• Istituto di Biologia e Patologia Molecolari


Tel :+39 06 49910556
Fax :+39 06 4440062
allegra.via@cnr.it
ALLEGRA VIA
Researcher

IBPM-CNR @ Biochemical Science A.Rossi Fanelli
Sapienza University of Rome
P.le Aldo Moro 5
RESEARCH INTERESTS
I’m a bioinformatician and scientific researcher at the Institute of Molecular Biology and Pathology (IBPM) of the National Research Council (CNR, Rome, IT). In 2003, I got my PhD at the University of Rome “Tor Vergata”, where I also worked six years as postdoc. In 2009 I moved to the Sapienza University as researcher, and, since January 2014, I’m the ELIXIR Italy Training Coordinator. I’m involved in the design, organisation and delivery of bioinformatics training courses, in Train the Trainer activities, and collaborate with other ELIXIR’s nodes on many training-related initiatives. My main research interests include protein structural bioinformatics, protein structure and function prediction and analysis, and protein interactions. I’m also strongly interested in what researchers have discovered about how people learn and how best to teach them, and how research findings in the science of learning (educational psychology) can be translated into common teaching practice. Since 2016, educational psychology is the main focus of my research activities. I’m a member of the Global Organisation of Bioinformatics Learning, Education and Training (GOBLET) and a Software/Data Carpentry Instructor and Instructor Trainer.
SELECTED PUBLICATIONS

PEER REVIEWED PUBLICATIONS (since 2010)

