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Items: 37

1.

Chromatin-Based Classification of Genetically Heterogeneous AMLs into Two Distinct Subtypes with Diverse Stemness Phenotypes.

Yi G, Wierenga ATJ, Petraglia F, Narang P, Janssen-Megens EM, Mandoli A, Merkel A, Berentsen K, Kim B, Matarese F, Singh AA, Habibi E, Prange KHM, Mulder AB, Jansen JH, Clarke L, Heath S, van der Reijden BA, Flicek P, Yaspo ML, Gut I, Bock C, Schuringa JJ, Altucci L, Vellenga E, Stunnenberg HG, Martens JHA.

Cell Rep. 2019 Jan 22;26(4):1059-1069.e6. doi: 10.1016/j.celrep.2018.12.098.

2.

miR-194-5p/BCLAF1 deregulation in AML tumorigenesis.

Dell'Aversana C, Giorgio C, D'Amato L, Lania G, Matarese F, Saeed S, Di Costanzo A, Belsito Petrizzi V, Ingenito C, Martens JHA, Pallavicini I, Minucci S, Carissimo A, Stunnenberg HG, Altucci L.

Leukemia. 2018 Feb;32(2):573. doi: 10.1038/leu.2017.310. Epub 2017 Dec 22.

PMID:
29271969
3.

Effect of methyl jasmonate on the aroma of Sangiovese grapes and wines.

D'Onofrio C, Matarese F, Cuzzola A.

Food Chem. 2018 Mar 1;242:352-361. doi: 10.1016/j.foodchem.2017.09.084. Epub 2017 Sep 18.

PMID:
29037700
4.

Predicting stimulation-dependent enhancer-promoter interactions from ChIP-Seq time course data.

Dzida T, Iqbal M, Charapitsa I, Reid G, Stunnenberg H, Matarese F, Grote K, Honkela A, Rattray M.

PeerJ. 2017 Sep 28;5:e3742. doi: 10.7717/peerj.3742. eCollection 2017.

5.

Time-resolved analysis of DNA-protein interactions in living cells by UV laser pulses.

Nebbioso A, Benedetti R, Conte M, Carafa V, De Bellis F, Shaik J, Matarese F, Della Ventura B, Gesuele F, Velotta R, Martens JHA, Stunnenberg HG, Altucci C, Altucci L.

Sci Rep. 2017 Sep 15;7(1):11725. doi: 10.1038/s41598-017-12010-5.

6.

miR-194-5p/BCLAF1 deregulation in AML tumorigenesis.

Dell'Aversana C, Giorgio C, D'Amato L, Lania G, Matarese F, Saeed S, Di Costanzo A, Belsito Petrizzi V, Ingenito C, Martens JHA, Pallavicini I, Minucci S, Carissimo A, Stunnenberg HG, Altucci L.

Leukemia. 2017 Nov;31(11):2315-2325. doi: 10.1038/leu.2017.64. Epub 2017 Feb 20. Erratum in: Leukemia. 2017 Dec 22;:.

7.

The Constitutive Endopolygalacturonase TvPG2 Regulates the Induction of Plant Systemic Resistance by Trichoderma virens.

Sarrocco S, Matarese F, Baroncelli R, Vannacci G, Seidl-Seiboth V, Kubicek CP, Vergara M.

Phytopathology. 2017 May;107(5):537-544. doi: 10.1094/PHYTO-03-16-0139-R. Epub 2017 Mar 20.

8.

Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells.

Chen L, Ge B, Casale FP, Vasquez L, Kwan T, Garrido-Martín D, Watt S, Yan Y, Kundu K, Ecker S, Datta A, Richardson D, Burden F, Mead D, Mann AL, Fernandez JM, Rowlston S, Wilder SP, Farrow S, Shao X, Lambourne JJ, Redensek A, Albers CA, Amstislavskiy V, Ashford S, Berentsen K, Bomba L, Bourque G, Bujold D, Busche S, Caron M, Chen SH, Cheung W, Delaneau O, Dermitzakis ET, Elding H, Colgiu I, Bagger FO, Flicek P, Habibi E, Iotchkova V, Janssen-Megens E, Kim B, Lehrach H, Lowy E, Mandoli A, Matarese F, Maurano MT, Morris JA, Pancaldi V, Pourfarzad F, Rehnstrom K, Rendon A, Risch T, Sharifi N, Simon MM, Sultan M, Valencia A, Walter K, Wang SY, Frontini M, Antonarakis SE, Clarke L, Yaspo ML, Beck S, Guigo R, Rico D, Martens JHA, Ouwehand WH, Kuijpers TW, Paul DS, Stunnenberg HG, Stegle O, Downes K, Pastinen T, Soranzo N.

