- Poggiali B, Ponzetti A, Malerba M, Landuzzi F, Furia F, Charrance D, Trova S, Perseghin V, Falcone PA, Alliod V, Malossi A, Carassai P, Familiari U, Vecchi M, Gustincich S, Schena M, Cavalli A, Coppe A. Multiomic analysis of HER2-enriched and AR-positive breast carcinoma with apocrine differentiation and an oligometastatic course: a case report. Front Oncol. 2023 Jul 31;13:1240865.
- Marzollo A, Maestrini G, La Starza R, Elia L, Malfona F, Pierini T, Tretti C, Coppe A, Bortoluzzi S, Biffi A, Mecucci C, Bresolin S, Testi AM. A novel germline variant in PIK3R1 results in SHORT syndrome associated with TAL/LMO T-cell Acute Lymphoblastic Leukemia. Am J Hematol. 2020 Sep 16. doi: 10.1002/ajh.25998.
- Binatti A, Bresolin S, Bortoluzzi S, Coppe A. iWhale: a computational pipeline based on Docker and SCons for detection and annotation of somatic variants in cancer WES data Briefings in Bioinformatics. 2020 May 20:bbaa065. doi: 10.1093/bib/bbaa065.
- Gasparini VR, Binatti A, Coppe A, Teramo A, Vicenzetto C, Calabretto G, Barila' G, Barizza A, Giussani E, Facco M, Mustjoki S, Semenzato G, Zambello R, Bortoluzzi S. A high definition picture of somatic mutations in chronic lymphoproliferative disorder of natural killer cells Blood Cancer Journal. 2020 Apr 22;10(4):42. doi: 10.1038/s41408-020-0309-2.
- Lovisa F, Binatti A, Coppe A, Primerano S, Carraro E, Pillon M, Pizzi M, Guzzardo V, Buffardi S, Porta F, Farruggia P, De Santis R, Bulian P, Basso G, Lazzari E, d'Amore ESG, Bortoluzzi S, Mussolin L. A high definition picture of key genes and pathways mutated in pediatric follicular lymphoma. Haematologica. 2019 Feb 18. 2020 Sep;104(9):e406-e409. doi: 10.3324/haematol.2018.211631. Epub 2019 Feb 28.
- Esposito MR, Binatti A, Pantile M, Coppe A, Mazzocco K, Longo L, Capasso M, Lasorsa VA, Luksch R, Bortoluzzi S, Tonini GP. Somatic mutations in specific and connected subpathways are associated with short neuroblastoma patients' survival and indicate proteins targetable at onset of disease. Int J Cancer. 2018 Nov 15;143(10):2525-2536. doi: 10.1002/ijc.31748. Epub 2018 Sep 17. PubMed PMID: 29992558.
- Salvoro C, Bortoluzzi S, Coppe A, Valle G, Feltrin E, Mostacciuolo ML, Vazza G. Rare Risk Variants Identification by Identity-by-Descent Mapping and Whole-Exome Sequencing Implicates Neuronal Development Pathways in Schizophrenia and Bipolar Disorder. Mol Neurobiol. 2018 Sep;55(9):7366-7376. doi: 10.1007/s12035-018-0922-2. Epub 2018 Feb 6. PubMed PMID: 29411265.
- Coppe A, Nogara L, Pizzuto MS, Cani A, Cesaro S, Masetti R, Locatelli F, Te Kronnie G, Basso G, Bortoluzzi S, Bresolin S. Somatic mutations activating Wiskott-Aldrich syndrome protein concomitant with RAS pathway mutations in juvenile myelomonocytic leukemia patients. Hum Mutat. 2018 Apr;39(4):579-587. doi: 10.1002/humu.23399. Epub 2018 Jan 19. PubMed PMID: 29316027.
- Andersson EI, Coppe A, Bortoluzzi S. A guilt-by-association mutation network in LGL leukemia. Oncotarget. 2017 Oct 9;8(55):93299-93300. doi: 10.18632/oncotarget.21699. eCollection 2017 Nov 7. PubMed PMID: 29212142; PubMed Central PMCID: PMC5706788.
- Coppe A, Andersson EI, Binatti A, Gasparini VR, Bortoluzzi S, Clemente M, Herling M, Maciejewski J, Mustjoki S, Bortoluzzi S. Genomic landscape characterization of large granular lymphocyte leukemia with a systems genetics approach. Leukemia. 2017 May;31(5):1243-1246. doi: 10.1038/leu.2017.49. Epub 2017 Feb 7. PubMed PMID: 28167832; PubMed Central PMCID: PMC5419584.
