Luca Zammataro
Personal Details:
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Current Position: 2011-Today. Senior Post Doc at Computational Research Unit, Center of
Genomic Science of IIT@SEMM.
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Date and Place of Birth: June, 20, 1970, Catania, Italy
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Work address: Computational Research Unit, Center of Genomic Science of IIT@SEMM, Via
Adamello 16, 20139 Milan
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Phone.: (+39) +39 02 94375274
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Fax.: (+39) 02 94375991
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Mobile: (+39) 338 9697236
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Emails: luca.zammataro@iit.it; luca.zammataro@gmail.com; luca.zammataro@ieo.eu;
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Citizenship: italian
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Foreign Languages: English;
Personal Home Pages:
 www.lucazammataro.com
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http://www.iit.it/en/people/iitsemm/senior-post-doc/luca-zammataro.html
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GoogleScolar: http://scholar.google.com/citations?user=RtD5I_sAAAAJ&hl=en
skypeID: lucazammataro
Research areas:
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Bioinformatics in the context of Oncogenomics (Next Generation Sequencing).
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Identification of tumor driver mutations by meta-analysis of re-sequencing studies.
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Structural Biology.
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Application of immunology to cancer studies.
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Developing of computational tools and web services for bioinformatics (java, C, Shell
programming).
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Computational modeling of development.
Education:
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2006: PhD program in “Complexity In Post-Genomic Biology” at University of Torino, Tutor:
Prof. Federico Bussolino. PhD Thesis: “Computational Geometry in Biology: From Proteins to
Embryo”.
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2004: Summer School at NKS (New Kind of Science), Brown University, Providence, USA,
Head: Stephen Wolfram. Research topic: “Using 3D Substitution Systems to Model
Compartmentalizations and Clusters Architectures in Nature: An NKS Approach.”
http://www.wolframscience.com/summerschool/2004/participants/zammataro.html
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2003: MSc Master in Bioinformatics, Faculty of Biotechnology, University of Torino, Italy.
Thesis: “Studying the relationship between the energy residues and their phi/psi angles in
proteins, by means of artificial neural networks: an approach to tertiary structure
prediction”.
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2003: Residency Program: Graduated at Clinical Pathology, (BSc Pathology) University of
Catania (Department of Biomedical Sciences . Director: Prof. S. Travali) Score: of 70/70
highest honors. Thesis: "Role of collapsin response mediator protein in the control of
endothelial cell migration and morphogenesis".
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1999: Acquisition of Italian Medical License for practicing (M.D. License). Registered in the
County of Catania, Italy. Registration Number: 11692.
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1998, July 29: Degree of Medicine, University of Catania (Italy) Score: 110/110 highest
honors. Thesis: "Action of IFN-gamma, IL-10, and TNF-alpha in MMP and TIMP-1 production
by human monocyte-macrophages cell lines".
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1988: Diploma of High School at Liceo-Ginnasio Statale “Nicola Spedalieri” of Catania, Italy
with vote of 60/60 highest honors.
Positions:
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2011-Today. Senior Post Doc at Computational Research Unit, Center of Genomic Science of
IIT@SEMM. Currently I'm focused on NGS and ChipSeq analysis, and in translating all these
analyses in the field of structural biology. Moreover, I'm working on the role of lowfrequency mutations in chemokine receptors in melanoma metastases developing new
concepts of "homing" of metastases versus specific tissue sites /organs, associated to those
mutations, in relation to the receptor desensitization of chemokine receptors.
Since June 2014 I’m collaborating with Dr Pier Framcesco Ferrucci, which is the Director of
Oncology of Melanoma Unit of IEO - Istituto Europeo di Oncologia, Milan, studying
melanoma patients, with the aim to create and test new computational and statistical
methods for melanoma subclassification, and therapy optimization.
2008-2011: Research assistant in Bioinformatics, Istituto Clinico Humanitas Milano, Italy.