  1. Via A, Attwood TK, Fernandes PL, Morgan SL, Schneider MV, Palagi PM, Rustici G and Tractenberg RE (2017) A new pan-European Train-the-Trainer Programme for bioinformatics: Pilot results on feasibility, utility and sustainability of learning. Briefings in Bioinformatics. In press.
  2. Morgan SL, Palagi PM, Fernandes PL, Koperlainen E,  Dimec J,  Marek D,  Larcombe L, Rustici G,  Attwood TK, Via A (2017) The ELIXIR-EXCELERATE Train-the-Trainer pilot programme: empower researchers to deliver high-quality training [version 1; referees: awaiting peer review]. F1000Research 2017, 6:1557. doi: 10.12688/f1000research.12332.1.
  3. Jiménez RC et al. (2017) Four simple recommendations to encourage best practices in research software. F1000Research. doi: http://dx.doi.org/10.12688/f1000research.11407.1
  4. Schiffthaler B, Kostadima M, the NGS Trainer Consortium, Delhomme N and Rustici G (2016) Training in High-Throughput Sequencing: Common Guidelines to Enable Material Sharing, Dissemination and Re-Usability. PLoS Computational Biology, 12(6): e1004937. doi: 10.1371/journal.pcbi.1004937
  5. 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. (2016) Tools and data services registry: a community effort to document bioinformatics resources. Nucleic Acids Res. 44(D1):D38-47. doi: 10.1093/nar/gkv1116.
  6. Lapatas V, Stefanidakis M, Jimenez RC, Via A, Schneider MV (2015) Data integration in biological research: an overview. J Biol Res (Thessalon). 22(1):9. doi: 10.1186/s40709-015-0032-5
  7. Attwood TK, Bongcam-Rudloff E, Brazas ME, Corpas M, Gaudet P, Lewitter F, Mulder N, Palagi PM, Schneider MV, van Gelder CW; GOBLET Consortium (2015) GOBLET: the Global Organisation for Bioinformatics Learning, Education and Training. PLoS Comput Biol. 11(4):e1004143. doi: 10.1371/journal.pcbi.1004281.
  8. Via A, Zanzoni A (2015) A prismatic view of protein phosphorylation in health and disease. Front. Genet. doi: 10.3389/fgene.2015.00131
  9. Via A, Uyar B, Brun C, Zanzoni A. (2015) How pathogens use linear motifs to perturb host cell networks. Trends Biochem Sci. 40(1):36-48. doi: 10.1016/j.tibs.2014.11.001.
  10. Di Marino D, Coletta A, D’Annessa I, Via A*, Tramontano A. (2015) Characterization of the differences in the cyclopiazonic acid binding mode to mammalian and P. falciparum Ca2+ pumps: a computational study. PROTEINS: Structure, Function and Bioinformatics. Jan 10. doi: 10.1002/prot.24734.
  11. Dias RO, Via A, Brandão MM, Tramontano A, Silva-Filho MC. (2015) Digestive peptidase evolution in holometabolous insects culminated in a specialized group of enzymes in Lepidoptera. Journal of Molecular Biology. 58C:1-11. doi: 10.1016/j.ibmb.2014.12.009.
  12. Corpas M, Jimenez RC, Bongcam-Rudloff E, Budd A, Brazas MD, Fernandes PL, Gaeta B, van Gelder C, Korpelainen E, Lewitter F, McGrath A, MacLean D, Palagi PM, Rother K, Taylor J, Via A, Watson M, Schneider MV, Attwood TK. (2015) The GOBLET training portal: a global repository of bioinformatics training materials, courses and trainers. Bioinformatics. 31(1):140-2. doi: 10.1093/bioinformatics/btu601.
  13. Fiorillo A, Di Marino D, Bertuccini L, Via A, Pozio E., Ilari A, Lalle M. (2014) The crystal structure of Giardia duodenalis g14-3-3 in the apo form reveals unique features of the 14-3-3 protein family. PLoS ONE. 9(3): e92902. doi: 13.1002/prot.24734.
  14. Via A, Blicher T, Bongcam-Rudloff E, Brazas MD, Brooksbank C, Budd A, De Las Rivas J, Dreyer J, Fernandes PL, van Gelder C, Jacob J, Jimenez RC, Loveland J, Moran F, Mulder N, Nyrönen T, Rother K, Schneider MV, Attwood TK. (2013) Best practices in bioinformatics training for life scientists. Briefings in Bioinformatics. 14(5):528-537. doi: 10.1093/bib/bbt043.
  15. Jimenez RC, Albar JP, Bhak J, Blatter MC, Blicher T, Brazas MD, Brooksbank C, Budd A, De Las Rivas J, Dreyer J, van Driel MA, Dunn MJ, Fernandes PL, van Gelder CW, Hermjakob H, Ioannidis V, Judge DP, Kahlem P, Korpelainen E, Kraus HJ, Loveland J, Mayer C, McDowall J, Moran F, Mulder N, Nyronen T, Rother K, Salazar GA, Schneider R, Via A, Villaveces JM, Yu P, Schneider MV, Attwood TK, Corpas M. (2013) iAnn: an event sharing platform for the life sciences. Bioinformatics. 29(15):1919-1921. doi: 10.1093/bioinformatics/btt306.
  16. Lepore R, Tramontano A, Via A (2013) TIPs: a database of therapeutic targets in pathogens and associated tools. Bioinformatics. 29(14):1821-1822. doi: 10.1093/bioinformatics/btt289.
  17. Pillai DR, Lau R, Khairnar K, Lepore R, Via A, Staines H.M., Krishna S (2012) Artemether resistance in vitro is linked to mutations in PfATP6 in travellers returning with Plasmodium falciparum infections. Malar J. 11:131. doi: 10.1186/1475-2875-11-131.
  18. Caroli A, Simeoni S, Lepore R, Tramontano A, Via A (2012) Investigation of a Potential Mechanism for the Inhibition of SmTGR by Auranofin and its implications for Plasmodium falciparum Inhibition. Biochem Biophys Res Commun. 417(1):576-581. doi: 10.1016/j.bbrc.2011.12.009;
  19. Dinkel H, Michael S, Weatheritt RJ, Davey NE, Van Roey K, Altenberg B, Toedt G, Uyar B, Seiler M, Budd A, Jödicke L, Dammert MA, Schroeter C, Hammer M, Schmidt T, Jehl P, McGuigan C, Dymecka M, Chica C, Luck K, Via A, Chatr-Aryamontri A, Haslam N, Grebnev G, Edwards RJ, Steinmetz MO, Meiselbach H, Diella F, Gibson TJ (2012) ELM–the database of eukaryotic linear motifs. Nucleic Acids Res. 40:D242-D251. doi: 10.1093/nar/gkr1064.
  20. Schneider MV, Walter P, Blatter MC, Watson J, Brazas MD, Rother K, Budd A, Via A, van Gelder C, Jacob J, Fernandes P, Nyronwn T, De Las Rivas J, Blicher T, Loveland J, McDowall J, Jones P, Vaughan BW, Lopez R, Attwood TK, Brooksbank C (2012) Bioinformatics Training Network (BTN): A community resource for bioinformatics trainers. Brief Bioinform 13(3):383-389. doi: 10.1093/bib/bbq021.
  21. Via A, De Las Rivas J, Attwood TK, Landsman D, Brazas MD, Leunissen JAM, Tramontano A, Schneider MV (2011) 10 simple rules for developing a short bioinformatics training course. PLoS Computational Biology. 7(10):e1002245. doi: 10.1371/journal.pcbi.1002245.
  22. Sayadi A, Briganti L, Tramontano A, Via A (2011) Exploiting Publicly Available Biological and Biochemical Information for the Discovery of Novel Short Linear Motifs. PLoS One 6(7): e22270. doi: 10.1371/journal.pone.0022270.
  23. Lepore A, Simeoni S, Raimondo D, Caroli A, Tramontano A, Via A (2011) Identification of the Schistosoma mansoni molecular target for the anti malarial drug artemether. J Chem Inf Model 51(11):3005-3016. doi: 10.1021/ci2001764.
  24. Mancini E, Tammaro F, Baldini F, Via A, Raimondo D, George P, Audisio P, Sharakhov I, Tramontano A, Catteruccia F, della Torre A (2011) Molecular evolution of a gene cluster of female serine proteases involved in reproductive processes of the malaria mosquito Anopheles gambiae. BMC Evolutionary Biology 11: 72. doi: 10.1186/1471-2148-11-72.
  25. Dinkel H, Chica C, Via A, Gould C, Jensen L, Gibson T, Diella F (2011) Phospho.ELM: a database of phosphorylation sites- update 2011 Nucleic Acid Research, 39:D261-D267. doi: 10.1093/nar/gkq1104.
  26. 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. doi: 10.2741/3787.
  27. 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. Nucleic Acid Research 39: D268-D271. doi: 10.1093/nar/gkl922;
  28. Chinappi M†, Via A†, Marcatili P, Tramontano A (2010) On the mechanism of chloroquine resistance in Plasmodium falciparum. PLoS ONE 5(11):e14064. Doi: 10.1371/journal.pone.0014064.
  29. Schneider MV, Watson J, Attwood T, Rother K, Budd A, McDowall J, Via A, Fernandes P, Nyronen T, Blicher T, Jones P, Blatter M-C, De Las Rivas J, Judge DP, van der Gool W, Brooksbank C (2010) Bioinformatics training: a review of challenges, actions and support requirements. Briefings in Bioinformatics 11(6): 544-551. doi: 544-551. 10.1093/bib/bbq021.
  30. 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, Hughes T, Pas J, Rychlewski L, Travé G, Aasland R, Helmer-Citterich M, Linding R, Gibson TJ. (2010) ELM: The status of the 2010 Eukaryotic Linear Motif Resource. Nucleic Acid Research 38:D167-D180. Doi: 10.1093/nar/gkp1016.
CV

