Manuela Helmer Citterich

Manuela Helmer-Citterich

CV

Personal information

1957

birth in Trieste, Italy

1987

married (a son in 1988, a daughter in 1990)

Education and training

1981

Degree in Physics, University of Rome La Sapienza

Thesis with prof. Mario Ageno in Biophysics

1981-1984

fellow with Giuseppe Macino, working on gene arrangement and transcription regulation in Neurospora crassa mitochondria (molecular biology)

1986-1988

EMBL (Heidelberg) post-doc with Gianni Cesareni, working on RNA-protein interaction in the ColE1 system (molecular biology)

1991-1993

guest scientist at IRBM with Anna Tramontano, developing a docking program, i.e. a software for the reconstruction of protein complexes starting from the 3d coordinates of their separated components (structural bioinformatics)

Employment

1984-1999

Research scientist, Dept of Biology, University of Rome Tor Vergata

1984-present

member of SIBBM (Italian Society of Biophysics and Molecular Biology)

1997-present

Group leader in the Dept of Biology, University of Rome, Tor Vergata

1998-present

Director of the Centre for Molecular Bioinformatics in the Dept of Biology, Univ of Rome Tor Vergata

2000-2004

Associate professor, Dept of Biology, University of Rome Tor Vergata

2003-present

member of BITS (Bioinformatics Italian Society)

2005 and present position

Full professor of Bioinformatics and Molecular Biology, Dept of Biology, University of Rome Tor Vergata

2004-2019

Coordinator of the Master Degree in Bioinformatics

Teaching

2002-present

Bioinformatics in the Degree in Biological Sciences (6 cfu)

2009-present

Molecular Biology and Bioinformatics in the Master Degree in Bioinformatics (9 cfu)

2013-present

Molecular Biology in the Degree in Biological Sciences (8 cfu)

Honours

2000-2004

Member of the Steering Committee of the European Science Foundation Programme in Functional Genomics

2009-2016

President of the Italian Society of Bioinformatics (BITS, http://bioinformatics.it)

2013-2017

Member of the PDBe Scientific Advisory Board (EBI)

2014-2019

Member of the INGM (National Institute of Molecular Genetics) Scientific Advisory Committee

2014-2019

Coordinator of the Master Degree in Bioinformatics in the University of Rome Tor Vergata

2016-present

Honorary President of the Italian Society of Bioinformatics

2017

BITS award 2017, Cagliari, July 2017

2019-present

Italian Representative in the 3D-Bioinfo ELIXIR Community

2020

Keynote speaker at RECOMB 2020

2020-present

Member of the Scientific Advisory Committee of ELIXIR Greece

2021

Member of the Advisory Committee Dipartimento di Eccellenza “Classe di Scienze” - Scuola Normale Superiore - Pisa

Research interests

Bioinformatics, Computational Biology, RNA analysis, Structure Bioinformatics, Molecular Interactions, Development of Computational Tools.

Autorizzo il trattamento dei dati personali contenuti nel mio curriculum vitae in base all’art. 13 del D. Lgs. 196/2003 e all’art. 13 del Regolamento UE 2016/679 relativo alla protezione delle persone fisiche con riguardo al trattamento dei dati personali.

Publications

- Latini S, Venafra V, Massacci G, Bica V, Graziosi S, Pugliese GM, Iannuccelli M, Frioni F, Minella J, Marra J, Chiusolo P, Pepe G, Helmer-Citterich M, Fischer T, Perfetto L, Sacco F. Unveiling the signaling network rewiring of FLT3-ITD AML improves drug sensitivity prediction. Molecular Systems Biology, in press.

- Latini A, Borgiani A, De Benedittis G, Ciccacci C, Novelli L, Pepe G, Helmer-Citterich M, Capulli M, Perricone C, Ceccarelli F, Conti F, Ianniciello G, Caceres J, Ottalevi R, Baldini I, Novelli G (2024). Large-scale DNA sequencing identifies rare variants associated with Systemic Lupus Erythematosus susceptibility in known risk genes. Gene, 13:148279.

- Candi E, Smirnov A, Lena AM, Tosetti G, Yang X, Cappello A, Helmer Citterich M, and Melino G. (2023). Epigenetic priming of an epithelial enhancer by p63 and CTCF controls expression of a skin-restricted gene XP33. Cell Death Discovery, 9(1):446.

- Marchionni E, D’Apice MR, Lupo V, Lattanzi G, Mattioli E, Lisignoli G, Gabusi E, Pepe G, Helmer Citterich M, Campione E, Nardone AM, Spitalieri P, Pucci N, Picchi E, Garaci F, Novelli A, Novelli G. (2023). Clinical and functional characterization of COL2A1 p.Gly444Ser variant: from a fetal phenotype to a previously undisclosed postnatal phenotype. Bone Rep.19:101728.

