Study plan | Catalogo dei Corsi di studio

Study plan

Curriculum unico

First year

Orientamento unico
Course		Semester	CFU	SSD	Language
1049371 - Principles of Mathematics	The aim of this course is to give the student sound mathematical basis in calculus of one or several variables, optimization and elementary graph theory in a way appropriate for a student bioinformatics. An emphasis will be given to applications and intuitive understanding of the underlying concepts.	First semester	6
Principles of Mathematics 2		First semester	6	MAT/09
1049372 - Organic and inorganic chemistry	This course is an introduction to chemistry fundamentals addressed to students with limited chemistry background. The purpose of the course is to provide students with the knowledge of general chemistry principles, and with the tools to solve simple chemistry problems. At the end of the course the students are expected to know ho to apply the acquired chemical concepts to different fields, including pharmaceutical chemistry and biochemistry which are the subjects of further courses. The course aims to provide a correct knowledge of the fundamental principles of organic chemistry, proposing the contents into two distinct phases that are closely and logically linked. In the first phase the teaching is addressed to provide basic knowledge about classification and nomenclature of organic compounds, about the symbolism used to represent both structures and reactions, as well as over the chemical-physics, acid-base, nucleophilic-electrophilic properties of the considered compounds. In the second phase the teaching is instead focused on the description of the different reactivity involved by different classes of compounds, rationalizing the study through the analysis of the relevant mechanisms. In the context of the described methodology the objectives to be achieved are: 1) attainment of a suitable degree of specialized knowledge, understood as the ability to invoke theories, rules, nomenclature etc.; 2) capacity to properly interpret and process the reaction schemes and propose alternatives to the encountered syntheses; 3) establish connections between different studied subjects.	First semester	6
Organic and inorganic chemistry 2		First semester	6	CHIM/03
1049251 - Principles of Physics	The Physics course has several distinct aims. First, it aims to full the gap between school and university level physics. Second, it aims to provide a much logical and analytical framework for classical physics, which will be essential for the course. Third, it includes bio-medical themes generally underestimated in basic physics courses. Such topics will be selected among those that will be developed in the subsequent years of the course. Fourth, single lectures aim to broaden the student’s perspectives, so that he can begin to appreciate the great flexibility and generality of the laws of physics and their application in emerging biomedical fields of research.	First semester	6	FIS/07
1049253 - Principles of Computer Science I	The goal of this course is to empower students with those basic programming skills needed to deal with bioinformatics data. More specifically, at the end of the course the students will be able to: - model problems of medium difficulty and solve them by programming; - decompose complex programming problems into simpler problems; - implement well-designed and well-coded software - test and debug programs - analyse programs with respect to their correctness and efficiency - use Python and its libraries These skills are essential in order to analyse bioinformatics data using software libraries and scripts	First semester	6	INF/01
1049373 - Biology of the cell	Students acquire the knowledge and thinking skills necessary to understand biological problems in a evolutionary perspective. The course will provide students with understanding of the basic molecular mechanisms that operate in living cells, with a focus on the flow of genetic information.	First semester	6
Biology of the cell 2		First semester	6	BIO/13
1049371 - Principles of Mathematics	The aim of this course is to give the student sound mathematical basis in calculus of one or several variables, optimization and elementary graph theory in a way appropriate for a student bioinformatics. An emphasis will be given to applications and intuitive understanding of the underlying concepts.	Second semester	6
Principles of Mathematics 1		Second semester	6	MAT/09
1049372 - Organic and inorganic chemistry	This course is an introduction to chemistry fundamentals addressed to students with limited chemistry background. The purpose of the course is to provide students with the knowledge of general chemistry principles, and with the tools to solve simple chemistry problems. At the end of the course the students are expected to know ho to apply the acquired chemical concepts to different fields, including pharmaceutical chemistry and biochemistry which are the subjects of further courses. The course aims to provide a correct knowledge of the fundamental principles of organic chemistry, proposing the contents into two distinct phases that are closely and logically linked. In the first phase the teaching is addressed to provide basic knowledge about classification and nomenclature of organic compounds, about the symbolism used to represent both structures and reactions, as well as over the chemical-physics, acid-base, nucleophilic-electrophilic properties of the considered compounds. In the second phase the teaching is instead focused on the description of the different reactivity involved by different classes of compounds, rationalizing the study through the analysis of the relevant mechanisms. In the context of the described methodology the objectives to be achieved are: 1) attainment of a suitable degree of specialized knowledge, understood as the ability to invoke theories, rules, nomenclature etc.; 2) capacity to properly interpret and process the reaction schemes and propose alternatives to the encountered syntheses; 3) establish connections between different studied subjects.	Second semester	6
Organic and inorganic chemistry 1		Second semester	6	CHIM/06
1049376 - Introduction to biomedical statistics	This course provides an introduction to basic concepts of Statistics and Probability for students in the biosciences.	Second semester	12
Introduction to biomedical statistics 1		Second semester	6	SECS-S/01
Introduction to biomedical statistics 2		Second semester	6	MED/01
1049373 - Biology of the cell	Students acquire the knowledge and thinking skills necessary to understand biological problems in a evolutionary perspective. The course will provide students with understanding of the basic molecular mechanisms that operate in living cells, with a focus on the flow of genetic information.	Second semester	6
Biology of the cell 1		Second semester	6	BIO/13

