Publications

E. Groppa, P. Martini, N. Derakhshan, M. Theret, M. Ritso, L.W. Tung, Y.X. Wang, H. Soliman, M.S. Hamer, L. Stankiewicz, C. Eisner, L.N. Erwan, C. Chang, L. Yi, J.H. Yuan, S. Kong, C. Weng, J. Adams, L. Chang, A. Peng, H.M. Blau, C. Romualdi, F.M.V. Rossi. Spatial compartmentalization of signaling imparts source-specific functions on secreted factors. Cell Reports, (42), 2, https://doi.org/10.1016/j.celrep.2023.112051, 2023.
E. Lazzarini, D.A. Silvestris, G. Benvenuto, D. Osti, L. Fattore, R. Paterra, G. Finocchiaro, P. Malatesta, A. Daga, A.L. Gallotti, R. Galli, G. Pelicci, A. Tesei, M. Bedeschi, R. Pallini, L. Pasqualini, C. Romualdi, A. Gallo, L. Ricci-Vitiani, S. Indraccolo. Genome-wide profiling of patient-derived glioblastoma stem-like cells reveals recurrent genetic and transcriptomic signatures associated with brain tumors. Journal of Neuro-Oncology, (163), 1, pp. 47-59, https://doi.org/10.1007/s11060-023-04287-6, 2023.
C. Marchioretti, G. Zanetti, M. Pirazzini, G. Gherardi, L. Nogara, R. Andreotti, P. Martini, L. Marcucci, M. Canato, S.R. Nath, E. Zuccaro, M. Chivet, C. Mammucari, M. Pacifici, A. Raffaello, R. Rizzuto, A. Mattarei, M.A. Desbats, L. Salviati, A. Megighian, G. Soraru, E. Pegoraro, E. Belluzzi, A. Pozzuoli, C. Biz, P. Ruggieri, C. Romualdi, A.P. Lieberman, G.J. Babu, M. Sandri, B. Blaauw, M. Basso, M. Pennuto. Defective excitation-contraction coupling and mitochondrial respiration precede mitochondrial Ca2+ accumulation in spinobulbar muscular atrophy skeletal muscle. Nature Communications, (14), 1, https://doi.org/10.1038/s41467-023-36185-w, 2023.
A. Velle, C. Pesenti, T. Grassi, L. Beltrame, P. Martini, M. Jaconi, F. Agostinis, E. Calura, D. Katsaros, F. Borella, R. Fruscio, M. D'Incalci, S. Marchini, C. Romualdi. A comprehensive investigation of histotype-specific microRNA and their variants in Stage I epithelial ovarian cancers. International Journal of Cancer, (152), 9, pp. 1989-2001, https://doi.org/10.1002/ijc.34408, 2023.
A. Dinarello, A. Tesoriere, P. Martini, C.M. Fontana, D. Volpato, L. Badenetti, F. Terrin, N. Facchinello, C. Romualdi, O. Carnevali, L. {Dalla Valle}, F. Argenton. Zebrafish Mutant Lines Reveal the Interplay between nr3c1 and nr3c2 in the GC-Dependent Regulation of Gene Transcription. International Journal of Molecular Sciences, (23), 5, https://doi.org/10.3390/ijms23052678, 2022.
G. Cattaneo, U.F. Petrillo, R. Giancarlo, F. Palini, C. Romualdi. The power of word-frequency-based alignment-free functions: a comprehensive large-scale experimental analysis. Bioinformatics, (38), 4, pp. 925-932, https://doi.org/10.1093/bioinformatics/btab747, 2022.
M. Borella, G. Martello, D. Risso, C. Romualdi. PsiNorm: a scalable normalization for single-cell RNA-seq data. Bioinformatics, (38), 1, pp. 164-172, https://doi.org/10.1093/bioinformatics/btab641, 2022.
F. Agostinis, C. Romualdi, G. Sales, D. Risso. NewWave: A scalable R/Bioconductor package for the dimensionality reduction and batch effect removal of single-cell RNA-seq data. Bioinformatics, (38), 9, pp. 2648-2650, https://doi.org/10.1093/bioinformatics/btac149, 2022.
E. Calura, C. Romualdi. miRNA bioinformatics and pathway analysis. MicroRNA in Human Malignancies, pp. 141-150, https://doi.org/10.1016/B978-0-12-822287-4.00021-9, 2022.
S. Negro, F. Lauria, M. Stazi, T. Tebaldi, G. D'Este, M. Pirazzini, A. Megighian, F. Lessi, C.M. Mazzanti, G. Sales, C. Romualdi, S. Fillo, F. Lista, J.N. Sleigh, A.P. Tosolini, G. Schiavo, G. Viero, M. Rigoni. Hydrogen peroxide induced by nerve injury promotes axon regeneration via connective tissue growth factor. Acta Neuropathologica Communications, (10), 1, https://doi.org/10.1186/s40478-022-01495-5, 2022.
A. Buratin, C. Romualdi, S. Bortoluzzi, E. Gaffo. Detecting differentially expressed circular RNAs from multiple quantification methods using a generalized linear mixed model. Computational and Structural Biotechnology Journal, (20), pp. 2495-2502, https://doi.org/10.1016/j.csbj.2022.05.026, 2022.
C. Pesenti, L. Beltrame, A. Velle, R. Fruscio, M. Jaconi, F. Borella, F.M. Cribiu, E. Calura, L.V. Venturini, D. Lenoci, F. Agostinis, D. Katsaros, N. Panini, T. Bianchi, F. Landoni, M. Miozzo, M. D'Incalci, J.D. Brenton, C. Romualdi, S. Marchini. Copy number alterations in stage I epithelial ovarian cancer highlight three genomic patterns associated with prognosis. European Journal of Cancer, (171), pp. 85-95, https://doi.org/10.1016/j.ejca.2022.05.005, 2022.
P. Martini, G. Sales, L. Diamante, V. Perrera, C. Colantuono, S. Riccardo, D. Cacchiarelli, C. Romualdi, G. Martello. BrewerIX enables allelic expression analysis of imprinted and X-linked genes from bulk and single-cell transcriptomes. Communications Biology, (5), 1, https://doi.org/10.1038/s42003-022-03087-4, 2022.
I. Urso, A. Biscontin, D. Corso, C. Bertolucci, C. Romualdi, C. {De Pitta}, B. Meyer, G. Sales. A thorough annotation of the krill transcriptome offers new insights for the study of physiological processes. Scientific Reports, (12), 1, https://doi.org/10.1038/s41598-022-15320-5, 2022.
L. Paracchini, L. Mannarino, I. Craparotta, C. Romualdi, R. Fruscio, T. Grassi, V. Fotia, G. Caratti, P. Perego, E. Calura, L. Clivio, M. D'Incalci, L. Beltrame, S. Marchini. Regional and temporal heterogeneity of epithelial ovarian cancer tumor biopsies: implications for therapeutic strategies. Oncotarget, (12), 24, pp. 2404-2417, https://doi.org/10.18632/oncotarget.10505, 2021.
D. Corso, F. Chemello, E. Alessio, I. Urso, G. Ferrarese, M. Bazzega, C. Romualdi, G. Lanfranchi, G. Sales, S. Cagnin. MyoData: An expression knowledgebase at single cell/nucleus level for the discovery of coding-noncoding RNA functional interactions in skeletal muscle. Computational and Structural Biotechnology Journal, (19), pp. 4142-4155, https://doi.org/10.1016/j.csbj.2021.07.020, 2021.
N. Laprovitera, M. Riefolo, E. Porcellini, G. Durante, I. Garajova, F. Vasuri, A. Aigelsreiter, N. Dandachi, G. Benvenuto, F. Agostinis, S. Sabbioni, I. {Berindan Neagoe}, C. Romualdi, A. Ardizzoni, D. Trere, M. Pichler, A. D'Errico, M. Ferracin. MicroRNA expression profiling with a droplet digital PCR assay enables molecular diagnosis and prognosis of cancers of unknown primary. Molecular Oncology, (15), 10, pp. 2732-2751, https://doi.org/10.1002/1878-0261.13026, 2021.
C. Romani, E. Salviato, A. Paderno, L. Zanotti, A. Ravaggi, A. Deganello, G. Berretti, T. Gualtieri, S. Marchini, M. D'Incalci, D. Mattavelli, C. Piazza, P. Bossi, C. Romualdi, P. Nicolai, E. Bignotti. Genome-wide study of salivary miRNAs identifies miR-423-5p as promising diagnostic and prognostic biomarker in oral squamous cell carcinoma. Theranostics, (11), 6, pp. 2987-2999, https://doi.org/10.7150/THNO.45157, 2021.
L. Paracchini, L. Beltrame, T. Grassi, A. Inglesi, R. Fruscio, F. Landoni, D. Ippolito, M.D. Marchette, M. Paderno, M. Adorni, M. Jaconi, C. Romualdi, M. D'Incalci, G. Siravegna, S. Marchini. Genome-wide copy-number alterations in circulating tumor DNA as a novel biomarker for patients with high-grade serous ovarian cancer. Clinical Cancer Research, (27), 9, pp. 2549-2560, https://doi.org/10.1158/1078-0432.CCR-20-3345, 2021.
