Identifying Data 2016/17
Subject (*) Xenómica 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 Optativa 3
Language
Spanish
Galician
English
Teaching method Face-to-face
Prerequisites
Department Bioloxía Celular e Molecular
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.

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 Skills of dominating the oral form expression and compression and written of a foreign language.
C3 Skills of Using basic tools of the information technologies and communications (ICT) necessary to the exercise of his profession and for the apprenticeship over his life.
C8 Considering the importance that the investigation has, the innovation and the technological development in the socioeconomic advance and cultural of the 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
Next Generation Sequencing (NGS) Platforms and applications
Structural Genomics Mapping, sequencing, annotation and databases
The Human Genome Project
Comparative Genomics How do genomes evolve?
Genomes of Prokaryotes Metagenomics
Genomes of Eukaryotes Taxonomy
Paleogenomics
Medicine
Functional Genomics DNA microarrays: methodology, types of platforms, experimental set up, data analysis
Computer lab 1. Using GALAXY (https://usegalaxy.org/) for genomic analysis
2. Gene expression analysis and microarrays

Planning
Methodologies / tests Competencies Ordinary class hours Student’s personal work hours Total hours
ICT practicals A3 A11 B1 7 14 21
Oral presentation B5 B9 C2 C3 C8 1.55 6.2 7.75
Guest lecture / keynote speech A3 A11 B1 C8 14 28 42
Objective test A3 A11 B1 C8 2 0 2
 
Personalized attention 2.38 0 2.38
 
(*)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 10-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).
Oral presentation Students may hold a 10-minute speech about a genomic issue previously agreed with the instructors.
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
Oral presentation
ICT practicals
Description
Instructors will typically be available via email. Students can arrange for in-person tutoring sessions.

Assessment
Methodologies Competencies Description Qualification
Oral presentation B5 B9 C2 C3 C8 Student may hold a 10-minute speech about an interesting topic within the field of Genomics. They will try to answer any question from the audience.
Distance learning students unable to attend this activity will have a maximum score of 85 in their objective test.
15
Objective test A3 A11 B1 C8 The exam will evaluate items discussed in the aforementioned activities. 70
ICT practicals A3 A11 B1 Attendance is mandatory.
Distance learning students will be required to follow certain guidelines/tutorials on their own and finally answer a questionnaire, so that comprehension and performance may be assessed.
15
 
Assessment comments

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
















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
Campbell, A.M & Heyer, L.J. (2007). Discovering Genomics, Proteomics & Bioinformatics. Pearson Benjamin Cummings
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
Lesk, Arthur M. (2012). Introduction to Genomics. Oxford University Press

Complementary Straalen, Nico M. van (2006). An introduction to ecological genomics. Oxford University Press
Zhanjiang, Liu (2007). Aquaculture genome techonologies. Blackwell
Futuyama, Douglas J. (2006). Evolution. Sinauer Associates
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
Técnicas Celulares/610441001
Técnicas Moleculares/610441002
Mecanismos de xeración da variación xenética/610441005
Regulación da expresión xénica/610441006
Bioinformática e Modelado de Biomoléculas/610441020

Subjects that are recommended to be taken simultaneously
Proteómica/610441013
Cromosomas: Estructura. Función e Evolución/610441015
Xenética Humana/610441016
Toxicología Xenética/610441017

Subjects that continue the syllabus
Traballo de Máster/610441022

Other comments


(*)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.