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Items: 1 to 50 of 128

1.

Correction for Tarallo et al., "Altered Fecal Small RNA Profiles in Colorectal Cancer Reflect Gut Microbiome Composition in Stool Samples".

Tarallo S, Ferrero G, Gallo G, Francavilla A, Clerico G, Realis Luc A, Manghi P, Thomas AM, Vineis P, Segata N, Pardini B, Naccarati A, Cordero F.

mSystems. 2020 Feb 18;5(1). pii: e00072-20. doi: 10.1128/mSystems.00072-20. No abstract available.

2.

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.

3.

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.

4.

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.

5.

Author Correction: Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation.

Thomas AM, Manghi P, Asnicar F, Pasolli E, Armanini F, Zolfo M, Beghini F, Manara S, Karcher N, Pozzi C, Gandini S, Serrano D, Tarallo S, Francavilla A, Gallo G, Trompetto M, Ferrero G, Mizutani S, Shiroma H, Shiba S, Shibata T, Yachida S, Yamada T, Wirbel J, Schrotz-King P, Ulrich CM, Brenner H, Arumugam M, Bork P, Zeller G, Cordero F, Dias-Neto E, Setubal JC, Tett A, Pardini B, Rescigno M, Waldron L, Naccarati A, Segata N.

Nat Med. 2019 Dec;25(12):1948. doi: 10.1038/s41591-019-0663-4.

PMID:
31664237
6.

Altered Fecal Small RNA Profiles in Colorectal Cancer Reflect Gut Microbiome Composition in Stool Samples.

Tarallo S, Ferrero G, Gallo G, Francavilla A, Clerico G, Realis Luc A, Manghi P, Thomas AM, Vineis P, Segata N, Pardini B, Naccarati A, Cordero F.

mSystems. 2019 Sep 17;4(5). pii: e00289-19. doi: 10.1128/mSystems.00289-19. Erratum in: mSystems. 2020 Feb 18;5(1):.

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.

Computational Investigation of the Selective Cleavage of Diastereotopic Cyclopropane Bonds in 5-Spirocyclopropane Isoxazolidines Rearrangement.

Briccolani-Bandini L, Brandi A, Cardini G, Chelli R, Cordero FM, Gellini C, Pagliai M.

J Org Chem. 2019 Jun 7;84(11):6757-6764. doi: 10.1021/acs.joc.9b00499. Epub 2019 May 10.

PMID:
31042393
9.

Stability of Cubic FAPbI3 from X-ray Diffraction, Anelastic, and Dielectric Measurements.

Cordero F, Craciun F, Trequattrini F, Generosi A, Paci B, Paoletti AM, Pennesi G.

J Phys Chem Lett. 2019 May 16;10(10):2463-2469. doi: 10.1021/acs.jpclett.9b00896. Epub 2019 May 2.

PMID:
31041864
10.

Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation.

Thomas AM, Manghi P, Asnicar F, Pasolli E, Armanini F, Zolfo M, Beghini F, Manara S, Karcher N, Pozzi C, Gandini S, Serrano D, Tarallo S, Francavilla A, Gallo G, Trompetto M, Ferrero G, Mizutani S, Shiroma H, Shiba S, Shibata T, Yachida S, Yamada T, Wirbel J, Schrotz-King P, Ulrich CM, Brenner H, Arumugam M, Bork P, Zeller G, Cordero F, Dias-Neto E, Setubal JC, Tett A, Pardini B, Rescigno M, Waldron L, Naccarati A, Segata N.

Nat Med. 2019 Apr;25(4):667-678. doi: 10.1038/s41591-019-0405-7. Epub 2019 Apr 1. Erratum in: Nat Med. 2019 Dec;25(12):1948.

PMID:
30936548
11.

Analytic Form of Planar Two-Loop Five-Gluon Scattering Amplitudes in QCD.

Abreu S, Dormans J, Cordero FF, Ita H, Page B.

Phys Rev Lett. 2019 Mar 1;122(8):082002. doi: 10.1103/PhysRevLett.122.082002.

PMID:
30932613
12.

Damage from Coexistence of Ferroelectric and Antiferroelectric Domains and Clustering of O Vacancies in PZT: An Elastic and Raman Study.

Cordero F, Buixaderas E, Galassi C.

Materials (Basel). 2019 Mar 22;12(6). pii: E957. doi: 10.3390/ma12060957.

