Su appuntamento

Giovanni Bacci

Curriculum vitae

 Corsi di formazione post-laurea

1     Writing in the Sciences course, Stanford University, piattaforma Coursera.

Completato (con lode) il: 24/04/2020

2     Machine Learning course, Stanford University, piattaforma Coursera.

Completato il: 04/06/2014

3     Corso di Inglese "Academic Writing", Università degli Studi di Firenze, Centro linguistico di Ateneo (CLA).

Completato nel 2013

4     Corso Java Avanzato, Università degli Studi di Firenze, Sistema informatico dell’ateneo fiorentino (SIAF), 32 ore totali. Completato il: 03/12/2012

 Esperienze professionali

Accademia

     2022–2023       Rinnovo assegno di ricerca (Art.            22 legge 30 Dicembre 2010 n.         240)_,

Università degli Studi di Firenze, attività svolta presso il laboratorio del Prof. Duccio Cavalieri, Dipartimento di Biologia, Università degli Studi di Firenze, progetto: "Sviluppo e mantenimento di pipeline bioinformatiche per analisi di dati di NextGeneration Sequencing".

Dal 01/07/2022 al 30/06/2023

     2021–2022       Rinnovo assegno di ricerca (Art.            22 legge 30 Dicembre 2010 n.         240)_,

Università degli Studi di Firenze, attività svolta presso il laboratorio del Prof. Duccio Cavalieri, Dipartimento di Biologia, Università degli Studi di Firenze, progetto: "Sviluppo e mantenimento di pipeline bioinformatiche per analisi di dati di NextGeneration Sequencing".

Dal 01/07/2021 al 30/06/2022

     2020–2021       Rinnovo assegno di ricerca (Art.            22 legge 30 Dicembre 2010 n.         240)_,

Università degli Studi di Firenze, attività svolta presso il laboratorio di Genomica avanzata, Dipartimento di Biologia, Università degli Studi di Firenze, progetto: "Sviluppo e mantenimento di pipeline bioinformatiche per analisi di dati di NextGeneration Sequencing".

Dal 01/07/2020 al 30/06/2021

Responsabile: Dott. Giuseppe Lombardi

2015 Collaborazione con Biomolecular Diagnostic Srl, messa a punto di metodi per l’identificazione del microbiota gengivale e valutazione del rischio di periodontite. Responsabile: Dott. Francesco Saverio Martelli

 Riconoscimenti e premi

1 Vincitore finanziamento da: "Federation of European Microbiological Societies" (FEMS), per la partecipazione a: 8^th Congress of European Microbiologists, Glasgow, Regno Unito.

Febbraio 2019

                   2                  Vincitore finanziamento da: "International Society for Microbial Ecology"

(ISME), per la partecipazione a: 14^th Symposium on Bacterial Genetics and Ecology (BAGECO), Aberdeen, Regno Unito. Aprile 2017

                   3            Vincitore premio per il miglior poster, XLV Congresso Nazionale "Associazione

Microbiologi Clinici Italiani" (AMCLI), Rimini, Italia.

Novembre 2016

                   4          Vincitore finanziamento da: "Fondazione Italiana Fibrosi Cistica"_{,            per la}

partecipazione al convegno: 13^th ECFS Basic Science Conference, Pisa, Italia. Marzo 2016

                   5      Vincitore del premio "Franco Tatò", conferito dalla "Società Italiana Microbiologia

Generale Biotecnologie Microbiche" (SIMGBM), per la migliore tesi di dottorato in Microbiologia.

Settembre 2015

 Pubblicazioni selezionate

Legenda ^*Primo nome condiviso

^†Corresponding author

Articoli pubblicati su riviste peer-reviewed

1       Bacci, G., Fratini, S., Meriggi, N., Cheng, C. L. Y., Ng, K. H., Pindo, M., ... &

Cannicci, S. (2023). Conserved Organ-Specific Microbial Assemblages in Different Populations of a Terrestrial Crab. Frontiers in Microbiology, 14.

2       Bacci, G., Mengoni, A., Emiliani, G., Chiellini, C., Cipriani, E. G., Bianconi, G.,

Canganella, F., & Fani, R. (2021). Defining the Resilience of the Human Salivary Microbiota by a 520-Day Longitudinal Study in a Confined Environment: The Mars500 Mission. Microbiome, 9(1), 152.