- Andersson EI, Tanahashi T, Sekiguchi N, Gasparini VR, Bortoluzzi S, Kawakami T, Matsuda K, Mitsui T, Eldfors S, Bortoluzzi S, Coppe A, Binatti A, Lagstrom S, Ellonen P, Fukushima N, Nishina S, Senoo N, Sakai H, Nakazawa H, Kwong YL, Loughran TP, Maciejewski JP, Mustjoki S, Ishida F. High incidence of activating STAT5B mutations in CD4-positive T-cell large granular lymphocyte leukemia. Blood. 2016 Nov 17;128(20):2465-2468. Epub 2016 Oct 3. PubMed PMID: 27697773; PubMed Central PMCID: PMC5114490.
- Calura E, Pizzini S, Bisognin A, Coppe A, Sales G, Gaffo E, Fanelli T, Mannarelli C, Zini R, Norfo R, Pennucci V, Manfredini R, Romualdi C, Guglielmelli P, Vannucchi AM, Bortoluzzi S. A data-driven network model of primary myelofibrosis: transcriptional and post-transcriptional alterations in CD34+ cells. Blood Cancer J. 2016 Jun 24;6(6):e439. doi: 10.1038/bcj.2016.47. PubMed PMID: 27341078; PubMed Central PMCID: PMC5141361.
- Guglielmelli P, Bisognin A, Saccoman C, Mannarelli C, Coppe A, Vannucchi AM, Bortoluzzi S. Small RNA Sequencing Uncovers New miRNAs and moRNAs Differentially Expressed in Normal and Primary Myelofibrosis CD34+ Cells. PLoS One. 2015 Oct 15;10(10):e0140445. doi: 10.1371/journal.pone.0140445. eCollection 2015. PubMed PMID: 26468945; PubMed Central PMCID: PMC4607157.
- Leite RB, Milan M, Coppe A, Bortoluzzi S, dos Anjos A, Reinhardt R, Saavedra C, Patarnello T, Cancela ML, Bargelloni L. mRNA-Seq and microarray development for the Grooved Carpet shell clam, Ruditapes decussatus: a functional approach to unravel host-parasite interaction. BMC Genomics. 2013 Oct 29;14:741. doi: 10.1186/1471-2164-14-741. PubMed PMID: 24168212; PubMed Central PMCID: PMC4007648.
- Coppe A, Agostini C, Marino IA, Zane L, Bargelloni L, Bortoluzzi S, Patarnello T. Genome evolution in the cold: Antarctic icefish muscle transcriptome reveals selective duplications increasing mitochondrial function. Genome Biol Evol. 2013;5(1):45-60. doi: 10.1093/gbe/evs108. PubMed PMID: 23196969; PubMed Central PMCID: PMC3595028.
- Vidotto M, Grapputo A, Boscari E, Barbisan F, Coppe A, Grandi G, Kumar A, Congiu L. Transcriptome sequencing and de novo annotation of the critically endangered Adriatic sturgeon. BMC Genomics. 2013 Jun 18;14:407. doi: 10.1186/1471-2164-14-407. PubMed PMID: 23773438; PubMed Central PMCID: PMC3691660.
- Coppe A, Bortoluzzi S, Murari G, Marino IA, Zane L, Papetti C. Sequencing and characterization of striped venus transcriptome expand resources for clam fishery genetics. PLoS One. 2012;7(9):e44185. doi: 10.1371/journal.pone.0044185. Epub 2012 Sep 18. PubMed PMID: 23028497; PubMed Central PMCID: PMC3445586.
- Pujolar JM, Marino IA, Milan M, Coppe A, Maes GE, Capoccioni F, Ciccotti E, Bervoets L, Covaci A, Belpaire C, Cramb G, Patarnello T, Bargelloni L, Bortoluzzi S, Zane L. Surviving in a toxic world: transcriptomics and gene expression profiling in response to environmental pollution in the critically endangered European eel. BMC Genomics. 2012 Sep 25;13:507. doi: 10.1186/1471-2164-13-507. PubMed PMID: 23009661; PubMed Central PMCID: PMC3532374.
- Bisognin A, Sales G, Coppe A, Bortoluzzi S, Romualdi C. MAGIA2: from miRNA and genes expression data integrative analysis to microRNA-transcription factor mixed regulatory circuits (2012 update). Nucleic Acids Res. 2012 Jul;40(Web Server issue):W13-21. doi: 10.1093/nar/gks460. Epub 2012 May 21. PubMed PMID: 22618880; PubMed Central PMCID: PMC3394337.
- Biasiolo M, Sales G, Lionetti M, Agnelli L, Todoerti K, Bisognin A, Coppe A, Romualdi C, Neri A, Bortoluzzi S. Impact of host genes and strand selection on miRNA and miRNA* expression. PLoS One. 2011;6(8):e23854. doi: 10.1371/journal.pone.0023854. Epub 2011 Aug 31. PubMed PMID: 21909367; PubMed Central PMCID: PMC3166117.
