The novel (TCTG)n motif in CNBP expanded alleles: composition, dynamics and genotype–phenotype correlation in Myotonic dystrophy type 2 (DM2) Federica Centofanti, Virginia Veronica Visconti, Maria Rosaria D’Apice, Marco Carlomagno, Simone Maestri, Dario Ciabini, Mario Bengala, Enrica Marchionni, Erica Frezza, Roberto Massa, Antonio Petrucci, Francesca Lupidi, Elena Pegoraro, Gabriele Siciliano, Matteo Garibaldi, Paola Origone, Massimo Delledonne, Marzia Rossato, Annalisa Botta, Giuseppe Novelli Human Genomics, 2026 Introduction. Myotonic dystrophy type 2 (DM2) is an autosomal dominant disorder caused by (CCTG)n repeat expansions in intron 1 of the CNBP gene. Recent evidence from long-read sequencing suggests these expansions may be more complex than previously recognized. Aim. To comprehensively characterize the composition, intergenerational dynamics, and clinical impact of novel (TCTG)n motifs within the CNBP expanded alleles in a large DM2 cohort. Methods. We analyzed 100 genetically confirmed DM2 individuals (45 sporadic, 55 familial). The presence of (TCTG)n blocks was detected using an optimized quadruplet-repeat primed PCR (QP-PCR) assay coupled with Sanger sequencing. In a subset of nine patients, Cas9-mediated enrichment followed by Nanopore Long-Read Sequencing (LRS) provided nucleotide-level resolution of the expanded alleles. Haplotype analysis was performed using STR markers. Results. We identified (TCTG)n blocks at the 3′ end of the expansion in 88% of patients. This refined assay corrected nine initial false-negative diagnoses from standard testing. LRS analysis confirmed the composition and revealed the dynamics of the (TCTG)n tract in familial transmission, showing a tendency for contraction and, in one case, complete loss. Genotype–phenotype correlation analysis indicated that the presence of the (TCTG)n motif acts as a disease modifier, significantly influencing the age of onset. Conclusion. The detailed characterization of the CNBP expansion reveals the novel (TCTG)n component that is integral to the DM2 genotype. Understanding its composition and dynamics enhances diagnostic accuracy and provides a new framework for genetic counselling, prognostic stratification and future personalized therapies. .
The lncRNA LOC100257036 and vvimiR156 modulate gibberellin signaling through AGAMOUS during cluster formation in Sistan Yaghooti grape Shahla Sahraei, Nafiseh Mahdinezhad, Abbasali Emamjomeh, Kaveh Kavousi, Mahmood Solouki, Massimo Delledonne Scientific Reports, 2025 The long non-coding RNAs (lncRNAs), despite lacking the ability to encode proteins, have become essential players in regulating gene expression in crops. Yaghooti grape in addition to its good flavor, is highly regarded by consumers due to its high nutritional value. However, the compact clusters and small berries are notable features that negatively impact its marketability. Gibberellin is widely used to reduce cluster density. This research aimed to identify lncRNAs involved in cluster formation and examine how their expression is influenced by gibberellin treatment. The expression of lncRNAs is spatiotemporally specific, and external stimuli can influence their expression. However, the role of lncRNA in modulating the transcriptional pathway of gibberellin is unknown. The length of grape clusters increased from 107 to 184 mm under gibberellin treatment, accompanied by a corresponding decrease in cluster density. RNA-seq data related to Sistan Yaghooti grape clusters were examined at three stages of formation and in response to gibberellin to identify lncRNA transcripts. A total of 2021 lncRNAs were identified, of which 262 lncRNAs showed differential expression. The numbers of lncRNAs and target genes that exhibited significant differential expression were 76, 100, and 86 lncRNAs and 146, 143, and 138 target genes, respectively, in stage2 vs. stage1, stage3 vs. stage2, and stage3 vs. stage1. The target genes of lncRNAs were significantly associated with (Catabolic Process, hydrolase activity, Phosphorylation, ATP binding, response to abiotic stimulus). Furthermore, pathway analysis indicated that majority of genes in the treated samples were primarily linked to metabolic pathways and secondary metabolite biosynthesis in comparison to the control group. Specifically, genes such as cytokinin (CK), Indole-3-acetic acid (IAA), squamosa-promoter binding protein-like2 (SPL2), LATERAL ORGAN BOUNDARIES DOMAIN (LBD), Domain of Unknown Function 1218 (DUF1218), the non-specific phospholipase C2 (NPC2), Cytochrome P450 (P450 CYP), pectin methylesterases (PMEs), and AGAMOUS (AG) showed significantly increased expression in response to gibberellin. Some of these genes are targets of lncRNAs that interact with microRNAs (miRNAs) vvi-miR156, vvi-miR159, vvi-miR172, and vvi-miR319. Among the differentially expressed non-coding RNAs, lncRNA LOC100257036 and vvi-miR156 may contribute to gibberellin-mediated regulation of AG, potentially influencing cluster architecture through a lncRNA-miRNA-mRNA regulatory pathway.
The unexplored diversity of rough-seeded lupins provides rich genomic resources and insights into lupin evolution Karolina Susek, Leonardo Vincenzi, Magdalena Tomaszewska, Magdalena Kroc, Edoardo Franco, Emanuela Cosentino, Antonina Rita Limongi, Umesh Kumar Tanwar, Humaira Jamil, Matthew Nicholas Nelson, Philipp E. Bayer, David Edwards, Roberto Papa, Massimo Delledonne, Scott A. Jackson Nature Communications, 2025 Lupin crops provide nutritious seeds as an excellent source of dietary protein. However, extensive genomic resources are needed for crop improvement, focusing on key traits such as nutritional value and climate resiliency, to ensure global food security based on sustainable and healthy diets for all. Such resources can be derived either from related lupin species or crop wild relatives, which represent a large and untapped source of genetic variation for crop improvement. Here, we report genome assemblies of the cross-compatible species Lupinus cosentinii (Mediterranean) and its pan-Saharan wild relative L. digitatus, which are well adapted to drought-prone environments and partially domesticated. We show that both species are tetraploids, and their repetitive DNA content differs considerably from that of the main lupin crops L. angustifolius and L. albus. We present the complex evolutionary process within the rough-seeded lupins as a species-based model involving polyploidization and rediploidization. Our data also provide the foundation for a systematic analysis of genomic diversity among lupin species to promote their exploitation for crop improvement and sustainable agriculture.
