CSE 427 Winter 2012
Course Calendar

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January
SundayMondayTuesdayWednesdayThursdayFridaySaturday
01 02
New Year's Day
03
HW0 assigned
10:30-11:50 Lecture
MGH 234
Basics of molecular biology: proteins, DNA
Hunter's primer
Molecular Biology handout
12:00-13:00 OH (Martin)
CSE 538
04 05
HW1 assigned
10:30 HW0 due
10:30-11:50 Lecture
MGH 234
Basics of molecular biology: replication, gene expression
06 07
08 09 10
10:30-11:50 Lecture
MGH 234
Basics of molecular biology: gene structure, genome organization
12:00-13:00 OH (Martin)
CSE 538
11 12
10:30-11:50 Lecture
MGH 234
Pairwise global alignment
Lectures 3-5 from CSE 527
13
14:30-15:30 OH (Kris)
CSE 218
14
15 16
Martin Luther King Day
17
HW2 assigned
10:00 HW1 due
10:30-11:50 Lecture
MGH 234
Pairwise local alignment, affine gap penalties
12:00-13:00 OH (Martin)
CSE 538
18 19
10:30-11:50 Lecture
MGH 234
Snow closure
20
14:30-15:30 OH (Kris)
CSE 218
21
22 23 24
10:30-11:50 Lecture
MGH 234
BLAST
Overview of the BLAST Algorithm
Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. (1990), "Basic local alignment search tool". Journal of Molecular Biology 215:403-410.
12:00-13:00 OH (Martin)
CSE 538
25 26
10:30-11:50 Lecture
MGH 234
BLAST statistics; amino acid substitution matrices
Section 6.5 from Ewens and Grant's book
Stephen Altschul's primer
27
14:30-15:30 OH (Kris)
CSE 218
28
29
22:00 HW2 due
30 31
HW3 assigned
10:30-11:50 Lecture
MGH 234
Multiple sequence alignment
Lectures 6 from CSE 527
12:00-13:00 OH (Martin)
CSE 538
01 02
10:30-11:50 Lecture
MGH 234
Extremely Conserved Elements
example of Theorem 2
03
14:30-15:30 OH (Kris)
CSE 218
04

February
SundayMondayTuesdayWednesdayThursdayFridaySaturday
05 06 07
10:30-11:50 Lecture
MGH 234
Progressive alignment; phylogeny construction
Building phylogenies
Overview of progressive alignment
12:00-13:00 OH (Martin)
CSE 538
08 09
10:30-11:50 Lecture
MGH 234
Markov chains
Markov Models
10
14:30-15:30 OH (Kris)
CSE 218
11
12 13 14
10:30-11:50 Lecture
MGH 234
Hidden Markov models; Viterbi algorithm
12:00-13:00 OH (Martin)
CSE 538
15 16
HW4 assigned
10:30-11:50 Lecture
MGH 234
Profile HMMs
Profile HMMs
17
14:30-15:30 OH (Kris)
CSE 218
18
19
22:00 HW3 due
20
Presidents Day
21
10:30-11:50 Lecture
MGH 234
Human microbiome
Microbes and you
22 23
10:30-11:50 Lecture
MGH 234
Human microbiome
Genome assembly
24
14:30-15:30 OH (Kris)
CSE 218
25
26 27 28
10:30-11:50 Lecture
MGH 234
Forward-backward algorithm
12:00-13:00 OH (Martin)
CSE 538
29 01
10:30-11:50 Lecture
MGH 234
Detecting recent positive selection
Gusfield's notes
02
14:30-15:30 OH (Kris)
CSE 218
03

March
SundayMondayTuesdayWednesdayThursdayFridaySaturday
04 05 06
10:30-11:50 Lecture
MGH 234
Detecting recent positive selection
12:00-13:00 OH (Martin)
CSE 538
07
15:00-16:00 OH (Kris)
CSE 216
08
10:30-11:50 Lecture
MGH 234
TBD
09
14:30-15:30 OH (Kris)
CSE 218
22:00 HW4 due
10