Second year

Orientamento unico
Course		Semester	CFU	SSD	Language
1052115 - Genetics and computational genomics	The purpose of the course is to provide students with a deep understanding of the theoretical and practical tools to solve genetic problems. Fundamentals concepts in genetics, functioning and evolution will be reconsidered in light of the sequencing and re-sequencing projects. Computational genetics has been an important area of science since the discovery of the first sequencing method and advances in tools and techniques for data generation are rapidly increasing the amount of data available to researchers. During the course, students will learn to rely on computational and data science tools for the storage, management, analysis, and visualization of genetic data.	First semester	6	BIO/18
1049261 - Principles of Computer Science II	The course aim to introduce the algorithmic approach to solving problems correctly and efficiently. Algorithms are ubiquitous in bioinformatics and are often at the interface of computer science and biology. Well established algorithmic techniques will be studied as well as ways to encode them in a computer programme using python.	First semester	6	ING-INF/05
1049256 - Microbiology	To introduce the microbial diversity, the structure/function relationship of prokaryotic cells and viruses, the microbial taxonomy and the basic principles of clinical, environmental and industrial microbiology.	First semester	6	BIO/19
1049375 - Molecular biology	Main goal of the course is to give to the students a general view of the molecular mechanisms which are at the base of the biological processes. For each argument a methodological section will introduce the students to the main technical approaches used at the state of the art. Practical training (2 CFU) will make the students to breath the atmosphere of a molecular biology laboratory. Particular attention will be given to the high throughput methods utilized in “Omic” approaches to the comprehension of biological processes which will be further illustrated in the course of Molecular Biology and Genomics.	First semester	6
Molecular biology 2		First semester	6	BIO/11
1049377 - Biochemistry	MAIN AIMS OF THE II MODULE KNOWLEDGE AND UNDERSTANDING The main goal of the module is to provide students with the necessary tools for a detailed analysis of the structure of proteins and their macromolecular complexes. The first part of the module is dedicated to the understanding of the physico-chemical properties of the amino acids and their interaction within a protein. During the second part of the module, students are challenged with practical sessions on the structural analysis of protein models, also by means of open source software. The module consists of lectures that cover the main topics of the program and practical exercises. Exercises are carried out in a computer room with the use of open source software for the visualization of the tridimensional structure of macromolecules. Beside textbooks, students have access to lectures' slides, scientific articles, and other teaching resources made available trough this web site. APPLYING KNOWLEDGE AND UNDERSTANDING The educational objective of the module is to achieve the necessary knowledge for a critical analysis of the structure of proteins and their interactors. By the end of the module students will have acquired the skills necessary to deal with the analysis and experimental study of biological macromolecules. They will learn how to retrieve the coordinates of macromolecules from the PDB database, recognize the fold and use software for a detailed analysis of their structure. MAKING JUDGEMENTS The module is aimed at increasing the ability to critically analyze the structure of proteins and other macromolecules. COMMUNICATION SKILLS The module includes significant activity of classroom discussion aimed at developing the ability of students to transfer skills acquired in support of their arguments. In the final exam, students must take an oral presentation on the structure and function of an assigned protein. LEARNING SKILLS The many advancements of scientific research, particularly in the field of biochemistry and molecular biology, require a constant updating. For this reason, the module aims to provide the necessary tools to achieve a wider knowledge and to align skills to the advancement in biology and bioinformatics research. Biochemistry 2 – (6 cfu) This module provides an overview of the basic principles of metabolism with emphasis on the structural and regulative aspects. The course will be supported by practical sessions in the computer room available at the Department of Biochemical sciences.	First semester	6
Biochemistry 2		First semester	6	BIO/10
1049260 - Immunology and molecular pathologies		Second semester	6	MED/04
1049375 - Molecular biology	Main goal of the course is to give to the students a general view of the molecular mechanisms which are at the base of the biological processes. For each argument a methodological section will introduce the students to the main technical approaches used at the state of the art. Practical training (2 CFU) will make the students to breath the atmosphere of a molecular biology laboratory. Particular attention will be given to the high throughput methods utilized in “Omic” approaches to the comprehension of biological processes which will be further illustrated in the course of Molecular Biology and Genomics.	Second semester	6
Molecular biology 1		Second semester	6	BIO/11
1049377 - Biochemistry	MAIN AIMS OF THE II MODULE KNOWLEDGE AND UNDERSTANDING The main goal of the module is to provide students with the necessary tools for a detailed analysis of the structure of proteins and their macromolecular complexes. The first part of the module is dedicated to the understanding of the physico-chemical properties of the amino acids and their interaction within a protein. During the second part of the module, students are challenged with practical sessions on the structural analysis of protein models, also by means of open source software. The module consists of lectures that cover the main topics of the program and practical exercises. Exercises are carried out in a computer room with the use of open source software for the visualization of the tridimensional structure of macromolecules. Beside textbooks, students have access to lectures' slides, scientific articles, and other teaching resources made available trough this web site. APPLYING KNOWLEDGE AND UNDERSTANDING The educational objective of the module is to achieve the necessary knowledge for a critical analysis of the structure of proteins and their interactors. By the end of the module students will have acquired the skills necessary to deal with the analysis and experimental study of biological macromolecules. They will learn how to retrieve the coordinates of macromolecules from the PDB database, recognize the fold and use software for a detailed analysis of their structure. MAKING JUDGEMENTS The module is aimed at increasing the ability to critically analyze the structure of proteins and other macromolecules. COMMUNICATION SKILLS The module includes significant activity of classroom discussion aimed at developing the ability of students to transfer skills acquired in support of their arguments. In the final exam, students must take an oral presentation on the structure and function of an assigned protein. LEARNING SKILLS The many advancements of scientific research, particularly in the field of biochemistry and molecular biology, require a constant updating. For this reason, the module aims to provide the necessary tools to achieve a wider knowledge and to align skills to the advancement in biology and bioinformatics research. Biochemistry 2 – (6 cfu) This module provides an overview of the basic principles of metabolism with emphasis on the structural and regulative aspects. The course will be supported by practical sessions in the computer room available at the Department of Biochemical sciences.	Second semester	6
Biochemistry 1		Second semester	6	BIO/10
1055572 - Bioinformatics I		Second semester	6	INF/01
1049264 - Pharmaceutical chemistry	During the course the student will learn the basics to design a drug through computational methods. The aim of the course is to impart an understanding of what medicinal chemists consider when attempting to design new pharmaceuticals. The course is twofold: a theoretical part and practical section. In the first part the course will describe the principles involved in modern drug design and drug discovery, usually with reference to compounds in current clinical usage. In the second part practical sections will be set up to teach the student some computational methods to apply in the drug design process.	Second semester	6	CHIM/08