The italian national genomic strategy: current status, challenges, and future perspectives in clinical practice and public health Francesco Andrea Causio, Sara Farina, Alessandra Maio, Flavia Beccia, Luigi Russo, Valentina Baccolini, Matteo Chiara, Americo Cicchetti, Gualtiero I. Colombo, Giovanni Comandé, Domenico Coviello, Ruggero De Maria, Massimo Delledonne, Corrado De Vito, Daniela Galeone, Paolo Gasparini, David Horner, Giovanni Martinelli, Carolina Marzuillo, Laura Palazzani, Erica Pitini, Maurizio Sanguinetti, Aldo Scarpa, Marco Tartaglia, Francesco Danilo Tiziano, Giovanni Tonon, Bruno Dallapiccola, Paolo Villari, Giovanna Elisa Calabrò, Stefania Boccia Journal of Community Genetics, 2025 This article presents the outcomes of a national initiative aimed at developing a technical document to support the future Italian National Genomic Strategy, carried out from 2021 to 2024 through the collaboration of 14 research institutions. The project was designed to align with major European genomic initiatives, particularly the “1 + Million Genomes” (1 + MG) Declaration and its supporting programs, including Beyond 1 Million Genomes (B1 + MG), the Genomic Data Infrastructure (GDI), and Genome of Europe (GoE). The initiative was structured around 12 National Mirror Groups (NMGs), each addressing a specific domain such as clinical implementation, ethical and legal issues, data governance, health economics, and public engagement. Through expert consensus and coordinated activities, the project produced a comprehensive technical document outlining seven strategic lines and related intervention areas. These include the integration of genomic testing into clinical practice, development of specialized genomic centers, creation of a national genomic data infrastructure, professional training, and public education. The proposed strategy emphasizes equitable access to genomic medicine, the use of health technology assessment to evaluate new technologies, and the importance of citizen engagement and literacy. By fostering collaboration among institutions, healthcare professionals, and the public, the final goal is to position Italy as a leader in genomic medicine and ensure the responsible, effective, and ethical use of genomics in public health and clinical care.
Exploring Bat–Virus Interactions: Insights from a Study in the Gobi Desert Sabrina Canziani, Davide Lelli, Paolo Agnelli, Claudio Augugliaro, Munkhtsetseg Bazarragchaa, Sandro Bertolino, Marco Carlomagno, Gantulga Davaakhuu, Massimo Delledonne, Fabrizio Gili, Renato Fani, Ana Moreno, Battogtokh Nasanbat, Francesco Riga, Marzia Rossato, Tiziana Trogu, Leonardo Vincenzi, Udval Uuganbayar, Antonio Lavazza, Marco Zaccaroni Pathogens, 2025 In May 2022, an expedition was conducted in the Gobi Desert, Mongolia, to investigate the viral diversity of bats, recognized as reservoirs of emerging zoonotic viruses. Bats were captured in six oases using mist nets and were identified morphologically and molecularly. Fecal samples were collected and screened using molecular protocol targeting viral agents of relevance to human and animal health, including coronaviruses, orthoreoviruses, herpesviruses, adenoviruses, flaviviruses, phleboviruses, paramyxoviruses, pestiviruses, and Influenza A viruses. In total, 74 bats were sampled. The most represented bat genus was Plecotus, followed by Hypsugo, Vespertilio, and Myotis. Coronavirus RNA was detected in eleven samples (14.86%), Mammalian orthoreovirus RNA in two samples (2.70%), and herpesvirus DNA in three samples (4.05%). No other targeted viruses were detected. These data expand our understanding of viral circulation in bats from previously unstudied regions. By expanding our understanding of the viral diversity harbored by bats, this study contributes to ongoing efforts to better characterize their role in the ecology and evolution of emerging zoonotic viruses. Continuous surveillance in remote and biodiverse areas is essential to identify potential threats to public and animal health and to improve preparedness for future viral emergence.
The evolutionary history of the common bean (Phaseolus vulgaris) revealed by chloroplast and nuclear genomes analysis Giulia Frascarelli, Teresa R. Galise, Nunzio D’Agostino, Donata Cafasso, Salvatore Cozzolino, Gaia Cortinovis, Francesca Sparvoli, Elisa Bellucci, Valerio Di Vittori, Laura Nanni, Alice Pieri, Marzia Rossato, Leonardo Vincenzi, Andrea Benazzo, Massimo Delledonne, Elena Bitocchi, Roberto Papa Theoretical and Applied Genetics, 2025 Key message The origin of common bean was investigated throughout chloroplast and nuclear WGS data considering recombination events. Our results support the Mesoamerican origin of common bean. Abstract The remarkable evolutionary history of the common bean (Phaseolus vulgaris L.) has led to the emergence of three wild main gene pools corresponding to three different eco-geographical areas: Mesoamerica, the Andes and northern Peru/Ecuador. Recent works proposed novel scenarios, and the northern Peru/Ecuador population has been described as a new species called P. debouckii, rekindling the debate about the origin of P. vulgaris. Here we shed light on the origin of P. vulgaris by analyzing the chloroplast and nuclear genomes of a large varietal collection representing the entire geographical distribution of wild forms including a large collection of Mesoamerican and Andean individuals. We assembled 37 chloroplast genomes de novo and used them to construct a time frame for the divergence of the genotypes under investigation, revealing that the separation of the Mesoamerican and northern Peru/Ecuador gene pools occurred ~ 0.15 Mya. Our results clearly support a Mesoamerican origin of the common bean and reject the recent P. deboukii hypothesis. These results also imply two independent migratory events from Mesoamerica to the North and South Andes, probably facilitated by birds. Our work represents a paradigmatic example of the importance of taking into account the genetic rearrangements produced by recombination when investigating phylogeny and of the analysis of wild forms when studying the evolutionary history of a crop species.
