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Items: 1 to 50 of 103

1.

Modeling cancer drug response through drug-specific informative genes.

Parca L, Pepe G, Pietrosanto M, Galvan G, Galli L, Palmeri A, Sciandrone M, Ferrè F, Ausiello G, Helmer-Citterich M.

Sci Rep. 2019 Oct 23;9(1):15222. doi: 10.1038/s41598-019-50720-0.

2.

Discovering sequence and structure landscapes in RNA interaction motifs.

Adinolfi M, Pietrosanto M, Parca L, Ausiello G, Ferrè F, Helmer-Citterich M.

Nucleic Acids Res. 2019 Jun 4;47(10):4958-4969. doi: 10.1093/nar/gkz250.

3.

Blood and skin-derived Sezary cells: differences in proliferation-index, activation of PI3K/AKT/mTORC1 pathway and its prognostic relevance.

Cristofoletti C, Bresin A, Picozza M, Picchio MC, Monzo F, Helmer Citterich M, Passarelli F, Frezzolini A, Scala E, Monopoli A, Cantonetti M, Benucci R, D'Atri S, Caprini E, Russo G, Narducci MG.

Leukemia. 2019 May;33(5):1231-1242. doi: 10.1038/s41375-018-0305-8. Epub 2018 Dec 5.

4.

Loss of the candidate tumor suppressor ZEB1 (TCF8, ZFHX1A) in Sézary syndrome.

Caprini E, Bresin A, Cristofoletti C, Helmer Citterich M, Tocco V, Scala E, Monopoli A, Benucci R, Narducci MG, Russo G.

Cell Death Dis. 2018 Dec 5;9(12):1178. doi: 10.1038/s41419-018-1212-7.

5.

T Cell Leukemia/Lymphoma 1A is essential for mouse epidermal keratinocytes proliferation promoted by insulin-like growth factor 1.

Bresin A, Ragone G, Cristofoletti C, Arcelli D, Bassi C, Caprini E, Fiorenza MT, Helmer Citterich M, Russo G, Narducci MG.

PLoS One. 2018 Oct 4;13(10):e0204775. doi: 10.1371/journal.pone.0204775. eCollection 2018.

6.

Kinome-wide identification of phosphorylation networks in eukaryotic proteomes.

Parca L, Ariano B, Cabibbo A, Paoletti M, Tamburrini A, Palmeri A, Ausiello G, Helmer-Citterich M.

Bioinformatics. 2019 Feb 1;35(3):372-379. doi: 10.1093/bioinformatics/bty545.

7.

BEAM web server: a tool for structural RNA motif discovery.

Pietrosanto M, Adinolfi M, Casula R, Ausiello G, Ferrè F, Helmer-Citterich M.

Bioinformatics. 2018 Mar 15;34(6):1058-1060. doi: 10.1093/bioinformatics/btx704.

8.

A novel method for the identification of conserved structural patterns in RNA: From small scale to high-throughput applications.

Pietrosanto M, Mattei E, Helmer-Citterich M, Ferrè F.

Nucleic Acids Res. 2016 Oct 14;44(18):8600-8609. Epub 2016 Aug 31.

9.

c-MYC inhibition impairs hypoxia response in glioblastoma multiforme.

Mongiardi MP, Savino M, Falchetti ML, Illi B, Bozzo F, Valle C, Helmer-Citterich M, Ferrè F, Nasi S, Levi A.

Oncotarget. 2016 May 31;7(22):33257-71. doi: 10.18632/oncotarget.8921.

10.

Genome-wide methylation analysis demonstrates that 5-aza-2-deoxycytidine treatment does not cause random DNA demethylation in fragile X syndrome cells.

Tabolacci E, Mancano G, Lanni S, Palumbo F, Goracci M, Ferrè F, Helmer-Citterich M, Neri G.

Epigenetics Chromatin. 2016 Mar 24;9:12. doi: 10.1186/s13072-016-0060-x. eCollection 2016.