3       Bacci, G., Rossi, A., Armanini, F., Cangioli, L., De Fino, I., Segata, N., ... & Bevivino, A. (2021). Lung and Gut Microbiota Changes Associated with Pseudomonas Aeruginosa Infection in Mouse Models of Cystic Fibrosis. International Journal of Molecular Sciences, 22(22), 12169.

4       Bellabarba, A., Bacci, G., Decorosi, F., Aun, E., Azzarello, E., Remm, M., ... &

Pini, F. (2021). Competitiveness for Nodule Colonization in Sinorhizobium Meliloti: Combined In Vitro -Tagged Strain Competition and Genome-Wide Association Analysis. mSystems, 6(4), e00550–21.

5       Fagorzi, C., Bacci, G.^†, Huang, R., Cangioli, L., Checcucci, A., Fini, M., ... & Mengoni, A. (2021). Nonadditive Transcriptomic Signatures of Genotype-by-Genotype Interactions during the Initiation of Plant-Rhizobium Symbiosis. mSystems, 6(1), 10–1128.

6       Bacci, G., Taccetti, G., Dolce, D., Armanini, F., Segata, N., Di Cesare, F., ... & Bevivino, A. (2020). Untargeted Metagenomic Investigation of the Airway Microbiome of Cystic Fibrosis Patients with Moderate-Severe Lung Disease. Microorganisms, 8(7), 1003.

7       Bacci, G., Amalfitano, S., Levantesi, C., Rossetti, S., Garrelly, L., Canganella, F., ...

& Perrin, E. (2019). Microbial Community Composition of Water Samples Stored inside the International Space Station. Research in Microbiology, 170(4-5), 230–234.

8       Bevivino, A., Bacci, G., Drevinek, P., Nelson, M. T., Hoffman, L., & Mengoni, A.

(2019). Deciphering the Ecology of Cystic Fibrosis Bacterial Communities: Towards Systems-Level Integration. Trends in Molecular Medicine, 25(12), 1110–1122.

9       Bacci, G.^†, Cerri, M., Lastrucci, L., Ferranti, F., Ferri, V., Foggi, B., ... & Coppi, A.

(2018). Applying Predictive Models to Decipher Rhizobacterial Modifications in Common Reed Die-Back Affected Populations. Science of The Total Environment, 642, 708–722.

10    Chiellini, C., Miceli, E., Bacci, G., Fagorzi, C., Coppini, E., Fibbi, D., ... & Fani, R.

(2018). Spatial Structuring of Bacterial Communities in Epilithic Biofilms in the Acquarossa River (Italy). FEMS Microbiology Ecology, 94(12).

11    Golanowska, M., Potrykus, M., Motyka-Pomagruk, A., Kabza, M., Bacci, G.,

Galardini, M., ... & Lojkowska, E. (2018). Comparison of Highly and Weakly Virulent Dickeya Solani Strains, With a View on the Pangenome and Panregulon of This Species. Frontiers in Microbiology, 9, 1940.

12    Perrin, E., Bacci, G.^*, Garrelly, L., Canganella, F., Bianconi, G., Fani, R., & Mengoni,

1. Research in Microbiology, 169(6), 289–295.

13     Russo, E., Bacci, G., Chiellini, C., Fagorzi, C., Niccolai, E., Taddei, A., ... & Amedei,

1. Frontiers in Microbiology, 8, 2699.

14     Abdelrhman, K. F., Bacci, G.^*, Marras, B., Nistri, A., Schintu, M., Ugolini, A., &

Mengoni, A. (2017). Exploring the Bacterial Gut Microbiota of Supralittoral Talitrid Amphipods. Research in Microbiology, 168(1), 74–84.

15     Bacci, G., Mengoni, A., Fiscarelli, E., Segata, N., Taccetti, G., Dolce, D., ... &

Bevivino, A. (2017). A Different Microbiome Gene Repertoire in the Airways of Cystic Fibrosis Patients with Severe Lung Disease. International Journal of Molecular Sciences, 18(8), 1654.

