Last modified by varvio@helsinki_fi on 2024/03/27 10:35
Show last authors
1 = (% style="color: rgb(0,51,102);" %)Genetic analysis and molecular evolution, fall 2012(%%) =
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 4-6 cu.
10
11 === (% style="color: rgb(0,51,102);" %)Type and time schedule(%%) ===
12
13 Lectures, home-exercises, computer class sessions.
14
15 Weeks 36-42, Tuesday 14-16, Thursday 14-16 B120 and computer class C128 Tuesday 16-18 and negotiable additional sessions.
16
17 === (% style="color: rgb(0,51,102);" %)Prerequisites(%%) ===
18
19 Basic probabilistics and interest in bio-applications of statistics. This course is suitable for students with planned orientation to biometry and bioinformatics and also for other students interested in all-round-education on biological applications of statistical inference. In HU Bioinformatics Master´s program (MBI) this is one of the optionally compulsory courses and in Aalto-MBI a compulsory course.
20
21 === (% style="color: rgb(0,51,102);" %)Short description(%%) ===
22
23 Characteristics of molecules and inheritance as statistical and computational challenges.
24 Sequence databases - how to retrieve sequence information and use it for comparative purposes - multiple sequence alignment.
25 The neutral theory of molecular evolution - sequence evolution models and phylogeny inference.
26 Basics of genetic inheritance and population genetics.
27
28 (% style="color: rgb(0,51,102);" %)**4cr**(%%) Exam, based on lectures and assignments. Exam will be in computer class and you have access to all material.
29 (% style="color: rgb(0,51,102);" %)**6cr**(%%) Participating also in the Journal Club.
30
31 (% style="color: rgb(0,51,102);" %)**Week 1**
32
33 (% style="color: rgb(0,51,102);" %)Thu 6.9(%%)
34 (% style="color: rgb(0,51,102);" %)14-16, B120(%%)
35 (% class="confluence-link" %)First lecture.pdf
36
37 (% style="color: rgb(0,51,102);" %)**Week 2**
38
39 (% style="color: rgb(0,51,102);" %)Tue 11.9,(%%)
40 (% style="color: rgb(0,51,102);" %)14-16, B120(%%)
41 (% class="confluence-link" %)Modelling sequence evolution.pdf(%%)
42 (% style="color: rgb(0,51,102);" %)16-18, C128 (=computer class),(%%) This is for those who have not worked with sequence databases before. [[http:~~/~~/www.ncbi.nlm.nih.gov/>>url:http://www.ncbi.nlm.nih.gov/||shape="rect"]].
43 Those who are familiar with NCBI-database working can (probably) do the initial part of Assignment 1 (1a, below) without attending this computer class session.
44 (% class="confluence-link" %)Assignment 1a - Instructions for collecting data from NCBI.pdf(%%), (% class="confluence-link" %)Assignment 1 - Initial dataset.txt(%%),
45 Read these: (% class="confluence-link" %)NCBI BLAST.pdf(%%), (% class="confluence-link" %)Multiple sequence alignment.pdf
46
47 (% style="color: rgb(0,51,102);" %)Thu 13.9(%%)
48 (% style="color: rgb(0,51,102);" %)14-16, B120,(%%) (% class="confluence-link" %)Sequence relationships - Phylogenetic trees.pdf(%%), Distance matrix phylogenies as a handout-copy.
49
50 (% style="color: rgb(0,51,102);" %)**Week 3**
51
52 (% style="color: rgb(0,51,102);" %)Tue 18.9, 16-18, C128(%%)
53 (% class="confluence-link" %)Assignment 1b - Phylogenetic trees.pdf(%%), [[http:~~/~~/www.megasoftware.net/>>url:http://www.megasoftware.net/||shape="rect"]], [[http:~~/~~/www.hiv.lanl.gov/content/sequence/findmodel/findmodel.html>>url:http://www.hiv.lanl.gov/content/sequence/findmodel/findmodel.html||shape="rect"]].
54
55 (% style="color: rgb(0,51,102);" %)Thu 20.9, 14-16, C128(%%)
56 (% class="confluence-link" %)Assignment 1c - Substitution patterns and rates.pdf
57
58 (% class="confluence-link" %)Useful Phylo tutorial.pdf(%%), http:~/~/tolweb.org/tree/, http:~/~/www.timetree.org/, (% class="confluence-link" %)Today in Nature.pdf(%%),
59 (% class="confluence-link" %)Assignment 1 - Instructions for writing the report.pdf
60
61 (% style="color: rgb(0,0,0);" %)Reserve time for further personal advise from here:(%%) [[http:~~/~~/doodle.com/6frkpgknw7m7exnr>>url:http://doodle.com/6frkpgknw7m7exnr||shape="rect"]]
62
63 (% style="color: rgb(0,51,102);" %)**Week 4**
64
65 (% style="color: rgb(0,51,102);" %)Tue 25.9, 14-16, B120(%%)
66 Topics on molecular evolution will be completed later. Now we switch to topics on population genetics so that there will be enough time for assignment 2.