- Pericoli G, Galardi A, Paolini A, Petrilli LL, Pepe G, Palma A, Colletti M, Ferretti M, Giorda E, Levi Mortera S, Marzano V, Burford A, Carai A, Mastronuzzi A, Mackay A, Putignani L, Jones C, Pascucci L, Peinado H, Helmer-Citterich M, de Billy E, Masotti A, Locatelli F, Di Giannatale A, Vinci M. Inhibition of exosome biogenesis affects cell motility in heterogeneous sub-populations of paediatric-type diffuse high-grade gliomas. Cell & Biosciences, 13:207.

- Cirotti C, Taddei I, Contadini C, Di Girolamo C, Pepe G, De Bardi M, Borsellino G, Helmer-Citterich M, and Barila M. NRF2 connects Src tyrosine kinase to ferroptosis resistance in glioblastoma". Life Science Alliance. 7(1):e202302205.

- 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.

- Olmi L, Pepe G, Helmer-Citterich M, Canini A, Gismondi A. (2023). Looking for Plant microRNAs in Human Blood Samples: Bioinformatics Evidence and Perspectives. Plant Foods for Human Nutrition, https://doi.org/10.1007/s11130-023-01063-9.

- Pepe G, Appierdo R, Carrino C, Ballesio F, Helmer-Citterich M, Gherardini PF. Artificial intelligence methods enhance the discovery of RNA interactions. Frontiers in Molecular Biosciences, in press.

- 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, Bruno T, De Nicola F, Corleone G, Di Benedetto A, Ercolani C, Pescarmona E, Pizzuti L, Guidi F, Sperati F, Vitale S, Schiavoni, Mattei F, De Ninno A, Businaro L, Lucarini L, Bracci L, Aricò E, Ziccheddu G, Facchiano F, Rossi S, Sanchez M, Boe A, Biffoni M, De Maria R, Vitale I and Sistigu A (2022) Type I IFNs promote cancer cell stemness by triggering the epigenetic regulator KDM1B. Nature Immunology, 23(9):1379-1392.

- Pepe G, Carrino C, Parca L, and Helmer-Citterich M. Dissecting the genome for drug response prediction. Data Mining Techniques for the Life Sciences (Methods in Molecular Biology series), Springer, in press.  

- Pepe G, Parca L, Viviani L, Ausiello G, Helmer-Citterich M. (2022). Variation in the co-expression profile highlights a loss of miRNA-mRNA regulation in multiple cancer types. Noncoding RNA Res., 7(2), pp. 98–105. 

- Di Fraia D, Anitei M, Mackmull MT, Parca L, Behrendt L, Andres-Pons A, Gilmour D, Helmer-Citterich M, Kaether C, Beck M, Ori A. (2022). Conserved exchange of paralog proteins during neuronal differentiation. Life Science Alliance 5(6):e202201397.

- Pepe G, Guarracino A, Ballesio F, Parca L, Ausiello G, Helmer-Citterich M. (2022). Evaluation of potential sponge effects of SARS genomes in human. Noncoding RNA Res. 7(1):48-53.

- Lo Iacono L, Mancini, Babicola , Pietrosanto M, Di Segni M, Lica D’Addario S, Ielpo D, Pascucci T, Cabib S, D'Amato FR, Andolina D, Helmer-Citterich M, Cifani C, Ventura R. (2021) Attachment bond interference alters Ventral Tegmental Area transcriptomic patterning in a sex-dependent manner. Neurobiology of Stress, 15:100406.

- Galfrè SG, Morandin F, Pietrosanto M, Cremisi F, Helmer-Citterich M. COTAN: Co-expression Table Analysis for scRNA-seq data. Nucl. Acids Res. Genomics and Bioinformatics, NAR Genom Bioinform. 3(3):lqab072.

- Guarracino A, Pepe G, Ballesio F, Adinolfi M, Pietrosanto M, Sangiovanni E, Vitale I, Ausiello G, Helmer-Citterich M.(2021). BRIO: a web server for RNA sequence and structure motif scan. Nucleic Acids Res., 49(W1):W67-W71.

- Ferradini V, Parca L, Martino A, Lanzillo C, Silvetti E, Calò L, Caselli S, Novelli G, Helmer-Citterich M, Sangiuolo FC and Mango R (2021). Variants in MHY7 gene cause Arrhythmogenic Cardiomyopathy. Genes, 12(6):793.

