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Items: 1 to 50 of 72

1.

hSWATH: Unlocking SWATH's full potential for an untargeted histone perspective.

De Clerck L, Willems S, Noberini R, Restellini C, Van Puyvelde B, Daled S, Bonaldi T, Deforce D, Dhaenens M.

J Proteome Res. 2019 Aug 20. doi: 10.1021/acs.jproteome.9b00214. [Epub ahead of print]

PMID:
31429292
2.

Therapeutic Targeting of RNA Splicing Catalysis through Inhibition of Protein Arginine Methylation.

Fong JY, Pignata L, Goy PA, Kawabata KC, Lee SC, Koh CM, Musiani D, Massignani E, Kotini AG, Penson A, Wun CM, Shen Y, Schwarz M, Low DH, Rialdi A, Ki M, Wollmann H, Mzoughi S, Gay F, Thompson C, Hart T, Barbash O, Luciani GM, Szewczyk MM, Wouters BJ, Delwel R, Papapetrou EP, Barsyte-Lovejoy D, Arrowsmith CH, Minden MD, Jin J, Melnick A, Bonaldi T, Abdel-Wahab O, Guccione E.

Cancer Cell. 2019 Aug 12;36(2):194-209.e9. doi: 10.1016/j.ccell.2019.07.003.

PMID:
31408619
3.

Profiling of Epigenetic Features in Clinical Samples Reveals Novel Widespread Changes in Cancer.

Noberini R, Restellini C, Savoia EO, Raimondi F, Ghiani L, Jodice MG, Bertalot G, Bonizzi G, Capra M, Maffini FA, Tagliabue M, Ansarin M, Lupia M, Giordano M, Osti D, Pelicci G, Chiocca S, Bonaldi T.

Cancers (Basel). 2019 May 24;11(5). pii: E723. doi: 10.3390/cancers11050723.

4.

Functional Landscape of PCGF Proteins Reveals Both RING1A/B-Dependent-and RING1A/B-Independent-Specific Activities.

Scelfo A, Fernández-Pérez D, Tamburri S, Zanotti M, Lavarone E, Soldi M, Bonaldi T, Ferrari KJ, Pasini D.

Mol Cell. 2019 Jun 6;74(5):1037-1052.e7. doi: 10.1016/j.molcel.2019.04.002. Epub 2019 Apr 24.

5.

Proteomics profiling of arginine methylation defines PRMT5 substrate specificity.

Musiani D, Bok J, Massignani E, Wu L, Tabaglio T, Ippolito MR, Cuomo A, Ozbek U, Zorgati H, Ghoshdastider U, Robinson RC, Guccione E, Bonaldi T.

Sci Signal. 2019 Apr 2;12(575). pii: eaat8388. doi: 10.1126/scisignal.aat8388.

PMID:
30940768
6.

hmSEEKER: Identification of hmSILAC Doublets in MaxQuant Output Data.

Massignani E, Cuomo A, Musiani D, Jammula S, Pavesi G, Bonaldi T.

Proteomics. 2019 Mar;19(5):e1800300. doi: 10.1002/pmic.201800300. Epub 2019 Feb 18.

7.

Alternative digestion approaches improve histone modification mapping by mass spectrometry in clinical samples.

Restellini C, Cuomo A, Lupia M, Giordano M, Bonaldi T, Noberini R.

Proteomics Clin Appl. 2019 Jan;13(1):e1700166. doi: 10.1002/prca.201700166. Epub 2018 Dec 6.

PMID:
30471193
8.

Mass Spectrometry-Based Proteomics to Unveil the Non-coding RNA World.

Giambruno R, Mihailovich M, Bonaldi T.

Front Mol Biosci. 2018 Nov 8;5:90. doi: 10.3389/fmolb.2018.00090. eCollection 2018. Review.

9.

The kinetochore module Okp1CENP-Q/Ame1CENP-U is a reader for N-terminal modifications on the centromeric histone Cse4CENP-A.

