Curriculum

CURRICULUM - EXTENDED

ENGLISH 

Email adresses       stefano.campanaro@unipd.it, stefano.campanaro@gmail.com

Personal Website   https://sites.google.com/site/stefanocampanaro/

Website of the research unit https://metabioinfomicslab.it/

Research Gate - Scientific Research social media                           https://www.researchgate.net/profile/Stefano_Campanaro

Google scholar profile         https://scholar.google.it/citations?user=SSXEe7AAAAAJ&hl=it

Education

I started my research activity in the molecular biology field during my master thesis by performing experiments to determine the function of yeast genes. 

I graduated in biology (Molecular Biology curriculum) at University of Padova in 1998 (14th July 1998) with a dissertation focused on the discrimination of Saccharomyces cerevisiae yeast strains using microsatellites length polymorphisms.

In 2002 (6th of February 2002) I obtained the PhD in Biotechnology at the University of Padova.

Positions held and scientific focus areas

My current position is Associate Professor (BIO/11) at the Department of Biology of the University of Padova (from March 2019).

From 2002 to 2005 I received various research contracts including a post-doctoral fellowship (a detailed description of the positions from 1998 to 2000 is reported below). I focused my work on gene expression analysis and genomic data integration in collaboration with various research groups (i.e. with Prof. Mathias Mann - Max Planck Institute of Biochemistry). During that period I was a pioneer in Italy in the implementation of transcriptomic analysis using microarrays. The work was mainly focused on the development of microarrays platforms for the analysis of normal and pathological samples in human and mouse.

In 2004 I shifted my research activity to microbial genomics and transcriptomics which is the field I am still working on. I was part of the team that sequenced the first microbial genome in Italy (published in Science, 2005). In 2008 I was invited as a visiting fellow at the University of New South Wales (Sydney). I collaborated with Prof. Ricardo Cavicchioli of the UNSW (Sydney, Australia) to study cold temperature adaptation in methanogenic Archaea at the gene expression level. A side project was also established to investigate the functional role of RNA polymerase subunits E/F in Methanococcoides burtonii.

In 2009 I coordinated a research project supported by the University of Padova and focused on the investigation of genomic variability among S. cerevisiae strains and their impact on gene expression profile.

In 2013 I started a project in collaboration with Prof. Irini Angelidaki of the Technical University of Denmark, Department of Environmental Engineering (DTU-Env) focused on the metagenomic analysis of the Anaerobic Digestion (AD) process in biogas reactors. In the last years I contributed to the development of new software for the improvement of the microbial community analysis, moving from 16S sequencing to high throughput metagenomics sequencing and to the “genome-centric metagenomics”. During this collaboration I visited the “Bioenergy group” at DTU-Env in 2014, 2015, 2016 and 2018 in order to coordinate research activities and to perform some target experiments. Considering my expertise in bioinformatics and microbial genomics, my role was focused on data analysis and interpretation: shotgun reads assembly, gene finding annotation, development of tools for management and integration of metagenomics data. More recently, investigation was expanded including innovative approaches like metabolic flux balance analysis, investigation of the virome structure and analysis of the microbiome structure at the strain level.  We envision that the application of innovative bioinformatics analyses to the “biogas microbial community” will generate an unprecedented improvement in the knowledge of the biological processes of the anaerobic digestion microbial community in response to the modification of the environmental conditions. The genome reconstruction of more than 4500 microbial species previously unknown and the investigation of their functional role was published in “Environmental Microbiome” in 2024. It is expected that these studies will have a positive effect on biogas production as renewable energy.

In 2017 I received the “abilitazione scientifica nazionale, SECONDA FASCIA” in Molecular Biology (BIO/11) and in Agricultural Microbiology (07/I1).

In 2021 I received the “abilitazione scientifica nazionale, PRIMA FASCIA” in Agricultural Microbiology (07/I1).

From January 2006 to February 2019, I worked as a Researcher at the Department of Biology (University of Padova).

From February 2019 to July 2022 Director of the Center for Innovative Biotechnologies (University of Padova).

https://www.cribi.unipd.it/en/

From June 2023 to "present", member of the scientific committee of the Interuniversity Consortium for Biotechnologies (CIB).

From July 2023 to "present", representative member for the University of Padova of the European Network of Bio-based Industries Consortium - BIC.

From August 2022 to "present", coordinator of the Genomics and Bioinformatics research group of the Biology department (University of Padova).

From August 2022 to "present": coordinator of the Next-Gen Sequencing service of the Biology Department (University of Padova).

Management experience and International collaborations

From 1999 to 2002 I took part to two international projects focused on S. cerevisiae gene disruption and phenotypic analysis. The more relevant research was focused on gene disruption analysis of all the 6000 genes of S. cerevisiae and its application to the generation of a collection of deleted strains tagged with molecular barcodes (published in Nature, 2002).

From 2004 to 2007 I participated to the genome analysis and the expression profiling of P. profundum, a project focused on the comprehension of the mechanisms involved in deep-sea adaptation. The study was developed in collaboration with Prof. Douglas Bartlett (Scripps Institution of Oceanography, San Diego, California).

In 2009 I shifted the focus of my research activity back to S. cerevisiae. I obtained a grant from University of Padova and I have coordinated the research project “Genomic characterization, transcriptomics and analysis of the metabolites in S. cerevisiae strains of great enological relevance” founded by University of Padova.

From 2014 I working on the metagenomics and systems biology of the anaerobic digestion microbiome in collaboration with many laboratories from EU, USA and China.

I am also actively collaborating with Prof. N. Kyrpides at the Joint Genome Institute (Department of Energy, Walnut Creek USA), with Prof. G. Luo at the Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3) (Fudan University (Shanghai, China), with Irini Angelidaki of the Technical University of Denmark (Copenhagen, Denmark) and with Panagiotis G Kougias (Hellenic Agricultural Organization - DIMITRA, Thessaloniki, Greece). The target is the creation of an international network of laboratories with complementary expertise to facilitate the investigation of the AD system.

From February 2019 to July 2022 I directed the Center for Innovative Biotechnologies, a network of laboratories belonging to the University of Padova that focus their research activity on genomics, proteomics, bioinformatics and biotechnologies.

People hosted in the research group

According to the strong international cooperation of our research group with other universities, I hosted many PhD and postdocs during the years from different countries, including Greece, Spain, China, Denmark, Argentina, Brazil, Hungary, Morocco, Turkey .

18th September 2016 - 18th December 2016. Josep Ruiz Sánchez, PhD student, supervisor Prof. Francesc X. Prenafeta-Boldú, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Barcelona (Spain).

01st June 2017 - 31st July 2017. Alessandra Fontana, PhD student, supervisor Prof. Lorenzo Morelli, Department for Sustainable Food Process – DiSTAS, Catholic University of the Sacred Heart, 29122 Piacenza (Italy).

01st Sept 2017 - 23rd Dic2017. Ruth Iglesias Iglesias, PhD student, supervisor  Prof. Maria Carmen Veiga, Department of Environmental Bioengineering, University of A Coruña (Spain). External period was supported by a scholarship granted by INDITEX for a pre-doctoral stay abroad.

01st April 2019 - 30st June 2019. Adam Kovalovzski,  PhD student, supervisor Prof. Irini Angelidaki, Bioenergy Group at DTU Environment, Denmark technical University, Copenhagen (Denmark). Financial support came from the Otto Mønsted Foundation. 

30th June 2019 - 2nd August 2019. Miao Yan, PhD student, supervisor Prof. Irini Angelidaki, Bioenergy Group at DTU Environment, Denmark technical University, Copenhagen (Denmark). 30th June to 2nd of August. Financial support came from the Otto Mønsted Foundation. 

08th July 2019 - 06th Sept 2019 - Furkan_Emre_Çiçek, Master student, supervisor Prof. Fatma Nese Kok, Department of Molecular Biology and Genetics, Istambul Technical University.  Erasmus+ placement student within the framework of Erasmus+.

01st July 2019 - 30th September 2019. Zhi-Jian_Shi, PhD student, supervisor Prof. Gang Luo, Department of Environmental Science & Engineering at Fudan University (China).

1st Oct 2019 - 30th Mar 2020 - Ayse Nur Tanis, Master student, supervisor Assoc. Prof. Dr. Muhammet KÖSE, Faculty of Agriculture/Animal Science, Graduate Scholl of Natural and Applied Science at Kahramanmaraş Sütçü İmam University (Turkey). Erasmus+ placement student within the framework of Erasmus+.

1st Oct 2019 - 30th Mar 2020 - TuğçeTurgut, PhD student, supervisor Prof. Emin Ozkose, Faculty of Agriculture/Animal Science, Institute of Science and Technology at Kahramanmaraş Sütçü İmam University. Erasmus+ placement student within the framework of Erasmus+.

1st November 2019 - 31st May 2020. Chao Liu, PhD student, supervisor Prof. Guang-qing Liu, Beijing University of Chemical Technology. Title "Novel ecological insights and functional roles during anaerobic digestion for efficient medium chain carboxylate production by chain elongation with syngas as electron donor by genome-centric metagenomics".

