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Lectures: During the first three weeks only Thursdays 14-16 in room B120 and tutoring sessions with negotiable times.
Assignments: exercises, computer work, simulations.

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Weeks 1-3,

  • Assignment set 1.pdf, Population genetics basics I.pdf,  NOTE: You don´t have to obey the originally given deadlines for submitting assignments 1,2,3,4,5. 
  • Assignment set 2.pdf, Population genetics basics II. pdf, relevant background: Genetic relatedness analysis.pdf

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  • Bayesian genetic analysis.pdf
  • Assignment 3.pdf, NOTE: this dataset works: Growth hormone DNA stop codons removed.txt, submit it to Selecton and take one sequence translated into protein and submit to SIFT. And concentrate on interpreting the results.
    Links to servers: http://sift.jcvi.org/, http://selecton.tau.ac.il/ (for collecting data you need this: http://www.ncbi.nlm.nih.gov/)
    • Diagnosing mutations.pdf, Bayesian inference in selection detecting at the level of proteins.pdf, SIFT algorithm for non-synonymous mutation prediction.pdf,

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Week 4,
We have the possibility to exploit the lecture program of Population genomics graduate school having an intensive course in Kumpula and topics closely related to our Statistical genetics course.
Lecturers: Matthieu Foll and Daniel Wegmann from Switzerland, Peter Tiffin from USA, Chris Wheat from UK/Viikki.

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Tue 29. Nov, 12.30--> in computer class C128, Assignment 4 introduction

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Thu 1. Dec, 14.15 -15 in B120, 15--> in computer class C128, Assignment 5 introduction

  • Assignment 5.pdf, Stat gen software.pdf, Lecture slides TBA,
    • Data: UK_FIN_MEX_alignedFASTA.txt, USA_before_vacc.txt, USA_after_vacc.txt, Skand_before_vacc.txt, Skand_after_vacc.txt

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Week 6
(Tue 6. Dec is the Independence day of Finland, University is closed)
Thu 8. Dec,
Seminar presentations:
Global distribution of human genomic diversity.pdf, Alejandra
Genetics of financial risk taking.pdf, Xiaofeng
Math-stat laws of genome evolution.pdf, Yang
Principal component analysis and unraveling gene expression, Juha
Protein Sequence and Structure prediction, Muhammed

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Week 7

Thu 15. Dec, 14.15> as long as needed    Wed 25. Jan 2012, 15.15 - 18 in D340; this is a meeting room in 3. floor
Seminar presentations:
Gene expression variance in neurology.pdf, Ping (not coming)
p-values and Bayes factors in genetic association studies.pdf, Christian
Markov random fields in GWAS.pdf, Hailin
Epigenetics.pdf, Khadeeja
Stat inference of natural selection shaping immunity genes.pdf, Jimmy
Genetic variants to be discovered.pdf, Jian
Genetic classification by supervised learning.pdf, Chunxiang (?)
Bayesian analysis of population structure, Fitsum
A family based association study, Anju (not coming)
Comparative Studies of de novo Assembly Tools for Nextgeneration Sequencing Technologies, Shafiqul

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