Filippo CastiglioneIstituto per le Applicazioni del Calcolo (IAC) “M. Picone”

Consiglio Nazionale delle Ricerche (CNR)Via dei Taurini, 19 – 00185 Roma

Tel: +39 (0)6 4993 7352 • Fax: +39 (0)6 4404 306filippo.castiglione@cnr.it • http://www.iac.cnr.it/~filippo

Curriculum Vitae

May 17, 2019

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CURRENT POSITIONS

Jan 2002 – today: Senior Research Scientist and Principal Investigator at the Institute for Applied Computing(IAC), of the National Research Council of Italy (CNR), Rome.

Sep 2015 – today: Adjunct Professor of ”Computational Biology” at the Department of Mathematics andPhysics of Roma Tre University, Rome, Italy.

Sep 2018 – today: Adjunct Professor of ”Machine Learning” at the Department of Mathematics and Physicsof Roma Tre University, Rome, Italy.

EDUCATION

Nov 2001 – Nov 2002: Postdoc at the Institute for Medical Bio-Mathematics (IMBM). Bene Ataroth, Tel Aviv,Israel.

Jun 2001 – Sept 2001: Research Fellow at the Harvard Medical School, as part of Cell Biology’s summer scholarprogram sponsored by the Harvard - Armenise Foundation, Boston, USA.

Mar 1998 – May 2001: PhD in Scientific Computing at the University of Cologne, Germany. Supported by theGraduirtenkollegs - Scientific Computing of the University of Cologne, Germany.

Oct 1987 – Jul 1993: Bachelor: Graduated in Computer Science at the University of Milan, Italy.

CITATION METRICS

Web of Science: Publons, Web of Science

https://publons.com/researcher/1325707/filippo-castiglione/

Publications: 99

Total Times Cited: 1206

H-index: 22

Average Citations per Article: 12.2

Last Update: 17/05/2019 10:00 GMT

Scopus: Scopus (Elsevier)

http://www.scopus.com/authid/detail.uri?authorId=56231681200

Documents: 104

Total citations : 1424 (by 958 documents)

h-index: 23

Last Update: 17/05/2019 10:00 GMT

PROFESSIONAL RECORDS

Sep 2017 – Dec 2017: Adjunct Professor of ”Information Systems” at the University ”LUISS Guido Carlo”, Rome,Italy.

Sep 2017 – Sep 2018: Research Fellow at the Institute for Advanced Study (IAS), Universiteit van Amsterdam,The Netherlands

Jan – Dec 2010: Visiting Research Fellow, School of Computer Science, China University of Geosciences,Wuhan, Hubei, China.

Nov 2000 – Jul 2001: Research Assistant with teaching assignment at the Department of Computer Science of theUniversity “La Sapienza”, Rome, Italy.

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Feb – Mar 2001: Research Fellow of the group “The Science of Complexity” at the Center for InterdisciplinaryResearch (Zentrum fur interdisziplinare Forschung - ZiF) of the University of Bielefeld,Germany.

Apr 1997 – Mar 1998: Information Technology and CAM support Engineer at ST-Microelectronics, IT facilities ofthe Power Bipolar Wafer Fab, Discrete and Standard IC’s Group, Catania, Italy.

Aug 1996: Visiting Research at the IBM Watson Research Center, Yorktown, NY and at the MolecularBiology department of the Princeton University, NJ, USA.

RESEARCH GRANTS

Jan 2019 - Dec 2022: Principal Investigator (Work Package Leader)Horizon 2020 - Research and Innovation Framework ProgrammeCall identifier: H2020-SC1-DTH-2018-1, Contract No 826121 (∼ 15 Mln, 386keCNR)iPC – “individualizedPaediatricCure: Cloud-based virtual-patient models for precision pae-diatric oncology”.

Feb 2017 - Jan 2019: Principal Investigator and Unit LeaderENI S.p.A.: Sviluppo di un sistema ad agenti per il monitoraggio efficiente degli impianti diproduzione (reference number 3500043486, 290ke )

Apr 2016 - Apr 2020: Management Committee (MC) MemberEuropean framework CA - Cost Action CA15120, Open Multiscale Systems Medicine (Open-MultiMed, ∼ 150ke ), http://www.cost.eu/COST_Actions/ca/CA15120

Mar 2013 – Feb 2016: Project Coordinator and Work Package leader7th Framework Programme - Priority 2 “Information Society Technologies”Call identifier: FP7-ICT-2011-9, Contract No 600803 (∼2.4 Mlne total, 600keCNR)MISSION-T2D – “Multiscale Immune System Simulator for the Onset of Type 2 Diabetesintegrating genetic, metabolic and nutritional data”

Mar 2007 – Feb 2010: Principal Investigator (Work Package leader)6th Framework Programme - Priority 2 “Information Society Technologies”Call identifier: FP6-2005-NEST-PATH, Contract No 043241 (∼2 Mlne total, 200keCNR)COMPLEXDIS – “Unravelling complex diseases with complexity theory: from networks tothe bedside”.

Feb 2006 – Jan 2009: Principal Investigator (Work Package leader)6th Framework Programme - Priority 2 “Information Society Technologies”Call identifier: FP6-2004-IST-Call4 , Contract No 028069 (∼2 Mlne total, 200keCNR)IMMUNOGRID – “The European Virtual Human Immune System Project”

AWARDS

Jun 2001 – Nov 2002: Research fellow at the Harvard Medical School, as part of Cell Biology’s summer scholarprogram supported by the Harvard - Armenise Foundation, Boston, USA.

Feb 1999 – Jul 2000: Fellowship of the University of Catania (G.U. n.55 9.07.1996 IV s.s.).

Oct 1995 – Apr 1996: Fellowship of the IBM, University of Catania and Italsiel consortium.

MEMBERSHIPS OF EVALUATION COMMITTEES

2012 - 2013, 2015 - 2018: Project proposal reviewer for the French National Alliance for Life and Health Science(AVISEAN) and the French Cancer Institute (INCa).

2017: Grant applications assessment for the Ministry of Education and Science of the RussianFederation.

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2017: Research proposal reviewer for the Marsden Fund Council of the New Zealand Royal SocietyTe Aparangi.

2016 - 2019: Scientific Committee Member of a technological laboratory on ”Complex Systems and In-novative methods for the Analysis of the Emerging Behaviour with particular interest to theImmune System” to carry out research activities, technological development, innovation andtraining within a collaboration with the University of Camerino (MC), Italy.

2017: Substitute Member of the jury for the evaluation of the final examination to achieve thetitle of Doctor of Philosophy in Physics (Sub. Applied Physics and Physics of Matter) atthe University of Bologna “Alma Mater Studiorum” (Italy).

2016: Research proposal reviewer for the Deutsches Krebsforschungszentrum (DKFZ) and theMinistry of Science, Technology and Space of Israel (MOST).

2015: Research proposal reviewer for the Netherlands Foundation for Fundamental Research onMatter (FOM).

2015: Project proposal reviewer for the National Sustainability Programme (NPU) of the CzechMinistry of Education, Youth and Sports.

2014: Project proposal reviewer for the Netherlands Organisation for Scientific Research (NWO).

2014: Project proposal reviewer for the Israeli Science Foundation (ISF).

2014: Member of the jury for the evaluation of the final examination to achieve the title of Doctorof Philosophy in Physics (Sub. Applied Physics and Physics of Matter) at the University ofBologna “Alma Mater Studiorum” (Italy).

2013: Project proposal reviewer for the U.S. Army Research Office (ARO).

2009-2013: Expert in monitoring the implementation of EU-funded project (FP7-ICT for Health) underthe technical aspect, including definition of research priorities and objectives.

2012: Project proposal reviewer for the Latvian Science Council (LSC).

2012: Project proposal reviewer for the Austrian Science Fund (FWF).

2010: Member of the jury for the evaluation of the final examination to achieve deil title of Doctorof Philosophy in Mathematics for Technology (XXII Ciclo - Settore Informatica) at theUniversity of Catania, Italy.

2009: Expert in the evaluation of grant proposals towards the objectives of ICT for Health themeof the FP7 European Union Framework Programme (Call FP7-ICT-2009-4).

2007: Expert in the evaluation of grant proposals towards the objectives of ICT for Health themeof the FP7 European Union Framework Programme (Call FP7-ICT-2007-2).

2007: Project proposal reviewer for the University of Hasselt, Belgium.

TEACHING

Sep 2017 – Dec 2017: Lecturer on “Information Systems” at the Department of Economics and Business of Luiss“Guido Carli” University in Rome, Italy.

Sep 2015 – Jan 2018: Lecturer on “Computational Biology” at the Department of Mathematics and Physics ofRoma Tre University in Rome, Italy.

Feb 9 – 13, 2015: Invited lecturer on “Bioinformatics” for the master and doctoral students of the Depar-tamento de Bioquımica e Imunologia of the Universidade Federal de Minas Gerais, BeloHorizonte, Brazil.

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Jun 2005: Graduate level course on “Computer Security” sponsored by the Regione Lazio, Rome, Italy.

2004 – 2005: Assistant Professor for a first level Master course in “Information Security” (content “Unix/Linuxand Windows Security” theory+practice), University La Sapienza, Rome, Italy.

