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Items: 1 to 50 of 103

1.

Live-animal imaging of native haematopoietic stem and progenitor cells.

Christodoulou C, Spencer JA, Yeh SA, Turcotte R, Kokkaliaris KD, Panero R, Ramos A, Guo G, Seyedhassantehrani N, Esipova TV, Vinogradov SA, Rudzinskas S, Zhang Y, Perkins AS, Orkin SH, Calogero RA, Schroeder T, Lin CP, Camargo FD.

Nature. 2020 Feb;578(7794):278-283. doi: 10.1038/s41586-020-1971-z. Epub 2020 Feb 5.

PMID:
32025033
2.

A regulatory microRNA network controls endothelial cell phenotypic switch during sprouting angiogenesis.

Rosano S, Corà D, Parab S, Zaffuto S, Isella C, Porporato R, Hoza RM, Calogero RA, Riganti C, Bussolino F, Noghero A.

Elife. 2020 Jan 24;9. pii: e48095. doi: 10.7554/eLife.48095.

3.

Docker4Circ: A Framework for the Reproducible Characterization of circRNAs from RNA-Seq Data.

Ferrero G, Licheri N, Coscujuela Tarrero L, De Intinis C, Miano V, Calogero RA, Cordero F, De Bortoli M, Beccuti M.

Int J Mol Sci. 2019 Dec 31;21(1). pii: E293. doi: 10.3390/ijms21010293.

4.

A computational approach based on the colored Petri net formalism for studying multiple sclerosis.

Pernice S, Pennisi M, Romano G, Maglione A, Cutrupi S, Pappalardo F, Balbo G, Beccuti M, Cordero F, Calogero RA.

BMC Bioinformatics. 2019 Dec 10;20(Suppl 6):623. doi: 10.1186/s12859-019-3196-4.

5.

Look for methods, not conclusions.

Bassi R, Bucci EM, Calogero RA, Carninci P, Ciliberto G, Conte P, De Luca M, Corbellini G, Giordano A, Marchionni L, Massaro Giordano G, Parini A, Sbardella G.

Cell Death Dis. 2019 Dec 5;10(12):931. doi: 10.1038/s41419-019-2179-8. No abstract available.

6.

BITS2018: the fifteenth annual meeting of the Italian Society of Bioinformatics.

Cordero F, Calogero RA, Caselle M.

BMC Bioinformatics. 2019 Nov 22;20(Suppl 9):562. doi: 10.1186/s12859-019-3175-9.

7.

rCASC: reproducible classification analysis of single-cell sequencing data.

Alessandrì L, Cordero F, Beccuti M, Arigoni M, Olivero M, Romano G, Rabellino S, Licheri N, De Libero G, Pace L, Calogero RA.

Gigascience. 2019 Sep 1;8(9). pii: giz105. doi: 10.1093/gigascience/giz105.

8.

Extracellular Vesicles Mediate Mesenchymal Stromal Cell-Dependent Regulation of B Cell PI3K-AKT Signaling Pathway and Actin Cytoskeleton.

Adamo A, Brandi J, Caligola S, Delfino P, Bazzoni R, Carusone R, Cecconi D, Giugno R, Manfredi M, Robotti E, Marengo E, Bassi G, Takam Kamga P, Dal Collo G, Gatti A, Mercuri A, Arigoni M, Olivero M, Calogero RA, Krampera M.

Front Immunol. 2019 Mar 12;10:446. doi: 10.3389/fimmu.2019.00446. eCollection 2019.

9.

MicroRNAs from saliva of anopheline mosquitoes mimic human endogenous miRNAs and may contribute to vector-host-pathogen interactions.

Arcà B, Colantoni A, Fiorillo C, Severini F, Benes V, Di Luca M, Calogero RA, Lombardo F.

Sci Rep. 2019 Feb 27;9(1):2955. doi: 10.1038/s41598-019-39880-1.

10.

DNA damage and transcriptional regulation in iPSC-derived neurons from Ataxia Telangiectasia patients.

Corti A, Sota R, Dugo M, Calogero RA, Terragni B, Mantegazza M, Franceschetti S, Restelli M, Gasparini P, Lecis D, Chrzanowska KH, Delia D.

Sci Rep. 2019 Jan 24;9(1):651. doi: 10.1038/s41598-018-36912-0.

11.

NUAK2 is a critical YAP target in liver cancer.

Yuan WC, Pepe-Mooney B, Galli GG, Dill MT, Huang HT, Hao M, Wang Y, Liang H, Calogero RA, Camargo FD.