Transcriptomic analysis reveals role of lncRNA LOC100257036 to regulate AGAMOUS during cluster compactness of Vitis vinifera cv. sistan yaghooti Shahla Sahraei, Nafiseh Mahdinezhad, Abbasali Emamjomeh, Kaveh Kavousi, Mahmood Solouki, Massimo Delledonne Scientific Reports, 2024 Yaghooti grape, as the earliest grape variety in Iran, is considered as more resistant to heat, drought, and salinity than other cultivars. Cluster compactness is regarded as an inappropriate feature for the productivity of Yaghooti grape as a critical commercial and nutritional product. In plants, lncRNAs play a critical role in regulating biological processes related to growth and development. However, the potential role of lncRNAs was not assessed in cluster compactness. Totally, 1549 lncRNAs were identified by RNA-Seq data analysis in three steps of cluster formation, berry formation, and final cluster size after a thorough screening process. In addition, 229 lncRNAs were differentially expressed in the cluster development steps. Based on the functional analysis, lncRNAs are related to AG and MYB, bHLH, LBD, NAC, and WRKY TFs. Further, the target genes enrichment analysis revealed a relationship between lncRNAs with grape growth and development, as well as resistance to abiotic stresses such as heat and drought, plant defense against pathogens, and early grapes ripening. The study identified four lncRNAs as precursors of miRNAs, predicting that 112 other lncRNAs could potentially be targeted by 166 miRNAs. The results provide new insights into the regulatory functions of lncRNAs in Yaghooti grape to improve overall understanding of the molecular mechanisms related to grape compactness.
Adaptive gene loss in the common bean pan-genome during range expansion and domestication Gaia Cortinovis, Leonardo Vincenzi, Robyn Anderson, Giovanni Marturano, Jacob Ian Marsh, Philipp Emanuel Bayer, Lorenzo Rocchetti, Giulia Frascarelli, Giovanna Lanzavecchia, Alice Pieri, Andrea Benazzo, Elisa Bellucci, Valerio Di Vittori, Laura Nanni, Juan José Ferreira Fernández, Marzia Rossato, Orlando Mario Aguilar, Peter Laurent Morrell, Monica Rodriguez, Tania Gioia, Kerstin Neumann, Juan Camilo Alvarez Diaz, Ariane Gratias, Christophe Klopp, Elena Bitocchi, Valérie Geffroy, Massimo Delledonne, David Edwards, Roberto Papa Nature Communications, 2024 The common bean (Phaseolus vulgaris L.) is a crucial legume crop and an ideal evolutionary model to study adaptive diversity in wild and domesticated populations. Here, we present a common bean pan-genome based on five high-quality genomes and whole-genome reads representing 339 genotypes. It reveals ~234 Mb of additional sequences containing 6,905 protein-coding genes missing from the reference, constituting 49% of all presence/absence variants (PAVs). More non-synonymous mutations are found in PAVs than core genes, probably reflecting the lower effective population size of PAVs and fitness advantages due to the purging effect of gene loss. Our results suggest pan-genome shrinkage occurred during wild range expansion. Selection signatures provide evidence that partial or complete gene loss was a key adaptive genetic change in common bean populations with major implications for plant adaptation. The pan-genome is a valuable resource for food legume research and breeding for climate change mitigation and sustainable agriculture.
Correction to: Adaptive gene loss in the common bean pan-genome during range expansion and domestication (Nature Communications, (2024), 15, 1, (6698), 10.1038/s41467-024-51032-2) Gaia Cortinovis, Leonardo Vincenzi, Robyn Anderson, Giovanni Marturano, Jacob Ian Marsh, Philipp Emanuel Bayer, Lorenzo Rocchetti, Giulia Frascarelli, Giovanna Lanzavecchia, Alice Pieri, Andrea Benazzo, Elisa Bellucci, Valerio Di Vittori, Laura Nanni, Juan José Ferreira Fernández, Marzia Rossato, Orlando Mario Aguilar, Peter Laurent Morrell, Monica Rodriguez, Tania Gioia, Kerstin Neumann, Juan Camilo Alvarez Diaz, Ariane Gratias, Christophe Klopp, Elena Bitocchi, Valérie Geffroy, Massimo Delledonne, David Edwards, Roberto Papa Nature Communications, 2024
Enhancer hijacking at the ARHGAP36 locus is associated with connective tissue to bone transformation Uirá Souto Melo, Jerome Jatzlau, Cesar A. Prada-Medina, Elisabetta Flex, Sunhild Hartmann, Salaheddine Ali, Robert Schöpflin, Laura Bernardini, Andrea Ciolfi, M-Hossein Moeinzadeh, Marius-Konstantin Klever, Aybuge Altay, Pedro Vallecillo-García, Giovanna Carpentieri, Massimo Delledonne, Melanie-Jasmin Ort, Marko Schwestka, Giovanni Battista Ferrero, Marco Tartaglia, Alfredo Brusco, Manfred Gossen, Dirk Strunk, Sven Geißler, Stefan Mundlos, Sigmar Stricker, Petra Knaus, Elisa Giorgio, Malte Spielmann Nature Communications, 2023
