Manuela Helmer-Citterich - Publications

Affiliations: 
Biology University of Rome “Tor Vergata”, Italy 

57 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Parca L, Pepe G, Pietrosanto M, Galvan G, Galli L, Palmeri A, Sciandrone M, Ferrè F, Ausiello G, Helmer-Citterich M. Modeling cancer drug response through drug-specific informative genes. Scientific Reports. 9: 15222. PMID 31645597 DOI: 10.1038/s41598-019-50720-0  0.52
2019 Adinolfi M, Pietrosanto M, Parca L, Ausiello G, Ferrè F, Helmer-Citterich M. Discovering sequence and structure landscapes in RNA interaction motifs. Nucleic Acids Research. 47: 4958-4969. PMID 31162604 DOI: 10.1093/nar/gkz250  0.52
2018 Parca L, Ariano B, Cabibbo A, Paoletti M, Tamburrini A, Palmeri A, Ausiello G, Helmer-Citterich M. Kinome-wide identification of phosphorylation networks in Eukaryotic proteomes. Bioinformatics (Oxford, England). PMID 30016513 DOI: 10.1093/bioinformatics/bty545  0.52
2018 Pietrosanto M, Adinolfi M, Casula R, Ausiello G, Ferrè F, Helmer-Citterich M. BEAM web server: a tool for structural RNA motif discovery. Bioinformatics (Oxford, England). 34: 1058-1060. PMID 29095974 DOI: 10.1093/bioinformatics/btx704  0.52
2015 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, ... ... Helmer-Citterich M, et al. Tools and data services registry: a community effort to document bioinformatics resources. Nucleic Acids Research. PMID 26538599 DOI: 10.1093/nar/gkv1116  0.52
2015 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, et al. Kinome-wide Decoding of Network-Attacking Mutations Rewiring Cancer Signaling. Cell. 163: 202-17. PMID 26388441 DOI: 10.1016/j.cell.2015.08.056  0.52
2015 Facchiano A, Angelini C, Bosotti R, Guffanti A, Marabotti A, Marangoni R, Pascarella S, Romano P, Zanzoni A, Helmer-Citterich M. Preface: BITS2014, the annual meeting of the Italian Society of Bioinformatics. Bmc Bioinformatics. 16: S1. PMID 26050789 DOI: 10.1186/1471-2105-16-S9-S1  0.52
2015 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, et al. Corrigendum: AMBRA1 links autophagy to cell proliferation and tumorigenesis by promoting c-Myc dephosphorylation and degradation. Nature Cell Biology. 17: 706. PMID 25925585 DOI: 10.1038/ncb3171  0.44
2015 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, et al. AMBRA1 links autophagy to cell proliferation and tumorigenesis by promoting c-Myc dephosphorylation and degradation. Nature Cell Biology. 17: 20-30. PMID 25438055 DOI: 10.1038/ncb3072  0.52
2014 Palmeri A, Ausiello G, Ferrè F, Helmer-Citterich M, Gherardini PF. A Proteome-wide Domain-centric Perspective on Protein Phosphorylation. Molecular & Cellular Proteomics : McP. 13: 2198-212. PMID 24830415 DOI: 10.1074/mcp.M114.039990  0.52
2014 Mattei E, Ausiello G, Ferrè F, Helmer-Citterich M. A novel approach to represent and compare RNA secondary structures. Nucleic Acids Research. 42: 6146-57. PMID 24753415 DOI: 10.1093/nar/gku283  0.52
2014 Tsigankov P, Gherardini PF, Helmer-Citterich M, Späth GF, Myler PJ, Zilberstein D. Regulation dynamics of Leishmania differentiation: deconvoluting signals and identifying phosphorylation trends. Molecular & Cellular Proteomics : McP. 13: 1787-99. PMID 24741111 DOI: 10.1074/mcp.M114.037705  0.44
2013 Bianchi V, Colantoni A, Calderone A, Ausiello G, Ferrè F, Helmer-Citterich M. DBATE: database of alternative transcripts expression. Database : the Journal of Biological Databases and Curation. 2013: bat050. PMID 23842462 DOI: 10.1093/database/bat050  0.52
2013 Colantoni A, Bianchi V, Gherardini PF, Tomba GS, Ausiello G, Helmer-Citterich M, Ferrè F. Alternative splicing tends to avoid partial removals of protein-protein interaction sites. Bmc Genomics. 14: 379. PMID 23758645 DOI: 10.1186/1471-2164-14-379  0.52
