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Jole Costanza Write a Message

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CGS@SEMM Milano

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Via Adamello

About

Jole Costanza received her Bachelor’s degree in Biomedical Engineering in 2007 and her Master’s degree in Bioengineering in 2010 at University of Padua. In Padua, she joined a project in collaboration with the Department of Information Engineering and the BMR Genomics for building an automatic troubleshooting algorithm for Sanger DNA sequencing. 

Moved by her big passion and love on the  research in November 2010 she started her PhD  in Computer Science at the University of Catania,  under the supervision of the Prof. Giuseppe Nicosia  where she joined a project on Computational Biology  and  Systems Biology. She has been involved on the development of the novel BioCAD tools for the  design  of optimal and robust biological systems for  synthetic and biofuel production. In 2012-2013, she spent several times at the  Computer Laboratory of the University of Cambridge where she collaborated  with the group of the Prof. Pietro Liò.

Currently, she is a postdoctoral fellow at the Center for Genomic Science of  IIT@SEMM  in  Milan. From February 2014 to August 2015 she joined the Computational Research group headed by Dr. Heiko Muller, where she designed a new machine learning algorithm based on the knowledge of viral mechanism in tumorigenesis for the discovery of driver somatic mutations and driver genes in human cancer. From September 2015, she started a new collaboration with the Computational Cancer Genomics and Systems Biology group, headed by Dr. Laura Riva, working on the genomics of chemoresistant acute myeloid leukemia.

Selected Publications

Journal articles

 

  • Melloni GE, de Pretis S, Riva L, Pelizzola M, Ceol A, Costanza JoleMuller H, Zammataro L (2016) LowMACA: exploiting protein family analysis for the identification of rare driver mutations in cancer. BMC Bioinformatics,  Feb 9;17(1):80. doi: 10.1186/s12859-016-0935-7.
  • Costanza Jole, Angione C, Carapezza G, Lió P, Nicosia G (2015) Multi-Target Analysis and Design of Mitochondrial Metabolism. PLoS ONE 10(9): e0133825. doi:10.1371/journal.pone.0133825.  Featured in "Le Scienze - Scientific American".
  • Angione C, Costanza Jole, Carapezza G, Lió P, Nicosia G (2015) Analysis and Design of Molecular Machines. Theoretical Computer Science. ISSN 0304-39710.1016/j.tcs.2015.01.030
  • Patane A, Santoro A, Costanza Jole, Carapezza G, Nicosia G (2015) Pareto Optimal Design for Synthetic Biology. Biomedical Circuits and Systems, IEEE Transactions on , vol.9, no.4, pp.555-571. doi: 10.1109/TCBB.2013.95
  • Angione C, Carapezza G, Costanza Jole, Liò P, Nicosia G (2013) Pareto Optimality in Organelle Energy Metabolism Analysis, in Computational Biology and Bioinformatics, IEEE/ACM Transactions on , vol.10, no.4, pp.1032-1044. doi: 10.1109/TCBB.2013.95
  • Angione C, Carapezza G, Costanza Jole, Lió P, Nicosia G (2013) Design and strain selection criteria for bacterial communication networks. Nano Communication Networks, DOI: 10.1016/j.nancom.2013.08.001
  • Angione C, Costanza Jole, Carapezza G, Lió P, Nicosia G (2013) A Design Automation Framework for Computational Bioenergetics in Biological Networks. Molecular BioSystems, DOI: 10.1039/C3MB25558A.
  • Umeton R, Stracquadanio G, Papini A, Costanza Jole, Lió P, Nicosia G (2012)  Identification of Sensitive Enzymes in the Photosynthetic Carbon Metabolism. Advances in experimental medicine and biology, DOI: 10.1007/978-1-4419-7210-1_26.
  • Carapezza G, Umeton R, Costanza Jole, Angione C, Stracquadanio G, Papini A, Lió P, Nicosia G (2012)  Efficient Behavior of Photosynthetic Organelles via Pareto Optimality, Identifiability and Sensitivity Analysis. ACS Synthetic Biology Journal, DOI: 10.1021/sb300102k
  • Costanza Jole, Carapezza G, Angione C, Liò P, Nicosia G (2012) Robust Design of Microbial Strains. Bioinformatics 28 (23), 3097-3104