Cell. 2016 Nov 17;167(5):1398-1414.e24. doi: 10.1016/j.cell.2016.10.026.

9.

β-Glucan Reverses the Epigenetic State of LPS-Induced Immunological Tolerance.

Novakovic B, Habibi E, Wang SY, Arts RJW, Davar R, Megchelenbrink W, Kim B, Kuznetsova T, Kox M, Zwaag J, Matarese F, van Heeringen SJ, Janssen-Megens EM, Sharifi N, Wang C, Keramati F, Schoonenberg V, Flicek P, Clarke L, Pickkers P, Heath S, Gut I, Netea MG, Martens JHA, Logie C, Stunnenberg HG.

Cell. 2016 Nov 17;167(5):1354-1368.e14. doi: 10.1016/j.cell.2016.09.034.

10.

eFORGE: A Tool for Identifying Cell Type-Specific Signal in Epigenomic Data.

Breeze CE, Paul DS, van Dongen J, Butcher LM, Ambrose JC, Barrett JE, Lowe R, Rakyan VK, Iotchkova V, Frontini M, Downes K, Ouwehand WH, Laperle J, Jacques PÉ, Bourque G, Bergmann AK, Siebert R, Vellenga E, Saeed S, Matarese F, Martens JHA, Stunnenberg HG, Teschendorff AE, Herrero J, Birney E, Dunham I, Beck S.

Cell Rep. 2016 Nov 15;17(8):2137-2150. doi: 10.1016/j.celrep.2016.10.059.

11.

The Hematopoietic Transcription Factors RUNX1 and ERG Prevent AML1-ETO Oncogene Overexpression and Onset of the Apoptosis Program in t(8;21) AMLs.

Mandoli A, Singh AA, Prange KHM, Tijchon E, Oerlemans M, Dirks R, Ter Huurne M, Wierenga ATJ, Janssen-Megens EM, Berentsen K, Sharifi N, Kim B, Matarese F, Nguyen LN, Hubner NC, Rao NA, van den Akker E, Altucci L, Vellenga E, Stunnenberg HG, Martens JHA.

Cell Rep. 2016 Nov 15;17(8):2087-2100. doi: 10.1016/j.celrep.2016.08.082.

12.

Study of the terpene profile at harvest and during berry development of Vitis vinifera L. aromatic varieties Aleatico, Brachetto, Malvasia di Candia aromatica and Moscato bianco.

D'Onofrio C, Matarese F, Cuzzola A.

J Sci Food Agric. 2017 Jul;97(9):2898-2907. doi: 10.1002/jsfa.8126. Epub 2016 Nov 28.

PMID:
27801497
13.

Distinct transcriptome responses to water limitation in isohydric and anisohydric grapevine cultivars.

Dal Santo S, Palliotti A, Zenoni S, Tornielli GB, Fasoli M, Paci P, Tombesi S, Frioni T, Silvestroni O, Bellincontro A, d'Onofrio C, Matarese F, Gatti M, Poni S, Pezzotti M.

BMC Genomics. 2016 Oct 20;17(1):815.

14.

Influence of vineyard altitude on Glera grape ripening (Vitis vinifera L.): effects on aroma evolution and wine sensory profile.

Alessandrini M, Gaiotti F, Belfiore N, Matarese F, D'Onofrio C, Tomasi D.

J Sci Food Agric. 2017 Jul;97(9):2695-2705. doi: 10.1002/jsfa.8093. Epub 2016 Nov 21.

PMID:
27747897
15.

ZMYND8 Co-localizes with NuRD on Target Genes and Regulates Poly(ADP-Ribose)-Dependent Recruitment of GATAD2A/NuRD to Sites of DNA Damage.

Spruijt CG, Luijsterburg MS, Menafra R, Lindeboom RG, Jansen PW, Edupuganti RR, Baltissen MP, Wiegant WW, Voelker-Albert MC, Matarese F, Mensinga A, Poser I, Vos HR, Stunnenberg HG, van Attikum H, Vermeulen M.

Cell Rep. 2016 Oct 11;17(3):783-798. doi: 10.1016/j.celrep.2016.09.037.

16.

Management of postharvest grape withering to optimise the aroma of the final wine: A case study on Amarone.

Bellincontro A, Matarese F, D'Onofrio C, Accordini D, Tosi E, Mencarelli F.

Food Chem. 2016 Dec 15;213:378-387. doi: 10.1016/j.foodchem.2016.06.098. Epub 2016 Jun 29.

PMID:
27451194
17.

Recruitment of the Mammalian Histone-modifying EMSY Complex to Target Genes Is Regulated by ZNF131.

