Year |
Citation |
Score |
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 |
0.353 |
|
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 |
0.385 |
|
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 |
0.311 |
|
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 |
0.318 |
|
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 |
0.421 |
|
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 |
0.373 |
|
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 |
0.638 |
|
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 |
0.355 |
|
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 |
0.308 |
|
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 |
0.401 |
|
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 |
0.467 |
|
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 |
0.343 |
|
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 |
0.311 |
|
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 |
0.319 |
|
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 |
0.469 |
|
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 |
0.445 |
|
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 |
0.452 |
|
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 |
0.374 |
|
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 |
0.429 |
|
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 |
0.322 |
|
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 |
0.343 |
|
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 |
0.469 |
|
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 |
0.307 |
|
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 |
0.421 |
|
2012 |
Palmeri A, Helmer-Citterich M, Gherardini P. Domain-context information for the improvement of phosphorylation site prediction Embnet.Journal. 18: 120. DOI: 10.14806/Ej.18.A.448 |
0.388 |
|
2012 |
Mangone I, Helmer-Citterich M, Ausiello G. Assessment of structure-based functional annotation methods on protein 3D models Embnet.Journal. 18: 115. DOI: 10.14806/Ej.18.A.445 |
0.47 |
|
2012 |
Mattei E, Gherardini P, Ausiello G, Helmer-Citterich M. A software pipeline for the discovery of variations in exome sequencing projects Embnet.Journal. 18: 103. DOI: 10.14806/Ej.18.A.434 |
0.344 |
|
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 |
0.429 |
|
2012 |
Gherardini P, Sacco F, Paoluzi S, Saez-Rodriguez J, Helmer-Citterich M, Ragnini-Wilson A, Castagnoli L, Cesareni G. A combined computational/experimental strategy to map phosphatases on growth pathways Embnet.Journal. 18: 28. DOI: 10.14806/Ej.18.A.395 |
0.371 |
|
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 |
0.481 |
|
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 |
0.343 |
|
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 |
0.47 |
|
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 |
0.362 |
|
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 |
0.407 |
|
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 |
0.456 |
|
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 |
0.71 |
|
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 |
0.38 |
|
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 |
0.439 |
|
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 |
0.361 |
|
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 |
0.427 |
|
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 |
0.508 |
|
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 |
0.493 |
|
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 |
0.443 |
|
2009 |
Sternberg M, Ali SN, Helmer-Citterich M, Gherardini PF, Fleming K, Kelley LA, Wass MN. Evolution of protein structure and function Comparative Biochemistry and Physiology Part a: Molecular & Integrative Physiology. 153: S47. DOI: 10.1016/J.Cbpa.2009.04.499 |
0.444 |
|
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 |
0.437 |
|
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 |
0.5 |
|
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 |
0.367 |
|
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 |
0.503 |
|
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 |
0.452 |
|
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 |
0.472 |
|
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 |
0.428 |
|
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 |
0.732 |
|
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 |
0.471 |
|
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 |
0.468 |
|
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 |
0.396 |
|
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 |
0.736 |
|
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 |
0.752 |
|
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 |
0.741 |
|
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 |
0.436 |
|
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 |
0.716 |
|
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 |
0.765 |
|
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 |
0.456 |
|
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 |
0.48 |
|
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 |
0.713 |
|
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 |
0.371 |
|
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 |
0.72 |
|
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 |
0.468 |
|
2000 |
Via A, Ferrè F, Brannetti B, Valencia A, Helmer-Citterich M. Three-dimensional view of the surface motif associated with the P-loop structure: cis and trans cases of convergent evolution. Journal of Molecular Biology. 303: 455-65. PMID 11054283 DOI: 10.1006/Jmbi.2000.4151 |
0.479 |
|
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 |
0.338 |
|
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 |
0.375 |
|
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 |
0.491 |
|
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 |
0.429 |
|
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 |
0.347 |
|
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 |
0.371 |
|
1997 |
Pazos F, Helmer-Citterich M, Ausiello G, Valencia A. Correlated mutations contain information about protein-protein interaction. Journal of Molecular Biology. 271: 511-23. PMID 9281423 DOI: 10.1006/Jmbi.1997.1198 |
0.486 |
|
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 |
0.437 |
|
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 |
0.407 |
|
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 |
