Wiki source code of Statistical genetics, fall 2011
Last modified by varvio@helsinki_fi on 2024/03/27 10:34
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| author | version | line-number | content |
|---|---|---|---|
| 1 | = (% style="color: rgb(0,51,102);" %)Statistical genetics, fall 2011(%%) = | ||
| 2 | |||
| 3 | === (% style="color: rgb(0,51,102);" %)Lecturer(%%) === | ||
| 4 | |||
| 5 | [[Sirkka-Liisa Varvio>>doc:mathstatHenkilokunta.Varvio, Sirkka-Liisa]] | ||
| 6 | |||
| 7 | === (% style="color: rgb(0,51,102);" %)Scope(%%) === | ||
| 8 | |||
| 9 | (% style="color: rgb(0,51,102);" %)**1-10 cu**(%%). | ||
| 10 | Credits by assignment sets, 5 sets, each 1cr, 3cr from a seminar. 1-2cr from Population genomics program during week 4. | ||
| 11 | You can collect credits by performing 1-5 assignment sets and by a seminar talk during the course and by listening and writing short reports from Population genomics lectures. | ||
| 12 | For getting 3cr from a seminar you also write an essay (this can be submitted later). | ||
| 13 | The course can be taken as intermediate or advanced studies in statistics. | ||
| 14 | In Bioinformatics master´s program (MBI) this course is one of the advanced bioinformatics courses and the seminar | ||
| 15 | can be taken as one of the compulsory seminars. | ||
| 16 | No exam; credits by assignments | ||
| 17 | |||
| 18 | === (% style="color: rgb(0,51,102);" %)Prerequisites, lectures, assignments, seminar(%%) === | ||
| 19 | |||
| 20 | (% style="color: rgb(0,0,0);" %)Prerequisites: Interest in genetics and knowledge on basic probability calculus. | ||
| 21 | |||
| 22 | Lectures: During the first three weeks only Thursdays 14-16 in room B120 and tutoring sessions with negotiable times. | ||
| 23 | Assignments: exercises, computer work, simulations. | ||
| 24 | |||
| 25 | ---- | ||
| 26 | |||
| 27 | (% style="color: rgb(0,51,102);" %)**Weeks 1-3,** | ||
| 28 | |||
| 29 | * (% class="confluence-link" %)Assignment set 1.pdf(%%), (% class="confluence-link" %)Population genetics basics I.pdf, (%%) | ||
| 30 | * (% class="confluence-link" %)Assignment set 2.pdf(%%), (% class="confluence-link" %)Population genetics basics II. pdf(%%), relevant background: (% class="confluence-link" %)Genetic relatedness analysis.pdf | ||
| 31 | |||
| 32 | ---- | ||
| 33 | |||
| 34 | * (% class="confluence-link" %)Bayesian genetic analysis.pdf(%%)((( | ||
| 35 | ---- | ||
| 36 | ))) | ||
| 37 | * (% class="confluence-link" %)Assignment 3.pdf(%%), (% style="color: rgb(255,0,0);" %)NOTE:(%%) this dataset works: (% class="confluence-link" %)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. | ||
| 38 | Links to servers: [[http:~~/~~/sift.jcvi.org/>>url:http://sift.jcvi.org/||shape="rect"]], [[http:~~/~~/selecton.tau.ac.il/>>url:http://selecton.tau.ac.il/||shape="rect"]] (for collecting data you need this: [[http:~~/~~/www.ncbi.nlm.nih.gov/>>url:http://www.ncbi.nlm.nih.gov/||shape="rect"]]) | ||
| 39 | ** (% class="confluence-link" %)Diagnosing mutations.pdf(%%), (% class="confluence-link" %)Bayesian inference in selection detecting at the level of proteins.pdf(%%), (% class="confluence-link" %)SIFT algorithm for non-synonymous mutation prediction.pdf(%%), | ||
| 40 | |||
| 41 | ---- | ||
| 42 | |||
| 43 | (% style="color: rgb(0,51,102);" %)**Week 4,**(%%) | ||
| 44 | 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. | ||
| 45 | Lecturers: Matthieu Foll and Daniel Wegmann from Switzerland, Peter Tiffin from USA, Chris Wheat from UK/Viikki. | ||
| 46 | |||
| 47 | (% style="color: rgb(0,51,102);" %)**Lecture slides and other material** | ||
| 48 | |||
| 49 | * [[attach:M Foll, Introduction to the coalescent.pdf]] | ||
| 50 | * [[attach:M Foll, Extensions of the coalescent.pdf]] | ||
| 51 | * [[M Foll, Selection and coalescent.pdf>>attach:M Foll, Selection and coalescent.pdf]] | ||
| 52 | * [[attach:M Foll, Practicals coalescent.pdf]], [[attach:fastsimcoal Manual.pdf]], [[http:~~/~~/cmpg.unibe.ch/software/fastsimcoal/>>url:http://cmpg.unibe.ch/software/fastsimcoal/||shape="rect"]] | ||
| 53 | * [[attach:D Wegmann, Demography inference from genetic data.pdf]], [[attach:ABC Manual.pdf]], [[http:~~/~~/www.cmpg.iee.unibe.ch/content/softwares~~_~~_services/computer_programs/abctoolbox/index_eng.html>>url:http://www.cmpg.iee.unibe.ch/content/softwares__services/computer_programs/abctoolbox/index_eng.html||shape="rect"]] | ||
| 54 | * P Tiffin, Nature of data sets and signals of selection, Selection and demography in ecological contexts. Slides will be added if they come available | ||
| 55 | * C Wheat, Functional genomics of life history variation. Slides will be added if they come available. | ||
| 56 | |||