Skewed X-chromosome inactivation in unsolved neurodevelopmental disease cases can guide re-evaluation For X-linked genes Chiara Giovenino, Slavica Trajkova, Lisa Pavinato, Simona Cardaropoli, Verdiana Pullano, Enza Ferrero, Elena Sukarova-Angelovska, Silvia Carestiato, Paola Salmin, Antonina Rinninella, Anthony Battaglia, Luca Bertoli, Antonio Fadda, Flavia Palermo, Diana Carli, Alessandro Mussa, Paola Dimartino, Alessandro Bruselles, Tawfiq Froukh, Giorgia Mandrile, Barbara Pasini, Silvia De Rubeis, Joseph D. Buxbaum, Tommaso Pippucci, Marco Tartaglia, Marzia Rossato, Massimo Delledonne, Giovanni Battista Ferrero, Alfredo Brusco European Journal of Human Genetics, 2023
An isoform of the giant protein titin is a master regulator of human T lymphocyte trafficking Lara Toffali, Beatrice D’Ulivo, Cinzia Giagulli, Alessio Montresor, Elena Zenaro, Massimo Delledonne, Marzia Rossato, Barbara Iadarola, Andrea Sbarbati, Paolo Bernardi, Gabriele Angelini, Barbara Rossi, Nicola Lopez, Wolfgang A. Linke, Andreas Unger, Dario Di Silvestre, Louise Benazzi, Antonella De Palma, Sara Motta, Gabriela Constantin, Pierluigi Mauri, Carlo Laudanna Cell Reports, 2023
CRISPR-Cas9-based repeat depletion for highthroughput genotyping of complex plant genomes Marzia Rossato, Luca Marcolungo, Luca De Antoni, Giulia Lopatriello, Elisa Bellucci, Gaia Cortinovis, Giulia Frascarelli, Laura Nanni, Elena Bitocchi, Valerio Di Vittori, Leonardo Vincenzi, Filippo Lucchini, Kirstin E. Bett, Larissa Ramsay, David James Konkin, Massimo Delledonne, Roberto Papa Genome Research, 2023
Metabolite and lipoprotein profiles reveal sex-related oxidative stress imbalance in de novo drug-naive Parkinson’s disease patients Gaia Meoni, Leonardo Tenori, Sebastian Schade, Cristina Licari, Chiara Pirazzini, Maria Giulia Bacalini, Paolo Garagnani, Paola Turano, Alessandra Dal Molin, Anna Bartoletti-Stella, Anna Gabellini, Astrid Daniela Adarmes-Gómez, Cesa Lorella Maria Scaglione, Christine Nardini, Cilea Rosaria, Claudia Boninsegna, Claudia Sala, Cristina Giuliani, Cristina Tejera-Parrado, Daniel Macias, Dolores Buiza-Rueda, Dylan Williams, Elisa Zago, Federica Provini, Francesca Magrinelli, Francesco Mignani, Francesco Ravaioli, Franco Valzania, Friederike Sixel-Döring, Giacomo Mengozzi, Giovanna Calandra-Buonaura, Giovanna Maria Dimitri, Giovanni Fabbri, Henry Houlden, Ismael Huertas, Ivan Doykov, Jenny Hällqvist, Juan Francisco Martín Rodríguez, Juulia Jylhävä, Kailash P. Bhatia, Kevin Mills, Luca Baldelli, Luciano Xumerle, Luisa Sambati, Maddalena Milazzo, Marcella Broli, Maria Giovanna Maturo, Maria Teresa Periñán-Tocino, Mario Carriòn-Claro, Marta Bonilla-Toribio, Massimo Delledonne, Miguel A. Labrador-Espinosa, Nancy L. Pedersen, Pablo Mir, Patrizia De Massis, Pietro Cortelli, Pietro Guaraldi, Pietro Liò, Pilar Gómez-Garre, Robert Clayton, Rocio Escuela-Martin, Rosario Vigo Ortega, Sabina Capellari, Sara Hägg, Sebastian R. Schreglmann, Silvia De Luca, Simeon Spasov, Stefania Alessandra Nassetti, Stefania Macrì, Tiago Azevedo, Wendy Heywood, Claudia Trenkwalder, Claudio Franceschi, Brit Mollenhauer, Claudio Luchinat, and Npj Parkinson S Disease, 2022
A Gain-of-Function Mutation on BCKDK Gene and Its Possible Pathogenic Role in Branched-Chain Amino Acid Metabolism Alice Maguolo, Giulia Rodella, Alejandro Giorgetti, Marion Nicolodi, Rui Ribeiro, Alice Dianin, Gaetano Cantalupo, Irene Monge, Sarah Carcereri, Margherita Lucia De Bernardi, Massimo Delledonne, Andrea Pasini, Natascia Campostrini, Florina Ion Popa, Giorgio Piacentini, Francesca Teofoli, Monica Vincenzi, Marta Camilot, Andrea Bordugo Genes, 2022
Heterogeneity of prodromal Parkinson symptoms in siblings of Parkinson disease patients Luca Baldelli, Sebastian Schade, Silvia Jesús, Sebastian R. Schreglmann, Luisa Sambati, Pilar Gómez-Garre, Claire Halsband, Giovanna Calandra-Buonaura, Astrid Daniela Adarmes-Gómez, Friederike Sixel-Döring, Corrado Zenesini, Chiara Pirazzini, Paolo Garagnani, Maria Giulia Bacalini, Kailash P. Bhatia, Pietro Cortelli, Brit Mollenhauer, Claudio Franceschi, Henry Houlden, Pietro Liò, Claudio Luchinat, Massimo Delledonne, Kevin Mills, Nancy L. Pedersen, Tiago Azevedo, Anna Bartoletti-Stella, Marta Bonilla-Toribio, Dolores Buiza-Rueda, Sabina Capellari, Mario Carriòn-Claro, Robert Clayton, Alessandra Dal Molin, Giovanna Maria Dimitri, Ivan Doykov, Cristina Giuliani, Sara Hägg, Jenny Hällqvist, Wendy Heywood, Ismael Huertas, Juulia Jylhävä, Miguel A. Labrador-Espinosa, Cristina Licari, Daniel Macias, Francesca Magrinelli, Juan Francisco Martín Rodríguez, Maria Giovanna Maturo, Giacomo Mengozzi, Gaia Meoni, Maddalena Milazzo, Christine Nardini, Nancy L. Pedersen, Maria Teresa Periñán-Tocino, Francesco Ravaioli, Claudia Sala, Simeon Spasov, Cristina Tejera-Parrado, Leonardo Tenori, Turano Paola, Dylan Williams, Luciano Xumerle, Elisa Zago, Marcella Broli, Dolores Buiza-Rueda, Patrizia De Massis, Rocio Escuela-Martin, Giovanni Fabbri, Anna Gabellini, Pietro Guaraldi, Henry Houlden, Stefania Macrì, Stefania Alessandra Nassetti, Cesa Lorella Maria Scaglione, Franco Valzania, Cilea Rosaria, Francesco Mignani, Rosario Vigo Ortega, Claudia Boninsegna, Silvia De Luca, Pablo Mir, Claudia Trenkwalder, Federica Provini, and Npj Parkinson S Disease, 2021