Anedchenko EA, Samel-Pommerencke A, Tran Nguyen TM, Shahnejat-Bushehri S, Pöpsel J, Lauster D, Herrmann A, Rappsilber J, Cuomo A, Bonaldi T, Ehrenhofer-Murray AE.

EMBO J. 2019 Jan 3;38(1). pii: e98991. doi: 10.15252/embj.201898991. Epub 2018 Nov 2.

PMID:
30389668
10.

Extensive and systematic rewiring of histone post-translational modifications in cancer model systems.

Noberini R, Osti D, Miccolo C, Richichi C, Lupia M, Corleone G, Hong SP, Colombo P, Pollo B, Fornasari L, Pruneri G, Magnani L, Cavallaro U, Chiocca S, Minucci S, Pelicci G, Bonaldi T.

Nucleic Acids Res. 2018 May 4;46(8):3817-3832. doi: 10.1093/nar/gky224.

11.

Zc3h10 is a novel mitochondrial regulator.

Audano M, Pedretti S, Cermenati G, Brioschi E, Diaferia GR, Ghisletti S, Cuomo A, Bonaldi T, Salerno F, Mora M, Grigore L, Garlaschelli K, Baragetti A, Bonacina F, Catapano AL, Norata GD, Crestani M, Caruso D, Saez E, De Fabiani E, Mitro N.

EMBO Rep. 2018 Apr;19(4). pii: e45531. doi: 10.15252/embr.201745531. Epub 2018 Mar 5.

12.

PARP14 Controls the Nuclear Accumulation of a Subset of Type I IFN-Inducible Proteins.

Caprara G, Prosperini E, Piccolo V, Sigismondo G, Melacarne A, Cuomo A, Boothby M, Rescigno M, Bonaldi T, Natoli G.

J Immunol. 2018 Apr 1;200(7):2439-2454. doi: 10.4049/jimmunol.1701117. Epub 2018 Mar 2.

13.

Microbiota derived short chain fatty acids promote histone crotonylation in the colon through histone deacetylases.

Fellows R, Denizot J, Stellato C, Cuomo A, Jain P, Stoyanova E, Balázsi S, Hajnády Z, Liebert A, Kazakevych J, Blackburn H, Corrêa RO, Fachi JL, Sato FT, Ribeiro WR, Ferreira CM, Perée H, Spagnuolo M, Mattiuz R, Matolcsi C, Guedes J, Clark J, Veldhoen M, Bonaldi T, Vinolo MAR, Varga-Weisz P.

Nat Commun. 2018 Jan 9;9(1):105. doi: 10.1038/s41467-017-02651-5.

14.

A role for CENP-A/Cse4 phosphorylation on serine 33 in deposition at the centromere.

Hoffmann G, Samel-Pommerencke A, Weber J, Cuomo A, Bonaldi T, Ehrenhofer-Murray AE.

FEMS Yeast Res. 2018 Feb 1;18(1). doi: 10.1093/femsyr/fox094.

PMID:
29272409
15.

Chromatin proteomics reveals novel combinatorial histone modification signatures that mark distinct subpopulations of macrophage enhancers.

Soldi M, Mari T, Nicosia L, Musiani D, Sigismondo G, Cuomo A, Pavesi G, Bonaldi T.

Nucleic Acids Res. 2017 Dec 1;45(21):12195-12213. doi: 10.1093/nar/gkx821.

16.

Design of KDM4 Inhibitors with Antiproliferative Effects in Cancer Models.

Chen YK, Bonaldi T, Cuomo A, Del Rosario JR, Hosfield DJ, Kanouni T, Kao SC, Lai C, Lobo NA, Matuszkiewicz J, McGeehan A, O'Connell SM, Shi L, Stafford JA, Stansfield RK, Veal JM, Weiss MS, Yuen NY, Wallace MB.

ACS Med Chem Lett. 2017 Jul 27;8(8):869-874. doi: 10.1021/acsmedchemlett.7b00220. eCollection 2017 Aug 10.

17.

PAT-H-MS coupled with laser microdissection to study histone post-translational modifications in selected cell populations from pathology samples.