Nat Commun. 2018 Nov 16;9(1):4834. doi: 10.1038/s41467-018-07394-5.

12.

Reproducible bioinformatics project: a community for reproducible bioinformatics analysis pipelines.

Kulkarni N, Alessandrì L, Panero R, Arigoni M, Olivero M, Ferrero G, Cordero F, Beccuti M, Calogero RA.

BMC Bioinformatics. 2018 Oct 15;19(Suppl 10):349. doi: 10.1186/s12859-018-2296-x.

13.

Development, Function, and Clinical Significance of Plasmacytoid Dendritic Cells in Chronic Myeloid Leukemia.

Inselmann S, Wang Y, Saussele S, Fritz L, Schütz C, Huber M, Liebler S, Ernst T, Cai D, Botschek S, Brendel C, Calogero RA, Pavlinic D, Benes V, Liu ET, Neubauer A, Hochhaus A, Burchert A.

Cancer Res. 2018 Nov 1;78(21):6223-6234. doi: 10.1158/0008-5472.CAN-18-1477. Epub 2018 Aug 30.

14.

MicroRNA miR-34a downregulates FOXP1 during DNA damage response to limit BCR signalling in chronic lymphocytic leukaemia B cells.

Cerna K, Oppelt J, Chochola V, Musilova K, Seda V, Pavlasova G, Radova L, Arigoni M, Calogero RA, Benes V, Trbusek M, Brychtova Y, Doubek M, Mayer J, Pospisilova S, Mraz M.

Leukemia. 2019 Feb;33(2):403-414. doi: 10.1038/s41375-018-0230-x. Epub 2018 Aug 15.

PMID:
30111844
15.

Correction: p190 RhoGAP promotes contact inhibition in epithelial cells by repressing YAP activity.

Frank SR, Köllmann CP, Luong P, Galli GG, Zou L, Bernards A, Getz G, Calogero RA, Frödin M, Hansen SH.

J Cell Biol. 2018 Sep 3;217(9):3313. doi: 10.1083/JCB.20171005807172018c. Epub 2018 Jul 25. No abstract available.

16.

YAP-TEAD signaling promotes basal cell carcinoma development via a c-JUN/AP1 axis.

Maglic D, Schlegelmilch K, Dost AF, Panero R, Dill MT, Calogero RA, Camargo FD.

EMBO J. 2018 Sep 3;37(17). pii: e98642. doi: 10.15252/embj.201798642. Epub 2018 Jul 23.

17.

p190 RhoGAP promotes contact inhibition in epithelial cells by repressing YAP activity.

Frank SR, Köllmann CP, Luong P, Galli GG, Zou L, Bernards A, Getz G, Calogero RA, Frödin M, Hansen SH.

J Cell Biol. 2018 Sep 3;217(9):3183-3201. doi: 10.1083/jcb.201710058. Epub 2018 Jun 22. Erratum in: J Cell Biol. 2018 Jul 25;:.

18.

Laser capture microdissection for transcriptomic profiles in human skin biopsies.

Santoro S, Lopez ID, Lombardi R, Zauli A, Osiceanu AM, Sorosina M, Clarelli F, Peroni S, Cazzato D, Marchi M, Quattrini A, Comi G, Calogero RA, Lauria G, Martinelli Boneschi F.

BMC Mol Biol. 2018 Jun 19;19(1):7. doi: 10.1186/s12867-018-0108-5.

19.

microRNA profiles in urine by next-generation sequencing can stratify bladder cancer subtypes.

Pardini B, Cordero F, Naccarati A, Viberti C, Birolo G, Oderda M, Di Gaetano C, Arigoni M, Martina F, Calogero RA, Sacerdote C, Gontero P, Vineis P, Matullo G.

Oncotarget. 2018 Apr 17;9(29):20658-20669. doi: 10.18632/oncotarget.25057. eCollection 2018 Apr 17.

20.

Luminal breast cancer-specific circular RNAs uncovered by a novel tool for data analysis.

Coscujuela Tarrero L, Ferrero G, Miano V, De Intinis C, Ricci L, Arigoni M, Riccardo F, Annaratone L, Castellano I, Calogero RA, Beccuti M, Cordero F, De Bortoli M.

Oncotarget. 2018 Feb 19;9(18):14580-14596. doi: 10.18632/oncotarget.24522. eCollection 2018 Mar 6.

21.