The INCREASE project: Intelligent Collections of food-legume genetic resources for European agrofood systems Elisa Bellucci, Orlando Mario Aguilar, Saleh Alseekh, Kirstin Bett, Creola Brezeanu, Douglas Cook, Lucía De la Rosa, Massimo Delledonne, Denise F. Dostatny, Juan J. Ferreira, Valérie Geffroy, Sofia Ghitarrini, Magdalena Kroc, Shiv Kumar Agrawal, Giuseppina Logozzo, Mario Marino, Tristan Mary‐Huard, Phil McClean, Vladimir Meglič, Tamara Messer, Frédéric Muel, Laura Nanni, Kerstin Neumann, Filippo Servalli, Silvia Străjeru, Rajeev K. Varshney, Marta W. Vasconcelos, Massimo Zaccardelli, Aleksei Zavarzin, Elena Bitocchi, Emanuele Frontoni, Alisdair R. Fernie, Tania Gioia, Andreas Graner, Luis Guasch, Lena Prochnow, Markus Oppermann, Karolina Susek, Maud Tenaillon, Roberto Papa Plant Journal, 2021
A geroscience approach for Parkinson's disease: Conceptual framework and design of PROPAG-AGEING project Chiara Pirazzini, Tiago Azevedo, Luca Baldelli, Anna Bartoletti-Stella, Giovanna Calandra-Buonaura, Alessandra Dal Molin, Giovanna Maria Dimitri, Ivan Doykov, Pilar Gómez-Garre, Sara Hägg, Jenny Hällqvist, Claire Halsband, Wendy Heywood, Silvia Jesús, Juulia Jylhävä, Katarzyna Malgorzata Kwiatkowska, Miguel A. Labrador-Espinosa, Cristina Licari, Maria Giovanna Maturo, Giacomo Mengozzi, Gaia Meoni, Maddalena Milazzo, Maria Teresa Periñán-Tocino, Francesco Ravaioli, Claudia Sala, Luisa Sambati, Sebastian Schade, Sebastian Schreglmann, Simeon Spasov, Leonardo Tenori, Dylan Williams, Luciano Xumerle, Elisa Zago, Kailash P. Bhatia, Sabina Capellari, Pietro Cortelli, Paolo Garagnani, Henry Houlden, Pietro Liò, Claudio Luchinat, Massimo Delledonne, Kevin Mills, Pablo Mir, Brit Mollenhauer, Christine Nardini, Nancy L. Pedersen, Federica Provini, Stephen Strom, Claudia Trenkwalder, Paola Turano, Maria Giulia Bacalini, Claudio Franceschi, Astrid Adarmes-Gómez, Tiago Azevedo, Maria Giulia Bacalini, Luca Baldelli, Anna Bartoletti-Stella, Kailash P. Bhatia, Marta Bonilla-Toribio, Claudia Boninsegna, Marcella Broli, Dolores Buiza-Rueda, Giovanna Calandra-Buonaura, Sabina Capellari, Mario Carrión-Claro, Rosalia Cilea, Robert Clayton, Pietro Cortelli, Alessandra Dal Molin, Silvia De Luca, Patrizia De Massis, Giovanna Maria Dimitri, Ivan Doykov, Rocio Escuela-Martin, Giovanni Fabbri, Claudio Franceschi, Anna Gabellini, Paolo Garagnani, Cristina Giuliani, Pilar Gómez-Garre, Pietro Guaraldi, Sara Hägg, Jenny Hällqvist, Claire Halsband, Wendy Heywood, Henry Houlden, Ismae Huertas, Silvia Jesús, Juulia Jylhävä, Miguel A. Labrador-Espinosa, Cristina Licari, Pietro Liò, Claudio Luchinat, Daniel Macias, Stefania Macrì, Francesca Magrinelli, Juan Francisco Martín Rodríguez, Massimo Delledonne, Maria Giovanna Maturo, Giacomo Mengozzi, Gaia Meoni, Francesco Mignani, Maddalena Milazzo, Kevin Mills, Pablo Mir, Brit Mollenhauer, Christine Nardini, Stefania Alessandra Nassetti, Nancy L. Pedersen, Maria Teresa Periñán-Tocino, Chiara Pirazzini, Federica Provini, Francesco Ravaioli, Claudia Sala, Luisa Sambati, Cesa Lorella Maria Scaglione, Sebastian Schade, Sebastian Schreglmann, Simeon Spasov, Stephen Strom, Cristina Tejera-Parrado, Leonardo Tenori, Claudia Trenkwalder, Paola Turano, Franco Valzania, Rosario Vigo Ortega, Dylan Williams, Luciano Xumerle, Elisa Zago Mechanisms of Ageing and Development, 2021
Pod indehiscence in common bean is associated with the fine regulation of PvMYB26 Valerio Di Vittori, Elena Bitocchi, Monica Rodriguez, Saleh Alseekh, Elisa Bellucci, Laura Nanni, Tania Gioia, Stefania Marzario, Giuseppina Logozzo, Marzia Rossato, Concetta De Quattro, Maria L Murgia, Juan José Ferreira, Ana Campa, Chunming Xu, Fabio Fiorani, Arun Sampathkumar, Anja Fröhlich, Giovanna Attene, Massimo Delledonne, Björn Usadel, Alisdair R Fernie, Domenico Rau, Roberto Papa Journal of Experimental Botany, 2021