Third year

Orientamento unico
Course		Semester	CFU	SSD	Language
1049266 - Bioinformatics II	The course aims to provide some bioinformatics tools to analyze and visualize data produce from next generation sequencing technologies. In particular the attendee will be to perform differential expression analysis of RNA-sequencing data and then integrate the results with other data coming from high-throughput technologies	First semester	6	ING-INF/06
1049265 - Bioethics	The course will introduce to the main historical and theoretical knowledge needed to understand the cultural and political relevance that in the western and democratic societies has taken the reflection on the ethical dimensions of biological and medical research. The course objectives are to provide students with the cognitive tools to understand the terms of the discussions on the various controversial bioethical issues, and to enable him to develop a personal and critical view on the various issues addressed in the lessons.	First semester	6	MED/02
1049258 - Molecular biology and genomics	The new generation of sequencing technologies offered extraordinary opportunities for high-throughput functional genomic studies. These tools have been applied in a variety of contexts, including whole-genome sequencing, discovery of transcription factor binding loci, mapping out DNA accessibility and RNA expression profiling. Intriguingly, recent efforts in annotation led to the discovery of novel noncoding RNA genes that control temporal and/or spatial gene expression along cell differentiation. Aim of the course is the integration of the knowledge of the modern molecular biology with high-throughput technologies. Besides RNA metabolism and noncoding content, the course will introduce NGS technologies, highlight different applications of these new tools and show ways to analyse data in the context of completed genome sequences of different model organisms. The course will also feature methods to assist the study and the prioritization of gene lists from large-scale gene expression data.	First semester	6	BIO/11
AAF1749 - For the final test	The final exams consists of writing, presenting and discussing a thesis, developed autonomously by the students, which illustrates in a coherent and detailed manner the problem tackled during the practical training and all the activities carried out to develop its solution.	Second semester	9
AAF1750 - Further linguistic knowledge		Second semester	3
AAF1752 - Stages and professional training	Acquisition of manual, methodological and organizational skills aimed at the elaboration of technical-scientific issues.	Second semester	3
AAF1753 - Other knowledge useful for entering into the work market	Basic training in laboratorytechniques aimed to improve professionalization.	Second semester	3
- Elective course		Second semester	12
Gruppo OPZIONALE		Go to group

