First cycle
degree courses
Second cycle
degree courses
Single cycle
degree courses
School of Science
Course unit
SCN1028833, A.A. 2017/18

Information concerning the students who enrolled in A.Y. 2017/18

Information on the course unit
Degree course Second cycle degree in
SC1175, Degree course structure A.Y. 2008/09, A.Y. 2017/18
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Degree course track Common track
Number of ECTS credits allocated 9.0
Type of assessment Mark
Course unit English denomination GENOMICS
Website of the academic structure
Department of reference Department of Biology
Mandatory attendance
Language of instruction English

Teacher in charge GIORGIO VALLE BIO/11

ECTS: details
Type Scientific-Disciplinary Sector Credits allocated
Core courses BIO/11 Molecular Biology 5.0
Core courses BIO/18 Genetics 4.0

Mode of delivery (when and how)
Period Second semester
Year 1st Year
Teaching method frontal

Organisation of didactics
Type of hours Credits Hours of
Hours of
Individual study
Laboratory 2.0 32 18.0 No turn
Lecture 7.0 56 119.0 No turn

Start of activities 26/02/2018
End of activities 01/06/2018

Prerequisites: The content of the course has been defined keeping in mind the program of the first level degree in Molecular Biology of the University of Padua. In particular it is expected that the students have a good knowledge of Genetics, Molecular Biology and Bioinformatics. The course is in English, therefore the students should have a reasonable command of spoken and written English.
Target skills and knowledge: The course is divided in three main parts: 1) DNA sequencing technology and genome sequencing; 2) Functional genomics, including transcriptomics, proteomics, interactomics, gene prediction, gene annotation, epigenomics; 3) Analysis of polymorphisms, genome and exome resequencing, personalized medicine, data integration, systems biology. Furthermore, the course includes practicals in which the students will learn to make NGS libraries and will apply bioinformatic approaches for analyzing genomic data.
Taking into consideration the complexity of the subject and in agreement with the Dublin Descriptors, a particular attention will be spent to promote the ability of the students to integrate knowledge and handle complexity, and formulate judgments with incomplete or limited information.
Examination methods: The exam will be written, but a continuous process of assessment will be carried out throughout the course, to verify the level of understanding of the students.
Assessment criteria: In their final examination the students should demonstrate a systematic understanding of the field and mastery of the methods of research associated with it. Furthermore, they should be capable of critical analysis, evaluation and synthesis of new and complex ideas, integrating the subjects of this course with other knowledge.
Course unit contents: This is a 9 credit course, 7 of which will be lessons, the remaining 2 will be practicals. Each title reported below corresponds to approximately two hours of classroom teaching plus four hours of home study. The lessons will be articulated as follows.

Part 1.
Presentation of course and practicals
Introduction: Life, Biology, Information, Genomes, Evolution
History of genomics
Next Generation sequencing (NGS)
NGS: data formats for reads
Classical sequence alignment and assembly algorithms
NGS read alignment
Alignment formats: gff, sam and bam
Genome assembly with NGS data
Mate pair libraries and scaffolding

Part 2
Transcriptome: Northern, EST, Full length, Microarrays
Analysis of RNAseq data
miRNA target prediction; lincRNA
Interactomics, and functional associations
Gene prediction, gene ontology and gene annotation
DNA methylation and methylome analysis
Histone modification and ChIP analysis"

Part 3
Analysis of human mutations and polymorphisms
Genome re-sequencing and Exome sequencing
Personalized medicine and related bioinformatics
Genome browsers
Data integration and systems biology
General summary, discussion and conclusions
Planned learning activities and teaching methods: The course will include lectures and practicals. The teaching activity will be supported by resources made available on the e-learning platform "Moodle". These resources include teaching material as well as tools for self-assessment. The motivation behind this implementation is the promotion of an activity of "blended learning" that would allow the student to learn, at least in part through delivery of content and instruction via digital and online media. When possible, the "flipped classroom paradigm" will be applied, thus reversing the traditional learning environment. Firstly the student learns the topics autonomously, then a thorough discussion will take place in the classroom, among the students and the teacher.
An ample selection of assessment questionnaires and exercises is made available on the Moodle platform, both to allow the students to self-assess and to stimulate arguments which will be further discussed in the classroom.
Additional notes about suggested reading: There are no official text books for this course. The students will be encouraged to find the information from multiple sources. Lecture notes and other teaching material will be available on the Moodle e-learning platform.
Textbooks (and optional supplementary readings)