A molecular signature associated with prolonged survival in glioblastoma patients treated with regorafenib Alessandra Santangelo, Marzia Rossato, Giuseppe Lombardi, Salvatore Benfatto, Denise Lavezzari, Gian Luca De Salvo, Stefano Indraccolo, Maria Cristina Dechecchi, Paola Prandini, Roberto Gambari, Chiara Scapoli, Gianfranco Di Gennaro, Mario Caccese, Marica Eoli, Roberta Rudà, Alba Ariela Brandes, Toni Ibrahim, Simona Rizzato, Ivan Lolli, Giuseppe Lippi, Massimo Delledonne, Vittorina Zagonel, Giulio Cabrini Neuro Oncology, 2021
Interaction between microarray design strategies and data pre-processing procedures in gene expression differential analysis: A computational statistical survey Research Journal of Biotechnology, 2020
The genetic basis of sex determination in grapes Mélanie Massonnet, Noé Cochetel, Andrea Minio, Amanda M. Vondras, Jerry Lin, Aline Muyle, Jadran F. Garcia, Yongfeng Zhou, Massimo Delledonne, Summaira Riaz, Rosa Figueroa-Balderas, Brandon S. Gaut, Dario Cantu Nature Communications, 2020
Genomic history of the Italian population recapitulates key evolutionary dynamics of both Continental and Southern Europeans Marco Sazzini, Paolo Abondio, Stefania Sarno, Guido Alberto Gnecchi-Ruscone, Matteo Ragno, Cristina Giuliani, Sara De Fanti, Claudia Ojeda-Granados, Alessio Boattini, Julien Marquis, Armand Valsesia, Jerome Carayol, Frederic Raymond, Chiara Pirazzini, Elena Marasco, Alberto Ferrarini, Luciano Xumerle, Sebastiano Collino, Daniela Mari, Beatrice Arosio, Daniela Monti, Giuseppe Passarino, Patrizia D’Aquila, Davide Pettener, Donata Luiselli, Gastone Castellani, Massimo Delledonne, Patrick Descombes, Claudio Franceschi, Paolo Garagnani BMC Biology, 2020
A chromosome-anchored eggplant genome sequence reveals key events in Solanaceae evolution Lorenzo Barchi, Marco Pietrella, Luca Venturini, Andrea Minio, Laura Toppino, Alberto Acquadro, Giuseppe Andolfo, Giuseppe Aprea, Carla Avanzato, Laura Bassolino, Cinzia Comino, Alessandra Dal Molin, Alberto Ferrarini, Louise Chappell Maor, Ezio Portis, Sebastian Reyes-Chin-Wo, Riccardo Rinaldi, Tea Sala, Davide Scaglione, Prashant Sonawane, Paola Tononi, Efrat Almekias-Siegl, Elisa Zago, Maria Raffaella Ercolano, Asaph Aharoni, Massimo Delledonne, Giovanni Giuliano, Sergio Lanteri, Giuseppe Leonardo Rotino Scientific Reports, 2019
Intronic ATTTC repeat expansions in STARD7 in familial adult myoclonic epilepsy linked to chromosome 2 Mark A. Corbett, Thessa Kroes, Liana Veneziano, Mark F. Bennett, Rahel Florian, Amy L. Schneider, Antonietta Coppola, Laura Licchetta, Silvana Franceschetti, Antonio Suppa, Aaron Wenger, Davide Mei, Manuela Pendziwiat, Sabine Kaya, Massimo Delledonne, Rachel Straussberg, Luciano Xumerle, Brigid Regan, Douglas Crompton, Anne-Fleur van Rootselaar, Anthony Correll, Rachael Catford, Francesca Bisulli, Shreyasee Chakraborty, Sara Baldassari, Paolo Tinuper, Kirston Barton, Shaun Carswell, Martin Smith, Alfredo Berardelli, Renee Carroll, Alison Gardner, Kathryn L. Friend, Ilan Blatt, Michele Iacomino, Carlo Di Bonaventura, Salvatore Striano, Julien Buratti, Boris Keren, Caroline Nava, Sylvie Forlani, Gabrielle Rudolf, Edouard Hirsch, Eric Leguern, Pierre Labauge, Simona Balestrini, Josemir W. Sander, Zaid Afawi, Ingo Helbig, Hiroyuki Ishiura, Shoji Tsuji, Sanjay M. Sisodiya, Giorgio Casari, Lynette G. Sadleir, Riaan van Coller, Marina A. J. Tijssen, Karl Martin Klein, Arn M. J. M. van den Maagdenberg, Federico Zara, Renzo Guerrini, Samuel F. Berkovic, Tommaso Pippucci, Laura Canafoglia, Melanie Bahlo, Pasquale Striano, Ingrid E. Scheffer, Francesco Brancati, Christel Depienne, Jozef Gecz Nature Communications, 2019
Not just a pathogen? Description of a plant-beneficial Pseudomonas syringae strain Alessandro Passera, Stéphane Compant, Paola Casati, Maria Giovanna Maturo, Giovanna Battelli, Fabio Quaglino, Livio Antonielli, Domenico Salerno, Milena Brasca, Silvia Laura Toffolatti, Francesco Mantegazza, Massimo Delledonne, Birgit Mitter Frontiers in Microbiology, 2019
SETD2 and histone H3 lysine 36 methylation deficiency in advanced systemic mastocytosis G Martinelli, M Mancini, C De Benedittis, M Rondoni, C Papayannidis, M Manfrini, M Meggendorfer, R Calogero, V Guadagnuolo, M C Fontana, L Bavaro, A Padella, E Zago, L Pagano, R Zanotti, L Scaffidi, G Specchia, F Albano, S Merante, C Elena, P Savini, D Gangemi, P Tosi, F Ciceri, G Poletti, L Riccioni, F Morigi, M Delledonne, T Haferlach, M Cavo, P Valent, S Soverini Leukemia, 2018
A novel analysis flow for fused transcripts discovery from paired-end RNA-SEQ data Bioinformatics 2012 Proceedings of the International Conference on Bioinformatics Models Methods and Algorithms, 2012