- Milan M, Coppe A, Reinhardt R, Cancela LM, Leite RB, Saavedra C, Ciofi C, Chelazzi G, Patarnello T, Bortoluzzi S, Bargelloni L. Transcriptome sequencing and microarray development for the Manila clam, Ruditapes philippinarum: genomic tools for environmental monitoring. BMC Genomics. 2011 May 12;12:234. doi: 10.1186/1471-2164-12-234. PubMed PMID: 21569398; PubMed Central PMCID: PMC3107815.
- Lenzi L, Facchin F, Piva F, Giulietti M, Pelleri MC, Frabetti F, Vitale L, Casadei R, Canaider S, Bortoluzzi S, Coppe A, Danieli GA, Principato G, Ferrari S, Strippoli P. TRAM (Transcriptome Mapper): database-driven creation and analysis of transcriptome maps from multiple sources. BMC Genomics. 2011 Feb 18;12:121. doi: 10.1186/1471-2164-12-121. PubMed PMID: 21333005; PubMed Central PMCID: PMC3052188.
- Coppe A, Pujolar JM, Maes GE, Larsen PF, Hansen MM, Bernatchez L, Zane L, Bortoluzzi S. Sequencing, de novo annotation and analysis of the first Anguilla anguilla transcriptome: EeelBase opens new perspectives for the study of the critically endangered European eel. BMC Genomics. 2010 Nov 16;11:635. doi: 10.1186/1471-2164-11-635. PubMed PMID: 21080939; PubMed Central PMCID: PMC3012609.
- Sales G, Coppe A, Bisognin A, Biasiolo M, Bortoluzzi S, Romualdi C. MAGIA, a web-based tool for miRNA and Genes Integrated Analysis. Nucleic Acids Res. 2010 Jul;38(Web Server issue):W352-9. doi: 10.1093/nar/gkq423. Epub 2010 May 19. PubMed PMID: 20484379; PubMed Central PMCID: PMC2896126.
- Sales G, Coppe A, Bicciato S, Bortoluzzi S, Romualdi C. Impact of probe annotation on the integration of miRNA-mRNA expression profiles for miRNA target detection. Nucleic Acids Res. 2010 Apr;38(7):e97. doi: 10.1093/nar/gkp1239. Epub 2010 Jan 13. PubMed PMID: 20071740; PubMed Central PMCID: PMC2853140.
- Bisognin A, Coppe A, Ferrari F, Risso D, Romualdi C, Bicciato S, Bortoluzzi S. A-MADMAN: annotation-based microarray data meta-analysis tool. BMC Bioinformatics. 2009 Jun 29;10:201. doi: 10.1186/1471-2105-10-201. PubMed PMID: 19563634; PubMed Central PMCID: PMC2711946.
- Coppe A, Ferrari F, Bisognin A, Danieli GA, Ferrari S, Bicciato S, Bortoluzzi S. Motif discovery in promoters of genes co-localized and co-expressed during myeloid cells differentiation. Nucleic Acids Res. 2009 Feb;37(2):533-49. doi: 10.1093/nar/gkn948. Epub 2008 Dec 5. PubMed PMID: 19059999; PubMed Central PMCID: PMC2632922.
- Ferrari F, Bortoluzzi S, Coppe A, Sirota A, Safran M, Shmoish M, Ferrari S, Lancet D, Danieli GA, Bicciato S. Novel definition files for human GeneChips based on GeneAnnot. BMC Bioinformatics. 2007 Nov 15;8:446. PubMed PMID: 18005434; PubMed Central PMCID: PMC2216044.
- Ferrari F, Bortoluzzi S, Coppe A, Basso D, Bicciato S, Zini R, Gemelli C, Danieli GA, Ferrari S. Genomic expression during human myelopoiesis. BMC Genomics. 2007 Aug 3;8:264. PubMed PMID: 17683550; PubMed Central PMCID: PMC2045681.
- Coppe A, Danieli GA, Bortoluzzi S. REEF: searching REgionally Enriched Features in genomes. BMC Bioinformatics. 2006 Oct 16;7:453. PubMed PMID: 17042935; PubMed Central PMCID: PMC1624853.
- Pizzi C, Bortoluzzi S, Bisognin A, Coppe A, Danieli GA. Detecting seeded motifs in DNA sequences. Nucleic Acids Res. 2005 Sep 1;33(15):e135. PubMed PMID: 16141193; PubMed Central PMCID: PMC1197136.
- Bortoluzzi S, Coppe A, Bisognin A, Pizzi C, Danieli GA. A multistep bioinformatic approach detects putative regulatory elements in gene promoters. BMC Bioinformatics. 2005 May 18;6:121. PubMed PMID: 15904489; PubMed Central PMCID: PMC1173081.