11.

Next Generation Sequencing and Linkage Analysis for the Molecular Diagnosis of a Novel Overlapping Syndrome Characterized by Hypertrophic Cardiomyopathy and Typical Electrical Instability of Brugada Syndrome.

Mango R, Luchetti A, Sangiuolo R, Ferradini V, Briglia N, Giardina E, Ferrè F, Helmer Citterich M, Romeo F, Novelli G, Sangiuolo F.

Circ J. 2016;80(4):938-49. doi: 10.1253/circj.CJ-15-0685. Epub 2016 Mar 9.

12.

The human rs1050286 polymorphism alters LOX-1 expression through modifying miR-24 binding.

Morini E, Rizzacasa B, Pucci S, Polidoro C, Ferrè F, Caporossi D, Helmer Citterich M, Novelli G, Amati F.

J Cell Mol Med. 2016 Jan;20(1):181-7. doi: 10.1111/jcmm.12716. Epub 2015 Nov 6.

13.

Tools and data services registry: a community effort to document bioinformatics resources.

Ison J, Rapacki K, Ménager H, Kalaš M, Rydza E, Chmura P, Anthon C, Beard N, Berka K, Bolser D, Booth T, Bretaudeau A, Brezovsky J, Casadio R, Cesareni G, Coppens F, Cornell M, Cuccuru G, Davidsen K, Vedova GD, Dogan T, Doppelt-Azeroual O, Emery L, Gasteiger E, Gatter T, Goldberg T, Grosjean M, Grüning B, Helmer-Citterich M, Ienasescu H, Ioannidis V, Jespersen MC, Jimenez R, Juty N, Juvan P, Koch M, Laibe C, Li JW, Licata L, Mareuil F, Mičetić I, Friborg RM, Moretti S, Morris C, Möller S, Nenadic A, Peterson H, Profiti G, Rice P, Romano P, Roncaglia P, Saidi R, Schafferhans A, Schwämmle V, Smith C, Sperotto MM, Stockinger H, Vařeková RS, Tosatto SC, de la Torre V, Uva P, Via A, Yachdav G, Zambelli F, Vriend G, Rost B, Parkinson H, Løngreen P, Brunak S.

Nucleic Acids Res. 2016 Jan 4;44(D1):D38-47. doi: 10.1093/nar/gkv1116. Epub 2015 Nov 3.

14.

Kinome-wide decoding of network-attacking mutations rewiring cancer signaling.

Creixell P, Schoof EM, Simpson CD, Longden J, Miller CJ, Lou HJ, Perryman L, Cox TR, Zivanovic N, Palmeri A, Wesolowska-Andersen A, Helmer-Citterich M, Ferkinghoff-Borg J, Itamochi H, Bodenmiller B, Erler JT, Turk BE, Linding R.

Cell. 2015 Sep 24;163(1):202-17. doi: 10.1016/j.cell.2015.08.056. Epub 2015 Sep 17.

15.

Preface: BITS2014, the annual meeting of the Italian Society of Bioinformatics.

Facchiano A, Angelini C, Bosotti R, Guffanti A, Marabotti A, Marangoni R, Pascarella S, Romano P, Zanzoni A, Helmer-Citterich M.

BMC Bioinformatics. 2015;16 Suppl 9:S1. doi: 10.1186/1471-2105-16-S9-S1. Epub 2015 Jun 1.

16.

Revealing protein-lncRNA interaction.

Ferrè F, Colantoni A, Helmer-Citterich M.

Brief Bioinform. 2016 Jan;17(1):106-16. doi: 10.1093/bib/bbv031. Epub 2015 Jun 2. Review.

17.

Web-Beagle: a web server for the alignment of RNA secondary structures.

Mattei E, Pietrosanto M, Ferrè F, Helmer-Citterich M.

Nucleic Acids Res. 2015 Jul 1;43(W1):W493-7. doi: 10.1093/nar/gkv489. Epub 2015 May 14.

18.