Oct 2004: Teacher on “Unix internals” Telecom Italia Learning Center (TILS), Rome, Italy.

Sep 2003 – Nov 2003: Teacher on “DNS, e-mail systems, multicasting and VoIP”. Ministero della Universita e dellaRicerca Scientifica (MIUR), Rome.

Jul 13 – 19, 2002: Invited lecturer on “Mathematical Modeling of Biological Systems”, at the Intstitute forTheoretical BioPhysics, Humboldt University, Berlin, Germany.

Nov 2000 – Jul 2001: Assistant lecturer on “Programming” at the University “La Sapienza”, Rome, Italy.

Oct 1997: Invited lecturer on “Numerical Simulations” at the University of Catania, Italy.

ORGANISATION/COMMITTEE OF INTERNATIONAL CONFERENCES

2018: Program Committee Member of the 3rd Workshop on Molecular Communications (MolCom2018) April 4-6, 2018Ghent, Belgium

2018: Program Committee Member of the 2nd International Workshop on Computational Methods for the ImmuneSystem Function (CMISF 2018) December 3, 2018 Madrid, Spain

2017: Program Committee Member of the 1st International Workshop on Computational Methods for the ImmuneSystem Function (CMISF 2017) November 13, 2017 Kansas City, MO, USA

2016: Program Chair or co-chair of the workshop Modeling and computational approaches to Biology and Medicine(MOBI-2016) June 26-28, 2017 Rome, Italy

2016: Programme Committee Member of the The 16th International Conference on Bioinformatics (InCoB 2017) Septem-ber 20-22, 2017 Tsinghua University, Shenzhen, China

2016: Programme Committee Member of the 5th International Young Scientists Conference in HPC and Simulation 26- 28 October, 2016 Krakow, Poland

2016: Programme Committee Member of the 15th International Conference on Bioinformatics (InCoB2016) 21-23September, 2016 Biopolis, The Matrix, Singapore

2015: Programme Committee Member of the 1st Genome Informatics Workshop / International Conference on Bioinfor-matics Joint Conference (GIW/InCoB2015) Sept 9-11, 2015 Odaiba, Tokyo, Japan

2015: Program Chair or co-chair of the 1st International Conference on Computational Modeling of Metabolic Health,Inflammation and Diabetes (MMH 2015) October 6-7, 2015 - Cambridge, UK

2014: Programme Committee Member of the 13th International Conference on Bioinformatics (InCoB2014) July 31st -Aug 2nd, 2014 - Sydney, New South Wales, Australia

2013: Programme Committee Member of the 12th International Conference on Bioinformatics (InCoB2013) Sep 20-22th,2013 - Taicang, China

2012: Programme Committee Member of the 11th International Conference on Bioinformatics and Computational Biology(InCoB2012) October 3-5, 2012 - Bangkok, Thailand.

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2012: Program Chair or co-chair the VPH2012 Integrative approaches to Computational Biomedicine conference.September 18th-20th, 2012, London, UK.

2011: Programme Committee Member of the 10th International Conference in Bioinformatics - 1st ISCB Asia JointConference (InCoB2011-ISCB Asia), Nov 27 - Dec 3, 2011, Kuala Lumpur, Malaysia.Chair of the Basic and Clinical Immunoinformatics and Immunomics (sub-)conference (BCII 2011).

2010: Program Committee Member of MathCell 2010, Dec 14-15, 2010, Rome, Italy.

2010: Programme Committee Member of the 9th International Conference on Bioinformatics (InCoB2010) September26-28, 2010, Tokyo, Japan.

2010: Programme Committee Member of the 3rd IASTED African Conference on Modelling and Simulation (“AfricaMS2010”) September 6-8, 2010, Gaborone, Botswana.

2009: Program Chair or co-chair of the workshop Optimal Control and Optimization for Individual-based and Agent-based Models. December 1-3, 2009 at the National Institute for Mathematical and Biological Synthesis (NIMBioS)at the University of Tennessee, Knoxville, TN, USA.

2008: Programme Committee Member of The 2nd IASTED African Conference on Modelling and Simulation (“AfricaMS2008”), September 8 - 10, 2008, Gaborone, Botswana.

2007: Programme Committee Member of the 6th International Conference on Artificial Immune Systems ( ICARIS 2007),26 - 29 August, 2007, Santos/SP, Brazil.

2006: Programme Committee Member of the 5th International Conference on Artificial Immune Systems ( ICARIS 2006),4 - 6 September, 2006, Oeiras, Portugal.

2005: Programme Committee Member of the 4th International Conference on Artificial Immune Systems ( ICARIS 2005),14 - 17 August, 2005, in Banff, Alberta, Canada.

2005: International Advisor of the International Symposium on Bio-Inspired Computing ( BIC’05). September 5 - 7,2005, Johor, Malaysia.

2004: Programme Committee Member of the 3rd International Conference on Artificial Immune Systems ( ICARIS 2004).13 - 16 September, 2004, Catania, Italy.

2004: Program Chair or co-chair of the invited session “Computational Biology” at the 43rd IEEE Conference onDecision and Control. 14 - 17 December, 2004, Nassau, Bahamas.

2004: Technical Program Committee Member for SimTecT 2004. 24 - 27 May, 2004, Canberra, Australia.

2003: Program Chair or co-chair of the IMA “Hot Topics” Workshop: Agent Based Modeling and Simulation. Novem-ber 3 - 6, 2003, Institute for Mathematics and its Applications (IMA) Minneapolis, MN, USA.

EDITORIAL AND RELATED ACTIVITIES

Since 2018 Editorial Board Member of “Computational and Mathematical Methods in Medicine”, Hindawi. https://www.

hindawi.com/journals/cmmm/

Since 2011 Editorial Board Member of “PLoS ONE” (open access, peer-reviewed, on-line journal), Public Library of Sciencehttp://www.plosone.org

Since 2005 Editorial Board Member of the “Immunome Research” (open access, peer-reviewed, on-line journal), BioMed Centralhttps://www.omicsonline.com/open-access/immunome-research.php

2015-2018 Editorial Advisory Board Member of “The Open Biochemistry Journal” (open access, peer-reviewed, on-line journal),Bentham Science Publishers https://www.benthamopen.com/TOBIOCJ/

2014 Guest Editor of the Special Issue “Computational Studies of Immune System Function”, Computation (ISSN 2079-3197). Published online by MDPI (2015)http://www.mdpi.com/journal/computation/special_issues/system-function

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2014 Guest Editor of the Special Issue “Computational and Bioinformatics Techniques for Immunology”, Eds. F. Pap-palardo, V. Brusic, F. Castiglione, C. Schonbach. BioMed Research International, Hindawi Publishing Corporation(2014). http://www.hindawi.com/journals/bmri/si/390574/cfp/

2012 Editorial Board Member of the (peer-reviewed, open access) journal “ISRN Computational Biology” (Hindawi Pub-lishing Corporation) http://www.hindawi.com/isrn/cbio/

2012–2015 Editorial Board Member of the Bioinformatics section of the journal “Conference Papers in Biology” (open access,peer-reviewed, on-line journal), of the series Conference Papers in Science (Hindawi Publishing Corporation) http:

//www.cpis.com/journals/biology/

2012–2017 Editorial Board Member of “Dataset Papers in Biology” (open access, peer-reviewed, on-line journal), DatasetsInternational (Hindawi Publishing Corporation) http://www.datasets.com/journals/biology

2007–2015 Editorial Advisory Board Member of “The Open Bioinformatics Journal” (open access, peer-reviewed, on-line journal),Bentham Science Publishers http://www.bentham.org/open/tobioij/index.htm

2009 Section Editor of “Agent based modeling and simulation” of the Encyclopedia of Complexity and System Science,Mayers Robert (Ed.), Springer Verlag (2009) http://refworks.springer-sbm.com/complexity/ and of a six-volume spin-off of the Encyclopedia titled Computational Complexity: Theory, Techniques, and Applicationshttp://www.springer.com/computer/theoretical+computer+science/book/978-1-4614-1799-6

• Served as referee for the following journals:? Advances in Complex Systems ? Advances in Difference Equations ? AIDS Research and Human Retrovirus ?Artificial Intelligence in Medicine ? Autoimmunity ? Bioinformatics ? BioSystems ? BMC Bioinformatics ? BMC Im-munology ? BMC Systems Biology ? Brazilian Journal of Pharmaceutical Sciences ? Bulletin of Mathematical Biology? Cancer Research ? Cancer Immunology, Immunotherapy ? Cardiovascular Diabetology ? Communications in Com-putational Physics ? Computational and Mathematical Methods in Medicine ? Computer Methods and Programs inBiomedicine ? Computers in Biology and Medicine ? EuroPhysics Letters ? Evolutionary Intelligence ? Expert ReviewClinical Immunology ? Frontiers In Immunology ? IEEE Transactions on Evolutionary Computation ? IET SystemsBiology ? Immunome Research ? International Journal of Computer Mathematics ? International Journal of Control,Automation, and Systems ? International Journal of Molecular Sciences ? ISRN Computational Biology ? Journalof Theoretical Biology ? Journal of Mathematical Biology ? Letters in Biomathematics ? Mathematical Bioscience? Mathematical Bioscience and Engineering ? Mathematical Methods in the Applied Sciences ? Mathematical Mod-eling of Natural Phenomena ? Mathematics and Computers in Simulation ? Oncotarget ? Pattern Recognition ?Pharmaceutics ? Physica A ? Physics Letters A ? PLoS ONE ? PLoS Computational Biology ? Quantitative Finance? Science Translational Medicine ? SIAM Journal on Applied Mathematics ? Simulation: Transactions of the Societyfor Modeling and Simulation International ? Swarm and Evolutionary Computation ? Systems BioMedicine ? TheOpen Bioinformatics Journal ? Vaccine ?

