahfoudi, Abderrahim, Besse, Jerome, Launay, Pierre, Passioukov, Alexandre, Chetaille, Eric, Favre, Gilles, Maldonado, Fabien, Cruzalegui, Francisco, Delfour, Olivier, Mazières, Julien, Pancaldi, Vera

“…Background Lung cancer is the leading cause of cancer death worldwide, with poor survival despite recent therapeutic advances. A better understanding of the…”
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Low Replicative Stress Triggers Cell-Type Specific Inheritable Advanced Replication Timing by Courtot, Lilas, Bournique, Elodie, Maric, Chrystelle, Guitton-Sert, Laure, Madrid-Mencía, Miguel, Pancaldi, Vera, Cadoret, Jean-Charles, Hoffmann, Jean-Sébastien, Bergoglio, Valérie

“…DNA replication timing (RT), reflecting the temporal order of origin activation, is known as a robust and conserved cell-type specific process. Upon low…”
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Molecular Inverse Comorbidity between Alzheimer's Disease and Lung Cancer: New Insights from Matrix Factorization by Greco, Alessandro, Sanchez Valle, Jon, Pancaldi, Vera, Baudot, Anaïs, Barillot, Emmanuel, Caselle, Michele, Valencia, Alfonso, Zinovyev, Andrei, Cantini, Laura

“…Matrix factorization (MF) is an established paradigm for large-scale biological data analysis with tremendous potential in computational biology. Here, we…”
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AnGeLi: A Tool for the Analysis of Gene Lists from Fission Yeast by Bitton, Danny A, Schubert, Falk, Dey, Shoumit, Okoniewski, Michal, Smith, Graeme C, Khadayate, Sanjay, Pancaldi, Vera, Wood, Valerie, Bähler, Jürg

“…Genome-wide assays and screens typically result in large lists of genes or proteins. Enrichments of functional or other biological properties within such lists…”
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Thoracic Cancers International COVID-19 Collaboration (TERAVOLT): Impact of type of cancer therapy and COVID therapy on survival by Horn, Leora, Whisenant, Jennifer G., Torri, Valter, Huang, Li-Ching, Trama, Annalisa, Paz-Ares, Luis G., Felip, Enriqueta, Pancaldi, Vera, De Toma, Alessandro, Tiseo, Marcello, Garrido, Pilar, Genova, Carlo, Cadranel, Jacques, Michielin, Olivier, Dingemans, Anne-Marie C., Van Meerbeeck, Jan P., Barlesi, Fabrice, Wakelee, Heather A., Peters, Solange, Garassino, Marina Chiara

“…Abstract only LBA111 Background: Early reports on cancer patients infected with COVID-19 have suggested a high mortality rate compared to the general…”
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An agent-based model of monocyte differentiation into tumour-associated macrophages in chronic lymphocytic leukemia by Verstraete, Nina, Marku, Malvina, Domagala, Marcin, Arduin, Hélène, Bordenave, Julie, Fournié, Jean-Jacques, Ysebaert, Loïc, Poupot, Mary, Pancaldi, Vera

“…Monocyte-derived macrophages help maintain tissue homeostasis and defend the organism against pathogens. In tumors, recent studies have uncovered complex…”
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Network models of chromatin structure by Pancaldi, Vera

“…Increasing numbers of datasets and experimental assays that capture the organization of chromatin inside the nucleus warrant an effort to develop tools to…”
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Systematic screen for mutants resistant to TORC1 inhibition in fission yeast reveals genes involved in cellular ageing and growth by Rallis, Charalampos, López-Maury, Luis, Georgescu, Teodora, Pancaldi, Vera, Bähler, Jürg

“…Target of rapamycin complex 1 (TORC1), which controls growth in response to nutrients, promotes ageing in multiple organisms. The fission yeast…”
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Publisher Correction: Epigenome-wide analysis of T-cell large granular lymphocytic leukemia identifies BCL11B as a potential biomarker by Johansson, Patricia, Laguna, Teresa, Ossowski, Julio, Pancaldi, Vera, Brauser, Martina, Dührsen, Ulrich, Keuneke, Lara, Queiros, Ana, Richter, Julia, Martín-Subero, José I, Siebert, Reiner, Schlegelberger, Brigitte, Küppers, Ralf, Dürig, Jan, Penas, Eva M Murga, Pau, Enrique Carrillo-de Santa, Bergmann, Anke K

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