3rd February 2020 - 12th December 2020. Victor Borin Centurion Biruel, PhD student, supervisor Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), Campinas University – UNICAMPDr. Valéria Maia de Oliveira. Project “Genome recovery from metagenomics data and functional analysis of soil microbiome from Whalers Bay – Antarctic samples”. External period was supported by Research Internship Abroad (BEPE-DD), FAPESP Process number: 2017/03172-8.

01st October 2020 - 22nd December 2020. Maria Gaspari, PhD student, supervisor Prof. Thomas Kotsopoulos, Faculty of Agriculture, Aristotele University, Thessaloniki (Greece). External period supported by Erasmus+ Higer Education Learning Agreement, title "Bioinformatic analysis for sequence data".

1st May 2021 - 31th July 2021. Esteban Orellana, PhD student, supervisor Prof. Leonardo Erijman, University of Buenos Aires, Buenos Aires (Argentina).

1st Sept 2021 - 23rd Dec 2021. Silvia Greses Huerta, Postdoctoral researcher, IMDEA Energy institute, Biotechnological processes unit, Móstoles (MADRID, Spain).

1st Jan 2022 - 23rd Dec 2022. Rebecca Serna, Postdoctoral researcher, Calagua research center, Chemical Engineering Department, Universitat de València (Valencia, Spain).

1st Oct 2022 - 23rd Dec 2022. Nuria Otero Logilde , PhD student, Prof. Maria Carmen Veiga, Department of Environmental Bioengineering, University of A Coruña (Spain). External period was supported by a scholarship granted by INDITEX for a pre-doctoral stay abroad.

1st Oct 2022 - 30th Apr 2023. Marina Mauro Gomes , PhD student, supervisor Prof.ssa Maria Bernadete Amancio Varesche. Faculty of Engenharia Hidráulica e Saneamento University of Sao Paolo, (São Carlos, Brasil). 

27th Aug 2022 - 27th Sep 2022; 24th Jul 2023 - 28th Jul 2023. Balasz Kakuk,  Postdoctoral researcher, supervisor Zsolt Boldogkői, Department of Medical Biology University of Szeged (Szeged, Hungary) Erasmus plus mobility program. 

Selected grant requests

During my research activity I was involved in conceiving, drafting and developing numerous research projects, both as participant and as coordinator. Some of the more relevant are listed below.

- April 2004-March 2007. Participation to the National research project (FIRB) “Post-genomics of the extremophilic bacterium Photobacterium profundum”. The project was focused on gene finding, annotation, functional analysis, gene expression of the piezophilic bacterium Photobacterium profundum, a model organism to study the adaptation of the microbial species to the deep-sea environment. My role in the project was mainly focused on the transcriptomic analysis in different temperature and pressure conditions.

- March 2009-February 2011. Coordinator of the research grant “Genomic characterization, transcriptomics and analysis of the metabolites in Saccharomyces cerevisiae strains of oenological interest” founded by the University of Padova (Italy). The aim of the project was the identification of the genomic characters influencing gene expression and having a relevant impact on phenotypic characters such as alcoholic fermentation efficiency, stress resistance in autochthonous yeast strains.

- January 2010-December 2012. Participation to the research project “Selection of new grape rootstocks resistant to abiotic stresses through the development and validation of physiological and molecular markers – SERRES”. Aim of the project was the study of the responses of newly established rootstocks to abiotic stresses. 

- March 2011-February 2014. Participation to the research project “Understanding protein-nucleic-acid interaction networks in cold-adapted archaea” presented as “Discovery-Project” to the Australian Research Council by Prof. Ricardo Cavicchioli (UNSW, Sydney, Australia).

- April 2011-March 2013. Participation to the research project granted by the University of Padova (Italy) “Ankrd2 signaling and gene expression during muscle differentiation” coordinated by Prof. Giorgio Valle (Department of Biology, University of Padova).

- March 2013 February 2014. Coordinator of the project “Development of new enological starters obtained from autochthonous yeast strains to improve the peculiar characters of the Venetian wines” granted by the Venetian region (Italy) in the framework of the European Social Found.

- March 2014-2017. Participation to the strategic research project of the University of Padova “Bioinformatics for Personal Genomics – BIOINFOGEN” (code: Year 2011 - prot. STPD11F33L_001) coordinated by Prof. Giorgio Valle (Department of Biology, University of Padova). Aim of the project was the development of new bioinformatics and molecular biology technologies applied to the field of "personal genomics".

- Aug 2018-July 2019. Participation to the project “New strategies for the identification of enological yeasts using genomic and metabolic profiling” (code: 2015-17-11-2018) granted by the Venetian region (Italy) in the framework of the European Social Found.

- January 2019-present. Participation to the research project “Unravelling the Ariadne’s thread into the microbiome of Anaerobic Digestion labyrinth” granted by the “Hellenic Foundation for Research and Innovation” and coordinated by Prof. Panagiotis G. Kougias of the Technical University of Denmark. My role in this project is to perform metagenomic and metatranscriptomic analyses and to support the “data mining” process.

- 2nd Mar 2020- 28th Jan 2021. Participation to the research project  "Genome recovery from metagenomics data and functional analysis of soil microbiome from Whalers Bay - Antarctic samples". Principal Investigator Valeria Maia Merzel. Fundação de Amparo à Pesquisa do Estado de São Paulo; Funding Line: Regular Programs / Fellowships / Abroad / RIA - Research Internship Abroad / RIA - Doctorate (applicant without MSc degree) - Continuous Funding Stream.

-October 2020-September 2021. Participation to the research project  "Biofermentors: new applications" within the framework of the competitive project supported by Italian MIUR “Development of the innovation in biotechnologies” MIUR ex D.M.738 dd 08/08/19-October 2020 (total funding 50,000 euros). My role in the project was the investigation of the putative interactions between microbial species involved in biogas upgrading process using bioinformatics strategies and metabolic modelling approaches.

-September 2020-December 2022. Participation to the research project as coordinator of the WP5 ("Development, validation and execution of microbiological tests aimed at evaluating the maintenance of functional properties of food ingredients" - "Sviluppo, validazione ed esecuzione di test microbiologici finalizzati alla valutazione del mantenimento delle proprietà funzionali degli ingredienti alimentari")  "The agriculture of the future and functional foods: a challenge for the research and revitalization of the Venetian region - "F.A. & A.F." (L'agricoltura del futuro e gli alimenti funzionali: una sfida per la ricerca e il rilancio del territorio veneto - "F.A.&A.F.") within the framework of the competitive project supported by POR FESR 2014-2020 (total funding 2.99 Meuros). My role in the project was to develop projects with the companies in order to investigate the connections existing between feed composition and gut microbiome in livestock.

- October 2021-September 2025. Participation to the research project "Harnessing potential of biological CO2 capture for Circular Economy" CooCE. ACT - Accelerating CCS Technologies. Budget funding from ACT 2,374,922 €.

- October 2021-September 2025. Participation to the research project "Demonstration of a mobile unit for hybrid energy storage based on CO2 capture and renewable energy sources" - LIFE CO2toCH4. In the framework of LIFE20 CCM/GR/001642 (LIFE Climate Change Mitigation). Total costs of the actions including overheads  3,888,985 €; Beneficiary's own contribution 1,750,044 €; Amount of EU contribution requested 2,138,941 €.

- March 2021-Feb 2024 -  Participation to the research project "Future-proof bioactive peptides from food by-products: an eco-sustainable bioprocessing for tailored multifunctional foods (PROACTIVE)". PRIN: PROGETTI DI RICERCA DI RILEVANTE INTERESSE NAZIONALE – Bando 2020. Total costs of the actions including overheads  725,382 €; Beneficiary's own contribution 99,091 €; Amount of MUR contribution requested 626,291 €.

- Aug 2022-July 2024 - Coordination of the research project "BioCO2-TRAPPING: development and optimization of a biological process for the trapping of carbon dioxide and its conversion into bioplastics in a circular economy context" (Italian: BioCO2-TRAPPING: sviluppo e ottimizzazione di un processo  biologico per l’intrappolamento dell’anidride carbonica e la sua conversione in bioplastiche in un contesto di economia circolare)  Fondazione CARIVERONA - Call Research and development 2022. Total costs of the actions including overheads  120,000 €; Beneficiary's own contribution 24,000 €; Amount of Fondazione CARIVERONA contribution requested 96,000 €.

- December 2022-November 2026 - Participation to the research project “Capture and Reuse Of biogenic gases for Negative-emission - sustainable biofUelS (CRONUS)”. HORIZON-CL5-2021-D3-03. Amount of EU contribution 4,999,570 €.

- November 2023-October 2025 - Coordination of the research project "MICRO-BIOfuels: Development and characterization of a microbial inoculum for use in the valorization of difficult-to-degrade byproducts through the production of biohydrogen and biogas" (Italian: MICRO-BIOfuels: Sviluppo e caratterizzazione di un inoculo microbico da impiegare nella valorizzazione di sottoprodotti difficilmente degradabili tramite produzione di bioidrogeno e biogas) University of Padova - Call: Uni-Impresa 2022. Total costs of the actions  80,000 €.

