Publications

2020

  1. NAT COMMUN
    RADICL-seq identifies general and cell type–specific principles of genome-wide RNA-chromatin interactions
    Bonetti, Alessandro, Agostini, Federico, Suzuki, Ana Maria, Hashimoto, Kosuke, Pascarella, Giovanni, Gimenez, Juliette, Roos, Leonie, Nash, Alex J, Ghilotti, Marco, Cameron, Christopher J F, Valentine, Matthew, Medvedeva, Yulia A., Noguchi, Shuhei, Agirre, Eneritz, Kashi, Kaori, Samudyata, , Luginbühl, Joachim, Cazzoli, Riccardo, Agrawal, Saumya, Luscombe, Nicholas M., Blanchette, Mathieu, Kasukawa, Takeya, Hoon, Michiel, Arner, Erik, Lenhard, Boris, Plessy, Charles, Castelo-Branco, Gonçalo, Orlando, Valerio, and Carninci, Piero
    Nature Communications 2020
  2. BIORXIV
    Intergenic RNA mainly derives from nascent transcripts of known genes
    Agostini, Federico, Zagalak, Julian A, Attig, Jan, Ule, Jernej, Luscombe, Nicholas M, Federico, Agostini, Julian, Zagalak, Jan, Attig, Jernej, Ule, and M, Luscombe Nicholas
    bioRxiv 2020
  3. NAT BIOTECHNOL
    GPSeq reveals the radial organization of chromatin in the cell nucleus
    Girelli, Gabriele, Custodio, Joaquin, Kallas, Tomasz, Agostini, Federico, Wernersson, Erik, Spanjaard, Bastiaan, Mota, Ana, Kolbeinsdottir, Solrun, Gelali, Eleni, Crosetto, Nicola, and Bienko, Magda
    Nature Biotechnology 2020
  4. NAT PROTOC
    Genome-wide detection of DNA double-strand breaks by in-suspension BLISS
    Bouwman, Britta A. M., Agostini, Federico, Garnerone, Silvano, Petrosino, Giuseppe, Gothe, Henrike J., Sayols, Sergi, Moor, Andreas E., Itzkovitz, Shalev, Bienko, Magda, Roukos, Vassilis, and Crosetto, Nicola
    Nature Protocols 2020

2019

  1. NAT COMMUN
    iFISH is a publically available resource enabling versatile DNA FISH to study genome architecture
    Gelali, Eleni, Girelli, Gabriele, Matsumoto, Masahiro, Wernersson, Erik, Custodio, Joaquin, Mota, Ana, Schweitzer, Maud, Ferenc, Katalin, Li, Xinge, Mirzazadeh, Reza, Agostini, Federico, Schell, John P., Lanner, Fredrik, Crosetto, Nicola, and Bienko, Magda
    Nature Communications 2019

2018

  1. EMBO J
    No way out: when RNA elements promote nuclear retention
    Agostini, Federico, Ule, Jernej, and Zagalak, Julian A
    The EMBO Journal 2018
  2. CELL
    Heteromeric RNP Assembly at LINEs Controls Lineage-Specific RNA Processing
    Attig, Jan, Agostini, Federico, Gooding, Clare, Chakrabarti, Anob M, Singh, Aarti, Haberman, Nejc, Zagalak, Julian A, Emmett, Warren, Smith, Christopher W.J., Luscombe, Nicholas M, and Ule, Jernej
    Cell 2018

2015

  1. PHD THESIS
    Predictions of RNA-binding ability and aggregation propensity of proteins
    Agostini, Federico
    2015