CURRENT POSITION

Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR), Rome, IT
Scientific Researcher and ELIXIR-ITA Training Coordinator, 2016-

University of Bologna, Master in Bioinformatics, Bologna, IT
Adjunct professor, 2016-Present

Sapienza University, Laurea in Scienze Biologiche, Laboratorio di Bioinformatica, Rome, IT
Adjunct professor, 2017-2018

NATIONAL SCIENTIFIC QUALIFICATION

Molecular Biology (05/E2 - SSD BIO/11) - Associate Professor
Applied Physics (02/B3 - SSD FIS/07) - Associate Professor
Biochemistry (05/E1 – SSD BIO/10) - Associate Professor

EDUCATION

Università di "Tor Vergata", Roma, IT
PhD, Cellular and Molecular Biology, 2003

  • Dissertation: "Protein structural study for the optimization and analysis of sequence functional motifs"
  • Supervisor: Prof. Manuela Helmer-Citterich

Sapienza Università, Roma, IT
Master Degree, Physics, 1997
  • Dissertation: "Analytical study of the Sherrington and Kirkpatrick spin-glass model"
  • Supervisor:  Prof. Giorgio Parisi
Université Paris Diderot – Paris 7, Paris, FR
Erasmus programme, Dept. of Mathematics, 1994-1995

RESEARCH EXPERIENCE

Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR), Rome, IT
Scientific Researcher and ELIXIR-ITA Training Coordinator, 2016-

  • Bioinformatics
  • Educational psycohlogy
  • Cognitive sciences
  • Learning and teaching sciences
Institute of Biomembranes and Bioenergetics (IBBE), National Research Council (CNR), Bari, IT
Researcher and ELIXIR-ITA Training Coordinator, 2016
  • Bioinformatics
  • Educational psycohlogy
  • Cognitive sciences
  • Learning and teaching sciences
Sapienza University, Department of Physics, Roma, IT
Research Associate (RTD), 2013-2015

Sapienza University, Department of Biochemical Sciences, Roma, IT
Research Associate (RTD), 2009-2012

  • Therapeutic targets and their inhibitors, host-pathogen interactions using state-of-the art tools in computational biology.
  • Modelling of biological systems. Development of bioinformatics resources. Building pipelines.

Sapienza University, Department of Biochemical Sciences, Roma, IT
Postdoctoral fellow, 2007-2009

  • Protein structure, function and disease using state-of-the art tools in computational biology
  • Development of bioinformatics methodologies and resources. Building pipelines.

University of Bologna, Department of Experimental Biology of Evolution, Bologna, IT
Postdoctoral fellow, 2006-2007

  • Protein structure and function; Protein phosphorylation; Linear motifs.
  • Development of bioinformatics methodologies and resources; Neural networks.
University of "Tor Vergata", Department of Biology, Roma, IT
Postdoctoral fellow, 2003-2006
  • Protein structure and function; PTM, modular domains and signalling; functional motifs.
  • Development of bioinformatics methodologies and resources.