Paolo Alessandro Cozzi

Nerviano 20014 (MI), Italy · paoloalessandro.cozzi@gmail.com

I'm a bioinformatician with a passion in programming applications that could be useful in biological problems. My research activities concern the development of softwares for doing bioinformatic analyses, genomic annotations, data management and visualization under linux environment. I have experience in software optimization, HPC infrastructures, databases, linux system administration and web applications. I'm interested in the open-source community and in improving my developer skills.

Experience

Researcher

National Research Council - Institute of Agricultural Biology and Biotechnology

Bioinformatic analyses and software development in the field of animal and plant Genomics. Pipelines and analyses development. Web development and data visualization with responsive applications. Databases management and software development using the Continuous integration approach. IT infrastructure configuration and management.

February 2022 - Present

Graduate Research Fellow

National Research Council - Institute of Agricultural Biology and Biotechnology

Web development and data visualization with responsive applications. Databases management and software development using the Continuous integration approach. IT infrastructure configuration and management.

October 2019 - December 2021

Graduate Research Fellow

National Research Council - Institute of biomedical technologies

Web development and data visualization with responsive applications. Databases management and software development using the Continuous integration approach.

March 2018 - June 2019

Bioinformatician

Parco Tecnologico Padano

Involved in bioinformatic analyses with the core bioinformatic team and developer of specific pipelines to address customer specific problems. IT infrastructure management and administration. Performed genomic annotations and supported the rice group in bioinformatic analyses.

November 2010 - December 2017

Bioinformatician

National Research Council - Institute of biomedical technologies

Involved in software development with the aim to detect similarities between protein relying on molecular surfaces using a computer vision technique. Develop and perform bioinformatic calculations on HPC and EGEE GRID environment.

July 2007 - November 2010

Education

University of Milan (Italy)

PhD in Molecular Medicine
  • Molecular genetics
  • Molecular genomics
  • Functional genomics
  • Molecular biology
  • Bioinformatics
December 2007 - October 2010

University of Milano - Bicocca (Italy)

Specialist degree in Bioinformatics
  • Biological Systems
  • Molecular Processes
  • Fundamentals of computer science

110/110 e Lode

2004-2007

University of Milano - Bicocca (Italy)

Degree in Biotechnologies
  • Biological Systems
  • Molecular Processes
  • Biotechnological techniques
  • English Language

99/110

2000-2004

Skills

Programming Languages & Tools
Workflow
  • HPC
  • Responsive Design
  • Continuous integration and continuous delivery
  • DevOps
  • Nexflow pipelines and modules development

Interests

I'm interested in open-source projects, HPC and code optimization. I like working in linux environment and contribute to open-source software. I'm interested in data analysis and visualization.