• Served as reviewer for books of the following publishers:? Springer Nature ? Oxford University Press

• Served as referee for the following conferences/proceedings:? the IEEE society ? the International Association of Science and Technology for Development (IASTED) ? theInternational Conferences on Intelligent Computing (ICIC) ? the International Conference on Bioinformatics (InCoB)of the Asia-Pacific Bioinformatics Network (APBioNet)

• Author and curator of the review article “Agent Based Modeling” of the Encyclopedia of Computational Neuroscience,hosted by Scholarpedia, the free peer reviewed encyclopedia. http://www.scholarpedia.org/article/Agent_

Based_Modeling

CURRENT AND PAST AFFILIATIONS

• 2012–2018: Virtual Physiological Human Institute (VPH-inst, www.vph-institute.org)

• 2004–2019: Gruppo Nazionale per la Fisica Matematica (GNFM) of the Istituto Nazionale di Alta Matematica(INdAM) (GNFM, http://gruppi.altamatematica.it/gnfm/)

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• 2011–2013: Centro Interuniversitario per la Matematica Applicata a Biologia, Medicina ed Ambiente (CIMAB,www.mat.unimi.it/users/CIMAB)

• 2006: Societa Italiana di Matematica Applicata e Industriale (SIMAI, http://www.simai.eu)

• 2006: European Society for Mathematical and Theoretical Biology (ESMTB, http://www.esmtb.org)

• 2004–2006: International Immunomics Society (IIMMS)

OTHER

FOREIGN LANGUAGES

English: TOEFL (Test Of English as Foreign Language - Jan 1997) – Education Testing Service (ETS).

German: DaF (Deutsch als Fremdsprache - Feb 2000), Zertifikat Deutsch (B1) – Goethe Institut (Cologne).

French: Niveau Intermediaire B1 - 2008 – Centro Linguistico Eurolingue (Rome).

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INVITED TALKS

1. Invited Speaker at IMMUNO 2018, the XLIII Congress of the Brazilian Society of Immunology, October 1-4, 2018,Ouro Preto, MG, Brazil.

2. Invited talk at the Workshop on Immune Fitness. May 17 - 18, 2017, Institute for Advanced Study, Amsterdam,The Netherlands

3. Invited Tutorial Speaker at the 2nd Workshop on Molecular Communications, May 9 - 11, 2017, Trinity College,Dublin, Ireland

4. Invited talk at Accademia Medica di Roma, Policlinico Umberto I, May 26 2016, Rome, Italy

5. Invited talk at the Center for Quantitative Medicine, UCONN Health, May 13 2016, Farmington, Connecticut, USA

6. Invited talk at the Workshop on Computational modeling in Systems Biology and Radiotherapy, Apr 11 2016, Catania,Italy

7. Invited talk at the Workshop on Systems Biology and Systems Medicine, University of Luxembourg, Nov 23-26 2015,Luxembourg.

8. Invited (virtual) seminar at Program for Research on Immune Modeling and Experimentation (PRIME), May 28,2014, Yale School of Medicine, USA

9. Invited talk at the workshop on Theoretical Approaches and Related Mathematical Methods in Biology, Medicineand Environment. Apr 4 - 6, 2013, Milano, Italy

10. Invited talk at the workshop Mathematical oncology: New challenges for systems biomedicine Sept 25 - Oct 1, 2011,Erice, Italy

11. Invited talk at the 7th ISABS Conference in Forensic, Anthropologic and Medical Genetics. “Optimal control in amodel of dendritic cell transfection cancer immunotherapy.” June 20–24, 2011, Bol, Island of Brac, Croatia.

12. Invited talk at the Workshop on Modern Vaccines and Delivery Technologies. “A computational model of cancerimmunoprevention.” October 14–15, 2010, Roma, ENEA Research Center Casaccia.

13. Invited talk at The First International Workshop on Virtual Tissues: v-Tissues 2009, EPA Campus, Research TrianglePark, Durham, April 21-22, 2009, North Carolina, USA

14. Invited talk at ICHM-2008, August 21-23, 2008, Kottayam, Kerala, India

15. Tutorial speaker at the First Immunomics Summer School (IIMMS). Computer modelling, from molecules to clinics.Catania, Aug 24 -Sep 03, 2007.

16. Invited talk at the Neural Stem cells Lab, Inbiomed Foundation “A mathematical model of neurogenesis in subven-tricular zone after oxigen/glucose deprivation ” San Sebastian, Spain, June 22, 2007.

17. Invited talk at the Center of Molecular Immunology (CIM). International Workshop Immunotherapy 2006: Targetingcomplexity. Havana, Cuba, on November 15th-19th, 2006.

18. Invited talk at Institute for Theoretical Medicine and Clinical Pharmacology Department, University of Lyon, Lyon,France, September 27-28, 2006.

19. HPC User Forum. “ImmunoGrid: large scale simulation of the immune system” Bologna, May 29-30, 2006.

20. Invited talk at the Institute for Protein Biochemistry IBP, CNR. “Modeling biology”. Naples, March 10, 2006.

21. Invited talk at the University of Geneva. “The ImmunoGrid Project”. Geneva, Switzerland, Feb 3 2006.

22. Invited talk at Virginia Biotechnoloy Institute. “Discrete mathematical/computational models of biological systems”Blacksburg, VA, USA, Nov 2 2004.

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23. Interactome Meeting, Heidelberg, Germany, Nov 17, 2004.

24. Invited talk at the Sixteenth International Symposium on Mathematical Theory of Networks and Systems (MTNS2004)July 5 - 9, 2004 – Katholieke Universiteit Leuven, Belgium.

25. Tutorial speaker at the 3rd International Conference on Artificial Immune Systems (ICARIS 2004), Catania, Italy,13-16 September 2004.

26. Invited talk at Bayer Technology, July 12, 2004 “C-ImmSim: playing with the immune response” Leverkusen,Germany.

27. Institute for Higher Education, Rezekne, Latvia, “Mathematical modeling of therapy” , March 5, 2004.

28. Invited speaker at the 1st International Immunoinformatics Symposium - Immunology meets Bioinformatics February26/27, 2004. RIKEN Yokohama Institute, Yokohama, Japan.

29. “Modeling Immunity: the Agent-Based approach”, 1st Bioinformatics Conference, University ”La Sapienza”, Rome,Italy, March 12, 2003.

30. “Mutation, fitness, viral diversity and disease progression in a computational model of HIV-1 (untreated) infection”,Los Alamos National Laboratory, Los Alamos, USA, November 2002.

31. “Modeling HIV-1 infection”, Spallanzani Hospital, Rome, Italy, September 2002.

32. “Agent-Based simulations of the Immune Response”, Universita Campus Bio-Medico, Roma, Italy, September 2002.

33. “Simulation of the immune system dynamics”, DMFCI University of Catania, Italy, April 2001.

34. “Microsimulations of Financial Markets: The Cont-Bouchaud model”, IAC-CNR, Roma, September 1999.

35. “Image processing for keratoconus diagnosis”, IAC-CNR, Roma, July 1998.

36. “The Celada-Seiden model of the humoral response”, IAC-CNR, Roma, 1997.

37. “Cellular Automata for the simulation of biological systems”, Department of Mathematics, University of Catania,Italy, September 1997.

38. “Dynamic memory management for a lattice-based model to simulate the immune response”, IBM Watson ResearchCenter, Yorktown NY, August 1996.

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PUBLICATIONS

BOOKS

1. F. Castiglione and F. Celada. Immune System Modeling and Simulation. CRC Press (2015). ISBN 978-1-4665-9748-8.http://www.crcpress.com/product/isbn/9781466597488

JOURNAL PAPERS

1. Alva Presbitero, Emiliano Mancini, F. Castiglione, Valeria V. Krzhizhanovskaya, Rick Quax. The Game of Neu-trophils: Modeling the Balance Between Apoptosis and Necrosis. Submitted to BMC Supplements (April 2019).