- Martins M, Galfrè SG, 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, Cremisi FA (2021) Eutherian-specific microRNA controls the translation of Satb2 in a model of cortical differentiation. Stem Cell Reports, S2213-6711(21)00215-0.

- Pietrosanto M, Ausiello G, Helmer-Citterich M. (2021). Motif Discovery from CLIP Experiments. Methods Mol Biol. 2284:43-50.

- Pietrosanto M, Adinolfi M, Guarracino A, Ferrè F, Ausiello G, Vitale I, Helmer-Citterich M (2021). Relative Information Gain: Shannon entropy-based measure of the relative structural conservation in RNA alignments. Nucl. Acids Res. Genomics and Bioinformatics, NAR Genom Bioinform. 3(1):lqab007.

- 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. (2020).  COVID-19 and Genetic Variants of Protein Involved in the SARS-CoV-2 Entry into the Host Cells. Genes (Basel). 11(9):E1010.

- Helmer-Citterich M. (2020) A time for cooperation. Commentary about the role of algorithmics and computational biology in responding to the COVID-19 pandemic, Cell Systems 10(5):379

- Novelli G, Novelli A, Borgiani P, Cocciadiferro D, Biancolella M, Agolini E, Pietrosanto M, Casalone R, Helmer-Citterich M, Giardina E, Jain S, Wei W, Eng C, Pandolfi PP. (2020). WWP1 Germline Variants are Associated with Normocephalic Autism Spectrum Disorder. Cell Death & Disease, 11(7):529.

- Babicola L, Pietrosanto M, Ielpo D, D'Addario SL, Cabib S, Ventura R, Ferlazzo F, Helmer-Citterich M, Andolina D, Lo Iacono L. (2020). RISC RNA sequencing in the Dorsal Raphè reveals microRNAs regulatory activities associated with behavioral and functional adaptations to chronic stress. Brain Research, 1736:146763.

- 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, Soares C, Sussman JL, Thornton JM, Tuffery P, Tusnady G, Wierenga R, Salminen T, Schneider B. 2020. A Community Proposal to Integrate Structural Bioinformatics Activities in ELIXIR (3D-Bioinfo Community). F1000Res. 2020;9:ELIXIR-278.

- PDBe-kb Consortium (Varadi M, Berrisford J, Deshpande M, Nair SS, Gutmanas A, Armstrong D, Pravda L, Al-Lazikani B, Anyango S, Barton GJ, Berka K, Blundell T, Borkakoti N, Dana J, Das S, Dey S, Di Micco P, Fraternali F, Gibson T, Helmer-Citterich M, Hoksza D, Huang LC, Jain R, Jubb H, Kannas C, Kannan N, Koca J, Krivak R, Kumar M, Levy ED, Madeira F, Madhusudhan MS, Martell HJ, MacGowan S, McGreig JE, Mir S, Mukhopadhyay A, Parca P, Paysan-Lafosse T, Radusky L, Ribeiro A, Serrano L, Sillitoe I, Singh G, Skoda P, Svobodova R, Tyzack J, Valencia A, Villasclaras Fernandez E, Vranken W, Wass M, Thornton J, Sternberg M, Orengo C, Velankar S (2020). PDBe-KB: a community-driven resource for structural and functional annotations. Nucleic Acids Res. 2020 Jan 8;48(D1):D344-D353.

- Parca L, Pepe G, Pietrosanto M, Galvan G, Galli Leonardo, Palmeri A, Sciandrone M, Ferrè F, Ausiello G, Helmer-Citterich M.(2019) .Modeling cancer drug response through drug-specific informative genes. Sci. Rep 9(1):15222.

- Adinolfi M, Pietrosanto M, Parca L, Ausiello G, Ferrè F, Helmer-Citterich M. (2019). Discovering sequence and structure landscapes in RNA interaction motifs. Nucleic Acids Res. 47(10):4958-4969.

- Parca L, Ariano B, Cabibbo A, Paoletti M, Tamburrini A, Palmeri A, Ausiello G, Helmer-Citterich M. (2019). Kinome-wide identification of phosphorylation networks in eukaryotic proteomes. Bioinformatics. 35(3):372-379.

- Pietrosanto M, Adinolfi M, Casula R, Ausiello G, Ferrè F, Helmer-Citterich M. (2018). BEAM web server: A tool for structural RNA motif discovery. Bioinformatics, 34(6):1058-1060. PubMed PMID:29095974.

- 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. 

- 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. 7(22):33257-33271. 

- Mango R, Luchetti A, Sangiuolo R, Ferradini V, Briglia N, Giardina E, Ferrè F, Helmer Citterich M, Romeo F, Novelli G, Sangiuolo F. (2016). 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. 80:938-949. 