- November 2023-October 2024 - Participation to the research project "Development of an organic food additive rich in polyphosphates: towards an eco-sustainable alternative to synthetic production processes” (Italian: Sviluppo di un additivo alimentare di origine biologica ricco in polifosfati: verso un’alternativa ecosostenibile ai processi di produzione sintetica)  granted by the Venetian region (Italy) in the framework of the European Social Found (FSE) 2023 ID PROGETTO: 10619978 CODICE PROGETTO 2105-0048-553-2023. Total cost of the action 82020 €.

Cooperation with private companies

I am very active in promoting University-Industry cooperation. This connection is critical for skills development, for innovation and technology transfer, and the promotion of entrepreneurship (start-ups and spin-offs).

I am a founding member of the BMR Genomics spinoff of the University of Padova.

(http://www.bmr-genomics.it/bmr_it/storia_2010.html). The spinoff raised from the pre-existing DNA sequencing service developed at the Genomics and Bioinformatics research group of CRIBI (University of Padova).

In the context of the projects funded by the Venetian region with the European Social Found in 2013 and 2018, I had the opportunity to establish collaborations with important Biotechnological and Agricultural companies such as “Italiana Biotecnologie”, “Ever” and “Pololab”. Projects supported by the European Social Found are very important not only to favor the cooperation between University and Private Companies, but also to support the integration of trained staff into private companies.

The scientific cooperation with many companies like "Agripharma", "BMR Genomics", "Cereal Docks", "Cortal Extrasoy", "Experteam", "Labomar", "Molino Favero", "LandLab", "Sicit Group" was strengthened with the project  "The agriculture of the future and functional foods: a challenge for the research and revitalization of the Venetian region - "F.A. & A.F." within the framework of the competitive project supported by POR FESR 2014-2020.

I have been scientific supervisor of funding agreements with Italian companies including Italiana Biotecnologie S.r.l. and BMR genomics S.r.l. for genomics and metagenomics studies (details below).

- July 2018 - September 2018.  Supervisor of the scientific agreement (Italian: convenzione scientifica). Title: "Genomic sequencing and bioinformatics analysis of 12 Saccharomyces cerevisiae strains". Italian: Sequenziamento genomico e analisi bioinformatica di 12 ceppi di Saccharomyces cerevisiae).  Company: Italiana Biotecnologie (head office: via San Cassiano 99, Trecate (NO), Italy). Total funding 18,300,000 euros.

- March 2020 - February 2021.  Supervisor of the scientific agreement (Italian: convenzione scientifica). Title: "Sequencing and custom bioinformatics analysis of Saccharomyces cerevisiae". Italian: Sequenziamento ed analisi bioinformatiche custom di ceppi di Saccharomyces cerevisiae).  Company: Italiana Biotecnologie (head office: via San Cassiano 99, Trecate (NO), Italy). Total funding 25,000,000 euros.

- April 2021-December 2021. Supervisor of the scientific agreement (Italian: convenzione scientifica). Title: "Custom bioinformatics analysis on the yeast strains collection of the company". (Italian: Analisi bioinformatiche custom sulla collezione di ceppi aziendali di Saccharomyces cerevisiae). Company: Italiana Biotecnologie (head office: via San Cassiano 99, Trecate (NO), Italy). Total funding 12,200,000 euros.

- August 2021-February 2022. Supervisor of the scientific agreement (Italian: convenzione scientifica). Title: "Next Generation Sequencing analysis of data obtained with different bioinformatics pipelines and investigation of the microbial populations involved in anaerobic digestion". (Italian: Analisi di dati di Next Generation Sequencing ottenuti con diverse pipeline bioinformatiche e studio delle popolazioni microbiche coinvolte nella digestione anaerobica). Company: BMR genomics (head office: via Redipuglia 22/a 35131, Padova (PD), Italy). Total funding 12,291 euros.

- April 2023 - August 2023. Supervisor of the scientific agreement (Italian: convenzione scientifica). Title: "Research contract 22-R047 Microbial consortium MarcoPolo".  (Italian: Contratto di ricerca 22-R047 MarcoPolo consorzio microbico). Company MarcoPolo Engineering (Via XI Settembre 37 - 12011, Borgo San Dalmazzo - Cuneo, Italy). Total funding 14274 €

- September 2022-August 2023. Supervisor of the scientific agreement (Italian: convenzione scientifica). Title: "Investigation of the dynamics of microbial populations involved in the anaerobic digestion of the municipal solid waste organic fraction". (Italian: studio della dinamica di popolazioni microbiche coinvolte nella digestione anaerobica della frazione organica dei rifiuti solidi urbani (FORSU)). Company: S.E.S.A. S.p.A. Società Estense Servizi Ambientali (head office: via Comuna 5/b - 35042, Este - (PD), Italy). Total funding 16,000 euros.

- May 2024-October 2024. Supervisor of the scientific agreement (Italian: prestazione per attività di ricerca). Title: "Analysis of homozygous and heterozygous single nucleotide variants distribution in the Saccharomyces cerevisiae genome ." (Italian: Verifica della distribuzione di varianti a singolo nucleotide (omozigoti ed eterozigoti) nel genoma di Saccharomyces cerevisiae). Company: Italiana Biotecnologie (head office: via San Cassiano 99, Trecate (NO), Italy). Total funding 3,600 euros.

Scientific supervisor for temporary research fellows

I served as scientific supervisor for many temporary Research Fellows selected through competitive evaluations and supported by grants mentioned in the previous sections.

March 2013-February 2014. Temporary Research Fellow (Italian: assegnista di ricerca); position assigned to Dr. Chiara Nadai; in the context of the project “Development of new enological starters obtained from autochthonous yeast strains to improve the peculiar characters of the Venetian wines” granted by the Venetian region (Italy) in the framework of the European Social Found.

August 2018-July 2019. Temporary Research Fellow (Italian: assegnista di ricerca) - position assigned to Dr. Fabio De Pascale; in the context of the project “New strategies for the identification of enological yeasts using genomic and metabolic profiling” granted by the Venetian region (Italy) in the framework of the European Social Found.

January 2021 - December 2021. Temporary Research Fellow (Italian: assegnista di ricerca) - position assigned to Dr. Matteo Palù; in the context of the project “Biofermentors: new applications” granted by the competitive project supported by Italian MIUR “Development of the innovation in biotechnologies” MIUR ex D.M.738 dd 08/08/19.

10th October 2020 - 31st December 2020. Temporary Research Fellow (Italian: borsa di studio per attività di ricerca) - position assigned to Dr. Matteo Palù; In the context of the scientific agreement "Sequencing and custom bioinformatics analysis of Saccharomyces cerevisiae". (Italian: Analisi bioinformatiche custom sulla collezione di ceppi aziendali di Saccharomyces cerevisiae). Economic support provided by the company Italiana Biotecnologie (head office: via San Cassiano 99, Trecate (NO), Italy).

Fabio De Pascale - borsista ItaBio?

15th October 2019 - 15 July 2020.  Temporary Research Fellow (Italian: borsa di studio per attività di ricerca) - position assigned to Dr. Federico Bianca; Title: Studio di popolazioni di lieviti enologici ed analisi metagenomica di comunità microbiche ambientali. In the context of the scientific agreement TREU_COMM19_01 Convenzione commerciale con Italiana Biotecnologie srl. Economic support provided by the company Italiana Biotecnologie (head office: via San Cassiano 99, Trecate (NO), Italy).

16th July 2020 - 30 September 2020.  Temporary Research Fellow (Italian: borsa di studio per attività di ricerca) - position assigned to Dr. Federico Bianca; In the context of the scientific agreement "Sequencing and custom bioinformatics analysis of Saccharomyces cerevisiae". Italian: Sequenziamento ed analisi bioinformatiche custom di ceppi di Saccharomyces cerevisiae). Economic support provided by the company Italiana Biotecnologie (head office: via San Cassiano 99, Trecate (NO), Italy).

Nov 2020 - March 2021.  Temporary Research Fellow (Italian: borsa di studio per attività di ricerca) - position assigned to Dr. Nicola De bernardini; Title: Analisi bioinformatiche di varianti in ceppi di lievito associati a fenotipi di interesse enologico (Bando sezione n.50 del 2020). In the context of the scientific agreement "Sequencing and custom bioinformatics analysis of Saccharomyces cerevisiae". (Italian: Sequenziamento ed analisi bioinformatiche custom di ceppi di Saccharomyces cerevisiae). Economic support provided by the company Italiana Biotecnologie (head office: via San Cassiano 99, Trecate (NO), Italy).

Apr 2021 - September 2021.  Temporary Research Fellow (Italian: borsa di studio per attività di ricerca) - position assigned to Dr. Nicola De bernardini; Title:  Analisi bioinformatiche di varianti in ceppi di Saccharomyces cerevisiae della collezione Italiana Biotecnologie s.r.l. (Bando sezione n.20 del 2021). In the context of the scientific agreement "Custom bioinformatics analysis on the yeast strains collection of the company". (Italian: Analisi bioinformatiche custom sulla collezione di ceppi aziendali di Saccharomyces cerevisiae).

