BIO520 Bioinformatics Syllabus (also listed as INF 520)
Spring 2010

Lecture MW 2-3 pm, BS 108 (Morgan biology building)
Lab	F 2-4 pm, Young B-35 (Library basement)

Course website: http://elegans.uky.edu/520/

Instructor:
	TA:	
	Jim Lund	 Tseten Yeshi	
	jiml@uky.edu	 tgyeshi@uky.edu	
	311 Morgan Building, 0225	 311 Morgan	
	257-1034	 257-9847	
	Office hours: 3-4 PM Wed.	 	
	Available after class		

Course Description
	BIO520 provides an introduction to applying computational approaches to biological problems.  This course describes how to acquire information from biological databases, use computational approaches to analyze this information, and interpret the results as a guide to experiments in biology.  The course surveys computational approaches to DNA, RNA, protein, and genomic data, as well as the use of biological databanks.  Prereq: BIO 315 or BIO 304 or BCH 304 or BCH 401 or BCH 501 or BCH 502 or BIO 510 or consent of instructor.

Texts:
One text is required:
	Understanding Bioinformatics.  (2008).  Marketa Zvelebil and Jeremy Baum.  

Other good books on bioinformatics that may be useful:
	Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, 3rd Edition 			(2001) Andreas D. Baxevanis (Editor) and B. F. Francis Ouellette (Editor).
-short but very good discussions of each topic along with descriptions of software tools.
	Bioinformatics: Sequence and Genome Analysis, 2nd ed. (2004) D.W. Mount
		-thorough treatment of sequence comparison
	Bioinformatics and Functional Genomics (2003) Jonathan Pevsner
		-great survey of the completed genomes
	Introduction to Protein Structure, 2nd ed (1999) C. Branden and J. Tooze
		-comprehensive information on proteins.

The biology in this class is covered best by:
Genes IX, Lewin (or earlier editions) 
Cell biology books (eg.by Watson, et al or Darnell, et al)  or 	
Genetics texts (Modern Genetic Analysis by Griffiths, et al) are 	useful.
Program documentation is usually INVALUABLE.

Objectives
Students completing BIO/INF520 should:
•	Understand biological concepts fundamental to bioinformatics:
o	gene structure, gene expression, and genome structure in a phylogenetic context
o	protein structure and function
•	Be able to evaluate information from molecular genetic experiments typical of genomic analyses (sequence analysis, transcriptome analysis, proteome analysis)
•	Understand functional analyses including genetic mapping, deletion analysis, and be exposed to other forms of functional analysis
•	Understand and be able to implement computer use including sophisticated use of the web-based programs, configuration of downloaded programs.  Computer programming is NOT taught nor essential.
•	Be familiar with bioinformatics software, including web-based tools such as Entrez, BLAST, and protein visualization tools
•	Have a command of all topics listed on the syllabus below, including:
o	Genomic data acquisition, access, and analysis
o	Comparative and predictive analyses of DNA and protein sequence
o	Phylogenetic inference

Computer Requirements 
University lab computers are sufficient for this course.  Experience has shown that most manipulations in this course can be satisfactorily accomplished on a typical computer with a net connection.

Grading (and cheating policy)
Each lab assignment is worth 10 points. The 2 hour exams are worth 50 points each. The final exam is worth 50 points. Grades will be no worse than the standard 90/80/70/60 scale, but I reserve the right to liberalize grades to achieve a distribution more typical of a graduate/undergraduate class.  PLEASE NOTE that student grades on weekly assignments are generally very high, but experience shows that grades on exams may be much lower.  The goal of weekly labs is MASTERY, not just completion.

Students may collaborate on assignments in general terms, but they should individually complete each assignment. Exams are to be done individually.  Inappropriate contact during an exam will be considered cheating and will be prosecuted as such via normal UK channels!  The minimum penalty for cheating is a disciplinary E, which cannot be removed from one’s transcript by a repeat option.

Date	Topic	Reading	
1/13	1. Intro. Bioinformatics 	Ch 1, 2 	
1/15	2. Biology review, lab familiarization	Biology textbooks	
1/18	MLK day, no class 	Ch 3	
1/20	3. DNA sequences-formats, databases 	Ch 4, 5	
1/22	Sequence databases and DNA sequence manipulations, Biology background.	LAB1	
1/25	4. Sequence comparison-alignment basics		
1/27	5. Multiple sequence alignment	Ch 6	
1/29	Pairwise sequence alignment 	LAB2	
2/1	6. Scoring matrices and PSSMs 	Baxevanis Ch 5	
2/3	7. Intro to Phylogenetics	Ch 7	
2/5	Multiple sequence alignment 	LAB3	
2/8	8. Phylogenetic infer ence	Ch 8	
2/10	Exam review		
2/12	Phylogenetic inference 	LAB7	
2/15	9. Protein structure and visualization	Ch 11	
2/17	10. Protein structure 	Ch 12	
2/19	EXAM1 covers 1/14 – 2/12		
2/22	11. Predicting protein properties	Ch 13, 14	
2/24	12. RNA structure prediction	Baxevanis Ch 6	
2/26	Protein motif prediction	LAB4	
3/1	13. DNA sequencing		
3/3	14. Genome sequencing	Ch 9	
3/5	3D protein structure	LAB5	
3/8	TBA		
3/10	15. Genefinding-Prokaryotes		
3/12	Protein structure prediction	LAB6	
3/15-3/19	NO CLASS, Spring Break		
3/22	16. Genefinding-Eukaryotes		
3/24	17. Genefinding-approaches and tools		
3/26	Gene prediction	LAB8	
3/29	18. Genomes, Genome Databases	Ch 10 	
3/21	Exam review		
4/2	EXAM2 covers 2/9 – 3/25		
4/5	Genome sequencing journal club		
4/7	19. Transcription Analyses	Ch 15	
4/9	DNA sequence assembly	LAB9	
4/12	20. Transcriptome	Ch 16	
4/14	21. Trait mapping, QTLs	Ch 17	
4/16	Microarrays/Transcriptome	LAB10	
4/19	22. Proteomics		
4/21	23. Functional genomics		
4/23	Proteomics/Functional Genomics	LAB11	
4/26	24. Comparative genomics	Baxevanis Ch 15	
4/28	Review Session		
4/30	Comparative genomics	LAB12 (due 5/4)	
5/8 Friday	FINAL EXAM 8-10 AM