2013 Bianchi V, Mangone I, Ferrè F, Helmer-Citterich M, Ausiello G. webPDBinder: a server for the identification of ligand binding sites on protein structures. Nucleic Acids Research. 41: W308-13. PMID 23737450 DOI: 10.1093/nar/gkt457  0.52
2013 Parca L, Ferré F, Ausiello G, Helmer-Citterich M. Nucleos: a web server for the identification of nucleotide-binding sites in protein structures. Nucleic Acids Research. 41: W281-5. PMID 23703207 DOI: 10.1093/nar/gkt390  0.52
2013 Tsigankov P, Gherardini PF, Helmer-Citterich M, Späth GF, Zilberstein D. Phosphoproteomic analysis of differentiating Leishmania parasites reveals a unique stage-specific phosphorylation motif. Journal of Proteome Research. 12: 3405-12. PMID 23688256 DOI: 10.1021/pr4002492  0.44
2013 Leclercq O, Bartho K, Duelsner E, von Kleist L, Gherardini PF, Palmeri A, Helmer-Citterich M, Baumgart S, Späth GF. Enrichment of Leishmania donovani ATP-binding proteins using a staurosporine capture compound. Journal of Proteomics. 86: 97-104. PMID 23684787 DOI: 10.1016/j.jprot.2013.05.002  0.44
2013 Gherardini PF, Helmer-Citterich M. Experimental and computational methods for the analysis and modeling of signaling networks. New Biotechnology. 30: 327-32. PMID 23165097 DOI: 10.1016/j.nbt.2012.11.007  0.44
2013 Perfetto L, Gherardini PF, Davey NE, Diella F, Helmer-Citterich M, Cesareni G. Exploring the diversity of SPRY/B30.2-mediated interactions. Trends in Biochemical Sciences. 38: 38-46. PMID 23164942 DOI: 10.1016/j.tibs.2012.10.001  0.52
2012 Parca L, Gherardini PF, Truglio M, Mangone I, Ferrè F, Helmer-Citterich M, Ausiello G. Identification of nucleotide-binding sites in protein structures: a novel approach based on nucleotide modularity. Plos One. 7: e50240. PMID 23209685 DOI: 10.1371/journal.pone.0050240  0.52
2012 Sacco F, Gherardini PF, Paoluzi S, Saez-Rodriguez J, Helmer-Citterich M, Ragnini-Wilson A, Castagnoli L, Cesareni G. Mapping the human phosphatome on growth pathways. Molecular Systems Biology. 8: 603. PMID 22893001 DOI: 10.1038/msb.2012.36  0.52
2012 Giacò L, Amicosante M, Fraziano M, Gherardini PF, Ausiello G, Helmer-Citterich M, Colizzi V, Cabibbo A. B-Pred, a structure based B-cell epitopes prediction server. Advances and Applications in Bioinformatics and Chemistry : Aabc. 5: 11-21. PMID 22888263 DOI: 10.2147/AABC.S30620  0.52
2012 Minguez P, Parca L, Diella F, Mende DR, Kumar R, Helmer-Citterich M, Gavin AC, van Noort V, Bork P. Deciphering a global network of functionally associated post-translational modifications. Molecular Systems Biology. 8: 599. PMID 22806145 DOI: 10.1038/msb.2012.31  0.52
2012 Bianchi V, Gherardini PF, Helmer-Citterich M, Ausiello G. Identification of binding pockets in protein structures using a knowledge-based potential derived from local structural similarities. Bmc Bioinformatics. 13: S17. PMID 22536963 DOI: 10.1186/1471-2105-13-S4-S17  0.52
2012 Tsigankov P, Gherardini PF, Helmer-Citterich M, Zilberstein D. What has proteomics taught us about Leishmania development? Parasitology. 139: 1146-57. PMID 22369930 DOI: 10.1017/S0031182012000157  0.44
2011 Palmeri A, Gherardini PF, Tsigankov P, Ausiello G, Späth GF, Zilberstein D, Helmer-Citterich M. PhosTryp: a phosphorylation site predictor specific for parasitic protozoa of the family trypanosomatidae. Bmc Genomics. 12: 614. PMID 22182631 DOI: 10.1186/1471-2164-12-614  0.52
2011 Parca L, Mangone I, Gherardini PF, Ausiello G, Helmer-Citterich M. Phosfinder: a web server for the identification of phosphate-binding sites on protein structures. Nucleic Acids Research. 39: W278-82. PMID 21622655 DOI: 10.1093/nar/gkr389  0.52