| 57 | 2cr from this program: attending all lectures (10-14h) + lecture diary (short reports). | ||
| 58 | 1cr from this program: attending ~~half of the lectures + lecture diary (short reports). | ||
| 59 | |||
| 60 | ---- | ||
| 61 | |||
| 62 | (% style="color: rgb(0,51,102);" %)**Week 5** | ||
| 63 | |||
| 64 | ---- | ||
| 65 | |||
| 66 | (% style="color: rgb(0,51,102);" %)**Tue 29. Nov, 12.30~-~->**(%%) in computer class C128, Assignment 4 introduction | ||
| 67 | |||
| 68 | * (% class="confluence-link" %)Assignment 4.doc | ||
| 69 | ** Data analysis by this software: [[http:~~/~~/www.ub.edu/dnasp/>>url:http://www.ub.edu/dnasp/||shape="rect"]], or by this: [[http:~~/~~/cmpg.unibe.ch/software/arlequin35/>>url:http://cmpg.unibe.ch/software/arlequin35/||shape="rect"]] | ||
| 70 | ** Population data from here: [[http:~~/~~/www.pypop.org/>>url:http://www.pypop.org/||shape="rect"]] and allele sequences here: (% class="confluence-link" %)drb1 sequences.txt | ||
| 71 | |||
| 72 | ---- | ||
| 73 | |||
| 74 | (% style="color: rgb(0,51,102);" %)**Thu 1. Dec, 14.15 -15**(%%) (% style="color: rgb(0,51,102);" %)**in B120, 15~-~-> in computer class C128**(%%), Assignment 5 introduction | ||
| 75 | |||
| 76 | * (% class="confluence-link" %)Assignment 5.pdf(%%), (% class="confluence-link" %)Stat gen software.pdf(%%), Lecture slides TBA, | ||
| 77 | ** Data: (% class="confluence-link" %)UK_FIN_MEX_alignedFASTA.txt(%%), (% class="confluence-link" %)USA_before_vacc.txt(%%), (% class="confluence-link" %)USA_after_vacc.txt(%%), (% class="confluence-link" %)Skand_before_vacc.txt(%%), (% class="confluence-link" %)Skand_after_vacc.txt | ||
| 78 | |||
| 79 | ---- | ||
| 80 | |||
| 81 | (% style="color: rgb(0,51,102);" %)**Week 6**(%%) | ||
| 82 | (Tue 6. Dec is the Independence day of Finland, University is closed) | ||
| 83 | (% style="color: rgb(0,51,102);" %)T**hu 8. Dec,**(%%) | ||
| 84 | Seminar presentations: | ||
| 85 | |||
| 86 | ---- | ||
| 87 | |||
| 88 | (% style="color: rgb(0,51,102);" %)**Week 7** | ||
| 89 | |||
| 90 | (% style="color: rgb(0, 51, 102); text-decoration: line-through" %)**Thu 15. Dec, 14.15**> as long as needed(%%) (% style="color: rgb(255,0,0);" %)**Wed 25. Jan 2012, 15.15 - 18 in D340; this is a meeting room in 3. floor**(%%) | ||
| 91 | Seminar presentations: | ||
| 92 | [[attach:Gene expression variance in neurology.pdf]], (% style="text-decoration: line-through;" %)Ping(%%) (not coming) | ||
| 93 | [[attach:p-values and Bayes factors in genetic association studies.pdf]], Christian | ||
| 94 | [[attach:Markov random fields in GWAS.pdf]], Hailin | ||
| 95 | [[attach:Epigenetics.pdf]], Khadeeja | ||
| 96 | [[attach:Stat inference of natural selection shaping immunity genes.pdf]], Jimmy | ||
| 97 | [[attach:Genetic variants to be discovered.pdf]], Jian | ||
| 98 | [[attach:Genetic classification by supervised learning.pdf]], Chunxiang (?) | ||
| 99 | Bayesian analysis of population structure, Fitsum | ||
| 100 | A family based association study, (% style="text-decoration: line-through;" %)Anju(%%) (not coming) | ||
| 101 | Comparative Studies of de novo Assembly Tools for Nextgeneration Sequencing Technologies, Shafiqul | ||
| 102 | |||
| 103 | ---- | ||
| 104 | |||
| 105 | [[attach:PC-analysis and allele surfing.pdf]] | ||
| 106 | [[attach:Gene-based tests of association.pdf]] | ||
| 107 | [[attach:Hitchhiking of deleterious mutations.pdf]] | ||
| 108 | [[attach:Mapping mobile elements in human genome.pdf]] | ||
| 109 | [[attach:Selection mapping of dog phenotypes.pdf]] | ||
| 110 | |||
| 111 | You can also suggest a topic of your own. | ||
| 112 | The presentation in December (~~20-30min) can be based on only one literature reference (the one here, above, or the one you have found by yourself). | ||
| 113 | The written essay (to be submitted in January), 5-8 pages, should include ~~ 3 additional references. These are the requirements for 3cr from a seminar | ||
| 114 | to be registered for you. You should also follow other student´s presentations. | ||
| 115 | If you want to give a presentation but not write an essay, you get 1cr. | ||
| 116 | |||
| 117 | ---- | ||
| 118 | |||
| 119 | === [[Registration>>url:https://oodi-www.it.helsinki.fi/hy/opintjakstied.jsp?html=1&Tunniste=57734||shape="rect"]] === | ||
| 120 | |||
| 121 | (% style="color: rgb(255,0,0);" %)**NOTE:**(%%) Information about time schedule and credits given here in the course home page is valid information and information given in Weboodi-registration page (initially constructed last spring) is not updated/valid information (i.e. getting credits is more flexible and there are more options, for example the seminar option). | ||
| 122 | |||
| 123 | Did you forget to register? [[What to do>>doc:mathstatOpiskelu.Kysymys4]]. |