13.

Integrative Analysis of Novel Metabolic Subtypes in Pancreatic Cancer Fosters New Prognostic Biomarkers.

Follia L, Ferrero G, Mandili G, Beccuti M, Giordano D, Spadi R, Satolli MA, Evangelista A, Katayama H, Hong W, Momin AA, Capello M, Hanash SM, Novelli F, Cordero F.

Front Oncol. 2019 Feb 27;9:115. doi: 10.3389/fonc.2019.00115. eCollection 2019.

14.

ACVR1 R206H cooperates with H3.1K27M in promoting diffuse intrinsic pontine glioma pathogenesis.

Hoeman CM, Cordero FJ, Hu G, Misuraca K, Romero MM, Cardona HJ, Nazarian J, Hashizume R, McLendon R, Yu P, Procissi D, Gadd S, Becher OJ.

Nat Commun. 2019 Mar 4;10(1):1023. doi: 10.1038/s41467-019-08823-9.

15.

Pregnancy Epigenetic Signature in T Helper 17 and T Regulatory Cells in Multiple Sclerosis.

Iannello A, Rolla S, Maglione A, Ferrero G, Bardina V, Inaudi I, De Mercanti S, Novelli F, D'Antuono L, Cardaropoli S, Todros T, Turrini MV, Cordioli C, Puorro G, Marsili A, Lanzillo R, Brescia Morra V, Cordero F, De Bortoli M, Durelli L, Visconti A, Cutrupi S, Clerico M.

Front Immunol. 2019 Jan 8;9:3075. doi: 10.3389/fimmu.2018.03075. eCollection 2018.

16.

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.

17.

Endoscopic Balloon Dilation for Treatment of Congenital Antral Web.

Peck J, Khalaf R, Marth R, Phen C, Sosa R, Cordero FB, Wilsey M.

Pediatr Gastroenterol Hepatol Nutr. 2018 Oct;21(4):351-354. doi: 10.5223/pghn.2018.21.4.351. Epub 2018 Oct 10.

18.

MMP23B expression and protein levels in blood and urine are associated with bladder cancer.

Allione A, Pardini B, Viberti C, Giribaldi G, Turini S, Di Gaetano C, Guarrera S, Cordero F, Oderda M, Allasia M, Gontero P, Sacerdote C, Vineis P, Matullo G.

Carcinogenesis. 2018 Oct 8;39(10):1254-1263. doi: 10.1093/carcin/bgy098.

PMID:
30052775
19.

Competition between Polar and Antiferrodistortive Modes and Correlated Dynamics of the Methylammonium Molecules in MAPbI3 from Anelastic and Dielectric Measurements.

Cordero F, Craciun F, Trequattrini F, Imperatori P, Paoletti AM, Pennesi G.

J Phys Chem Lett. 2018 Aug 2;9(15):4401-4406. doi: 10.1021/acs.jpclett.8b01761. Epub 2018 Jul 23.

PMID:
30027742
20.

Combined use of Mössbauer spectroscopy, XPS, HRTEM, dielectric and anelastic spectroscopy for estimating incipient phase separation in lead titanate-based multiferroics.

Craciun F, Cordero F, Vasile BS, Fruth V, Zaharescu M, Atkinson I, Trusca R, Diamandescu L, Tanase LC, Galizia P, Cernea M, Galassi C.

Phys Chem Chem Phys. 2018 May 30;20(21):14652-14663. doi: 10.1039/c8cp01456f.

PMID:
29770415
21.

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.

22.

A probabilistic view on the deterministic mutation-selection equation: dynamics, equilibria, and ancestry via individual lines of descent.

Baake E, Cordero F, Hummel S.

J Math Biol. 2018 Sep;77(3):795-820. doi: 10.1007/s00285-018-1228-8. Epub 2018 Apr 19.

PMID:
29675600
23.

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.

24.

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.

25.

HashClone: a new tool to quantify the minimal residual disease in B-cell lymphoma from deep sequencing data.

Beccuti M, Genuardi E, Romano G, Monitillo L, Barbero D, Boccadoro M, Ladetto M, Calogero R, Ferrero S, Cordero F.

BMC Bioinformatics. 2017 Nov 23;18(1):516. doi: 10.1186/s12859-017-1923-2.

26.

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.

27.

Two-Loop Four-Gluon Amplitudes from Numerical Unitarity.