P. Todeschini, E. Salviato, C. Romani, V. Raimondi, F. Ciccarese, F. Ferrari, G. Tognon, S. Marchini, M. D'Incalci, L. Zanotti, A. Ravaggi, F. Odicino, E. Sartori, D.M. D'agostino, M. Samaja, C. Romualdi, E. Bignotti. Comprehensive profiling of hypoxia-related mirnas identifies mir-23a-3p overexpression as a marker of platinum resistance and poor prognosis in high-grade serous ovarian cancer. Cancers, (13), 13, https://doi.org/10.3390/cancers13133358, 2021.
C. Sacchetto, Z. Mohseni, R.M.W. Colpaert, L. Vitiello, M.D. Bortoli, I.G.C. Vonhogen, K. Xiao, G. Poloni, A. Lorenzon, C. Romualdi, R. Bariani, E. Mazzotti, L. Daliento, B. Bauce, D. Corrado, T. Thum, A. Rampazzo, L.J. {de Windt}, M. Calore. Circulating mir-185-5p as a potential biomarker for arrhythmogenic right ventricular cardiomyopathy. Cells, (10), 10, https://doi.org/10.3390/cells10102578, 2021.
A.I. Pisani, A. Scalfari, F. Crescenzo, C. Romualdi, M. Calabrese. A novel prognostic score to assess the risk of progression in relapsing−remitting multiple sclerosis patients. European Journal of Neurology, (28), 8, pp. 2503-2512, https://doi.org/10.1111/ene.14859, 2021.
R. Magliozzi, A. Scalfari, A.I. Pisani, S. Ziccardi, D. Marastoni, F.B. Pizzini, A. Bajrami, A. Tamanti, M. Guandalini, S. Bonomi, S. Rossi, V. Mazziotti, M. Castellaro, S. Montemezzi, S. Rasia, R. Capra, M. Pitteri, C. Romualdi, R. Reynolds, M. Calabrese. The CSF Profile Linked to Cortical Damage Predicts Multiple Sclerosis Activity. Annals of Neurology, (88), 3, pp. 562-573, https://doi.org/10.1002/ana.25786, 2020.
V. Barili, P. Fisicaro, B. Montanini, G. Acerbi, A. Filippi, G. Forleo, C. Romualdi, M. Ferracin, F. Guerrieri, G. Pedrazzi, C. Boni, M. Rossi, A. Vecchi, A. Penna, A. Zecca, C. Mori, A. Orlandini, E. Negri, M. Pesci, M. Massari, G. Missale, M. Levrero, S. Ottonello, C. Ferrari. Targeting p53 and histone methyltransferases restores exhausted CD8+ T cells in HCV infection. Nature Communications, (11), 1, https://doi.org/10.1038/s41467-019-14137-7, 2020.
V. Djordjilovic, M. Chiogna, C. Romualdi. Simulating gene silencing through intervention analysis. Journal of the Royal Statistical Society. Series C: Applied Statistics, (69), 4, pp. 887-907, https://doi.org/10.1111/rssc.12412, 2020.
V. Djordjilovic, M. Chiogna, C. Romualdi, E. Salviato. Searching for the Source of Difference: A Graphical Model Approach. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), (11925 LNBI), pp. 131-138, https://doi.org/10.1007/978-3-030-34585-3_12, 2020.
S. Gagno, M. Bartoletti, C. Romualdi, E. Poletto, S. Scalone, R. Sorio, M. Zanchetta, E. {De Mattia}, R. Roncato, E. Cecchin, G. Giorda, G. Toffoli. Pharmacogenetic score predicts overall survival, progression-free survival and platinum sensitivity in ovarian cancer. Pharmacogenomics, (21), 14, pp. 995-1010, https://doi.org/10.2217/pgs-2020-0049, 2020.
B. Gris, L. Treu, R.M. Zampieri, F. Caldara, C. Romualdi, S. Campanaro, N. {La Rocca}. Microbiota of the therapeutic Euganean thermal muds with a focus on the main cyanobacteria species. Microorganisms, (8), 10, pp. 1-23, https://doi.org/10.3390/microorganisms8101590, 2020.
S. Facchin, N. Vitulo, M. Calgaro, A. Buda, C. Romualdi, D. Pohl, B. Perini, G. Lorenzon, C. Marinelli, R. D'Inca, G.C. Sturniolo, E.V. Savarino. Microbiota changes induced by microencapsulated sodium butyrate in patients with inflammatory bowel disease. Neurogastroenterology and Motility, (32), 10, https://doi.org/10.1111/nmo.13914, 2020.
G. Benvenuto, P. Todeschini, L. Paracchini, E. Calura, R. Fruscio, C. Romani, L. Beltrame, P. Martini, A. Ravaggi, L. Ceppi, G. Sales, F. Donati, P. Perego, L. Zanotti, S. Ballabio, T. Grassi, M. {delle Marchette}, G. Tognon, E. Sartori, M. Adorni, F. Odicino, M. D'Incalci, E. Bignotti, C. Romualdi, S. Marchini. Expression profiles of PRKG1, SDF2L1 and PPP1R12A are predictive and prognostic factors for therapy response and survival in high-grade serous ovarian cancer. International Journal of Cancer, (147), 2, pp. 565-574, https://doi.org/10.1002/ijc.32935, 2020.
F. Finotello, E. Calura, D. Risso, S. Hautaniemi, C. Romualdi. Editorial: Multi-omic Data Integration in Oncology. Frontiers in Oncology, (10), https://doi.org/10.3389/fonc.2020.01768, 2020.
M. Calgaro, C. Romualdi, L. Waldron, D. Risso, N. Vitulo. Assessment of statistical methods from single cell, bulk RNA-seq, and metagenomics applied to microbiome data. Genome Biology, (21), 1, https://doi.org/10.1186/s13059-020-02104-1, 2020.
S. Gagno, E. Poletto, M. Bartoletti, L. Quartuccio, C. Romualdi, M. Garziera, S. Scalone, R. Sorio, E. Dreussi, C. Zanusso, E. {De Mattia}, R. Roncato, E. Cecchin, G. Giorda, S. {De Vita}, M. {Dal Bo}, F. Puglisi, G. Toffoli. A TGF-β associated genetic score to define prognosis and platinum sensitivity in advanced epithelial ovarian cancer. Gynecologic Oncology, (156), 1, pp. 233-242, https://doi.org/10.1016/j.ygyno.2019.10.019, 2020.
F. Chemello, F. Grespi, A. Zulian, P. Cancellara, E. Hebert-Chatelain, P. Martini, C. Bean, E. Alessio, L. Buson, M. Bazzega, A. Armani, M. Sandri, R. Ferrazza, P. Laveder, G. Guella, C. Reggiani, C. Romualdi, P. Bernardi, L. Scorrano, S. Cagnin, G. Lanfranchi. Transcriptomic Analysis of Single Isolated Myofibers Identifies miR-27a-3p and miR-142-3p as Regulators of Metabolism in Skeletal Muscle. Cell Reports, (26), 13, pp. 3784-3797.e8, https://doi.org/10.1016/j.celrep.2019.02.105, 2019.
M.D. Corno, A. Baldassarre, E. Calura, L. Conti, P. Martini, C. Romualdi, R. Vari, B. Scazzocchio, M. D'Archivio, A. Masotti, S. Gessani. Transcriptome profiles of human visceral adipocytes in obesity and colorectal cancer unravel the effects of body mass index and polyunsaturated fatty acids on genes and biological process related to tumorigenesis. Frontiers in Immunology, (10), FEB, https://doi.org/10.3389/fimmu.2019.00265, 2019.
E. Calura, M. Ciciani, A. Sambugaro, L. Paracchini, G. Benvenuto, S. Milite, P. Martini, L. Beltrame, F. Zane, R. Fruscio, M.D. Marchette, F. Borella, G. Tognon, A. Ravaggi, D. Katsaros, E. Bignotti, F. Odicino, M. D'Incalci, S. Marchini, C. Romualdi. Transcriptional characterization of stage i epithelial ovarian cancer: A multicentric study. Cells, (8), 12, https://doi.org/10.3390/cells8121554, 2019.
E. Salviato, V. Djordjilovic, M. Chiogna, C. Romualdi. SourceSet: A graphical model approach to identify primary genes in perturbed biological pathways. PLoS Computational Biology, (15), 10, https://doi.org/10.1371/journal.pcbi.1007357, 2019.
E. Alessio, L. Buson, F. Chemello, C. Peggion, F. Grespi, P. Martini, M.L. Massimino, B. Pacchioni, C. Millino, C. Romualdi, A. Bertoli, L. Scorrano, G. Lanfranchi, S. Cagnin. Single cell analysis reveals the involvement of the long non-coding RNA Pvt1 in the modulation of muscle atrophy and mitochondrial network. Nucleic Acids Research, (47), 4, pp. 1653-1670, https://doi.org/10.1093/nar/gkz007, 2019.
L. Suter, A.M. Polanowski, R. King, C. Romualdi, G. Sales, S. Kawaguchi, S.N. Jarman, B.E. Deagle. Sex identification from distinctive gene expression patterns in Antarctic krill (Euphausia superba). Polar Biology, (42), 12, pp. 2205-2217, https://doi.org/10.1007/s00300-019-02592-3, 2019.