- Morini E, Rizzacasa B, Pucci S, Polidoro C, Ferrè F, Caporossi D, Helmer Citterich M, Novelli G, Amati F. (2016). The human rs1050286 polymorphism alters LOX-1 expression through modifying miR-24 binding. J Cell Mol Med.  20:181-187. 

- 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. 9:12.  

- 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.

- 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., [Epub ahead of print] PubMed PMID: 26542080.

- 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].

- 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.,43:W493-497. 

- 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. (2015). AMBRA1 links  autophagy to cell proliferation and tumorigenesis by promoting c-Myc dephosphorylation and degradation. Nat Cell Biol. 17:706. 

- 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. 

- 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. (2015) AMBRA1 links autophagy to cell proliferation  and tumorigenesis by promoting c-Myc dephosphorylation and degradation. Nat Cell  Biol. 17:20-30. 

- Palmeri A, Ferrè F, Helmer-Citterich M. (2014). Exploiting holistic approaches to model specificity in protein phosphorylation. Front Genet, 5:315.   80) Ferrè F, Palmeri A, Helmer-Citterich M. (2014). Computational methods for analysis and inference of kinase/inhibitor relationships. Front Genet. 5:196.

- Palmeri A, Ausiello G, Ferrè F, Helmer-Citterich M, Gherardini PF (2014). A proteome-wide domain-centric perspective on protein phosphorylation. Mol. Cell. proteomics, :13,9; 2198-2212.

- Mattei E, Ausiello G, Ferrè F, Helmer-Citterich M. (2014). A novel approach to represent and compare RNA secondary structures. Nucleic Acids Res. 42(10):6146-6157.   

- Tsigankov P, Gherardini PF, Helmer-Citterich M, Späth GF, Myler PJ, Zilberstein D. (2014) Regulation dynamics of Leishmaniadifferentiation: deconvoluting signals and identifying phosphorylation trends. Mol. Cell. Proteomics 2014 Apr 16. [Epub ahead of print]

- Lanni S, Goracci M, Borrelli L, Mancano G, Chiurazzi P, Moscato U, Ferre' F, Helmer-Citterich M, Tabolacci E, Neri G. (2013). Role of CTCF Protein in Regulating FMR1 Locus Transcription. PLoS Genet. 2013 Jul;9(7):e1003601.    

- Bianchi V, Colantoni A, Calderone A, Ausiello G, Ferre' F, Helmer-Citterich M. (2013). DBATE: DataBase of Alternative Transcripts Expression. Database, 2013:bat050.   

- Colantoni A, Bianchi V, Gherardini PF, Scalia Tomba G, Ausiello G, Helmer-Citterich M, Ferre' F. (2013). Alternative splicing tends to avoid partial removals of protein-protein interaction sites. BMC Genomics, 14:379.   

- Parca L, Ferre' F, Ausiello G, Helmer Citterich M. Nucleos: a web server for the identification of nucleotide-binding sites in protein structures. Nucl Acids Res 2013 May 22. [Epub ahead of print] PubMed PMID: 23703207.   

- Bianchi V, Mangone I, Ferre' F, Helmer-Citterich M, Ausiello G. The webPDBinder server for the identification of ligand binding sites on protein structures. Nucl Acids Res 2013 Jun 3. [Epub ahead of print] PubMed PMID: 23737450.   

- Tsigankov P, Gherardini PF, Helmer Citterich M, Spaeth GF, Zilberstein D. (2013). Phosphoproteomic analysis of differentiating Leishmania parasites reveals unique stage-specific phosphorylation motif. J Proteome Res. 2013 May 21. [Epub ahead of print]   

- Leclercq O, Bartho K, Duelsner E, von Kleist L, Gherardini PF, Palmeri A, Helmer-Citterich M, Baumgart S, Spaeth GF. (2013). Enrichment of Leishmania donovani ATP-binding proteins using a staurosporine Capture Compound. J Proteomics. 2013 May 15. [Epub ahead of print]

- 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. (2013). Peamaclein – A new peach allergenic protein: similarities, differences and misleading features compared to Pru p 3. Clinical And Experimental Allergy, 43(1):128-140.

- Gherardini PF, Helmer-Citterich M. (2012). Experimental and computational methods for the analysis and modeling of signaling networks. N. Biotechnol, S1871-6784(12)00864-3.   67) Parca L, Gherardini PF, Truglio M, Mangone I, Ferre' F, Helmer-Citterich M, Ausiello G. (2012). Identification of nucleotide-binding sites in protein structures: a novel approach based on nucleotide modularity. PLoS One, 7(11):e50240.