MYO1E mutations and childhood familial focal segmental glomerulosclerosis Caterina Mele, Paraskevas Iatropoulos, Roberta Donadelli, Andrea Calabria, Ramona Maranta, Paola Cassis, Simona Buelli, Susanna Tomasoni, Rossella Piras, Mira Krendel, Serena Bettoni, Marina Morigi, Massimo Delledonne, Carmine Pecoraro, Isabella Abbate, Maria Rosaria Capobianchi, Friedhelm Hildebrandt, Edgar Otto, Franz Schaefer, Fabio Macciardi, Fatih Ozaltin, Sevinc Emre, Tulin Ibsirlioglu, Ariela Benigni, Giuseppe Remuzzi, Marina Noris New England Journal of Medicine, 2011
Microarray system: A system for managing data produced by DNA-microarray experiments Bioinformatics 2011 Proceedings of the International Conference on Bioinformatics Models Methods and Algorithms, 2011
Transformation of korean chrysanthemum (Dendranthema zawadskii x D. x grandiflorum) and insertion of the maize autonomous element Ac using Agrobacterium tumefaciens Journal of Genetics and Breeding, 2000
Afzelia corallina (Fabaceae), a new micro-endemic tree from Pemba Island, Zanzibar, Tanzania A Bianchi, G Baldesi, D Calzoni, M Delledonne, R Focaia, Q Luke, ... PhytoKeys 273, 55 , 2026 2026
The novel (TCTG) n motif in CNBP expanded alleles: composition, dynamics and genotype–phenotype correlation in Myotonic dystrophy type 2 (DM2) F Centofanti, VV Visconti, MR D’Apice, M Carlomagno, S Maestri, ... Human Genomics , 2026 2026
The novel (TCTG) MG Siciliano, P Origone, M Delledonne, M Rossato, A Botta, G Novelli 2026
On-site microbial community analysis in rivers: integrating autonomous sampling with a portable sequencing workflow S Martínez-Campos, M Ordeix, M Soria, JL Balcazar, F Fontana, N Rossi, ... bioRxiv, 2025.12. 24.695448 , 2025 2025
Genetic mosaicism in diffuse Malformations of Cortical Development: Insights and Implications in the diagnostic workflow F Fineschi, B Straka, C Mandorlini, V Cetica, E Cellini, P Krsek, AI Timis, ... EUROPEAN JOURNAL OF HUMAN GENETICS 33, 780-780 , 2025 2025
Identification, characterization and segregation analysis of DM1 alleles containing non-CTG variant repeats (VRs) in a two-generation Italian family VV Visconti, MR D'Apice, F Centofanti, M Carlomagno, S Maestri, ... EUROPEAN JOURNAL OF HUMAN GENETICS 33, 830-831 , 2025 2025
Optimizing insert size ditribution in whole exome sequencing for improved variant detection L Bertoli, M Orlandi, F Lucchini, CD Esposti, M Delledonne EUROPEAN JOURNAL OF HUMAN GENETICS 33, 1012-1012 , 2025 2025
The italian national genomic strategy: current status, challenges, and future perspectives in clinical practice and public health FA Causio, S Farina, A Maio, F Beccia, L Russo, V Baccolini, M Chiara, ... Journal of Community Genetics, 1-5 , 2025 2025 Citations: 1
Exploring Bat–Virus Interactions: Insights from a Study in the Gobi Desert S Canziani, D Lelli, P Agnelli, C Augugliaro, M Bazarragchaa, S Bertolino, ... Pathogens 14 (9), 870 , 2025 2025 Citations: 1
A journey of discovery: a multi-stage diagnostic procedure identifies Curtobacterium flaccumfaciens pv. allii as a new potential threat to maize F Gaffuri, I Ferraris, A Follador, A Travaglino, L Angheben, AR Limongi, ... Crop Protection 195, 107254 , 2025 2025 Citations: 1
The lncRNA LOC100257036 and vvimiR156 modulate gibberellin signaling through AGAMOUS during cluster formation in Sistan Yaghooti grape S Sahraei, N Mahdinezhad, A Emamjomeh, K Kavousi, M Solouki, ... Scientific Reports 15 (1), 29687 , 2025 2025
di Firenze L Leonardelli, M Delledonne, A Brusco, K Chrzanowska, A Schinzel, ... 2025
Bats as reservoir hosts of emerging viruses in Italy: eco-epidemiological investigations to protect public health and biodiversity D Lelli, A Lavazza, T Trogu, E Sozzi, M Carrera, A Castelli, C Tolini, ... 9th National Congress of the Italian Society for Virology-One Virology One … , 2025 2025
The unexplored diversity of rough-seeded lupins provides rich genomic resources and insights into lupin evolution K Susek, L Vincenzi, M Tomaszewska, M Kroc, E Franco, E Cosentino, ... Nature Communications 16 (1), 4358 , 2025 2025 Citations: 4
The evolutionary history of the common bean ( Phaseolus vulgaris ) revealed by chloroplast and nuclear genomes analysis G Frascarelli, TR Galise, N D’Agostino, D Cafasso, S Cozzolino, ... Theoretical and Applied Genetics 138 (2), 47 , 2025 2025 Citations: 7
Differentiation of long non-coding RNA expression profiles in three fruiting stages of grape S Sahraei, N Mahdinezhad, A Emamjomeh, K Kavousi, M Solouki, ... Gene 934, 149029 , 2025 2025 Citations: 2
Transcriptomic analysis reveals role of lncRNA LOC100257036 to regulate AGAMOUS during cluster compactness of Vitis vinifera cv. sistan yaghooti S Sahraei, N Mahdinezhad, A Emamjomeh, K Kavousi, M Solouki, ... Scientific Reports 14 (1), 28331 , 2024 2024 Citations: 4
Mosaicism in malformations of cortical development: Implications for the diagnostic workflow F Fineschi, B Straka, C Mandorlini, M Vlckova, V Cetica, ... EPILEPSIA 65, 48-48 , 2024 2024