C. Zanusso, E. Dreussi, R. Bortolus, C. Romualdi, S. Gagno, E. {De Mattia}, L. Romanato, F. Sartor, L. Quartuccio, E. Cecchin, G. Toffoli. Rs4143815-PDL1, a new potential immunogenetic biomarker of biochemical recurrence in locally advanced prostate cancer after radiotherapy. International Journal of Molecular Sciences, (20), 9, https://doi.org/10.3390/ijms20092082, 2019.
S. Ballabio, I. Craparotta, L. Paracchini, L. Mannarino, S. Corso, M.G. Pezzotta, M. Vescio, R. Fruscio, C. Romualdi, E. Dainese, L. Ceppi, E. Calura, S. Pileggi, G. Siravegna, L. Pattini, P. Martini, M. {delle Marchette}, C. Mangioni, A. Ardizzoia, A. Pellegrino, F. Landoni, M. D'Incalci, L. Beltrame, S. Marchini. Multisite analysis of high-grade serous epithelial ovarian cancers identifies genomic regions of focal and recurrent copy number alteration in 3q26.2 and 8q24.3. International Journal of Cancer, (145), 10, pp. 2670-2681, https://doi.org/10.1002/ijc.32288, 2019.
P. Martini, M. Chiogna, E. Calura, C. Romualdi. MOSClip: multi-omic and survival pathway analysis for the identification of survival associated gene and modules. Nucleic acids research, (47), 14, pp. e80, https://doi.org/10.1093/nar/gkz324, 2019.
G. Sales, E. Calura, C. Romualdi. Meta Graphite-a new layer of pathway annotation to get metabolite networks. Bioinformatics, (35), 7, pp. 1258-1260, https://doi.org/10.1093/bioinformatics/bty719, 2019.
E. Palumbo, C. Piotto, E. Calura, E. Fasanaro, E. Groff, F. Busato, B. {El Khouzai}, M. Rigo, L. Baggio, C. Romualdi, D. Zafiropoulos, A. Russo, M. Mognato, L. Corti. Individual Radiosensitivity in Oncological Patients: Linking Adverse Normal Tissue Reactions and Genetic Features. Frontiers in Oncology, (9), https://doi.org/10.3389/fonc.2019.00987, 2019.
D. Marastoni, A. Buriani, A.I. Pisani, F. Crescenzo, C. Zuco, S. Fortinguerra, V. Sorrenti, B. Marenda, C. Romualdi, R. Magliozzi, S. Monaco, M. Calabrese. Increased NK Cell Count in Multiple Sclerosis Patients Treated With Dimethyl Fumarate: A 2-Year Longitudinal Study. Frontiers in immunology, (10), pp. 1666, https://doi.org/10.3389/fimmu.2019.01666, 2019.
R.A. Tassi, A. Gambino, L. Ardighieri, E. Bignotti, P. Todeschini, C. Romani, L. Zanotti, M. Bugatti, F. Borella, D. Katsaros, G. Tognon, E. Sartori, F. Odicino, C. Romualdi, A. Ravaggi. FXYD5 (Dysadherin) upregulation predicts shorter survival and reveals platinum resistance in high-grade serous ovarian cancer patients. British Journal of Cancer, (121), 7, pp. 584-592, https://doi.org/10.1038/s41416-019-0553-z, 2019.
S. Giulitti, M. Pellegrini, I. Zorzan, P. Martini, O. Gagliano, M. Mutarelli, M.J. Ziller, D. Cacchiarelli, C. Romualdi, N. Elvassore, G. Martello. Direct generation of human naive induced pluripotent stem cells from somatic cells in microfluidics. Nature Cell Biology, (21), 2, pp. 275-286, https://doi.org/10.1038/s41556-018-0254-5, 2019.
A. Bajrami, M. Pitteri, M. Castellaro, F. Pizzini, C. Romualdi, S. Montemezzi, S. Monaco, M. Calabrese. The effect of fingolimod on focal and diffuse grey matter damage in active MS patients. Journal of Neurology, (265), 9, pp. 2154-2161, https://doi.org/10.1007/s00415-018-8952-2, 2018.
A. Scalfari, C. Romualdi, R.S. Nicholas, M. Mattoscio, R. Magliozzi, A. Morra, S. Monaco, P.A. Muraro, M. Calabrese. The cortical damage, early relapses, and onset of the progressive phase in multiple sclerosis. Neurology, (90), 24, pp. e2099-e2106, https://doi.org/10.1212/WNL.0000000000005685, 2018.
C. Scaroni, N. Albiger, A. Daniele, F. Dassie, C. Romualdi, G. Vazza, D. Regazzo, F. Ferrau, V. Barresi, V. Maffeis, M.P. Gardiman, S. Cannavo, P. Maffei, F. Ceccato, M. Losa, G. Occhi. Paradoxical GH Increase during OGTT Is Associated with First-Generation Somatostatin Analog Responsiveness in Acromegaly. Journal of Clinical Endocrinology and Metabolism, (104), 3, pp. 856-862, https://doi.org/10.1210/jc.2018-01360, 2018.
R. Magliozzi, O.W. Howell, R. Nicholas, C. Cruciani, M. Castellaro, C. Romualdi, S. Rossi, M. Pitteri, M.D. Benedetti, A. Gajofatto, F.B. Pizzini, S. Montemezzi, S. Rasia, R. Capra, A. Bertoldo, F. Facchiano, S. Monaco, R. Reynolds, M. Calabrese. Inflammatory intrathecal profiles and cortical damage in multiple sclerosis. Annals of Neurology, (83), 4, pp. 739-755, https://doi.org/10.1002/ana.25197, 2018.
E. Ferrazzi, C. Romualdi, M. Ocello, G. Frighetto, M. Turco, S. Vigolo, F. Fabris, P. Angeli, G. Vettore, R. Costa, S. Montagnese. Changes in Accident & Emergency Visits and Return Visits in Relation to the Enforcement of Daylight Saving Time and Photoperiod. Journal of Biological Rhythms, (33), 5, pp. 555-564, https://doi.org/10.1177/0748730418791097, 2018.
L. Mannarino, L. Paracchini, I. Craparotta, M. Romano, S. Marchini, R. Gatta, E. Erba, L. Clivio, C. Romualdi, M. D'Incalci, L. Beltrame, L. Pattini. A systems biology approach to investigate the mechanism of action of trabectedin in a model of myelomonocytic leukemia. Pharmacogenomics Journal, (18), 1, pp. 56-63, https://doi.org/10.1038/tpj.2016.76, 2018.
E. Salviato, V. Djordjilovic, M. Chiogna, C. Romualdi. SimPATHy: A new method for simulating data from perturbed biological PATHways. Bioinformatics, (33), 3, pp. 456-457, https://doi.org/10.1093/bioinformatics/btw642, 2017.
L. Tombolan, E. Poli, P. Martini, A. Zin, C. Romualdi, G. Bisogno, G. Lanfranchi. NELL1, whose high expression correlates with negative outcomes, has different methylation patterns in alveolar and embryonal rhabdomyosarcoma. Oncotarget, (8), 20, pp. 33086-33099, https://doi.org/10.18632/oncotarget.16526, 2017.
P. Martini, L. Paracchini, G. Caratti, M. Mello-Grand, R. Fruscio, L. Beltrame, E. Calura, G. Sales, A. Ravaggi, E. Bignotti, F.E. Odicino, E. Sartori, P. Perego, D. Katsaros, I. Craparotta, G. Chiorino, S. Cagnin, L. Mannarino, L. Ceppi, C. Mangioni, C. Ghimenti, M. D'Incalci, S. Marchini, C. Romualdi. LncRNAs as novel indicators of patients' prognosis in stage i epithelial ovarian cancer: A retrospective and multicentric study. Clinical Cancer Research, (23), 9, pp. 2356-2366, https://doi.org/10.1158/1078-0432.CCR-16-1402, 2017.
A. Imperatori, N. Sahnane, N. Rotolo, F. Franzi, E. Nardecchia, L. Libera, C. Romualdi, M. Cattoni, F. Sessa, L. Dominioni, D. Furlan. LINE-1 hypomethylation is associated to specific clinico-pathological features in Stage I non-small cell lung cancer. Lung Cancer, (108), pp. 83-89, https://doi.org/10.1016/j.lungcan.2017.03.003, 2017.
G. Sales, B.E. Deagle, E. Calura, P. Martini, A. Biscontin, C. {De Pitta}, S. Kawaguchi, C. Romualdi, B. Meyer, R. Costa, S. Jarman. KrillDB: A de novo transcriptome database for the Antarctic krill (Euphausia superba). PLoS ONE, (12), 2, https://doi.org/10.1371/journal.pone.0171908, 2017.
A. Palombit, M. Castellaro, M. Calabrese, C. Romualdi, F.B. Pizzini, S. Montemezzi, E. Grisan, A. Bertoldo. Cortical Thickness variability in Multiple Sclerosis: The role of lesion segmentation and filling. Proceedings - International Symposium on Biomedical Imaging, pp. 792-795, https://doi.org/10.1109/ISBI.2017.7950637, 2017.
M. Pitteri, C. Romualdi, R. Magliozzi, S. Monaco, M. Calabrese. Cognitive impairment predicts disability progression and cortical thinning in MS: An 8-year study. Multiple Sclerosis, (23), 6, pp. 848-854, https://doi.org/10.1177/1352458516665496, 2017.
