Identifying Data 2019/20
Subject (*) Genomics Code 610441014
Study programme
Mestrado Universitario en Bioloxía Molecular , Celular e Xenética
Descriptors Cycle Period Year Type Credits
Official Master's Degree 2nd four-month period
First Optional 3
Language
Spanish
Galician
English
Teaching method Face-to-face
Prerequisites
Department Bioloxía
Coordinador
Vila Taboada, Marta
E-mail
marta.vila.taboada@udc.es
Lecturers
Becerra Fernandez, Manuel
Vila Taboada, Marta
E-mail
manuel.becerra@udc.es
marta.vila.taboada@udc.es
Web
General description Denomínase xenómica ao estudo integral do funcionamento, evolución e orixe dos xenomas. A xenómica utiliza coñecementos derivados de distintas disciplinas como xenética, bioloxía molecular, bioquímica, informática, estatística, matemáticas e física.
A diferenza da xenética clásica que a partires dun fenotipo (xeralmente mutante) procura o xene ou xenes responsables dese fenotipo, a xenómica ten como obxectivo predicir a función dos xenes a partir da súa secuencia ou das súas interaccións con outros xenes.
As denominadas ciencias ómicas están na vangarda da ciencia, feito debido ás posibilidades abertas polas novas tecnoloxías de secuenciación masiva, aos avances en bioinformática e aos algoritmos cada vez máis sofisticados para análise de xenomas completos.
Contingency plan

Study programme competencies
Code Study programme competences
A3 Skills of understanding the functioning of cells through the structural organization, biochemistry, gene expression and genetic variability.
A11 Skills of understanding the structure, dynamics and evolution of genomes and to apply tools necessary to his study.
B1 Analysis skills to understand biological problems in connection with the Molecular and Cellular Biology and Genetics.
B5 Correct oral and written communication on scientific topics in the native language and at least in another International diffusion language.
B9 Skills of preparation, show and defense of a work.
C2 Mastering oral and written expression in a foreign language.
C3 Using ICT in working contexts and lifelong learning.
C8 Valuing the importance of research, innovation and technological development for the socioeconomic and cultural progress of society.

Learning aims
Learning outcomes Study programme competences
To learn the basics of the different molecular techniques used in genomics, with particular emphasis in NGS AR3
AR11
CC3
To acquire an updated view about the current scope and future perspectives of structural, functional and evolutionary genomics AR3
AR11
BR1
BR5
BR9
CC2
CC8
To understand how genomes evolve and how molecular and bioinformatic tools are used for that purpose AR3
AR11
BR1
BR5
BR9
CC2
CC8
DNA microarrays: experimental set up and data analysis. AR3
AR11

Contents
Topic Sub-topic
The Human Genome Project History and results
Whole Genome Sequencing Mate-pair libraries
Annotation
Comparative genomics
Palaeogenomics
Next Generation Sequencing (NGS) Platforms
Paired-end libraries
Introduction to data analysis
Metagenomics Metabarcoding
Clinical genomics Amplicon-seq
Panel-seq
Exome-seq
Pharmacogenomics
Single Nucleotide Polymorphisms (SNPs) Genome wide association studies (GWAS)
Digital genetic testing
Functional genomics Transcriptome analysis: microarrays and NGS (RNA-seq)
Epigenomics
Computer lab 1. Using GALAXY for analysis of NGS data.
2. Gene expression analysis using BABELOMICS.
3. Farmacogenomic analysis using PHARMKGB.
4. Introduction to the Intregative Genomics Viewer (IGV).

Planning
Methodologies / tests Competencies Ordinary class hours Student’s personal work hours Total hours
ICT practicals A3 A11 B1 B5 B9 C2 C3 7 21 28
Guest lecture / keynote speech A3 A11 B1 C8 14 28 42
Objective test A3 A11 B1 C8 2 0 2
 
Personalized attention 3 0 3
 
(*)The information in the planning table is for guidance only and does not take into account the heterogeneity of the students.

Methodologies
Methodologies Description
ICT practicals OUr 7-hour, computer lab curriculum was developed to accompany the lecture course in Genomics. The students work on their own web-based investigations and present their results to each other (active learnning).
Guest lecture / keynote speech The instructors explain the main contents of each topic interacting as much as possible with the students.
Objective test Written exam.

Personalized attention
Methodologies
ICT practicals
Description
Instructors will typically be available via email/SKYPE. Students can arrange for in-person tutoring sessions.

Assessment
Methodologies Competencies Description Qualification
Objective test A3 A11 B1 C8 In order to pass the subject, all students will have to score at least 28 (out of 70) points in a multiple choice test and/or short-answer questionnaire. 70
ICT practicals A3 A11 B1 B5 B9 C2 C3 Attendance to computer labs is mandatory.
In order to pass the subject, all students will have to score at least 15 (out of 30) points in a hands-on exam: a set of bioinformatic exercises to be solved using the software introduced during the computer labs.
30
 
Assessment comments

Students scoring at least 50 (out of 100) points but not reaching the aforementioned thresholds (ICT practicals and Objective test) will be awarded a 4.5 (out of 10) score. When resitting, they can choose to take both exams or only the failed one.

Mark "A with distinction" will only be awarded to outstanding students passing the subject in May.

