Giacomo Baruzzo, PhD

Postdoctoral Research Fellow (RTDA)

Systems Biology and Bioinformatics Group

giacomo dot baruzzo at unipd dot it

Department of Information Engineering

University of Padova

Short Bio

Giacomo Baruzzo got a Bachelor Degree in Information Engineering at University of Padova in 2011. He got a Master Degree in Computer Engineering (110/110) at University of Padova in 2013, working on bioinformatics methods for genome assembly from high-throughput sequencing technology (Next Generation Sequencing - NGS) data. He got a Ph.D. in Information Engineering at University of Padova in 2017, working on bioinformatics methods for the analysis of transcriptomics NGS data (RNA-sequencing). From 2017, he is working as postdoctoral researcher at the Department of Information Engineering, University of Padova.
His current research is aimed at developing algorithms, methods and software for the preprocessing and analysis of biological data from high-throughput sequencing technologies, especially single cell RNA-Sequencing, bulk RNA-Sequencing and 16S rDNA-Sequencing.

Academic Degree

PhD in Information Engineering at the University of Padova, Padova, Italy

Jan 2014 - Dec 2016
Thesis title: Improving the RNA-Seq analysis pipeline: read alignment and expression level quantification.
Advisor: Prof. Barbara Di Camillo

Master's Degree in Computer Engineering at the University of Padova, Padova, Italy

Oct 2011 - Oct 2013
Thesis title: A maximum likelihood approach to genome assembly.
Advisor: Prof. Gianfranco Bilardi

Bachelor's degree in Information Engineering at the University of Padova, Padova, Italy

Oct 2008 - Sep 2011

Appointments

Postdoctoral Researcher (RTDA)
at the Department of Information Engineering, University of Padova, Padova, Italy

Jan 2022 - Present
Research project: "Environmental Antimicrobial Resistance Load Tackling via Intelligent Systems (EARLIeSt)". Funding: REACT EU – PON “Ricerca e Innovazione 2014-2020” - DM 1062/2021

Senior Postdoctoral Researcher
at the Department of Information Engineering, University of Padova, Padova, Italy

Nov 2020 - Dec 2021
Research project: "Development of single cell RNA-seq bioinformatics methods and tools to study cell-cell communication and spatio-temporal evolution of multi-cells systems".

Junior Postdoctoral Researcher
at the Department of Information Engineering, University of Padova, Padova, Italy

Oct 2017 - Oct 2020
Research project: DEI PROACTIVE 2017 - "From Single-Cell to Multi-Cells Information Systems Analysis"

Visiting Postdoctoral Researcher
at Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia

Mar 2019 - Apr 2019
Research project: 1° Session of the Italian–Slovenian Joint Commission on Scientific and Technological Cooperation: "Computational and data visualization approaches to mining of large-scale data in single-cell genomics".

Junior Postdoctoral Researcher
at the Department of Information Engineering, University of Padova, Padova, Italy

Jan 2017 - Sep 2017
Research project: BIOBIG - “Analisi di Big Data in Bioinformatica”

Visiting PhD Student
at ITMAT Bioinformatics Group, Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, USA.

Jun 2015 - Dec 2015

Awards

"Best performing teams (3rd place)" at "Metagenomics Diagnosis for Inflammatory Bowel Disease Challenge (MEDIC)", sbv IMPROVER Computational Challenge series 2019-2020

Team GiGi, University of Padova, Italy: Barbara Di Camillo, Marco Cappellato, Mehdi Poursheikhali Asghari, Sebastian Daberdaku, Giacomo Baruzzo, Filippo Pietrobon, Ilaria Patuzzi.