P. Todeschini, E. Salviato, L. Paracchini, M. Ferracin, M. Petrillo, L. Zanotti, G. Tognon, A. Gambino, E. Calura, G. Caratti, P. Martini, L. Beltrame, L. Maragoni, D. Gallo, F.E. Odicino, E. Sartori, G. Scambia, M. Negrini, A. Ravaggi, M. D'Incalci, S. Marchini, E. Bignotti, C. Romualdi. Circulating miRNA landscape identifies miR-1246 as promising diagnostic biomarker in high-grade serous ovarian carcinoma: A validation across two independent cohorts. Cancer Letters, (388), pp. 320-327, https://doi.org/10.1016/j.canlet.2016.12.017, 2017.
G. Beffagna, A. Sammarco, C. Bedin, C. Romualdi, M. Mainenti, A. Mollo, L. Cavicchioli, S. Ferro, D. Trez, R.D. Maria, D. Nitti, A. Saccani, M. Campanella, M. Agostini, V. Zappulli. Circulating cell-free DNA in dogs with mammary tumors: Short and long fragments and integrity index. PLoS ONE, (12), 1, https://doi.org/10.1371/journal.pone.0169454, 2017.
A. Paolin, C. Romualdi, L. Romagnoli, D. Trojan. Analysis of potential factors affecting allografts contamination at retrieval. Cell and Tissue Banking, (18), 4, pp. 539-545, https://doi.org/10.1007/s10561-017-9667-9, 2017.
V. Daidone, G. Barbon, M.G. Cattini, E. Pontara, C. Romualdi, I. {Di Pasquale}, K. Hosokawa, A. Casonato. Usefulness of the Total Thrombus-Formation Analysis System (T-TAS) in the diagnosis and characterization of von Willebrand disease. Haemophilia, (22), 6, pp. 949-956, https://doi.org/10.1111/hae.12971, 2016.
F. Serra, C. Romualdi, F. Fogolari. Similarity Measures Based on the Overlap of Ranked Genes Are Effective for Comparison and Classification of Microarray Data. Journal of Computational Biology, (23), 7, pp. 603-614, https://doi.org/10.1089/cmb.2015.0057, 2016.
M. Petrillo, G.F. Zannoni, L. Beltrame, E. Martinelli, A. Difeo, L. Paracchini, I. Craparotta, L. Mannarino, G. Vizzielli, G. Scambia, M. D'Incalci, C. Romualdi, S. Marchini. Identification of high-grade serous ovarian cancer miRNA species associated with survival and drug response in patients receiving neoadjuvant chemotherapy: A retrospective longitudinal analysis using matched tumor biopsies. Annals of Oncology, (27), 4, pp. 625-634, https://doi.org/10.1093/annonc/mdw007, 2016.
L. Tombolan, E. Poli, P. Martini, A. Zin, C. Millino, B. Pacchioni, B. Celegato, G. Bisogno, C. Romualdi, A. Rosolen, G. Lanfranchi. Global DNA methylation profiling uncovers distinct methylation patterns of protocadherin alpha4 in metastatic and non-metastatic rhabdomyosarcoma. BMC Cancer, (16), 1, https://doi.org/10.1186/s12885-016-2936-3, 2016.
E. Calura, A. Bisognin, M. Manzoni, K. Todoerti, E. Taiana, G. Sales, G.J. Morgan, G. Tonon, N. Amodio, P. Tassone, A. Neri, L. Agnelli, C. Romualdi, S. Bortoluzzi. Disentangling the microRNA regulatory milieu in multiple myeloma: Integrative genomics analysis outlines mixed miRNATF circuits and pathway-derived networks modulated in t(4;14) patients. Oncotarget, (7), 3, pp. 2367-2378, https://doi.org/10.18632/oncotarget.6151, 2016.
M. Moretto, P. Sonego, N. Dierckxsens, M. Brilli, L. Bianco, D. Ledezma-Tejeida, S. Gama-Castro, M. Galardini, C. Romualdi, K. Laukens, J. Collado-Vides, P. Meysman, K. Engelen. COLOMBOS v3.0: Leveraging gene expression compendia for cross-species analyses. Nucleic Acids Research, (44), D1, pp. D620-D623, https://doi.org/10.1093/nar/gkv1251, 2016.
J.W. Kim, O.B. Botvinnik, O. Abudayyeh, C. Birger, J. Rosenbluh, Y. Shrestha, M.E. Abazeed, P.S. Hammerman, D. Dicara, D.J. Konieczkowski, C.M. Johannessen, A. Liberzon, A.R. Alizad-Rahvar, G. Alexe, A. Aguirre, M. Ghandi, H. Greulich, F. Vazquez, B.A. Weir, E.M. {Van Allen}, A. Tsherniak, D.D. Shao, T.I. Zack, M. Noble, G. Getz, R. Beroukhim, L.A. Garraway, M. Ardakani, C. Romualdi, G. Sales, D.A. Barbie, J.S. Boehm, W.C. Hahn, J.P. Mesirov, P. Tamayo. Characterizing genomic alterations in cancer by complementary functional associations. Nature Biotechnology, (34), 5, pp. 539-546, https://doi.org/10.1038/nbt.3527, 2016.
P. Benedetti, A.M. Sefton, M. Menegozzo, C. Guerriero, G. Bordignon, G. {Da Rin}, C. Romualdi, G. Pellizzer, D.M. Livermore. Antimicrobial use and microbiological testing in district general hospital ICUs of the Veneto region of north-east Italy. European Journal of Clinical Microbiology and Infectious Diseases, (35), 10, pp. 1627-1638, https://doi.org/10.1007/s10096-016-2701-1, 2016.
E. Calura, L. Paracchini, R. Fruscio, A. Difeo, A. Ravaggi, J. Peronne, P. Martini, G. Sales, L. Beltrame, E. Bignotti, G. Tognon, R. Milani, L. Clivio, T. Dell'Anna, G. Cattoretti, D. Katsaros, E. Sartori, C. Mangioni, L. Ardighieri, M. D'Incalci, S. Marchini, C. Romualdi. A prognostic regulatory pathway in stage I epithelial ovarian cancer: New hints for the poor prognosis assessment. Annals of Oncology, (27), 8, pp. 1511-1519, https://doi.org/10.1093/annonc/mdw210, 2016.
E. Calura, S. Pizzini, G. Sales, E. Gaffo, R. Norfo, V. Pennucci, R. Manfredini, C. Romualdi, P. Guglielmelli, A.M. Vannucchi, M. Balliu, N. Bartalucci, C. Bogani, A. Bosi, T. Fanelli, R. Fjerza, C. Mannarelli, S. Martinelli, A. Pancrazzi, C. Paoli, L. Pieri, A. Bisognin, S. Bortoluzzi, A. Coppe, C. Saccoman, A. Masciulli, B. Giovani, C. Azzan, S. Badalucco, A. Balduini, E. Bonetti, R. Campanelli, P. Catarsi, M.A. Isgro, M.L. Lupo, U. Magrini, M. Massa, V. Poletto, V. Rosti, L. Villani, M. Cazzola, I. Ambaglio, P. Bernasconi, I.C. Casetti, S. Catricala, C. Elena, E. Fugazza, A. Galli, L. Malcovati, C. Milanesi, C. Pascutto, D. Pietra, F. Ripamonti, M. Rossi, E. Rumi, E. Dejana, F. Breviario, M. Corada, B.G. Erba, A. Rambaldi, T. Barbui, M.L. Ferrari, G. Finazzi, M.C. Finazzi, G. Gritti, C. Belotti, C. Boroni, S. Salmoiraghi, A. Amaru, J. Golay, D. Cilloni, V. Campia, S. Carturan, A. Guerrasio, E. Bianchi, M. Montanari, S. Salati, E. Tagliafico, E. Tenedini, R. Zini. A data-driven network model of primary myelofibrosis: Transcriptional and post-transcriptional alterations in CD34+ cells. Blood Cancer Journal, (6), 6, https://doi.org/10.1038/bcj.2016.47, 2016.
M. Turco, M. Corrias, F. Chiaromanni, M. Bano, M. Salamanca, L. Caccin, C. Merkel, P. Amodio, C. Romualdi, C. {De Pitta}, R. Costa, S. Montagnese. The self-morningness/eveningness (Self-ME): An extremely concise and totally subjective assessment of diurnal preference. Chronobiology International, (32), 9, pp. 1192-1200, https://doi.org/10.3109/07420528.2015.1078807, 2015.
M. Calabrese, R. Reynolds, R. Magliozzi, M. Castellaro, A. Morra, A. Scalfari, G. Farina, C. Romualdi, A. Gajofatto, M. Pitteri, M.D. Benedetti, S. Monaco. Regional distribution and evolution of gray matter damage in different populations of multiple sclerosis patients. PLoS ONE, (10), 8, https://doi.org/10.1371/journal.pone.0135428, 2015.
B. Meyer, P. Martini, A. Biscontin, C. {De Pitta}, C. Romualdi, M. Teschke, S. Frickenhaus, L. Harms, U. Freier, S. Jarman, S. Kawaguchi. Pyrosequencing and de novo assembly of Antarctic krill (Euphausia superba) transcriptome to study the adaptability of krill to climate-induced environmental changes. Molecular Ecology Resources, (15), 6, pp. 1460-1471, https://doi.org/10.1111/1755-0998.12408, 2015.