Small non-coding RNA profiling in human biofluids and surrogate tissues from healthy individuals: description of the diverse and most represented species.

Ferrero G, Cordero F, Tarallo S, Arigoni M, Riccardo F, Gallo G, Ronco G, Allasia M, Kulkarni N, Matullo G, Vineis P, Calogero RA, Pardini B, Naccarati A.

Oncotarget. 2017 Dec 14;9(3):3097-3111. doi: 10.18632/oncotarget.23203. eCollection 2018 Jan 9.

22.

Clonal analysis of lineage fate in native haematopoiesis.

Rodriguez-Fraticelli AE, Wolock SL, Weinreb CS, Panero R, Patel SH, Jankovic M, Sun J, Calogero RA, Klein AM, Camargo FD.

Nature. 2018 Jan 11;553(7687):212-216. doi: 10.1038/nature25168. Epub 2018 Jan 3.

23.

SeqBox: RNAseq/ChIPseq reproducible analysis on a consumer game computer.

Beccuti M, Cordero F, Arigoni M, Panero R, Amparore EG, Donatelli S, Calogero RA.

Bioinformatics. 2018 Mar 1;34(5):871-872. doi: 10.1093/bioinformatics/btx674.

24.

Deregulation of MicroRNAs mediated control of carnitine cycle in prostate cancer: molecular basis and pathophysiological consequences.

Valentino A, Calarco A, Di Salle A, Finicelli M, Crispi S, Calogero RA, Riccardo F, Sciarra A, Gentilucci A, Galderisi U, Margarucci S, Peluso G.

Oncogene. 2017 Oct 26;36(43):6030-6040. doi: 10.1038/onc.2017.216. Epub 2017 Jul 3.

PMID:
28671672
25.

LSD1 mediates MYCN control of epithelial-mesenchymal transition through silencing of metastatic suppressor NDRG1 gene.

Ambrosio S, Amente S, Saccà CD, Capasso M, Calogero RA, Lania L, Majello B.

Oncotarget. 2017 Jan 17;8(3):3854-3869. doi: 10.18632/oncotarget.12924.

26.

A novel infection- and inflammation-associated molecular signature in peripheral blood of myasthenia gravis patients.

Barzago C, Lum J, Cavalcante P, Srinivasan KG, Faggiani E, Camera G, Bonanno S, Andreetta F, Antozzi C, Baggi F, Calogero RA, Bernasconi P, Mantegazza R, Mori L, Zolezzi F.

Immunobiology. 2016 Nov;221(11):1227-36. doi: 10.1016/j.imbio.2016.06.012. Epub 2016 Jun 15.

PMID:
27387891
27.

A hypoxic signature marks tumors formed by disseminated tumor cells in the BALB-neuT mammary cancer model.

Msaki A, Pastò A, Curtarello M, Arigoni M, Barutello G, Calogero RA, Macagno M, Cavallo F, Amadori A, Indraccolo S.

Oncotarget. 2016 May 31;7(22):33081-95. doi: 10.18632/oncotarget.8859.

28.

Erratum for Baddal et al., Dual RNA-seq of Nontypeable Haemophilus influenzae and Host Cell Transcriptomes Reveals Novel Insights into Host-Pathogen Cross Talk.

Baddal B, Muzzi A, Censini S, Calogero RA, Torricelli G, Guidotti S, Taddei AR, Covacci A, Pizza M, Rappuoli R, Soriani M, Pezzicoli A.

mBio. 2016 Apr 12;7(2):e00373-16. doi: 10.1128/mBio.00373-16. No abstract available.

29.

Dual RNA-seq of Nontypeable Haemophilus influenzae and Host Cell Transcriptomes Reveals Novel Insights into Host-Pathogen Cross Talk.

Baddal B, Muzzi A, Censini S, Calogero RA, Torricelli G, Guidotti S, Taddei AR, Covacci A, Pizza M, Rappuoli R, Soriani M, Pezzicoli A.

mBio. 2015 Nov 17;6(6):e01765-15. doi: 10.1128/mBio.01765-15. Erratum in: MBio. 2016;7(2). pii: e00373-16. doi: 10.1128/mBio.00373-16.

30.

Immunotargeting of Antigen xCT Attenuates Stem-like Cell Behavior and Metastatic Progression in Breast Cancer.

Lanzardo S, Conti L, Rooke R, Ruiu R, Accart N, Bolli E, Arigoni M, Macagno M, Barrera G, Pizzimenti S, Aurisicchio L, Calogero RA, Cavallo F.

