MO640	Computational Biology	2015
		Instructor: Joao Meidanis
		TENTATIVE SCHEDULE	CONSULT OFTEN, CHANGES MAY OCCUR
WD	Date	Topic	Text	Date	Relevant Events
ter	02/24/2015
qui	02/26/2015	Course presentation		02/27/2015	Special Student Registration
ter	03/03/2015	Molecular Biology Concepts	SM 1997 (chap.1), C-B 2010	02/28/2015	Special Student Registration
qui	03/05/2015	Molecular Biology Concepts	SM 1997 (chap.1), C-B 2010
ter	03/10/2015	Informatics Concepts	SM 1997 (chap.2)
qui	03/12/2015	Multidisciplinarity	Eddy 2005
ter	03/17/2015	Sequence comparison	SM 1997 (sec.3.2.1), PS 2011 (sec.4.4)
qui	03/19/2015	Sequence comparison	SM 1997 (sec.3.2.2,3.3.1,3.3.4,3.5.1,3.5.2,3.6.1), PS 2011 (sec.4.4)
ter	03/24/2015	Jukes-Cantor and Kimura Models	Durand 2014, Felsenstein 2004 (p.196-200)
qui	03/26/2015	Evaluation 1
ter	03/31/2015	Phylogenetic trees: Parsimony	Felsenstein 2004 (chap.1)
qui	04/02/2015	No lecture: Holy Thursday
ter	04/07/2015	Characters and Distances	SM 1997 (p.175-196), Felsenstein 2004 (p.1-96,p.147-176)
qui	04/09/2015	GR: representation of signed, multi-chromossomal genomes	FM 2011, PS 2011 (chap.9), SM 1997 (chap.7)
ter	04/14/2015	GR: Single-Cut-or-Join, distance, weighted median, median	FM 2011
qui	04/16/2015	GR: Single-Cut-or-Join, small phylogeny, big phylogeny	FM 2011
ter	04/21/2015	No lecture: Tiradentes Holiday		04/28/2015	Last day for class withdrawal
qui	04/23/2015	GR: Double-Cut-and-Join, distance	YAF 2005
ter	04/28/2015	Evaluation 2
qui	04/30/2015	GR: Algebraic distance, permutations	FM 2013
ter	05/05/2015	GR: DCJ, adjacency graph	YAF 2005, FM 2011
qui	05/07/2015	GR: Algebraic distance, definition, relationship with DCJ	FM 2013
ter	05/12/2015	GR: Matrix median approximation	ZBM 2013, algorithm.pdf
qui	05/14/2015	GR: Unichromosomal genomes: reversal	HP 1999, Bergeron 2005
ter	05/19/2015	GR: Unichromosomal genomes: block interchange	Christie 1996	05/19/2015	Last day for course withdrawal
qui	05/21/2015	Evaluation 3
ter	05/26/2015	Fine gene structure	Benzer 1959
qui	05/28/2015	Prob.dict.order, Consecutive ones property	Benzer 1959, SM 1997 (p.149-159)
ter	06/02/2015	PQ Trees: introduction	BL 1976
qui	06/04/2015	No lecture: Corpus Christi Holiday
ter	06/09/2015	Consecutive ones property: Solving components	SM 1997 (p.154-157)
qui	06/11/2015	PQR Trees: off-line algorithm	MPT 1998
ter	06/16/2015	PQ/PQR Trees: on-line algorithm	BL 1976, ?
qui	06/18/2015	Evaluation 4
ter	06/23/2015
qui	06/25/2015
ter	06/30/2015				Last day of classes
qui	07/02/2015	Study Week (for undergrads)
ter	07/07/2015	Study Week (for undergrads)
qui	07/09/2015
ter	07/14/2015	Exam (for undergrads)
qui	07/16/2015