Adaptive gene loss in the common bean pan-genome during range expansion and domestication G Cortinovis, L Vincenzi, R Anderson, G Marturano, JI Marsh, PE Bayer, ... Nature communications 15 (1), 6698 , 2024 2024 Citations: 47
Landscape genomics highlights the adaptive evolution of chickpea L Rocchetti, M Rodriguez, A Pieri, S Papalini, L De Antoni, E Vitali, ... bioRxiv, 2024.06. 06.597750 , 2024 2024 Citations: 1
MOST CITED SCHOLAR PUBLICATIONS
The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla French nature 449 (7161), 463-467 , 2007 2007 Citations: 4266
Nitric oxide functions as a signal in plant disease resistance M Delledonne, Y Xia, RA Dixon, C Lamb Nature 394 (6693), 585-588 , 1998 1998 Citations: 2546
Phased diploid genome assembly with single-molecule real-time sequencing CS Chin, P Peluso, FJ Sedlazeck, M Nattestad, GT Concepcion, A Clum, ... Nature methods 13 (12), 1050-1054 , 2016 2016 Citations: 2088
International network of cancer genome projects W Anderson, A Aretz, AD Barker, C Bell, RR Bernabé, MK Bhan, F Calvo, ... Nature 464 (7291), 993-998 , 2010 2010 Citations: 1932
Signal interactions between nitric oxide and reactive oxygen intermediates in the plant hypersensitive disease resistance response M Delledonne, J Zeier, A Marocco, C Lamb Proceedings of the National Academy of Sciences 98 (23), 13454-13459 , 2001 2001 Citations: 1438
The involvement of cysteine proteases and protease inhibitor genes in the regulation of programmed cell death in plants M Solomon, B Belenghi, M Delledonne, E Menachem, A Levine The Plant Cell 11 (3), 431-443 , 1999 1999 Citations: 1005
NO news is good news for plants M Delledonne Current opinion in plant biology 8 (4), 390-396 , 2005 2005 Citations: 624
Insight into the evolution of the Solanaceae from the parental genomes of Petunia hybrida A Bombarely, M Moser, A Amrad, M Bao, L Bapaume, CS Barry, M Bliek, ... Nature plants 2 (6), 16074 , 2016 2016 Citations: 441
Characterization of Transcriptional Complexity during Berry Development in Vitis vinifera Using RNA-Seq S Zenoni, A Ferrarini, E Giacomelli, L Xumerle, M Fasoli, G Malerba, ... Plant physiology 152 (4), 1787-1795 , 2010 2010 Citations: 438
Arabidopsis nonsymbiotic hemoglobin AHb1 modulates nitric oxide bioactivity M Perazzolli, P Dominici, MC Romero-Puertas, E Zago, J Zeier, M Sonoda, ... The Plant Cell 16 (10), 2785-2794 , 2004 2004 Citations: 437
Genome analysis of Bifidobacterium bifidum PRL2010 reveals metabolic pathways for host-derived glycan foraging F Turroni, F Bottacini, E Foroni, I Mulder, JH Kim, A Zomer, B Sánchez, ... Proceedings of the National Academy of Sciences 107 (45), 19514-19519 , 2010 2010 Citations: 436
The grapevine expression atlas reveals a deep transcriptome shift driving the entire plant into a maturation program M Fasoli, S Dal Santo, S Zenoni, GB Tornielli, L Farina, A Zamboni, ... The Plant Cell 24 (9), 3489-3505 , 2012 2012 Citations: 432
S-nitrosylation of peroxiredoxin II E promotes peroxynitrite-mediated tyrosine nitration MC Romero-Puertas, M Laxa, A Matte, F Zaninotto, I Finkemeier, ... The Plant Cell 19 (12), 4120-4130 , 2007 2007 Citations: 417
Decreased epigenetic age of PBMCs from Italian semi-supercentenarians and their offspring S Horvath, C Pirazzini, MG Bacalini, D Gentilini, AM Di Blasio, ... Aging (Albany NY) 7 (12), 1159 , 2015 2015 Citations: 416
Nitric oxide signalling functions in plant–pathogen interactions MC Romero‐Puertas, M Perazzolli, ED Zago, M Delledonne Cellular Microbiology 6 (9), 795-803 , 2004 2004 Citations: 334
Annotating genomes with massive-scale RNA sequencing F Denoeud, JM Aury, C Da Silva, B Noel, O Rogier, M Delledonne, ... Genome biology 9 (12), R175 , 2008 2008 Citations: 324
Proteomic analysis of S‐nitrosylated proteins in Arabidopsis thaliana undergoing hypersensitive response MC Romero‐Puertas, N Campostrini, A Mattè, PG Righetti, M Perazzolli, ... Proteomics 8 (7), 1459-1469 , 2008 2008 Citations: 323
MYO1E mutations and childhood familial focal segmental glomerulosclerosis C Mele, P Iatropoulos, R Donadelli, A Calabria, R Maranta, P Cassis, ... New England Journal of Medicine 365 (4), 295-306 , 2011 2011 Citations: 317
NO signals in the haze: nitric oxide signalling in plant defence M Leitner, E Vandelle, F Gaupels, D Bellin, M Delledonne Current opinion in plant biology 12 (4), 451-458 , 2009 2009 Citations: 308
Metacaspase activity of Arabidopsis thaliana is regulated by S-nitrosylation of a critical cysteine residue B Belenghi, MC Romero-Puertas, D Vercammen, A Brackenier, D Inzé, ... Journal of Biological Chemistry 282 (2), 1352-1358 , 2007 2007 Citations: 304