L. Beltrame, M. {Di Marino}, R. Fruscio, E. Calura, B. Chapman, L. Clivio, F. Sina, C. Mele, P. Iatropoulos, T. Grassi, V. Fotia, C. Romualdi, P. Martini, M. Noris, L. Paracchini, I. Craparotta, M. Petrillo, R. Milani, P. Perego, A. Ravaggi, A. Zambelli, E. Ronchetti, M. D'Incalci, S. Marchini. Profiling cancer gene mutations in longitudinal epithelial ovarian cancer biopsies by targeted next-generation sequencing: A retrospective study. Annals of Oncology, (26), 7, pp. 1363-1371, https://doi.org/10.1093/annonc/mdv164, 2015.
N. Sahnane, D. Furlan, M. Monti, C. Romualdi, A. Vanoli, E. Vicari, E. Solcia, C. Capella, F. Sessa, S. {La Rosa}. Microsatellite unstable gastrointestinal neuroendocrine carcinomas: A new clinicopathologic entity. Endocrine-Related Cancer, (22), 1, pp. 35-45, https://doi.org/10.1530/ERC-14-0410, 2015.
V. Djordjilovic, M. Chiogna, M.S. Massa, C. Romualdi. Graphical modeling for gene set analysis: A critical appraisal. Biometrical Journal, (57), 5, pp. 852-866, https://doi.org/10.1002/bimj.201300287, 2015.
E. Baldan, S. Nigris, C. Romualdi, S. D'Alessandro, A. Clocchiatti, M. Zottini, P. Stevanato, A. Squartini, B. Baldan. Beneficial bacteria isolated from grapevine inner tissues shape arabidopsis Thaliana roots. PLoS ONE, (10), 10, https://doi.org/10.1371/journal.pone.0140252, 2015.
N. Sahnane, F. Magnoli, B. Bernasconi, M.G. Tibiletti, C. Romualdi, M. Pedroni, M.P. {De Leon}, G. Magnani, L. Reggiani-Bonetti, L. Bertario, S. Signoroni, C. Capella, F. Sessa, D. Furlan. Aberrant DNA methylation profiles of inherited and sporadic colorectal cancer. Clinical Epigenetics, (7), 1, https://doi.org/10.1186/s13148-015-0165-2, 2015.
C. Calore, M. {De Bortoli}, C. Romualdi, A. Lorenzon, A. Angelini, C. Basso, G. Thiene, S. Iliceto, A. Rampazzo, P. Melacini. A founder MYBPC3 mutation results in HCM with a high risk of sudden death after the fourth decade of life. Journal of Medical Genetics, (52), 5, pp. 338-347, https://doi.org/10.1136/jmedgenet-2014-102923, 2015.
E. Calura, P. Martini, G. Sales, L. Beltrame, G. Chiorino, M. D'Incalci, S. Marchini, C. Romualdi. Wiring miRNAs to pathways: A topological approach to integrate miRNA and mRNA expression profiles. Nucleic Acids Research, (42), 11, https://doi.org/10.1093/nar/gku354, 2014.
P. Martini, G. Sales, M. Brugiolo, A. Gandaglia, F. Naso, C. {De Pitta}, M. Spina, G. Gerosa, F. Chemello, C. Romualdi, S. Cagnin, G. Lanfranchi. Tissue-specific expression and regulatory networks of pig microRNAome. PLoS ONE, (9), 4, https://doi.org/10.1371/journal.pone.0089755, 2014.
P. Martini, G. Sales, E. Calura, S. Cagnin, M. Chiogna, C. Romualdi. TimeClip: Pathway analysis for time course data without replicates. BMC Bioinformatics, (15), https://doi.org/10.1186/1471-2105-15-S5-S3, 2014.
M. Stefanoli, S. {La Rosa}, N. Sahnane, C. Romualdi, R. Pastorino, A. Marando, C. Capella, F. Sessa, D. Furlan. Prognostic relevance of aberrant DNA methylation in G1 and G2 pancreatic neuroendocrine tumors. Neuroendocrinology, (100), 1, pp. 26-34, https://doi.org/10.1159/000365449, 2014.
A. Parikh, C. Lee, P. Joseph, S. Marchini, A. Baccarini, V. Kolev, C. Romualdi, R. Fruscio, H. Shah, F. Wang, G. Mullokandov, D. Fishman, M. D'Incalci, J. Rahaman, T. Kalir, R.W. Redline, B.D. Brown, G. Narla, A. Difeo. MicroRNA-181a has a critical role in ovarian cancer progression through the regulation of the epithelial-mesenchymal transition. Nature Communications, (5), https://doi.org/10.1038/ncomms3977, 2014.
A.N. Mininni, M. Milan, S. Ferraresso, T. Petochi, P. {Di Marco}, G. Marino, S. Livi, C. Romualdi, L. Bargelloni, T. Patarnello. Liver transcriptome analysis in gilthead sea bream upon exposure to low temperature. BMC Genomics, (15), 1, https://doi.org/10.1186/1471-2164-15-765, 2014.
C. Girardi, C. {De Pitta}, S. Casara, E. Calura, C. Romualdi, L. Celotti, M. Mognato. Integration analysis of MicroRNA and mRNA expression profiles in human peripheral blood lymphocytes cultured in modeled microgravity. BioMed Research International, (2014), https://doi.org/10.1155/2014/296747, 2014.
G. {Della Vittoria Scarpati}, E. Calura, M. {Di Marino}, C. Romualdi, L. Beltrame, U. Malapelle, G. Troncone, A. {De Stefano}, S. Pepe, S. {De Placido}, M. D'Incalci, S. Marchini, C. Carlomagno. Analysis of differential miRNA expression in primary tumor and stroma of colorectal cancer patients. BioMed Research International, (2014), https://doi.org/10.1155/2014/840921, 2014.
L. Mussolin, A.B. Holmes, C. Romualdi, G. Sales, E.S.G. D'Amore, M. Ghisi, M. Pillon, A. Rosolen, K. Basso. An aberrant microRNA signature in childhood T-cell lymphoblastic lymphoma affecting CDKN1B expression, NOTCH1 and growth factor signaling pathways. Leukemia, (28), 9, pp. 1909-1912, https://doi.org/10.1038/leu.2014.134, 2014.
M. Calabrese, C. Romualdi, V. Poretto, A. Favaretto, A. Morra, F. Rinaldi, P. Perini, P. Gallo. The changing clinical course of multiple sclerosis: A matter of gray matter. Annals of Neurology, (74), 1, pp. 76-83, https://doi.org/10.1002/ana.23882, 2013.
P. Martini, G. Sales, E. Calura, M. Brugiolo, G. Lanfranchi, C. Romualdi, S. Cagnin. Systems biology approach to the dissection of the complexity of regulatory networks in the S. scrofa cardiocirculatory system. International Journal of Molecular Sciences, (14), 11, pp. 23160-23187, https://doi.org/10.3390/ijms141123160, 2013.
M. Frangini, E. Franzolin, F. Chemello, P. Laveder, C. Romualdi, V. Bianchi, C. Rampazzo. Synthesis of mitochondrial DNA precursors during myogenesis, an analysis in purified C2C12 myotubes. Journal of Biological Chemistry, (288), 8, pp. 5624-5635, https://doi.org/10.1074/jbc.M112.441147, 2013.
S.R. Pigozzo, L. {Da Re}, C. Romualdi, P.G. Mazzara, E. Galletta, S. Fletcher, S.D. Wilton, L. Vitiello. Revertant Fibers in the mdx Murine Model of Duchenne Muscular Dystrophy: An Age- and Muscle-Related Reappraisal. PLoS ONE, (8), 8, https://doi.org/10.1371/journal.pone.0072147, 2013.
S. Marchini, R. Fruscio, L. Clivio, L. Beltrame, L. Porcu, I.F. Nerini, D. Cavalieri, G. Chiorino, G. Cattoretti, C. Mangioni, R. Milani, V. Torri, C. Romualdi, A. Zambelli, M. Romano, M. Signorelli, S.D. Giandomenico, M. D'Incalci. Resistance to platinum-based chemotherapy is associated with epithelial to mesenchymal transition in epithelial ovarian cancer. European Journal of Cancer, (49), 2, pp. 520-530, https://doi.org/10.1016/j.ejca.2012.06.026, 2013.
E. Calura, R. Fruscio, L. Paracchini, E. Bignotti, A. Ravaggi, P. Martini, G. Sales, L. Beltrame, L. Clivio, L. Ceppi, M. {Di Marino}, I.F. Nerini, L. Zanotti, D. Cavalieri, G. Cattoretti, P. Perego, R. Milani, D. Katsaros, G. Tognon, E. Sartori, S. Pecorelli, C. Mangioni, M. D'Incalci, C. Romualdi, S. Marchini. MiRNA landscape in stage i epithelial ovarian cancer defines the histotype specificities. Clinical Cancer Research, (19), 15, pp. 4114-4123, https://doi.org/10.1158/1078-0432.CCR-13-0360, 2013.
