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Items: 1 to 50 of 51

1.

Benchmarking software tools for detecting and quantifying selection in evolve and resequencing studies.

Vlachos C, Burny C, Pelizzola M, Borges R, Futschik A, Kofler R, Schlötterer C.

Genome Biol. 2019 Aug 15;20(1):169. doi: 10.1186/s13059-019-1770-8.

2.

An early Myc-dependent transcriptional program orchestrates cell growth during B-cell activation.

Tesi A, de Pretis S, Furlan M, Filipuzzi M, Morelli MJ, Andronache A, Doni M, Verrecchia A, Pelizzola M, Amati B, Sabò A.

EMBO Rep. 2019 Jul 23:e47987. doi: 10.15252/embr.201947987. [Epub ahead of print]

PMID:
31334602
3.

Prognostic Significance of Organ Dysfunction in Cats With Polytrauma.

Murgia E, Troia R, Bulgarelli C, Pelizzola M, Foglia A, Dondi F, Giunti M.

Front Vet Sci. 2019 Jun 21;6:189. doi: 10.3389/fvets.2019.00189. eCollection 2019.

4.

m6A RNA modification and its writer/reader VIRMA/YTHDF3 in testicular germ cell tumors: a role in seminoma phenotype maintenance.

Lobo J, Costa AL, Cantante M, Guimarães R, Lopes P, Antunes L, Braga I, Oliveira J, Pelizzola M, Henrique R, Jerónimo C.

J Transl Med. 2019 Mar 12;17(1):79. doi: 10.1186/s12967-019-1837-z.

5.

m6A-Dependent RNA Dynamics in T Cell Differentiation.

Furlan M, Galeota E, de Pretis S, Caselle M, Pelizzola M.

Genes (Basel). 2019 Jan 8;10(1). pii: E28. doi: 10.3390/genes10010028.

6.

DNA methylation dynamics during embryonic development and postnatal maturation of the mouse auditory sensory epithelium.

Yizhar-Barnea O, Valensisi C, Jayavelu ND, Kishore K, Andrus C, Koffler-Brill T, Ushakov K, Perl K, Noy Y, Bhonker Y, Pelizzola M, Hawkins RD, Avraham KB.

Sci Rep. 2018 Nov 26;8(1):17348. doi: 10.1038/s41598-018-35587-x.

7.

Positioning Europe for the EPITRANSCRIPTOMICS challenge.

Jantsch MF, Quattrone A, O'Connell M, Helm M, Frye M, Macias-Gonzales M, Ohman M, Ameres S, Willems L, Fuks F, Oulas A, Vanacova S, Nielsen H, Bousquet-Antonelli C, Motorin Y, Roignant JY, Balatsos N, Dinnyes A, Baranov P, Kelly V, Lamm A, Rechavi G, Pelizzola M, Liepins J, Holodnuka Kholodnyuk I, Zammit V, Ayers D, Drablos F, Dahl JA, Bujnicki J, Jeronimo C, Almeida R, Neagu M, Costache M, Bankovic J, Banovic B, Kyselovic J, Valor LM, Selbert S, Pir P, Demircan T, Cowling V, Schäfer M, Rossmanith W, Lafontaine D, David A, Carre C, Lyko F, Schaffrath R, Schwartz S, Verdel A, Klungland A, Purta E, Timotijevic G, Cardona F, Davalos A, Ballana E, O Carroll D, Ule J, Fray R.

RNA Biol. 2018;15(6):829-831. doi: 10.1080/15476286.2018.1460996. Epub 2018 May 9.

8.

Identification of Differentially Methylated Regions in the Genome of Arabidopsis thaliana.

Kishore K, Pelizzola M.

Methods Mol Biol. 2018;1675:61-69. doi: 10.1007/978-1-4939-7318-7_4.

PMID:
29052185
9.

Integrative analysis of RNA polymerase II and transcriptional dynamics upon MYC activation.

de Pretis S, Kress TR, Morelli MJ, Sabò A, Locarno C, Verrecchia A, Doni M, Campaner S, Amati B, Pelizzola M.

Genome Res. 2017 Oct;27(10):1658-1664. doi: 10.1101/gr.226035.117. Epub 2017 Sep 13.

10.

DNA methylation variations are required for epithelial-to-mesenchymal transition induced by cancer-associated fibroblasts in prostate cancer cells.