2    Bacci G. (2018). Are microbiomes predictable? The challenge of big data, lesson learned from host-associated microbiomes. Symbiomes: Frontiers in host-microbiota symbiotic interactions from humans to insects. Università di Hong Kong (HKU). Hong Kong, Repubblica Popolare Cinese

3    Bacci G. (2015). Reading Genomes: solving the puzzle of microbial complexity.

European PhD Network in “Insect Science” - 6^th Annual Meeting. Università degli Studi di Firenze. Firenze, Italia

4    Bacci, G. (2015). Mining Microbiomes: Computational Biology approaches to uncover the complexity of bacterial communities. XXXI congresso della SIMGBM. Ravenna, Italia

5    Bacci G. (2012). DNA Sequencing - Reading Genomes. Master degree in Biology class of Bioinformatics. Università degli Studi di Firenze. Firenze, Italia

6    Bacci G. (2012). Genomic and Metagenomic. Master degree course in Molecular

Biotechnology class of Genomics. Università degli Studi di Firenze. Firenze, Italia

7    Bacci G. (2012). Fundamentals of Bioinformatics. School of Bioindication and

Organizzazione di convegni nazionali ed internazionali

1    Bioinformatiha 10, Decima edizione della Giornata Toscana di Bioinformatica e

Systems Biology, Membro del comitato organizzatore. Siena, 2023

2    Bioinformatiha 9, Nona edizione della Giornata Toscana di Bioinformatica e Systems Biology, Membro del comitato organizzatore. Pisa, 2022

3    Bioinformatiha 8, Ottava edizione della Giornata Toscana di Bioinformatica e

Systems Biology, Membro del comitato organizzatore. Firenze, 2019

4    Microbiology 2019, XXXIII congresso della "Società italiana di Microbiologia generale e Biotecnologie microbiche" (SIMGBM), Membro del comitato organizzatore. Firenze, 2019

5    BioSaturdays 2018, 2019 e 2021, Serie di simposi incentrati su varie tematiche biologiche, Organizzatore insieme al Prof. Renato Fani. Firenze, 2018, 2019 e 2021

Attività editoriale

1    Guest Editor dello special issue: "From sequence to model" pubblicato sulla rivista "Frontiers in Genetics" sezione: "Computational Genomics"

2    Associate Editor della rivista "Frontiers in Genetics" sezione: "Computational Genomics"

3    Associate Editor della rivista "Frontiers in Microbiology" sezione "Microbial Symbioses"

4    Leading guest editor dello special issue: "New Advances in Environmental Microbiology" pubblicato sulla rivista "International Journal of Environmental Research and Public Health"

5    Editor del libro: "Bacterial Pangenomics" della serie "Book in the Methods in

Molecular Biology" (MiMB) pubblicato da Springer, New York

Membro di commissioni giudicatrici

Il candidato ha fatto parte, come membro attivo o supplente, di 24 commissioni di Laurea Triennale in "Scienze Biologiche" o di Laurea Magistrale in "Biologia" e "Biologia Molecolare e Applicata".

Membro di società scientifiche

Il candidato è membro della "Società Italiana Microbiologia Generale Biotecnologie Microbiche" (SIMGBM) dal 2019.

Abilitazione Scientifica Nazionale (ASN)

1    Abilitazione Scientifica Nazionale, Seconda Fascia, Settore Concorsuale 05/I2:

Valida dal 15/09/2021 al 15/09/2030

2    Abilitazione Scientifica Nazionale, Seconda Fascia, Settore Concorsuale 05/I1:

Valida dal 15/04/2021 al 15/04/2030

Giovanni Bacci

Curriculum vitae

 Statements

1     Writing in the Sciences course, Stanford University, Coursera platform.

Accomplished (cum laude): 2020-04-24

2     Machine Learning course, Stanford University, Coursera platform.

Accomplished: 2014-06-04

3     English course "Academic Writing", University of Florence, Centro linguistico di

Ateneo (CLA).

Accomplished in 2013

4     Advanced Java course, University of Florence, Sistema informatico dell’ateneo fiorentino (SIAF), 32 hours. Accomplished: 2012-12-03

 Experience

Academic experience

    2022–2023          Researcher, University of Florence_.