- Perfetto L, Gherardini PF, Davey NE, Diella F, Helmer-Citterich M, Cesareni G. (2012). Exploring the diversity of SPRY/B30.2-mediated interactions. TiBS, 38:38-46.

- Sacco F, Gherardini PF, Paoluzi S, Saez-Rodriguez J, Helmer-Citterich M, Ragnini A, Castagnoli L, Cesareni C. (2012). Mapping the human phosphatome on growth pathways. Mol. Syst. Biol., 8:603. 

- Giaco' L, Amicosante M, Fraziano M, Gherardini PF, Ausiello G, Helmer-Citterich M, Colizzi V, Cabibbo A. (2012). B-Pred, a structure based B-cell epitopes prediction server. Adv Appl Bioinform Chem, 5:11-21. 

- Minguez P, Parca L, Diella F, Mende DR, Kumar R, Helmer-Citterich M, Gavin AC, van Noort V, Bork P (2012). Deciphering a global network of functionally associated post-translational modifications. Mol. Syst. Biol, 8:599.

- Fioravanti F, Helmer-Citterich M, Nardelli E. (2012). Modeling Gene Regulatory Network Motifs using Statecharts. BMC Bioinformatics,13(Suppl 4):S20.

- Bianchi V, Gherardini PF, Helmer-Citterich M, Ausiello G. (2012). Identification of binding pockets in protein structures using a knowledge-based potential derived from local structural similarities. BMC Bioinformatics, 13(Suppl 4):S17.

- Tsigankov P, Gherardini PF, Helmer-Citterich M, Zilberstein D. (2012). What have proteomics taught us about Leishmaniadevelopment inside its host? Parasitology, 28:1-12.

- Palmeri A, Gherardini PF, Tsigankov P, Ausiello G, Späth GF, Zilberstein D, Helmer-Citterich M. (2011) PhosTryp: a phosphorylation sites predictor specific for parasitic protozoa of the family trypanosomatidae. BMC Genomics, 12:614.

- Parca L, Mangone I, Gherardini PF, Ausiello G, Helmer-Citterich M (2011). Phosfinder: a web server for the identification of phosphate binding sites on protein structures. Nucl. Acids Res. 39(Web Server issue):W278-282. May 26. [Epub ahead of print].

- Schmidt-Arras,D., Leclercq, O., Gherardini, P.F., Helmer-Citterich, M., Faigle, W., Loew, D., Spaeth, G. (2011). Adaptation of a 2D in-gel kinase assay to trace phosphotransferase activities in the human pathogen Leishmania donovani. J Proteomics, 74(9):1644-1651.   

- Via, A., Diella, F., Gibson, TJ., Helmer-Citterich, M. (2011). From sequence to structural analysis in protein phosphorylation motifs. Frontiers in Bioscience, 16: 1261-1275.   

- Zanzoni A, Carbajo D, Diella F, Gherardini PF, Tramontano A, Helmer-Citterich M, Via A (2011). Phospho3D 2.0: An enhanced database of three-dimensional structures of phosphorylation sites. Nucl. Acids Res., 39 (Database issue): D268-71.    

- Parca L, Gherardini PF, Helmer-Citterich M, Ausiello G (2010). Phosphate binding-sites identification in protein structures. Nucl. Acids Res., 39(4):1231-1242.   

- Gherardini, PF, Ausiello, A, Helmer-Citterich, M. (2010). Superpose3D: a local structural comparison program that allows for user-defined structure representations. PLoS One, 5(8): e11988.   

- Hem, S, Gherardini, PF, Fortea, JO, Hourdel, V, Morales, MA, Watanabe, R, Pescher, P, Kuzyk, MA, Smith, D, Borchers, CH, Zilberstein, D, Helmer-Citterich, M, Namane, A, Spaeth GF (2010). Identification of Leishmania-specific protein phosphorylation sites by LC-MS/MS and comparative genomics analyses. Proteomics, 21: 3868-6883.   

- 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, Spaeth GF (2010). Cyclosporin A treatment of Leishmania donovani reveals stage-specific functions of cyclophilins in parasite differentiation, proliferation, and viability. PLoS Negl Trop Dis., 4(6):e729.   

- Gherardini, PF, Ausiello, G, Russell, RB, Helmer-Citterich, M (2010). Modular architecture of nucleotide binding pockets. Nucl. Acids Res., 38: 3809-3816. [Epub 2010 Feb 25].   

