Bioinformatics - Bioinformatica

Obiettivi formativi

Principles of mathematics 1:
The aim of this course is to give the student sound mathematical basis in calculus of one or several variables and optimization in a way appropriate for a student of bioinformatics. An emphasis is given to applications and intuitive understanding of the underlying concepts. The first semester (Principles of Mathematics 1) will be devoted mainly to the study of functions of one variables, including limits, derivative and integrals. Basic optimisation results for functions of one variable will also be considered

Knowledge and understanding

The aim of the course is to give students a basic

understanding of calculus in a way appropriate to bioinformatics students. Students will also be exposed to mathematics proofs as an example of rigorous scientific reasoning.

Applying knowledge and understanding

By the end of the course, students will be able to use basic mathematical tools as applied to different environments. They will also be able to interpret in a critical way

results obtained by applying mathematical modelling technique.

Making judgements

Lectures and practical exercises will provide students with the basic ability in

assessing the main strengths and weaknesses of mathematical models when used to explain empirical evidence.

Communication

By the end of the course, students will have basic mathematical skills that will help them to talk in an appropriate way about quantitative models.

Lifelong learning skills

Students are expected to develop learning skills necessary to undertake additional and more advanced studies involving mathematics and mathematical modelling in biology.

Principles of Mathematics 2:

The aim of this course is to give the student sound mathematical basis in calculus of one or several variables and optimization in a way appropriate for a student of bioinformatics. An emphasis is given to applications and intuitive understanding of the underlying concepts. The second semester (Principles of Mathematics 2) will be devoted mainly to the study of functions of several variables, linear algebra, and differential equations. Basic optimization results for functions of several variables will also be considered.

Knowledge and understanding

The aim of the course is to give students a basic

understanding of calculus in a way appropriate to bioinformatics students. Students will also be exposed to mathematics proofs as an example of rigorous scientific reasoning.

Applying knowledge and understanding

By the end of the course, students will be able to use basic mathematical tools as applied to different environments. They will also be able to interpret in a critical way

results obtained by applying mathematical modelling technique.

Making judgements

Lectures and practical exercises will provide students with the basic ability in

assessing the main strengths and weaknesses of mathematical models when used to explain empirical evidence.

Communication

By the end of the course, students will have basic mathematical skills that will help them to talk in an appropriate way about quantitative models.

Lifelong learning skills

Students are expected to develop learning skills necessary to undertake additional and more advanced studies involving mathematics and mathematical modelling in biology.

Obiettivi formativi

Principles of mathematics 1:
The aim of this course is to give the student sound mathematical basis in calculus of one or several variables and optimization in a way appropriate for a student of bioinformatics. An emphasis is given to applications and intuitive understanding of the underlying concepts. The first semester (Principles of Mathematics 1) will be devoted mainly to the study of functions of one variables, including limits, derivative and integrals. Basic optimisation results for functions of one variable will also be considered

Knowledge and understanding

The aim of the course is to give students a basic

understanding of calculus in a way appropriate to bioinformatics students. Students will also be exposed to mathematics proofs as an example of rigorous scientific reasoning.

Applying knowledge and understanding

By the end of the course, students will be able to use basic mathematical tools as applied to different environments. They will also be able to interpret in a critical way

results obtained by applying mathematical modelling technique.

Making judgements

Lectures and practical exercises will provide students with the basic ability in

assessing the main strengths and weaknesses of mathematical models when used to explain empirical evidence.

Communication

By the end of the course, students will have basic mathematical skills that will help them to talk in an appropriate way about quantitative models.

Lifelong learning skills

Students are expected to develop learning skills necessary to undertake additional and more advanced studies involving mathematics and mathematical modelling in biology.

Principles of Mathematics 2:

The aim of this course is to give the student sound mathematical basis in calculus of one or several variables and optimization in a way appropriate for a student of bioinformatics. An emphasis is given to applications and intuitive understanding of the underlying concepts. The second semester (Principles of Mathematics 2) will be devoted mainly to the study of functions of several variables, linear algebra, and differential equations. Basic optimization results for functions of several variables will also be considered.

Knowledge and understanding

The aim of the course is to give students a basic

understanding of calculus in a way appropriate to bioinformatics students. Students will also be exposed to mathematics proofs as an example of rigorous scientific reasoning.

Applying knowledge and understanding

By the end of the course, students will be able to use basic mathematical tools as applied to different environments. They will also be able to interpret in a critical way

results obtained by applying mathematical modelling technique.

Making judgements

Lectures and practical exercises will provide students with the basic ability in

assessing the main strengths and weaknesses of mathematical models when used to explain empirical evidence.

Communication

By the end of the course, students will have basic mathematical skills that will help them to talk in an appropriate way about quantitative models.

Lifelong learning skills

Students are expected to develop learning skills necessary to undertake additional and more advanced studies involving mathematics and mathematical modelling in biology.

Obiettivi formativi

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.

Obiettivi formativi

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.