2014

  1. BIOINFORMATICS
    The cleverSuite approach for protein characterization: predictions of structural properties, solubility, chaperone requirements and RNA-binding abilities
    Klus, Petr, Bolognesi, Benedetta, Agostini, Federico, Marchese, Domenica, Zanzoni, Andreas, and Tartaglia, Gian Gaetano
    Bioinformatics 2014
  2. MOL BIOSYST
    Discovery of protein–RNA networks
    Cirillo, Davide, Livi, Carmen Maria, Agostini, Federico, and Tartaglia, Gian Gaetano
    Mol. BioSyst. 2014
  3. BBA-PROTEINS PROTEOM
    Molecular landscape of the interaction between the urease accessory proteins UreE and UreG
    Merloni, Anna, Dobrovolska, Olena, Zambelli, Barbara, Agostini, Federico, Bazzani, Micaela, Musiani, Francesco, and Ciurli, Stefano
    Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics 2014
  4. BIOINFORMATICS
    ccSOL omics: a webserver for solubility prediction of endogenous and heterologous expression in Escherichia coli
    Agostini, Federico, Cirillo, Davide, Livi, C. M., Delli Ponti, Riccardo, and Tartaglia, G. G.
    Bioinformatics 2014
  5. BMC GENOMICS
    SeAMotE: a method for high-throughput motif discovery in nucleic acid sequences
    Agostini, Federico, Cirillo, Davide, Ponti, Riccardo, and Tartaglia, Gian
    BMC Genomics 2014
  6. GENOME BIOL
    Constitutive patterns of gene expression regulated by RNA-binding proteins
    Cirillo, Davide, Marchese, Domenica, Agostini, Federico, Livi, Carmen, Botta-Orfila, Teresa, and Tartaglia, Gian
    Genome Biology 2014

2013

  1. WIREs
    Predictions of protein-RNA interactions
    Cirillo, Davide, Agostini, Federico, and Tartaglia, Gian Gaetano
    Wiley Interdisciplinary Reviews: Computational Molecular Science 2013
  2. NAR
    Principles of self-organization in biological pathways: a hypothesis on the autogenous association of alpha-synuclein
    Zanzoni, Andreas, Marchese, Domenica, Agostini, Federico, Bolognesi, Benedetta, Cirillo, Davide, Botta-Orfila, Maria, Livi, Carmen Maria, Rodriguez-Mulero, Silvia, and Tartaglia, Gian Gaetano
    Nucleic Acids Research 2013
  3. NAR
    X-inactivation: quantitative predictions of protein interactions in the Xist network
    Agostini, Federico, Cirillo, Davide, Bolognesi, Benedetta, and Tartaglia, Gian Gaetano
    Nucleic Acids Research 2013
  4. BIOINFORMATICS
    catRAPID omics: a web server for large-scale prediction of protein-RNA interactions
    Agostini, Federico, Zanzoni, Andreas, Klus, Petr, Marchese, Domenica, Cirillo, Davide, and Tartaglia, Gian Gaetano
    Bioinformatics 2013
  5. RNA
    Neurodegenerative diseases: Quantitative predictions of protein-RNA interactions
    Cirillo, Davide, Agostini, Federico, Klus, Petr, Marchese, Domenica, Rodriguez, Silvia, Bolognesi, Benedetta, and Tartaglia, Gian Gaetano
    RNA 2013

2012

  1. JMB
    Sequence-Based Prediction of Protein Solubility
    Agostini, Federico, Vendruscolo, Michele, and Tartaglia, Gian Gaetano
    Journal of Molecular Biology 2012
  2. CELL REP
    DnaK Functions as a Central Hub in the E. coli Chaperone Network
    Calloni, Giulia, Chen, Taotao, Schermann, Sonya M., Chang, Hung-chun, Genevaux, Pierre, Agostini, Federico, Tartaglia, Gian Gaetano, Hayer-Hartl, Manajit, and Hartl, F. Ulrich
    Cell Reports 2012

2011

  1. NAT METHODS
    Predicting protein associations with long noncoding RNAs
    Bellucci, Matteo, Agostini, Federico, Masin, Marianela, and Tartaglia, Gian Gaetano
    Nature Methods 2011
  2. ANGEW CHEM INT EDIT
    Disulfide Bonds Reduce the Toxicity of the Amyloid Fibrils Formed by an Extracellular Protein
    Mossuto, Maria F., Bolognesi, Benedetta, Guixer, Bernat, Dhulesia, Anne, Agostini, Federico, Kumita, Janet R., Tartaglia, Gian G., Dumoulin, Mireille, Dobson, Christopher M., and Salvatella, Xavier
    Angewandte Chemie International Edition 2011