D. Cimino, C. {De Pitta}, F. Orso, M. Zampini, S. Casara, E. Penna, E. Quaglino, M. Forni, C. Damasco, E. Pinatel, R. Ponzone, C. Romualdi, C. Brisken, M. {De Bortoli}, N. Biglia, P. Provero, G. Lanfranchi, D. Taverna. miR148b is a major coordinator of breast cancer progression in a relapse-associated microRNA signature by targeting ITGA5, ROCK1, PIK3CA, NRAS, and CSF1. FASEB Journal, (27), 3, pp. 1223-1235, https://doi.org/10.1096/fj.12-214692, 2013.
M. Calabrese, A. Favaretto, V. Poretto, C. Romualdi, F. Rinaldi, I. Mattisi, A. Morra, P. Perini, P. Gallo. Low degree of cortical pathology is associated with benign course of multiple sclerosis. Multiple Sclerosis Journal, (19), 7, pp. 904-911, https://doi.org/10.1177/1352458512463767, 2013.
G. Sales, E. Calura, P. Martini, C. Romualdi. Graphite Web: Web tool for gene set analysis exploiting pathway topology.. Nucleic acids research, (41), Web Server issue, pp. W89-97, https://doi.org/10.1093/nar/gkt386, 2013.
P. Martini, G. Sales, M.S. Massa, M. Chiogna, C. Romualdi. Along signal paths: An empirical gene set approach exploiting pathway topology. Nucleic Acids Research, (41), 1, https://doi.org/10.1093/nar/gks866, 2013.
A. Bisognin, G. Sales, A. Coppe, S. Bortoluzzi, C. Romualdi. MAGIA2: From miRNA and genes expression data integrative analysis to microRNA-transcription factor mixed regulatory circuits (2012 update). Nucleic Acids Research, (40), W1, pp. W13-W21, https://doi.org/10.1093/nar/gks460, 2012.
M. Calabrese, D. Seppi, C. Romualdi, F. Rinaldi, S. Alessio, P. Perini, P. Gallo. Gray matter pathology in MS: A 3-year longitudinal study in a pediatric population. American Journal of Neuroradiology, (33), 8, pp. 1507-1511, https://doi.org/10.3174/ajnr.A3011, 2012.
G. Sales, E. Calura, D. Cavalieri, C. Romualdi. Graphite - a Bioconductor package to convert pathway topology to gene network. BMC Bioinformatics, (13), 1, https://doi.org/10.1186/1471-2105-13-20, 2012.
S. Mirandola, G. Sebastiani, C. Rossi, E. Velo, E.M. Erne, A. Vario, D. Tempesta, C. Romualdi, D. Campagnolo, A. Alberti. Genotype-specific mutations in the polymerase gene of hepatitis B virus potentially associated with resistance to oral antiviral therapy. Antiviral Research, (96), 3, pp. 422-429, https://doi.org/10.1016/j.antiviral.2012.09.014, 2012.
M. Calabrese, P. Grossi, A. Favaretto, C. Romualdi, M. Atzori, F. Rinaldi, P. Perini, M. Saladini, P. Gallo. Cortical pathology in multiple sclerosis patients with epilepsy: A 3 year longitudinal study. Journal of Neurology, Neurosurgery and Psychiatry, (83), 1, pp. 49-54, https://doi.org/10.1136/jnnp-2011-300414, 2012.
M. Calabrese, V. Poretto, A. Favaretto, S. Alessio, V. Bernardi, C. Romualdi, F. Rinaldi, P. Perini, P. Gallo. Cortical lesion load associates with progression of disability in multiple sclerosis. Brain, (135), 10, pp. 2952-2961, https://doi.org/10.1093/brain/aws246, 2012.
P. Bonvini, E. Zorzi, L. Mussolin, M. Pillon, C. Romualdi, M. Peron, E.S.G. D'Amore, L. Lamant, A. Rosolen. Consequences of heat shock protein 72 (Hsp72) expression and activity on stress-induced apoptosis in CD30 NPM-ALK anaplastic large-cell lymphomas. Leukemia, (26), 6, pp. 1375-1382, https://doi.org/10.1038/leu.2011.367, 2012.
S. Uboldi, E. Calura, L. Beltrame, I. Nerini, S. Marchini, D. Cavalieri, E. Erba, G. Chiorino, P. Ostano, D. D'Angelo, M. D'Incalci, C. Romualdi. A systems biology approach to characterize the regulatory networks leading to trabectedin resistance in an in vitro model of myxoid liposarcoma. PLoS ONE, (7), 4, https://doi.org/10.1371/journal.pone.0035423, 2012.
L. Beltrame, E. Calura, R.R. Popovici, L. Rizzetto, D.R. Guedez, M. Donato, C. Romualdi, S. Draghici, D. Cavalieri. The biological Connection Markup Language: A SBGN-compliant format for visualization, filtering and analysis of biological pathways. Bioinformatics, (27), 15, pp. 2127-2133, https://doi.org/10.1093/bioinformatics/btr339, 2011.
P. Martini, D. Risso, G. Sales, C. Romualdi, G. Lanfranchi, S. Cagnin. Statistical Test of Expression Pattern (STEPath): A new strategy to integrate gene expression data with genomic information in individual and meta-analysis studies. BMC Bioinformatics, (12), https://doi.org/10.1186/1471-2105-12-92, 2011.
G. Sales, C. Romualdi. Parmigene-a parallel R package for mutual information estimation and gene network reconstruction. Bioinformatics, (27), 13, pp. 1876-1877, https://doi.org/10.1093/bioinformatics/btr274, 2011.
M. Biasiolo, G. Sales, M. Lionetti, L. Agnelli, K. Todoerti, A. Bisognin, A. Coppe, C. Romualdi, A. Neri, S. Bortoluzzi. Impact of host genes and strand selection on miRNA and miRNA* expression. PLoS ONE, (6), 8, https://doi.org/10.1371/journal.pone.0023854, 2011.
L. Tombolan, F. Orso, V. Guzzardo, S. Casara, A. Zin, M. Bonora, C. Romualdi, C. Giorgi, G. Bisogno, R. Alaggio, P. Pinton, C. {De Pitt}, D. Taverna, A. Rosolen, G. Lanfranchi. High IGFBP2 expression correlates with tumor severity in pediatric rhabdomyosarcoma. American Journal of Pathology, (179), 5, pp. 2611-2624, https://doi.org/10.1016/j.ajpath.2011.07.018, 2011.
D.M. Tiago, V. Laize, L. Bargelloni, S. Ferraresso, C. Romualdi, M.L. Cancela. Global analysis of gene expression in mineralizing fish vertebra-derived cell lines: New insights into anti-mineralogenic effect of vanadate. BMC Genomics, (12), https://doi.org/10.1186/1471-2164-12-310, 2011.
S. Marchini, D. Cavalieri, R. Fruscio, E. Calura, D. Garavaglia, I.F. Nerini, C. Mangioni, G. Cattoretti, L. Clivio, L. Beltrame, D. Katsaros, L. Scarampi, G. Menato, P. Perego, G. Chiorino, A. Buda, C. Romualdi, M. D'Incalci. Association between miR-200c and the survival of patients with stage I epithelial ovarian cancer: A retrospective study of two independent tumour tissue collections. The Lancet Oncology, (12), 3, pp. 273-285, https://doi.org/10.1016/S1470-2045(11)70012-2, 2011.
M. Calabrese, F. Rinaldi, I. Mattisi, P. Grossi, A. Favaretto, M. Atzori, V. Bernardi, L. Barachino, C. Romualdi, L. Rinaldi, P. Perini, P. Gallo. Widespread cortical thinning characterizes patients with MS with mild cognitive impairment. Neurology, (74), 4, pp. 321-328, https://doi.org/10.1212/WNL.0b013e3181cbcd03, 2010.
D. Segat, M. Cassaro, E. Dazzo, L. Cavallini, C. Romualdi, R. Salvador, M.P. Vitale, L. Vitiello, M. Fassan, M. Rugge, G. Zaninotto, E. Ancona, M.D. Baroni. Pericentriolar material analyses in normal esophageal mucosa, Barrett's metaplasia and adenocarcinoma. Histology and Histopathology, (25), 5, pp. 551-560, 2010.
V. Daidone, E. Pontara, C. Romualdi, M.G. Cattini, C. Scaroni, N. Albiger, A. Pagnan, A. Casonato. Microsatellite (GT)n is part of the von Willebrand factor (VWF) promoter region that influences the glucocorticoid-induced increase in VWF in Cushing's syndrome. Thrombosis Research, (125), 6, pp. e275-e280, https://doi.org/10.1016/j.thromres.2010.01.031, 2010.
M. Calabrese, I. Mattisi, F. Rinaldi, A. Favaretto, M. Atzori, V. Bernardi, L. Barachino, C. Romualdi, L. Rinaldi, P. Perini, P. Gallo. Magnetic resonance evidence of cerebellar cortical pathology in multiple sclerosis. Journal of Neurology, Neurosurgery and Psychiatry, (81), 4, pp. 401-404, https://doi.org/10.1136/jnnp.2009.177733, 2010.
G. Sales, A. Coppe, A. Bisognin, M. Biasiolo, S. Bortoluzzi, C. Romualdi. Magia, a web-based tool for miRNA and genes integrated analysis. Nucleic Acids Research, (38), SUPPL. 2, pp. W352-W359, https://doi.org/10.1093/nar/gkq423, 2010.
G. Sales, A. Coppe, S. Bicciato, S. Bortoluzzi, C. Romualdi. Impact of probe annotation on the integration of miRNA-mRNA expression profiles for miRNA target detection. Nucleic Acids Research, (38), 7, https://doi.org/10.1093/nar/gkp1239, 2010.