2. V. Prana, P. Tieri, M.C. Palumbo, E. Mancini, F. Castiglione. Modeling the effect of high calorie diet on the interplaybetween adipose tissue, inflammation and diabetes. Computational and Mathematical Methods in Medicine, ArticleID 7525834 (2019)https://doi.org/10.1155/2019/7525834

3. A. Palma, A. S Jarrah, P. Tieri, G. Cesareni and F. Castiglione. Gene regulatory network modeling of macrophagedifferentiation corroborates the continuum hypothesis of polarization states Frontiers in Physiology, 9: 1659 (2018)https://www.frontiersin.org/articles/10.3389/fphys.2018.01659/full

doi: 10.3389/fphys.2018.01659

4. M-C. Palumbo, M. Morettini, P. Tieri, F. Diele, M. Sacchetti, F. Castiglione. Personalizing physical exercise in acomputational model of fuel homeostasis. PLOS Computat Biol., 14(4):e1006073 (2018)doi: 10.1371/journal.pcbi.1006073

http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006073

5. M. Zanin, I. Chorbev, B. Stres, E. Stalidzans, J. Vera, P. Tieri, F. Castiglione, D. Groen, H. Zheng, J. Baumbach, J.Schmid, J. Basilio, P. Klimek, N. Debeljak, D. Rozman, H. Schmidt. Community effort endorsing multiscale modeling,multiscale data science and multiscale computing for systems medicine. Briefings in Bioinformatics, bbx160 (2017)https://doi.org/10.1093/bib/bbx160

6. H. De Assis Lopes Ribeiro, T. Uceli Maioli, L. Martins Freitas, Paolo Tieri, F. Castiglione. Modeling immuneresponse to Leishmania species indicates adenosine as an important inhibitor of Th-cell activation. Frontiers inCellular and Infection Microbiology, 7:309 (2017)https://www.frontiersin.org/article/10.3389/fcimb.2017.00309

doi: 10.3389/fcimb.2017.00309

7. M. Morettini, M-C. Palumbo, M. Sacchetti, F. Castiglione, C. Mazza. A system model of the effects of exercise onplasma Interleukin-6 dynamics in healthy individuals: role of skeletal muscle and adipose tissue. PLoS ONE, 12(7):e0181224 (2017)https://doi.org/10.1371/journal.pone.0181224

8. A. Madonia, C. Melchiorri, S. Bonamano, M. Marcelli, C. Bulfon, F. Castiglione, M. Galeotti, D. Volpatti, F. Mosca,P-G. Tiscar and N. Romano. Computational modeling of immune system of the fish for a more effective vaccinationin aquaculture. Bioinformatics, (2017) btx341.doi: 10.1093/bioinformatics/btx341

9. A. Liso, Castellani, F. Massenzio, A. Pucciarini, B. Bigerna, P. De Luca, P. Zoppoli, F. Castiglione, M-C. Palumbo,M. Conese, S. Castellani, F. Stracci, M. Landriscina, G. Specchia and B. Falini. Human monocyte-derived dendriticcells exposed to hyperthermia show a distinct gene expression profile and selective upregulation of IGFBP6. Onco-target, 8(37):60826-40 (2017)doi: 10.18632/oncotarget.18338

10. J-F. Moreau, T. Pradeu, A. GRignolio, C. Nardini, F. Castiglione, P. Tieri, M. Capri, S. Salvioli, J-L. Taupin, P.Garagnani, C. Franceschi. The emerging role of ECM crosslinking in T cell mobility as a hallmark of immunosenes-cence in humans. Ageing Research Reviews, 35:322-335 (2017)http://dx.doi.org/10.1016/j.arr.2016.11.005

http://www.sciencedirect.com/science/article/pii/S1568163716301015

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11. F. Castiglione, P. Tieri, A. Palma, A.S. Jarrah. Statistical ensemble of gene regulatory networks of macrophagedifferentiation. BMC Bioinformatics 17(Suppl 19):1363 (2016)doi: 10.1186/s12859-016-1363-4

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1363-4

12. A-R. Garbuglia, U. Visco-Comandini, R. Lionetti, D. Lapa, F. Castiglione, G. D’Offizi, C. Taibi, M. Montalbano,M-R. Capobianchi, P. Paci. Ultrasensitive HCV-RNA quantification in antiviral triple therapy: new insight on viralclearance dynamic and treatment outcome predictors. PLoS ONE, 11(8):e0158989 (2016)doi: 10.1371/journal.pone.0158989

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0158989

13. C. Sansom, F. Castiglione, P. Lio. Metabolic disorders: how can systems modelling help? The Lancet Diabetes andEndocrinology, 4(4):305-6 (2016)doi:http://dx.doi.org/10.1016/S2213-8587(16)00047-4

http://www.sciencedirect.com/science/article/pii/S2213858716000474

14. A-R. Garbuglia, R. Lionetti; D. Lapa, C. Taibi, U. Visco-Comandini, M. Montalbano, G. D’Offizi, F. Castiglione, M.R.Capobianchi, P. Paci. The clinical significance of HCV core antigen detection during Telaprevir/Peg-Interferon/Ribavirintherapy in patients with HCV 1 genotype infection. Journal of Clinical Virology, 69:68–73 (2015)http://dx.doi.org/10.1016/j.jcv.2015.06.002

15. E. Galeota, C. Gavrila, F. Castiglione, M. Bernaschi and G. Cesareni. The hierarchical organization of natural proteininteraction networks confers self-organization properties on pseudocells. BMC Systems Biology 9(3):S3 (2015)doi:10.1186/1752-0509-9-S3-S3

http://www.biomedcentral.com/1752-0509/9/S3/S3/

16. A. Cappuccio, P. Tieri and F. Castiglione. Multiscale modelling in immunological: a review. Briefings in Bioinfor-matics 1-11 (2015)doi:10.1093/bib/bbv012

17. F. Pappalardo, V. Brusic, F. Castiglione, and C. Schonbach. Computational and Bioinformatics Techniques forImmunology. BioMed Research International, vol. 2014, Article ID 263189 (2014)http://dx.doi.org/10.1155/2014/263189

18. P. Tieri, A. de Graaf, S. Krishnan, M. Ernst and F. Castiglione. Pre-empting Type 2 Diabetes. InternationalInnovation, 140:40-43 (2014)

19. M-C. Palumbo, L. Farina, F. Castiglione, M. Fasoli, S. Zenoni, M. Pezzotti and P. Paci. Integrated network analysisidentifies key switch genes that control major transcriptome reprogramming during grapevine development. ThePlant Cell, 26(12): 4617–4635 (2014) Published online before print December 2014,doi:http://dx.doi.org/10.1105/tpc.114.133710

http://www.plantcell.org/content/26/12/4617

20. F. Castiglione. Immunoinformatics. International Innovation, 133:23-25 (2014)

21. A.S. Jarrah, F. Castiglione, N.P. Evans, R.W. Grange, R. Laubenbacher. A mathematical model of skeletal muscledisease and immune response in the mdx mouse. BioMed Research International, Article ID 871810 (2014)doi:10.1155/2014/871810

http://www.hindawi.com/journals/bmri/2014/871810/

22. F. Castiglione, F. Pappalardo, C. Bianca and S. Motta Modeling biology spanning different scales: An open challenge.BioMed Research International, Article ID 902545, (2014)doi:10.1155/2014/902545

http://www.hindawi.com/journals/bmri/2014/902545/

23. F. Castiglione, P. Tieri, A. De Graaf, C. Franceschi, P. Lio, B. Van Ommen, C. Mazza, A. Tuchel, M. Bernaschi,C. Samson, T. Colombo, G. Castellani, M. Capri, P. Garagnani, S. Salvioli, V. Anh Nguyen, I. Bobeldijk-Pastorova,S. Krishnan, A. Cappozzo, M. Sacchetti, M. Morettini, M. Ernst. The Onset of Type 2 Diabetes: Proposal for aMulti-Scale Model. JMIR Research Protocols, 01/2013 2(2):e44 (2013)doi:10.2196/resprot.2854

http://www.researchprotocols.org/2013/2/e44/

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24. J. von Eichborn, A-L. Woelke, F. Castiglione, R. Preissner. VaccImm: Simulating peptide vaccination in cancertherapy BMC Bioinformatics 14:127 (2013)doi:10.1186/1471-2105-14-127

http://www.biomedcentral.com/1471-2105/14/127

25. D. Santoni,F. Castiglione, P. Paci. Identifying Correlations between Chromosomal Proximity of Genes and Distanceof Their Products in Protein-Protein Interaction Networks of Yeast. PLoS ONE 8(3): e57707 (2013)doi:10.1371/journal.pone.0057707

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0057707

26. F. Castiglione, V. Diaz, A. Gaggioli, P. Lio, C. Mazza, E. Merelli, C.G.M. Meskers, F. Pappalardo and R. vonAmmon. Physio-environmental sensing and live modeling. Interactive Journal of Medical Research 2(1): e3 (2013)doi:10.2196/ijmr.2092

http://www.i-jmr.org/article/view/ijmr_v2i1e3/1

27. B. Ribba, H. El Garch, S. Brunet, E. Grenier, F. Castiglione, H. Poulet and P. Vanhems. Time-course analysis ofmain markers of primary infection in cats with the feline immunodeficiency virus. Computational and MathematicalMethods in Medicine, 2012: 342602 (2012)doi:10.1155/2012/342602

http://www.hindawi.com/journals/cmmm/2012/342602/

28. F. Castiglione, F. Mantile, P. De Berardinis, A. Prisco How the interval between prime and boost injection affectsthe immune response in a computational model of the immune system. Computational and Mathematical Methodsin Medicine, 2012: 842329 (2012)doi:10.1155/2012/842329

http://www.hindawi.com/journals/cmmm/2012/842329/

29. E. Mancini, F. Castiglione, M. Bernaschi, A. de Luca, P.M.A. Sloot. HIV reservoirs and immune surveillance evasioncause the failure of structured treatment interruptions: A computational study. PLoS ONE, 7(4): e36108 (2012)doi:10.1371/journal.pone.0036108