Unify biological and ’omics data into a single framework.

Detailed studies and activities:

{ Developing Harmony ontology for nutritional science.

{ Link metabolic information to subject data.

{ Represent microbial data together with nutritional data and subject information.

    2019–2022          Researcher, University of Florence_.

Development of Bioinformatic pipeline for NGS data analysis.

Detailed studies and activities:

{ Optimizing sequencing platforms (Illumina and PacBio).

{ Analysing sequencing data from different species.

{ Developing method for big data interpretation.

    2018–2019          Researcher, University of Florence_.

Analysis of the coevolution of microorganisms and their host. Predicting host phenotype from microbiome characteristics.

Detailed studies and activities:

{ Studying plant/microbes interactions in model systems.

{ Predicting phenotype from microbiome in animal species.

{ Developing method to simulate bacterial assemblages from shotgun metagenomic data. 2015–2018 Researcher, University of Florence_.

Developing methods for the analysis of metagenomic sequences related to peculiar environments or correlated with human diseases.

Detailed studies and activities:

{ Variability in the salivary microbiome during the mission MARS500 (NASA).

{ Gut microbiome alterations in patients affected by colorectal cancer.

{ Exploring the airway metagenome of cystic fibrosis patients through DNA massive sequencing approach.

    2012–2014           PhD Student, University of Florence_.

Developing Bioinformatic pipelines for mining microbiome data of both particular environments and associated with macro-organisms.

Acquired skills:

{ Developing scalable bioinformatic pipelines for interpreting microbiome data.

{ Quality control of biological sequences obtained through massive sequencing.

{ Modelling biological data for predicting outcome variables.

Other experience

              2017                    Collaboration with "Azienda Ospedaliero Universitaria Careggi" (AOUC,

Neurology unit), assess the response in spinal cord injured patients alternatively treated with different types and dosages of Botulinum neurotoxin type A.

Supervisor: Dr. Giuseppe Lombardi

2015 Collaboration with "Biomolecular Diagnostic Srl", periodontitis early diagnosis from gingival microbiome.

Supervisor: Dott. Francesco Saverio Martelli

 Awards

1     Congress attendance grant from: "Federation of European Microbiological

Societies" (FEMS), 8^th Congress of European Microbiologists (FEMS), Glasgow,

United Kingdom.

February 2019

2     Young scientists travel grant from: "International Society for Microbial

Ecology" (ISME), 14^th Symposium on Bacterial Genetics and Ecology (BAGECO),

Aberdeen, United Kingdom.

April 2017

3     Best poster award from: "Associazione Microbiologi Clinici Italiani" (AMCLI)_,

XLV National AMCLI Conference, Rimini, Italy.

Novembre 2016

4     Young researcher award winner from: "Italian cystic fibrosis foundation"_,

13^th ECFS Basic Science Conference, Pisa, Italy.

March 2016

5     “Franco Tatò” prize from: "Società Italiana Microbiologia Generale Biotecnologie Microbiche" (FEMS affiliated), Best PhD Thesis in Microbiology.

September 2015  Selected publications

Legend ^*First authorship shared

^†Corresponding author

Peer-reviewed papers

1       Bacci, G., Fratini, S., Meriggi, N., Cheng, C. L. Y., Ng, K. H., Pindo, M., ... &

Cannicci, S. (2023). Conserved Organ-Specific Microbial Assemblages in Different Populations of a Terrestrial Crab. Frontiers in Microbiology, 14.

2       Bacci, G., Mengoni, A., Emiliani, G., Chiellini, C., Cipriani, E. G., Bianconi, G.,

Canganella, F., & Fani, R. (2021). Defining the Resilience of the Human Salivary Microbiota by a 520-Day Longitudinal Study in a Confined Environment: The Mars500 Mission. Microbiome, 9(1), 152.

3       Bacci, G., Rossi, A., Armanini, F., Cangioli, L., De Fino, I., Segata, N., ... & Bevivino, A. (2021). Lung and Gut Microbiota Changes Associated with Pseudomonas Aeruginosa Infection in Mouse Models of Cystic Fibrosis. International Journal of Molecular Sciences, 22(22), 12169.

