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Masters
Course: Introduction to Bioinformatics for Molecular Biologists
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AIM:
To introduce commonly used bioinformatic concepts, tools and
resources in molecular biological research.
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Date:
12-11-2012 till 23-11-2012 (2 weeks full time, 3 ECTS), Venue
Stratenum str. 2.106 / 2.112
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Description:
“Introduction to Bioinformatics for Molecular Biologists”
is a joint course for the various life science Masters programs at
the Utrecht University. This introductory course provides an
overview of the importance of bioinformatics in various biological
disciplines. While a biological background is required, no
programming skills are needed. The course can be considered a
general introduction to bioinformatics, with a focus on the
research that is performed at Utrecht University. The theory and
tools for bioinformatics provided are very useful for any life
science researcher. The course will be partially theoretical with
lectures taking up to 30% of the day while the major focus will be
on working with various tools and datasets. These computer tasks
are performed in groups of 2 students. The maximum number of
participants for this course is 40 students. The course will be
concluded on the last day with an exam that consists of normal
pen-and-paper questions but also of tasks that should be completed
on the computer. Active participation during the course provides
sufficient preparation to complete the exam. Furthermore,
follow-up courses are organized later in the year that will allow
you to specialize in specific directions. Students are expected to
be familiar with the subjects from this introductory course when
participating in any of the follow-up courses.
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Course
coordinator: Berend Snel, b.snel@uu.nl,030-253 8102
Registration:
http://www.cgdb.nl/courses/
The
maximum number of participants for this course is 40 students.
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Part
1: Exploration of Genomes Coordinator Van den Ackerveken
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To
understand how genome sequences are generated, annotated and can
be accessed and browsed
To
understand and work with Ensembl, and NCBI genome browsers
To
understand genomic contents, e.g. protein coding genes, regulatory
elements, non-coding genes, alternative introns, UTRs
To
understand that there is variation in sequences within populations
and how this affects the phenotype and disease. (genetic
variation/SNP/disease/ phenotypes)
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Monday
9:00-16:30
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Genome Sequencing
Lecture Genome
Sequencing
Lecture Introduction
to similarity searching
Hands-on Sequence
assembly and annotation
Lecture Ensembl Genome
browser
Hands-on
Ensembl Genome browser
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Tuesday
9:00-16:30
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Exploring
the Genome
Lecture
Next Generation Sequencing (NGS)
Hands-on
exersise: Working with NGS data
Lecture:
Genome mining tools
Hands-on
Biomart
Lecture
Genome Variation
Hands
on SNPs, haplotypes and CNVs
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Wednesday
9:00-14:30
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Genome
Variations and their Relevance to Human Traits and Diseases
Lecture:
Mapping disease genes
Hands-on
exercises: Linkage and association
Lecture
Next Generation Sequencing Applications
Lecture
Personal Genomics
Hands-on
exercise Personal genomics
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Wednesday
14:30-17:00
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Self
study
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Part
2: Protein sequence and structure analysis Coordinator
Snel
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To
understand sequence comparison methods and to use them in DNA and
protein analysis
To
learn to use tools to predict the three dimensional protein
structure based on the primary sequences
To
understand the relationship between sequence conservation and
structure and function
To
be able to construct and interpret a phylogenetic tree of genes or
proteins in terms of gene duplications and orthology.
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Thursday
9:00-15:00
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Using
sequence analysis to find homologs
Lecture
pairwise alignment
Hands-on
pairwise alignment
Lecture
sequence database searching
Hands-on
sequence database searching
Lecture
profile searches
Hands-on
profile searches
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Friday
9:00-16:30
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Structure-function
relationships of proteins Lecture: From primary sequence
information to tertiary protein structure
Hands-on:
Structure predictions based on protein sequences
Lecture:
Homology modeling
Hands-on/demo:
structure viewers JMOL and Deep-View (Swiss-PDB viewer)
Hands-on:
Homology modeling
Lecture
Structure-Function relationship
Hands-on:
Functional annotation through structural similarity
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Monday
9:00-14:30
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Phylogeny
and comparative genomics
Lecture:
Construction and primary interpretation of phylogenetic tree
Hands-on
exercise Construction and primary interpretation of phylogenetic
trees
Lecture:
interpretation of phylogenetic trees
Hands-on
exercise: interpretation of phylogenetic trees
Lecture:
genome duplications
hands-on
exercise: genome duplications
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Monday
14:30-17:00
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Self
study
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Part
3: Systems Biology Coordinator
Lijnzaad
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To
learn the basics of a number of high through-put quantitative
experiments and their analysis, in particular microarrays and
protein mass-spectrometry. This requires the use of statistics and
multivariate analysis methods such as clustering, which are also
introduced.
To
know how to bioinformatically interrogate functional networks of
interactions between genes and proteins as obtained from
high-throughput experiments of protein-protein interactions and
protein-DNA interactions.
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Tuesday
9:00-16:30
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Transcriptomics
Introduction
to microarrays
Introduction
to microarray statistics
Clustering
Gene
Ontology
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Wednesday
9:00-16:30
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Proteomics
Lecture
Introduction proteomics
Hands-on
Mass Spectrometry Finger Printing (MS-FP)
Lecture(s)
Tandem Mass Spectrometry
Hands-on
Tandem Mass Spectrometry (MS/MS)
Lecture
De Novo Peptide sequencing
ands-on
De Novo sequencing (optional)
Lecture
Applications in proteomics
Hands-on
using NetworKIN
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Thursday
9:00-14:30
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Networks
Lecture
Interactome networks
Hands-on
Interactome networks
Lecture
'From Tandem Affinity Purification (TAP) to protein complexes'
Hands-on
'From Tandem Affinity Purification (TAP) to protein complexes'
Lecture
Complementary Data integration
Hands-on
Complementary Data integration
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Thursday
9:00-14:30
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Self
study
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Exam
and Question Hour
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Friday
12:00-12:30
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questions
regarding the topics and tasks that were covered during the week
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Friday
13:00-16:00
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Exam:OPEN
BOOK, pen&paper and PC-exercises
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Lecturers:
dr. Berend Snel
(b.snel@uu.nl) Department of Biology, Faculty of Science
dr. Guido Van den
Ackerveken (g.vandenackerveken@uu.nl) Department of Biology,
Faculty of Science
dr. Bas van Breukelen
(b.vanbreukelen@uu.nl) Department of Pharmaceutical Sciences,
Faculty of Science
dr. Gert Folkers
(gert@nmr.chem.uu.nl) Department of Chemistry, Faculty of Science
dr. Philip Lijnzaad
(p.lijnzaad@umcutrecht.nl) Molecular Cancer Research, University
Medical Center Utrecht
dr. Patrick Kemmeren
(p.kemmeren@umcutrecht.nl) Molecular Cancer Research, University
Medical Center Utrecht
dr. Carolien de Kovel
(C.deKovel@umcutrecht.nl) Department of Medical Genetics,
University Medical Center Utrecht
dr.
Ies Nijman (i.nijman@niob.knaw.nl) Hubrecht
Institute, University Medical Center Utrecht
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