Studying at the University of Verona
Here you can find information on the organisational aspects of the Programme, lecture timetables, learning activities and useful contact details for your time at the University, from enrolment to graduation.
Academic calendar
The academic calendar shows the deadlines and scheduled events that are relevant to students, teaching and technical-administrative staff of the University. Public holidays and University closures are also indicated. The academic year normally begins on 1 October each year and ends on 30 September of the following year.
Course calendar
The Academic Calendar sets out the degree programme lecture and exam timetables, as well as the relevant university closure dates..
Period | From | To |
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I semestre | Oct 1, 2015 | Jan 29, 2016 |
II semestre | Mar 1, 2016 | Jun 10, 2016 |
Session | From | To |
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Sessione straordinaria Appelli d'esame | Feb 1, 2016 | Feb 29, 2016 |
Sessione estiva Appelli d'esame | Jun 13, 2016 | Jul 29, 2016 |
Sessione autunnale Appelli d'esame | Sep 1, 2016 | Sep 30, 2016 |
Session | From | To |
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Sess. autun. App. di Laurea | Nov 25, 2015 | Nov 25, 2015 |
Sess. invern. App. di Laurea | Mar 16, 2016 | Mar 16, 2016 |
Sess. estiva App. di Laurea | Jul 12, 2016 | Jul 12, 2016 |
Sess. autun 2016 App. di Laurea | Nov 23, 2016 | Nov 23, 2016 |
Sess. invern. 2017 App. di Laurea | Mar 20, 2017 | Mar 20, 2017 |
Period | From | To |
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Festività dell'Immacolata Concezione | Dec 8, 2015 | Dec 8, 2015 |
Vacanze di Natale | Dec 23, 2015 | Jan 6, 2016 |
Vancanze di Pasqua | Mar 24, 2016 | Mar 29, 2016 |
Anniversario della Liberazione | Apr 25, 2016 | Apr 25, 2016 |
Festa del S. Patrono S. Zeno | May 21, 2016 | May 21, 2016 |
Festa della Repubblica | Jun 2, 2016 | Jun 2, 2016 |
Vacanze estive | Aug 8, 2016 | Aug 15, 2016 |
Exam calendar
Exam dates and rounds are managed by the relevant Science and Engineering Teaching and Student Services Unit.
To view all the exam sessions available, please use the Exam dashboard on ESSE3.
If you forgot your login details or have problems logging in, please contact the relevant IT HelpDesk, or check the login details recovery web page.
Academic staff

Bloisi Domenico Daniele
Ugolini Simone
Study Plan
The Study Plan includes all modules, teaching and learning activities that each student will need to undertake during their time at the University. Please select your Study Plan based on your enrolment year.
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1° Year
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2° Year activated in the A.Y. 2016/2017
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3° Year activated in the A.Y. 2017/2018
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Legend | Type of training activity (TTA)
TAF (Type of Educational Activity) All courses and activities are classified into different types of educational activities, indicated by a letter.
Bio-information technology workshop (2017/2018)
Teaching code
4S003713
Credits
12
Language
Italian
Scientific Disciplinary Sector (SSD)
BIO/10 - BIOCHEMISTRY
The teaching is organized as follows:
Modulo 1
Modulo 2
Learning outcomes
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MM: Modulo 1
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The course will provide the theoretical and practical basis to understand and employ algorithms and programs currently used in Bioinformatics. Major biological databases will be introduced with a special focus on genomic, proteomic and biochemical information. The students will also be introduced to the most modern fields of structural bioinformatics and systems biology. The theoretical part will be taught in the classroom, and it is aimed at understanding and learning bioinformatic topics and paradigms. The laboratory part will be useful to develop problem solving skills in classical and structural bioinformatics. Students will also work in groups and present databases of their choice, which will improve their communication skills and self criticism.