Obiettivi formativi

The goal of this course is to teach students the basic programming skills needed to deal with bioinformatics data. 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;
- design and implement programs;
- test programs;
- analyze programs in terms of their correctness and efficiency;
- use Python and its libraries.

Obiettivi formativi

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.

Obiettivi formativi

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.

Obiettivi formativi

A - Knowledge and understanding
OF 1) Possess a basic knowledge of physical phenomena that play an important role in biology, medicine and other fields related to bionformatics.
OF 2) Knowledge of the main units and of the laws that describe the physical phenomena that are object of the course.
B - Application skills
OF 3) Being able to place a physical phenomenon in a correct conceptual framework.
OF 4) Being able to use the notions acquired to face and solve simple theoretical and numerical problems.
C - Autonomy of judgment
OF 5) Being able to synthesize the studied phenomenologies in order to be able to formulate pertinent and relevant questions.
D - Communication skills
OF 6) Knowing how to organize a coherent presentation of the phenomena studied.
E - Ability to learn
OF 7) Being able to consult with sufficient authonomy both textbooks and scientific articles

Obiettivi formativi

Principles of mathematics 1:
The aim of this course is to give the student sound mathematical basis in calculus of one or several variables and optimization in a way appropriate for a student of bioinformatics. An emphasis is given to applications and intuitive understanding of the underlying concepts. The first semester (Principles of Mathematics 1) will be devoted mainly to the study of functions of one variables, including limits, derivative and integrals. Basic optimisation results for functions of one variable will also be considered

Knowledge and understanding

The aim of the course is to give students a basic

understanding of calculus in a way appropriate to bioinformatics students. Students will also be exposed to mathematics proofs as an example of rigorous scientific reasoning.

Applying knowledge and understanding

By the end of the course, students will be able to use basic mathematical tools as applied to different environments. They will also be able to interpret in a critical way

results obtained by applying mathematical modelling technique.

Making judgements

Lectures and practical exercises will provide students with the basic ability in

assessing the main strengths and weaknesses of mathematical models when used to explain empirical evidence.

Communication

By the end of the course, students will have basic mathematical skills that will help them to talk in an appropriate way about quantitative models.

Lifelong learning skills

Students are expected to develop learning skills necessary to undertake additional and more advanced studies involving mathematics and mathematical modelling in biology.

Principles of Mathematics 2:

The aim of this course is to give the student sound mathematical basis in calculus of one or several variables and optimization in a way appropriate for a student of bioinformatics. An emphasis is given to applications and intuitive understanding of the underlying concepts. The second semester (Principles of Mathematics 2) will be devoted mainly to the study of functions of several variables, linear algebra, and differential equations. Basic optimization results for functions of several variables will also be considered.

Knowledge and understanding

The aim of the course is to give students a basic

understanding of calculus in a way appropriate to bioinformatics students. Students will also be exposed to mathematics proofs as an example of rigorous scientific reasoning.

Applying knowledge and understanding

By the end of the course, students will be able to use basic mathematical tools as applied to different environments. They will also be able to interpret in a critical way

results obtained by applying mathematical modelling technique.

Making judgements

Lectures and practical exercises will provide students with the basic ability in

assessing the main strengths and weaknesses of mathematical models when used to explain empirical evidence.

Communication

By the end of the course, students will have basic mathematical skills that will help them to talk in an appropriate way about quantitative models.

Lifelong learning skills

Students are expected to develop learning skills necessary to undertake additional and more advanced studies involving mathematics and mathematical modelling in biology.

Obiettivi formativi

Principles of mathematics 1:
The aim of this course is to give the student sound mathematical basis in calculus of one or several variables and optimization in a way appropriate for a student of bioinformatics. An emphasis is given to applications and intuitive understanding of the underlying concepts. The first semester (Principles of Mathematics 1) will be devoted mainly to the study of functions of one variables, including limits, derivative and integrals. Basic optimisation results for functions of one variable will also be considered

Knowledge and understanding

The aim of the course is to give students a basic

understanding of calculus in a way appropriate to bioinformatics students. Students will also be exposed to mathematics proofs as an example of rigorous scientific reasoning.

Applying knowledge and understanding

By the end of the course, students will be able to use basic mathematical tools as applied to different environments. They will also be able to interpret in a critical way

results obtained by applying mathematical modelling technique.

Making judgements

Lectures and practical exercises will provide students with the basic ability in

assessing the main strengths and weaknesses of mathematical models when used to explain empirical evidence.

Communication

By the end of the course, students will have basic mathematical skills that will help them to talk in an appropriate way about quantitative models.

Lifelong learning skills

Students are expected to develop learning skills necessary to undertake additional and more advanced studies involving mathematics and mathematical modelling in biology.

Principles of Mathematics 2:

The aim of this course is to give the student sound mathematical basis in calculus of one or several variables and optimization in a way appropriate for a student of bioinformatics. An emphasis is given to applications and intuitive understanding of the underlying concepts. The second semester (Principles of Mathematics 2) will be devoted mainly to the study of functions of several variables, linear algebra, and differential equations. Basic optimization results for functions of several variables will also be considered.