16th November 2020 - 16th April 2020. Temporary Research Fellow (Italian: borsa di studio per attività di ricerca) - position assigned to Dr. Maria Silvia Morlino; In the context of the scientific agreement "Sequencing and custom bioinformatics analysis of Saccharomyces cerevisiae". (Italian: Sequenziamento ed analisi bioinformatiche custom di ceppi di Saccharomyces cerevisiae). Economic support provided by the company Italiana Biotecnologie (head office: via San Cassiano 99, Trecate (NO), Italy).

17th April 2020 - 16th May 2020. Temporary Research Fellow (Italian: borsa di studio per attività di ricerca) - position assigned to Dr. Maria Silvia Morlino; In the context of the scientific agreement "Sequencing and custom bioinformatics analysis of Saccharomyces cerevisiae". (Italian: Sequenziamento ed analisi bioinformatiche custom di ceppi di Saccharomyces cerevisiae). Economic support provided by the company Italiana Biotecnologie (head office: via San Cassiano 99, Trecate (NO), Italy).

January 2021 - December 2021.  Temporary Research Fellow (Italian: borsa di studio per attività di ricerca) - position assigned to Dr. Laura Treu. In the context of the scientific agreement "Next Generation Sequencing analysis of data obtained with different bioinformatics pipelines and investigation of the microbial populations involved in anaerobic digestion". (Italian: Analisi di dati di Next Generation Sequencing ottenuti con diverse pipeline bioinformatiche e studio delle popolazioni microbiche coinvolte nella digestione anaerobica). Economic support provided by the company BMR genomics (head office: via Redipuglia 22/a 35131, Padova (PD), Italy).

Aug 2022 - July 2023. Temporary Research Fellow (Italian: assegnista di ricerca) - position assigned to Dr. Victor Borin Centurion Biruel; in the context of the project “Future-proof bioactive peptides from food by-products: an eco-sustainable bioprocessing for tailored multifunctional foods (PROACTIVE)” granted by the competitive project supported by Italian PRIN: PROGETTI DI RICERCA DI RILEVANTE INTERESSE NAZIONALE – Bando 2020.

October 2022 - February 2023.  Temporary Research Fellow (Italian: borsa di studio per attività di ricerca) - position assigned to Dr. Luca Bucci. In the context of the scientific agreement "Investigation of the microbial populations dynamics in the anaerobic digestion of the organic fraction of municipal solid waste". (Italian: Studio della dinamica di popolazioni microbiche coinvolte nella digestione anaerobica della frazione organica dei rifiuti solidi urbani - FORSU). Economic support provided by the company S.E.S.A. S.p.A. Società Estense Servizi Ambientali (head office: Via Comuna, 5/b 35042 - Este - PD).

January 2022 - present. Temporary Research Fellow (Italian: assegnista di ricerca) - position assigned to Dr. Tatiana Spatola Rossi; in the context of the project “BioCO2-TRAPPING: development and optimization of a biological process for the trapping of carbon dioxide and its conversion into bioplastics in a circular economy context” (Italian: BioCO2-TRAPPING: sviluppo e ottimizzazione di un processo  biologico per l’intrappolamento dell’anidride carbonica e la sua conversione in bioplastiche in un contesto di economia circolare)  Fondazione CARIVERONA - Call Research and development 2022.

January 2022 - present. Temporary Research Fellow (Italian: assegnista di ricerca) - position assigned to Dr. Junior Lemos Fernandes; in the context of the project “.” (Italian:)  granted by the Venetian region (Italy) in the framework of the European Social Found (FSE) 2023.

June 2023 - September 2023. Temporary Research Fellow (Italian: borsa di studio per attività di ricerca) - position assigned to Dr. Maria Chiara Valerin; in the context of the project “CONTRATTO DI RICERCA 22-R047_MARCO POLO_ CONSORZIO MICROBICO” granted by Marco Polo Engineering Srl through UniSMART.

October 2023 - November 2023. Temporary Research Fellow (Italian: borsa di studio per attività di ricerca) - position assigned to Dr. Maria Chiara Valerin; in the context of the project "Sviluppo, validazione ed esecuzione di test microbiologici finalizzati alla valutazione del mantenimento delle proprietà funzionali degli ingredienti alimentari")  "The agriculture of the future and functional foods: a challenge for the research and revitalization of the Venetian region - "F.A. & A.F." (L'agricoltura del futuro e gli alimenti funzionali: una sfida per la ricerca e il rilancio del territorio veneto - "F.A.&A.F.") within the framework of the competitive project supported by POR FESR 2014-2020

November 2023 - January 2024. Temporary Research Fellow (Italian: borsa di studio per attività di ricerca) - position assigned to Dr. Mengyuan Ji; "Development of a customized bioinformatics pipeline for the analysis of transcriptome sequencing data of Coniella granati" (Italian: "Sviluppo di una pipeline bioinformatica personalizzata per l'analisi dei dati di sequenziamento del trascrittoma di Coniella granati") granted by the Sequencing Service of the Biology Department (University of Padova).

December 2023 - February 2024. Temporary Research Fellow (Italian: borsa di studio per attività di ricerca) - position assigned to Dr. Maria Chiara Valerin; in the context of the project “CONTRATTO DI RICERCA 22-R047_MARCO POLO_ CONSORZIO MICROBICO” granted by Marco Polo Engineering Srl through UniSMART.

February 2024 - present. Temporary Research Fellow (Italian: borsa di studio per attività di ricerca) - position assigned to Dr. Luca Francescato; in the context of the project “MICRO-BIOfuels: Development and characterization of a microbial inoculum for use in the valorization of difficult-to-degrade byproducts through the production of biohydrogen and biogas.” (Italian: MICRO-BIOfuels: Sviluppo e caratterizzazione di un inoculo microbico da impiegare nella valorizzazione di sottoprodotti difficilmente degradabili tramite produzione di bioidrogeno e biogas)  granted by the University of Padova - Call: Uni-Impresa 2022.

March 2024 - September 2024. Temporary Research Fellow (Italian: borsa di studio per attività di ricerca) - position assigned to Dr. Maria Chiara Valerin; in the context of the project “MICRO-BIOfuels: Development and characterization of a microbial inoculum for use in the valorization of difficult-to-degrade byproducts through the production of biohydrogen and biogas.” (Italian: MICRO-BIOfuels: Sviluppo e caratterizzazione di un inoculo microbico da impiegare nella valorizzazione di sottoprodotti difficilmente degradabili tramite produzione di bioidrogeno e biogas)  granted by the University of Padova - Call: Uni-Impresa 2022.

Supervision and Teaching

I have many years of teaching experience (2004-2021) in different disciplines like "Molecular Biology", "Genomics", "Bioinformatics" "Microbial Metagenomics". At present, I teach "Molecular Biology 2" and the Molecular Biology Bachelor Degree and "Microbial Metagenomics" at the Master Degree in Molecular Biology (both at the University of Padova).

In the link are reported the details of the teaching activity in the Molecular Biology degree (bachelor and master) from 2004. Data are the same reported in the “reserved area of the School of Sciences” website (University of Padova) (https://docenti.scienze.unipd.it/).

Teaching activity details

International teaching courses

10th Aug 2022 - Three hours of online lecture on "Biological aspects of anaerobic microbiomes" via Classroom USP and Google system at the online course "Metabolic approaches and microbial characterization in anaerobic microbiomes and biorefineries" sponsored by CNPq (Brazil) and the Latin American Biotechnology Center (CABBIO). Number of  participants:  78 from Brazil, Argentina, Uruguay, Mexico, and Colombia.

31st Oct - 4th Nov 2022 - Invited teacher at the postgraduate course: “Genome-centric metagenomics for bioremediation and resource recovery” supported by the United Nations University - BIOLAC (Biotechnology Programme for Latin America and the Caribbean). Number of participants: 22 from Latin America (Colombia, Uruguay, Chile, Brazil, Ecuador and Argentina). The teaching activity was in presence at the Instituto de Investigaciones en Ingeniería Genética y Biología Molecular “Dr Héctor N. Torres” (INGEBI-CONICET), Buenos Aires, Argentina. 

7th Nov 2023 - Invited teacher in the postgraduate course "Frontiers of organic wastes utilization" Fudan University Shanghai, China. Number of participants: 30.

PhD students

Academic year (2009-2011). PhD in Viticulture, Enology and Marketing, Department of Agricultural Biotechnology, University of Padua. Student: Laura Treu; Thesis title: A genomic and transcriptomic strategy to characterize oenological Saccharomyces cerevisiae strains. (co-supervisor with Prof. Viviana Corich).

Academic year October 2019-September 2022. PhD school of Biosciences. Student: Alessandro Rossi; Thesis title: The metagenomics revolution and its impact on virology: the case of anaerobic environments.

Academic year October 2020-present. PhD school of Biosciences. Student: Mengyuan Ji; Thesis title: Integrated metagenomic model insight towards understanding the effects of biochar on microplastics degradation in flooded soil. (People’s Republic of China Scholarship Financed by the China Scholarship Council).