M.S. Massa, M. Chiogna, C. Romualdi. Gene set analysis exploiting the topology of a pathway. BMC Systems Biology, (4), https://doi.org/10.1186/1752-0509-4-121, 2010.
C. Romualdi, G. Lanfranchi. Statistical tools for gene expression analysis and systems biology and related web resources. Bioinformatics for Systems Biology, (9781597454407), pp. 181-205, https://doi.org/10.1007/978-1-59745-440-7_11, 2009.
A. Malerba, L. Vitiello, D. Segat, E. Dazzo, M. Frigo, I. Scambi, P. {De Coppi}, L. Boldrin, L. Martelli, A. Pasut, C. Romualdi, R.G. Bellomo, J. Vecchiet, M.D. Baroni. Selection of multipotent cells and enhanced muscle reconstruction by myogenic macrophage-secreted factors. Experimental Cell Research, (315), 6, pp. 915-927, https://doi.org/10.1016/j.yexcr.2009.01.005, 2009.
D. Cavalieri, E. Calura, C. Romualdi, E. Marchi, M. Radonjic, B. {Van Ommen}, M. Muller. Filling gaps in PPAR-alpha signaling through comparative nutrigenomics analysis. BMC Genomics, (10), https://doi.org/10.1186/1471-2164-10-596, 2009.
L. Carraro, S. Ferraresso, B. Cardazzo, C. Romualdi, C. Montesissa, F. Gottardo, T. Patarnello, M. Castagnaro, L. Bargelloni. Expression profiling of skeletal muscle in young bulls treated with steroidal growth promoters. Physiological Genomics, (38), 2, pp. 138-148, https://doi.org/10.1152/physiolgenomics.00014.2009, 2009.
M. Calabrese, M. Filippi, M. Rovaris, V. Bernardi, M. Atzori, I. Mattisi, A. Favaretto, P. Grossi, L. Barachino, L. Rinaldi, C. Romualdi, P. Perini, P. Gallo. Evidence for relative cortical sparing in benign multiple sclerosis: A longitudinal magnetic resonance imaging study. Multiple Sclerosis, (15), 1, pp. 36-41, https://doi.org/10.1177/1352458508096686, 2009.
M. Calabrese, M.A. Rocca, M. Atzori, I. Mattisi, V. Bernardi, A. Favaretto, L. Barachino, C. Romualdi, L. Rinaldi, P. Perini, P. Gallo, M. Filippi. Cortical lesions in primary progressive multiple sclerosis: A 2-year longitudinal MR study. Neurology, (72), 15, pp. 1330-1336, https://doi.org/10.1212/WNL.0b013e3181a0fee5, 2009.
C. Romualdi, A. Giuliani, C. Millino, B. Celegato, R. Benigni, G. Lanfranchi. Correlation between gene expression and clinical data through linear and nonlinear principal components analyses: Muscular dystrophies as case studies. OMICS A Journal of Integrative Biology, (13), 3, pp. 173-184, https://doi.org/10.1089/omi.2009.0003, 2009.
A. Bisognin, A. Coppe, F. Ferrari, D. Risso, C. Romualdi, S. Bicciato, S. Bortoluzzi. A-MADMAN: Annotation-based microarray data meta-analysis tool. BMC Bioinformatics, (10), https://doi.org/10.1186/1471-2105-10-201, 2009.
D. Risso, M.S. Massa, M. Chiogna, C. Romualdi. A modified LOESS normalization applied to microRNA arrays: A comparative evaluation. Bioinformatics, (25), 20, pp. 2685-2691, https://doi.org/10.1093/bioinformatics/btp443, 2009.
M. Chiogna, M.S. Sofia, D. Risso, C. Romualdi. A comparison on effects of normalisations in the detection of differentially expressed genes. BMC Bioinformatics, (10), https://doi.org/10.1186/1471-2105-10-61, 2009.
P. Gatto, U. Vrhovsek, J. Muth, C. Segala, C. Romualdi, P. Fontana, D. Pruefer, M. Stefanini, C. Moser, F. Mattivi, R. Velasco. Ripening and genotype control stilbene accumulation in healthy grapes. Journal of Agricultural and Food Chemistry, (56), 24, pp. 11773-11785, https://doi.org/10.1021/jf8017707, 2008.
A. Casonato, V. Daidone, F. Sartorello, N. Albiger, C. Romualdi, F. Mantero, A. Pagnan, C. Scaroni. Polymorphisms in von Willebrand factor gene promoter influence the glucocorticoid-induced increase in von Willebrand factor: The lesson learned from Cushing syndrome. British Journal of Haematology, (140), 2, pp. 230-235, https://doi.org/10.1111/j.1365-2141.2007.06907.x, 2008.
M. Calabrese, M. Filippi, M. Rovaris, I. Mattisi, V. Bernardi, M. Atzori, A. Favaretto, L. Barachino, L. Rinaldi, C. Romualdi, P. Perini, P. Gallo. Morphology and evolution of cortical lesions in multiple sclerosis. A longitudinal MRI study. NeuroImage, (42), 4, pp. 1324-1328, https://doi.org/10.1016/j.neuroimage.2008.06.028, 2008.
E. Calura, S. Cagnin, A. Raffaello, P. Laveder, G. Lanfranchi, C. Romualdi. Meta-analysis of expression signatures of muscle atrophy: Gene interaction networks in early and late stages. BMC Genomics, (9), https://doi.org/10.1186/1471-2164-9-630, 2008.
S. Ferraresso, N. Vitulo, A.N. Mininni, C. Romualdi, B. Cardazzo, E. Negrisolo, R. Reinhardt, A.V.M. Canario, T. Patarnello, L. Bargelloni. Development and validation of a gene expression oligo microarray for the gilthead sea bream (Sparus aurata). BMC Genomics, (9), https://doi.org/10.1186/1471-2164-9-580, 2008.
M. Lodovici, C. Luceri, C. {De Filippo}, C. Romualdi, F. Bambi, P. Dolara. Smokers and passive smokers gene expression profiles: Correlation with the DNA oxidation damage. Free Radical Biology and Medicine, (43), 3, pp. 415-422, https://doi.org/10.1016/j.freeradbiomed.2007.04.018, 2007.
M. Calabrese, N. {De Stefano}, M. Atzori, V. Bernardi, I. Mattisi, L. Barachino, A. Morra, L. Rinaldi, C. Romualdi, P. Perini, L. Battistin, P. Gallo. Detection of cortical inflammatory lesions by double inversion recovery magnetic resonance imaging in patients with multiple sclerosis. Archives of Neurology, (64), 10, pp. 1416-1422, https://doi.org/10.1001/archneur.64.10.1416, 2007.
M. Calabrese, M. Atzori, V. Bernardi, A. Morra, C. Romualdi, L. Rinaldi, M.J.M. McAuliffe, L. Barachino, P. Perini, B. Fischl, L. Battistin, P. Gallo. Cortical atrophy is relevant in multiple sclerosis at clinical onset. Journal of Neurology, (254), 9, pp. 1212-1220, https://doi.org/10.1007/s00415-006-0503-6, 2007.
N. Vitulo, A. Vezzi, C. Romualdi, S. Campanaro, G. Valle. A global gene evolution analysis on Vibrionaceae family using phylogenetic profile. BMC Bioinformatics, (8), SUPPL. 1, https://doi.org/10.1186/1471-2105-8-S1-S23, 2007.
B. Celegato, D. Capitanio, M. Pescatori, C. Romualdi, B. Pacchioni, S. Cagnin, A. Vigano, L. Colantoni, S. Begum, E. Ricci, R. Wait, G. Lanfranchi, C. Gelfi. Parallel protein and transcript profiles of FSHD patient muscles correlate to the D4Z4 arrangement and reveal a common impairment of slow to fast fibre differentiation and a general deregulation of MyoD-dependent genes. Proteomics, (6), 19, pp. 5303-5321, https://doi.org/10.1002/pmic.200600056, 2006.
L. Rinaldi, P. Gallo, M. Calabrese, F. Ranzato, D. Luise, D. Colavito, M. Motta, A. Guglielmo, E. {Del Giudice}, C. Romualdi, E. Ragazzi, A. D'Arrigo, M. {Dalle Carbonare}, B. Leontino, A. Leon. Longitudinal analysis of immune cell phenotypes in early stage multiple sclerosis: Distinctive patterns characterize MRI-active patients. Brain, (129), 8, pp. 1993-2007, https://doi.org/10.1093/brain/awl179, 2006.
C. {De Pitta}, L. Tombolan, G. Albiero, F. Sartori, C. Romualdi, G. Jurman, M. Carli, C. Furlanello, G. Lanfranchi, A. Rosolen. Gene expression profiling identifies potential relevant genes in alveolar rhabdomyosarcoma pathogenesis and discriminates PAX3-FKHR positive and negative tumors. International Journal of Cancer, (118), 11, pp. 2772-2781, https://doi.org/10.1002/ijc.21698, 2006.
C. Millino, M. Bellin, M. Fanin, C. Romualdi, E. Pegoraro, C. Angelini, G. Lanfranchi. Expression profiling characterization of laminin α-2 positive MDC. Biochemical and Biophysical Research Communications, (350), 2, pp. 345-351, https://doi.org/10.1016/j.bbrc.2006.09.063, 2006.
