Pscan: finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes von Zambelli, Federico, Pesole, Graziano, Pavesi, Giulio

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Next generation sequencing of SARS-CoV-2 genomes: challenges, applications and opportunities von Chiara, Matteo, D’Erchia, Anna Maria, Gissi, Carmela, Manzari, Caterina, Parisi, Antonio, Resta, Nicoletta, Zambelli, Federico, Picardi, Ernesto, Pavesi, Giulio, Horner, David S, Pesole, Graziano

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Motif discovery and transcription factor binding sites before and after the next-generation sequencing era von Zambelli, Federico, Pesole, Graziano, Pavesi, Giulio

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ChIP-Seq Data Analysis to Define Transcriptional Regulatory Networks von Pavesi, Giulio

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On the NF-Y regulome as in ENCODE (2019) von Ronzio, Mirko, Bernardini, Andrea, Pavesi, Giulio, Mantovani, Roberto, Dolfini, Diletta

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A perspective of promoter architecture from the CCAAT box von Dolfini, Diletta, Zambelli, Federico, Pavesi, Giulio, Mantovani, Roberto

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The evolutionary history of the polyQ tract in huntingtin sheds light on its functional pro-neural activities von Iennaco, Raffaele, Formenti, Giulio, Trovesi, Camilla, Rossi, Riccardo Lorenzo, Zuccato, Chiara, Lischetti, Tiziana, Bocchi, Vittoria Dickinson, Scolz, Andrea, Martínez-Labarga, Cristina, Rickards, Olga, Pacifico, Michela, Crottini, Angelica, Møller, Anders Pape, Chen, Richard Zhenghuan, Vogt, Thomas Francis, Pavesi, Giulio, Horner, David Stephen, Saino, Nicola, Cattaneo, Elena

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The Short Isoform of NF-YA Belongs to the Embryonic Stem Cell Transcription Factor Circuitry von Dolfini, Diletta, Minuzzo, Mario, Pavesi, Giulio, Mantovani, Roberto

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UTRdb and UTRsite (RELEASE 2010): a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs von Grillo, Giorgio, Turi, Antonio, Licciulli, Flavio, Mignone, Flavio, Liuni, Sabino, Banfi, Sandro, Gennarino, Vincenzo Alessandro, Horner, David S, Pavesi, Giulio, Picardi, Ernesto, Pesole, Graziano

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RNentropy: an entropy-based tool for the detection of significant variation of gene expression across multiple RNA-Seq experiments von Zambelli, Federico, Mastropasqua, Francesca, Picardi, Ernesto, D'Erchia, Anna Maria, Pesole, Graziano, Pavesi, Giulio

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Mapping the Global Chromatin Connectivity Network for Sox2 Function in Neural Stem Cell Maintenance von Bertolini, Jessica A., Favaro, Rebecca, Zhu, Yanfen, Pagin, Miriam, Ngan, Chew Yee, Wong, Chee Hong, Tjong, Harianto, Vermunt, Marit W., Martynoga, Ben, Barone, Cristiana, Mariani, Jessica, Cardozo, Marcos Julián, Tabanera, Noemi, Zambelli, Federico, Mercurio, Sara, Ottolenghi, Sergio, Robson, Paul, Creyghton, Menno P., Bovolenta, Paola, Pavesi, Giulio, Guillemot, Francois, Nicolis, Silvia K., Wei, Chia-Lin

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The coding and long noncoding single-cell atlas of the developing human fetal striatum von Bocchi, Vittoria Dickinson, Conforti, Paola, Vezzoli, Elena, Besusso, Dario, Cappadona, Claudio, Lischetti, Tiziana, Galimberti, Maura, Ranzani, Valeria, Bonnal, Raoul J. P., De Simone, Marco, Rossetti, Grazisa, He, Xiaoling, Kamimoto, Kenji, Espuny-Camacho, Ira, Faedo, Andrea, Gervasoni, Federica, Vuono, Romina, Morris, Samantha A., Chen, Jian, Felsenfeld, Dan, Pavesi, Giulio, Barker, Roger A., Pagani, Massimiliano, Cattaneo, Elena

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Human PNPase causes RNA stabilization and accumulation of R-loops in the Escherichia coli model system von Falchi, Federica A., Forti, Francesca, Carnelli, Cristina, Genco, Aurelia, Pizzoccheri, Roberto, Manzari, Caterina, Pavesi, Giulio, Briani, Federica

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Evaluation of Quality Assessment Protocols for High Throughput Genome Resequencing Data von Chiara, Matteo, Pavesi, Giulio

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Birth, evolution, and transmission of satellite-free mammalian centromeric domains von Nergadze, Solomon G, Piras, Francesca M, Gamba, Riccardo, Corbo, Marco, Cerutti, Federico, McCarter, Joseph G W, Cappelletti, Eleonora, Gozzo, Francesco, Harman, Rebecca M, Antczak, Douglas F, Miller, Donald, Scharfe, Maren, Pavesi, Giulio, Raimondi, Elena, Sullivan, Kevin F, Giulotto, Elena

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Assessing computational tools for the discovery of transcription factor binding sites von Eskin, Eleazar, Ye, Chun, Mironov, Andrei A, Fu, Yutao, Favorov, Alexander V, Pavesi, Giulio, Li, Nan, Pesole, Graziano, Vandenbogaert, Mathias, Noble, William Stafford, Weng, Zhiping, Régnier, Mireille, Sinha, Saurabh, Makeev, Vsevolod J, Kent, W James, De Moor, Bart, Simonis, Nicolas, Zhu, Zhou, Thijs, Gert, Bailey, Timothy L, Frith, Martin C, Workman, Christopher, Church, George M, Tompa, Martin, van Helden, Jacques

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Integrating Peak Colocalization and Motif Enrichment Analysis for the Discovery of Genome-Wide Regulatory Modules and Transcription Factor Recruitment Rules von Ronzio, Mirko, Zambelli, Federico, Dolfini, Diletta, Mantovani, Roberto, Pavesi, Giulio

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Targeting the scaffolding role of LSD1 (KDM1A) poises acute myeloid leukemia cells for retinoic acid-induced differentiation von Ravasio, Roberto, Ceccacci, Elena, Nicosia, Luciano, Hosseini, Amir, Rossi, Pier Luigi, Barozzi, Iros, Fornasari, Lorenzo, Dal Zuffo, Roberto, Valente, Sergio, Fioravanti, Rossella, Mercurio, Ciro, Varasi, Mario, Mattevi, Andrea, Mai, Antonello, Pavesi, Giulio, Bonaldi, Tiziana, Minucci, Saverio

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Sox2 conditional mutation in mouse causes ataxic symptoms, cerebellar vermis hypoplasia, and postnatal defects of Bergmann glia von Cerrato, Valentina, Mercurio, Sara, Leto, Ketty, Fucà, Elisa, Hoxha, Eriola, Bottes, Sara, Pagin, Miriam, Milanese, Marco, Ngan, Chew‐Yee, Concina, Giulia, Ottolenghi, Sergio, Wei, Chia‐Lin, Bonanno, Giambattista, Pavesi, Giulio, Tempia, Filippo, Buffo, Annalisa, Nicolis, Silvia K.

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Histone acetylation landscape in S. cerevisiae nhp6ab mutants reflects altered glucose metabolism von Durano, Diletta, Di Felice, Francesca, Caldarelli, Federica, Lukacs, Andrea, D'Alfonso, Anna, Saliola, Michele, Sciubba, Fabio, Miccheli, Alfredo, Zambelli, Federico, Pavesi, Giulio, Bianchi, Marco E., Camilloni, Giorgio

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