Manuela Helmer-Citterich
Socio Ordinario
Professore ordinario
Universita' di Roma Tor Vergata
Contact Information
email
phone
+39-06-72594324
RESEARCH AREA
sequence analysis,structure analysis,structural genomics
RESEARCH ACTIVITY
- Development of computational tools for the study of protein structure-function relationships;
- Molecular recognition: protein-protein and RNA-protein interaction;
- RNA sequence and structure analysis.
- Specificity of kinase/substrate interaction in eukaryotes
- Molecular recognition: protein-protein and RNA-protein interaction;
- RNA sequence and structure analysis.
- Specificity of kinase/substrate interaction in eukaryotes
SELECTED PUBLICATIONS
- Parca L, Ariano B, Cabibbo A, Paoletti M, Tamburrini A, Palmeri A, Ausiello G, Helmer-Citterich M. (2018). Kinome-wide identification of phosphorylation networks in Eukaryotic proteomes. Bioinformatics. [Epub ahead of print] (free full-text)
- Pietrosanto M, Adinolfi M, Casula R, Ausiello G, Ferrè F, Helmer-Citterich M. (2017). BEAM web server: A tool for structural RNA motif discovery. Bioinformatics. [Epub ahead of print] (free full-text)
- El Hachem M, Fortugno P, Palmeri A, Helmer-Citterich M, Diociaiuti A, Proto V, Boldrini R, Zambruno G, Castiglia D (2016). Structural Defects of Laminin β3 N-terminus Underlie Junctional Epidermolysis Bullosa with Altered Granulation Tissue Response. Acta Derm Venereol, in press. (free full-text)
- Pietrosanto M, Mattei E, Helmer-Citterich M, Ferrè F. (2016). A novel method for the identification of conserved structural patterns in RNA: From small scale to high-throughput applications. Nucleic Acids Res. 44(18):8600-8609. (free-full-text)
- Mongiardi MP, Savino M, Falchetti ML, Illi B, Bozzo F, Valle C, Helmer-Citterich M, Ferrè F, Nasi S, Levi A. (2016). c-MYC inhibition impairs hypoxia response in glioblastoma multiforme. Oncotarget, doi:10.18632/oncotarget.8921. [Epub ahead of print] PMID: 27119353.
- Tabolacci E, Mancano G, Lanni S, Palumbo F, Goracci M, Ferrè F, Helmer-Citterich M, Neri G. (2016). Genome-wide methylation analysis demonstrates that 5-aza-2-deoxycytidine treatment does not cause random DNA demethylation in fragile X syndrome cells. Epigenetics Chromatin. 2016 Mar 24;9:12. (free full-text)
- Mango R, Luchetti A, Sangiuolo R, Ferradini V, Briglia N, Giardina E, Ferrè F, Helmer Citterich M, Romeo F, Novelli G, Sangiuolo F. 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. Circ J. 2016 Mar 25;80(4):938-49.
- 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. (2015). Tools and data services registry: a community effort to document bioinformatics resources. Nucleic Acids Res. [Epub ahead of print] PubMed PMID: 26538599. (free full-text)
- Morini E, Rizzacasa B, Pucci S, Polidoro C, Ferrè F, Caporossi D, Helmer-Citterich M, Novelli G, Amati F. (2015). The human rs1050286 polymorphism alters LOX-1 expression through modifying miR-24 binding. J Cell Mol Med., 20(1):181-187 PubMed PMID: 26542080. (free full-text)
- 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. (2015). Kinome-wide Decoding of Network-Attacking Mutations Rewiring Cancer Signaling. Cell, pii: S0092-8674(15)01108-3.
- Ferrè F, Colantoni A, Helmer-Citterich M. (2015). Revealing protein-lncRNA interaction. Brief Bioinform., pii: bbv031. [Epub ahead of print] (free full-text)
- Mattei E, Pietrosanto M, Ferrè F, Helmer-Citterich M. (2015). Web-Beagle: a web server for the alignment of RNA secondary structures. Nucleic Acids Res., pii: gkv489. (free full-text)
- Mattei E, Helmer-Citterich M, Ferrè F. (2015). A simple protocol for the inference of RNA global pairwise alignments. Methods Mol Biol.;1269:39-47. doi:10.1007/978-1-4939-2291-8_3.
- 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, Gretzmeier C, Helmer-Citterich M, Dengjel J, Fimia GM, Piacentini M, Di Bartolomeo S, Velasco G, and Cecconi F. (2015). AMBRA1 links autophagy to cell proliferation and tumorigenesis by promoting c-MYC dephosphorylation and degradation. Nature Cell Biology, 17:20-30.
- Palmeri A, Ferrè F, Helmer-Citterich M. (2014). Exploiting holistic approaches to model specificity in protein phosphorylation. Front Genet. 5:315 (free full-text)
- Ferrè F, Palmeri A, Helmer-Citterich M. (2014). Computational methods for analysis and inference of kinase/inhibitor relationships. Front Genet. 5:196 (free full-text).
- Palmeri A, Helmer-Citterich M, Gherardini PF (2014). A proteome-wide domain-centric perspective on protein phosphorylation. Mol. Cell. proteomics:13,9; 2198-2212 (free full-text).
- Mattei E, Ausiello G, Ferrè F, Helmer-Citterich M. (2014). A novel approach to represent and compare RNA secondary structures. Nucleic Acids Res. 2014 Apr 21. [Epub ahead of print] (free full-text).
- Tsigankov P, Gherardini PF, Helmer-Citterich M, Späth GF, Myler PJ, Zilberstein D. (2014) Regulation dynamics of Leishmania differentiation: deconvoluting signals and identifying phosphorylation trends. Mol. Cell. Proteomics, 13:1787-1799. (free full-text).
