Federico Agostini

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Articles

Article: BIOLOGY OPEN. 2023;12(10):bio060113
Deficiency of the Heterogeneous Nuclear Ribonucleoprotein U locus leads to delayed hindbrain neurogenesis
Mastropasqua F; Oksanen M; Soldini C; Alatar S; Arora A; Ballarino R; Molinari M; Agostini F; Poulet A; Watts M; Rabkina I; Becker M; Li D; Anderlid B-M; Isaksson J; Remnelius KL; Moslem M; Jacob Y; Falk A; Crosetto N; Bienko M; Santini E; Borgkvist A; Bo''lte S; Tammimies K
Article: SCIENCE ADVANCES. 2023;9(30):eadg1805
Control of protein synthesis through mRNA pseudouridylation by dyskerin
Pederiva C; Trevisan DM; Peirasmaki D; Chen S; Savage SA; Larsson O; Ule J; Baranello L; Agostini F; Farnebo M
Article: CELL. 2022;185(16):3025-3040.e6
Recombination of repeat elements generates somatic complexity in human genomes
Pascarella G; Hon CC; Hashimoto K; Busch A; Luginbuhl J; Parr C; Yip WH; Abe K; Kratz A; Bonetti A; Agostini F; Severin J; Murayama S; Suzuki Y; Gustincich S; Frith M; Carninci P
Article: SCIENTIFIC DATA. 2022;9(1):400
An atlas of endogenous DNA double-strand breaks arising during human neural cell fate determination
Ballarino R; Bouwman BAM; Agostini F; Harbers L; Diekmann C; Wernersson E; Bienko M; Crosetto N
Article: GENOME BIOLOGY. 2021;22(1):136
Intergenic RNA mainly derives from nascent transcripts of known genes.
Agostini F; Zagalak J; Attig J; Ule J; Luscombe NM
Article: FRONTIERS IN ONCOLOGY. 2021;11:700568
Somatic Copy Number Alterations in Human Cancers: An Analysis of Publicly Available Data From The Cancer Genome Atlas
Harbers L; Agostini F; Nicos M; Poddighe D; Bienko M; Crosetto N
Article: NATURE PROTOCOLS. 2020;15(12):3894-3941
Genome-wide detection of DNA double-strand breaks by in-suspension BLISS
Bouwman BAM; Agostini F; Garnerone S; Petrosino G; Gothe HJ; Sayols S; Moor AE; Itzkovitz S; Bienko M; Roukos V; Crosetto N
Article: NATURE BIOTECHNOLOGY. 2020;38(10):1184-1193
GPSeq reveals the radial organization of chromatin in the cell nucleus
Girelli G; Custodio J; Kallas T; Agostini F; Wernersson E; Spanjaard B; Mota A; Kolbeinsdottir S; Gelali E; Crosetto N; Bienko M
Article: NATURE COMMUNICATIONS. 2020;11(1):1018
RADICL-seq identifies general and cell type-specific principles of genome-wide RNA-chromatin interactions
Bonetti A; Agostini F; Suzuki AM; Hashimoto K; Pascarella G; Gimenez J; Roos L; Nash AJ; Ghilotti M; Cameron CJF; Valentine M; Medvedeva YA; Noguchi S; Agirre E; Kashi K; Samudyata; Luginbuhl J; Cazzoli R; Agrawal S; Luscombe NM; Blanchette M; Kasukawa T; de Hoon M; Arner E; Lenhard B; Plessy C; Castelo-Branco G; Orlando V; Carninci P
Article: NATURE COMMUNICATIONS. 2019;10(1):1636
iFISH is a publically available resource enabling versatile DNA FISH to study genome architecture
Gelali E; Girelli G; Matsumoto M; Wernersson E; Custodio J; Mota A; Schweitzer M; Ferenc K; Li X; Mirzazadeh R; Agostini F; Schell JP; Lanner F; Crosetto N; Bienko M
Article: CELL. 2018;174(5):1067-1081.e17
Heteromeric RNP Assembly at LINEs Controls Lineage-Specific RNA Processing.
Attig J; Agostini F; Gooding C; Chakrabarti AM; Singh A; Haberman N; Zagalak JA; Emmett W; Smith CWJ; Luscombe NM; Ule J
Article: BMC GENOMICS. 2014;15(1):925
SeAMotE: a method for high-throughput motif discovery in nucleic acid sequences.
Agostini F; Cirillo D; Ponti RD; Tartaglia GG
Article: BIOINFORMATICS. 2014;30(20):2975-2977
ccSOL omics: a webserver for solubility prediction of endogenous and heterologous expression in Escherichia coli.