Heads: Prof Massimo Locati and Alberto Mantovani; Research topics: 1) Identification of new
promoter regions regulating micro RNA complexes involved in inflammation 2) Identification
of transcriptional factors specifically oriented in macrophage alternative polarization. 3)
Identification of new markers and functions of alternative macrophage polarization M2: the
regulation and functional role of iron in macrophage activation (clustering of iron
homeostasis-related genes). (Project in collaboration with Dr S. Recalcati and G. Cairo,
University of Milan) 4. NF-kB DNA binding investigation: Molecular design, folding and
docking prediction of peptides interacting with p50/p65 NF-kB dimer (head of project: Prof A.
Sica, Istituto Clinico Humanitas) Nobel Project: “Modelling of Gene Regulation, Transcription
and Translation. Modelling the role of transcription factors and microRNAs in macrophage
activation” (project in collaboration with Dr A. Ihekwaba and Dr I. Mura of The Microsoft
Research – University of Trento, Centre for Computational and Systems Biology (CoSBI).
2007-2008: Research assistant in Bioinformatics. Consiglio Nazionale delle Ricerche CNR,
Istituto di Scienze Neurologiche ISN, Head: Dr Sebastiano Cavallaro.
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2001-2007: Visiting Fellow in the Div. of Molecular Angiogenesis, Institute for Cancer
Research and Treatment, University of Torino School of Medicine. Head: Prof. Federico
Bussolino. Research activities in the Division of Molecular Angiogenesis, Institute for Cancer
Research and Treatment, University of Torino School of Medicine. Head: Prof. Federico
Bussolino. Research topics: 1) Studying the role of collapsin response mediator protein
(CRMP-1) as signal transducers of semaphorin signaling in endothelial cell. 2) Developing
algorithms based on geometric hashing, for 3D-alignments of molecular coordinates in
structural biology. 3) Developing algorithms analyzing “atypical SH2 domains” and their in
vivo validation. 4) Embryonic Cleavage algorithm.
Acquired techniques: a) Cell biology of endothelium. b) Experience in angiogenesis
mechanisms, cell migration and endothelial cell polarisation. c) Expertises in fluorescence
microscopy. d) Expertises in molecular and cell biology (plasmid preparations, and Green
Fluor Protein (GFP) fusion constructs). e) Know-how in microRNAs biological mechanisms
and seed prediction algorithms. f) Structural biology and protein folding know-how. g)
Biochemical background on macrophages Iron metabolisms and inflammation.
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2000-2001: Clinical activities in Hospital Ascoli-Tomaselli, and Hospital Garibaldi, Catania,
Italy.
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1998-2000: Visiting Fellow in, Dept. of Biomedical Sciences, University of Catania School of
Medicine Head: Prof. A. Messina. 1998-2000: Frequency before as student and after as
professional trainer in the Department of of Biomedical Sciences. Head: Prof. A. Messina.
Research topic: “Function of IRF-1 in the regulation of FAS-Receptor transcription.”
Professional programming
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I have also developed apps for iPhone. The most recent is “Wamoz (WAke Me up On Zone).
Wamoz is a pretty iPhone application that advice you when you are nearby a place, (that
could be a bus stop, train stations.. etc) with a delicate sound.
https://itunes.apple.com/it/app/wamoz/id504530681?mt=8
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Wolfram Mathematica Demonstrations:
http://demonstrations.wolfram.com/author.html?author=Luca+Zammataro
Publications:
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1: Selmi C, Cavaciocchi F, Lleo A, Cheroni C, De Francesco R, Lombardi SA, De Santis M, Meda
F, Raimondo MG, Crotti C, Folci M, Zammataro L, Mayo MJ, Bach N, Shimoda S, Gordon SC,
Miozzo M, Invernizzi P, Podda M, Scavelli R, Martin MR, Lasalle JM, Gershwin ME. Genomewide analysis of DNA methylation, copy number variation, and gene expression in
monozygotic twins discordant for primary biliary cirrhosis. Front Immunol. 2014 Mar
28;5:128. doi: 10.3389/fimmu.2014.00128. e Collection 2014. PubMed PMID: 24734033;
PubMed Central PMCID: PMC3975093.