Cancer Res. 2016 Jan 1;76(1):62-72. doi: 10.1158/0008-5472.CAN-15-1208. Epub 2015 Nov 13.

31.

Novel insights into Notum and glypicans regulation in colorectal cancer.

De Robertis M, Arigoni M, Loiacono L, Riccardo F, Calogero RA, Feodorova Y, Tashkova D, Belovejdov V, Sarafian V, Cavallo F, Signori E.

Oncotarget. 2015 Dec 1;6(38):41237-57. doi: 10.18632/oncotarget.5652.

32.

YAP Drives Growth by Controlling Transcriptional Pause Release from Dynamic Enhancers.

Galli GG, Carrara M, Yuan WC, Valdes-Quezada C, Gurung B, Pepe-Mooney B, Zhang T, Geeven G, Gray NS, de Laat W, Calogero RA, Camargo FD.

Mol Cell. 2015 Oct 15;60(2):328-37. doi: 10.1016/j.molcel.2015.09.001. Epub 2015 Oct 1.

33.

Alternative splicing detection workflow needs a careful combination of sample prep and bioinformatics analysis.

Carrara M, Lum J, Cordero F, Beccuti M, Poidinger M, Donatelli S, Calogero RA, Zolezzi F.

BMC Bioinformatics. 2015;16 Suppl 9:S2. doi: 10.1186/1471-2105-16-S9-S2. Epub 2015 Jun 1.

34.

A versatile mathematical work-flow to explore how Cancer Stem Cell fate influences tumor progression.

Fornari C, Balbo G, Halawani SM, Ba-Rukab O, Ahmad AR, Calogero RA, Cordero F, Beccuti M.

BMC Syst Biol. 2015;9 Suppl 3:S1. doi: 10.1186/1752-0509-9-S3-S1. Epub 2015 Jun 1.

35.

RAP: RNA-Seq Analysis Pipeline, a new cloud-based NGS web application.

D'Antonio M, D'Onorio De Meo P, Pallocca M, Picardi E, D'Erchia AM, Calogero RA, Castrignanò T, Pesole G.

BMC Genomics. 2015;16:S3. doi: 10.1186/1471-2164-16-S6-S3. Epub 2015 Jun 1.

36.

Bisphenol A effects on gene expression in adipocytes from children: association with metabolic disorders.

Menale C, Piccolo MT, Cirillo G, Calogero RA, Papparella A, Mita L, Del Giudice EM, Diano N, Crispi S, Mita DG.

J Mol Endocrinol. 2015 Jun;54(3):289-303. doi: 10.1530/JME-14-0282. Epub 2015 Apr 15.

PMID:
25878060
37.

Quantifying entire transcriptomes by aligned RNA-seq data.

Calogero RA, Zolezzi F.

Methods Mol Biol. 2015;1269:163-72. doi: 10.1007/978-1-4939-2291-8_10.

PMID:
25577378
38.

Chimera: a Bioconductor package for secondary analysis of fusion products.

Beccuti M, Carrara M, Cordero F, Lazzarato F, Donatelli S, Nadalin F, Policriti A, Calogero RA.

Bioinformatics. 2014 Dec 15;30(24):3556-7. doi: 10.1093/bioinformatics/btu662. Epub 2014 Oct 6.

39.

Histone methyltransferase MMSET/NSD2 alters EZH2 binding and reprograms the myeloma epigenome through global and focal changes in H3K36 and H3K27 methylation.

Popovic R, Martinez-Garcia E, Giannopoulou EG, Zhang Q, Zhang Q, Ezponda T, Shah MY, Zheng Y, Will CM, Small EC, Hua Y, Bulic M, Jiang Y, Carrara M, Calogero RA, Kath WL, Kelleher NL, Wang JP, Elemento O, Licht JD.

PLoS Genet. 2014 Sep 4;10(9):e1004566. doi: 10.1371/journal.pgen.1004566. eCollection 2014 Sep.

40.

A mathematical-biological joint effort to investigate the tumor-initiating ability of Cancer Stem Cells.

Fornari C, Beccuti M, Lanzardo S, Conti L, Balbo G, Cavallo F, Calogero RA, Cordero F.

PLoS One. 2014 Sep 3;9(9):e106193. doi: 10.1371/journal.pone.0106193. eCollection 2014.

41.

The Hippo transducer YAP1 transforms activated satellite cells and is a potent effector of embryonal rhabdomyosarcoma formation.