Varier RA, Carrillo de Santa Pau E, van der Groep P, Lindeboom RG, Matarese F, Mensinga A, Smits AH, Edupuganti RR, Baltissen MP, Jansen PW, Ter Hoeve N, van Weely DR, Poser I, van Diest PJ, Stunnenberg HG, Vermeulen M.

J Biol Chem. 2016 Apr 1;291(14):7313-24. doi: 10.1074/jbc.M115.701227. Epub 2016 Feb 3.

18.

Genome-wide modeling of transcription kinetics reveals patterns of RNA production delays.

Honkela A, Peltonen J, Topa H, Charapitsa I, Matarese F, Grote K, Stunnenberg HG, Reid G, Lawrence ND, Rattray M.

Proc Natl Acad Sci U S A. 2015 Oct 20;112(42):13115-20. doi: 10.1073/pnas.1420404112. Epub 2015 Oct 5.

19.

Physiological parameters and protective energy dissipation mechanisms expressed in the leaves of two Vitis vinifera L. genotypes under multiple summer stresses.

Palliotti A, Tombesi S, Frioni T, Silvestroni O, Lanari V, D'Onofrio C, Matarese F, Bellincontro A, Poni S.

J Plant Physiol. 2015 Aug 1;185:84-92. doi: 10.1016/j.jplph.2015.07.007. Epub 2015 Jul 31.

PMID:
26310367
20.

Epigenetic programming of monocyte-to-macrophage differentiation and trained innate immunity.

Saeed S, Quintin J, Kerstens HH, Rao NA, Aghajanirefah A, Matarese F, Cheng SC, Ratter J, Berentsen K, van der Ent MA, Sharifi N, Janssen-Megens EM, Ter Huurne M, Mandoli A, van Schaik T, Ng A, Burden F, Downes K, Frontini M, Kumar V, Giamarellos-Bourboulis EJ, Ouwehand WH, van der Meer JW, Joosten LA, Wijmenga C, Martens JH, Xavier RJ, Logie C, Netea MG, Stunnenberg HG.

Science. 2014 Sep 26;345(6204):1251086. doi: 10.1126/science.1251086.

21.

Expression of terpene synthase genes associated with the formation of volatiles in different organs of Vitis vinifera.

Matarese F, Cuzzola A, Scalabrelli G, D'Onofrio C.

Phytochemistry. 2014 Sep;105:12-24. doi: 10.1016/j.phytochem.2014.06.007. Epub 2014 Jul 7.

PMID:
25014656
22.

Genome-wide binding of MBD2 reveals strong preference for highly methylated loci.

Menafra R, Brinkman AB, Matarese F, Franci G, Bartels SJ, Nguyen L, Shimbo T, Wade PA, Hubner NC, Stunnenberg HG.

PLoS One. 2014 Jun 13;9(6):e99603. doi: 10.1371/journal.pone.0099603. eCollection 2014.

23.

Inference of RNA polymerase II transcription dynamics from chromatin immunoprecipitation time course data.

wa Maina C, Honkela A, Matarese F, Grote K, Stunnenberg HG, Reid G, Lawrence ND, Rattray M.

PLoS Comput Biol. 2014 May 15;10(5):e1003598. doi: 10.1371/journal.pcbi.1003598. eCollection 2014 May.

24.

Context-selective death of acute myeloid leukemia cells triggered by the novel hybrid retinoid-HDAC inhibitor MC2392.

De Bellis F, Carafa V, Conte M, Rotili D, Petraglia F, Matarese F, Françoijs KJ, Ablain J, Valente S, Castellano R, Goubard A, Collette Y, Mandoli A, Martens JH, de Thé H, Nebbioso A, Mai A, Stunnenberg HG, Altucci L.

Cancer Res. 2014 Apr 15;74(8):2328-39. doi: 10.1158/0008-5472.CAN-13-2568. Epub 2014 Feb 24.

25.

Dnmt3L antagonizes DNA methylation at bivalent promoters and favors DNA methylation at gene bodies in ESCs.

Neri F, Krepelova A, Incarnato D, Maldotti M, Parlato C, Galvagni F, Matarese F, Stunnenberg HG, Oliviero S.

Cell. 2013 Sep 26;155(1):121-34. doi: 10.1016/j.cell.2013.08.056.

26.

Whole-genome bisulfite sequencing of two distinct interconvertible DNA methylomes of mouse embryonic stem cells.

Habibi E, Brinkman AB, Arand J, Kroeze LI, Kerstens HH, Matarese F, Lepikhov K, Gut M, Brun-Heath I, Hubner NC, Benedetti R, Altucci L, Jansen JH, Walter J, Gut IG, Marks H, Stunnenberg HG.