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0036108

30. N. Arrigo, P. Paci, L. Di Paola, D. Santoni, M. De Ruvo, A. Giuliani, F. Castiglione. Characterizing protein shapeby a volume distribution asymmetry index. The Open Bionformatics Journal, 6: 20–27 (2012)doi:10.2174/1875036201206010020

http://benthamscience.com/open/tobioij/articles/V006/20TOBIOIJ.htm

31. F. Castiglione, S. Motta, F. Pappalardo and M. Pennisi. A modeling framework for immune-related diseases.Mathematical Modelling of Natural Phenomena, 7(3): 40–48 (2012)http://dx.doi.org/10.1051/mmnp/20127304

32. F. Pappalardo, A. Palladini, M.Pennisi, F. Castiglione, S. Motta. Mathematical and computational models in tumorimmunology. Mathematical Modelling of Natural Phenomena, 7(3): 186–203 (2012)http://dx.doi.org/10.1051/mmnp/20127312

33. A-L. Woelke, J. von Eichborn, M.S. Murgueitio, C.L. Worth, F. Castiglione, R. Preissner. Development of Immune-Specific Interaction Potentials and Their Application in the Multi-Agent-System VaccImm. PLoS ONE, 6(8): e23257(2011)doi:10.1371/journal.pone.0023257

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0023257

34. N. Rapin, O. Lund and F. Castiglione. Immune System Simulation Online. Bioinformatics, 27(14): 2013-2014(2011)doi:10.1093/bioinformatics/btr335

35. T. Clancy, M. Pedicini, F. Castiglione, D. Santoni, V. Nygaard, T. J. Lavelle, M. Benson and E. Hovig. Immunologicalnetwork signatures of cancer progression and survival. BMC Medical Genomics, 4:28 (2011)doi:10.1186/1755-8794-4-28

http://www.biomedcentral.com/1755-8794/4/28

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36. P. Paci, F. Martini, M. Bernaschi, G. D’Offizi and F. Castiglione. Earlier is better: a timely HAART initiation maypave the way for best controllers. BMC Infectious Diseases, 11:56 (2011)doi:10.1186/1471-2334-11-56

http://www.biomedcentral.com/1471-2334/11/56/

37. F. Castiglione, D. Santoni, N. Rapin. CTLs’ repertoire shaping in the thymus: a Montecarlo simulation. Autoim-munity, 44(4): 1–10 (2011)doi:10.3109/08916934.2011.523272

38. M. Pedicini, F. Barrenas, T. Clancy, F. Castiglione, E. Hovig, K. Kanduri, D. Santoni, M. Benson. Combiningnetwork modeling and gene expression microarray analysis to explore the dynamics of Th1 and Th2 cell regulation.PLoS Computational Biology, 6(12): e1001032 (2010)doi:10.1371/journal.pcbi.1001032

39. F. Castiglione and P.Paci. Criticality of timing for anti-HIV therapy initiation. PLoS ONE, 5(12): e15294 (2010)doi:10.1371/journal.pone.0015294

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0015294

40. M. Halling-Brown, F. Pappalardo, N. Rapin, P. Zhang, D. Alemani, A. Emerson, F. Castiglione, P. Doroux, M.Penissi, O. Miotto, D. Churchill, E. Rossi, D. S. Moss, C. E. Sansom, M. Bernaschi, M-P. Lefranc, S. Brunak, S.Motta, P-L. Lollini, K. E. Basford, V. Brusic, A. J. Shepherd. ImmunoGrid: towards agent-based simulations of thehuman immune system at a natural scale. Philosophical Transactions of the Royal Society A, 368(1920): 2799–2815(2010)doi:10.1098/rsta.2010.0067

http://rsta.royalsocietypublishing.org/content/368/1920/2799.abstract

41. N. Rapin, O. Lund, M. Bernaschi and F. Castiglione. Computational Immunology Meets Bioinformatics: The Useof Prediction Tools for Molecular Binding in the Simulation of the Immune System. PLoS ONE, 5(4): e9862 (2010)doi:10.1371/journal.pone.0009862

http://dx.plos.org/10.1371/journal.pone.0009862

42. F. Pappalardo, M. Pennisi, F. Castiglione and S. Motta. Vaccine protocols optimization: in silico experiences.Biotechnology Advances, 28: 82–93 (2010)doi:10.1016/j.biotechadv.2009.10.001

http://dx.doi.org/10.1016/j.biotechadv.2009.10.001

43. T. Avitabile, Francesco Castiglione, V. Bonfiglio and Filippo Castiglione. Transconjunctival sutureless 25-gaugeversus 20-gauge standard vitrectomy: correlation between corneal topography and ultrasound biomicroscopy mea-surements of sclerotomy sites. Cornea, 29(1): 19–25 (2010).doi:10.1097/ICO.0b013e3181ab98ae

44. V. Baldazzi, P. Paci, M. Bernaschi and F. Castiglione. Modeling lymphocytes homing and encounters in lymphnodes. BMC Bioinformatics, 10: 387 (2009)doi:10.1186/1471-2105-10-387

45. P. Paci, R. Carello, M. Bernaschi, G. D’Offizi and F. Castiglione. Immune control of HIV-1 infection after therapyinterruption: immediate versus deferred antiretroviral therapy. BMC Infectious Diseases, 9: 172 (2009)doi:10.1186/1471-2334-9-172

http://www.biomedcentral.com/1471-2334/9/172

46. G. Dell’Acqua and F. Castiglione. Stability and phase transitions in a mathematical model of Duchenne musculardystrophy. Journal of Theoretical Biology, 260(2): 283–289 (2009)doi:10.1016/j.jtbi.2009.05.037

47. D. Vergni, F. Castiglione, M. Briani, S. Middei, E. Alberdi, K. G. Reymann, R. Natalini, C. Volonte, C. Matute, F.Cavaliere. A Model of Ischemia-Induced Neuroblast Activation in the Adult Subventricular Zone. PLoS ONE, 4(4):e5278 (2009)doi:10.1371/journal.pone.0005278

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48. F. Pappalardo, M. D. Halling-Brown, N. Rapin, P. Zhang, D. Alemani, A. Emerson, P. Paci, P. Duroux, M. Pennisi, A.Palladini, O. Miotto, D. Churchill, E. Rossi, A. J. Shepherd, D. S. Moss, F. Castiglione, M. Bernaschi, M-P. Lefranc,S. Brunak, S. Motta, P-L. Lollini, K. E. Basford and V. Brusic. ImmunoGrid, an integrative environment for large-scale simulation of the immune system for vaccine discovery, design, and optimization. Briefing in Bioinformatics,10(3):330-40 (2009).doi:10.1093/bib/bbp014

49. A. Cappuccio, F. Castiglione, B. Piccoli and V. Tozzi. Evaluation of HIV/CD4+ T cell dynamic parameters inpatients treated with genotypic resistance testing-guided HAART. Current HIV Research, 6(4):363–369 (2008)

50. A. Liso, F. Castiglione, A. Cappuccio, F. Stracci, R. Schlenk, S. Amadori, C. Thiede, S. Schnittger, P. J.M. Valk,K. Dohner, M. F. Martelli, M. Schaich, J. Krauter, A. Ganser, M. P. Martelli, N. Bolli, B. Lowenberg, T. Haferlach,G. Ehninger, F. Mandelli, H. Dohner, F. Michor, and B. Falini. A one-mutation mathematical model can explain theage incidence of AML with mutated nucleophosmin (NPM1). Haematologica/The Hematology Journal, 93(8):1219–1226 (2008)doi:10.3324/haematol.13209

51. D. Santoni, M.Pedicini, F. Castiglione. Implementation of a regulatory gene network to simulate the TH1/2differentiation in an agent-based model of hyper-sensitivity reactions. Bioinformatics, 24:1374–1380 (2008)doi:10.1093/bioinformatics/btn135

52. V. Tozzi, R. Bellagamba, F. Castiglione, A. Amendola, J. Ivanovic, E. Nicastri, R. Libertone, G. D’Offizi, G. Liuzzi,C. Gori, F. Forbici, R. D’Arrigo, A. Bertoli, M-F. Salvatori, M-R. Capobianchi, A. Antinori, C-F. Perno, P. Narciso.Plasma HIV RNA decline and drug resistance evolution among patients with multiple virologic failures receivingresistance testing-guided HAART. AIDS Research and Human Retroviruses, 24:6:787–796 (2008)

53. M. Bernaschi and F. Castiglione. A comment to “Optimization and parallelisation strategies for Monte Carlosimulation of HIV infection” by D. Hecqueta , H.J. Ruskinb , M. Crane. Computers in Biology and Medicine, 38:281(2008).