Publications

Peer-reviewed journal articles

  • Manunza A, Diaz JR, Sayre BL, Cozzi P, Bobbo T, Deniskova T, Dotsev A, Zinovieva N, Stella A (2023) Discovering novel clues of natural selection on four worldwide goat breeds. Sci Rep 13:1–19., https://doi.org/10.1038/s41598-023-27490-x
  • Lorenzini EC, Lazzari B, Tartaglia GM, Farronato G, Lanteri V, Botti S, Biscarini F, Cozzi P, Stella A (2022) Oral ecological environment modifications by hard-cheese: from pH to microbiome: a prospective cohort study based on 16S rRNA metabarcoding approach. J Transl Med 20:312., https://doi.org/10.1186/s12967-022-03506-4
  • M. Chialva, S. Ghignone, P. Cozzi, B. Lazzari, P. Bonfante, P. Abbruscato, E. Lumini, "Water management and phenology influence the root-associated rice field microbiota", FEMS Microbiology Ecology, Volume 96, Issue 9, September 2020, fiaa146, https://doi.org/10.1093/femsec/fiaa146
  • Maccaferri, M., Harris, N. S., Twardziok, S. O., Pasam, R. K., Gundlach, H., Spannagl, M., …, Cattivelli, L. (2019). Durum wheat genome highlights past domestication signatures and future improvement targets. Nature Genetics, 51(5), 885–895, https://doi.org/10.1038/s41588-019-0381-3
  • F. Biscarini, P. Cozzi and P. Orozco‐ter Wengel, "Lessons learnt on the analysis of large sequence data in animal genomics". Anim Genet. Volume: 49 Issue: 3 Pages: 147-158, 10.1111/age.12655
  • A. Volante, F. Desiderio, A. Tondelli, R. Perrini, G. Orasen, C. Biselli, P. Riccardi, A. Vattari, D. Cavalluzzo, S. Urso, M. Ben Hassen, A. Fricano, P. Piffanelli, P. Cozzi, F. Biscarini, G. A. Sacchi, L. Cattivelli, G. Valè, "Genome-wide analysis of japonica rice performance under limited water and permanent flooding conditions", Frontiers in Plant Science, 8, 1862. Oct. 2017, 10.3389/fpls.2017.01862
  • N. Nazzicari, F. Biscarini, P. Cozzi, E. C. Brummer, and P. Annicchiarico, "Marker imputation efficiency for genotyping-by-sequencing data in rice (Oryza sativa) and alfalfa (Medicago sativa)," Mol. Breed., vol. 36, no. 6, pp. 1–16, 2016.
  • F. Biscarini, P. Cozzi, L. Casella, P. Riccardi, A. Vattari, G. Orasen, R. Perrini, G. Tacconi, A. Tondelli, C. Biselli, L. Cattivelli, J. Spindel, S. McCouch, P. Abbruscato, G. Valé, P. Piffanelli, and R. Greco, "Genome-Wide Association Study for Traits Related to Plant and Grain Morphology, and Root Architecture in Temperate Rice Accessions.," PLoS One, vol. 11, no. 5, p. e0155425, Jan. 2016.
  • P. Cozzi, L. Milanesi, and G. Bernardi, "Segmenting the Human Genome into Isochores," Evol. Bioinforma., vol. 11, pp. 253–261, Nov. 2015.
  • I. Merelli, P. Cozzi, E. Ronchieri, D. Cesini, and D. D’Agostino, "Porting bioinformatics applications from grid to cloud: a macromolecular surface analysis application case study", Int. J. High Perform. Comput. Vol 31 (3), pp 182-195, Jun 2015, 10.1177/1094342015588565