Knowledge and understanding

The aim of the course is to give students a basic

understanding of calculus in a way appropriate to bioinformatics students. Students will also be exposed to mathematics proofs as an example of rigorous scientific reasoning.

Applying knowledge and understanding

By the end of the course, students will be able to use basic mathematical tools as applied to different environments. They will also be able to interpret in a critical way

results obtained by applying mathematical modelling technique.

Making judgements

Lectures and practical exercises will provide students with the basic ability in

assessing the main strengths and weaknesses of mathematical models when used to explain empirical evidence.

Communication

By the end of the course, students will have basic mathematical skills that will help them to talk in an appropriate way about quantitative models.

Lifelong learning skills

Students are expected to develop learning skills necessary to undertake additional and more advanced studies involving mathematics and mathematical modelling in biology.

Obiettivi formativi

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.

Obiettivi formativi

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.

Obiettivi formativi

Obiettivi formativi
Obiettivo formativo dell’insegnamento è l'apprendimento da parte degli studenti dei fondamenti del calcolo delle probabilità e della statistica.

Conoscenza e capacità di comprensione
Alla fine del corso gli studenti conoscono e comprendono come formalizzare l’incertezza, descrivere quantitativamente le caratteristiche di una popolazione e come fare inferenza su parametri non noti.

Capacità di applicare conoscenza e comprensione
Gli studenti apprendono come impostare un problema di probabilità o statistica.

Autonomia di giudizio
La discussione dei vari metodi fornisce agli studenti le capacità necessarie per analizzare criticamente, ed in autonomia, situazioni reali.

Abilità comunicativa
Gli studenti acquisiscono gli elementi di base per ragionare, e far ragionare, in termini quantitativi su problemi di incertezza e statistica.

Capacità di apprendimento
Gli studenti che superano l’esame sono in grado di applicare i metodi appresi in diversi contesti applicativi.

Obiettivi formativi

Obiettivi formativi
Obiettivo formativo dell’insegnamento è l'apprendimento da parte degli studenti dei fondamenti del calcolo delle probabilità e della statistica.

Conoscenza e capacità di comprensione
Alla fine del corso gli studenti conoscono e comprendono come formalizzare l’incertezza, descrivere quantitativamente le caratteristiche di una popolazione e come fare inferenza su parametri non noti.

Capacità di applicare conoscenza e comprensione
Gli studenti apprendono come impostare un problema di probabilità o statistica.

Autonomia di giudizio
La discussione dei vari metodi fornisce agli studenti le capacità necessarie per analizzare criticamente, ed in autonomia, situazioni reali.

Abilità comunicativa
Gli studenti acquisiscono gli elementi di base per ragionare, e far ragionare, in termini quantitativi su problemi di incertezza e statistica.

Capacità di apprendimento
Gli studenti che superano l’esame sono in grado di applicare i metodi appresi in diversi contesti applicativi.

Obiettivi formativi

The course has the objective to deepen the practical understanding of the use of probability and statistics in the context of epidemiological/biomedical research.

In particular the students will learn the differences between the main epidemiological study designs, suitable measures of treatment/exposure effect , the concepts of bias, variability, confounding and causality in epidemiology. They will also learn the concept and application of linear regression and have an introduction to logistic regression. Furthermore they will learn how to manage data and apply statistical methods using the software Stata.

Obiettivi formativi

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.

Obiettivi formativi

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.

Obiettivi formativi

General skills
The course of Genetics and computational genomics provides students with a basic knowledge of Genetics aimed at understanding the rules of inheritance, their molecular bases, their main applications and their implications for evolution. In addition, the course will allow students to understand how genetic information is encoded at the DNA level and how it contribute to phenotypic variability. Fundamentals concepts in functional genetics and evolution will be reconsidered in light of the sequencing and re-sequencing projects. The student will be also provided of practical and theoretical tools to solve genetic problems and to use databases for storage, management, analysis, and visualization of genetic data.

Specific skills

A) Knowledge and understanding
-Knowledge and understanding of the characteristics of the genetic material
-Knowledge and understanding of the rules of genetic transmission
-Knowledge and understanding of mutations and their implications
-Basic knowledge on the dynamics of genes in populations as well as on the genetic mechanisms underlying evolution
- Knowledge and understanding of informatic methods used for genomic analyses

B) Applying knowledge and understanding
- Usage of a proper genetic terminology
- Identification of the right procedures to solve genetic problems
- Formulation of hypotheses on the hereditary transmission of characters
- Constructing and interpreting genetic maps and genealogical trees
- Acquisition of conceptual tools for the genetic dissection of biological systems
- Management of genomic browsers and programs for storage, management analysis, and visualization of “big data”

C) Making judgements
- Acquisition of a critical judgment capacity on solving problems of formal genetics, through the study of the evolution of the gene concept from Mendel to the present day and the detailed analysis of some fundamental experiments
- Addressing questions for the elaboration and deepening of the gained information

D) Communication skills
- Communicating the genetic concepts acquired during the course with appropriate terminology

E) Learning skills
- Logically connecting the acquired knowledge
- Identification of the most relevant topics of the issues discussed during the course

Obiettivi formativi

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.