0.313 |
|
1994 |
Helmer-Citterich M, Tramontano A. PUZZLE: a new method for automated protein docking based on surface shape complementarity. Journal of Molecular Biology. 235: 1021-31. PMID 7507171 DOI: 10.1006/Jmbi.1994.1054 |
0.395 |
|
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 |
0.342 |
|
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 |
0.38 |
|
Low-probability matches (unlikely to be authored by this person) |
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 |
0.299 |
|
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 |
0.299 |
|
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 |
0.296 |
|
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 |
0.292 |
|
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 |
0.291 |
|
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 |
0.288 |
|
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 |
0.287 |
|
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 |
0.287 |
|
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 |
0.286 |
|
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 |
0.285 |
|
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 |
0.283 |
|
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 |
0.277 |
|
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 |
0.274 |
|
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 |
0.27 |
|
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 |
0.262 |
|
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 |
0.259 |
|
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 |
0.249 |
|
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 |
0.244 |
|
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 |
0.241 |
|
2012 |
Ferro A, Giugno R, Pulvirenti A, D'Elia D, Helmer-Citterich M, Romano P. Preface - BITS 2012: Ninth Annual Meeting of the Bioinformatics Italian Society Embnet.Journal. 18: 4. DOI: 10.14806/Ej.18.A.466 |
0.241 |
|
2012 |
Helmer-Citterich M, Romano P. The Bioinformatics Italian Society Embnet.Journal. 18: 3. DOI: 10.14806/Ej.18.A.467 |
0.24 |
|
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 |
0.238 |
|
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 |
0.233 |
|
2020 |
Orengo C, Velankar S, Wodak S, Zoete V, Bonvin AM, 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: 278. DOI: 10.12688/f1000research.20559.1 |
0.229 |
|
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 |
0.228 |
|
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 |
0.223 |
|
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 |
0.22 |
|
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 |
0.216 |
|
2007 |
Mari A, Palazzo P, Pomponi D, Helmer-Citterich M, Zennaro D, Giani M, Scala E. Comparative Analysis of Extract-based Skin Test and IgE detection, Singleplexed Molecule-based IgE Detection and a Molecule-based Microarray System Journal of Allergy and Clinical Immunology. 119: S266. DOI: 10.1016/J.Jaci.2006.12.412 |
0.21 |
|
2023 |
Ballarino M, Pepe G, Helmer-Citterich M, Palma A. Exploring the landscape of tools and resources for the analysis of long non-coding RNAs. Computational and Structural Biotechnology Journal. 21: 4706-4716. PMID 37841333 DOI: 10.1016/j.csbj.2023.09.041 |
0.208 |
|
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 |
0.186 |
|
2023 |
Olmi L, Pepe G, Helmer-Citterich M, Canini A, Gismondi A. Looking for Plant microRNAs in Human Blood Samples: Bioinformatics Evidence and Perspectives. Plant Foods For Human Nutrition (Dordrecht, Netherlands). PMID 37256506 DOI: 10.1007/s11130-023-01063-9 |
0.17 |
|
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 |
0.127 |
|
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 |
0.123 |
|
2022 |
Pepe G, Carrino C, Parca L, Helmer-Citterich M. Dissecting the Genome for Drug Response Prediction. Methods in Molecular Biology (Clifton, N.J.). 2449: 187-196. PMID 35507263 DOI: 10.1007/978-1-0716-2095-3_7 |
0.118 |
|
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 |
0.113 |
|
2023 |
Cirotti C, Taddei I, Contadini C, Di Girolamo C, Pepe G, De Bardi M, Borsellino G, Helmer-Citterich M, Barilà D. NRF2 connects Src tyrosine kinase to ferroptosis resistance in glioblastoma. Life Science Alliance. 7. PMID 37879937 DOI: 10.26508/lsa.202302205 |
0.078 |
|
2021 |
Lo Iacono L, Mancini C, Babicola L, Pietrosanto M, Di Segni M, D'Addario SL, Municchi D, Ielpo D, Pascucci T, Cabib S, Ferlazzo F, D'Amato FR, Andolina D, Helmer-Citterich M, Cifani C, et al. Early life adversity affecting the attachment bond alters ventral tegmental area transcriptomic patterning and behavior almost exclusively in female mice. Neurobiology of Stress. 15: 100406. PMID 34660854 DOI: 10.1016/j.ynstr.2021.100406 |
0.077 |
|
2022 |
Pepe G, Parca L, Viviani L, Ausiello G, Helmer-Citterich M. Variation in the co-expression profile highlights a loss of miRNA-mRNA regulation in multiple cancer types. Non-Coding Rna Research. 7: 98-105. PMID 35387279 DOI: 10.1016/j.ncrna.2022.03.003 |
0.074 |
|
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 |
0.071 |
|
2008 |
Pesole G, Helmer-Citterich M. Bioinformatics in Italy: BITS2007, the fourth annual meeting of the Italian Society of Bioinformatics Bmc Bioinformatics. 9. DOI: 10.1186/1471-2105-9-S2-S1 |
0.071 |
|
2007 |
Casadio R, Helmer-Citterich M, Pesole G. Bioinformatics in Italy: BITS2006, the third annual meeting of the Italian Society of Bioinformatics Bmc Bioinformatics. 8. DOI: 10.1186/1471-2105-8-S1-S1 |
0.07 |
|
2023 |
Pericoli G, Galardi A, Paolini A, Petrilli LL, Pepe G, Palma A, Colletti M, Ferretti R, Giorda E, Levi Mortera S, Burford A, Carai A, Mastronuzzi A, Mackay A, Putignani L, ... ... Helmer-Citterich M, et al. Inhibition of exosome biogenesis affects cell motility in heterogeneous sub-populations of paediatric-type diffuse high-grade gliomas. Cell & Bioscience. 13: 207. PMID 37957701 DOI: 10.1186/s13578-023-01166-5 |
0.059 |
|
2022 |
Musella M, Guarracino A, Manduca N, Galassi C, Ruggiero E, Potenza A, Maccafeo E, Manic G, Mattiello L, Soliman Abdel Rehim S, Signore M, Pietrosanto M, Helmer-Citterich M, Pallocca M, Fanciulli M, et al. Type I IFNs promote cancer cell stemness by triggering the epigenetic regulator KDM1B. Nature Immunology. PMID 36002648 DOI: 10.1038/s41590-022-01290-3 |
0.059 |
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