54. F. Castiglione, F. Pappalardo, M. Bernaschi and S. Motta. Optimization of HAART with genetic algorithms andagent based models of HIV infection. Bioinformatics, 23(24):3350–3355 (2007);doi:10.1093/bioinformatics/btm408

55. F. Castiglione and B. Piccoli. Cancer immunotherapy, mathematical modeling and optimal control. Journal ofTheoretical Biology, 247(4):723–732 (2007)doi:10.1016/j.jtbi.2007.04.003

http://dx.doi.org/10.1016/j.jtbi.2007.04.003

56. F. Castiglione, K.A. Duca, A. Jarrah, R. Laubenbacher, K. Luzuriaga, D. Hochberg and D.A. Thorley-Lawson.Simulating Epstein Barr Virus Infection with C-ImmSim. Bioinformatics, 23:1371–1377 (2007)doi:10.1093/bioinformatics/btm044

57. A. Cappuccio, F. Castiglione and B. Piccoli. Determination of the optimal therapeutic protocol in cancer im-munotherapy. Mathematical Biosciences, 209(1):1–13 (2007)doi:10.1016/j.mbs.2007.02.009

58. M. Bernaschi, F. Castiglione, A. Ferranti, C. Gavrila, and G. Cesareni. Protnet: a stochastic tool for dynamicsimulation of protein interaction networks. BMC Bioinformatics, 8(1):S4 (2007)doi:10.1186/1471-2105-8-S1-S4

59. F. Castiglione, A. Liso, M. Bernaschi and S. Succi. Microscopic simulation in biology and medicine. CurrentMedicinal Chemistry, 14(6): 625–637 (2007)

60. V. Baldazzi, F. Castiglione and M. Bernaschi. An Enhanced Agent Based Model of the Immune System Response.Cellular Immunology, 244:77–79 (2006)

61. B. Piccoli and F. Castiglione. Optimal vaccine scheduling in cancer immunotherapy. Physica A, 370(2):672–680(2006)doi:10.1016/j.physa.2006.03.011

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62. F. Castiglione and B. Piccoli. Optimal control in a model of dendritic cell transfection cancer immunotherapy.Bulletin of Mathematical Biology, 68(2):255–274 (2006)doi:10.1007/s11538-005-9014-3

63. F. Castiglione and M. Bernaschi. HIV-1 strategies of immune evasion. International Journal of Modern Physics C,16(12):1869–1879 (2005)

64. F. Massaioli, F. Castiglione and M. Bernaschi. OpenMP parallelization of agent-based models. Parallel Computing,31(10-12):1066–1081 (2005)doi:10.1016/j.parco.2005.03.012

65. S. Motta, F. Castiglione, P.-L. Lollini and F. Pappalardo. Modelling vaccination schedules for a cancer immunopre-vention vaccine. Immunome Research, 1(1):5 (2005)doi:10.1186/1745-7580-1-5

http://www.immunome-research.com/content/1/1/5

66. F. Castiglione and A. Liso. The role of computational models of the immune system in designing vaccinationstrategies. Immunopharmacology and Immunotoxicology, 27(3):417–432 (2005)

67. F. Castiglione, F. Toschi, M. Bernaschi, S. Succi, R. Benedetti, B. Falini and A. Liso. Computational modeling of theimmune response to tumor antigens: implications for vaccination. Journal of Theoretical Biology, 237(4):390–400(2005)doi:10.1016/j.jtbi.2005.04.024

68. F. Pappalardo, P.-L. Lollini, F. Castiglione and S. Motta. Modelling and Simulation of Cancer ImmunopreventionVaccine. Bioinformatics, 21(12):2891–2897 (2005)doi:10.1093/bioinformatics/bti426

69. F. Castiglione and S. Succi. Simulating the G-protein cAMP pathway with a two-compartment reactive lattice gas.Theory in Bioscience, 123:413–429 (2005)

70. M. Bernaschi and F. Castiglione. Computational features of agent-based models. International Journal of Compu-tational Methods, 2(1):33–48 (2005)doi:10.1142/S0219876205000399

71. F. Castiglione, F. Poccia, G. D’Offizi and M. Bernaschi. Mutation, fitness, viral diversity and predictive mark-ers of disease progression in a computational model of HIV-1 infection. AIDS Research and Human Retrovirus,20(12):1316–1325 (2004)doi:10.1089/aid.2004.20.1314

72. T. Avitabile, L. Franco, E. Ortisi, Francesco Castiglione, M. Pulvirenti, B. Torrisi, Filippo Castiglione and A. Reibaldi.Keratoconus Staging: A Computer-Assisted Ultrabiomicroscopic Method Compared With Videokeratographic Anal-ysis. Cornea, 23(7):655–660, (2004).

73. F. Castiglione, M. Bernaschi, S. Succi, R. Heinrich and M.W. Kirschner. Intracellular signal propagation in a two-dimensional auto-catalytic reaction model. Physical Review E, 66(3), 031905 (2002)doi:10.1103/PhysRevE.66.031905

74. M. Bernaschi and F. Castiglione. Selection of escape mutants from immune recognition during HIV infection,Immunology and Cell Biology : 80, 307–313 (2002)

75. F. Castiglione and D. Stauffer. Multi-scaling in the Cont-Bouchaud microscopic stock market model. Physica A,300(3-4): 531–538 (2001)

76. K.E. Kurten and F. Castiglione. A dynamical model of B-T cell regulation. International Journal of Modern PhysicsC, 12(3): 367–375 (2001)doi:10.1142/S0129183101001766

77. M. Bernaschi and F. Castiglione. Design and implementation of an Immune System Simulator. Computers inBiology and Medicine, 31(5): 303–331 (2001)

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78. F. Castiglione, S. Motta and G. Nicosia. Pattern Recognition by primary and secondary response of an ArtificialImmune System. Theory in Bioscience, 120(2): 93–106 (2001)

79. F. Castiglione, R.B. Pandey and D. Stauffer. Effect of Trading Momentum and Price Resistance on Stock MarketDynamics: A Glauber Monte Carlo Simulation, Physica A, 289(1-2): 223–228 (2001)

80. F. Castiglione. Forecasting price increments using an artificial Neural Network, in Complex Dynamics in Economics,a Special Issue of Advances in Complex Systems, 4(1): 45–56, Hermes-Oxford (2001)doi:10.1142/S0219525901000097

http://www.worldscientific.com/doi/abs/10.1142/S0219525901000097

81. M. Bernaschi and F. Castiglione. Effects of technical traders in a synthetic Stock Market. International Journal ofModern Physics C, 11(7): 1437–1454 (2000)doi:10.1142/S0129183100001255

82. Filippo Castiglione and Francesco Castiglione. Estimating the Keratoconus Index from ultrasound images of thehuman cornea, IEEE Transaction on Medical Imaging, 19(12): 1268–1227 (2000)

83. F. Castiglione. Diffusion and Aggregation in an Agent Based Model of Stock Market Fluctuations. InternationalJournal of Modern Physics C, 11(5): 865–880 (2000)doi:10.1142/S0129183100000754

84. Francesco Castiglione and Filippo Castiglione. Estrapolalazione automatica del Keratoconus index dall’analisi com-puterizzata di immagini ultrabiomicroscopiche. Bollettino di Oculistica, 79(1) (2000)

85. M. Bernaschi, S. Succi and F. Castiglione. Large-scale Cellular Automata simulations of the Immune Systemresponse, Physical Review E, 61(2): 1851–1854 (2000)

86. F. Castiglione, G. Mannella, S. Motta and G. Nicosia. A Network of Cellular Automata for the simulation of theimmune system. International Journal of Modern Physics C, 10(4): 677–686 (1999)doi:10.1142/S0129183199000516

87. M. Bernaschi, F. Castiglione, P.E. Seiden and S. Succi. Learning cascade in the immune system dynamics: anumerical simulation. Computer Physics Communications, 121(1-3): 122–125 (1999)

88. F. Castiglione. Antigen recognition and evolution in a bit-string population model. International Journal of ModernPhysics C, 10(6): 989–1002 (1999)doi:10.1142/S0129183199000796

89. M. Bernaschi, F. Castiglione and S. Succi. A high performance simulator of the immune response, Future GenerationComputer Systems, 15(3): 333-342 (1999), Elsevier Science ed.