AMBRA1 links autophagy to cell proliferation and tumorigenesis by promoting c-Myc dephosphorylation and degradation.

Cianfanelli V, Fuoco C, Lorente M, Salazar M, Quondamatteo F, Gherardini PF, De Zio D, Nazio F, Antonioli M, D'Orazio M, Skobo T, Bordi M, Rohde M, Dalla Valle L, Helmer-Citterich M, Gretzmeier C, Dengjel J, Fimia GM, Piacentini M, Di Bartolomeo S, Velasco G, Cecconi F.

Nat Cell Biol. 2015 May;17(5):706. doi: 10.1038/ncb3171. No abstract available.

PMID:
25925585
19.

A simple protocol for the inference of RNA global pairwise alignments.

Mattei E, Helmer-Citterich M, Ferrè F.

Methods Mol Biol. 2015;1269:39-47. doi: 10.1007/978-1-4939-2291-8_3.

PMID:
25577371
20.

AMBRA1 links autophagy to cell proliferation and tumorigenesis by promoting c-Myc dephosphorylation and degradation.

Cianfanelli V, Fuoco C, Lorente M, Salazar M, Quondamatteo F, Gherardini PF, De Zio D, Nazio F, Antonioli M, D'Orazio M, Skobo T, Bordi M, Rohde M, Dalla Valle L, Helmer-Citterich M, Gretzmeier C, Dengjel J, Fimia GM, Piacentini M, Di Bartolomeo S, Velasco G, Cecconi F.

Nat Cell Biol. 2015 Jan;17(1):20-30. doi: 10.1038/ncb3072. Epub 2014 Dec 1. Erratum in: Nat Cell Biol. 2015 May;17(5):706.

21.

Exploiting holistic approaches to model specificity in protein phosphorylation.

Palmeri A, Ferrè F, Helmer-Citterich M.

Front Genet. 2014 Sep 30;5:315. doi: 10.3389/fgene.2014.00315. eCollection 2014. Review.

22.

Computational methods for analysis and inference of kinase/inhibitor relationships.

Ferrè F, Palmeri A, Helmer-Citterich M.

Front Genet. 2014 Jun 30;5:196. doi: 10.3389/fgene.2014.00196. eCollection 2014. Review.

23.

A Proteome-wide Domain-centric Perspective on Protein Phosphorylation.

Palmeri A, Ausiello G, Ferrè F, Helmer-Citterich M, Gherardini PF.

Mol Cell Proteomics. 2014 Sep;13(9):2198-212. doi: 10.1074/mcp.M114.039990. Epub 2014 May 15.

24.

A novel approach to represent and compare RNA secondary structures.

Mattei E, Ausiello G, Ferrè F, Helmer-Citterich M.

Nucleic Acids Res. 2014 Jun;42(10):6146-57. doi: 10.1093/nar/gku283. Epub 2014 Apr 21.

25.

Regulation dynamics of Leishmania differentiation: deconvoluting signals and identifying phosphorylation trends.

Tsigankov P, Gherardini PF, Helmer-Citterich M, Späth GF, Myler PJ, Zilberstein D.

Mol Cell Proteomics. 2014 Jul;13(7):1787-99. doi: 10.1074/mcp.M114.037705. Epub 2014 Apr 16.

26.

Role of CTCF protein in regulating FMR1 locus transcription.

Lanni S, Goracci M, Borrelli L, Mancano G, Chiurazzi P, Moscato U, Ferrè F, Helmer-Citterich M, Tabolacci E, Neri G.

PLoS Genet. 2013;9(7):e1003601. doi: 10.1371/journal.pgen.1003601. Epub 2013 Jul 18.

27.

Bioinformatics in Italy: BITS 2012, the ninth annual meeting of the Italian Society of Bioinformatics.

Gissi C, Romano P, Ferro A, Giugno R, Pulvirenti A, Facchiano A, Helmer-Citterich M.

