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Lecture

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Lab

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January
Sunday	Monday	Tuesday	Wednesday	Thursday	Friday	Saturday
06	07	08 HW0 out 10:30-11:50 Lecture SAV 139 Basics of molecular biology: proteins, DNA, replication Hunter's primer Molecular Biology handout 15:00-16:00 OH (PV) CSE 218	09 17:00 HW0 due	10 HW1 out 10:30-11:50 Lecture SAV 139 Basics of molecular biology: gene expression and structure 12:30-13:25 OH (MT) CSE 538	11	12
13	14	15 10:30-11:50 Lecture SAV 139 Pairwise global alignment Lectures 3-5 from CSE 527 15:00-16:00 OH (PV) CSE 218	16	17 10:30-11:50 Lecture SAV 139 Pairwise local alignment, affine gap penalties 12:30-13:25 OH (MT) CSE 538	18	19
20	21 Martin Luther King Day 22:00 HW1 due	22 HW2 out 10:30-11:50 Lecture SAV 139 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. 15:00-16:00 OH (PV) CSE 218	23	24 10:30-11:50 Lecture SAV 139 BLAST statistics; amino acid substitution matrices Section 6.5 from Ewens and Grant's book Stephen Altschul's primer 12:30-13:25 OH (MT) CSE 538	25	26
27	28	29 10:30-11:50 Lecture SAV 139 Multiple sequence alignment Lectures 6 from CSE 527 Overview of progressive alignment 15:00-16:00 OH (PV) CSE 218	30	31 10:30-11:50 Lecture SAV 139 UCSC Genome Browser, Extremely Conserved Elements example of Theorem 2 12:30-13:25 OH (MT) CSE 538	01	02

February
Sunday	Monday	Tuesday	Wednesday	Thursday	Friday	Saturday
03 22:00 HW2 due	04	05 HW3 out 10:30-11:50 Lecture SAV 139 Phylogeny construction Building phylogenies 15:00-16:00 OH (PV) CSE 218	06	07 10:30-11:50 Lecture SAV 139 Markov chains and classification Markov Models 12:30-13:25 OH (MT) CSE 538	08	09
10	11	12 10:30-11:50 Lecture SAV 139 Hidden Markov models 15:00-16:00 OH (PV) CSE 218	13	14 10:30-11:50 Lecture SAV 139 Profile HMMs Profile HMMs 12:30-13:25 OH (MT) CSE 538	15	16
17	18 Presidents Day	19 HW4 out 10:30-11:50 Lecture SAV 139 Motif discovery; statistical overrepresentation; MEME Prediction of sequence motifs 15:00-16:00 OH (PV) CSE 218 22:00 HW3 due	20	21 10:30-11:50 Lecture SAV 139 Gibbs sampling; FootPrinter 12:30-13:25 OH (MT) CSE 538	22	23
24	25	26 10:30-11:50 Lecture SAV 139 MicroFootPrinter MEME and Gibbs demo 15:00-16:00 OH (PV) CSE 218	27	28 10:30-11:50 Lecture SAV 139 Technical details of profile HMMs 12:30-13:25 OH (MT) CSE 538	01	02

March
Sunday	Monday	Tuesday	Wednesday	Thursday	Friday	Saturday
03	04	05 10:30-11:50 Lecture SAV 139 Microbiomes Microbes and You 15:00-16:00 OH (PV) CSE 218	06	07 10:30-11:50 Lecture SAV 139 More profile HMMs and microbiomes 12:30-13:25 OH (MT) CSE 538	08 22:00 HW4 due	09
10	11	12 10:30-11:50 Lecture SAV 139 Colonization of infant gut Infant gut microbiome 15:00-16:00 OH (PV) CSE 218	13	14 10:30-11:50 Lecture SAV 139 Other directions, Schnapsen Challenges in computational biology 12:30-13:25 OH (MT) CSE 538	15	16