90. M. Bernaschi, F. Castiglione and S. Succi. A parallel simulator of the Immune response. Lecture Notes on ComputerScience, 1401: 163–172 (1998)

91. S. Succi, F. Castiglione and M. Bernaschi. Collective Dynamics in the Immune System Response. Physical ReviewLetters, 79(22): 4493–4496 (1997)

92. F. Castiglione, M. Bernaschi and S. Succi. Simulating the Immune Response on a Distributed Parallel Computer.International Journal of Modern Physics C, 8(3): 527–545 (1997)doi:10.1142/S0129183197000424

BOOK CHAPTERS

1. F. Castiglione, E. Mancini, M. Pedicini, A. S. Jarrah. Quantitative Modelling Approaches. In: Ranganathan, S.,Nakai, K., Schonbach C. and Gribskov, M. (eds.) Encyclpedia of Bioinformatics and Computational Biology, Oxford:Elsevier. (2018) https://www.sciencedirect.com/science/article/pii/B9780128096338204548

2. Paolo Tieri, Lorenzo Farina, Manuela Petti, Laura Astolfi, Paola Paci, F. Castiglione. Network inference andreconstruction in bioinformatics. In: Ranganathan, S., Nakai, K., Schonbach C. and Gribskov, M. (eds.) Encyclopedaof Bioinformatics and Computational Biology, Oxford: Elsevier. (2018)

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3. Pedicini M., Palumbo M.C., F. Castiglione. Computing Hierarchical Transition Graphs of Asynchronous GeneticRegulatory Networks. In: Pelillo M., Poli I., Roli A., Serra R., Slanzi D., Villani M. (eds.) “Artificial Life and Evo-lutionary Computation.” WIVACE 2017. Communications in Computer and Information Science, vol 830. Springer,Cham (2018) https://www.springer.com/us/book/9783319786575

4. T. Mendes, F. Castiglione, P. Tieri and L. Felicori. Systems and Synthetic Biology Applied to Health, In CurrentDevelopments in Biotechnology and Bioengineering, Elsevier, Pages 183-213, (2017) (ISBN 9780444636607) http:

//dx.doi.org/10.1016/B978-0-444-63660-7.00009-7

http://www.sciencedirect.com/science/article/pii/B9780444636607000097

5. P. Tieri, V. Prana, T. Colombo, D. Santoni, F. Castiglione. Multi-scale simulation of T helper lymphocyte dif-ferentiation, in “Advances in Bioinformatics and Computational Biology”, Sergio Campos (Ed.), Lecture Notes inComputer Science, Vol. 8826, pp. 123-134 Springer Verlag (2014) (ISBN 978-3-319-12417-9)

6. F. Castiglione, P-L. Lollini, S. Motta, A. Paladini, F. Pappalardo, M. Pennisi. Computational models as novel toolsfor cancer vaccines, in “New Challenges for Cancer Systems Biomedicine (Simai Springer Series)”, A. D’Onofrio, P.Cerrai, A. Gandolfi (Eds.), Springer Verlag (2012) (ISBN: 978-8847025707)

7. F. Castiglione, B. Ribba, O. Brass. Comparing in-silico results to in vivo and ex-vivo of influenza-specific immuneresponses after vaccination or infection in humans. In “Innovation in Vaccinology, from design, through to deliveryand testing ”, Selene Baschieri (Ed.), Springer Verlag (2012) (ISBN: 978-94-007-4542-1)

8. F. Castiglione. A Monte Carlo simulation for the construction of cytotoxic T lymphocytes repertoire. In “Applicationsof Monte Carlo Methods in Biology, Medicine and Other Fields of Science”, Charles J. Mode (Ed.), Intech Publishing.Wien, Austria (2011) (ISBN: 978-953-307-427-6)

9. F. Castiglione, D. Santoni, M. Pedicini. Implementing agent’s rules with gene regulatory networks in mesoscopic-level models of cellular interactions. In “A practical guide to bioinformatics analysis.” iConcept Press. Annerley,Australia (2010) (ISBN: 978-1-4536086-2-3).

10. F. Castiglione. Agent Based Modeling and Simulation, Introduction to. In Meyers, Robert (Ed.) Encyclopedia ofComplexity and Systems Science, Vol X. Springer, New York (2009).http://www.springer.com/physics/complexity/book/978-0-387-75888-6 (ISBN 978-0-387-75888-6)

11. M. Bernaschi and F. Castiglione. Understanding the immune system by computer-aided modeling. In Schonbach,Christian; Ranganathan, Shoba; Brusic, Vladimir (Eds.) Immunoinformatics, Series: Immunomics Reviews: , Vol. 1,Springer, New York (2007) (ISBN: 978-0-387-72967-1)

12. F. Castiglione, V. Sleitser and Z. Agur. Analyzing hypersensitivity to chemotherapy in a Cellular Automata modelof the immune system. In Preziosi L. (Ed), Cancer Modeling and Simulation, Chapman & Hall/CRC Press (UK), pp333–365, London (2003).

13. F. Castiglione. Forecasting price increments using an artificial Neural Network. In Schweitzer (Ed.), ModelingComplexity in Economic and Social Systems, 395 pp. 45–56, World Scientific, Singapore (2002) (ISBN: 981-238-034-5).

14. F. Castiglione, M. Bernaschi and S. Succi. Simulating the immune response on a distributed parallel computer. InBagnoli, Franco and Ruffo, Stefano (Eds.), Dynamical Modeling in Biotechnologies, World Scientific textbook eds.(2000).

15. F. Castiglione. A Users Guide to CimmSim 1.1. In Bagnoli, Franco and Ruffo, Stefano (Eds.), Dynamical Modelingin Biotechnologies, World Scientific textbook eds (2000).

WEB PUBLICATIONS

1. F. Castiglione. Mathematical Immunology. Expert Review of Immunology Vaccines and Informatics, 2(1):49–51(2015)http://erivijournal.org/articles/Mathematical-Immunology.pdf. Regularly refereed paper.

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2. F. Castiglione Agent Based Modeling. Scholarpedia, 1(10):1562 (2006)doi:10.4249/scholarpedia.1562

http://www.scholarpedia.org/article/Agent_Based_Modeling. Regularly refereed paper.

IN PREPARATION OR UNDER REVIEW

1. F. Castiglione, D. Ghersi, F. Celada. Submitted to Frontiers in Immunology, 2018

CONFERENCE PROCEEDINGS

1. Leandro Martins de Freitas, Tatiani Uceli Maioli, Henrique de Assis Lopes Ribeiro, Paolo Tieri and F. Castiglione Amathematical model of Chagas disease infection predicts inhibition of the immune system. 2018 IEEE InternationalConference on Bioinformatics and Biomedicine (BIBM), Madrid, Spain, 2018, pp. 1374-1379.doi:10.1109/BIBM.2018.8621389

2. Henrique de Assis Lopes Ribeiro, Tatiani Uceli Maioli, Leandro Martins de Freitas, Paolo Tieri and F. Castiglione.A mathematical model of murine macrophage infected with Leishmania sp. 2018 IEEE International Conference onBioinformatics and Biomedicine (BIBM), Madrid, Spain, 2018, pp. 1425-1430.doi:10.1109/BIBM.2018.8621351

3. Alva Presbitero, Emiliano Mancini, F. Castiglione, Valeria V. Krzhizhanovskaya, Rick Quax. Evolutionary gametheory can explain the choice between apoptotic and necrotic pathways in neutrophils. 2018 IEEE InternationalConference on Bioinformatics and Biomedicine (BIBM), Madrid, Spain, 2018, pp. 1401-1405.doi:10.1109/BIBM.2018.8621127

4. F. Castiglione, D. Ghersi, F. Celada. In-Silico Analysis of the “Memory Anti-Naıve” Effect in Anti-Viral Cross-Reactive. 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Kansas City, MO, USA,2017, pp. 1433-1437.doi:10.1109/BIBM.2017.8217873

5. Liso, A, Massenzio, F, Pucciarini, A , Bigerna, B, Luca, P, Zoppoli, P , F. Castiglione, Palumbo, MC, Conese, M,Castellani, S , Stracci, F, Landriscina, M, Specchia, G, Bach, L, Falini, B. Human monocyte-derived dendritic cellsexposed to hyperthermia show a distinct gene expression profile and selective upregulation of IGFBP-6. Haemato-logica, 99(1):440-441. Proceedings of the 19th Congress of the European-Hematology-Association Milan, Italy, Jun12-15, 2014

6. M. Rucco, F. Castiglione, E. Merelli, M. Pettini. Characterisation of the idiotypic immune network through per-sistent entropy. S. Battiston et al. (eds.), Proceedings of ECCS 2014, Springer Proceedings in Complexity, doi

10.1007/978-3-319-29228-1

7. F. Pappalardo, F. Castiglione Castiglione, C. Bianca, G. Russo, M. Pennisi, S. Motta. Multiscale modelling of livingsystems: a mathematical and computational perspective SIMAI2014, Taormina, Italy, July 7-10, 2014

8. F. Castiglione, Merelli E., Pettini M. and Rucco M. Correlation between topological complexity and entropy inIdiotypic Network ECCS’14: Satellite Meeting - Information Processing in Complex Systems (IPCS’14) Lucca, Italy,September 24, 2014.

9. F. Castiglione and F. Pappalardo. “Computational biology modeling across different scales” in Simulation and Mod-eling Methodologies, Technologies and Applications (SIMULTECH 2013), 3rd International Conference on (Reykjavik,Iceland, July 29 - 31, 2013)

10. F. Castiglione and Bernaschi M. “Epitope screening and cell cooperation in the immune response” in IntelligentSystems, Modelling and Simulation (ISMS2011), International Conference on, (Kuala Lumpur 24 January, PhnomPenh 27-28 January 2011) ISMS2010 papers in the IEEE computer Society Digital Library (CSDL) IEEE ComputerSociety, Los Alamitos, CA, USA 0: 127–132 (2011) ISBN 978-0-7695-4336-9 http://doi.ieeecomputersociety.

org/10.1109/ISMS.2011.30

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11. F. Castiglione and Pappalardo F. “Toward multi-organs simulations of immune-pathogen interactions”, in NinthInternational Conference on Intelligent Systems Design and Applications, ISDA 2009, Pisa, Italy, Nov 30 – Dec2, 2009, pg. 330–334, 2009. IEEE Computer Society Washington, DC, USA (ISBN: 978-0-7695-3872-3). doi:

10.1109/ISDA.2009.119

http://www.computer.org/portal/web/csdl/doi/10.1109/ISDA.2009.119

12. G. Dell’Acqua and F. Castiglione. “A mathematical model of Duchenne muscular dystrophy”, in Applied andIndustrial Mathematics in Italy III (AIMI III) Proceedings of the SIMAI IX Congress, Rome, September 15–19, 2008.World Scientific Press (2009).