4       Bellabarba, A., Bacci, G., Decorosi, F., Aun, E., Azzarello, E., Remm, M., ... &

Pini, F. (2021). Competitiveness for Nodule Colonization in Sinorhizobium Meliloti: Combined In Vitro -Tagged Strain Competition and Genome-Wide Association Analysis. mSystems, 6(4), e00550–21.

5       Fagorzi, C., Bacci, G.^†, Huang, R., Cangioli, L., Checcucci, A., Fini, M., ... & Mengoni, A. (2021). Nonadditive Transcriptomic Signatures of Genotype-by-Genotype Interactions during the Initiation of Plant-Rhizobium Symbiosis. mSystems, 6(1), 10–1128.

6       Bacci, G., Taccetti, G., Dolce, D., Armanini, F., Segata, N., Di Cesare, F., ... & Bevivino, A. (2020). Untargeted Metagenomic Investigation of the Airway Microbiome of Cystic Fibrosis Patients with Moderate-Severe Lung Disease. Microorganisms, 8(7), 1003.

7       Bacci, G., Amalfitano, S., Levantesi, C., Rossetti, S., Garrelly, L., Canganella, F., ...

& Perrin, E. (2019). Microbial Community Composition of Water Samples Stored inside the International Space Station. Research in Microbiology, 170(4-5), 230–234.

8       Bevivino, A., Bacci, G., Drevinek, P., Nelson, M. T., Hoffman, L., & Mengoni, A.

(2019). Deciphering the Ecology of Cystic Fibrosis Bacterial Communities: Towards Systems-Level Integration. Trends in Molecular Medicine, 25(12), 1110–1122.

9       Bacci, G.^†, Cerri, M., Lastrucci, L., Ferranti, F., Ferri, V., Foggi, B., ... & Coppi, A.

(2018). Applying Predictive Models to Decipher Rhizobacterial Modifications in Common Reed Die-Back Affected Populations. Science of The Total Environment, 642, 708–722.

10    Chiellini, C., Miceli, E., Bacci, G., Fagorzi, C., Coppini, E., Fibbi, D., ... & Fani, R.

(2018). Spatial Structuring of Bacterial Communities in Epilithic Biofilms in the Acquarossa River (Italy). FEMS Microbiology Ecology, 94(12).

11    Golanowska, M., Potrykus, M., Motyka-Pomagruk, A., Kabza, M., Bacci, G.,

Galardini, M., ... & Lojkowska, E. (2018). Comparison of Highly and Weakly Virulent Dickeya Solani Strains, With a View on the Pangenome and Panregulon of This Species. Frontiers in Microbiology, 9, 1940.

12    Perrin, E., Bacci, G.^*, Garrelly, L., Canganella, F., Bianconi, G., Fani, R., & Mengoni,

1. Research in Microbiology, 169(6), 289–295.

13     Russo, E., Bacci, G., Chiellini, C., Fagorzi, C., Niccolai, E., Taddei, A., ... & Amedei,

1. Frontiers in Microbiology, 8, 2699.

14     Abdelrhman, K. F., Bacci, G.^*, Marras, B., Nistri, A., Schintu, M., Ugolini, A., &

Mengoni, A. (2017). Exploring the Bacterial Gut Microbiota of Supralittoral Talitrid Amphipods. Research in Microbiology, 168(1), 74–84.

15     Bacci, G., Mengoni, A., Fiscarelli, E., Segata, N., Taccetti, G., Dolce, D., ... &

Bevivino, A. (2017). A Different Microbiome Gene Repertoire in the Airways of Cystic Fibrosis Patients with Severe Lung Disease. International Journal of Molecular Sciences, 18(8), 1654.

16     Bosi, E., Bacci, G.^*, Mengoni, A., & Fondi, M. (2017). Perspectives and Challenges in Microbial Communities Metabolic Modeling. Frontiers in Genetics, 8, 88.

17     Bacci, G., Paganin, P., Lopez, L., Vanni, C., Dalmastri, C., Cantale, C., ... &

Mengoni, A. (2016). Pyrosequencing Unveils Cystic Fibrosis Lung Microbiome Differences Associated with a Severe Lung Function Decline. PLOS ONE, 11(6), e0156807.