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2: Zammataro L, DeMolfetta R, Bucci G, Ceol A, Muller H. AnnotateGenomicRegions: a web
application. BMC Bioinformatics. 2014;15 Suppl 1:S8. doi: 10.1186/1471-2105-15-S1-S8.
Epub 2014 Jan 10. PubMed PMID: 24564446; PubMed Central PMCID: PMC4015944.
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3: Pangrazio A, Puddu A, Oppo M, Valentini M, Zammataro L, Vellodi A, Gener B, Llano-Rivas
I, Raza J, Atta I, Vezzoni P, Superti-Furga A, Villa A, Sobacchi C. Exome sequencing identifies
CTSK mutations in patients originally diagnosed as intermediate osteopetrosis. Bone. 2013
Nov 20;59C:122-126. doi: 10.1016/j.bone.2013.11.014. [Epub ahead of print] PubMed PMID:
24269275.
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4: Ficara F, Crisafulli L, Lin C, Iwasaki M, Smith KS, Zammataro L, Cleary ML. Pbx1 restrains
myeloid maturation while preserving lymphoid potential in hematopoietic progenitors. J Cell
Sci. 2013 Jul 15;126(Pt 14):3181-91. doi: 10.1242/jcs.125435. Epub 2013 May 9. PubMed
PMID: 23660001.
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5: Selmi C, Feghali-Bostwick CA, Lleo A, Lombardi SA, De Santis M, Cavaciocchi F, Zammataro
L, Mitchell MM, Lasalle JM, Medsger T Jr, Gershwin ME. X chromosome gene methylation in
peripheral lymphocytes from monozygotic twins discordant for scleroderma. Clin Exp
Immunol. 2012 Sep;169(3):253-62. doi: 10.1111/j.1365-2249.2012.04621.x. PubMed PMID:
22861365; PubMed Central PMCID: PMC3445002.
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6: X chromosome gene methylation in peripheral lymphocytes from monozygotic twins
discordant for scleroderma. C Selmi, C A Feghali-Bostwick, A Lleo, S A Lombardi, M De Santis,
F Cavaciocchi, L Zammataro, M M Mitchell, J M Lasalle, T Medsger, M E Gershwin Clinical &
Experimental
Immunology
(impact
factor:
3.01).
09/2012;
169(3):253-62.
DOI:10.1111/j.1365-2249.2012.04621.x
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7: Pangrazio A, Cassani B, Guerrini MM, Crockett JC, Marrella V, Zammataro L, Strina D,
Schulz A, Schlack C, Kornak U, Mellis DJ, Duthie A, Helfrich MH, Durandy A, Moshous D,
Vellodi A, Chiesa R, Veys P, Lo Iacono N, Vezzoni P, Fischer A, Villa A, Sobacchi C. RANKdependent autosomal recessive osteopetrosis: characterization of five new cases with novel
mutations. J Bone Miner Res. 2012 Feb;27(2):342-51. doi: 10.1002/jbmr.559. PubMed PMID:
22271396; PubMed Central PMCID: PMC3306792
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8: Pangrazio A, Cassani B, Guerrini MM, Crockett JC, Marrella V, Zammataro L, Strina
D, Schulz A, Schlack C, Kornak U, Mellis DJ, Duthie A, Helfrich MH,
Durandy A, Moshous D,
Vellodi A, Chiesa R, Veys P, Iacono NL, Vezzoni P, Fischer A, Villa A, Sobacchi C. RANKdependent autosomal recessive osteopetrosis:
characterisation of 5 new cases with novel
mutations. J Bone Miner Res. 2011 Nov 9. doi: 10.1002/jbmr.559. [Epub ahead of print]
PubMed PMID: 22072319.
