Manuela Helmer-Citterich - Publications

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

103 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
2021 Galfrè SG, Morandin F, Pietrosanto M, Cremisi F, Helmer-Citterich M. COTAN: scRNA-seq data analysis based on gene co-expression. Nar Genomics and Bioinformatics. 3: lqab072. PMID 34396096 DOI: 10.1093/nargab/lqab072  1
2021 Ferradini V, Parca L, Martino A, Lanzillo C, Silvetti E, Calò L, Caselli S, Novelli G, Helmer-Citterich M, Sangiuolo FC, Mango R. Variants in Gene Cause Arrhythmogenic Cardiomyopathy. Genes. 12. PMID 34067482 DOI: 10.3390/genes12060793  1
2021 Guarracino A, Pepe G, Ballesio F, Adinolfi M, Pietrosanto M, Sangiovanni E, Vitale I, Ausiello G, Helmer-Citterich M. BRIO: a web server for RNA sequence and structure motif scan. Nucleic Acids Research. PMID 34038531 DOI: 10.1093/nar/gkab400  1
2021 Martins M, Galfrè S, Terrigno M, Pandolfini L, Appolloni I, Dunville K, Marranci A, Rizzo M, Mercatanti A, Poliseno L, Morandin F, Pietrosanto M, Helmer-Citterich M, Malatesta P, Vignali R, et al. A eutherian-specific microRNA controls the translation of Satb2 in a model of cortical differentiation. Stem Cell Reports. 16: 1496-1509. PMID 34019815 DOI: 10.1016/j.stemcr.2021.04.020  1
2021 Pietrosanto M, Ausiello G, Helmer-Citterich M. Motif Discovery from CLIP Experiments. Methods in Molecular Biology (Clifton, N.J.). 2284: 43-50. PMID 33835436 DOI: 10.1007/978-1-0716-1307-8_3  1
2021 Pietrosanto M, Adinolfi M, Guarracino A, Ferrè F, Ausiello G, Vitale I, Helmer-Citterich M. Relative Information Gain: Shannon entropy-based measure of the relative structural conservation in RNA alignments. Nar Genomics and Bioinformatics. 3: lqab007. PMID 33615214 DOI: 10.1093/nargab/lqab007  1
2020 Latini A, Agolini E, Novelli A, Borgiani P, Giannini R, Gravina P, Smarrazzo A, Dauri M, Andreoni M, Rogliani P, Bernardini S, Helmer-Citterich M, Biancolella M, Novelli G. COVID-19 and Genetic Variants of Protein Involved in the SARS-CoV-2 Entry into the Host Cells. Genes. 11. PMID 32867305 DOI: 10.3390/Genes11091010  0.01
2020 Novelli G, Novelli A, Borgiani P, Cocciadiferro D, Biancolella M, Agolini E, Pietrosanto M, Casalone R, Helmer-Citterich M, Giardina E, Jain SK, Wei W, Eng C, Pandolfi PP. WWP1 germline variants are associated with normocephalic autism spectrum disorder. Cell Death & Disease. 11: 529. PMID 32699206 DOI: 10.1038/S41419-020-2681-Z  1
2020 Orengo C, Velankar S, Wodak S, Zoete V, Bonvin AMJJ, Elofsson A, Feenstra KA, Gerloff DL, Hamelryck T, Hancock JM, Helmer-Citterich M, Hospital A, Orozco M, Perrakis A, Rarey M, et al. A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community). F1000research. 9. PMID 32566135 DOI: 10.12688/F1000Research.20559.1  0.01
2020 Babicola L, Pietrosanto M, Ielpo D, Luca D'Addario S, Cabib S, Ventura R, Ferlazzo F, Helmer-Citterich M, Andolina D, Lo Iacono L. Title: RISC RNA sequencing in the Dorsal Raphè reveals microRNAs regulatory activities associated with behavioral and functional adaptations to chronic stress. Brain Research. 146763. PMID 32169579 DOI: 10.1016/J.Brainres.2020.146763  1
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  1
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  1
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  1
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  1
2016 Pietrosanto M, Mattei E, Helmer-Citterich M, Ferrè F. A novel method for the identification of conserved structural patterns in RNA: From small scale to high-throughput applications. Nucleic Acids Research. 44: 8600-8609. PMID 27580722 DOI: 10.1093/Nar/Gkw750  1
2016 Mongiardi MP, Savino M, Falchetti ML, Illi B, Bozzo F, Valle C, Helmer-Citterich M, Ferrè F, Nasi S, Levi A. c-MYC inhibition impairs hypoxia response in glioblastoma multiforme. Oncotarget. 7: 33257-71. PMID 27119353 DOI: 10.18632/Oncotarget.8921  1
2016 Tabolacci E, Mancano G, Lanni S, Palumbo F, Goracci M, Ferrè F, Helmer-Citterich M, Neri G. Genome-wide methylation analysis demonstrates that 5-aza-2-deoxycytidine treatment does not cause random DNA demethylation in fragile X syndrome cells. Epigenetics & Chromatin. 9: 12. PMID 27014370 DOI: 10.1186/S13072-016-0060-X  1
2016 Ferrè F, Colantoni A, Helmer-Citterich M. Revealing protein-lncRNA interaction. Briefings in Bioinformatics. 17: 106-16. PMID 26041786 DOI: 10.1093/Bib/Bbv031  1
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  1
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  1
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  1