Obiettivi formativi

Microorganisms play a key role in the environment, in human health and in biotechnological research. The course of Microbiology aims to provide the basic principles of structure, function and evolution of microbial cells, with particular regard to bacterial cells.
The knowledge and skills acquired during this course will represent a framework for the study of bioinformatics and biotechnological applications of microorganisms, and for the analysis of their impact on human health and the environment.

Students who have passed the exam will know and understand (acquired knowledge)

- The structural and functional diversity which is present in the microbial world;
- The mechanisms responsible for the structure and functioning of bacterial cells;
- The mechanisms responsible for the evolution of bacterial species;
- The structure and life cycles of viruses;
- The methods and strategies for the control of microbial growth.

Students who have passed the exam will be able to (acquired skills):
- Understand and analyse microbiological data;
- Critically analyze the issues related to the evolution and diffusion of multi-resistant antibiotic bacteria;
- Understand and design experimental and bioinformatics approaches for the study and exploitation of bacteria for biotechnological and environmental purposes;
- Identify and develop key themes to build educational paths in microbiology.

Obiettivi formativi

General goals
The course aims to introduce the students to the links between DNA, RNA and protein structure and their relevant biological functions with particular emphasis on the bioinformatic approaches to their analysis.
Specific goals:
1. Knowledge and comprehension: the students will have to know the molecular mechanisms which regulate cellular homeostasis and gene expression and the most utilized methodologies in Molecular Biology.
2. Ability in applying Knowledge and comprehension: the students will have to be able to apply this knowledge in the discussion of specific arguments of recent and general interest with a particular focus on the bioinformatic approaches.
3. Abilities in judging methodologic approaches and communication skill: The students will have to show skills in judging strategies in biological problems solving and to communicate their conclusions to the teacher and to the colleagues. This is also applicable to the practical training sessions.
4. The students will have to show skill in applying what they have learned in molecular biology to specific problems to be solved with a bioinformatic approach.

Obiettivi formativi

General goals
The course aims to introduce the students to the links between DNA, RNA and protein structure and their relevant biological functions with particular emphasis on the bioinformatic approaches to their analysis.

Specific goals
1. Knowledge and comprehension: the students will have to know the molecular mechanisms which regulate cellular homeostasis and gene expression and the most utilized methodologies in Molecular Biology.
2. Ability in applying Knowledge and comprehension: the students will have to be able to apply this knowledge in the discussion of specific arguments of recent and general interest with a particular focus on the bioinformatic approaches.
3. Abilities in judging methodologic approaches and communication skill: The students will have to show skills in judging strategies in biological problems solving and to communicate their conclusions to the teacher and to the colleagues. This is also applicable to the practical training sessions.
4. The students will have to show skill in applying what they have learned in molecular biology to specific problems to be solved with a bioinformatic approach.

Obiettivi formativi

KNOWLEDGE AND UNDERSTANDING
The students will acquire the knowledge necessary for the understanding of the structures and functions of the living matter in molecular terms. Structures and functions of proteins, lipids, phospholipids. Structure-function relationship of protein and folding. Fibrous and globular proteins. Antibodies and their applications in analytical biochemistry. Importance of kinetics and thermodynamics in biochemistry. Biological membranes and transport systems. Mechanisms of enzymic reactions, Michaelis-Menten kinetics. The most important metabolic pathways of carbohydrates, lipids, fatty acids and amino acids. Mechanisms of regulation of metabolic pathways, production and conservation of energy. Connections between the metabolic pathways. Some aspects of the forefront research in biochemistry and, in particular, in metabolomic research, will also be illustrated, supported by advanced textbooks and scientific articles.

APPLYING KNOWLEDGE AND UNDERSTANDING

The students will gain an insight into the relevance of the knowledge of biochemistry for pharmaceutical chemistry, biotechnology and, in particular, metabolomic research applied to human health. The knowledge acquired during the lectures will be consolidated by exercises regarding the single topics. Also, examples of problems which can be solved only by applying the knowledge on the enzymic mechanisms, metabolic pathways and their connections, will be proposed. The students will be encouraged to tackle the problems and to put forward the ideas on the possible solutions. The importance of the constant updating on the progress in the research will also be highlighted.
MAKING JUDGEMENTS
The knowledge and the understanding of the single topics will be consolidated through discussions regarding the conceptual and methodological approaches used in the studies on the metabolic reactions and on the connections among the metabolic pathways. The students will be encouraged to apply the acquired knowledge to new problems.
The discussions on the topics regarding the programme, presented in an interdisciplinary framework, together with the acquired knowledge, will help to develop the ability to make autonomous judgements, to gather and interpret relevant data regarding issues in biochemistry. In particular, examples of metabolomic research will be presented and the students will be encouraged to tackle the problems and put forward the ideas on the possible solutions.