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9: Pello OM, De Pizzol M, Mirolo M, Soucek L, Zammataro L, Amabile A, Doni A,
Nebuloni M,
Swigart LB, Evan GI, Mantovani A, Locati M. Role of c-Myc in
alternative activation of human
macrophages and tumor-associated macrophage
biology. Blood. 2011 Nov 8. [Epub ahead
of print] PubMed PMID: 22067385.
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10: Mitchell MM, Lleo A, Zammataro L, Mayo MJ, Invernizzi P, Bach N, Shimoda S, Gordon S,
Podda M, Gershwin ME, Selmi C, LaSalle JM. Epigenetic investigation of variably X
chromosome inactivated genes in monozygotic female twins discordant for primary biliary
cirrhosis. Epigenetics. 2011 Jan;6(1):95-102. Epub 2011 Jan1. PubMed PMID: 20864813;
PubMed Central PMCID: PMC3029486.
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11: Mitola S, Ravelli C, Moroni E, Salvi V, Leali D, Ballmer-Hofer K, Zammataro L, Presta M.
Gremlin is a novel agonist of the major proangiogenic receptor VEGFR2. Blood. 2010 Nov
4;116(18):3677-80. Epub 2010 Jul 21. PubMed PMID: 20660291.
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12: Large scale agent-based modeling of the humoral and cellular immune response
Giovanni Stracquadanio, Renato Umeton, Jole Costanza, Viviana Annibali, Rosella Mechelli,
Mario Pavone, Luca Zammataro, Giuseppe Nicosia. LNCS 01/2011; 6825:15-29.
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13: Solinas G, Schiarea S, Liguori M, Fabbri M, Pesce S, Zammataro L, Pasqualini F, Nebuloni
M, Chiabrando C, Mantovani A, Allavena P. Tumor-conditioned macrophages secrete
migration-stimulating factor: a new marker for M2-polarization, influencing tumor cell
motility. J Immunol. 2010 Jul 1;185(1):642-52. Epub 2010 Jun 7. PubMed PMID: 20530259.
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14: Recalcati S, Locati M, Marini A, Santambrogio P, Zaninotto F, De Pizzol M, Zammataro L,
Girelli D, Cairo G. Differential regulation of iron homeostasis during human macrophage
polarized activation. Eur J Immunol. 2010 Mar;40(3):824-35. PubMed PMID: 20039303.
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15: Mantovani A, Savino B, Locati M, Zammataro L, Allavena P, Bonecchi R. The chemokine
system in cancer biology and therapy. Cytokine Growth Factor Rev. 2010 Feb;21(1):27-39.
Epub 2009 Dec 8. Review. PubMed PMID: 20004131.
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16: Zammataro L, Serini G, Rowland T, Bussolino F. Embryonic cleavage modeling as a
computational approach to sphere packing problem. J Theor Biol. 2007 Mar 7;245(1):77-82.
Epub 2006 Oct 4. PubMed PMID: 17087975.
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17: Mitola S, Brenchio B, Piccinini M, Tertoolen L, Zammataro L, Breier G, Rinaudo MT, den
Hertog J, Arese M, Bussolino F. Type I collagen limits VEGFR-2 signaling by a SHP2 proteintyrosine phosphatase-dependent mechanism 1. Circ Res. 2006 Jan 6;98(1):45-54. Epub 2005
Dec 8. PubMed PMID: 16339483.
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18: Serini G, Valdembri D, Zanivan S, Morterra G, Burkhardt C, Caccavari F, Zammataro L,
Primo L, Tamagnone L, Logan M, Tessier-Lavigne M, Taniguchi M, Puschel AW, Bussolino F.
Class 3 semaphorins control vascular morphogenesis by inhibiting integrin function. Nature.
2003 Jul 24;424(6947):391-7. Erratum in: Nature. 2003 Aug 21;424(6951):974. PubMed
PMID: 12879061.