2015 Mattei E, Pietrosanto M, Ferrè F, Helmer-Citterich M. Web-Beagle: a web server for the alignment of RNA secondary structures. Nucleic Acids Research. 43: W493-7. PMID 25977293 DOI: 10.1093/Nar/Gkv489  1
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  1
2015 Mattei E, Helmer-Citterich M, Ferrè F. A simple protocol for the inference of RNA global pairwise alignments. Methods in Molecular Biology (Clifton, N.J.). 1269: 39-47. PMID 25577371 DOI: 10.1007/978-1-4939-2291-8_3  1
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  1
2014 Palmeri A, Ferrè F, Helmer-Citterich M. Exploiting holistic approaches to model specificity in protein phosphorylation. Frontiers in Genetics. 5: 315. PMID 25324856 DOI: 10.3389/Fgene.2014.00315  1
2014 Ferrè F, Palmeri A, Helmer-Citterich M. Computational methods for analysis and inference of kinase/inhibitor relationships. Frontiers in Genetics. 5: 196. PMID 25071826 DOI: 10.3389/Fgene.2014.00196  1
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  1
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  1
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  1
2014 Pietrosanto M, Mattei E, Helmer-Citterich M, Ferré F. BEAM: a new method for RNA secondary structure motif discovery F1000research. 5. DOI: 10.7490/F1000Research.1096798.1  1
2013 Lanni S, Goracci M, Borrelli L, Mancano G, Chiurazzi P, Moscato U, Ferrè F, Helmer-Citterich M, Tabolacci E, Neri G. Role of CTCF protein in regulating FMR1 locus transcription. Plos Genetics. 9: e1003601. PMID 23874213 DOI: 10.1371/Journal.Pgen.1003601  1
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  1
2013 Gissi C, Romano P, Ferro A, Giugno R, Pulvirenti A, Facchiano A, Helmer-Citterich M. Bioinformatics in Italy: BITS 2012, the ninth annual meeting of the Italian Society of Bioinformatics. Bmc Bioinformatics. 14: S1. PMID 23815154 DOI: 10.1186/1471-2105-14-S7-S1  1
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  1
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  1
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  1
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  1
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  1
2013 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, et al. Peamaclein - A new peach allergenic protein: Similarities, differences and misleading features compared to Pru p 3 Clinical and Experimental Allergy. 43: 128-140. PMID 23278887 DOI: 10.1111/Cea.12028  1
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  1
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  1
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  1
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  1
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  1
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  1
2012 Fioravanti F, Helmer-Citterich M, Nardelli E. Modeling gene regulatory network motifs using Statecharts. Bmc Bioinformatics. 13: S20. PMID 22536967 DOI: 10.1186/1471-2105-13-S4-S20  0.01
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: 10.7490/F1000Research.2144.1  1
2012 Romano P, Helmer-Citterich M. Bioinformatics in Italy: BITS2011, the Eighth Annual Meeting of the Italian Society of Bioinformatics. Bmc Bioinformatics. 13: I1. PMID 22536954 DOI: 10.1186/1471-2105-13-S4-I1  1
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  1
2012 Bianchi V, Colantoni A, Helmer-Citterich M, Ferrè F. Role of alternative splicing in modulating protein-protein interactions Embnet.Journal. 18: 86-87. DOI: 10.14806/Ej.18.A.428  1
2012 Colantoni A, Ferrè F, Helmer-Citterich M. Alternative splicing as regulator of protein-protein interactions Embnet.Journal. 18: 35. DOI: 10.14806/Ej.18.A.383  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
2006 Ferraro E, Via A, Ausiello G, Helmer-Citterich M. A novel structure-based encoding for machine-learning applied to the inference of SH3 domain specificity. Bioinformatics (Oxford, England). 22: 2333-9. PMID 16870929 DOI: 10.1093/Bioinformatics/Btl403  1
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  1
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  1
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  1
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  1
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  1
2005 Helmer-Citterich M, Casadio R, Guffanti A, Mauri G, Milanesi L, Pesole G, Valle G, Saccone C. Overview of BITS2005, the Second Annual Meeting of the Italian Bioinformatics Society Bmc Bioinformatics. 6. DOI: 10.1186/1471-2105-6-S4-S1  1
2004 Via A, Helmer-Citterich M. A structural study for the optimisation of functional motifs encoded in protein sequences. Bmc Bioinformatics. 5: 50. PMID 15119965 DOI: 10.1186/1471-2105-5-50  1