COMMUNICATION

The knowledge of the biochemical bases of biological processes oriented towards applications in medicine and pharmaceutical research and framed in an interdisciplinary context, as well as the correct use of the biochemical terminology, contributes to develop the ability to communicate with specialist and nonspecialist interlocutors.

LEARNING SKILLS

The knowledge of the fundamentals of biochemistry and the ability to interpret the data, as well as the insight gained into the strategies of biochemical research, will enable the students to develop those skills needed to undertake further studies requiring a higher level of autonomy, such as the Master degree

Obiettivi formativi

KNOWLEDGE AND UNDERSTANDING
The students will acquire the knowledge necessary for the understanding of the structures and functions of the living matter in molecular terms. Structures and functions of proteins, lipids, phospholipids. Structure-function relationship of protein and folding. Fibrous and globular proteins. Antibodies and their applications in analytical biochemistry. Importance of kinetics and thermodynamics in biochemistry. Biological membranes and transport systems. Mechanisms of enzymic reactions, Michaelis-Menten kinetics. The most important metabolic pathways of carbohydrates, lipids, fatty acids and amino acids. Mechanisms of regulation of metabolic pathways, production and conservation of energy. Connections between the metabolic pathways. Some aspects of the forefront research in biochemistry and, in particular, in metabolomic research, will also be illustrated, supported by advanced textbooks and scientific articles.

APPLYING KNOWLEDGE AND UNDERSTANDING

The students will gain an insight into the relevance of the knowledge of biochemistry for pharmaceutical chemistry, biotechnology and, in particular, metabolomic research applied to human health. The knowledge acquired during the lectures will be consolidated by exercises regarding the single topics. Also, examples of problems which can be solved only by applying the knowledge on the enzymic mechanisms, metabolic pathways and their connections, will be proposed. The students will be encouraged to tackle the problems and to put forward the ideas on the possible solutions. The importance of the constant updating on the progress in the research will also be highlighted.
MAKING JUDGEMENTS
The knowledge and the understanding of the single topics will be consolidated through discussions regarding the conceptual and methodological approaches used in the studies on the metabolic reactions and on the connections among the metabolic pathways. The students will be encouraged to apply the acquired knowledge to new problems.
The discussions on the topics regarding the programme, presented in an interdisciplinary framework, together with the acquired knowledge, will help to develop the ability to make autonomous judgements, to gather and interpret relevant data regarding issues in biochemistry. In particular, examples of metabolomic research will be presented and the students will be encouraged to tackle the problems and put forward the ideas on the possible solutions.

COMMUNICATION

The knowledge of the biochemical bases of biological processes oriented towards applications in medicine and pharmaceutical research and framed in an interdisciplinary context, as well as the correct use of the biochemical terminology, contributes to develop the ability to communicate with specialist and nonspecialist interlocutors.

LEARNING SKILLS

The knowledge of the fundamentals of biochemistry and the ability to interpret the data, as well as the insight gained into the strategies of biochemical research, will enable the students to develop those skills needed to undertake further studies requiring a higher level of autonomy, such as the Master degree

Obiettivi formativi

Learning results
This course is aimed at providing an overview of the most important cellular and molecular mechanisms involved in the regulation of the immune response. The factors regulating immune system will be put in relation to the molecular mechanisms governing resistance against pathogens and promoting pathologies related to a defective immune response.
Specific aims
Student will acquire fundamental knowledge on
- how immune cells function and interplay to participate to immune responses
- how immune system protects us from pathogens and how mechanisms that inhibit immune responses lead to disease state.
- how interpretation of transcriptomic and proteomic data helps to elucidate mechanisms of development of the immune response.
At the end of the course, students will be able to explain how immune system works and to understand and explain data obtained from multiparametric analysis of immune cell function at transcriptional and post-transcriptional levels. The use of bioinformatics tools to clarify the molecular processes underlying pathologies and their use in diagnosis and treatment of diseases will be discussed.
At the end of the course, students will be able to perform bibliographic searches in public scientific data banks (i.e. PubMed) to develop the topics covered in the course. This will be instrumental to identify the most recent methods of bioinformatic analysis used to approach immunology issues. The independent ability of the student to propose solutions to solve immunological questions is and aim of the course.
Communication skills will be verified during the course by stimulating discussion and implemented by suggestions and the critical analysis of the slides presented during the course

Obiettivi formativi

General goals
The course aims to introduce the students to the links between DNA, RNA and protein structure and their relevant biological functions with particular emphasis on the bioinformatic approaches to their analysis.
Specific goals:
1. Knowledge and comprehension: the students will have to know the molecular mechanisms which regulate cellular homeostasis and gene expression and the most utilized methodologies in Molecular Biology.
2. Ability in applying Knowledge and comprehension: the students will have to be able to apply this knowledge in the discussion of specific arguments of recent and general interest with a particular focus on the bioinformatic approaches.
3. Abilities in judging methodologic approaches and communication skill: The students will have to show skills in judging strategies in biological problems solving and to communicate their conclusions to the teacher and to the colleagues. This is also applicable to the practical training sessions.
4. The students will have to show skill in applying what they have learned in molecular biology to specific problems to be solved with a bioinformatic approach.

