Logo UAB

Advanced Genomics and Proteomics

Code: 43473 ECTS Credits: 9
2024/2025
Degree Type Year
4313794 Biochemistry, Molecular Biology and Biomedicine OT 0

Contact

Name:
Julia Lorenzo Rivera
Email:
julia.lorenzo@uab.cat

Teachers

Francesc Xavier Avilés Puigvert
Antoni Barbadilla Prados
Enric Querol Murillo
Sebastián Martin Tanco
Jaime Luis Martinez Urtaza
Julia Lorenzo Rivera
Sonia Casillas Viladerrams

Teaching groups languages

You can view this information at the end of this document.


Prerequisites

     The Catalan, English or Spanish languages will be mostly used depending of the lecturer that will give a particular topic and the conjoint of attendees.

     Addressed to post-graduate students in Biochemistry, Biotechnology, Biology, Biomedicine, Genetics, Microbiology, Chemistry, Informatics/Bioinformatics, Pharmacy, Medicine and Veterinary.


Objectives and Contextualisation

     The overall aim of the subject is to provide students with an overview of Genomics and Proteomics, including the fundamentals, common techniques, and applications. The specific objectives of GENOMICS include understanding the following aspects. the diversity and complexity of eukaryotic genomes, the historical and evolutionary perspective of genomic content, the meaning and consequences of intraspecific variability, techniques commonly employed in studies of genomics and transcriptomics, and applications derived from the knowledge provided by this science.

The objective of the PROTEOMICS classes is to introduce students to new methods of proteomics and interactomics and their application in biomedical research. It aims to understand how proteins interact and regulate each other, how they change in response to diseases or treatments, and how these alterations can be used to diagnose diseases, identify biomarkers, or develop new therapeutic approaches.

 


Competences

  • Analyse and correctly interpret the molecular mechanisms operating in living beings and identify their applications.
  • Communicate and justify conclusions clearly and unambiguously to both specialist and non-specialist audiences.
  • Continue the learning process, to a large extent autonomously.
  • Develop critical reasoning within the subject area and in relation to the scientific or business context.
  • Identify and use bioinformatic tools to solve problems in biochemistry, molecular biology and biomedicine.
  • Integrate contents in biochemistry, molecular biology, biotechnology and biomedicine from a molecular perspective.
  • Solve problems in new or little-known situations within broader (or multidisciplinary) contexts related to the field of study.
  • Use and manage bibliography and IT resources related to biochemistry, molecular biology or biomedicine.
  • Use scientific terminology to account for research results and present these orally and in writing.

Learning Outcomes

  1. Communicate and justify conclusions clearly and unambiguously to both specialist and non-specialist audiences.
  2. Continue the learning process, to a large extent autonomously.
  3. Develop critical reasoning within the subject area and in relation to the scientific or business context.
  4. Identify and describe the different components in prokaryotic and eukaryotic genomes and proteomes.
  5. Identify molecular mechanisms responsible for diseases.
  6. Solve problems in new or little-known situations within broader (or multidisciplinary) contexts related to the field of study.
  7. Use and manage bibliography and IT resources related to biochemistry, molecular biology or biomedicine.
  8. Use scientific terminology to account for research results and present these orally and in writing.
  9. Use the different methodologies, techniques and tools commonly used in genome sequencing, assembly and annotation.
  10. Use the different methodologies, techniques and tools commonly used in proteomics and interactomics and metabolomics.

Content

GENOMICS: Introduction to Genomics. The human genome project. Genomic technologies. Transposable elements. Comparative genomics nucleotide-level changes. Comparative genomics: chromosomal changes. Population genomics: Theory. Population genomics in model species. Nucleotide variation in humans. Structural variation. Association Studies/System genetics. Functional Genomics and Transcriptomics. Epigenomics.

PROTEOMICS: Instrumentation and methods of proteomics. Session of proteomics practices. Introduction to biomedical proteomics and its applications: biomarkers in biomedicine; identification of pharmacological targets; Moonlighting proteins in human diseases and in vaccine design. Interactomics and the role of protein interactions in the disease. Applications from proteomics to custom medicine.


Activities and Methodology

Title Hours ECTS Learning Outcomes
Type: Directed      
Lectures 45 1.8 5, 6, 8
Type: Supervised      
Oral presentations 40 1.6 1, 7, 8
Type: Autonomous      
Student work and learning 137 5.48 2, 3, 5, 6, 7, 8

Subject teaching includes three types of activities:
 
- Lectures. PowerPoint presentations accompany spoken explanations of the subject to be learned to help students visualize questions and answers.
- Reading and discussion. Students are expected to read a number of research papers during the course and participate in the critical discussion of the papers in the classroom.
- Oral presentations. Students will prepare a subject and make an oral and PowerPoint presentation of the subject to their peers.
 
15 minutes of a class will be dedicated to answer the institutional surveys of the UAB

Annotation: Within the schedule set by the centre or degree programme, 15 minutes of one class will be reserved for students to evaluate their lecturers and their courses or modules through questionnaires.


Assessment

Continous Assessment Activities

Title Weighting Hours ECTS Learning Outcomes
Exams 40% 2 0.08 1, 2, 3, 4, 5, 6, 8, 9, 10
Lecture attendance 20% 0 0 1, 6
Oral presentation 40% 1 0.04 1, 6, 7

 Continuos evaluation subject (the unique evaluation does not apply): 

Final grades are a weighted average of items:

- Attendance and participation in the classroom (20%)
- Oral presentation and defense (40%)
- Exam (40%)
The student will be "not qualifiable" when the number of evaluable tests/tasks/activities done by he student do not reach to a global minimal qualification of 5.0 
 

Important: If plagiarism is detected in any of the works submitted, the student will fail the whole module.

 

 

I

 



Bibliography

Basic books
- Gibson, G. i S. V. Muse. A Primer of Genome Science. Sinauer, Massachusetts. USA. 2009, 3rd edition.
- Brown, T. A. Genomes. Garland Science, UK. 2009, 3rd edition.
- Kraj, A. & Silberring J. Introduction to Proteomics. Ed. Wiley, UK 2008.
- Lovrik, J. Introducting Proteomics: From concepts to sample separation, mass spectroetry and data analysis. Ed. Wiley-Blackwell, UK, 2011.
- Klipp, E. et al. Systems Biology: A textbook. Ed. Wiley-Blackwell, UK, 2009.
- Baldwin, G. et al. Synthetic Biology: A primer. Imperial College Press, UK, 2012
- Belinda Pitman. Proteomics: Proteome and proteomics analysis. Ed Syrawood 2019
- Manual de Proteómica. Ed. Sociedad Española de Proteómica. Pdf 15€ en https://payhip.com/b/FNt7
Additional journal references will be commented in thelectures
 
 
 
Useful links
UAB Virtual Campus: https://cv2008.uab.cat/
Entrez Genome Database: http://www.ncbi.nlm.nih.gov/genome

Expasy: http://www.expasy.org

Human Proteome Map: http://www.humanproteomemap.org/

ProteomicsDB: : http://www.proteomicsdb.org/


Software

None


Language list

Name Group Language Semester Turn
(PLABm) Practical laboratories (master) 1 Catalan/Spanish first semester morning-mixed
(SEMm) Seminars (master) 1 English first semester morning-mixed
(TEm) Theory (master) 1 Catalan/Spanish first semester morning-mixed