Seminars organized or recommended by the Ph.D: Program in Information Engineering

Dates and location of each seminar can be found on the Ph.D. Course Calendar (open it in Google Calendar or in any browser).

  1. “Science, Reality and Credibility – The Role of Scientific Critical Thinking to Contrast Disinformation and Face the Great Challenges of the Future”, a talk with Nobel Laureate Saul Perlmutter (organization by Città della Scienza, project Futuro Remoto)
Instructor: Professor Saul Perlmutter, University of California, Berkeley


There is a body of techniques and practices, a language and culture, that is usually implicitly taught by apprenticeship and osmosis to graduate students and postdocs in the sciences. This is the underpinning of an approach to building a credible sense of the “real world” that is shared by scientists, but not much used (or understood) by the rest of society.

Equipping future generations with this scientific-style critical thinking could be one of our most reasonable defenses against confused thinking and misinformation, both major challenges to our democratic societies’ ability to make deliberative decisions.

Can we make these implicit concepts explicit, and teach them to scientists and non-scientists alike? Could this help our society address difficult issues such as are raised by the global environment and economics? And how could citizen scientists use these tools to help build sources of credibility on the web and in the news.


Saul Perlmutter is a 2011 Nobel Laureate, sharing the prize in Physics for the discovery of the
accelerating expansion of the Universe. He is a professor of physics at the University of California, Berkeley, where he holds the Franklin W. and Karen Weber Dabby Chair, and a senior scientist at Lawrence Berkeley National Laboratory. He is the leader of the international Supernova Cosmology Project, and director of the Berkeley Institute for Data Science and executive director of the Berkeley Center for Cosmological Physics. His undergraduate degree was from Harvard and his PhD from UC Berkeley. In addition to other awards and honors, he is a member of the National Academy of Sciences and the American Academy of Arts and Sciences and a fellow of the American Physical Society and the American Association for the Advancement of Science. An author of over 200 scientific publications, Perlmutter has also written popular articles and appeared in numerous PBS, Discovery Channel, and BBC documentaries. His interest in teaching scientific-style critical thinking for scientists and non-scientists alike led to Berkeley courses on “Sense and Sensibility and Science” and “Physics and Music”.

  1. “Building a Research Career: A Success Story”, Prof. Fabrizio Nestola, June 23rd 2021, 9:00, Aula Magna “Antonio Lepschy”, building DEI/A
Instructor: Professor Fabrizio Nestola, Department of Earth Sciences, Università di Padova



Fabrizio Nestola, Full Professor in Mineralogy at the University of Padova, ERC Grant recipient, explains how to start planning a successful career as an academic or industrial researcher right from the beginning of the Ph.D.

  1. Seminar “Bioinformatics, System Biology and Synthetic Biology: where Information Engineering meets Molecular Biology” (in three parts)
  • Introduction to Systems Biology, Irene Zorzan, PhD, May 24th 2021 14:30, Zoom Meeting - Read More...

    Link to Zoom Meeting


    Systems Biology is an interdisciplinary field of study that integrates Molecular Biology and Dynamical Systems Theory to investigate the interactions between components of biological systems (e.g. genes and proteins) and to understand how these interactions bring about dynamic behaviors and biological functions (e.g. circadian oscillations, cellular differentiation).
    The seminar is thought to introduce engineering students/researchers with no biological background to the Systems Biology field by showing, with examples of increasing complexity, how mathematical modeling, theoretical and computational analysis of the models can be powerful tools to address biological questions and to formulate testable hypothesis about the functioning of biological systems. First of all, to exemplify the process of translating biological interactions into mathematical equations, analytical derivation of the Hill equation, commonly adopted to describe molecular interactions that exhibit nonlinear, sigmoidal response curve, is presented. Then, to provide an idea of how knowledge and tools from Systems Theory can help to unveil essential functioning principles of biological systems, three case study are presented: positive autoregulation circuit, a simple but widely spread network motif; a minimal gene regulatory network responsible for cellular differentiation; a complex stress response network responsible for persistence development in bacterial population exposed to stress.

  • Introduction to Synthetic Biology, Massimo Bellato, PhD, May 31st 2021 14:30, Zoom Meeting - Read More...

    Link to Zoom Meeting


    Synthetic biology is a new interdisciplinary area that involves the application of engineering principles to molecular biology. This field of science consist in redesigning organisms for useful purposes, by engineering them to have new abilities through the (re-)designing and fabrication of novel biological components and systems that do not already exist in the natural world. Synthetic biology researchers and companies around the world are harnessing the power of nature to solve problems in medicine, manufacturing, green energy, and agriculture.
    This seminar is aimed to provide a brief introduction on Synthetic Biology framework, methods, and research topics. Furthermore – as a multidisciplinary research area which taps into different fields – some case studies on how different engineering disciplines have been used in synthetic biology will be provided, from control theory to electronics and machine learning.
    The lecture will inspire attendants to think about how they can get involved in the Synthetic Biology world, envisioning how their research and knowledge could be exploited for possible future contribution in this exciting and cutting-edge emerging field. Even researchers who do not deal with these topics will find this excursus on the methodologies of engineering applied to biology instructive and formative.

  • Introduction to Single-Cell Bioinformatics, Giacomo Baruzzo, PhD, June 7th 10:00, Zoom Meeting - Read More...

    Link to Zoom Meeting


    Many biological mechanisms, such as cancer progression and stem cell differentiation, are the results of complex spatio-temporal interactions among cells. Similarly, tissues and organs are collections of cells that are spatially and temporally organized to fulfill their biological functions and respond to external stimuli. Therefore, the ability to study what single cells are doing in a living organism and how they interact across time and space is a key element to better understand biological processes and characterize diseases progression.
    Few years ago, a novel technology called single cell RNA-sequencing (scRNA-seq) enabled for the first time ever the characterization at single cell resolution of thousands of cells in parallel, resulting in a revolutionary tool for biology and medicine.
    What does this have to do with engineering?
    The output of a single cell RNA-sequencing experiment are thousands of text files containing tons of strings made up of characters “A”, “C”, “G” and “T”. The way information about cells and their activities is extracted from such data is through several methodologies and techniques from engineering, such as high-performance computing, string alignment, missing data imputation, statistical modelling and machine learning. This is what the novel field of scRNA-seq bioinformatics is about: an interdisciplinary field aimed at developing algorithm, data structure, methods and software to pre-process and analyze scRNA-seq data, combining knowledge from engineering, computer science, data analysis, biology and biotechnology.
    This seminar aims to provide an overview on the novel research area of scRNA-seq bioinformatics. First, a brief biological background will be provided to the audience, together with an introduction to the single cell RNA-sequencing field. Then, the bioinformatics pre-processing and analysis of single cell RNA-sequencing data will be described, focusing on some technical and methodological aspects (e.g. compositional data, string alignment, missing data imputation, dimensionality reduction) that attendant may find useful even in their research area.

Please, remember that students may have their attendance to the seminar recognized in order to fulfill the Seminar Requirements (see the PhD Course Catalogue for details). To this aim, students shall bring with them the Seminar Certificate of Attendance sheet (an empty one is attached to this message), fill it in with the required information and have it signed by the seminar instructor.