Selected
Publications

G. Baruzzo and K. Hayer, E. Ji Kim, B. Di Camillo, G. Fitzgerald, G. Grant,
“Simulation-based comprehensive benchmarking of RNA-seq aligners”,
Nature Methods, 2016, 14(2):135–139. (DOI: 10.1038/nmeth.4106)

A. Dal Molin, G. Baruzzo, B. Di Camillo,
“Single-cell RNA-sequencing: assessment of differential expression analysis methods”,
Frontiers in Genetics, 2017, 8:62. (DOI: 10.3389/fgene.2017.00062)

F. Sambo, F. Finotello, E. Lavezzo, G. Baruzzo, G. Masi, E. Peta, M. Falda, S. Toppo, L. Barzon, B. Di Camillo,
“Optimizing PCR primers targeting the bacterial 16S ribosomal RNA gene”,
BMC Bioinformatics, 2018, 19(1):343. (DOI: 10.1186/s12859-018-2360-6)

G. Baruzzo, I. Patuzzi, B. Di Camillo,
“SPARSim single cell: a count data simulator for scRNA-seq data”,
Bioinformatics, 2019, 36(5): 1468-1475. (DOI: 10.1093/bioinformatics/btz752)

I. Patuzzi, G. Baruzzo, C. Losasso, A. Ricci, B. Di Camillo,
“metaSPARSim: a 16S rRNA gene sequencing count data simulator”,
BMC Bioinformatics, 2019, 20(9): 1-13. (DOI: 10.1186/s12859-019-2882-6)

G. Baruzzo and I. Patuzzi, B. Di Camillo,
“Beware to ignore the rare: how imputing zero-values can improve the quality of 16S rRNA gene studies results”,
BMC Bioinformatics, 2021, 22(15). (DOI: 10.1186/s12859-022-04587-0)

G. Baruzzo, G. Cesaro, B. Di Camillo,
“Identify, quantify and characterize cellular communication from single cell RNA sequencing data with scSeqComm”,
Bioinformatics, 2022, 38(7):1920-1929. (DOI: 10.1093/bioinformatics/btac036)

The complete list of publications is avaiable here link to CV.

Articles and citation metrics (May 2022)

Number of peer-reviewed journals articles: 14 (13 research articles, 1 commentary article)

Number of conference contributions: 17 (11 abstract+poster, 6 abstract-only)

Number of journal article citations:

h-index: 6 (Scopus) - 7 (Google Scholar)

Scopus ID: 57192312589

Google Scholar: Link

The complete list of articles and conference contributions is avaiable here link to CV.

Role in organization of international scientific conferences

Publicity co-chair, Proceedings co-chair, Organizing committee, Program committee
at 16th IEEE International Conference on Computational Intelligence in Bioinformatics and Computational Biology

Certosa di Pontignano, Siena, Italy, from July 9 to July 11, 2019

Refereeing and editorial activities

Journal referee: BMC Bioinformatics, BMC Genomics, Briefings In Bioinformatics, Bioinformatics Advances, IEEE/ACM Transactions on Computational Biology and Bioinformatics, IEEE Journal of Biomedical and Health Informatics

Conference referee: Research in Computational Molecular Biology (RECOMB) 2022, IEEE-EMBS International Conference on Biomedical and Health Informatics (BHI) 2021, Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB) 2021, Research in Computational Molecular Biology (RECOMB) 2021, Research in Computational Molecular Biology (RECOMB) 2020

Proceedings editor: Proceedings of the 16th IEEE International Conference on Computational Intelligence in Bioinformatics and Computational Biology

Oral presentations and invited speaker

Invited seminar: "Working with RNA sequencing data: challenges and strategies for data analysis" at ITMAT Bioinformatics, Institute for Translational Medicine and Therapeutics, University of Pennsylvania

Philadelphia, USA, May 3, 2018

Conference oral presentation: "SPARSim: taking account of data sparsity in single cell and 16S rRNA gene sequencing" at 15th Annual Meeting of the Bioinformatics Italian Society (BITS)

Turin, Italy, June 28, 2018

Conference oral presentation: "SPARSim Single Cell: a count data simulator for single cell RNA-seq data" at 3rd Annual MAQC Society Conference