January 2022-present. Student: Ginevra Giangieri; Department of Chemical and Biochemical Engineering. Thesis title (To be defined). (co supervisor with Irini Angelidaki).

Academic year October 2022-September 2025. PhD school of Biosciences. Student: Edoardo Bizzotto; Thesis title (To be defined).

Academic year October 2023-September 2026. PhD school of Biosciences. Student: Sofia Fraulini; Thesis title (To be defined).

Academic year November 2023-Octoer 2025. PhD school of Biosciences. Student: Davide Santinello; Thesis title (To be defined).

Master students

Academic Year 2006-2007. Master Degree in Molecular Biology, University of Padova. Student: Andrea Telatin; Thesis title: Investigating high pressure adaptation of Photobacterium profundum by means of custom microarray  (co-tutor with Prof. Giorgio Valle).

Academic Year 2008-2009. Master Degree in Molecular Biology, University of Padova. Student: Fabio De Pascale; Thesis title: A detail characterization of the Photobacterium

profundum SS9 transcriptome with next-generation sequencing.

Academic Year 2008-2009. Master Degree in Molecular Biology, University of Padova. Student: Valerio Zaffalon; Thesis title: Survey of Begomoviruses and associated satellites infecting plants in the cotton-growing area of Northwestern India. Co-tutors: Dr. Jeremy R. Thompson, Dr. Mark Tepfer, plant virology group ICGEB Biosafety Outstation.

Academic Year 2009-2010. Master Degree in Molecular Biology, University of Padova. Student: Lisa Marchioretto; Thesis title: Promoter methylation contributes to the regulation of c-MET expression in pediatric LAL-B. (Italian: La metilazione del promotore contribuisce alla regolazione dell'espressione di c-MET nelle LAL-B pediatriche). (co-tutor with Prof. Giuseppe Basso).

Academic Year 2009-2010. Master Degree in Molecular Biology, University of Padova. Student: Chiara Sartor; Thesis title: Clinicopathological and molecular analysis of microscopic gastrointestinal stromal tumors - micro GIST. (Italian: Analisi clinicopatologica e molecolare di tumori stromali gastrointestinali microscopici - micro GIST) molecolare omoter methylation contributes to the regulation of c-MET expression in pediatric LAL-B. (Italian: La metilazione del promotore contribuisce alla regolazione dell'espressione di c-MET nelle LAL-B pediatriche). (co-tutor with Prof. Giuseppe Basso).

Academic Year 2010-2011. Master Degree in Molecular Biology, University of Padova. Student: Chiara Toniolo; Thesis title:  Correlation between differences in promoter regions and transcriprtional profile of Six Saccharomyces cerevisiae strains. Evaluation: 110/110 cum laude.

Academic Year 2011-2012. Master Degree in Molecular Biology, University of Padova. Student: Alessandro Sardu; Thesis title:  Analysis of the yeast transcriptome structure using a new bioinformatic tool. Evaluation: 110/110 cum laude.

Academic Year 2020-2021. Master Degree in Biotechnology, University of Padova. Student: Sara Agostini; Thesis title: Study of the microbiome of anaerobic digestion with techniques of isolation and optimization of the process through bioaugmentation. (Studio del microbioma della digestione anaerobica con tecniche di isolamento e ottimizzazione del processo tramite bioaugmentazione) (co-tutor with Dr. Laura Treu). Evaluation: 110/110.

Academic Year 2020-2021. Master Degree in Molecular Biology. Student: Francesco Moro; Thesis title: Identification of the main environmental factors impacting the gut microbiota composition in 167 healthy Danish children: a high throughput 16S rRNA sequencing investigation. Evaluation: 106/110.

Academic Year 2020-2021. Master Degree in Industrial Biotechnology, University of Padova. Student: Ginevra Giangieri; Thesis title: Preliminary investigation of microorganisms potentially involved in microplastic degradation using Next Generation Sequencing and degradation assays. Evaluation: 110/110 cum laude.

Academic Year 2020-2021. Master Degree in Industrial Biotechnology, University of Padova. Student: Luca Bucci; Thesis title: Ammonia stress in anaerobic digestion: isolation of bacteria and bioaugmentation with adapted cultures and resistant microorganisms. Evaluation: 110/110 cum laude.

Academic Year 2020-2021. Master Degree in Industrial Biotechnology, University of Padova. Student: Luca Carlon; Thesis title: Setup of anaerobic reactors to study microbial syntrophies in biogas upgrading. (Italian: Allestimento di reattori anaerobici per studiare le sintrofie microbiche nel biogas upgrading).  Evaluation: 110/110.

Academic Year 2021-2022. Master Degree in Molecular Biology (curriculum Bioinformatics), University of Padova. Student: Gabriele Ghiotto; Thesis title: Analysis of strains distribution in the anaerobic digestion microbiome and effects of variants on key metabolic pathways.  Evaluation: 110/110 cum laude.

Academic Year 2021-2022. Master Degree in Molecular Biology (curriculum Bioinformatics), University of Padova. Student: Artur Sannikov; Thesis title: Marine sediments: interaction partners of cable bacteria revealed through metagenomics​.  Evaluation: 110/110 cum laude.

Academic Year 2021-2022. Master Degree in Molecular Biology (curriculum Molecular Biology), University of Padova. Student: Davide Santinello; Thesis title: Metagenomic and metatranscriptomic analysis of microbial communities to investigate syntrophic interactions in the anaerobic digestion process.  Evaluation: 110/110 cum laude.

Academic Year 2022-2023. Master Degree in Industrial Biotechnology, University of Padova. Student: Nicholas Rizzetto; Thesis title: Impact of humic acids on methane emissions from microplastic contaminated paddy soils. Evaluation: 110/110 cum laude.

Academic Year 2022-2023. Master Degree in Molecular Biology (curriculum Molecular Biology), University of Padova. Student: Giulia Fiorito; Thesis title:.  Evaluation: 110/110.

Academic Year 2022-2023. Master Degree in Molecular Biology (curriculum Molecular Biology), University of Padova. Student: Davide Sanguineti; Thesis title: Accurate species detection and assessment of functional redundancy in microbial communities.  Evaluation: 110/110 cum laude.

Academic Year 2022-2023. Master Degree in Molecular Biology (curriculum Bioinformatics), University of Padova. Student: Sofia Fraulini; Thesis title: Development of a new tool for functional investigation of microbial communities: empowering the analysis through machine learning .  Evaluation: 110/110 cum laude.

Academic Year 2023-2024. Master Degree in Molecular Biology (curriculum Bioinformatics), University of Padova. Student: Maria Augustina Biancalani; Thesis title: TO BE DEFINED.  Evaluation: PENDING.

Academic Year 2023-2024. Master Degree in Molecular Biology (curriculum Bioinformatics), University of Padova. Student: Claudia Mojo Nomagugu; Thesis title: TO BE DEFINED.  Evaluation: PENDING.

Academic Year 2023-2024. Master Degree in Molecular Biology (curriculum Molecular Biology), University of Padova. Student: Retno Supardi; Thesis title: TO BE DEFINED.  Evaluation: PENDING.

Academic Year 2023-2024. Master Degree in Biotechnologies for food science, University of Padova. Student: Somayeh Mohammadzadeh; Thesis title: TO BE DEFINED.  Evaluation: PENDING.

Bachelor students

Academic Year 2005-2006. Bachelor Degree in Molecular Biology. Student: Giorgia Busolin; Thesis title: (English: Contribution to the project: drug resistance in breast cancer using the microarray technique) (Italian: Contributo al progetto: farmacoresistenza nel tumore al seno mediante la tecnica dei microarray).

Academic Year 2006-2007. Bachelor Degree in Molecular Biology. Student: Michele Bridda; Thesis title: (English: Gene expression analysis in Danio rerio embryos inactivated at the olig3 gene level) (Italian: Analisi dell'espressione genica in embrioni di Danio rerio inattivati a livello del gene olig3).

Academic Year 2007-2008. Bachelor Degree in Molecular Biology. Student: Lisa Marchioretto; Thesis title: (English: cloning tests on the ToxR transcription factor of Photobacterium profundum SS9) (Italian: Prove di clonaggio del fattore di trascrizione ToxR di Photobacterium profundum SS9). 

Academic Year 2008-2009. Bachelor Degree in Molecular Biology. Student: Michela Serena; Thesis title: (English: Preparation of cDNA for meta-transcriptomic analysis) (Italian: Preparazione di cDNA per analisi metatrascrittomica).

Academic Year 2009-2010. Student: Giulia Furlan; Thesis title:  (English: Transcriptome structure analysis and discovery of conditional operons in archaea Halobacterium salinarum by tiling array and ChIP-chip techniques). (Italian: Analisi della struttura del trascrittoma e scoperta di operoni condizionali nell'archaea Halobacterium salinarum tramite tecniche di tiling array e ChIP-chip). 

Academic Year 2010-2011. Bachelor Degree in Molecular Biology. Student: Tinto Daniel; Thesis title: (English: Finishing of yeast genomes and production of libraries for transcriptome analysis with SOLiD sequencing). (Italian: Finishing del genoma di ceppi di lievito e costruzione di librerie per l'analisi del trascrittoma mediante sequenziamento SOLiD).