Obiettivi formativi

General goals
The course aims to introduce the students to the links between DNA, RNA and protein structure and their relevant biological functions with particular emphasis on the bioinformatic approaches to their analysis.
Specific goals:
1. Knowledge and comprehension: the students will have to know the molecular mechanisms which regulate cellular homeostasis and gene expression and the most utilized methodologies in Molecular Biology.
2. Ability in applying Knowledge and comprehension: the students will have to be able to apply this knowledge in the discussion of specific arguments of recent and general interest with a particular focus on the bioinformatic approaches.
3. Abilities in judging methodologic approaches and communication skill: The students will have to show skills in judging strategies in biological problems solving and to communicate their conclusions to the teacher and to the colleagues. This is also applicable to the practical training sessions.
4. The students will have to show skill in applying what they have learned in molecular biology to specific problems to be solved with a bioinformatic approach.

Obiettivi formativi

KNOWLEDGE AND UNDERSTANDING
The students will acquire the knowledge necessary for the understanding of the structures and functions of the living matter in molecular terms. Structures and functions of proteins, lipids, phospholipids. Structure-function relationship of protein and folding. Fibrous and globular proteins. Antibodies and their applications in analytical biochemistry. Importance of kinetics and thermodynamics in biochemistry. Biological membranes and transport systems. Mechanisms of enzymic reactions, Michaelis-Menten kinetics. The most important metabolic pathways of carbohydrates, lipids, fatty acids and amino acids. Mechanisms of regulation of metabolic pathways, production and conservation of energy. Connections between the metabolic pathways. Some aspects of the forefront research in biochemistry and, in particular, in metabolomic research, will also be illustrated, supported by advanced textbooks and scientific articles.

APPLYING KNOWLEDGE AND UNDERSTANDING

The students will gain an insight into the relevance of the knowledge of biochemistry for pharmaceutical chemistry, biotechnology and, in particular, metabolomic research applied to human health. The knowledge acquired during the lectures will be consolidated by exercises regarding the single topics. Also, examples of problems which can be solved only by applying the knowledge on the enzymic mechanisms, metabolic pathways and their connections, will be proposed. The students will be encouraged to tackle the problems and to put forward the ideas on the possible solutions. The importance of the constant updating on the progress in the research will also be highlighted.
MAKING JUDGEMENTS
The knowledge and the understanding of the single topics will be consolidated through discussions regarding the conceptual and methodological approaches used in the studies on the metabolic reactions and on the connections among the metabolic pathways. The students will be encouraged to apply the acquired knowledge to new problems.
The discussions on the topics regarding the programme, presented in an interdisciplinary framework, together with the acquired knowledge, will help to develop the ability to make autonomous judgements, to gather and interpret relevant data regarding issues in biochemistry. In particular, examples of metabolomic research will be presented and the students will be encouraged to tackle the problems and put forward the ideas on the possible solutions.

COMMUNICATION

The knowledge of the biochemical bases of biological processes oriented towards applications in medicine and pharmaceutical research and framed in an interdisciplinary context, as well as the correct use of the biochemical terminology, contributes to develop the ability to communicate with specialist and nonspecialist interlocutors.

LEARNING SKILLS

The knowledge of the fundamentals of biochemistry and the ability to interpret the data, as well as the insight gained into the strategies of biochemical research, will enable the students to develop those skills needed to undertake further studies requiring a higher level of autonomy, such as the Master degree

Obiettivi formativi

Educational aims
i.e what is the purpose of the course and general statements about the learning that
takes place over the duration of the course

1. To give students a good understanding of the major areas of Biochemistry
2. To develop students’ understanding of the application of biochemical principles to
other areas of biology and biomedical sciences
3. To develop students’ awareness of the role of Biochemistry both as a research
discipline and its applications
4. Develop the key skills required for independent evaluation of data, critical appraisal of scientific literature.
5. Develop confidence in oral presentation skills to specialized audiences, and the
ability to write scientific reports.

Knowledge and understanding

The course provides a knowledge and understanding of the following:
1. Key concepts in areas of direct relevance to biochemistry
2. Structure and function of proteins
3. Key concepts in enzymology, metabolic pathways and their regulation
4. Mechanisms of enzymatic reactions, Michaelis-Menten kinetics. The most important metabolic pathways of carbohydrates, lipids, fatty acids and amino acids and connections between the metabolic pathways
5. Relevance of the knowledge of enzymic mechanisms, the metabolic pathways for research in metabolomics applied to human health issues and to pharmaceutical chemistry.
6. 7. Role of hormones in cellular communications and signal transduction
8. Theoretical basis of key biochemical and immunological practical techniques
9. Theoretical basis of the determination of protein structure
10. Basis of bioinformatics and sequence/structure analysis
11. Awareness of major issues currently at the forefront of Biochemistry research

Teaching/learning methods and strategies

The above mentioned points are achieved through lectures, group work and formative assessments, and are reviewed and reinforced in tutorials.