Conference proceedings

  • Costanza Jole, Ceol A, Zammataro L, Muller H (2015) Identification of virally encoded missense somatic mutations in human cancer. Viruses and Human Cancer, Keystone Symposia, Big Sky Resort, Big Sky, Montana, USA. March 29 - April 3, 2015. 
  • Costanza Jole, Zammataro L, Nicosia G (2015) A class of Pareto optimal Escherichia coli strains for production of 1,4 -butanediol (2015) Precision Genome Engineering and Synthetic Biology, Keystone Symposia, Big Sky Resort, Big Sky, Montana, USA. January 11-16, 2015.
  • Costanza Jole, Zammataro L, Nicosia G (2014) Programming Living Machines: the case study of Escherichia coli. Biomimetic and Biohybrid Systems, Third International Conference Living Machines 2014 - Milan, Italy, July 30 - August 1, 2014. Proceedings, Lecture Notes in Computer Science Volume 8608, 2014, pp 377-379.
  • Angione C, Costanza Jole, Carapezza G, Lió P, Nicosia G (2013) Identifiability Analysis to Characterize Mitochondrial Diseases, in Proceedings of the 5th International Workshop on Bio-Design Automation - IWBDA 2013 at Imperial College, London, UK, July 12-13, 2013.

  • Costanza Jole, Carapezza G, Angione C, Lió P, Nicosia G (2012) Multi-Objective Optimization, Sensitivity and Robustness Analysis in FBA Modeling, in Proceedings of the 10th Conference on Computational Methods in Systems Biology - CMSB 2012, October 3-5, 2012 The Royal Society, London, UK, Springer. DOI: 10.1007/978-3-642-33636-2_9; ISBN: 978-3-642-33635-5

  • Angione C, Carapezza G, Costanza Jole, Lió P, Nicosia G (2012) Computing with Metabolic Machines,

     in Proceedings of the Turing100, 

    The Alan Turing Centenary Conference, University of Manchester, June 22-25, 2012. Best Paper Award 

    presented by Sir Roger Penrose.

Awards

  • "BITS Travel Grants", the 12th Annual Meeting of the Bioinformatics Italian Society - BITS  2015, June  3- 5, Milan, Italy.
  • "Young Researcher Travel Award", the  5th International Workshop on Bio-Design Automation -IWBDA 2013 at Imperial College, London, UK, July  12- 13,  2013.
  • "Best Paper Award" presented by Sir Roger Penrose, Computing with Metabolic Machine at Turing100, The Alan Turing Centenary Conference, University of Manchester - UK, June  22- 25,  2012.
  • "Young Researcher Travel Award", the  4th International Workshop on Bio-Design Automation - IWBDA 2012 at the  49th ACM/EDAC/IEEE Design Automation Conference (DAC), June  3- 7,  2012 at the Moscone Center, San Francisco, CA, USA.
  • "Young Researcher Travel Award", the  8th Annual Meeting of the Bioinformatics Italian Society - BITS 2011, June  20- 22, Pisa, Italy.
  • "BioBricks Foundation SB 5. 0 Young Researcher Travel Award", the  5th International Meeting on Synthetic Biology - SB 5. 0 2011, Stanford University, Stanford, California USA, June  15- 17,  2011.
  • "Best Paper Award" presented by Sir Roger Penrose, Computing with Metabolic Machine at Turing100, The Alan Turing Centenary Conference, University of Manchester - UK, June 22 -25, 2012.

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I numeri di IIT

L’Istituto Italiano di Tecnologia (IIT) è una fondazione di diritto privato - cfr. determinazione Corte dei Conti 23/2015 “IIT è una fondazione da inquadrare fra gli organismi di diritto pubblico con la scelta di un modello di organizzazione di diritto privato per rispondere all’esigenza di assicurare procedure più snelle nella selezione non solo nell’ambito nazionale dei collaboratori, scienziati e ricercatori ”.