Optional Groups

**Gruppo OPZIONALE: The student must acquire 12 CFU from the exams below**
Course		Year	Semester	CFU	SSD	Language
1049267 - Modelling and simulation of biomolecular dynamical systems	This course aims to provide students with a practical and hands-on experience with common modeling and simulation tools in molecular biology. It would be expected that after completing this course a student would be able to model and simulate using Matlab a biomolecular systems like, for example, a gene regulatory network using the appropriate methodology. Further, students will understand the basic theory behind these modeling tecniques and critically analyze the results of their analysis.	Third year	First semester	6	ING-INF/06
1049268 - Signal processing and information theory		Third year	First semester	6	ING-INF/03
1049269 - Algorithms	this course is an introduction to algorithms with special emphasis given to those algorithmic problems and techniques that have the greatest impact for bioinformatics.	Third year	First semester	6	INF/01
1049270 - Complex biomolecular networks	The course aims to provide basics concepts and tools for complex networks analysis. The attendee will be able to apply complex networks concepts to biological networks and explore the underlying process and molecular related issues.	Third year	First semester	6	ING-INF/05
1049271 - Plant functional genomics	The aim of the course is to provide a theoretical knowledge of plant genomes, and practical explanation of the techniques used in plant functional genomics, i.e. a large-scale analysis of the function of the different gene products to understand how the genome generates the phenotype of the plant. Insights will be given into the new information that will be generated from whole genome-/proteome-/metabolome analysis. The course will cover the following concepts: array and sequencing based methods; reverse and forward genetics; comparison of plant genomes; epigenomics; proteomics and metabolomics. Also covered are robotization, miniaturization (single-cell studies) and high-throughput-screenings. Finally, the course will introduce methods for visualization and analysis of high-density data.	Third year	First semester	6	BIO/04
1049272 - Principles of general pathology		Third year	First semester	6	MED/46
1049273 - Optimization methods for computational biology	We aim to introduce students to the analysis of decision problems that arise in bioinformatics and health management. Students would be able to: model as mathematical programming problem to be used as a support to the decision maker, use algorithm suitable to each model for the solution, make post-optimality analysis.	Third year	First semester	6	MAT/09
1049285 - Bioinformatics in plant pathology	Recent advances in -omics technology, namely genomics, proteomics and metabolomics allow to go deeper into the understanding of the subtle mechanism underlying host-pathogen interactions. This is made possible by next generation sequencers that uncover entire genome or exome of host and pathogens while interacting, skipping complicate procedures for separating the two challengers. Moreover, we are moving faster in re-shaping plant pathology from the one disease-one pathogen dogma, as embodied in Koch's postulate, to the pathobiome concept. Meta-omic tools shed light on the inter-reign network originating the disease of the host in its complexity. The analysis and understanding of the huge amount of data generated by a single experiment represents currently the classical bottleneck. In relation to this, bioinformatics plays a crucial role in data capture, analysis and integration. Plant pathologists have to answer to very concrete and problematic question, today, more, and more in the next future: food security, food safety and food quality. Actually, plant disease burden current food production, accounting for more than 40% of food losses. Climate change and globalization enhance pathogens ability and mobility worldwide. Nevertheless, for environmental as well as political reasons, pathogens cannot be controlled anymore by using pesticides and/or GMO plants. A more sustainable, "green" and integrated pest management is needed. A modern plant pathologist has to face this complex reality, plan experiments at real scale, "sucks the marrow out of -omics" (par. Walt Whitman) by using bioinformatics tools, individuate biocontrol agents and stimulate plant self-defences. In relation to this, the main aim of this course is forming young scientists in managing plant diseases tout court by the mean of the -omics plus bioinformatics tools.	Third year	First semester	6	AGR/12