Agostini F; Cirillo D; Livi CM; Delli Ponti R; Tartaglia GG
Article: BIOCHIMICA ET BIOPHYSICA ACTA: INTERNATIONAL JOURNAL OF BIOCHEMISTRY AND BIOPHYSICS. 2014;1844(9):1662-1674
Molecular landscape of the interaction between the urease accessory proteins UreE and UreG.
Merloni A; Dobrovolska O; Zambelli B; Agostini F; Bazzani M; Musiani F; Ciurli S
Article: BIOINFORMATICS. 2014;30(11):1601-1608
The cleverSuite approach for protein characterization: predictions of structural properties, solubility, chaperone requirements and RNA-binding abilities.
Klus P; Bolognesi B; Agostini F; Marchese D; Zanzoni A; Tartaglia GG
Article: GENOME BIOLOGY. 2014;15(1):R13
Constitutive patterns of gene expression regulated by RNA-binding proteins.
Cirillo D; Marchese D; Agostini F; Livi CM; Botta-Orfila T; Tartaglia GG
Article: NUCLEIC ACIDS RESEARCH. 2013;41(22):9987-9998
Principles of self-organization in biological pathways: a hypothesis on the autogenous association of alpha-synuclein.
Zanzoni A; Marchese D; Agostini F; Bolognesi B; Cirillo D; Botta-Orfila M; Livi CM; Rodriguez-Mulero S; Tartaglia GG
Article: BIOINFORMATICS. 2013;29(22):2928-2930
catRAPID omics: a web server for large-scale prediction of protein-RNA interactions.
Agostini F; Zanzoni A; Klus P; Marchese D; Cirillo D; Tartaglia GG
Article: RNA. 2013;19(2):129-140
Neurodegenerative diseases: quantitative predictions of protein-RNA interactions.
Cirillo D; Agostini F; Klus P; Marchese D; Rodriguez S; Bolognesi B; Tartaglia GG
Article: NUCLEIC ACIDS RESEARCH. 2013;41(1):e31
X-inactivation: quantitative predictions of protein interactions in the Xist network.
Agostini F; Cirillo D; Bolognesi B; Tartaglia GG
Article: JOURNAL OF MOLECULAR BIOLOGY. 2012;421(2-3):237-241
Sequence-based prediction of protein solubility.
Agostini F; Vendruscolo M; Tartaglia GG
Article: CELL REPORTS. 2012;1(3):251-264
DnaK functions as a central hub in the E. coli chaperone network.
Calloni G; Chen T; Schermann SM; Chang H-C; Genevaux P; Agostini F; Tartaglia GG; Hayer-Hartl M; Hartl FU
Article: ANGEWANDTE CHEMIE-INTERNATIONAL EDITION. 2011;50(31):7048-7051
Disulfide bonds reduce the toxicity of the amyloid fibrils formed by an extracellular protein.
Mossuto MF; Bolognesi B; Guixer B; Dhulesia A; Agostini F; Kumita JR; Tartaglia GG; Dumoulin M; Dobson CM; Salvatella X
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Corrigendum: NATURE COMMUNICATIONS. 2021;12(1):3128
RADICL-seq identifies general and cell type-specific principles of genome-wide RNA-chromatin interactions (vol 11, 1018, 2020)
Bonetti A; Agostini F; Suzuki AM; Hashimoto K; Pascarella G; Gimenez J; Roos L; Nash AJ; Ghilotti M; Cameron CJF; Valentine M; Medvedeva YA; Noguchi S; Agirre E; Kashi K; Samudyata; Luginbuehl J; Cazzoli R; Agrawal S; Luscombe NM; Blanchette M; Kasukawa T; de Hoon M; Arner E; Lenhard B; Plessy C; Castelo-Branco G; Orlando V; Carninci P
Editorial comment: EMBO JOURNAL. 2018;37(6):e99123
No way out: when RNA elements promote nuclear retention.
Agostini F; Ule J; Zagalak JA
Review: MOLECULAR BIOSYSTEMS. 2014;10(7):1632-1642
Discovery of protein-RNA networks.
Cirillo D; Livi CM; Agostini F; Tartaglia GG
Review: WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE. 2013;3(2):161-175
Predictions of protein-RNA interactions
Cirillo D; Agostini F; Gaetano Tartaglia G
Letter: NATURE METHODS. 2011;8(6):444-445
Predicting protein associations with long noncoding RNAs.
Bellucci M; Agostini F; Masin M; Tartaglia GG

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