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19: Conte E, Manzella L, Zeuner A, Cocchiaro G, Conticello C, Zammataro L,
Messina CG, De
Maria R, Messina A. Involvement of interferon regulatory factor-1 in monocyte CD95
expression and CD95-mediated apoptosis. Cell Death Differ. 2003 May;10(5):615-7.
PubMed PMID: 12728261.
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20: Castiglione F., Motta S., Nicosia G. and Zammataro L. The effects of an apoptosis
mechanism on the immune response. Proceedings of the 4th International Eurosim 2001
Congress, Delft, The Netherlands, 26-29 June, 2001, ISBN 90-806441-1-0
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21: Zammataro L, Serini G, Botta M and Bussolino F. SEquences Analysis by Structural
Hashing Alignment. (SEASHAL). Abstract published in Ital J Biochem. 2006 Mar-Jun;55(1-2):3164. SIB 2006. Abstracts of the 51st National Congress of the Italian Society of Biochemistry
and Molecular Biology, Riccione, Italy, 28-30 September 2006. PMID: 17225340 [PubMed indexed for MEDLINE]
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22: Effective Calibration of Artificial Gene Regulatory Networks D. Agostini, J. Costanza, V.
Cutello, L. Zammataro, N. Krasnogor, M. Pavone, G. Nicosia 01/2011; In proceeding of: 20th
European Conference on Artificial Life (ECAL), At MIT Press, Paris, France, August 8-12, 2011
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23: Large Scale Agent-Based Modeling of the Humoral and Cellular Immune Response.
Giovanni Stracquadanio, Renato Umeton, Jole Costanza, Viviana Annibali, Rosella Mechelli,
Mario Pavone, Luca Zammataro, Giuseppe Nicosia 01/2011; In proceeding of: Artificial
Immune Systems - 10th International Conference, ICARIS 2011, Cambridge, UK, July 18-21,
2011. Proceedings
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24: Nicosia, G.; Sciacca, E.; Zammataro, L. Detecting constituent sequences by means of HP
pattern-based grammars to synthesize proteins: Inferring sequence-structurefunction
relationship. Bioinformatics and Biomedicine Workshops, 2007. BIBMW 2007. IEEE
International Conference on Volume , Issue , 2-4 Nov. 2007 Page(s):53 –59 Digital Object
Identifier 10.1109/BIBMW.2007.4425400
Abstracts:
 T.N.3 A GENOME-WIDE DNA METHYLATION STUDY IN MONOZYGOTIC TWINS
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DISCORDANT FOR PRIMARY BILIARY CIRRHOSIS by A. Lleo, M.R. Martin, L. Zammataro, M.J.
Mayo, N. Bach, S. Shimoda, S. Gordon, M. Folci, P. Invernizzi, M. Podda, M.E. Gershwin, J.M.
Lasalle, C. Selmi Digestive and Liver Disease (Vol.42)
Communications:
 # G. Nicosia, E. Sciacca, L. Zammataro, Detecting Constituent Sequences by means of HP
Pattern-Based Grammars to Synthesize AmPs, Synthetic Biology 3.0, 24th-26th June 2007,
ETH, Swiss Federal Institute of Technology, Zurich, Switzerland.
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# G. Nicosia, G. Stracquadanio, L. Zammataro, Modelling infections with stochastic picalculus,
Synthetic Biology 3.0, 24th-26th June 2007, ETH, Swiss Federal Institute of Technology,
Zurich, Switzerland.
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# F. Castiglione, S. Motta, G. Nicosia, L. Zammataro, The effects of an apoptosis mechanism
on the immune response, Eurosim 2001 Congress Shaping Future With Simulation, June 2629, 2001, Delft, The Netherlands.
Books.