Students will be scored as "ABSENT" (Non presentado) only when not involved in any of the assessed activities.

In the case of exceptional circumstances, lecturers may assist the student to improve his/her learning process and/or catch up on missed work/assessments. The student is responsible for liaising with his/her lecturer to organise this assistance by e.g. applying for: an extended deadline to present his/her work or taking an exam in a different date. The coordinator can request evidence about the reason for such an application.


Sources of information
Basic McLachlan, G. J., Do, K-A., Ambroise, C (2004). Analyzing Microarray Gene Expression Data. Wiley-Interscience. John Wiley & Sons
Pevsner, J. (2015). Bioinformatics and Functional Genomics. Wiley Blackwell
Kulkarni, S., Pfeifer, J. (2015). Clinical Genomics. A guide to Clinical NGS. Academic Press, Elsevier
Robison, P.N., Piro, R.M., Jäger, M. (2018). Computational Exome and Genome Analysis. CRC Press, Taylor & Francis Group
Bowtell, D., Sambrook, J. (2003). DNA Microarrays. Cold Spring Harbor Laboratory Press.
Allison, David B., et al (2006). DNA microarrays and related genomics techniques design, analysis, and interpretation of experiments. Chapman & Hall/CRC
E. Rinaldis, A. Lahm. (2007). DNA microarrays: current applications. Wymondham: Horizon Bioscience
Brown, T. A. (2018). Genomes4. Garland Science

Complementary (). .
Zhanjiang, Liu (2007). Aquaculture genome techonologies. Blackwell
Dale Jeremy (2008). From genes to genomes: concepst and applications of DNA technology. John Wiley & Sons
Sensen, Christoph W. (2005). Handbook of genome research genomics, proteomics, metabolism, bioinformatics, ethical & legal issues . Wiley-VCH

RECURSOS EN INTERNET:


Biological database compilation at NAR:
http://nar.oupjournals.org/content/vol29/issue1

DOE Joint Genome Institut. Why sequence them?
http://www.jgi.doe.gov/sequencing/why/index.html

EMBL (European Molecular BIology Laboratory), Bioinformatics.
http://www-db.embl.de/jss/servlet/de.embl.bk.emblGroups.EmblGroupsOrg/serv_0?t=0

ExPASy (Expert Protein Analysis System).
http://us.expasy.org/

GeneMark:
http://opal.biology.gatech.edu/GeneMark/

GenomeNet (Kyoto University Bioinformatics Center).
http://www.genome.jp/

Genoscope. Le séquençage des génomes.
http://www.genoscope.cns.fr/externe/Francais/Sequencage/

GOLD (Genomes Online Database).
http://www.genomesonline.org/

Human genome: advanced annotation tutorial.

http://www.mad-cow.org/00/annotation_tutorial.html

Human Genome Project Information.

http://www.ornl.gov/sci/techresources/Human_Genome/home.shtml

Iañez Pareja, E. (1997). Introducción a los Proyectos Genoma.
http://www.ugr.es/~eianez/Biotecnologia/genoma-2.html

KEGG (Kyoto Encyclopedia of Genes and Genomes).
http://www.genome.jp/kegg/kegg2.html

Nacional Human Genome Research Institute:
http://www.genome.gov/

NCBI (National Center for Biotechnology Information).
http://www.ncbi.nlm.nih.gov/

The Sanger Institute.
http://www.sanger.ac.uk/

TIGR (The Institute for Genomic Research).
http://www.tigr.org/

tRNAscan-SE 1.21.
http://www.genetics.wustl.edu/eddy/tRNAscan-SE/

The WWW Virtual Library: Model Organisms:
http://www.ceolas.org/VL/mo/

ALGUNAS BASES DE DATOS DE MICROARRAYS DE ADN

ArrayExpress

http://www.ebi.ac.uk/arrayexpress/

ChipDB

http://staffa.wi.mit.edu/chipdb/public/

ExpressDB

http://twod.med.harvard.edu/ExpressDB/

Gene Expression Omnibus (GEO)

http://www.ncbi.nlm.nih.gov/geo/

READ (RIKEN cDNA Expression Array Database)

http://read.gsc.riken.go.jp/

Saccharomyces Genome Database (SGD)

http://genome-www4.Stanford.EDU/cgi-bin/SGD/expression/expressionConnection.pl

Standford Microarray Database ( SMD)

http://genome-www5.stanford.edu/

The Yale Microarray Database

http://www.med.yale.edu/microarray/

yeast Microarray Global Viewer (yMGV)

http://www.transcriptome.ens.fr/ymgv/


Recommendations
Subjects that it is recommended to have taken before
Cellular Techniques/610441001
Molecular Techniques/610441002
Genetic Variation Mechanisms/610441005
Regulation of gene expression/610441006
Bioinformatics and Biomolecular models /610441020

Subjects that are recommended to be taken simultaneously
Proteomics/610441013
Chromosomes. structure. function and evolution /610441015
Human Genetics/610441016
Genetic Toxicology /610441017

Subjects that continue the syllabus
Project/610441022

Other comments

Do not take this subject if your level of English is lower than B1.



(*)The teaching guide is the document in which the URV publishes the information about all its courses. It is a public document and cannot be modified. Only in exceptional cases can it be revised by the competent agent or duly revised so that it is in line with current legislation.