- Pietrosanto M, Adinolfi M, Casula R, Ausiello G, Ferrè F, Helmer-Citterich M. (2017). BEAM web server: A tool for structural RNA motif discovery. Bioinformatics. [Epub ahead of print] (free full-text)
- El Hachem M, Fortugno P, Palmeri A, Helmer-Citterich M, Diociaiuti A, Proto V, Boldrini R, Zambruno G, Castiglia D (2016). Structural Defects of Laminin β3 N-terminus Underlie Junctional Epidermolysis Bullosa with Altered Granulation Tissue Response. Acta Derm Venereol, in press. (free full-text)
- Pietrosanto M, Mattei E, Helmer-Citterich M, Ferrè F. (2016). A novel method for the identification of conserved structural patterns in RNA: From small scale to high-throughput applications. Nucleic Acids Res. 44(18):8600-8609. (free-full-text)
- Mongiardi MP, Savino M, Falchetti ML, Illi B, Bozzo F, Valle C, Helmer-Citterich M, Ferrè F, Nasi S, Levi A. (2016). c-MYC inhibition impairs hypoxia response in glioblastoma multiforme. Oncotarget, doi:10.18632/oncotarget.8921. [Epub ahead of print] PMID: 27119353.
- Tabolacci E, Mancano G, Lanni S, Palumbo F, Goracci M, Ferrè F, Helmer-Citterich M, Neri G. (2016). Genome-wide methylation analysis demonstrates that 5-aza-2-deoxycytidine treatment does not cause random DNA demethylation in fragile X syndrome cells. Epigenetics Chromatin. 2016 Mar 24;9:12. (free full-text)
- Mango R, Luchetti A, Sangiuolo R, Ferradini V, Briglia N, Giardina E, Ferrè F, Helmer Citterich M, Romeo F, Novelli G, Sangiuolo F. 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. Circ J. 2016 Mar 25;80(4):938-49.
- 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. (2015). Tools and data services registry: a community effort to document bioinformatics resources. Nucleic Acids Res. [Epub ahead of print] PubMed PMID: 26538599. (free full-text)
- Morini E, Rizzacasa B, Pucci S, Polidoro C, Ferrè F, Caporossi D, Helmer-Citterich M, Novelli G, Amati F. (2015). The human rs1050286 polymorphism alters LOX-1 expression through modifying miR-24 binding. J Cell Mol Med., 20(1):181-187 PubMed PMID: 26542080. (free full-text)
- 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. (2015). Kinome-wide Decoding of Network-Attacking Mutations Rewiring Cancer Signaling. Cell, pii: S0092-8674(15)01108-3.
- Ferrè F, Colantoni A, Helmer-Citterich M. (2015). Revealing protein-lncRNA interaction. Brief Bioinform., pii: bbv031. [Epub ahead of print] (free full-text)
- Mattei E, Pietrosanto M, Ferrè F, Helmer-Citterich M. (2015). Web-Beagle: a web server for the alignment of RNA secondary structures. Nucleic Acids Res., pii: gkv489. (free full-text)
- Mattei E, Helmer-Citterich M, Ferrè F. (2015). A simple protocol for the inference of RNA global pairwise alignments. Methods Mol Biol.;1269:39-47. doi:10.1007/978-1-4939-2291-8_3.
- 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, Gretzmeier C, Helmer-Citterich M, Dengjel J, Fimia GM, Piacentini M, Di Bartolomeo S, Velasco G, and Cecconi F. (2015). AMBRA1 links autophagy to cell proliferation and tumorigenesis by promoting c-MYC dephosphorylation and degradation. Nature Cell Biology, 17:20-30.
- Palmeri A, Ferrè F, Helmer-Citterich M. (2014). Exploiting holistic approaches to model specificity in protein phosphorylation. Front Genet. 5:315 (free full-text)
- Ferrè F, Palmeri A, Helmer-Citterich M. (2014). Computational methods for analysis and inference of kinase/inhibitor relationships. Front Genet. 5:196 (free full-text).
- Palmeri A, Helmer-Citterich M, Gherardini PF (2014). A proteome-wide domain-centric perspective on protein phosphorylation. Mol. Cell. proteomics:13,9; 2198-2212 (free full-text).
- Mattei E, Ausiello G, Ferrè F, Helmer-Citterich M. (2014). A novel approach to represent and compare RNA secondary structures. Nucleic Acids Res. 2014 Apr 21. [Epub ahead of print] (free full-text).
- Tsigankov P, Gherardini PF, Helmer-Citterich M, Späth GF, Myler PJ, Zilberstein D. (2014) Regulation dynamics of Leishmania differentiation: deconvoluting signals and identifying phosphorylation trends. Mol. Cell. Proteomics, 13:1787-1799. (free full-text).
OTHER MEMBERSHIPS
BITS, Bioinformatics ITalian Society
SIBBM, Società Italiana di Biofisica e Biologia Molecolare
ISCB, International Society of Computational Biology
SIBBM, Società Italiana di Biofisica e Biologia Molecolare
ISCB, International Society of Computational Biology
EDITORIAL BOARDS
PLoSOne
MAIN TEACHINGS
Bioinformatica (Laurea triennale in Scienze Biologiche)
Biologia Molecolare (Laurea triennale in Scienze Biologiche)
Biologia Molecolare e Bioinformatica (Laurea Magistrale in Bioinformatica)
Biologia Molecolare (Laurea triennale in Scienze Biologiche)
Biologia Molecolare e Bioinformatica (Laurea Magistrale in Bioinformatica)