Abreu S, Cordero FF, Ita H, Jaquier M, Page B, Zeng M.

Phys Rev Lett. 2017 Oct 6;119(14):142001. doi: 10.1103/PhysRevLett.119.142001. Epub 2017 Oct 5.

PMID:
29053299
28.

Dissecting the genomic activity of a transcriptional regulator by the integrative analysis of omics data.

Ferrero G, Miano V, Beccuti M, Balbo G, De Bortoli M, Cordero F.

Sci Rep. 2017 Aug 17;7(1):8564. doi: 10.1038/s41598-017-08754-9.

29.

Peculiar Genes Selection: A new features selection method to improve classification performances in imbalanced data sets.

Martina F, Beccuti M, Balbo G, Cordero F.

PLoS One. 2017 Aug 14;12(8):e0177475. doi: 10.1371/journal.pone.0177475. eCollection 2017.

30.

[Clinical features of patients with Basedow Graves disease seen at a university hospital].

Lanas A, Díaz P, Eugenin D, González F, Cid P, Cordero F, Araya V, Liberman C, Barberan M, Gac P, Saldías N, Pineda P.

Rev Med Chil. 2017 Apr;145(4):436-440. doi: 10.4067/S0034-98872017000400003. Spanish.

31.

Histone H3.3K27M Represses p16 to Accelerate Gliomagenesis in a Murine Model of DIPG.

Cordero FJ, Huang Z, Grenier C, He X, Hu G, McLendon RE, Murphy SK, Hashizume R, Becher OJ.

Mol Cancer Res. 2017 Sep;15(9):1243-1254. doi: 10.1158/1541-7786.MCR-16-0389. Epub 2017 May 18.

32.

Erratum to: 'NETTAB 2014: From high-throughput structural bioinformatics to integrative systems biology'.

Romano P, Cordero F.

BMC Bioinformatics. 2016 Jul 29;17(1):293. No abstract available.

33.

Biologic Data of Cynomolgus Monkeys Maintained under Laboratory Conditions.

Rosso MC, Badino P, Ferrero G, Costa R, Cordero F, Steidler S.

PLoS One. 2016 Jun 9;11(6):e0157003. doi: 10.1371/journal.pone.0157003. eCollection 2016.

34.

A picture is worth a thousand words: maps of HIV indicators to inform research, programs, and policy from NA-ACCORD and CCASAnet clinical cohorts.

Althoff KN, Rebeiro PF, Hanna DB, Padgett D, Horberg MA, Grinsztejn B, Abraham AG, Hogg R, Gill MJ, Wolff MJ, Mayor A, Rachlis A, Williams C, Sterling TR, Kitahata MM, Buchacz K, Thorne JE, Cesar C, Cordero FM, Rourke SB, Sierra-Madero J, Pape JW, Cahn P, McGowan C; North American Aids Cohort Collaboration on Research and Design (NA-ACCORD) and Caribbean, Central and South America Network for Hiv Epidemiology (CCASAnet).

J Int AIDS Soc. 2016 Apr 4;19(1):20707. doi: 10.7448/IAS.19.1.20707. eCollection 2016.

35.

NETTAB 2014: From high-throughput structural bioinformatics to integrative systems biology.

Romano P, Cordero F.

BMC Bioinformatics. 2016 Mar 2;17 Suppl 4:62. doi: 10.1186/s12859-016-0907-y. Erratum in: BMC Bioinformatics. 2016;17(1):293.

36.

A Stereoselective Synthesis of Lentiginosine.

Cordero FM, Vurchio C, Brandi A.

J Org Chem. 2016 Feb 19;81(4):1661-4. doi: 10.1021/acs.joc.5b02804. Epub 2016 Feb 3.

PMID:
26800332
37.

Implementation and Outcomes of a Community-Based Educational Program for Colorectal Cancer Prevention in Hispanics.

Cruz-Correa M, Cordero F, Betancourt JP, Diaz-Algorri Y, Lopez SM, Rivera M, Mosquera R, Carlo-Chevere V, Rodriguez-Quilichini S.

J Fam Med Dis Prev. 2016;2(3). pii: 42. doi: 10.23937/2469-5793/1510042. Epub 2016 Aug 25.

38.

Luminal long non-coding RNAs regulated by estrogen receptor alpha in a ligand-independent manner show functional roles in breast cancer.