Tremblay AM, Missiaglia E, Galli GG, Hettmer S, Urcia R, Carrara M, Judson RN, Thway K, Nadal G, Selfe JL, Murray G, Calogero RA, De Bari C, Zammit PS, Delorenzi M, Wagers AJ, Shipley J, Wackerhage H, Camargo FD.

Cancer Cell. 2014 Aug 11;26(2):273-87. doi: 10.1016/j.ccr.2014.05.029. Epub 2014 Jul 31.

42.

Critical roles for Rictor/Sin1 complexes in interferon-dependent gene transcription and generation of antiproliferative responses.

Kaur S, Kroczynska B, Sharma B, Sassano A, Arslan AD, Majchrzak-Kita B, Stein BL, McMahon B, Altman JK, Su B, Calogero RA, Fish EN, Platanias LC.

J Biol Chem. 2014 Mar 7;289(10):6581-91. doi: 10.1074/jbc.M113.537852. Epub 2014 Jan 27.

43.

Recombinant human lactoferrin induces human and mouse dendritic cell maturation via Toll-like receptors 2 and 4.

Spadaro M, Montone M, Arigoni M, Cantarella D, Forni G, Pericle F, Pascolo S, Calogero RA, Cavallo F.

FASEB J. 2014 Jan;28(1):416-29. doi: 10.1096/fj.13-229591. Epub 2013 Oct 2.

PMID:
24088817
44.

Genomic and proteomic analyses of Prdm5 reveal interactions with insulator binding proteins in embryonic stem cells.

Galli GG, Carrara M, Francavilla C, de Lichtenberg KH, Olsen JV, Calogero RA, Lund AH.

Mol Cell Biol. 2013 Nov;33(22):4504-16. doi: 10.1128/MCB.00545-13. Epub 2013 Sep 16.

45.

Functional and pharmacodynamic evaluation of metronomic cyclophosphamide and docetaxel regimen in castration-resistant prostate cancer.

Cardillo I, Spugnini EP, Galluzzo P, Contestabile M, Dell'Anna ML, Picardo M, Crispi S, Calogero RA, Piccolo MT, Arigoni M, Cantarella D, Boccellino M, Quagliuolo L, Ferretti G, Carlini P, Felici A, Boccardo F, Cognetti F, Baldi A.

Future Oncol. 2013 Sep;9(9):1375-88. doi: 10.2217/fon.13.99.

PMID:
23980684
46.

The noninflammatory role of high mobility group box 1/Toll-like receptor 2 axis in the self-renewal of mammary cancer stem cells.

Conti L, Lanzardo S, Arigoni M, Antonazzo R, Radaelli E, Cantarella D, Calogero RA, Cavallo F.

FASEB J. 2013 Dec;27(12):4731-44. doi: 10.1096/fj.13-230201. Epub 2013 Aug 22.

PMID:
23970797
47.

Prdm5 suppresses Apc(Min)-driven intestinal adenomas and regulates monoacylglycerol lipase expression.

Galli GG, Multhaupt HA, Carrara M, de Lichtenberg KH, Christensen IB, Linnemann D, Santoni-Rugiu E, Calogero RA, Lund AH.

Oncogene. 2014 Jun 19;33(25):3342-50. doi: 10.1038/onc.2013.283. Epub 2013 Jul 22.

48.

State of art fusion-finder algorithms are suitable to detect transcription-induced chimeras in normal tissues?

Carrara M, Beccuti M, Cavallo F, Donatelli S, Lazzarato F, Cordero F, Calogero RA.

BMC Bioinformatics. 2013;14 Suppl 7:S2. doi: 10.1186/1471-2105-14-S7-S2. Epub 2013 Apr 22.

49.

Intelligent informatics in biomedicine.

Chang HT, Calogero RA, Draghici S, Ray O, Pai TW.

Biomed Res Int. 2013;2013:185839. doi: 10.1155/2013/185839. Epub 2013 Apr 22. No abstract available.

50.

miR-135b coordinates progression of ErbB2-driven mammary carcinomas through suppression of MID1 and MTCH2.

Arigoni M, Barutello G, Riccardo F, Ercole E, Cantarella D, Orso F, Conti L, Lanzardo S, Taverna D, Merighi I, Calogero RA, Cavallo F, Quaglino E.

Am J Pathol. 2013 Jun;182(6):2058-70. doi: 10.1016/j.ajpath.2013.02.046. Epub 2013 Apr 23.

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