2011 Schmidt-Arras D, Leclercq O, Gherardini PF, Helmer-Citterich M, Faigle W, Loew D, Späth GF. Adaptation of a 2D in-gel kinase assay to trace phosphotransferase activities in the human pathogen Leishmania donovani. Journal of Proteomics. 74: 1644-51. PMID 21443974 DOI: 10.1016/j.jprot.2011.03.024  0.44
2011 Via A, Diella F, Gibson TJ, Helmer-Citterich M. From sequence to structural analysis in protein phosphorylation motifs. Frontiers in Bioscience (Landmark Edition). 16: 1261-75. PMID 21196230 DOI: 10.2741/3787  0.52
2011 Parca L, Gherardini PF, Helmer-Citterich M, Ausiello G. Phosphate binding sites identification in protein structures. Nucleic Acids Research. 39: 1231-42. PMID 20974634 DOI: 10.1093/nar/gkq987  0.52
2011 Zanzoni A, Carbajo D, Diella F, Gherardini PF, Tramontano A, Helmer-Citterich M, Via A. Phospho3D 2.0: an enhanced database of three-dimensional structures of phosphorylation sites. Nucleic Acids Research. 39: D268-71. PMID 20965970 DOI: 10.1093/nar/gkq936  0.52
2010 Hem S, Gherardini PF, Osorio y Fortéa J, Hourdel V, Morales MA, Watanabe R, Pescher P, Kuzyk MA, Smith D, Borchers CH, Zilberstein D, Helmer-Citterich M, Namane A, Späth GF. Identification of Leishmania-specific protein phosphorylation sites by LC-ESI-MS/MS and comparative genomics analyses. Proteomics. 10: 3868-83. PMID 20960452 DOI: 10.1002/pmic.201000305  0.44
2010 Gherardini PF, Ausiello G, Helmer-Citterich M. Superpose3D: a local structural comparison program that allows for user-defined structure representations. Plos One. 5: e11988. PMID 20700534 DOI: 10.1371/journal.pone.0011988  0.52
2010 Yau WL, Blisnick T, Taly JF, Helmer-Citterich M, Schiene-Fischer C, Leclercq O, Li J, Schmidt-Arras D, Morales MA, Notredame C, Romo D, Bastin P, Späth GF. Cyclosporin A treatment of Leishmania donovani reveals stage-specific functions of cyclophilins in parasite proliferation and viability. Plos Neglected Tropical Diseases. 4: e729. PMID 20614016 DOI: 10.1371/journal.pntd.0000729  0.52
2010 Gherardini PF, Ausiello G, Russell RB, Helmer-Citterich M. Modular architecture of nucleotide-binding pockets. Nucleic Acids Research. 38: 3809-16. PMID 20185567 DOI: 10.1093/nar/gkq090  0.52
2010 Gould CM, Diella F, Via A, Puntervoll P, Gemünd C, Chabanis-Davidson S, Michael S, Sayadi A, Bryne JC, Chica C, Seiler M, Davey NE, Haslam N, Weatheritt RJ, Budd A, ... ... Helmer-Citterich M, et al. ELM: the status of the 2010 eukaryotic linear motif resource. Nucleic Acids Research. 38: D167-80. PMID 19920119 DOI: 10.1093/nar/gkp1016  0.52
2009 Via A, Gould CM, Gemünd C, Gibson TJ, Helmer-Citterich M. A structure filter for the Eukaryotic Linear Motif Resource. Bmc Bioinformatics. 10: 351. PMID 19852836 DOI: 10.1186/1471-2105-10-351  0.52
2009 Ausiello G, Gherardini PF, Gatti E, Incani O, Helmer-Citterich M. Structural motifs recurring in different folds recognize the same ligand fragments. Bmc Bioinformatics. 10: 182. PMID 19527512 DOI: 10.1186/1471-2105-10-182  0.52
2008 Gherardini PF, Helmer-Citterich M. Structure-based function prediction: approaches and applications. Briefings in Functional Genomics & Proteomics. 7: 291-302. PMID 18599513 DOI: 10.1093/bfgp/eln030  0.44
2008 Ausiello G, Gherardini PF, Marcatili P, Tramontano A, Via A, Helmer-Citterich M. FunClust: a web server for the identification of structural motifs in a set of non-homologous protein structures. Bmc Bioinformatics. 9: S2. PMID 18387204 DOI: 10.1186/1471-2105-9-S2-S2  0.52
2007 Gherardini PF, Wass MN, Helmer-Citterich M, Sternberg MJ. Convergent evolution of enzyme active sites is not a rare phenomenon. Journal of Molecular Biology. 372: 817-45. PMID 17681532 DOI: 10.1016/j.jmb.2007.06.017  0.44