18     Galardini, M., Brilli, M., Spini, G., Rossi, M., Roncaglia, B., Bani, A., ... Bacci, G.,

... & Mengoni, A. (2015). Evolution of Intra-specific Regulatory Networks in a Multipartite Bacterial Genome. PLOS Computational Biology, 11(9), e1004478.

19     Bacci, G., Bazzicalupo, M., Benedetti, A., & Mengoni, A. (2014). StreamingTrim

1. Molecular Ecology Resources, 14(2), 426–434.

20     Canfora, L., Bacci, G., Pinzari, F., Lo Papa, G., Dazzi, C., & Benedetti, A. (2014).

Salinity and Bacterial Diversity: To What Extent Does the Concentration of Salt Affect the Bacterial Community in a Saline Soil? PLOS ONE, 9(9), e106662.

 Technical skills

Programming languages

Basic Matlab_, MySQL

Intermediate html, JavaScript, GNU Octave

Advanced Java, R, LAT_EX, Beamer, Bash

Bioinformatics skills

             Basic    Protein-structure modelling algorithms

Intermediate      Biological databases mining, Motif recognition algorithms

      Advanced           Sequence alignment (DNA, RNA, and proteins), Database searching algorithms,

Clustering algorithms, Sequence comparison, Statistics applied to biological data

(linear models, IA and machine lerning algorithm)

 Academic activity

Invited conferences (oral presentations)

1     Bacci, G., Panov, P., Cavalieri, D. (2022). Annotation of samples with controlled metadata: The role of ontologies in the FNS-cloud project. FNS-Cloud M33 Consortium Meeting. Sassari, Italy

2     Bacci G. (2018). Are microbiomes predictable? The challenge of big data, lesson learned from host-associated microbiomes. Symbiomes: Frontiers in host-microbiota symbiotic interactions from humans to insects. Hong Kong University (HKU). Hong Kong, People’s Republic of China (PRC)

3     Bacci G. (2015). Reading Genomes: solving the puzzle of microbial complexity.

European PhD Network in “Insect Science” - 6^th Annual Meeting. University of Florence. Florence, Italy

4     Bacci, G. (2015). Mining Microbiomes: Computational Biology approaches to uncover the complexity of bacterial communities. XXXI congresso della SIMGBM. Ravenna, Italy

5     Bacci G. (2012). DNA Sequencing - Reading Genomes. Master degree in Biology class of Bioinformatics. University of Florence. Florence, Italy

6     Bacci G. (2012). Genomic and Metagenomic. Master degree course in Molecular Biotechnology class of Genomics. University of Florence. Florence, Italy

7     Bacci G. (2012). Fundamentals of Bioinformatics. School of Bioindication and Biodiversity. Council for Agricultural Research and Economics (CREA). Rome, Italy

Conference organization

1     Bioinformatiha 10, Tenth edition of Bioinformatics and Systems Biology day,

Organizing committee.

Siena, 2023

2     Bioinformatiha 9, Ninth edition of Bioinformatics and Systems Biology day, Organizing committee.

Pisa, 2022

3     Bioinformatiha 8, Eigth edition of Bioinformatics and Systems Biology day, Organizing committee.

Firenze, 2019

4     Microbiology 2019, XXXIII congress of "Società italiana di Microbiologia generale e Biotecnologie microbiche" (SIMGBM, FEMS-affiliated), Organizing committee. Firenze, 2019

5     BioSaturdays 2018, 2019 e 2021, Serie di simposi incentrati su varie tematiche biologiche, Organizing committee. Firenze, 2018, 2019 e 2021

Editor

1     Guest Editor "From sequence to model" special issue published on Frontiers in

Genetics (Computational Genomics section)

2     Associate Editor Frontiers in Genetics (Computational Genomics section)

3     Associate Editor Frontiers in Microbiology (Microbial Symbioses section)

4     Leading guest editor "New Advances in Environmental Microbiology" special issue published in International Journal of Environmental Research and Public Health (IJERPH)

5     Editor "Bacterial Pangenomics", Methods in Molecular Biology book serie (MiMB) published by Springer, New York