dna microarray analysis - cbs · 2011. 1. 2. · dna microarray analysis course #27612 3-21 january...
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DNA Microarray AnalysisCourse #27612
3-21 January 2011
DTU
Center for Biological Sequence analysis (CBS)
søndag den 2. januar 2011
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Carsten FriisAssistant professorChemical Engineer and PhD from DTUWorked with bioinformatics since 1997 and microarray data since 2000
Teaching on this course: R and Exercises in Statistics.
of the course
Teachers
søndag den 2. januar 2011
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Agnieszka JunkerGraduate Engineer and PhD in Bioinformatics from DTUWorked with bioinformatics and microarray data since 2000
Teaching on this course: Dimension reduction, several exercises & assistant course coordinator.
of the course
Teachers
søndag den 2. januar 2011
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Nils Weinhold & Tune PersPhD studentsSpecializes in Human Disease Genetics
Teaching on this course: Genome Wide Association
of the course
Teachers
Nils
Tune
søndag den 2. januar 2011
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5
of the course
Additional Teachers
Hanne Jarmer
søndag den 2. januar 2011
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5
of the course
Additional Teachers
Hanne Jarmer
Aron C. Eklund
søndag den 2. januar 2011
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5
of the course
Additional Teachers
Hanne Jarmer
Aron C. Eklund
Chris Workman
søndag den 2. januar 2011
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5
of the course
Additional Teachers
Hanne Jarmer
Aron C. Eklund
Chris Workman
Simon Rasmussen
søndag den 2. januar 2011
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5
of the course
Additional Teachers
Hanne Jarmer
Aron C. Eklund
Chris Workman
Simon Rasmussen
Ramneek Gupta
søndag den 2. januar 2011
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5
of the course
Additional Teachers
Hanne Jarmer
Aron C. Eklund
Chris Workman
Simon Rasmussen
Ramneek Gupta
Kirstine Belling
søndag den 2. januar 2011
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5
of the course
Additional Teachers
Hanne Jarmer
Aron C. Eklund
Chris Workman
Simon Rasmussen
Ramneek Gupta
Kirstine Belling
Agata Wesolowska
søndag den 2. januar 2011
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5
of the course
Additional Teachers
Hanne Jarmer
Aron C. Eklund
Chris Workman
Simon Rasmussen
Ramneek Gupta
Kirstine Belling
Ulrik Plate
Agata Wesolowska
søndag den 2. januar 2011
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H. Bjørn Nielsen Associate professorMC in Biology (KU), PhD from DTUWorked with microarray data since 1999
Teaching on this course:, Preprocessing, Statistics, Project work and Course organizer
of the course
Teachers
søndag den 2. januar 2011
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The course has 36 students signed up
2 Bachelor students (2 bioteknologi)
22 Master students (11 System Biology, 11 bioteknologi)
10 PhD students
2 guest students
the students
Who are you
søndag den 2. januar 2011
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・ Account for the individual steps in a general microarray analysis・ Explain the overall theoretical principles behind the individual steps in the
analysis・ Account for the preconditions and assumptions in the individual steps of
the analysis・ Independently apply a basal microarray analysis・ Read into and manipulate simple data structures in the statistical
computing environment R・ Formulate problem formulations that may be answered by microarray
analysis・ Answer the problem formulated by the students・ Collaborate in a group about the project work
for the course
Learning Objectives (L.O.)
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for the course
Learning Objectives (L.O.)
That the student learn
A) To apply the methods for microarray analysis on real data
C) To manipulate simple data structures in the statistical computing environment R
B) To formulate interesting hypotheses that can be addressed by microarray data analysis
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of the course
Content
Tree main tracksA) Lectures, discussions and exercises
on microarray analysis
B) Lectures and exercises on R
C) Problem formulation and project
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Project Period
time schedule
The Course Tracks
Intro The Pipeline Advanced Analysis
Project Intro ProblemFormulation Project
PosterSessionR Learning by doing
Array exercises
12th of January 21th of January3th of January
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Track A: The DNA Array Analysis Pipeline
Sample PreparationHybridization
Design Arrayor bye a
standard array
Experimental Design
Statistical AnalysisFit to Model (time series)
Expression IndexCalculation
Advanced Data AnalysisClustering PCA Gene Annotation Analysis Promoter Analysis
Classification Meta analysis Survival analysis Regulatory Network
ComparableGene Expression Data
Normalization
Image analysis
Question/hypothesis
NGS data
Mapping
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problem formulation
Track C
Group formation
Problem formulation (Finalized, Wednesday week 2)
Projects (Initialized Wednesday week 2)
Poster session (21th of January, exam)
søndag den 2. januar 2011
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Course web page
• Course program• Lecture Slides• Exercises• And more
www.cbs.dtu.dk/chipcourse
søndag den 2. januar 2011