Cell Stem Cell. 2013 Sep 5;13(3):360-9. doi: 10.1016/j.stem.2013.06.002. Epub 2013 Jul 11.

27.

Integrative analysis of deep sequencing data identifies estrogen receptor early response genes and links ATAD3B to poor survival in breast cancer.

Ovaska K, Matarese F, Grote K, Charapitsa I, Cervera A, Liu C, Reid G, Seifert M, Stunnenberg HG, Hautaniemi S.

PLoS Comput Biol. 2013;9(6):e1003100. doi: 10.1371/journal.pcbi.1003100. Epub 2013 Jun 20.

28.

Comparative genome-wide DNA methylation analysis of colorectal tumor and matched normal tissues.

Simmer F, Brinkman AB, Assenov Y, Matarese F, Kaan A, Sabatino L, Villanueva A, Huertas D, Esteller M, Lengauer T, Bock C, Colantuoni V, Altucci L, Stunnenberg HG.

Epigenetics. 2012 Dec 1;7(12):1355-67. doi: 10.4161/epi.22562. Epub 2012 Oct 18.

29.

Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk.

Brinkman AB, Gu H, Bartels SJ, Zhang Y, Matarese F, Simmer F, Marks H, Bock C, Gnirke A, Meissner A, Stunnenberg HG.

Genome Res. 2012 Jun;22(6):1128-38. doi: 10.1101/gr.133728.111. Epub 2012 Mar 30.

30.

5-Hydroxymethylcytosine: a new kid on the epigenetic block?

Matarese F, Carrillo-de Santa Pau E, Stunnenberg HG.

Mol Syst Biol. 2011 Dec 20;7:562. doi: 10.1038/msb.2011.95.

31.

Death receptor pathway activation and increase of ROS production by the triple epigenetic inhibitor UVI5008.

Nebbioso A, Pereira R, Khanwalkar H, Matarese F, García-Rodríguez J, Miceli M, Logie C, Kedinger V, Ferrara F, Stunnenberg HG, de Lera AR, Gronemeyer H, Altucci L.

Mol Cancer Ther. 2011 Dec;10(12):2394-404. doi: 10.1158/1535-7163.MCT-11-0525. Epub 2011 Oct 6.

32.

Biocontrol of Fusarium head blight: interactions between Trichoderma and mycotoxigenic Fusarium.

Matarese F, Sarrocco S, Gruber S, Seidl-Seiboth V, Vannacci G.

Microbiology. 2012 Jan;158(Pt 1):98-106. doi: 10.1099/mic.0.052639-0. Epub 2011 Oct 6.

PMID:
21980117
33.

RAD21 cooperates with pluripotency transcription factors in the maintenance of embryonic stem cell identity.

Nitzsche A, Paszkowski-Rogacz M, Matarese F, Janssen-Megens EM, Hubner NC, Schulz H, de Vries I, Ding L, Huebner N, Mann M, Stunnenberg HG, Buchholz F.

PLoS One. 2011 May 12;6(5):e19470. doi: 10.1371/journal.pone.0019470.

34.

Quantitative interaction proteomics and genome-wide profiling of epigenetic histone marks and their readers.

Vermeulen M, Eberl HC, Matarese F, Marks H, Denissov S, Butter F, Lee KK, Olsen JV, Hyman AA, Stunnenberg HG, Mann M.

Cell. 2010 Sep 17;142(6):967-80. doi: 10.1016/j.cell.2010.08.020.

35.

Analysis of subgroup C of fungal chitinases containing chitin-binding and LysM modules in the mycoparasite Trichoderma atroviride.

Gruber S, Vaaje-Kolstad G, Matarese F, López-Mondéjar R, Kubicek CP, Seidl-Seiboth V.

Glycobiology. 2011 Jan;21(1):122-33. doi: 10.1093/glycob/cwq142. Epub 2010 Sep 14.

PMID:
20843785
36.

Distinct signaling pathways mediate stimulation of cell cycle progression and prevention of apoptotic cell death by estrogen in rat pituitary tumor PR1 cells.

Caporali S, Imai M, Altucci L, Cancemi M, Caristi S, Cicatiello L, Matarese F, Penta R, Sarkar DK, Bresciani F, Weisz A.

Mol Biol Cell. 2003 Dec;14(12):5051-9. Epub 2003 Sep 5.

37.

Estrogens do not modify MAP kinase-dependent nuclear signaling during stimulation of early G(1) progression in human breast cancer cells.

Caristi S, Galera JL, Matarese F, Imai M, Caporali S, Cancemi M, Altucci L, Cicatiello L, Teti D, Bresciani F, Weisz A.

Cancer Res. 2001 Sep 1;61(17):6360-6.

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