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MM: Modulo 2
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Knowledge of the basical bioinformatic tools for the analysis, interpretation and prediction of biological data in: genomics, structural and functional biology. This course offers the possibility of applying state of the art bioinformatic tools to solve biological problems
Program
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MM: Modulo 1
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Theoretical Module ---------------------------- - Overview of the main structural features of proteins and nucleic acids in relation to the concept of evolution. Introduction to biomolecular databases: online resources and their use - Biological databases: organization and integration of information concerning: a) protein and nucleic acid sequences; b) biomolecular structures; c) bibliographic and scientific literature. Retrieve of specific information: use of limitations and Boolean operators. - Sequence comparison and alignments: static and dynamic algorithms; substitution matrices (PAM,BLOSUM) - Search-algorithms: dynamic algorithms; Smith-Waterman; Needleman-Wunsch; statistic significance for an alignment (z-score, expectation values and probability); heuristic methods for local alignments; BLAST - Multiple sequence alignments: ClustalW, search on specific databases, other algorithms, PSI-BLAST - Introduction to Structural Bioinformatics: visualization and analysis of protein and nucleic acid 3D structures - Methods to predict protein secondary structure elements starting from the sequence; introduction to neural networks. NN-based methods - Introduction to Systems Biology: Spatial and temporal scales, static and dynamic models, mathematical frameworks, introduction on signal transduction networks Laboratory Module ---------------------------- - NCBI databases: Entrez interface, Gene, UniGene, Protein, Uniprot and EBI - Single and multiple sequence alignments, score matrices, optimal methods; online resources and spreadsheets - BLAST,PSI-BLAST and BLAT: online tools and their use - Tools for multiple alignments, the Homologene databank, computation and visualization of multiple alignments - Introduction to PyMol and molecular visualization. Use of PSI-PRED and JPRED for predicting secondary structures from sequences - Systems biology: numerical simulation of simple biochemical reactions. Building simple kinetic models by using SBOTOOLBOX2 for Matlab; application to G-potein signalling cycles. RECOMMENDED BOOKS ----------------------------------- The main recommended book is: - Stefano Pascarella, Alessandro Paiardini. "Bioinformatica: dalla sequenza alla struttura delle proteine". Ed. Zanichelli The following books are also recommended: - Valle, Helmer Citterich, Attimonelli, Pesole. "Introduzione alla Bioinformatica". Ed. Zanichelli - Tramontano. "Bioinformatica". Ed. Zanichelli -J. Pevsner. "Bioinformatics and Functional Genomics, II edition". Ed. Wiley-Blackwell
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MM: Modulo 2
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Bioinformatic tools for the analysis of molecular evolution and phylogenesis: Molecular clock, substitution models, methods for the construction of phylogenetic trees. Protein structural preditions: Comparative modeling, Fold recognition and ab initio methods. Gene prediction Functional annotation Microarrays: databases and programs for the analysis of expression data. Introduction to the energetic treatment of proteins: MD simulations, ligand-protein and protein-protein docking. Reference Text: Testi di riferimento: Bioinformatica di di Stefano Pascarella, Alessandro Paiardini - Zanichelli The teaching includes: front lectures and hands-on excersices on the PC. The students are also involved in a project to be developed in groups.
Bibliography
Activity | Author | Title | Publishing house | Year | ISBN | Notes |
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Modulo 1 | Stefano Pascarella e Alessandro Paiardini | Bioinformatica | Zanichelli | 2011 | 9788808062192 | |
Modulo 2 | Stefano Pascarella e Alessandro Paiardini | Bioinformatica | Zanichelli | 2011 | 9788808062192 |
Examination Methods
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MM: Modulo 1
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In order to pass the examination, students shall demonstrate: - to understand the concept of homology and its practical implications in bioinformatics - to understand the difference between similarity and identity of biological sequences - to know how to query bioinformatics databases, in order to obtain and store relevant data and to conduct appropriate cross-searches on different databases - to know how to use algorithms for comparison of nucleotide and amino acid sequences - to know how to use software for molecular graphics and visualization - to know how to build simple interaction networks of biomolecules and simulate their time course. Theory -------- The exam consists of a written test with 5 open questions on the topics discussed in the course. Each correct question will score a maximum of 6 points. The test will last 75 minutes. Laboratory ----------------- The exam, which can be given on the same day of the theory part, is made of 3 exercises to be solved using the computer (each one has a maximum 10 points-score). The test will last 75 minutes. Presentations -------------------- At the end of January, groups of 2 or 3 students will present a database of their choice, which has been described in the January issue of Nucleic Acids Research (Database issue). A10 minute presentation (+ 3 minute for questions / discussion) shall be given, illustrating the database goals and an original test-case. Presentation will be given a score of 1 to 4, taking into account the depth of the presented subject, clarity and effectiveness of communication and mastery of the tools used. Final score --------------- The final score, in thirty's (/30), will be given by the average score of the theoretical and laboratory part, plus the score for the presentation.
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MM: Modulo 2
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The written exam is divided in two: a session of open questions regarding the theoretical arguments of the course: modelling, docking and gene annotation. The second phase consists in the preparation of a scientific-like article presenting the results obtained during the project development
Type D and Type F activities
Modules not yet included
Career prospects
Module/Programme news
News for students
There you will find information, resources and services useful during your time at the University (Student’s exam record, your study plan on ESSE3, Distance Learning courses, university email account, office forms, administrative procedures, etc.). You can log into MyUnivr with your GIA login details: only in this way will you be able to receive notification of all the notices from your teachers and your secretariat via email and soon also via the Univr app.
Erasmus+ and other experiences abroad
Graduation
List of theses and work experience proposals
Stage | Research area |
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Correlated mutations | Various topics |
Attendance
As stated in the Teaching Regulations for the A.Y. 2022/2023, attendance at the course of study is not mandatory.
Please refer to the Crisis Unit's latest updates for the mode of teaching.