Pistore C, Giannoni E, Colangelo T, Rizzo F, Magnani E, Muccillo L, Giurato G, Mancini M, Rizzo S, Riccardi M, Sahnane N, Del Vescovo V, Kishore K, Mandruzzato M, Macchi F, Pelizzola M, Denti MA, Furlan D, Weisz A, Colantuoni V, Chiarugi P, Bonapace IM.

Oncogene. 2017 Oct 5;36(40):5551-5566. doi: 10.1038/onc.2017.159. Epub 2017 Jun 5.

PMID:
28581528
11.

Integrative classification of human coding and noncoding genes through RNA metabolism profiles.

Mukherjee N, Calviello L, Hirsekorn A, de Pretis S, Pelizzola M, Ohler U.

Nat Struct Mol Biol. 2017 Jan;24(1):86-96. doi: 10.1038/nsmb.3325. Epub 2016 Nov 21.

PMID:
27870833
12.

Mycobacterium tuberculosis exploits the formation of new blood vessels for its dissemination.

Polena H, Boudou F, Tilleul S, Dubois-Colas N, Lecointe C, Rakotosamimanana N, Pelizzola M, Andriamandimby SF, Raharimanga V, Charles P, Herrmann JL, Ricciardi-Castagnoli P, Rasolofo V, Gicquel B, Tailleux L.

Sci Rep. 2016 Sep 12;6:33162. doi: 10.1038/srep33162.

13.

Compensatory RNA polymerase 2 loading determines the efficacy and transcriptional selectivity of JQ1 in Myc-driven tumors.

Donato E, Croci O, Sabò A, Muller H, Morelli MJ, Pelizzola M, Campaner S.

Leukemia. 2017 Feb;31(2):479-490. doi: 10.1038/leu.2016.182. Epub 2016 Jun 24.

14.

Integrated Systems for NGS Data Management and Analysis: Open Issues and Available Solutions.

Bianchi V, Ceol A, Ogier AG, de Pretis S, Galeota E, Kishore K, Bora P, Croci O, Campaner S, Amati B, Morelli MJ, Pelizzola M.

Front Genet. 2016 May 6;7:75. doi: 10.3389/fgene.2016.00075. eCollection 2016.

15.

Ontology-based annotations and semantic relations in large-scale (epi)genomics data.

Galeota E, Pelizzola M.

Brief Bioinform. 2017 May 1;18(3):403-412. doi: 10.1093/bib/bbw036.

16.

LowMACA: exploiting protein family analysis for the identification of rare driver mutations in cancer.

Melloni GE, de Pretis S, Riva L, Pelizzola M, Céol A, Costanza J, Müller H, Zammataro L.

BMC Bioinformatics. 2016 Feb 9;17:80. doi: 10.1186/s12859-016-0935-7.

17.

Degradation dynamics of microRNAs revealed by a novel pulse-chase approach.

Marzi MJ, Ghini F, Cerruti B, de Pretis S, Bonetti P, Giacomelli C, Gorski MM, Kress T, Pelizzola M, Muller H, Amati B, Nicassio F.

Genome Res. 2016 Apr;26(4):554-65. doi: 10.1101/gr.198788.115. Epub 2016 Jan 28.

18.

Transcription of Mammalian cis-Regulatory Elements Is Restrained by Actively Enforced Early Termination.

Austenaa LM, Barozzi I, Simonatto M, Masella S, Della Chiara G, Ghisletti S, Curina A, de Wit E, Bouwman BA, de Pretis S, Piccolo V, Termanini A, Prosperini E, Pelizzola M, de Laat W, Natoli G.

Mol Cell. 2015 Nov 5;60(3):460-74. doi: 10.1016/j.molcel.2015.09.018. Epub 2015 Oct 22.

19.

methylPipe and compEpiTools: a suite of R packages for the integrative analysis of epigenomics data.

Kishore K, de Pretis S, Lister R, Morelli MJ, Bianchi V, Amati B, Ecker JR, Pelizzola M.

BMC Bioinformatics. 2015 Sep 29;16:313. doi: 10.1186/s12859-015-0742-6.

20.

Selective transcriptional regulation by Myc: Experimental design and computational analysis of high-throughput sequencing data.

Pelizzola M, Morelli MJ, Sabò A, Kress TR, de Pretis S, Amati B.

Data Brief. 2015 Feb 12;3:40-6. doi: 10.1016/j.dib.2015.02.003. eCollection 2015 Jun.