2007 Via A, Peluso D, Gherardini PF, de Rinaldis E, Colombo T, Ausiello G, Helmer-Citterich M. 3dLOGO: a web server for the identification, analysis and use of conserved protein substructures. Nucleic Acids Research. 35: W416-9. PMID 17488847 DOI: 10.1093/nar/gkm228  0.52
2007 Ferraro E, Peluso D, Via A, Ausiello G, Helmer-Citterich M. SH3-Hunter: discovery of SH3 domain interaction sites in proteins. Nucleic Acids Research. 35: W451-4. PMID 17485474 DOI: 10.1093/nar/gkm296  0.52
2007 Ausiello G, Peluso D, Via A, Helmer-Citterich M. Local comparison of protein structures highlights cases of convergent evolution in analogous functional sites. Bmc Bioinformatics. 8: S24. PMID 17430569 DOI: 10.1186/1471-2105-8-S1-S24  0.52
2007 Via A, Gherardini PF, Ferraro E, Ausiello G, Scalia Tomba G, Helmer-Citterich M. False occurrences of functional motifs in protein sequences highlight evolutionary constraints. Bmc Bioinformatics. 8: 68. PMID 17331242 DOI: 10.1186/1471-2105-8-68  0.52
2007 Zanzoni A, Ausiello G, Via A, Gherardini PF, Helmer-Citterich M. Phospho3D: a database of three-dimensional structures of protein phosphorylation sites. Nucleic Acids Research. 35: D229-31. PMID 17142231 DOI: 10.1093/nar/gkl922  0.52
2005 Ausiello G, Via A, Helmer-Citterich M. Query3d: a new method for high-throughput analysis of functional residues in protein structures. Bmc Bioinformatics. 6: S5. PMID 16351754 DOI: 10.1186/1471-2105-6-S4-S5  0.52
2005 Ferraro E, Via A, Ausiello G, Helmer-Citterich M. A neural strategy for the inference of SH3 domain-peptide interaction specificity. Bmc Bioinformatics. 6: S13. PMID 16351739 DOI: 10.1186/1471-2105-6-S4-S13  0.52
2005 Ferrè F, Ausiello G, Zanzoni A, Helmer-Citterich M. Functional annotation by identification of local surface similarities: a novel tool for structural genomics. Bmc Bioinformatics. 6: 194. PMID 16076399 DOI: 10.1186/1471-2105-6-194  0.52
2005 Ausiello G, Zanzoni A, Peluso D, Via A, Helmer-Citterich M. pdbFun: mass selection and fast comparison of annotated PDB residues. Nucleic Acids Research. 33: W133-7. PMID 15980442 DOI: 10.1093/nar/gki499  0.52
2005 Via A, Zanzoni A, Helmer-Citterich M. Seq2Struct: a resource for establishing sequence-structure links. Bioinformatics (Oxford, England). 21: 551-3. PMID 15454411 DOI: 10.1093/bioinformatics/bti049  0.52
2004 Ferrè F, Ausiello G, Zanzoni A, Helmer-Citterich M. SURFACE: a database of protein surface regions for functional annotation. Nucleic Acids Research. 32: D240-4. PMID 14681403 DOI: 10.1093/nar/gkh054  0.52
2003 Ferrè F, Via A, Ausiello G, Brannetti B, Zanzoni A, Helmer-Citterich M. Development of computational tools for the inference of protein interaction specificity rules and functional annotation using structural information. Comparative and Functional Genomics. 4: 416-9. PMID 18629081 DOI: 10.1002/cfg.304  0.52
2003 Cesareni G, Helmer-Citterich M. Searching the MINT database for protein interaction information. Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. Unit 8.5. PMID 18428712 DOI: 10.1002/0471250953.bi0805s02  1
2003 Puntervoll P, Linding R, Gemünd C, Chabanis-Davidson S, Mattingsdal M, Cameron S, Martin DM, Ausiello G, Brannetti B, Costantini A, Ferrè F, Maselli V, Via A, Cesareni G, Diella F, ... ... Helmer-Citterich M, et al. ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins. Nucleic Acids Research. 31: 3625-30. PMID 12824381 DOI: 10.1093/nar/gkg545  0.52
2002 Zanzoni A, Montecchi-Palazzi L, Quondam M, Ausiello G, Helmer-Citterich M, Cesareni G. MINT: a Molecular INTeraction database. Febs Letters. 513: 135-40. PMID 11911893 DOI: 10.1016/S0014-5793(01)03293-8  0.52
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