BMC Bioinformatics. 2013;14 Suppl 7:S1. doi: 10.1186/1471-2105-14-S7-S1. Epub 2013 Apr 22.

28.

DBATE: database of alternative transcripts expression.

Bianchi V, Colantoni A, Calderone A, Ausiello G, Ferrè F, Helmer-Citterich M.

Database (Oxford). 2013 Jul 9;2013:bat050. doi: 10.1093/database/bat050. Print 2013.

29.

Alternative splicing tends to avoid partial removals of protein-protein interaction sites.

Colantoni A, Bianchi V, Gherardini PF, Tomba GS, Ausiello G, Helmer-Citterich M, Ferrè F.

BMC Genomics. 2013 Jun 7;14:379. doi: 10.1186/1471-2164-14-379.

30.

webPDBinder: a server for the identification of ligand binding sites on protein structures.

Bianchi V, Mangone I, Ferrè F, Helmer-Citterich M, Ausiello G.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W308-13. doi: 10.1093/nar/gkt457. Epub 2013 Jun 3.

31.

Nucleos: a web server for the identification of nucleotide-binding sites in protein structures.

Parca L, Ferré F, Ausiello G, Helmer-Citterich M.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W281-5. doi: 10.1093/nar/gkt390. Epub 2013 May 22.

32.

Phosphoproteomic analysis of differentiating Leishmania parasites reveals a unique stage-specific phosphorylation motif.

Tsigankov P, Gherardini PF, Helmer-Citterich M, Späth GF, Zilberstein D.

J Proteome Res. 2013 Jul 5;12(7):3405-12. doi: 10.1021/pr4002492. Epub 2013 Jun 11.

PMID:
23688256
33.

Enrichment of Leishmania donovani ATP-binding proteins using a staurosporine capture compound.

Leclercq O, Bartho K, Duelsner E, von Kleist L, Gherardini PF, Palmeri A, Helmer-Citterich M, Baumgart S, Späth GF.

J Proteomics. 2013 Jun 28;86:97-104. doi: 10.1016/j.jprot.2013.05.002. Epub 2013 May 16.

PMID:
23684787
34.

Peamaclein--a new peach allergenic protein: similarities, differences and misleading features compared to Pru p 3.

Tuppo L, Alessandri C, Pomponi D, Picone D, Tamburrini M, Ferrara R, Petriccione M, Mangone I, Palazzo P, Liso M, Giangrieco I, Crescenzo R, Bernardi ML, Zennaro D, Helmer-Citterich M, Mari A, Ciardiello MA.

Clin Exp Allergy. 2013 Jan;43(1):128-40. doi: 10.1111/cea.12028.

PMID:
23278887
35.

Identification of nucleotide-binding sites in protein structures: a novel approach based on nucleotide modularity.

Parca L, Gherardini PF, Truglio M, Mangone I, Ferrè F, Helmer-Citterich M, Ausiello G.

PLoS One. 2012;7(11):e50240. doi: 10.1371/journal.pone.0050240. Epub 2012 Nov 27.

36.

Experimental and computational methods for the analysis and modeling of signaling networks.

Gherardini PF, Helmer-Citterich M.

N Biotechnol. 2013 Mar 25;30(3):327-32. doi: 10.1016/j.nbt.2012.11.007. Epub 2012 Nov 16. Review.

PMID:
23165097
37.

Exploring the diversity of SPRY/B30.2-mediated interactions.

Perfetto L, Gherardini PF, Davey NE, Diella F, Helmer-Citterich M, Cesareni G.

Trends Biochem Sci. 2013 Jan;38(1):38-46. doi: 10.1016/j.tibs.2012.10.001. Epub 2012 Nov 17. Review.

PMID:
23164942
38.

Mapping the human phosphatome on growth pathways.

Sacco F, Gherardini PF, Paoluzi S, Saez-Rodriguez J, Helmer-Citterich M, Ragnini-Wilson A, Castagnoli L, Cesareni G.