  • E. L. Nicolazzi, A. Caprera, N. Nazzicari, P. Cozzi, F. Strozzi, C. Lawley, A. Pirani, C. Soans, F. Brew, H. Jorjani, G. Evans, B. Simpson, G. Tosser-Klopp, R. Brauning, J. L. Williams and A. Stella, "SNPchiMp v.3: integrating and standardizing single nucleotide polymorphism data for livestock species", BMC Genomics. 2015 Apr 10;16(1):283, 10.1186/s12864-015-1497-1
  • I. Merelli, A. Calabria, P. Cozzi, F. Viti, E. Mosca and L. Milanesi, "SNPranker 2.0: a gene-centric data mining tool for diseases associated SNP prioritization in GWAS", BMC Bioinformatics 2013, 14(Suppl 1):S9
  • F. Viti, I. Merelli, A. Calabria, P. Cozzi, E. Mosca, R. Alfieri, L. Milanesi, "Ontology-based resources for bioinformatics analysis", International Journal of Metadata, Semantics and Ontologies, 2011, Volume 6 Issue 1, September 2011.
  • A. Calabria, D. Di Pasquale, M. Gnocchi, P. Cozzi, A. Orro, G. Trombetti, L. Milanesi, "Grid Based Genome Wide Studies on Atrial Flutter", Journal of Grid Computing, 2010, 1-17
  • Torri F, Akelai A, Lupoli S, Sironi M, Amann-Zalcenstein D, Fumagalli M, Dal Fiume C, Ben-Asher E, Kanyas K, Cagliani R, Cozzi P, Trombetti G, Strik Lievers L, Salvi E, Orro A, Beckmann JS, Lancet D, Kohn Y, Milanesi L, Ebstein RB, Lerer B, Macciardi F, "Fine mapping of AHI1 as a schizophrenia susceptibility gene: from association to evolutionary evidence", FASEB J. 2010 Aug;24(8):3066-3082
  • I. Merelli, P. Cozzi, D. D’Agostino, A. Clematis, L. Milanesi, "Image Based Surface Matching Algorithm Oriented to Structural Biology", in IEEE/ACM Transactions on Computational Biology and Bioinformatics, Volume PP, Issue 99, 1.
  • P. Cozzi, I. Merelli, L. Milanesi, "A Visualization ToolKit based application for representing macromolecular surfaces", in Lecture Notes in Computer Science 2009 Jun 23, Volume 5488/2009, 284-292, 10.1007/978-3-642-02504-4_26
  • P. D'Ursi, F. Chiappori, I. Merelli, P. Cozzi, E. Rovida, L. Milanesi, "Virtual screening pipeline and ligand modelling for H5N1 neuraminidase", Biochem Biophys Res Commun. 2009 Jun 12;383(4):445-449.
  • D. D’Agostino, A. Clematis, I. Merelli, P. Cozzi and L. Milanesi, "Parallel Decomposition of 3D Surfaces in Images of Local Descriptors for Molecular Screening", in Parallel, Distributed and Network-based Processing, pp.261-267, 2009.
  • P. Cozzi, I. Merelli, L. Milanesi, "A Visualization ToolKit based application for representing macromolecular surfaces", in Lecture Notes in Computer Science 2009 Jun 23, Volume 5488/2009, 284-292, 10.1007/978-3-642-02504-4_26.
  • I. Merelli, P. Cozzi, D. D’Agostino, A. Clematis and L. Milanesi, "Images Based System for Surface Matching in Macromolecular Screening", IEEE International Conference on Bioinformatics and Biomedicine, pp.397-401, 2008
  • L. Milanesi, I. Merelli, G. Trombetti, P. Cozzi, A. Orro, "Functional Genomics Applications in Grid", in: Handbook of Research on Computational Grid Technologies for Life Sciences, Biomedicine and Healtcare, Ed. Mario Catannaro. ed. IGI Global, p. 149, 168.