Noberini R, Longuespée R, Richichi C, Pruneri G, Kriegsmann M, Pelicci G, Bonaldi T.

Clin Epigenetics. 2017 Jul 11;9:69. doi: 10.1186/s13148-017-0369-8. eCollection 2017.

18.

Reticulon 3-dependent ER-PM contact sites control EGFR nonclathrin endocytosis.

Caldieri G, Barbieri E, Nappo G, Raimondi A, Bonora M, Conte A, Verhoef LGGC, Confalonieri S, Malabarba MG, Bianchi F, Cuomo A, Bonaldi T, Martini E, Mazza D, Pinton P, Tacchetti C, Polo S, Di Fiore PP, Sigismund S.

Science. 2017 May 12;356(6338):617-624. doi: 10.1126/science.aah6152.

19.

High constitutive activity of a broad panel of housekeeping and tissue-specific cis-regulatory elements depends on a subset of ETS proteins.

Curina A, Termanini A, Barozzi I, Prosperini E, Simonatto M, Polletti S, Silvola A, Soldi M, Austenaa L, Bonaldi T, Ghisletti S, Natoli G.

Genes Dev. 2017 Feb 15;31(4):399-412. doi: 10.1101/gad.293134.116. Epub 2017 Mar 8.

20.

A Super-SILAC Strategy for the Accurate and Multiplexed Profiling of Histone Posttranslational Modifications.

Noberini R, Bonaldi T.

Methods Enzymol. 2017;586:311-332. doi: 10.1016/bs.mie.2016.09.036. Epub 2016 Nov 8.

PMID:
28137569
21.
22.

Mass-spectrometry analysis of histone post-translational modifications in pathology tissue using the PAT-H-MS approach.

Noberini R, Pruneri G, Minucci S, Bonaldi T.

Data Brief. 2016 Feb 16;7:188-94. doi: 10.1016/j.dib.2016.02.028. eCollection 2016 Jun.

23.

Quantitative assessment of chemical artefacts produced by propionylation of histones prior to mass spectrometry analysis.

Soldi M, Cuomo A, Bonaldi T.

Proteomics. 2016 Jul;16(14):1952-4. doi: 10.1002/pmic.201600173.

PMID:
27373704
24.

Spatiotemporal plasticity of miRNAs functions: The miR-17-92 case.

Bonaldi T, Mihailovich M.

Mol Cell Oncol. 2016 Apr 15;3(3):e1156216. doi: 10.1080/23723556.2016.1156216. eCollection 2016 May.

25.

The EGFR-specific antibody cetuximab combined with chemotherapy triggers immunogenic cell death.

Pozzi C, Cuomo A, Spadoni I, Magni E, Silvola A, Conte A, Sigismund S, Ravenda PS, Bonaldi T, Zampino MG, Cancelliere C, Di Fiore PP, Bardelli A, Penna G, Rescigno M.

Nat Med. 2016 Jun;22(6):624-31. doi: 10.1038/nm.4078. Epub 2016 May 2.

PMID:
27135741
26.

MYC/miR-17-92 interplay maintains B-lymphoma cell homeostasis.

Mihailovich M, Bonaldi T.

Cell Cycle. 2016;15(8):1025-6. doi: 10.1080/15384101.2016.1157977. No abstract available.

27.

MS-analysis of SILAC-labeled MYC-driven B lymphoma cells overexpressing miR-17-19b.

Mihailovich M, Bonaldi T.

Data Brief. 2016 Feb 24;7:349-53. doi: 10.1016/j.dib.2016.02.031. eCollection 2016 Jun.

28.

Recent advances in mass spectrometry analysis of histone post-translational modifications: potential clinical impact of the PAT-H-MS approach.

Bonaldi T, Noberini R.

Expert Rev Proteomics. 2016;13(3):245-50. doi: 10.1586/14789450.2016.1147960. Epub 2016 Feb 18. Review.

PMID:
26822344
29.

The contribution of mass spectrometry-based proteomics to understanding epigenetics.