Intellectual/Communication skills and Judgements

1. Interpret and analyze biochemical data with a critical understanding of the appropriate contexts for their use
2. Integrate subject knowledge and understanding to explore and solve familiar and unfamiliar problems
3. Understand Biochemistry literature
4. Produce critical and original pieces of written work on biochemical topics
5. Think critically about their own work/research and to input into the formulation of future hypotheses and experiments
7. Ability to present Biochemistry to audiences of differing scientific knowledge
8. Computer skills, to include molecular viewers, data analysis/presentation, spreadsheets and statistical analysis.

Obiettivi formativi

This course provides the students with the theoretical knowledge and technical skills and introduce them to the structure and properties of pharmaceutical agents and metabolites. The course outlines the structure, bonding and chemical reactivity of various important classes of organic molecules, ranging from simpler examples of hydrocarbons or those containing a single functional group, to some of the important biological molecules such as carbohydrates, nucleic acids and proteins. Topics include basic concepts in medicinal chemistry: 1) the drug discovery and development process, 2) review of organic functional groups found in drug molecules, 3) drug-target interactions, 4) physicochemical properties related to drug action such as acid-base properties, equilibrium, and stereochemistry, 5) Effect of chemical structure on the metabolism of drug molecules.
By completing Pharmaceutical Chemistry, the student acquires:
1. Recognize and describe zero-, first- and second-order kinetics, perform elementary calculations of rate constants and appreciate the role of enzymes in catalysis.
2. Integrate knowledge from foundational sciences to explain how specific drugs or drug classes work and evaluate their potential value in individuals and populations.
3. Apply knowledge in foundational sciences to solve therapeutic problems.
4. Demonstrate an understanding of the therapeutic potential of a candidate molecule and how chemical properties can affect its potential to become a new drug.

Obiettivi formativi

Obiettivi insegnamento
General skills
Bioinformatics is a new multidisciplinary field that includes the development and implementation of
computational methods and tools suitable to handle, decipher and interpret the large amount of
biomolecular data derived today. It is recognized that bioinformatics is fundamental in the rise of
translational research and the success of molecular medicine.
The aim of the course is to enable students to get familiar with several bioinformatics tools,
databases and programming languages, be able to implement and competently interpret and
present the results of a typical bioinformatics analyses, critically discuss the current limitations and
design the next generation of tools. The course will consist of lectures, tutorials, and literature
studies focusing on learning how to analyze “omics” sequencing data using a combination of
cutting-edge tools and programming languages.

Specific skills
The students who have passed the exam will be able to know and to understand (acquired
knowledge)
- how to analyze transcriptomics data (RNA-seq and Microarray data)
- how to develop a lightweight and reusable RNA-seq pipeline (Mapping and Transcripts
reconstruction)
- how mapping the reads from deep sequencing data.
- knowledge of most common file formats for “omics” data
- interpret omics data with functional analysis
- basic knowledge of R programming language
- basic knowledge of Linux command line and shell scripting
- be able to report results in a reproducible way
- understand and choose appropriate bioinformatics tools and databases for their
investigation.

Applying knowledge and understanding
To apply the acquired knowledge to integrate information gathered from different sources
(datasets, material obtained during lectures, and scientific literature) with particular focus on NGS-
based technologies; to set-up a bioinformatic pipeline to analyze transcriptomics data using open-
source software.
Communication skills
The student will be able to perform oral presentation of scientific data analysis, creating an analysis
report and a presentation.
Notions acquired during the course will be evaluated during the exam.
Learning skills
- Logically connecting the acquired knowledge
- Identification of the most relevant topics of the issues discussed during the course

Competenze generali
La bioinformatica è un nuovo campo multidisciplinare che include lo sviluppo e l'implementazione
di metodi e strumenti computazionali adatti a gestire, decifrare e interpretare la grande quantità di
dati biomolecolari che sono disponibili oggi. È riconosciuto che la bioinformatica è fondamentale
nell'ascesa dell’importanza della ricerca traslazionale e del successo della medicina molecolare.
L'obiettivo del corso è quello di consentire agli studenti di familiarizzare con diversi strumenti
bioinformatici, database e linguaggi di programmazione, essere in grado di implementare e
interpretare e presentare con competenza i risultati di una tipica analisi bioinformatica, discutere
criticamente i limiti attuali e progettare la prossima generazione di strumenti. Il corso consisterà in
lezioni, esercitazioni e studi di letteratura incentrati sull'apprendimento di come analizzare i dati di
sequenziamento "omici" utilizzando una combinazione di strumenti e linguaggi di programmazione
all'avanguardia.
Competenze specifiche
Gli studenti che avranno superato l'esame saranno in grado di conoscere e comprendere
(conoscenze acquisite)
- come analizzare i dati di trascrittomica (dati RNA-seq e Microarray)
- come sviluppare una pipeline RNA-seq leggera e riutilizzabile (ricostruzione di Mapping
and Transcripts)
- come mappare le letture dai dati di sequenziamento profondo.
- conoscenza dei formati di file più comuni per i dati "omics" Interpretare i dati omici con
l'analisi funzionale
- conoscenza di base del linguaggio di programmazione R
- conoscenza di base all’utilizzo del terminale Linux
- essere in grado di riportare i risultati in modo riproducibile
- comprendere e scegliere strumenti bioinformatici e database appropriati a seconda del
problema biologico.
Capacità di applicare conoscenza e comprensione
Applicare le conoscenze acquisite per integrare informazioni raccolte da diverse fonti (dataset,
materiale ottenuto durante le lezioni frontali e letteratura scientifica) con particolare attenzione alle
tecnologie basate su NGS; impostare una pipeline bioinformatica per analizzare dati di
trascrittomica utilizzando software open source.
Abilità comunicative
Lo studente sarà in grado di eseguire presentazioni orali di analisi di dati scientifici, creando un
rapporto di analisi e una presentazione. Le nozioni acquisite durante il corso saranno valutate
durante l'esame.
Capacità di apprendimento
- Collegare logicamente le conoscenze acquisite
- Individuazione degli argomenti più rilevanti delle tematiche trattate durante il corso