1049267 - Modelling and simulation of biomolecular dynamical systems	This course aims to provide students with a practical and hands-on experience with common modeling and simulation tools in molecular biology. It would be expected that after completing this course a student would be able to model and simulate using Matlab a biomolecular systems like, for example, a gene regulatory network using the appropriate methodology. Further, students will understand the basic theory behind these modeling tecniques and critically analyze the results of their analysis.	Third year	Second semester	6	ING-INF/06
1049268 - Signal processing and information theory		Third year	Second semester	6	ING-INF/03
1049269 - Algorithms	this course is an introduction to algorithms with special emphasis given to those algorithmic problems and techniques that have the greatest impact for bioinformatics.	Third year	Second semester	6	INF/01
1049270 - Complex biomolecular networks	The course aims to provide basics concepts and tools for complex networks analysis. The attendee will be able to apply complex networks concepts to biological networks and explore the underlying process and molecular related issues.	Third year	Second semester	6	ING-INF/05
1049271 - Plant functional genomics	The aim of the course is to provide a theoretical knowledge of plant genomes, and practical explanation of the techniques used in plant functional genomics, i.e. a large-scale analysis of the function of the different gene products to understand how the genome generates the phenotype of the plant. Insights will be given into the new information that will be generated from whole genome-/proteome-/metabolome analysis. The course will cover the following concepts: array and sequencing based methods; reverse and forward genetics; comparison of plant genomes; epigenomics; proteomics and metabolomics. Also covered are robotization, miniaturization (single-cell studies) and high-throughput-screenings. Finally, the course will introduce methods for visualization and analysis of high-density data.	Third year	Second semester	6	BIO/04
1049272 - Principles of general pathology		Third year	Second semester	6	MED/46
1049273 - Optimization methods for computational biology	We aim to introduce students to the analysis of decision problems that arise in bioinformatics and health management. Students would be able to: model as mathematical programming problem to be used as a support to the decision maker, use algorithm suitable to each model for the solution, make post-optimality analysis.	Third year	Second semester	6	MAT/09
1049285 - Bioinformatics in plant pathology	Recent advances in -omics technology, namely genomics, proteomics and metabolomics allow to go deeper into the understanding of the subtle mechanism underlying host-pathogen interactions. This is made possible by next generation sequencers that uncover entire genome or exome of host and pathogens while interacting, skipping complicate procedures for separating the two challengers. Moreover, we are moving faster in re-shaping plant pathology from the one disease-one pathogen dogma, as embodied in Koch's postulate, to the pathobiome concept. Meta-omic tools shed light on the inter-reign network originating the disease of the host in its complexity. The analysis and understanding of the huge amount of data generated by a single experiment represents currently the classical bottleneck. In relation to this, bioinformatics plays a crucial role in data capture, analysis and integration. Plant pathologists have to answer to very concrete and problematic question, today, more, and more in the next future: food security, food safety and food quality. Actually, plant disease burden current food production, accounting for more than 40% of food losses. Climate change and globalization enhance pathogens ability and mobility worldwide. Nevertheless, for environmental as well as political reasons, pathogens cannot be controlled anymore by using pesticides and/or GMO plants. A more sustainable, "green" and integrated pest management is needed. A modern plant pathologist has to face this complex reality, plan experiments at real scale, "sucks the marrow out of -omics" (par. Walt Whitman) by using bioinformatics tools, individuate biocontrol agents and stimulate plant self-defences. In relation to this, the main aim of this course is forming young scientists in managing plant diseases tout court by the mean of the -omics plus bioinformatics tools.	Third year	Second semester	6	AGR/12

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