21.

INSPEcT: a computational tool to infer mRNA synthesis, processing and degradation dynamics from RNA- and 4sU-seq time course experiments.

de Pretis S, Kress T, Morelli MJ, Melloni GE, Riva L, Amati B, Pelizzola M.

Bioinformatics. 2015 Sep 1;31(17):2829-35. doi: 10.1093/bioinformatics/btv288. Epub 2015 May 7.

PMID:
25957348
22.

Computational epigenomics: challenges and opportunities.

Robinson MD, Pelizzola M.

Front Genet. 2015 Mar 5;6:88. doi: 10.3389/fgene.2015.00088. eCollection 2015. No abstract available.

23.

DOTS-Finder: a comprehensive tool for assessing driver genes in cancer genomes.

Melloni GE, Ogier AG, de Pretis S, Mazzarella L, Pelizzola M, Pelicci PG, Riva L.

Genome Med. 2014 Jun 10;6(6):44. doi: 10.1186/gm563. eCollection 2014.

24.

Computational and experimental methods to decipher the epigenetic code.

de Pretis S, Pelizzola M.

Front Genet. 2014 Sep 23;5:335. doi: 10.3389/fgene.2014.00335. eCollection 2014.

25.

Selective transcriptional regulation by Myc in cellular growth control and lymphomagenesis.

Sabò A, Kress TR, Pelizzola M, de Pretis S, Gorski MM, Tesi A, Morelli MJ, Bora P, Doni M, Verrecchia A, Tonelli C, Fagà G, Bianchi V, Ronchi A, Low D, Müller H, Guccione E, Campaner S, Amati B.

Nature. 2014 Jul 24;511(7510):488-492. doi: 10.1038/nature13537. Epub 2014 Jul 9.

26.

Relationship between genome and epigenome--challenges and requirements for future research.

Almouzni G, Altucci L, Amati B, Ashley N, Baulcombe D, Beaujean N, Bock C, Bongcam-Rudloff E, Bousquet J, Braun S, Bressac-de Paillerets B, Bussemakers M, Clarke L, Conesa A, Estivill X, Fazeli A, Grgurević N, Gut I, Heijmans BT, Hermouet S, Houwing-Duistermaat J, Iacobucci I, Ilaš J, Kandimalla R, Krauss-Etschmann S, Lasko P, Lehmann S, Lindroth A, Majdič G, Marcotte E, Martinelli G, Martinet N, Meyer E, Miceli C, Mills K, Moreno-Villanueva M, Morvan G, Nickel D, Niesler B, Nowacki M, Nowak J, Ossowski S, Pelizzola M, Pochet R, Potočnik U, Radwanska M, Raes J, Rattray M, Robinson MD, Roelen B, Sauer S, Schinzer D, Slagboom E, Spector T, Stunnenberg HG, Tiligada E, Torres-Padilla ME, Tsonaka R, Van Soom A, Vidaković M, Widschwendter M.

BMC Genomics. 2014 Jun 18;15:487. doi: 10.1186/1471-2164-15-487.

27.

Systematic mapping of occluded genes by cell fusion reveals prevalence and stability of cis-mediated silencing in somatic cells.

Looney TJ, Zhang L, Chen CH, Lee JH, Chari S, Mao FF, Pelizzola M, Zhang L, Lister R, Baker SW, Fernandes CJ, Gaetz J, Foshay KM, Clift KL, Zhang Z, Li WQ, Vallender EJ, Wagner U, Qin JY, Michelini KJ, Bugarija B, Park D, Aryee E, Stricker T, Zhou J, White KP, Ren B, Schroth GP, Ecker JR, Xiang AP, Lahn BT.

Genome Res. 2014 Feb;24(2):267-80. doi: 10.1101/gr.143891.112. Epub 2013 Dec 5.

28.

Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis.

Chang KN, Zhong S, Weirauch MT, Hon G, Pelizzola M, Li H, Huang SS, Schmitz RJ, Urich MA, Kuo D, Nery JR, Qiao H, Yang A, Jamali A, Chen H, Ideker T, Ren B, Bar-Joseph Z, Hughes TR, Ecker JR.

Elife. 2013 Jun 11;2:e00675. doi: 10.7554/eLife.00675.

29.

Patterns of population epigenomic diversity.