Academic Year 2010-2011. Bachelor Degree in Molecular Biology. Student: Elena Porto; Thesis title: (English: Identification of the Saccharomyces cerevisiae transcriptome secondary structure by means of PARS technique). (Italian: Determinazione della struttura seconda del trascrittoma di Saccharomyces cerevisiae tramite tecnica PARS).

Academic Year 2011-2012. Bachelor Degree in Molecular Biology.  Student: Benedetta Scarpari; Thesis title: (English: Bioinformatics analysis of RNA-seq data for the identification of polyadenylation sites in Saccharomyces cerevisiae) (Italian: Analisi informatica di dati di RNA-seq per l'identificazione di siti di poliadenilazione in Saccharomyces cerevisiae).

Academic Year 2012-2013. Bachelor Degree in Molecular Biology. Student: Marco Necci; Thesis title: (English: Genomic analysis of the binding sites of the proteins present on the transcripts of Saccharomyces cerevisiae) (Italian: Analisi genomica dei siti di legame delle proteine presenti sui trascritti di Saccharomyces cerevisiae).

Academic Year 2012-2013. Bachelor Degree in Molecular Biology. Student: Mattia Bolzan; Thesis title: (English: Effects of sulfur dioxide on the transcriptional profile of oenological yeasts ) (Italian: Effetti dell'anidride solforosa sul profilo trascrizionale di lieviti enologici).

Academic Year 2015-2016. Bachelor Degree in Molecular Biology. Student: Davide Steffan; "Thesis title" (English: PGC-1alpha1 induced by exercise modify the kinurenine methabolism and protects from stress-induced depression). (Italian: PGC-1alpha1 indotto dall'esercizio fisico cambia il metabolismo della chinurenina e protegge dalla depressione indotta dallo stress). 

Academic Year 2015-2016. Student: Martina Bazzega; Thesis title: (English: The microbiome of mice treated with a prebiotic reveals new targets involved in the host response during the condition of obesity) (Italian: Il microbioma dei topi trattati con un prebiotico rivela nuovi target coinvolti nella risposta dell'ospite durante la condizione di obesità).

Academic Year 2016-2017. Bachelor Degree in Molecular Biology. Student: Alessia Cerchiaro; Thesis title: (English: Screening of yeast mutants using microfluidic techniques and genomic sequencing for the identification of variants associated with an increase in protein secretion) (Italian: Vaglio di mutanti di lievito tramite tecniche microfluidiche e sequenziamento genomico per l'identificazione di varianti associate ad un incremento di secrezione proteica).

Academic Year 2016-2017. Bachelor Degree in Molecular Biology. Student: Denise Pezzutto; Thesis title: (English: Isolation and culture of single bacterial cells in agarose microcapsules to obtain genomic sequences with a high degree of completeness) (Italian: Isolamento e coltura di singole cellule batteriche in microcapsule di agarosio per l'ottenimento di sequenze genomiche ad elevato grado di completezza).

Academic Year 2017-2018. Bachelor Degree in Molecular Biology. Student: Beatrice De Cortà Fumei; Thesis title: (English: Modulation of the intestinal microbiota through fecal microRNAs produced by the host) (Italian: Modulazione del microbiota intestinale attraverso microRNA fecali prodotti dall'ospite).

Academic Year 2017-2018. Bachelor Degree in Molecular Biology. Student: Donato D'Angelo; Thesis title: (English: Kynurenic acid and its Gpr35 receptor regulate energy homeostasis and inflammation in adipose tissue) (Italian: L'acido chinurenico ed il suo recettore Gpr35 regolano l'omeostasi energetica e l'infiammazione nel tessuto adiposo).

Academic Year 2018-2019. Bachelor Degree in Molecular Biology. Student: Giada Benedetti; Thesis title: (English: Using the PacBio sequencing technology to analyze the splicing process in Schizosaccharomyces pombe) (Italian:Utilizzo della Tecnologia PacBio per lo Studio del Processo di Splicing in Schizosaccharomyces pombe).

Academic Year 2019-2020. Bachelor Degree in Molecular Biology. Student: Elisabetta Offer; "Thesis title" (English: Genome- and Community-Level Interaction Insights into Carbon Utilization and Element Cycling Functions of Hydrothermarchaeota in Hydrothermal Sediment) (Italian: Interazione tra specie nel microbioma dei sedimenti idrotermali: un'esplorazione condotta tramite approcci genomici). 

Academic Year 2020-2021. Bachelor Degree in Molecular Biology. Student: Marta Bottega; "Thesis title" (English: Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals) (Italian: Analisi delle correlazioni tra microbioma, metabolismo dell'ospite e dieta in una coorte di 1098 individui altamente caratterizzati a livello fenotipico). 

Academic Year 2021-2022. Bachelor Degree in Molecular Biology. Student: Filippo Fiorin; "Thesis title" (English: Complete genome sequencing of Cupriavidus necator NH9 and reclassification of the strains of the genera Cupriavidus and Ralstonia) (Italian: Sequenziamento completo del genoma di Cupriavidus necator NH9 e ri-classificazione tassonomica dei ceppi appartenenti ai generi Cupriavidus e Ralstonia). 

Academic Year 2021-2022. Bachelor Degree in Biology. Student: Carraro Simone; "Thesis title" (English: New genomic methods in the analysis of virus-prokaryiotes interactions in hot springs biofilm) (Italian: Nuovi approcci genomici nell'analisi delle interazioni virus-procarioti nei biofilm delle sorgenti termali). 

Academic Year 2021-2022. Bachelor Degree in Molecular Biology. Student: Anna Caporello; "Thesis title" (English: Machine learning-aided analyses of thousands of draft genomes reveal specific features of activated sludge processes) (Italian: Machine learning applicato all’analisi della complessità genomica degli ecosistemi dei fanghi attivi rivela caratteristiche funzionali specifiche).

Academic Year 2022-2023. Bachelor Degree in Molecular Biology. Student: Alberto Maggio; "Thesis title" (English:  A metatranscriptomic analysis and its validation using the human small intestine microbiota dataset) (Italian: La procedura sviluppata permette una efficiente rimozione degli rRNA seguita da una affidabile assegnazione delle funzioni e dell'origine tassonomica previste, delle reads di mRNA del campoine).

Academic Year 2022-2023. Bachelor Degree in Molecular Biology. Student: Carlo Nicolin; "Thesis title" (English: DNA-directed termination of RNA polymerase II transcription) (Italian: Terminazione diretta dal DNA della trascrizione dell' RNA polimerasi II).

Academic Year 2022-2023. Bachelor Degree in Molecular Biology. Student: Lorenzo Barletta; "Thesis title" (English: TO BE DEFINED) (Italian: TITOLO DA DEFINIRE).

Academic Year 2023-2024. Bachelor Degree in Molecular Biology. Student: Alessandra Carpanese; "Thesis title" (English: TO BE DEFINED) (Italian: TITOLO DA DEFINIRE).

Academic Year 2023-2024. Bachelor Degree in Molecular Biology. Student: Lucas Cappelletti; "Thesis title" (English: TO BE DEFINED) (Italian: TITOLO DA DEFINIRE).

Participation to PhD Schools

I participated to the Medical PhD School as expert of genomics and transcriptomics from 2006 to 2014 and to the PhD school of Biosciences (genetics, genomics and bioinformatics) starting from 2017.

- Participation to the PhD program in Nephrological Sciences cycle XXII (AA 2006/2007 - AA 2008/2009), Referent Prof. D'Angelo Angela.

- Participation to the PhD program in Nephrological Sciences cycle XXIV (AA 2009/2010 - AA 2011/2012), Referent Prof. D'Angelo Angela.

- Participation to the PhD program in Clinical Physiopathology and Nephrological Sciences cycle XXV (AA 2010/2011 – AA 2012/2013), Referent Prof. Ossi Elena.

- Participation to the PhD program in Clinical Physiopathology and Nephrological Sciences cycle XXVI (AA 2011/2012 – AA 2013/2014), Referent Prof. Ossi Elena.

- Participation to the PhD program in Biosciences (genetics, genomics and bioinformatics) cycles XXXIII-XXXIV (AA 2017/2018 - AA 2019/2020), Referent Prof. Szabò Ildiko.

- Participation to the PhD program in Biosciences (genetics, genomics and bioinformatics) cycles XXXIV-XXXV (AA 2018/2019 - AA 2020/2021), Referent Prof. Szabò Ildiko.

- Participation to the PhD program in Biosciences (genetics, genomics and bioinformatics) cycles XXXV-XXXVI (AA 2019/2020 - AA 2021/2022), Referent Prof. Szabò Ildiko.

- Participation to the PhD program in Biosciences (genetics, genomics and bioinformatics) cycles XXXVI-XXXVII (AA 2020/2021 - AA 2022/2023), Referent Prof. Szabò Ildiko.

- Participation to the PhD program in Biosciences (genetics, genomics and bioinformatics) cycles XXXVII-XXXVIII (AA 2021/2022 - AA 2023/2024), Referent Prof. Szabò Ildiko.