Noberini R, Sigismondo G, Bonaldi T.

Epigenomics. 2016 Mar;8(3):429-45. doi: 10.2217/epi.15.108. Epub 2015 Nov 25. Review.

30.

miR-17-92 fine-tunes MYC expression and function to ensure optimal B cell lymphoma growth.

Mihailovich M, Bremang M, Spadotto V, Musiani D, Vitale E, Varano G, Zambelli F, Mancuso FM, Cairns DA, Pavesi G, Casola S, Bonaldi T.

Nat Commun. 2015 Nov 10;6:8725. doi: 10.1038/ncomms9725.

31.

Pathology Tissue-quantitative Mass Spectrometry Analysis to Profile Histone Post-translational Modification Patterns in Patient Samples.

Noberini R, Uggetti A, Pruneri G, Minucci S, Bonaldi T.

Mol Cell Proteomics. 2016 Mar;15(3):866-77. doi: 10.1074/mcp.M115.054510. Epub 2015 Oct 13.

32.

Extracellular vesicle-mediated transfer of CLIC1 protein is a novel mechanism for the regulation of glioblastoma growth.

Setti M, Osti D, Richichi C, Ortensi B, Del Bene M, Fornasari L, Beznoussenko G, Mironov A, Rappa G, Cuomo A, Faretta M, Bonaldi T, Lorico A, Pelicci G.

Oncotarget. 2015 Oct 13;6(31):31413-27. doi: 10.18632/oncotarget.5105.

33.

ARGONAUTE2 cooperates with SWI/SNF complex to determine nucleosome occupancy at human Transcription Start Sites.

Carissimi C, Laudadio I, Cipolletta E, Gioiosa S, Mihailovich M, Bonaldi T, Macino G, Fulci V.

Nucleic Acids Res. 2015 Feb 18;43(3):1498-512. doi: 10.1093/nar/gku1387. Epub 2015 Jan 20.

34.

DEPDC1B coordinates de-adhesion events and cell-cycle progression at mitosis.

Marchesi S, Montani F, Deflorian G, D'Antuono R, Cuomo A, Bologna S, Mazzoccoli C, Bonaldi T, Di Fiore PP, Nicassio F.

Dev Cell. 2014 Nov 24;31(4):420-33. doi: 10.1016/j.devcel.2014.09.009. Epub 2014 Nov 24.

35.

Improved bottom-up strategy to efficiently separate hypermodified histone peptides through ultra-HPLC separation on a bench top Orbitrap instrument.

Soldi M, Cuomo A, Bonaldi T.

Proteomics. 2014 Oct;14(19):2212-25. doi: 10.1002/pmic.201400075. Epub 2014 Aug 28.

PMID:
25073962
36.

Proteomics meets genetics: SILAC labeling of Drosophila melanogaster larvae and cells for in vivo functional studies.

Cuomo A, Sanfilippo R, Vaccari T, Bonaldi T.

Methods Mol Biol. 2014;1188:293-311. doi: 10.1007/978-1-4939-1142-4_21.

PMID:
25059620
37.
38.

Quantitative chemical proteomics identifies novel targets of the anti-cancer multi-kinase inhibitor E-3810.

Colzani M, Noberini R, Romanenghi M, Colella G, Pasi M, Fancelli D, Varasi M, Minucci S, Bonaldi T.

Mol Cell Proteomics. 2014 Jun;13(6):1495-509. doi: 10.1074/mcp.M113.034173. Epub 2014 Apr 2.

39.

Biochemical systems approaches for the analysis of histone modification readout.

Soldi M, Bremang M, Bonaldi T.

Biochim Biophys Acta. 2014 Aug;1839(8):657-68. doi: 10.1016/j.bbagrm.2014.03.008. Epub 2014 Mar 27. Review.

40.

Polycomb-dependent H3K27me1 and H3K27me2 regulate active transcription and enhancer fidelity.

Ferrari KJ, Scelfo A, Jammula S, Cuomo A, Barozzi I, Stützer A, Fischle W, Bonaldi T, Pasini D.