Obiettivi formativi

This course offers an introduction to network medicine, a rapidly emerging field that integrates systems biology and network science. It runs counter to the prevailing scientific reductionist trend that dominates current medical research on disease etiology and treatment. Reductionism relies on single molecules or single genes to provide comprehensive and robust insights into the pathophysiology of complex diseases. Similarly, current drug development methodologies target single molecules that very frequently fail because of the unforeseen and unintended effects that result from the application of this piecemeal approach to pharmacology. In contrast, network medicine emphasizes a more holistic approach through the identification and investigation of networks of interacting molecular and cellular components. When network medicine is integrated into biomedical research, it has the potential to transform investigations of disease etiology, diagnosis, and treatment.

The course will explore the concept of network medicine through: (1) a review of the role, identification, and behavior of networks in biology and disease, (2) the integration of multiple types of -omics data into networks as a paradigm for understanding disease expression and course, and (3) systems pharmacology approaches for the development and evaluation of effective therapies of complex disease.

Moreover, this course will provide hands-on experience in the analysis of two specific types of biological networks—gene co-expression networks and drug-disease networks. During the course, attendees will apply the theory to real data sets.
After completing the course, attendees should to be able to apply these methods in their own research.

The course goals are:

Understand the role of networks in biology and disease.
Understand networks as a paradigm for disease expression and course.
Understand the challenges of developing effective therapies for complex diseases.
Understand the role of omics data in networks.
Understand network medicine in terms of investigation for disease etiology, diagnosis, and treatment.

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The Bioethics course provides the students with tools to understand, discuss, present and address ethical issues relevant to bioinformatics, at the intersection between biological and technological sciences.
In order to respond to the course requirements, the students will also acquire general skills such as doing a bibliographic research on academic databases, speaking and arguing in public by using specialized bioethical concepts and theories, and writing a little paper in an academic format including a bibliography.

Obiettivi formativi

General skills
The new generation of sequencing technologies has provided unforeseen chances for high-throughput functional genomic studies. These technologies have been applied in a variety of contexts, including whole-genome sequencing, discovery of transcription factor binding sites, mapping out the DNA accessibility and RNA expression profiling. Intriguingly, recent annotation efforts focused on the discovery of novel noncoding RNA genes and regulatory elements that control temporal or spatial gene expression along cell differentiation. The course of Molecular Biology and Genomics is designed to provide students with an introduction to the structure and function of genomes and transcripts in humans and in other model organisms. Topics discussed will include modern genome sequencing technologies, as well the recent in silico and in vivo approaches used for functional genomics and for the functional role of emerging non-coding RNA classes (practical examples taken from recent literature will be used). The course also provides students with basic knowledge for accessing browsers and public databases for the analysis of gene expression data, GO and miRNA target prediction software.
By the end of the course, students will be able to apply the acquired knowledge to the study of the basic mechanisms of gene expression, as well as of complex processes such as development, cell division and differentiation, and to exploit them for a practical use in both basic and applied research.

Specific skills
The students who have passed the exam will be able to know and to understand (acquired knowledge)

- the origin and the maintenance of the biological complexity;
- the structure and function of the genome in humans and in the main model systems;
- the problems and technologies of genome-wide analyses applied to biological processes;
- the influence of the modern sequencing technologies for a better description and for the study of transcriptome dynamics in humans and in the main model systems;
- the network of interactions between the biological molecules in the mechanisms of regulation of gene expression.

The students who have passed the exam will be able to (acquired expertise):
- interpret the biological phenomena in a multi-scale and multi-factorial context;
- interpret the results of genomic studies and to discriminate which techniques to apply according to the different problems to be dealt with in the genomic field;
- report works already present in the literature in the form of an oral presentation.

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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.

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Acquisition of manual, methodological and organizational skills aimed at the elaboration of technical-scientific issues.

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Basic training in laboratorytechniques aimed to improve professionalization.