- Gould, C., Diella, F., Via, A., Puntervoll, P., Gemuend, C., Michael, S., Sayadi, A., Bryne, JC., Chica, C., Davey, N., Haslam, N., Budd, A., Hughes, T., Pas, J., Rychlewski, L., Trave', G., Aasland, R., Helmer-Citterich, M., Linding, R., Gibson, TJ. (2010) ELM: The status of the 2010 Eukaryotic Linear Motif Resource. Nucl. Acids Res., 38(Database issue):D167-180.    

- Via, A., Gould, C.M., Gemuend, C., Gibson, TJ, Helmer-Citterich, M. (2009) A structure filter for the Eukaryotic Linear Motif Resource. BMC Bioinformatics, 10(1):351.   

- Ausiello, G., Gherardini, P.F., Gatti, E., Incani, O., Helmer-Citterich, M. (2009). Structural motifs recurring in different folds recognize the same ligand fragments. BMC Bioinformatics, 10:182.

- Gherardini, PF, Helmer-Citterich, M. (2008). Structure-based function prediction: approaches and applications. Brief Funct Genomic Proteomic, 7:291-302.

- Ausiello, G., Gherardini, P.F., Marcatili, P., Tramontano, A., Via, A., Helmer-Citterich, M. (2008). FunClust: A web server for the identification of structural motifs in a set of non-homologous protein structures. BMC Bioinformatics, 9,(Suppl. 2): S1.

- Gherardini, P.F., Wass, M.N., Helmer-Citterich, M., Sternberg, M.J. (2007). Convergent Evolution of Enzyme Active Sites Is not a Rare Phenomenon. J Mol Biol., 372:817-845.

- Ferraro, E., Peluso, D., Via, A., Ausiello, G., Helmer-Citterich, M. (2007) SH3-Hunter: discovery of SH3 domain interaction sites in proteins. Nucl. Acids Res., 35:W451-454.

- Via, A., Peluso, D., Gherardini, P.F., de Rinaldis, E., Colombo, T., Ausiello, G., Helmer-Citterich, M. (2007) 3dLOGO: a web server for the identification, analysis and use of conserved protein substructures. Nucl. Acids Res., 35:W416-419.

- Ausiello, G., Peluso, D., Via, A., Helmer-Citterich, M. (2007). Local comparison of protein structures highlights cases of convergent evolution in analogous functional sites. BMC Bioinformatics, 8(Suppl.1): S24.

- Via, A., Gherardini, P.F., Ferraro, E., Ausiello, G., Scalia Tomba, G. and Helmer-Citterich, M. (2007). False occurrences of functional motifs in protein sequences highlight evolutionary constraints. BMC Bioinformatics, 8:68.

- Casadio, R., Helmer-Citterich, M., Pesole, G. (2007). Bioinformatics in Italy: BITS2006, the third annual meeting of the Italian Society of Bioinformatics. BMC Bioinformatics, 8 (Suppl.1): S1.

- Zanzoni, A., Ausiello, G., Via, A., Gherardini, P.F., Helmer-Citterich, M. (2007). Phospho3D: a database of three-dimensional structures of protein phosphorylation sites. Nucl. Acids Res., 35:D229-D23.

- Ferraro, E., Via, A., Ausiello, G., Helmer-Citterich, M. (2006) A novel structure-based encoding for machine-learning applied to the inference of SH3 domain specificity. Bioinformatics, 22:2333-2339.

- Ferraro, E., Via, A., Ausiello, G., Helmer-Citterich, M. (2005). A neural strategy for the inference of SH3 domain-peptide interaction specificity. BMC Bioinformatics, 6(Suppl 4):S13.

- Ausiello, G., Via, A., Helmer-Citterich, M. (2005). Query3d: a new method for high-throughput analysis of functional residues in protein structures. BMC Bioinformatics, 6(Suppl 4):S5.

- Helmer-Citterich, M., Casadio, R., Guffanti, A., Mauri, G., Milanesi, L., Pesole, G., Valle, G., Saccone, C. (2005). Overview of BITS2005, the Second Annual Meeting of the Italian Bioinformatics Society. BMC Bioinformatics, 6(Suppl 4):S1.

- Ferrè, F., Ausiello, G., Zanzoni, A., Helmer-Citterich, M. (2005). Functional annotation by identification of local surface similarities: a novel tool for structural genomics. BMC Bioinformatics, 6:19.

- Ausiello, G., Zanzoni, A., Peluso, D., Via, A., Helmer-Citterich, M. (2005) pdbFun: Mass selection and fast comparison of annotated PDB residues. Nucl.Acids Res., 33:133-137.

- Via, A., Zanzoni, A., Helmer-Citterich, M (2005). Seq2Struct: a resource for establishing sequence-structure links. Bioinformatics,21:551-552. Epub 2004 Sep 28.