Mol Cell. 2014 Jan 9;53(1):49-62. doi: 10.1016/j.molcel.2013.10.030. Epub 2013 Nov 27.

41.

Threshold-controlled ubiquitination of the EGFR directs receptor fate.

Sigismund S, Algisi V, Nappo G, Conte A, Pascolutti R, Cuomo A, Bonaldi T, Argenzio E, Verhoef LG, Maspero E, Bianchi F, Capuani F, Ciliberto A, Polo S, Di Fiore PP.

EMBO J. 2013 Jul 31;32(15):2140-57. doi: 10.1038/emboj.2013.149. Epub 2013 Jun 25.

42.

Mass spectrometry-based identification and characterisation of lysine and arginine methylation in the human proteome.

Bremang M, Cuomo A, Agresta AM, Stugiewicz M, Spadotto V, Bonaldi T.

Mol Biosyst. 2013 Sep;9(9):2231-47. doi: 10.1039/c3mb00009e.

PMID:
23748837
43.

Cell reprogramming requires silencing of a core subset of polycomb targets.

Fragola G, Germain PL, Laise P, Cuomo A, Blasimme A, Gross F, Signaroldi E, Bucci G, Sommer C, Pruneri G, Mazzarol G, Bonaldi T, Mostoslavsky G, Casola S, Testa G.

PLoS Genet. 2013;9(2):e1003292. doi: 10.1371/journal.pgen.1003292. Epub 2013 Feb 28.

44.

Mass spectrometry-based proteomics for the analysis of chromatin structure and dynamics.

Soldi M, Cuomo A, Bremang M, Bonaldi T.

Int J Mol Sci. 2013 Mar 6;14(3):5402-31. doi: 10.3390/ijms14035402.

45.

Reply to "Chaetocin is a nonspecific inhibitor of histone lysine methyltransferases".

Greiner D, Bonaldi T, Eskeland R, Roemer E, Imhof A.

Nat Chem Biol. 2013 Mar;9(3):137. doi: 10.1038/nchembio.1188. No abstract available.

PMID:
23416388
46.

Tet proteins connect the O-linked N-acetylglucosamine transferase Ogt to chromatin in embryonic stem cells.

Vella P, Scelfo A, Jammula S, Chiacchiera F, Williams K, Cuomo A, Roberto A, Christensen J, Bonaldi T, Helin K, Pasini D.

Mol Cell. 2013 Feb 21;49(4):645-56. doi: 10.1016/j.molcel.2012.12.019. Epub 2013 Jan 24.

47.

The proteomic investigation of chromatin functional domains reveals novel synergisms among distinct heterochromatin components.

Soldi M, Bonaldi T.

Mol Cell Proteomics. 2013 Mar;12(3):764-80. doi: 10.1074/mcp.M112.024307. Epub 2013 Jan 14.

48.

Methylation of CenH3 arginine 37 regulates kinetochore integrity and chromosome segregation.

Samel A, Cuomo A, Bonaldi T, Ehrenhofer-Murray AE.

Proc Natl Acad Sci U S A. 2012 Jun 5;109(23):9029-34. doi: 10.1073/pnas.1120968109. Epub 2012 May 21.

49.

Yin Yang 1 extends the Myc-related transcription factors network in embryonic stem cells.

Vella P, Barozzi I, Cuomo A, Bonaldi T, Pasini D.

Nucleic Acids Res. 2012 Apr;40(8):3403-18. doi: 10.1093/nar/gkr1290. Epub 2011 Dec 30.

50.

Substantial histone reduction modulates genomewide nucleosomal occupancy and global transcriptional output.

Celona B, Weiner A, Di Felice F, Mancuso FM, Cesarini E, Rossi RL, Gregory L, Baban D, Rossetti G, Grianti P, Pagani M, Bonaldi T, Ragoussis J, Friedman N, Camilloni G, Bianchi ME, Agresti A.

PLoS Biol. 2011 Jun;9(6):e1001086. doi: 10.1371/journal.pbio.1001086. Epub 2011 Jun 28.

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