Conference proceedings

  • P. Cozzi, J. Fan, A. Sokolov, O. Selmoni, E. Vajana, S. Joost, E. Groeneveld, P. Flicek, P. Harrison, A. Stella & the IMAGE Consortium "The Innovative Management of Animal Genetic Resources (IMAGE) unified data portal to integrate and represent European gene bank data" in Proceedings of 70th EAAP Annual Meeting, Ghent, Belgium, 26-30 August 2019
  • J. Fan, P. Cozzi, A Sokolov, O Selmoni, E. Vajana, S. Joost, E. Groeneveld, G. Cochrane, P. Flicek, P. W. Harrison, A. Stella & the IMAGE Consortium, "A metadata ruleset solution for the Innovative Management of Animal Genetic Resources (IMAGE) unification of European Gene Bank Data" in Proceedings of International Society for Animal Genetics Conference, Lleida, Spain, 7-12 July 2019
  • F. Biscarini, B. Castiglioni, A. Stella, P. Cozzi, A. Ianni, G. Masetti, P. Cremonesi, "Upgrading the pipeline to analyse 16S rRNA-gene sequencing data" in Proceedings of 23° Congresso dell'Associazione per la Scienza e le Produzioni Animali (ASPA), Sorrento, Italy, 11-13 June 2019
  • J. Fan, P. Cozzi, E. Vajana, E. Groeneveld, O. Selmoni, A. Stella, P. Harrison, P. Flicek, "Innovative Management of Animal Genetic Resources (IMAGE): Unifying European Gene Bank data" in Proceedings of Livestock Genomics Cambridge conference, Cambridge, UK, 21-22 September 2018
  • A. Volante, A. Tondelli, F. Biscarini, F. Desiderio, R. Perrini, P. Cozzi, P. Riccardi, G. Orasen, C. Biselli, A. Vattari, D. Cavalluzzo, S. McCouch, P. Abbruscato, R. Greco, P. Piffanelli, L. Cattivelli, G. Valè, "GWA studies for rice adaptation to alternate wetting and drying water management system" in Proceedings of the Joint Congress SIBV-SIGA, Milano, Italy – 8/11 September, 2015
  • E. Ronchieri, D. Cesini, D. D'Agostino, V. Ciaschini, G. Dalla Torre, P. Cozzi, D. Salomoni, A. Clematis, L. Milanesi, I. Merelli, "The WNoDeS Cloud virtualization framework: a macromolecular surface analysis application case study" in Proceedings of 22nd Euromicro International Conference on Parallel, Distributed and network-based Processing (PDP), Turin, Italy, 12-14 February 2014
  • E. Lumini, S. Ghignone, P. Abbruscato, B. Lazzari, P. Cozzi, M. Vallino, E. Lupotto, P. Piffanelli, P. Bonfante, "Multiple molecular approaches reveal how bacterial and fungal communities thrive in the rice rhizosphere" in Proceedings of the International Workshop: "Crop Improvement in a Changing Environment: the RISINNOVA Project for sustainable rice production in Italy", Venezia , Italy -29/30 October 2012
  • P. Cozzi, L. Milanesi and G. Bernardi, "Segmenting the human genome into isochores" in Proceedings of Evolution in the time of Genomics, Venezia, Italy. 7-9 May 2012
  • P. Cozzi, L. Milanesi and G. Bernardi, "Segmenting the human genome" in Proceedings of Molecular Evolution in the Genomic Era, Roma, Italy. 29 September – 1 October 2011.
  • P. Cozzi, I. Merelli, D. D’Agostino and L. Milanesi, "A parallel implementation of Genetic Algorithms for parameters estimation of Molecular Surfaces similarity analysis", in Proceedings of BITS 2010, Bari, Italy. 14-16 April, 2010.
  • D. D’Agostino, A. Clematis, I. Merelli, P. Cozzi, L. Milanesi, "A Parallel Algorithm for Molecular Surface Matching Through Image representation", in Procedings of Parallel, Distributed and Network-Based Processing (PDP), 17-19 Feb. 2010.
  • P. Cozzi, F. Viti, I. Merelli and L. Milanesi, "Exploitation of a 3D-oriented ontology for choosing the representative proteins in protein surfaces comparison.", in Proceedings of FOCUS K3D Conference on Semantic 3D Media and Content, INRIA Sophia Antipolis %3A Méditerranée, France. 11-12 February 2010.
  • A. Calabria, D. Di Pasquale, G. Trombetti, P. Cozzi, A. Orro, M, Gnocchi, L. Milanesi, "Genome Wide Linkage analysis and Systems Knowledge: an Integrated Web Framework for Distributed Excecution and Results Annotation", in: Proceedings of Sysbiohealth 2008, Bologna, 24-25 November 2008
  • P. Cozzi, I. Merelli, L. Milanesi, A Visualization ToolKit based application for representing macromolecular surfaces., in: Proceedings of Computational Intelligence Methods For Bioinformatics And Biostatistic, Vietri sul Mare (Salerno), 3-4 October 2008.
  • I. Merelli, P. Cozzi, L. Milanesi, "A reference database for protein surface comparison using grid technology", in: Proceedings of NETTAB, Santa Margherita di Pula, 10-13 July 2006.
  • P. Cozzi, I. Merelli, L. Milanesi, Creazione di un database di supporto per analisi delle superfici proteiche tramite un approccio di calcolo ad alte prestazioni., in: Proceedings of AITIM, Torino, 11-13 December 2006.

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