Miano V, Ferrero G, Reineri S, Caizzi L, Annaratone L, Ricci L, Cutrupi S, Castellano I, Cordero F, De Bortoli M.

Oncotarget. 2016 Jan 19;7(3):3201-16. doi: 10.18632/oncotarget.6420.

39.

Elastic Properties and Enhanced Piezoelectric Response at Morphotropic Phase Boundaries.

Cordero F.

Materials (Basel). 2015 Dec 2;8(12):8195-8245. doi: 10.3390/ma8125452. Review.

40.

A computational analysis of S-(2-succino)cysteine sites in proteins.

Miglio G, Sabatino AD, Veglia E, Giraudo MT, Beccuti M, Cordero F.

Biochim Biophys Acta. 2016 Feb;1864(2):211-8. doi: 10.1016/j.bbapap.2015.11.003. Epub 2015 Nov 14.

41.

Tumor location, but not H3.3K27M, significantly influences the blood-brain-barrier permeability in a genetic mouse model of pediatric high-grade glioma.

Subashi E, Cordero FJ, Halvorson KG, Qi Y, Nouls JC, Becher OJ, Johnson GA.

J Neurooncol. 2016 Jan;126(2):243-51. doi: 10.1007/s11060-015-1969-9. Epub 2015 Oct 28.

42.

Pre-Clinical Models of Diffuse Intrinsic Pontine Glioma.

Misuraca KL, Cordero FJ, Becher OJ.

Front Oncol. 2015 Jul 24;5:172. doi: 10.3389/fonc.2015.00172. eCollection 2015. Review.

43.

Sequencing of 15 622 gene-bearing BACs clarifies the gene-dense regions of the barley genome.

Muñoz-Amatriaín M, Lonardi S, Luo M, Madishetty K, Svensson JT, Moscou MJ, Wanamaker S, Jiang T, Kleinhofs A, Muehlbauer GJ, Wise RP, Stein N, Ma Y, Rodriguez E, Kudrna D, Bhat PR, Chao S, Condamine P, Heinen S, Resnik J, Wing R, Witt HN, Alpert M, Beccuti M, Bozdag S, Cordero F, Mirebrahim H, Ounit R, Wu Y, You F, Zheng J, Simková H, Dolezel J, Grimwood J, Schmutz J, Duma D, Altschmied L, Blake T, Bregitzer P, Cooper L, Dilbirligi M, Falk A, Feiz L, Graner A, Gustafson P, Hayes PM, Lemaux P, Mammadov J, Close TJ.

Plant J. 2015 Oct;84(1):216-27. doi: 10.1111/tpj.12959. Epub 2015 Sep 21.

44.

Differentially methylated microRNAs in prediagnostic samples of subjects who developed breast cancer in the European Prospective Investigation into Nutrition and Cancer (EPIC-Italy) cohort.

Cordero F, Ferrero G, Polidoro S, Fiorito G, Campanella G, Sacerdote C, Mattiello A, Masala G, Agnoli C, Frasca G, Panico S, Palli D, Krogh V, Tumino R, Vineis P, Naccarati A.

Carcinogenesis. 2015 Oct;36(10):1144-53. doi: 10.1093/carcin/bgv102. Epub 2015 Jul 13.

45.

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.

46.

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.

47.

The molecular landscape of colorectal cancer cell lines unveils clinically actionable kinase targets.

Medico E, Russo M, Picco G, Cancelliere C, Valtorta E, Corti G, Buscarino M, Isella C, Lamba S, Martinoglio B, Veronese S, Siena S, Sartore-Bianchi A, Beccuti M, Mottolese M, Linnebacher M, Cordero F, Di Nicolantonio F, Bardelli A.

Nat Commun. 2015 Apr 30;6:7002. doi: 10.1038/ncomms8002.

48.

A high-throughput in vitro drug screen in a genetically engineered mouse model of diffuse intrinsic pontine glioma identifies BMS-754807 as a promising therapeutic agent.

Halvorson KG, Barton KL, Schroeder K, Misuraca KL, Hoeman C, Chung A, Crabtree DM, Cordero FJ, Singh R, Spasojevic I, Berlow N, Pal R, Becher OJ.

PLoS One. 2015 Mar 6;10(3):e0118926. doi: 10.1371/journal.pone.0118926. eCollection 2015.

49.

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.

50.

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.

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