- Via, A, Helmer-Citterich, M (2004). A structural study for the optimisation of functional motifs encoded in protein sequences BMC Bioinformatics, 5, 50.

- Ferrè, F., Ausiello, G., Zanzoni, A., Helmer-Citterich, M. (2004). SURFACE: a database of protein surface regions for functional annotation. Nucl.Acids Res., 32, 240-244.

- Ferrè, F., Via, A., Ausiello, G., Brannetti, B., Zanzoni, A., Helmer-Citterich, M. (2003). Development of computational tools for the inference of protein interaction specificity rules and functional annotation using structural information. Comparative and Functional Genomics, 4, 416-419.

- Cesareni, G., Helmer-Citterich, M. (2003) Searching the MINT database for protein interaction information. Protocols in Bioinformatics, John Wiley & Sons, Inc., 8.5.1-8.5.13.

- Brannetti, B., Helmer-Citterich, M. (2003) iSPOT: a web tool to infer the interaction specificity of families of protein modules. Nucl. Acids Res., 31: 3709-3711.

- Puntervoll, P., Linding, R., Gemuend, C., Chabanis-Davidson, S., Mattingsdal, M., Cameron, S., Martin, D.M.A., Ausiello, G., Brannetti, B., Costantini, A., Ferrè, F., Maselli, V., Via, A., Cesareni, G., Diella, F., Superti-Furga, G., Wyrwicz, Ramu, C., McGuigan, C., Gudavalli, R., Letunic, I., Bork, P., Rychlewski, Kuester, B., Helmer-Citterich, M., Hunter, W.N., Aasland, R. and Gibson, T. (2003) ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins. Nucl. Acids Res., 31: 3625-3630

- Politou, A.S., Spadaccini, R., Joseph, C., Brannetti, B., Guerrini, R., Helmer-Citterich, M., Salvadori, S., Temussi, P.A. and Pastore, A. (2002). The SH3 domain of nebulin binds selectively to type II peptides: theoretical prediction and experimental validation. J Mol Biol. 316:305-315.

- Zanzoni, A., Montecchi-Palazzi, L., Quondam, M., Ausiello, G., Helmer-Citterich, M. and Cesareni, G. (2002). MINT: a Molecular INTeraction database. FEBS Letters.513, 135-140.

- Brannetti, B., Zanzoni, A., Montecchi Palazzi, L., Cesareni, G. and Helmer-Citterich, M. (2001). iSPOT: a web tool for the analysis and recognition of protein domain specificity. Comparative and Functional Genomics, 2, 314-318.

- Vaccaro, P., Brannetti, B., Montecchi Palazzi, L., Philipp, S., Helmer Citterich, M., Cesareni, G. and Dente, L. (2001). Distinct binding specificity of the multiple PDZ domains of the human INADL, a human protein with homology to INAD from Drosophila melanogaster. J.Biol.Chem., 276, 42122-42130.

- Citarella, F., Velthuis, H., Helmer Citterich, M. and Hack, C.E. (2000). Identification of a 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.

- Via, A., Ferre' F., Brannetti, B. and Helmer Citterich, M. (2000) Protein surface similarities: a survey of methods to describe and compare protein surfaces. Cell. Mol.Life Sci., 57, 1970-1977.

- Via, A., Ferre', F., Brannetti, B., Valencia, A. and Helmer Citterich, M. (2000). 3D view of the surface motif associated to the Ploop structure: cis and trans cases of convergent evolution. J.Mol.Biol., 303, 455-465.

- Brannetti, B., Via, A., Cestra, G., Cesareni, G. and Helmer Citterich, M. (2000) SH3-SPOT: an algorithm to predict preferred ligands of different members of the SH3 gene family. J.Mol.Biol, 298, 313-328.

- De Rinaldis, M., Ausiello, G., Cesareni, G. and Helmer Citterich, M. (1998) Three-dimensional profiles: a new tool to identify protein surface similarities. J.Mol.Biol., 284,1211-1221.

- Soucek, L., Helmer Citterich, M., Sacco, A., Jucker, R., Cesareni, G. and Nasi, S. (1998) Design and properties of a Myc derivative that efficiently homodimerizes. Oncogene, 17:2463-2472.

- Murali, R., Helmer Citterich, M., Sharkey, D.J., Scalice, E., Daiss, J. and Murthy, K. (1998) Structural studies on a inhibitory antibody against Thermus aquaticus DNA polymerase suggest mode of inhibition. Prot. Eng., 11(2):79-86.

