Search Results - "PAVESI, Giulio"

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

“…The first step in gene expression, transcription, is modulated by the interaction of transcription factors with their corresponding binding sites on the DNA…”
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Next generation sequencing of SARS-CoV-2 genomes: challenges, applications and opportunities by 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

“…Abstract Various next generation sequencing (NGS) based strategies have been successfully used in the recent past for tracing origins and understanding the…”
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Motif discovery and transcription factor binding sites before and after the next-generation sequencing era by Zambelli, Federico, Pesole, Graziano, Pavesi, Giulio

“…Motif discovery has been one of the most widely studied problems in bioinformatics ever since genomic and protein sequences have been available. In particular,…”
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ChIP-Seq Data Analysis to Define Transcriptional Regulatory Networks by Pavesi, Giulio

“…The first step in the definition of transcriptional regulatory networks is to establish correct relationships between transcription factors (TFs) and their…”
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On the NF-Y regulome as in ENCODE (2019) by Ronzio, Mirko, Bernardini, Andrea, Pavesi, Giulio, Mantovani, Roberto, Dolfini, Diletta

“…NF-Y is a trimeric Transcription Factor -TF- which binds with high selectivity to the conserved CCAAT element. Individual ChIP-seq analysis as well as ENCODE…”
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A perspective of promoter architecture from the CCAAT box by Dolfini, Diletta, Zambelli, Federico, Pavesi, Giulio, Mantovani, Roberto

“…The CCAAT box is an important promoter element regulated by NF-Y, a conserved trimer with histone-like features. We describe a new Position Specific Frequency…”
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The Short Isoform of NF-YA Belongs to the Embryonic Stem Cell Transcription Factor Circuitry by Dolfini, Diletta, Minuzzo, Mario, Pavesi, Giulio, Mantovani, Roberto

“…Totipotency of embryonic stem cells (ESCs) is controlled at the transcriptional level by a handful of transcription factors (TFs) that promote stemness and…”
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UTRdb and UTRsite (RELEASE 2010): a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs by Grillo, Giorgio, Turi, Antonio, Licciulli, Flavio, Mignone, Flavio, Liuni, Sabino, Banfi, Sandro, Gennarino, Vincenzo Alessandro, Horner, David S, Pavesi, Giulio, Picardi, Ernesto, Pesole, Graziano

“…The 5' and 3' untranslated regions of eukaryotic mRNAs (UTRs) play crucial roles in the post-transcriptional regulation of gene expression through the…”
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RNentropy: an entropy-based tool for the detection of significant variation of gene expression across multiple RNA-Seq experiments by Zambelli, Federico, Mastropasqua, Francesca, Picardi, Ernesto, D'Erchia, Anna Maria, Pesole, Graziano, Pavesi, Giulio

“…Abstract RNA sequencing (RNA-Seq) has become the experimental standard in transcriptome studies. While most of the bioinformatic pipelines for the analysis of…”
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Mapping the Global Chromatin Connectivity Network for Sox2 Function in Neural Stem Cell Maintenance by 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

“…The SOX2 transcription factor is critical for neural stem cell (NSC) maintenance and brain development. Through chromatin immunoprecipitation (ChIP)…”
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The coding and long noncoding single-cell atlas of the developing human fetal striatum by 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

“…Deciphering how the human striatum develops is necessary for understanding the diseases that affect this region. To decode the transcriptional modules that…”
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Human PNPase causes RNA stabilization and accumulation of R-loops in the Escherichia coli model system by Falchi, Federica A., Forti, Francesca, Carnelli, Cristina, Genco, Aurelia, Pizzoccheri, Roberto, Manzari, Caterina, Pavesi, Giulio, Briani, Federica

“…Polyribonucleotide phosphorylase (PNPase) is a phosphorolytic RNA exonuclease highly conserved throughout evolution. In Escherichia coli , PNPase controls…”
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Evaluation of Quality Assessment Protocols for High Throughput Genome Resequencing Data by Chiara, Matteo, Pavesi, Giulio

“…Large-scale initiatives aiming to recover the complete sequence of thousands of human genomes are currently being undertaken worldwide, concurring to the…”
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The evolutionary history of the polyQ tract in huntingtin sheds light on its functional pro-neural activities by 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

“…Huntington’s disease is caused by a pathologically long (>35) CAG repeat located in the first exon of the Huntingtin gene ( HTT ). While pathologically…”
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Birth, evolution, and transmission of satellite-free mammalian centromeric domains by 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

“…Mammalian centromeres are associated with highly repetitive DNA (satellite DNA), which has so far hindered molecular analysis of this chromatin domain…”
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Integrating Peak Colocalization and Motif Enrichment Analysis for the Discovery of Genome-Wide Regulatory Modules and Transcription Factor Recruitment Rules by Ronzio, Mirko, Zambelli, Federico, Dolfini, Diletta, Mantovani, Roberto, Pavesi, Giulio

“…Chromatin immunoprecipitation followed by next-generation sequencing (ChIP-Seq) has opened new avenues of research in the genome-wide characterization of…”
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Targeting the scaffolding role of LSD1 (KDM1A) poises acute myeloid leukemia cells for retinoic acid-induced differentiation by Ravasio, Roberto, Ceccacci, Elena, Nicosia, Luciano, Hosseini, Amir, Rossi, Pier Luigi, Barozzi, Iros, Fornasari, Lorenzo, Zuffo, Roberto Dal, Valente, Sergio, Fioravanti, Rossella, Mercurio, Ciro, Varasi, Mario, Mattevi, Andrea, Mai, Antonello, Pavesi, Giulio, Bonaldi, Tiziana, Minucci, Saverio

“…The histone demethylase LSD1 is deregulated in several tumors, including leukemias, providing the rationale for the clinical use of LSD1 inhibitors. In acute…”
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Sox2 conditional mutation in mouse causes ataxic symptoms, cerebellar vermis hypoplasia, and postnatal defects of Bergmann glia by 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.

“…Sox2 is a transcription factor active in the nervous system, within different cell types, ranging from radial glia neural stem cells to a few specific types of…”
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Assessing computational tools for the discovery of transcription factor binding sites by 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

“…The prediction of regulatory elements is a problem where computational methods offer great hope. Over the past few years, numerous tools have become available…”
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Histone acetylation landscape in S. cerevisiae nhp6ab mutants reflects altered glucose metabolism by 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

“…The execution of many genetic programs, influenced by environmental conditions, is epigenetically controlled. Thus, small molecules of the intermediate…”
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