- Participation to the PhD program in Biosciences (genetics, genomics and bioinformatics) cycles XXXVIII-XXXIX (AA 2022/2023 - AA 2024/2025), Referent Prof. Szabò Ildiko.

- Participation to the PhD program in Biosciences (genetics, genomics and bioinformatics) cycles XXXIX-XL (AA 2023/2024 - AA 2025/2026), Referent Prof. Chiara Romualdi.

Participation to PhD evaluation committee

2011. Student: WaiYin Chong. Thesis title: Characterization of the TATA-box binding protein (TBP) from the Antarctic archaeon Methanococcoides burtonii. Student number 3040337. Supervisor: Prof. Ricardo Cavicchioli. School of biotechnology and biomolecular sciences, faculty of Sciencs. University of New South Wales.

2013. Student: Marta Antonioli. Thesis title: Effects of natural drivers on marine prokaryotic community structure. Supervisor: Prof. Serena Fonda Umani. XXVI cycle PhD in environmental biology. Department of Life Sciences. University of Trieste (Italy).

2019 - Student: Núria Zamorano-López.  Thesis title: The role of microbial ecology during biogas production from renewable energy sources. Characterizing microbial community structures in bioenergy production systems for future water resource recovery facilities. Supervisor: Dr. Luis Borrás Falomir. Department of chemical engineering. University of Valencia, CALAGUA research group.

2021. Student: Borja Lagoa Costa. Thesis title: Polyhydroxyalkanoate production from cheese whey and other carbón sources using mixed microbial cultures. Supervisor: Prof. María del Carmen Veiga Barbazán, Prof. Christian Kennes. PhD program in advanced biotechnology. Department of Environmental Bioingeneering (BIOENGIN)Faculty of Sciences, University of A Coruña (Spain).

2021. Student: Abhjeet Singh. Thesis title: Microbiological surveillance of biogas plants focusing on the acetogenic community. Doctoral thesis No. 2021:12. Supervisor: Prof. Anna Schnürer. Faculty of natural resources and agricultural sciences. Department of molecular sciences. Swedish University of Agricultural Sciences. Uppsala (Sweden).

2022 (26th July). Student: Balázs Kakuk. Thesis title: Anaerobic digestion of Green Willow Biomass, a novel lignocellulosic substrate, and the evaluation of H2-induced stress in anaerobic bioreactors by genome-resolved metatranscriptomics. Supervisors: Kornél L. Kovács, Zoltán Bagi. Environmental Sciences Doctoral School, Department of Biotechnology, Faculty of Science and Informatics, University of Szeged. Szeged (Hungary).

Innovative teaching

I am very interested in innovative forms of teaching in the higher education system and I am involved in the development of Faculty Learning Communities. These activities allow to share new teaching formats and to promote innovative teaching. For this reason in 2018 I followed the “Teaching 4 Learning” course at the University of Padova.

Dissemination of molecular biology in secondary schools and career guidance

I am actively involved in helping students to choose the degree both during secondary school, and, as mentor, I support students of the bachelor and master degrees. As member of the “Didactic committee” and of the “Mentoring committee” in the Molecular Biology Course of the University of Padova, I have many years of experience in the interaction with the students and in the organization of the University Degree.

I constantly take part to the activity “scegli con noi il tuo domani” organized by the University of Padova, which is aimed to meet and discuss with the students of the secondary schools in order to help them to gather the relevant information and to make a decision on the Degree.

I was involved for three years in the “Progetto Nazionale Lauree Scientifiche” coordinated by Dr. Paolo Laveder (University of Padova); the project aimed to disseminate the new discoveries of the molecular biology in the secondary schools and to support teachers in performing new practical activities focused on molecular biology, developmental biology, etc.. The project was granted for other three years from 2019 to 2021.

I was involved in the project "Active orientation in the secondary school-to-university transition" (Italian: Orientamento attivo nella transizione scuola-Università) granted by Next-Generation EU, "Piano Nazionale di ripresa e resilienza (PNRR) Italia domani" with a series of three seminars in the topic "From genomic analysis to forensic genetics investigations" (Italian: Dall'analisi genomica alle indagini di genetica forense) from February to May 2024. Three secondary schools were involved: Secondary school IIS T. Lucrezio Caro (Cittadella, Padova) (22nd February 2024); Secondary school IS Giorgio Fermi (Treviso) (5th March 2024); Secondary school IS Ugo Morin (Mestre, Venezia) (9th May 2024).

Participation to congresses and selected oral presentations

Invited speaker S. Campanaro. Metabolic profiling of anaerobic digestion microbiomes: implications for biogas production and upgrading. 8th  IWA Resource Recovery Conference. Shenzhen (China) 1-3 November 2023.

Invited speaker S. Campanaro. From genome-centric metagenomics to metabolic network models: reconstruction and analysis in the anaerobic digestion system. Westlake University. Guangdhou (China) 1st November 2023.

Invited speaker S. Campanaro. From genome-centric metagenomics to metabolic network models: reconstruction and analysis in the anaerobic digestion system. Guangzhou Institute of Energy Conversion. Hangzhou (China) 6th November 2023.

Member of the organizing Scientific Committee 31st International Conference on Yeast Genetics and Molecular  Biology - ICYGMB31. Innovation Center (IC Auditorium) by Fondazione CR - Florence, Italy 2O-25 August 2O23.

Invited keynote speaker S. Campanaro. Using genome-centric metagenomics and metabolic flux balance analysis to investigate biogas upgrading and CO2 methanation. 8th International Conference on Biorefinery and Biomanufacturing, ICB 2023. Athens (Greece) 23-27 July 2023.

Invited speaker S. Campanaro. From Genome-centric Metagenomics to Metabolic Flux Balance Analysis: Tackling the Complexity of the Anaerobic Microbiomes. Symposium Resilience and Diversity in Complex Systems. Hamburg (Germany) 9-10 December 2022.

Invited speaker S. Campanaro. World food day 2022. Impact of diet on the gut microbiome: a metagenomic approach (Giornata Mondiale dell’Alimentazione 16th October 2022. Effetti dell'alimentazione sul microbiota intestinale: un approccio metagenomico). Department of Biology, University of Padova. 14th October 2022. https://www.fao.org/world-food-day/en#:~:text=16%2F10%2F2022

Invited speaker S. Campanaro. Metagenomics and metabolic flux balance approaches for the improvement of biological biogas upgrading (https://ebnet.ac.uk/biometh22/) Online webminar organized by the Carbon Recycling Network (https://carbonrecycling.net) and Environmental Biotechnology Network (EBNet) (www.ebnet.ac.uk)  26 May 2022.

Selected speaker  S. Campanaro, G. Zampieri, M.S. Morlino, N. De bernardini, X. Zhu, I. Angelidaki, P.G. Kougias, L. Treu. Analysis of the replication index on hundreds of metagenome-assembled genomes collected from different biogas reactors shed light on the growth characteristics of microbes in the anaerobic digestion process. 4th International conference on biogas microbiology (ICBM-4). Braga (Portugal) 9-12 May 2022. 

Invited speaker From metagenomics to metabolic modelling: how to increase our understanding of the anaerobic digestion microbial maze. MIKROBIOKOSMOS "Beneficial Microbes at the heart of Mikrobiokosmos”. Athens (Greece) 16-18 December 2021.

Selected speaker   S. Campanaro, G. Luo, L. Treu, P. G. Kougias, X. Zhu, I. Angelidaki D. Genome-Contric metagenomic investigation of 134 samples collected from biogas reactors revealed important functional roles for microbial species belonging to unexplored Taxa. Heraklion 2019 – 7th International conference on sustainable solid waste management. Heraklion (Greece) 26-29 June 2019.

Selected speaker   Campanaro S, Treu L, Kougias PG, Zhu X, Luo G, Angelidaki I. Definition of a novel strategy for assembly and binning of 148 shotgun sequenced samples collected from biogas reactors. Hellenic Bioinformatics. Thessalonica (Greece) 15-18 November 2018.

Selected speaker   S. Campanaro, G. Luo, L. Treu, P. G. Kougias, X. Zhu, I. Angelidaki D. Metagenomic investigation of 148 samples collected from biogas reactors revealed important functional roles for microbial species belonging to underexplored taxa. Biogas Science 2018. Turin (Italy) 17-19 September 2018.

Selected speaker   Campanaro S, Treu L, Kougias PG, Zhu X, Luo G, Angelidaki I. 700 microbial genomes assembled from the biogas microbiome shed light on functional roles in the anaerobic digestion process. Metaorganisms, Microbial Biorefineries and Human Health. Fondazione Golinelli (Bologna, Italy) 18-19 June 2018.

Selected speaker   Campanaro S, Treu L, Kougias P.G. and Angelidaki I. Do high throughput sequencing techniques provide the same phylogenetic result in anaerobic digestion system? 3rd International Conference on Biogas Microbiology (ICBM-3). Hotel de Wageningse Berg (Wageningen) The Netherlands. 1-3 May 2017.