13. P. Paci, F. Castiglione, M. Bernaschi and V. Baldazzi. “A Discrete/Continuous Model of Anti-HIV Response andTherapy”, uksim, pp. 481–486, Tenth International Conference on Computer Modeling and Simulation (uksim 2008),2008 (ISBN: 0-7695-3114-8).http://doi.ieeecomputersociety.org/10.1109/UKSIM.2008.26

14. F. Castiglione, F. Toschi, M. Bernaschi, S. Succi, R. Benedetti, B. Falini and A. Liso. Computational modeling ofthe immune response to tumor antigens: implications for vaccination. In: “Decision and Control, 2004. CDC. 43rdIEEE Conference on” 14-17 Dec. 2004 Volume: 1, On page(s): 585- 590 Vol.1 ISBN: 0-7803-8682-5

15. F. Castiglione and B. Piccoli. Optimal control in a model of dendritic cell transfection cancer immunotherapy. In:“Decision and Control, 2004. CDC. 43rd IEEE Conference on” 14-17 Dec. 2004 Volume: 1, On page(s): 585- 590Vol.1 ISBN: 0-7803-8682-5

16. F. Castiglione and M. Bernaschi. C-ImmSim: Playing with the immune response. In: Proceedings of the SixteenthInternational Symposium on Mathematical Theory of Networks and Systems (MTNS2004, July 5-9, 2004 – KatholiekeUniversiteit Leuven, Belgium) Eds.: B. de Moor, B. Motmans, J. Willems, P. van Dooren, V. Blondel, (ISBN: 90-5682-517-8).

17. F. Castiglione, M. Bernaschi and M. Spizzichino. From un-realistic to quasi-realistic rules for trading in a microscopicmodel of financial markets with N >> 1 assets, International Conference, “Scientific achievements for wellbeing anddevelopment of society”, March 4-5, 2004, Rezeknes Augstskola, 2004 (ISBN: 9984-585-34-4).

18. F. Castiglione. Agent-based micro-simulations in Immunology and Finance, Proceedings of the 4th InternationalScientific and Practical Conference, June 26-28, 2003, Rezeknes Augstskola, Latvia, 2003 (ISBN: 9984-585-68-9).

19. S. Motta, F. Castiglione and G. Nicosia. Pattern Recognition with a Multi-Agent model of the Immune System, In:Proceedings of the International NAISO Symposium on Information Science Innovations in Engineering of Naturaland Artificial Intelligent Systems (ENAIS’2001), ICSC Academic Press, March 17-21, 2001 at the American Universityin Dubai, U.A.E., ICSC Academic Press, pp. 788-794, 2001.

20. F. Castiglione. The joint meeting of the 4th World Multiconference on Systemics, Cybernetics and Informatics(SCI’2000) and the 6th International Conference on Information Systems Analysis and Synthesis (ISAS’2000), Or-lando, USA, July 23 - 26, 2000. SCI proceedings 2000/ISAS 2000 VOLUME X

21. M. Bernaschi, F. Castiglione and S. Succi. A Parallel Simulator of the Immune Response, In: Proceedings ofHPCN98 “High Performance Computing and Networking”, Amsterdam, 1998. M. Bubak, B. Hertzberger and P.Sloot (eds), Lecture Notes in Computer Science, Springer, n. 1401.

COMMUNICATIONS, ABSTRACTS AND POSTERS

1. I. Valentini, P. Tieri, F. Castiglione. MISSION-T2D - Multiscale Immune System SImulator for the ONset of Type2 Diabetes. 65th International Congress of Aviation and Space Medicine Rome, 10-14 September 2017

2. M. Pedicini, M-C. Palumbo, F. Castiglione. Attractors in synchronous and asynchronous genetic regulatory networks.Italian Workshop on Artificial Life and Evolutionary Computation (WIVACE) 2017 Edition - 19th-21st September2017, Venice, Italy.

3. F. Caixeta; A. B. Sa Campos, V. D. Martins, L. Martins de Freitas, F. Castiglione, P. Tieri, H. de Assis, T. UceliMaioli. Analyses of different expressed genes in C57BL/6 dentritic cell infected wiyh L. Amazonensis. XLI AnnualMeeting of the Brazilian Society of Immunology, Campos do Jordao, State of Sao Paulo, October 29th - November2nd, 2016

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4. Statistical ensemble of gene regulatory networks of macrophage differentiation. 15th International Conference onBioinformatics (InCoB 2016) - Singapore Sept 21–23, 2016

5. E-health week - Speakers’ Corner: EU Funded Projects, ”Multi scale Immune System Simulator for the Onset ofType 2 Diabetes integrating genetic, metabolic and nutritional data”. Budapest, Hungary, June 14–16, 2015

6. A multi-scale computational model of helper T lymphocytes differentiation. The Second International Conference onMathematics and Statistics AUS-ICMS’15 American University of Sharjah, UAE, April 2–5, 2015

7. Do closely located genes have a higher likelihood to interact? InCoB/ISCB - Asia 2011, Kuala Lumpur 30.11 – 02.122011

8. TH1/2 differentiation in an agent-based model. Workshop on Discrete models of biological networks: from structureto dynamics. Marseille, France, November 3–7, 2008

9. Stability and phase transitions in a mathematical model of Duchenne Muscular Dystrophy. Mini EURO Conferenceon Computational Biology, Bioinformatics and Medicine, Rome, September 15–17, 2008

10. Immunotherapy 2006: Targeting complexity. La Habana, Cuba, November 15–19, 2006.

11. International Conference of Immunogenomics and Immunomics. Budapest, Hungary, October 8–12, 2006.

12. Workshop on Cancer Modelling and Therapeutic Innovation: From Theory to Clinic (University of Lyon, France,from Sept 26/27, 2006. Workshop organized by the Institute for Theoretical Medicine and Clinical PharmacologyDepartment, University of Lyon, France).

13. HPC User Forum, May 29/30, 2006. “ImmunoGrid; large scale simulation of the immune system”.

14. “Inter- and intra-cellular scales with cellular automata”. VIII Congresso SIMAI Baia Samuele (Ragusa), 22-26 May2006.

15. “Dynamic simulation of protein interaction networks”. Interactome Network, Hinxton Genome Campus, Cambridge,Aug 31 - Sept 4, 2005.

16. II Congresso Nazionale della Societa Italiana di Virologia Medica - SIVIM Roma 16-18 Maggio 2005.

17. Workshop of the INDAM intergroup project. Control Systems, Theory, Numerics and Applications Rome, 30-31March, 1 April 2005.

18. “OpenMP parallelization of agent-based models” Fifth European Workshop on OpenMP, Aachen University, GermanySeptember 22-26, 2003.

19. ScalPerf 03: Scalable Approaches to High Performance and High Productivity Computing, 14-17 April 2003, Univer-sity of Bologna Residential Center Bertinoro (Forlı), Italy

20. Computer experiments of HIV-1 infection, 5th official ESMTB tri-annual Conference (ECMTB2002) of the Societyof Mathematical and Theoretical Biology (ESMTB) on “Mathematical Modelling and Computing in Biology andMedicine” Milan, Italy, July 2 - 6, 2002.

21. Annual Meeting of the Israeli Society of Theoretical BioMathematics (ISTBM), Bar Ilan University, Tel Aviv, IsraelMarch 25, 2002.

22. International EUROSIM Congress 2001, part of the 2nd Conference on Modelling and Simulation in Biology, Medicineand Biomedical Engineering. Delft, The Netherlands, June 26 - 29, 2001.

23. International Workshop on “Frontier in the physics of Complex Systems”, Ein Bokek, Dead Sea, Israel March 25 -28, 2001.

24. International Workshop “Economic Dynamics from the Physics Point of View”, Physikzentrum Bad Honnef, Germany,27 - 30 March 2000.

25. ZiF Meeting “Theory in Immunology”, Bielefeld, 16 - 19 October, 1999.

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26. The Fourth International Congress on Industrial and Applied Mathematics, ICIAM 99. Edinburgh, Scotland, 5-9 July1999.

27. International Conference on Computational Physics (CCP’98), Grenada, Spain 1998.

28. WAE’97 (Workshop on Algorithms Engineering), Venice, September 1997.

29. ACRI ’96 (Cellular Automata for Research and Industry), Milan, October 1996.

30. “Simulation of Cellular Interactions in the Immune System. Computational Complexity”, Proceedings of SIMAI 96(Conferenza della “Societa Italiana di Matematica Applicata Industriale”), Salice Terme (Pavia), 1996.

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