L. Toffolatti, L. {Rosa Gastaldo}, T. Patarnello, C. Romualdi, R. Merlanti, C. Montesissa, L. Poppi, M. Castagnaro, L. Bargelloni. Expression analysis of androgen-responsive genes in the prostate of veal calves treated with anabolic hormones. Domestic Animal Endocrinology, (30), 1, pp. 38-55, https://doi.org/10.1016/j.domaniend.2005.05.008, 2006.
L. Nanni, C. Romualdi, A. Maseri, G. Lanfranchi. Differential gene expression profiling in genetic and multifactorial cardiovascular diseases. Journal of Molecular and Cellular Cardiology, (41), 6, pp. 934-948, https://doi.org/10.1016/j.yjmcc.2006.08.009, 2006.
P. Venier, C. {De Pitta}, A. Pallavicini, F. Marsano, L. Varotto, C. Romualdi, F. Dondero, A. Viarengo, G. Lanfranchi. Development of mussel mRNA profiling: Can gene expression trends reveal coastal water pollution?. Mutation Research - Fundamental and Molecular Mechanisms of Mutagenesis, (602), 1-2, pp. 121-134, https://doi.org/10.1016/j.mrfmmm.2006.08.007, 2006.
A. Raffaello, P. Laveder, C. Romualdi, C. Bean, L. Toniolo, E. Germinario, A. Megighian, D. Danieli-Betto, C. Reggiani, G. Lanfranchi. Denervation in murine fast-twitch muscle: Short-term physiological changes and temporal expression profiling. Physiological Genomics, (25), 1, pp. 60-74, https://doi.org/10.1152/physiolgenomics.00051.2005, 2006.
C. Romualdi, C. {De Pitta}, L. Tombolan, S. Bortoluzzi, F. Sartori, A. Rosolen, G. Lanfranchi. Defining the gene expression signature of rhabdomyosarcoma by meta-analysis. BMC Genomics, (7), https://doi.org/10.1186/1471-2164-7-287, 2006.
M. Scaggiante, M.B. Rasotto, C. Romualdi, A. Pilastro. Territorial male gobies respond aggressively to sneakers but do not adjust their sperm expenditure. Behavioral Ecology, (16), 6, pp. 1001-1007, https://doi.org/10.1093/beheco/ari081, 2005.
D. Campagna, C. Romualdi, N. Vitulo, M. {Del Favero}, M. Lexa, N. Cannata, G. Valle. RAP: A new computer program for de novo identification of repeated sequences in whole genomes. Bioinformatics, (21), 5, pp. 582-588, https://doi.org/10.1093/bioinformatics/bti039, 2005.
S. Bortoluzzi, A. Bisognin, C. Romualdi, G.A. Danieli. Novel genes, possibly relevant for molecular diagnosis or therapy of human rhabdomyosarcoma, detected by genomic expression profiling. Gene, (348), 1-2 SUPPL., pp. 65-71, https://doi.org/10.1016/j.gene.2004.12.024, 2005.
C. Romualdi, N. Vitulo, M. {Del Favero}, G. Lanfranchi. MIDAW: A web tool for statistical analysis of microarray data. Nucleic Acids Research, (33), SUPPL. 2, pp. W644-W649, https://doi.org/10.1093/nar/gki497, 2005.
A. Vezzi, S. Campanaro, M. D'Angelo, F. Simonato, N. Vitulo, F.M. Lauro, A. Cestaro, G. Malacrida, B. Simionati, N. Cannata, C. Romualdi, D.H. Bartlett, G. Valle. Life at depth: Photobacterium profundum genome sequence and expression analysis. Science, (307), 5714, pp. 1459-1461, https://doi.org/10.1126/science.1103341, 2005.
C. {De Pitta}, L. Tombolan, M.C. Dell'Orto, B. Accordi, G.T. Kronnie, C. Romualdi, N. Vitulo, G. Basso, G. Lanfranchi. A leukemia-enriched cDNA microarray platform identifies new transcripts with relevance to the biology of pediatric acute lymphoblastic leukemia. Haematologica, (90), 7, pp. 890-898, 2005.
S. Bortoluzzi, C. Romualdi, A. Bisognin, G.A. Danieli. Disease genes and intracellular protein networks. Physiological Genomics, (15), pp. 223-227, https://doi.org/10.1152/physiolgenomics.00095.2003, 2004.
D. Basso, C. Millino, E. Greco, C. Romualdi, P. Fogar, A. Valerio, M. Bellin, C.-F. Zambon, F. Navaglia, N. Dussini, A. Avogaro, S. Pedrazzoli, G. Lanfranchi, M. Plebani. Altered glucose metabolism and proteolysis in pancreatic cancer cell conditioned myoblasts: Searching for a gene expression pattern with a microarray analysis of 5000 skeletal muscle genes. Gut, (53), 8, pp. 1159-1166, https://doi.org/10.1136/gut.2003.024471, 2004.
S. Toppo, N. Cannata, P. Fontana, C. Romualdi, P. Laveder, E. Bertocco, G. Lanfranchi, G. Valle. TRAIT (TRAnscript Integrated Table): A knowledgebase of human skeletal muscle transcripts. Bioinformatics, (19), 5, pp. 661-662, https://doi.org/10.1093/bioinformatics/btg045, 2003.
C. Romualdi, S. Campanaro, D. Campagna, B. Celegato, N. Cannata, S. Toppo, G. Valle, G. Lanfranchi. Pattern recognition in gene expression profiling using DNA array: A comparative study of different statistical methods applied to cancer classification. Human Molecular Genetics, (12), 8, pp. 823-836, https://doi.org/10.1093/hmg/ddg093, 2003.
C. Romualdi, S. Trevisan, B. Celegato, G. Costa, G. Lanfranchi. Improved detection of differentially expressed genes in microarray experiments through multiple scanning and image integration.. Nucleic acids research, (31), 23, https://doi.org/10.1093/nar/gng149, 2003.
C. Romualdi, S. Bortoluzzi, F. D'Alessi, G.A. Danieli. IDEG6: A web tool for detection of differentially expressed genes in multiple tag sampling experiments. Physiological Genomics, (12), pp. 159-162, https://doi.org/10.1152/physiolgenomics.00096.2002, 2003.
S. Campanaro, C. {De Pitta}, B. Celegato, C. Millino, C. Romualdi, B. Pacchioni, S. Trevisan, M. Bellin, S. Cagnin, L. Tombolan, M. Fanin, E. Pegoraro, G. {Te Kronnie}, M. Pescatori, G. Valle, G. Basso, E. Ricci, C. Angelini, G. Lanfranchi. Application of a cDNA micoarray for the analysis of muscular dystrophies and childhood leukemias. Minerva Biotecnologica, (15), 4, pp. 235-244, 2003.
N. Cannata, S. Toppo, C. Romualdi, G. Valle. Simplifying amino acid alphabets by means of a branch and bound algorithm and substitution matrices. Bioinformatics, (18), 8, pp. 1102-1108, https://doi.org/10.1093/bioinformatics/18.8.1102, 2002.
C. Romualdi, D. Balding, I.S. Nasidze, G. Risch, M. Robichaux, S.T. Sherry, M. Stoneking, M.A. Batzer, G. Barbujani. Patterns of human diversity, within and among continents, inferred from biallelic DNA polymorphisms. Genome Research, (12), 4, pp. 602-612, https://doi.org/10.1101/gr.214902, 2002.
S. Campanaro, C. Romualdi, C. {De Pitta}, M. Fanin, B. Celegato, B. Pacchioni, S. Trevisan, P. Laveder, S. Toppo, S. Cagnin, G. Valle, C. Angelini, G. Lanfranchi. Gene expression profiling in skeletal muscle using a dedicated microarray. Minerva Biotecnologica, (14), 3-4, pp. 273-279, 2002.
S. Bortoluzzi, F. D'Alessi, C. Romualdi, G.A. Danieli. Differential expression of genes coding of ribosomal proteins in different human tissues. Bioinformatics, (17), 12, pp. 1152-1157, https://doi.org/10.1093/bioinformatics/17.12.1152, 2002.
C. Romualdi, S. Bortoluzzi, G.A. Danieli. Detecting differentially expressed genes in multiple tag sampling experiments: Comparative evaluation of statistical tests. Human Molecular Genetics, (10), 19, pp. 2133-2141, https://doi.org/10.1093/hmg/10.19.2133, 2001.
S. Bortoluzzi, F. D'Alessi, C. Romualdi, G.A. Danieli. The human adult skeletal muscle transcriptional profile reconstructed by a novel computational approach. Genome Research, (10), 3, pp. 344-349, https://doi.org/10.1101/gr.10.3.344, 2000.
J.R. Freeland, C. Romualdi, B. Okamura. Gene flow and genetic diversity: A comparison of freshwater bryozoan populations in Europe and North America. Heredity, (85), 5, pp. 498-508, https://doi.org/10.1046/j.1365-2540.2000.00780.x, 2000.
G. Masarotto, C. Romualdi. Probability of conception on different days of the menstrual cycle: An ongoing exercise. Advances in Contraception, (13), 2-3, pp. 105-115, https://doi.org/10.1023/A:1006583300746, 1997.