- Quondam,M., Barbato,C., Pickford,A., Helmer Citterich,M. and Macino,G. (1997) Structural conservation in prenyltransferases: structural analysis and modeling of Neurospora crassa geranylgeranyl pyrophosphate synthase. Prot. Eng., 10, 1047-1055.

- Pazos,F., Helmer Citterich,M., Ausiello,G. and Valencia,A. (1997).Protein docking with sequences. Correlated mutations contain information about protein-protein interaction. J.Mol.Biol., 271, 511-523.

- Ausiello,G., Cesareni,G. and Helmer Citterich,M. (1997). ESCHER: a new docking procedure applied to the reconstruction of protein tertiary structure. Proteins, 28, 556-567. 

- Zappavigna,V., Falciola,L., Helmer Citterich,M., Mavilio,F. and Bianchi,M.E. (1996) HMG1 cooperates with HOX proteins in DNA binding and transcriptional activation. EMBO Journal, 15, 4981 - 4991.

- Hubbard,T., Tramontano,A., Barton,G., Jones,D., Sippl,M., Valencia,A., Lesk,A., Moult,J., Rost,B., Sander,C., Schneider,R., Lahm,A., Leplae,R., Buta,C., Eisenstein,M., Fjellstr^m,O., Floeckner,H., Grossman,G., Hansen,J., Helmer Citterich,M., Joergensen,F.S., Marchler-Bauer, A., Osuna,J., Park,J., Reinhardt,A., Ribas de Pouplana,L., Rojo-Dominguez,A., Saudek,V., Sinclair,J., Sturrock,S., Venclovas,C., Vinals,C. (1996). Update on protein structure prediction: results of the IRBM 1995 workshop. Folding and Design, 1, 55-63.

- Helmer Citterich,M., Rovida,E., Luzzago,A. and Tramontano,A. (1995). Modelling antibody antigen interactions: ferritin as a case study. Molecular Immunology, 32, 1001-1010.

7) Helmer Citterich,M. and Tramontano,A. (1994). PUZZLE: a new method for automated protein docking based on surface shape complementarity. J.Mol.Biol., 235, 1021-1031.

6) Marvin,D.A., Hale,R.D., Nave,C. and Helmer Citterich,M. (1994). Molecular models and structural comparisons of native and mutant class I filamentous bacteriophages Ff (fd, f1, M13), If1 and IKe. J.Mol.Biol., 235, 260-286.

5) Cesareni, G., Helmer Citterich, M. and Castagnoli, L. (1991). Control of ColE1 replication by antisense RNA. Trends in Genetics, 7, 230-235.

4) Helmer Citterich,M. (1988). Il presunto secondo codice. Sapere, 8/9, 79-84.

3) Helmer Citterich,M., Anceschi,M., Banner,D.W. and Cesareni,G. (1988). Control of ColE1 replication: Low affinity specific binding of Rop to RNAI and RNAII. EMBO Journal, 7, 557-566.

2) Burger,G., Helmer Citterich,M., Nelson,M.A., Werner,S. and Macino,G. (1985). RNA processing in Neurospora crassamitochondria: transfer RNAs punctuate a large precursor transcript. EMBO Journal, 4,197-204.

1) Helmer Citterich,M., Morelli,G. and Macino,G. (1983). Nucleotide sequence and intron structure of the apocytochrome b gene of Neurospora crassa mitochondria. EMBO Journal, 2,1235-1242. 

Books

1)  The Internet for Cell and Molecular Biologists - ed. A. Cabibbo, R.P. Grant, M. Helmer-Citterich , Horizon Scientific Press, 368 pages, April 2002, ISBN: 1-898486-32-8  (hbk).  

2) Valle, G., Helmer-Citterich, M. , Attimonelli,  M., Pesole, G. (2003) Introduzione alla Bioinformatica -  ed. Zanichelli, ISBN 8808079678.

3) The Internet for Cell and Molecular Biologists (2nd edition) - ed. A. Cabibbo, R.P. Grant, M. Helmer-Citterich , Horizon Scientific Press, 452 pages, August 2004, ISBN: 0-9545232-0-2, paperback.

4) Helmer-Citterich M, Ferrè F, Pavesi G, Romualdi C, Pesole G (2018). Fondamenti di Bioinformatica. Ed Zanichelli ISBN-10: 880862112X

Autorizzo il trattamento dei dati personali contenuti nel mio curriculum vitae in base all’art. 13 del D. Lgs. 196/2003 e all’art. 13 del Regolamento UE 2016/679 relativo alla protezione delle persone fisiche con riguardo al trattamento dei dati personali.

Roma 13 luglio 2021

(Manuela Helmer Citterich)