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  1
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  1
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 Brannetti B, Helmer-Citterich M. iSPOT: A web tool to infer the interaction specificity of families of protein modules. Nucleic Acids Research. 31: 3709-11. PMID 12824399 DOI: 10.1093/Nar/Gkg592  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  1
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  1
2002 Politou AS, Spadaccini R, Joseph C, Brannetti B, Guerrini R, Helmer-Citterich M, Salvadori S, Temussi PA, Pastore A. The SH3 domain of nebulin binds selectively to type II peptides: theoretical prediction and experimental validation. Journal of Molecular Biology. 316: 305-15. PMID 11851340 DOI: 10.1006/Jmbi.2001.5312  1
2001 Brannetti B, Zanzoni A, Montecchi-Palazzi L, Cesareni G, Helmer-Citterich M. iSPOT: a web tool for the analysis and recognition of protein domain specificity. Comparative and Functional Genomics. 2: 314-8. PMID 18629248 DOI: 10.1002/Cfg.104  1
2000 Via A, Ferrè F, Brannetti B, Helmer-Citterich M. Protein surface similarities: a survey of methods to describe and compare protein surfaces Cellular and Molecular Life Sciences. 57: 1970-1977. PMID 11215522 DOI: 10.1007/Pl00000677  1
2000 Brannetti B, Via A, Cestra G, Cesareni G, Helmer-Citterich M. SH3-SPOT: an algorithm to predict preferred ligands to different members of the SH3 gene family. Journal of Molecular Biology. 298: 313-28. PMID 10764600 DOI: 10.1006/jmbi.2000.3670  0.36
2000 Citarella F, Velthuis Ht, Helmer-Citterich M, Hack CE. Identification of a putative binding site for negatively charged surfaces in the fibronectin type II domain of human factor XII--an immunochemical and homology modeling approach. Thrombosis and Haemostasis. 84: 1057-1065. DOI: 10.1055/S-0037-1614171  0.01
1998 de Rinaldis M, Ausiello G, Cesareni G, Helmer-Citterich M. Three-dimensional profiles: a new tool to identify protein surface similarities. Journal of Molecular Biology. 284: 1211-21. PMID 9837739 DOI: 10.1006/Jmbi.1998.2248  1
1998 Soucek L, Helmer-Citterich M, Sacco A, Jucker R, Cesareni G, Nasi S. Design and properties of a Myc derivative that efficiently homodimerizes. Oncogene. 17: 2463-72. PMID 9824157 DOI: 10.1038/Sj.Onc.1202199  1
1998 Murali R, Helmer-Citterich M, Sharkey DJ, Scalice ER, Daiss JL, Sullivan MA. Structural studies on an inhibitory antibody against Thermus aquaticus DNA polymerase suggest mode of inhibition. Protein Engineering. 11: 79-86. PMID 9605541 DOI: 10.1093/Protein/11.2.79  0.01
1997 Quondam M, Barbato C, Pickford A, Helmer-Citterich M, Macino G. Homology modeling of Neurospora crassa geranylgeranyl pyrophosphate synthase: structural interpretation of mutant phenotypes. Protein Engineering. 10: 1047-1055. PMID 9464568 DOI: 10.1093/Protein/10.9.1047  1
1997 Ausiello G, Cesareni G, Helmer-Citterich M. ESCHER: a new docking procedure applied to the reconstruction of protein tertiary structure. Proteins. 28: 556-67. PMID 9261871 DOI: 10.1002/(Sici)1097-0134(199708)28:4<556::Aid-Prot9>3.0.Co;2-7  1
1996 Zappavigna V, Falciola L, Helmer-Citterich M, Mavilio F, Bianchi ME. HMG1 interacts with HOX proteins and enhances their DNA binding and transcriptional activation The Embo Journal. 15: 4981-4991. DOI: 10.1002/J.1460-2075.1996.Tb00878.X  0.01
1995 Helmer-Citterich M, Rovida E, Luzzago A, Tramontano A. Modelling Antibody-Antigen Interactions : Ferritin As A Case Study Molecular Immunology. 32: 1001-1010. PMID 7476997 DOI: 10.1016/0161-5890(95)00027-C  1
1994 Marvin DA, Hale RD, Nave C, Helmer-Citterich M. Molecular models and structural comparisons of native and mutant class I filamentous bacteriophages Ff (fd, f1, M13), If1 and IKe. Journal of Molecular Biology. 235: 260-86. PMID 8289247 DOI: 10.1016/S0022-2836(05)80032-4  0.01
1991 Cesareni G, Helmer-Citterich M, Castagnoli L. Control of ColE1 plasmid replication by antisense RNA. Trends in Genetics : Tig. 7: 230-5. PMID 1887504 DOI: 10.1016/0168-9525(91)90370-6  1
1988 Helmer-Citterich M, Anceschi MM, Banner DW, Cesareni G. Control of ColE1 replication: low affinity specific binding of Rop (Rom) to RNAI and RNAII. The Embo Journal. 7: 557-566. DOI: 10.1002/J.1460-2075.1988.Tb02845.X  1
1983 Helmer-Citterich M, Morelli G, Macino G. Nucleotide sequence and intron structure of the apocytochrome b gene of Neurospora crassa mitochondria. The Embo Journal. 2: 1235-1242. DOI: 10.1002/J.1460-2075.1983.Tb01575.X  1
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