Mol Syst Biol. 2012;8:603. doi: 10.1038/msb.2012.36.

39.

B-Pred, a structure based B-cell epitopes prediction server.

Giacò L, Amicosante M, Fraziano M, Gherardini PF, Ausiello G, Helmer-Citterich M, Colizzi V, Cabibbo A.

Adv Appl Bioinform Chem. 2012;5:11-21. doi: 10.2147/AABC.S30620. Epub 2012 Jul 25.

40.

Deciphering a global network of functionally associated post-translational modifications.

Minguez P, Parca L, Diella F, Mende DR, Kumar R, Helmer-Citterich M, Gavin AC, van Noort V, Bork P.

Mol Syst Biol. 2012 Jul 17;8:599. doi: 10.1038/msb.2012.31.

41.

Modeling gene regulatory network motifs using Statecharts.

Fioravanti F, Helmer-Citterich M, Nardelli E.

BMC Bioinformatics. 2012 Mar 28;13 Suppl 4:S20. doi: 10.1186/1471-2105-13-S4-S20.

42.

Identification of binding pockets in protein structures using a knowledge-based potential derived from local structural similarities.

Bianchi V, Gherardini PF, Helmer-Citterich M, Ausiello G.

BMC Bioinformatics. 2012 Mar 28;13 Suppl 4:S17. doi: 10.1186/1471-2105-13-S4-S17.

43.

Bioinformatics in Italy: BITS2011, the Eighth Annual Meeting of the Italian Society of Bioinformatics.

Romano P, Helmer-Citterich M.

BMC Bioinformatics. 2012 Mar 28;13 Suppl 4:I1. doi: 10.1186/1471-2105-13-S4-I1.

44.

What has proteomics taught us about Leishmania development?

Tsigankov P, Gherardini PF, Helmer-Citterich M, Zilberstein D.

Parasitology. 2012 Aug;139(9):1146-57. doi: 10.1017/S0031182012000157. Epub 2012 Feb 28. Review.

PMID:
22369930
45.

PhosTryp: a phosphorylation site predictor specific for parasitic protozoa of the family trypanosomatidae.

Palmeri A, Gherardini PF, Tsigankov P, Ausiello G, Späth GF, Zilberstein D, Helmer-Citterich M.

BMC Genomics. 2011 Dec 19;12:614. doi: 10.1186/1471-2164-12-614.

46.

Phosfinder: a web server for the identification of phosphate-binding sites on protein structures.

Parca L, Mangone I, Gherardini PF, Ausiello G, Helmer-Citterich M.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W278-82. doi: 10.1093/nar/gkr389. Epub 2011 May 26.

47.

Adaptation of a 2D in-gel kinase assay to trace phosphotransferase activities in the human pathogen Leishmania donovani.

Schmidt-Arras D, Leclercq O, Gherardini PF, Helmer-Citterich M, Faigle W, Loew D, Späth GF.

J Proteomics. 2011 Aug 24;74(9):1644-51. doi: 10.1016/j.jprot.2011.03.024. Epub 2011 Mar 26.

PMID:
21443974
48.

From sequence to structural analysis in protein phosphorylation motifs.

Via A, Diella F, Gibson TJ, Helmer-Citterich M.

Front Biosci (Landmark Ed). 2011 Jan 1;16:1261-75. Review.

49.

Phosphate binding sites identification in protein structures.

Parca L, Gherardini PF, Helmer-Citterich M, Ausiello G.

Nucleic Acids Res. 2011 Mar;39(4):1231-42. doi: 10.1093/nar/gkq987. Epub 2010 Oct 24.

50.

Phospho3D 2.0: an enhanced database of three-dimensional structures of phosphorylation sites.

Zanzoni A, Carbajo D, Diella F, Gherardini PF, Tramontano A, Helmer-Citterich M, Via A.

Nucleic Acids Res. 2011 Jan;39(Database issue):D268-71. doi: 10.1093/nar/gkq936. Epub 2010 Oct 21.

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