Riva del Garda, Italy, April 9, 2019

Conference oral presentation: "Reliable simulation of count data for single cell RNA sequencing" at Network Tools and Applications for Biology (NETTAB) and Bioinformatics and Computational Biology Conference (BBCC) 2019 Meeting

Fisciano, Italy, November 13, 2019

Conference oral presentation: "Zero-imputation in 16S rRNA gene studies: do we need it?" at Bioinformatics and Computational Biology Conference (BBCC) 2020 Meeting

Virtual conference, November 18, 2020

Conference oral presentation: "scSeqComm: a bioinformatic tool to identify, quantify and characterize cellular communication from single cell RNA sequencing data" at 18th Annual Meeting of the Bioinformatics Italian Society (BITS)

Virtual conference, July 2, 2021

Conference oral presentation: "Analyze cellular communication from single cell RNA sequencing data with scSeqComm" at Bioinformatics and Computational Biology Conference (BBCC) 2021 Meeting

Virtual conference, December 2, 2021

Teaching

2021-2022: Lecturer (with responsibility of the course) at “Scientific Computing and Object Oriented Programming” (48 hours, 6 CFU)

Master Degree course of Mathematical Engineering (A.Y. 2021/2022) - Department of Civil, Environmental and Architectural Engineering, University of Padova, Padova, Italy

2021-2022: Lecturer (with responsibility of the course) at “Advanced topics in scientific and parallel programming with practical application to the CAPRI HPC infrastructure” (20 hours, 5 credits)

PhD Program in Information Engineering, XXXVII series - Department of Information Engineering, University of Padova, Padova, Italy

2021-2022: Teaching assistant at “Fondamenti di Informatica e Programmazione” (Didattica integrativa, 30 hours)

Bachelor Degree course of Biomedical Engineering (A.Y. 2021/2022) - Department of Information Engineering, University of Padova, Padova, Italy

2020-2021: Lecturer (with responsibility of the course) at “Advanced topics in scientific and parallel programming with practical application to the CAPRI HPC infrastructure” (20 hours, 5 credits)

PhD Program in Information Engineering, XXXVI series - Department of Information Engineering, University of Padova, Padova, Italy

2020-2021: Teaching assistant at “Fondamenti di Informatica e Programmazione” (Didattica integrativa, 30 hours)

Bachelor Degree course of Biomedical Engineering (A.Y. 2020/2021) - Department of Information Engineering, University of Padova, Padova, Italy

2019-2020: Co-Lecturer (with responsibility of the course) at “Advanced topics in scientific and parallel programming with practical application to the CAPRI HPC infrastructure” (10 hours, 2.5 credits)

PhD Program in Information Engineering, XXXV series - Department of Information Engineering, University of Padova, Padova, Italy

2019-2020: Teaching assistant at “Fondamenti di Informatica e Programmazione” (Didattica integrativa, 40 hours)

Bachelor Degree course of Biomedical Engineering (A.Y. 2019/2020) - Department of Information Engineering, University of Padova, Padova, Italy

2018-2019: Teaching assistant at “Fondamenti di Informatica e Programmazione” (Didattica integrativa, 50 hours)

Bachelor Degree course of Biomedical Engineering (A.Y. 2018/2019) - Department of Information Engineering, University of Padova, Padova, Italy

2015-2016: Teaching assistant at “Bioingegneria per la Genomica”

Master Degree course of Bioengineering (A.Y. 2015/2016) - Department of Information Engineering, University of Padova, Padova, Italy

Students Supervision

Giacomo Baruzzo has served as co-supervisor for one PhD student's thesis (PhD Course in Information Engineering), 9 Master Degree students's thesis (Computer Engineering and Bioengineering) and 4 Bachelor Degree students's thesis (Information Engineering and Biomedical Engineering) at the University of Padova. He is currently co-supervising 2 PhD students (PhD Course in Information Engineering) at the University of Padova.

Last update: 06-05-2022