Selected speaker   Campanaro S. Utilizzo di un microarray a cDNA per lo studio delle patologie neuromuscolari. 7° Congresso nazionale S.I.G.U. Società Italiana di Genetica Umana. Pisa (Pisa), Palazzo dei Congressi 13-15 October 2004.

Selected speaker   Campanaro S, De Pittà C, Millino C, Celegato B, Pacchioni B, Trevisan S, Bellin M, Romualdi C, Tombolan L, Cagnin S, Valle G, Lanfranchi G. Application of a platform of 3’-end cDNAs for gene expression profiling in human diseases. Microarray Meeting 2003: III° convegno italiano sulla tecnologia. Segrate (Milano), Italy, Palazzo LITA, 09 June 2003.

Selected speaker   Campanaro S, Casalone E, Valle G. Polimorfismi di lunghezza dei microsatelliti in ceppi differenti di Saccharomyces cerevisiae. Convegno congiunto ABCD AGI-SIBBM-SIMGBM, Montesilvano Lido (Pescara) 1-4 October 1998.

Selected speaker   Campanaro S, Casalone E, Valle G. Microsatellites length polymorphism in different strains of Saccharomyces cerevisiae. 2nd Italian Workshop on Genome Research, Baia delle Zagare (Foggia) 8-10 June 1998.

Reviewing activity

I am very active as reviewer and I perform evaluations for various prestigious international journals including Nature Communications, Microbiome, Water Research, Bioresource Technolgy, etc.. The figure below reports a summary of my activity obtained from Publons, a website and free service for academics to track, verify and showcase their peer review.

Review editor

From January 2018 I am part of the “Frontiers Community” as Review Editor in the journal “Frontiers in Microbiology” (IF 5.64).

Guest editor

I served as guest editor for the research topic "Meta-omic Approaches to the Complex Anaerobic Communities in Wastewater Treatment Plants and Digesters"  Published on 02 December 2020. Front. Microbiol. doi: 10.3389/fmicb.2020.595036.

I served as editor for the special issue "Microorganisms with Probiotic Properties" (Deadline for manuscript submissions: 30 September 2021) in the journal Foods (ISSN 2304-8158).

Bibliometric indices (according to SCOPUS on April 2023 - https://www.scopus.com/authid/detail.uri?authorId=6506669806) 

Total number of publications: 143

Total number of citations: 9081 total citations by 7558 documents - h-index 40

Bibliometric indices (according to Web of Science on January 2022 - https://app.webofknowledge.com/author/record/769155,34711495)

Total number of publications: 139

Total number of citations: 8247 in 6897 documenti - h-index 38

Bibliometric indices (according to Google Scholar April 2023 - https://scholar.google.it/citations?user=SSXEe7AAAAAJ&hl=it)

Total number of citations: 1261 - h-index 46

CURRICULUM - SHORT

ENGLISH 

Email address: stefano.campanaro@unipd.it

Personal website https://sites.google.com/site/stefanocampanaro/

research unit Website https://metabioinfomicslab.it/

EDUCATION: 

I graduated at University of Padua in 1998, in 2002 I obtained a PhD in Biotechnology at the University of Padua.

POSITIONS AND MANAGEMENT:

My current position is Associate Professor (Molecular Biology), at the Department of Biology (UniPd).

2008: I was invited as Visiting fellow at the "University of New South Wales" (Sydney).

2006-2019: Researcher at the Department of Biology of the UniPd.

February 2019-July 2022: Director of the Research Center for Innovative Biotechnologies (CRIBI).

2023-"present": member of the scientific committee of the Interuniversity Consortium for Biotechnologies (CIB).

July 2023-"present": representative member for the University of Padova of the European Network of Bio-based Industries Consortium - BIC.

August 2022-"present": coordinator of the Genomics and Bioinformatics research group of the Biology department (University of Padova).

August 2022-"present": coordinator of the Next-Gen Sequencing service of the Biology Department (University of Padova).

GRANT REQUESTS:

I participated or coordinated 19 national and international research projects founded by: University of Padova (2009, 2011, Strategic research 2014, University of Padova (Uni-Impresa MICRO-BIOfuels 2022), Italian Ministry of University (FIRB 2004, SERRES 2010, CIB 2021, PRIN 2021), European Social Found (FSE) (2013, 2018, 2023), POR-FESR (F.A. & A.F. 2020), Australian Research Council (2011), Hellenic Foundation for Research and Innovation (2019), EU Accelerating CCS Technologies (CooCE 2021), EU LIFE Climate Change Mitigation (CO2toCH4 2021), CARIVERONA (BioCO2-TRAPPING 2022), EU HORIZON (CRONUS 2022).

From 2011 my research activity is focused on genomics, metagenomics, transcriptomics and bioinformatics and is mainly related to the investigation of the anaerobic digestion microbiome and Saccharomyces cerevisiae genomics and population structure.

INTERACTION WITH INDUSTRIES:

I am a founding member of the BMR Genomics spinoff of the University of Padova.

Starting from 2018 I received financial supports for eight different collaborative projects from companies including Italiana Biotecnologie, Marco Polo Engineering, BMR Genomics.

SUPERVISION AND TEACHING:

I have supervised 27 bachelor students, 23 master students (mainly from Molecular Biology and Biotechnologies), 7 PhD students (mainly from the Life Sciences PhD). 

I participated to the Medical PhD school from 2006 to 2014 and to the PhD school of Biosciences (Genetics, genomics and bioinformatics) starting from 2017.

I have supervised more than 20 temporary research fellows strting from 2013.

Bibliometric indices (SCOPUS): Total number of publications: 143 - 9081 total citations by 7558 documents - h-index 40.

ITALIAN

Indirizzo email: stefano.campanaro@unipd.it

Sito web personale: https://sites.google.com/site/stefanocampanaro/

Sito web dell'unità di ricerca: https://metabioinfomicslab.it/

ISTRUZIONE:

Mi sono laureato presso l'Università di Padova nel 1998 e nel 2002 ho conseguito il dottorato in Biotecnologie presso l'Università di Padova.

POSIZIONI E GESTIONE:

La mia attuale posizione è di Professore Associato (Biologia Molecolare) presso il Dipartimento di Biologia (UniPd).

Nel 2008: sono stato invitato come Visiting fellow presso l'Università di New South Wales (Sydney).

Dal 2006 al 2019: Ricercatore presso il Dipartimento di Biologia dell'UniPd.

Febbraio 2019-luglio 2022: Direttore del Centro di Ricerca per le Biotecnologie Innovative (CRIBI).

Dal 2023: membro del comitato scientifico del Consorzio Interuniversitario per le Biotecnologie (CIB).

Da luglio 2023: membro rappresentativo per l'Università di Padova della European Network of Bio-based Industries Consortium - BIC.

Da agosto 2022: coordinatore del gruppo di ricerca in Genomica e Bioinformatica del Dipartimento di Biologia (Università di Padova).

Da agosto 2022: coordinatore del servzio di sequenziamento NGS del Dipartimento di Biologia  (Università di Padova).

RICHIESTE DI FINANZIAMENTO:

Ho partecipato a 19 progetti di ricerca nazionali e internazionali finanziati da: Università di Padova (2009, 2011, Ricerca strategica 2014, Uni-Impresa MICRO-BIOfuels 2022), Ministero dell'Università (FIRB 2004, SERRES 2010, CIB 2021, PRIN 2021), Fondo Sociale Europeo (FSE) (2013, 2018, 2023), POR-FESR (F.A. & A.F. 2020), Consiglio Australiano per la Ricerca (2011), Fondazione Ellenica per la Ricerca e l'Innovazione (2019), EU Accelerating CCS Technologies (CooCE 2021), EU LIFE Climate Change Mitigation (CO2toCH4 2021), CARIVERONA (BioCO2-TRAPPING 2022), EU HORIZON (CRONUS 2022).

Dal 2011 la mia attività di ricerca è focalizzata sulla genomica, metagenomica, trascrittomica e bioinformatica ed è principalmente legata all'indagine del microbioma della digestione anaerobica e alla genomica e struttura della popolazione di Saccharomyces cerevisiae.

INTERAZIONE CON L'INDUSTRIA:

Sono uno dei membri fondatori della spin-off BMR Genomics dell'Università di Padova.

A partire dal 2018 ho ricevuto supporti finanziari per otto diversi progetti collaborativi da aziende tra cui Italiana Biotecnologie, Marco Polo Engineering, BMR Genomics.

SUPERVISIONE E INSEGNAMENTO:

Ho supervisionato 27 studenti laureati, 23 studenti magistrali (principalmente in Biologia Molecolare e Biotecnologie) e 7 dottorandi (principalmente nel dottorato in Scienze della Vita).

Ho partecipato alla Scuola di Dottorato in Medicina dal 2006 al 2014 e alla Scuola di Dottorato in Bioscienze (Genetica, genomica e bioinformatica) a partire dal 2017.

Ho supervisionato più di 20 borsisti di ricerca temporanei a partire dal 2013.

Indicatori bibliometrici (SCOPUS): Numero totale di pubblicazioni: 143 - 9081 citazioni totali in 7558 documenti - indice h 40.