Schmitz RJ, Schultz MD, Urich MA, Nery JR, Pelizzola M, Libiger O, Alix A, McCosh RB, Chen H, Schork NJ, Ecker JR.

Nature. 2013 Mar 14;495(7440):193-8. doi: 10.1038/nature11968. Epub 2013 Mar 6.

30.

Widespread dynamic DNA methylation in response to biotic stress.

Dowen RH, Pelizzola M, Schmitz RJ, Lister R, Dowen JM, Nery JR, Dixon JE, Ecker JR.

Proc Natl Acad Sci U S A. 2012 Aug 7;109(32):E2183-91. doi: 10.1073/pnas.1209329109. Epub 2012 Jun 25.

31.

Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer.

Hon GC, Hawkins RD, Caballero OL, Lo C, Lister R, Pelizzola M, Valsesia A, Ye Z, Kuan S, Edsall LE, Camargo AA, Stevenson BJ, Ecker JR, Bafna V, Strausberg RL, Simpson AJ, Ren B.

Genome Res. 2012 Feb;22(2):246-58. doi: 10.1101/gr.125872.111. Epub 2011 Dec 7.

32.

Methylated DNA immunoprecipitation genome-wide analysis.

Pelizzola M, Molinaro A.

Methods Mol Biol. 2011;791:113-23. doi: 10.1007/978-1-61779-316-5_9.

PMID:
21913075
33.

Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells.

Lister R, Pelizzola M, Kida YS, Hawkins RD, Nery JR, Hon G, Antosiewicz-Bourget J, O'Malley R, Castanon R, Klugman S, Downes M, Yu R, Stewart R, Ren B, Thomson JA, Evans RM, Ecker JR.

Nature. 2011 Mar 3;471(7336):68-73. doi: 10.1038/nature09798. Epub 2011 Feb 2. Erratum in: Nature. 2014 Oct 2;514(7520):126.

34.

Germline competency of parthenogenetic embryonic stem cells from immature oocytes of adult mouse ovary.

Liu Z, Hu Z, Pan X, Li M, Togun TA, Tuck D, Pelizzola M, Huang J, Ye X, Yin Y, Liu M, Li C, Chen Z, Wang F, Zhou L, Chen L, Keefe DL, Liu L.

Hum Mol Genet. 2011 Apr 1;20(7):1339-52. doi: 10.1093/hmg/ddr016. Epub 2011 Jan 14.

35.

The DNA methylome.

Pelizzola M, Ecker JR.

FEBS Lett. 2011 Jul 7;585(13):1994-2000. doi: 10.1016/j.febslet.2010.10.061. Epub 2010 Nov 5. Review.

36.

Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications.

Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, Downey SL, Johnson BE, Fouse SD, Delaney A, Zhao Y, Olshen A, Ballinger T, Zhou X, Forsberg KJ, Gu J, Echipare L, O'Geen H, Lister R, Pelizzola M, Xi Y, Epstein CB, Bernstein BE, Hawkins RD, Ren B, Chung WY, Gu H, Bock C, Gnirke A, Zhang MQ, Haussler D, Ecker JR, Li W, Farnham PJ, Waterland RA, Meissner A, Marra MA, Hirst M, Milosavljevic A, Costello JF.

Nat Biotechnol. 2010 Oct;28(10):1097-105. doi: 10.1038/nbt.1682. Epub 2010 Sep 19.

37.

Distinct epigenomic landscapes of pluripotent and lineage-committed human cells.

Hawkins RD, Hon GC, Lee LK, Ngo Q, Lister R, Pelizzola M, Edsall LE, Kuan S, Luu Y, Klugman S, Antosiewicz-Bourget J, Ye Z, Espinoza C, Agarwahl S, Shen L, Ruotti V, Wang W, Stewart R, Thomson JA, Ecker JR, Ren B.

Cell Stem Cell. 2010 May 7;6(5):479-91. doi: 10.1016/j.stem.2010.03.018.

38.

Temporal gene expression profile of the hippocampus following trace fear conditioning.

Sirri A, Bianchi V, Pelizzola M, Mayhaus M, Ricciardi-Castagnoli P, Toniolo D, D'Adamo P.

Brain Res. 2010 Jan 13;1308:14-23. doi: 10.1016/j.brainres.2009.10.049. Epub 2009 Oct 24.

PMID:
19857472
39.

Human DNA methylomes at base resolution show widespread epigenomic differences.

Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, Nery JR, Lee L, Ye Z, Ngo QM, Edsall L, Antosiewicz-Bourget J, Stewart R, Ruotti V, Millar AH, Thomson JA, Ren B, Ecker JR.

Nature. 2009 Nov 19;462(7271):315-22. doi: 10.1038/nature08514. Epub 2009 Oct 14.

40.

Genome-wide screen of promoter methylation identifies novel markers in melanoma.

Koga Y, Pelizzola M, Cheng E, Krauthammer M, Sznol M, Ariyan S, Narayan D, Molinaro AM, Halaban R, Weissman SM.

Genome Res. 2009 Aug;19(8):1462-70. doi: 10.1101/gr.091447.109. Epub 2009 Jun 2.

41.

Integrative analysis of epigenetic modulation in melanoma cell response to decitabine: clinical implications.

Halaban R, Krauthammer M, Pelizzola M, Cheng E, Kovacs D, Sznol M, Ariyan S, Narayan D, Bacchiocchi A, Molinaro A, Kluger Y, Deng M, Tran N, Zhang W, Picardo M, Enghild JJ.

PLoS One. 2009;4(2):e4563. doi: 10.1371/journal.pone.0004563. Epub 2009 Feb 23.

42.

MEDME: an experimental and analytical methodology for the estimation of DNA methylation levels based on microarray derived MeDIP-enrichment.

Pelizzola M, Koga Y, Urban AE, Krauthammer M, Weissman S, Halaban R, Molinaro AM.

Genome Res. 2008 Oct;18(10):1652-9. doi: 10.1101/gr.080721.108. Epub 2008 Sep 2.

43.

Probing host pathogen cross-talk by transcriptional profiling of both Mycobacterium tuberculosis and infected human dendritic cells and macrophages.

Tailleux L, Waddell SJ, Pelizzola M, Mortellaro A, Withers M, Tanne A, Castagnoli PR, Gicquel B, Stoker NG, Butcher PD, Foti M, Neyrolles O.

PLoS One. 2008 Jan 2;3(1):e1403. doi: 10.1371/journal.pone.0001403.

44.

Statistical similarities between transcriptomics and quantitative shotgun proteomics data.

Pavelka N, Fournier ML, Swanson SK, Pelizzola M, Ricciardi-Castagnoli P, Florens L, Washburn MP.

Mol Cell Proteomics. 2008 Apr;7(4):631-44. Epub 2007 Nov 19.

45.

The genopolis microarray database.

Splendiani A, Brandizi M, Even G, Beretta O, Pavelka N, Pelizzola M, Mayhaus M, Foti M, Mauri G, Ricciardi-Castagnoli P.

BMC Bioinformatics. 2007 Mar 8;8 Suppl 1:S21.

46.

AMDA: an R package for the automated microarray data analysis.

Pelizzola M, Pavelka N, Foti M, Ricciardi-Castagnoli P.

BMC Bioinformatics. 2006 Jul 6;7:335.

47.

Effects of dexamethazone on LPS-induced activationand migration of mouse dendritic cells revealed by a genome-wide transcriptional analysis.

Vizzardelli C, Pavelka N, Luchini A, Zanoni I, Bendickson L, Pelizzola M, Beretta O, Foti M, Granucci F, Nilsen-Hamilton M, Ricciardi-Castagnoli P.

Eur J Immunol. 2006 Jun;36(6):1504-15.

48.

Dendritic cells in pathogen recognition and induction of immune responses: a functional genomics approach.

Foti M, Granucci F, Pelizzola M, Beretta O, Ricciardi-Castagnoli P.

J Leukoc Biol. 2006 May;79(5):913-6. Review.

PMID:
16641136
49.

A critical role for lipophosphoglycan in proinflammatory responses of dendritic cells to Leishmania mexicana.

Aebischer T, Bennett CL, Pelizzola M, Vizzardelli C, Pavelka N, Urbano M, Capozzoli M, Luchini A, Ilg T, Granucci F, Blackburn CC, Ricciardi-Castagnoli P.

Eur J Immunol. 2005 Feb;35(2):476-86.

50.

A power law global error model for the identification of differentially expressed genes in microarray data.

Pavelka N, Pelizzola M, Vizzardelli C, Capozzoli M, Splendiani A, Granucci F, Ricciardi-Castagnoli P.

BMC Bioinformatics. 2004 Dec 17;5:203.

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