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Luca Zammataro. “Il computer emozionale, coscienza, emozioni, cibernetica.” Bonanno
editore. ISBN-13: 978-88-7796-305-5
Talks and seminars:
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8 Oct 2010: Luca Zammataro “An hypothesis of emotional engine” Centre of Robotics and
Neural
Systems,
University
of
Plymouth,
Speaker:
Luca
Zammataro
http://www.tech.plym.ac.uk/SOCCE/CRNS/events.html
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2007: Wolfram NKS2007 conference Presentation title: “The Universal Vision of Organismal
Forms through NKS’s Eyes” Speaker: Luca Zammataro July 13-15 2007, Burlington, University
of Vermont, USA. (Selected Speaker)
SBH2007 (Sysbiohealth symposioum 2007) Presentation title: “Analysis of atypical SH2
domains and their in vivo validation” 16-19 october 2007, University of Milano-Bicocca.
(Selected Speaker: Luca Zammataro) Miniworkshop at SYSBIOM (Complex Systems In
Molecular Biology and Medicine), on “Structural Biology and Bionformatics tools”.December
2006, University of Torino (Organizer: Luca Zammataro).
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January 23-27, 2006 : I FIMA International Conference "Models and Methods for Human
Genomics Ayas-Champoluc, Aosta Valley (Italy), January 23-27, 2006 Speaker: Luca
Zammataro. Presentation title: “Embryonic Cleavage Modeling as a biocomputational
approach to Keplero’s Sphere Packing Problem”. Luca Zammataro, Todd Rowland, Guido
Serini, Federico Bussolino
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28-30 September 2006: SIB (Società Italiana Biochimica e Biologia Molecolare) 28-30
September 2006. Poster presentation: SEquences Analysis by Structural Hashing Alignment.
(SEASHAL). Luca Zammataro°, Guido Serini°, Marco Botta§ and Federico Bussolino. Published
on Ital J Biochem. 2006 Mar-Jun;55(1-2):3-164. SIB 2006. Abstracts of the 51st National
Congress of the Italian Society of Biochemistry and Molecular Biology, Riccione, Italy, 28-30
September 2006. PMID: 17225340 [PubMed - indexed for MEDLINE] (Presenting author)
Recent posters:
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2012 poster BITS 2012: Bioinformatic Italian Society annual meeting 02-04 May, Catania
AnnotateGenomicRegions: A web application Heiko Muller, Bucci Gabriele, Luca Zammataro
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2012 poster BITS 2012: Bioinformatic Italian Society annual meeting 02-04 May, Catania
Integrated Analysis of Epigenetic and Transcriptional Circuits in Gliomagenesis Gabriele
Bucci, Elena Signaroldi, Pasquale Laise, Pierre-Luc Germain, Luca Zammataro, Heiko Muller,
Giuseppe Testa
Teaching Activity:
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During the last 5 years, I have reached a good experience in teaching. In particular, From
2003 to 2008, I organised a Computational Biology Practical Course at the Department of
Human and Animal Biology, University of Torino, and a Theoretical Neurosciences Course at
University of Catania. The overall feedback was very positive from students. For the
Theoretical Neuroscience Course I wrote a book, titled “The Emotional Computer”, in which I
have explained the current theory on “Affecting Computing”, that was inspired to Antonio
Damasio’s studies, on emotional aspects of brains, in decision making.
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2006-2007 B8610 – Computational Biology Practical Course, DBAU (Department of Human
and Animal Biology). University of Torino, Biological Sciences .Credits 4 Arguments treated:
1) Basic knowledge of instruments for data processing and treatment 2. Using genomic
database: ENTREZ; 3. Using genomic database: ENSEMBL; 4. Introduction to sequences
alignment: Needleman-Wunsch and Smith-Waterman algorithms 5. heuristical algorithms for
alignment: BLAST and FASTA; 6. Analysis of gene expression data: 7. Using databases for
biomedical literature (PubMed of NCBI) 8. Introduction to algorithms for of secondary
protein structure prediction. 9. Introduction to hashing algorithms for geometric alignment
of 3D protein structures 10; Analysis of protein data in molecular pathology.
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2007-2008: Theoretical Neurosciences Course. University of Catania. M-PSI/01: Credits 3