67 (% class="confluence-link" %)Inheritance, pedigree analysis.pdf(%%), (% class="confluence-link" %)The basic model in population genetics, Hardy-Weinberg.pdf(%%)
68 (% class="confluence-link" %)Assignment 2a.pdf
69
70 (% style="color: rgb(0,51,102);" %)Thu 27.9, 14-16, B120(%%)
71 Population genetics continues.
72 [[http:~~/~~/www.radford.edu/~~~~rsheehy/Gen_flash/popgen/>>url:http://www.radford.edu/%7Ersheehy/Gen_flash/popgen/||shape="rect"]], (% class="confluence-link" %)The basic selection model and Random genetic drift.pdf(%%)
73 (% class="confluence-link" %)Assignment 2b.pdf
74
75 (% style="color: rgb(0,51,102);" %)**Week 5**
76
77 (% style="color: rgb(0,51,102);" %)Tue 2.10, 14-16, B120 and 16-18 C128(%%)
78 The basic selection model and Random genetic drift continues.
79 Computer simulations. (% class="confluence-link" %)Assignment 2c.pdf
80
81 (% style="color: rgb(0,51,102);" %)**Week 6**
82
83 (% style="color: rgb(0,51,102);" %)Tue 9.10,(%%) (% style="color: rgb(0,51,102);" %)16-18, C128(%%)
84 (% style="color: rgb(0,51,102);" %)Assignment 1 presentations.
85
86 (% style="color: rgb(0,51,102);" %)Thu 11.10,(%%) (% style="color: rgb(0,51,102);" %)12.30-14, B120, 14-16, C128. Note the extra time 12.30-14 (the slot is free for this lecture because there will not be Algorithms for bioinformatics lecture.)(%%)
87 (% class="confluence-link" %)Last lecture.pdf(%%)
88 Assignment 1 presentations continue.
89 Assignment 2c presentations.
90 (% class="confluence-link" %)Assignment 2a Solutions.pdf(%%)
91 (% class="confluence-link" %)Assignment 2b Solutions.pdf
92
93 (% style="color: rgb(0,51,102);" %)**Week 7**
94
95 EXAM in computer class C128, Tue 16. October, 12-20.
96
97 === (% style="color: rgb(0,51,102);" %)**[[Course Moodle-area >>url:https://moodle.helsinki.fi/course/view.php?id=7366||shape="rect"]]**(%%) ===
98
99 === (% style="color: rgb(0,51,102);" %)Journal club(%%) ===
100
101 (% class="confluence-link" %)**Read instructions here.pdf**
102
103
104
105 (% class="confluence-link" %)Tree_of_life_1.pdf(%%), (% class="confluence-link" %)Human_pop_evo_1.pdf(%%), (% class="confluence-link" %)Human_pop_evo_3.pdf(%%), (% class="confluence-link" %)Human_pop_evo_6.pdf(%%), (% class="confluence-link" %)Human_pop_evo_7.pdf(%%), (% class="confluence-link" %)Disease_1.pdf(%%), (% class="confluence-link" %)Disease_2.pdf(%%), (% class="confluence-link" %)Disease_3.pdf(%%), (% class="confluence-link" %)Disease_4.pdf(%%), (% class="confluence-link" %)Animals_2.pdf(%%), (% class="confluence-link" %)Animals_3.pdf(%%), (% class="confluence-link" %)Bacteria_2.pdf(%%), (% class="confluence-link" %)Virus_1.pdf(%%), (% class="confluence-link" %)Virus_2.pdf(%%), (% class="confluence-link" %)General_1.pdf(%%), (% class="confluence-link" %)General_2.pdf(%%), (% class="confluence-link" %)General_4.pdf
106
107
108
109 (% class="confluence-link" %)Extra assignment 1.pdf
110
111 === [[Registration>>url:https://oodi-www.it.helsinki.fi/hy/opintjakstied.jsp?html=1&Tunniste=57748||shape="rect"]] ===
112
113 (% class="confluence-link" %)EXAM 16102012.pdf(%%), (% class="confluence-link" %)UK_MEX_FIN_data.txt