IIT è sotto la vigilanza del Ministero dell'Istruzione, dell'Università e della Ricerca e del Ministero dell'Economia e delle Finanze ed è stato istituito con la Legge 326/2003. La Fondazione ha l'obiettivo di promuovere l'eccellenza nella ricerca di base e in quella applicata e di favorire lo sviluppo del sistema economico nazionale. La costruzione dei laboratori iniziata nel 2006 si è conclusa nel 2009.

Lo staff complessivo di IIT conta circa 1440 persone. L’area scientifica è rappresentata da circa l’85% del personale. Il 45% dei ricercatori proviene dall’estero: di questi, il 29% è costituito da stranieri provenienti da oltre 50 Paesi e il 16% da italiani rientrati. Oggi il personale scientifico è composto da circa 60 principal investigators, circa 110 ricercatori e tecnologi di staff, circa 350 post doc, circa 500 studenti di dottorato e borsisti, circa 130 tecnici. Oltre 330 posti su 1400 creati su fondi esterni. Età media 34 anni. 41% donne / 59 % uomini.

Nel 2015 IIT ha ricevuto finanziamenti pubblici per circa 96 milioni di euro (80% del budget), conseguendo fondi esterni per 22 milioni di euro (20% budget) provenienti da 18 progetti europei17 finanziamenti da istituzioni nazionali e internazionali, circa 60 progetti industriali

La produzione di IIT ad oggi vanta circa 6990 pubblicazioni, oltre 130 finanziamenti Europei e 11 ERC, più di 350 domande di brevetto attive, oltre 12 start up costituite e altrettante in fase di lancio. Dal 2009 l’attività scientifica è stata ulteriormente rafforzata con la creazione di dieci centri di ricerca nel territorio nazionale (a Torino, Milano, Trento, Parma, Roma, Pisa, Napoli, Lecce, Ferrara) e internazionale (MIT ed Harvard negli USA) che, unitamente al Laboratorio Centrale di Genova, sviluppano i programmi di ricerca del piano scientifico 2015-2017.

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IIT: the numbers

Istituto Italiano di Tecnologia (IIT) is a public research institute that adopts the organizational model of a private law foundation. IIT is overseen by Ministero dell'Istruzione, dell'Università e della Ricerca and Ministero dell'Economia e delle Finanze (the Italian Ministries of Education, Economy and Finance).  The Institute was set up according to Italian law 326/2003 with the objective of promoting excellence in basic and applied research andfostering Italy’s economic development. Construction of the Laboratories started in 2006 and finished in 2009.

IIT has an overall staff of about 1,440 people. The scientific staff covers about 85% of the total. Out of 45% of researchers coming from abroad 29% are foreigners coming from more than 50 countries and 16% are returned Italians. The scientific staff currently consists of approximately 60 Principal Investigators110 researchers and technologists350 post-docs and 500 PhD students and grant holders and 130 technicians. External funding has allowed the creation of more than 330 positions . The average age is 34 and the gender balance proportion  is 41% female against 59% male.

In 2015 IIT received 96 million euros in public funding (accounting for 80% of its budget) and obtained 22 million euros in external funding (accounting for 20% of its budget). External funding comes from 18 European Projects, other 17 national and international competitive projects and approximately 60 industrial projects.

So far IIT accounts for: about 6990 publications, more than 130 European grants and 11 ERC grants, more than 350 patents or patent applications12 up start-ups and as many  which are about to be launched. The Institute’s scientific activity has been further strengthened since 2009 with the establishment of 11 research nodes throughout Italy (Torino, Milano, Trento, Parma, Roma, Pisa, Napoli, Lecce, Ferrara) and abroad (MIT and Harvard University, USA), which, along with the Genoa-based Central Lab, implement the research programs included in the 2015-2017 Strategic Plan.