Introduction to Bioinformatics Fall 2007-2008

Current Course found here

Overview:

This course is an introduction to the field of bioinformatics for students from Life Sciences and Medicine.
The aim of the course is to familiarize students with modern methods bioinformatics used for current Biology research.

Teaching instructors: Tal Pupko and Adi Stern.
Teaching assistant: Adi Doron, Nimrod Rubinstein and Dudu Burstein.
Course hours: Sunday, 14:00-16:00, Sherman 105.


Exercises:

Exercises will be held in the computer classroom (Sherman 03) on Sunday, 16:00-18:00. Monday, 12:00-14:00, and 14:00-16:00.
Each student will participate once in two weeks.

Announcements:

The average of the HW assignments will be determined according to the 5 best scores. This means that HW6 is optional and is due to April 6nd 2008!!!

Note that the following exercise will take place on 17/2 and 18/2 (instead of 10/2 and 11/2 as previously announced). The exercise after that will only be one week later (24/2, 25/2).

HW and CW grades
For questions email: Adi Doron

Updated Syllabus

Class Date Topic Presentation
Lesson 1 20.01.2008  Computational biology -
 revolutionizing science at the turn of the century		 1-Revolution.ppt
LargeScaleUpdated.ppt
*presentation updated to include only what was taught, 9/3/08
Lesson 2 27.01.2008  Large scale analyses 2-LargeScale.ppt
Lesson 3 01.02.2008 Friday 09:15  Sequence alignment & BLAST 3-4-SequenceAlignment.ppt
Lesson 4 03.02.2008  Sequence alignment & BLAST  
Lesson 5 10.02.2008  Predictions from protein sequence 5-6-Proteins predictions&Into the genomes.ppt *
*Slides 65, 67 added, slides 62,77 changed
Lesson 6 17.02.2008  Into the genome  
Lesson 7 24.02.2008  Phylogenetic trees 7phylogeny.ppt
Lesson 8 02.03.2008  Functional prediction in proteins (purifying and positive selection) using evolution 8_functional_prediction
Lesson 9 09.03.2008  Large-scale molecular biology, Part II: Expression data and networks 9_largeScale part2(lesson1)
9.5_E-Predict
Lesson 10 16.03.2008  Protein structures 10_proteinStructures
Lesson 11 23.03.2008  Machine learning 11_MachineLearning


Exercises Dates Topic Presentation Class work Class work solution Home work Home work solution
Exercise 1 21,22.01.2008   Introduction to databases Databases.ppt CW1   HW1  
Exercise 2 3,4.02.2008   Pairwise alignment PairwiseAlignment.ppt CW2   HW2*  
Exercise 3 17,18.02.2008   Genome browsers / protein domains InterPro_prosite_UCSC.ppt CW3   HW3**  
Exercise 4 24,25.02.2008   MSA and trees msa_phylogeny.ppt CW4  
HW4
globin_human.aln 		 
Exercise 5 9,10.03.2008   Evolutionary rates evolutionary_rates.ppt CW5
pp2c.aln 1t82.aln 		 
HW5***
protease.fas protease.tree

 
Exercise 6 23,24.03.2008   Protein structure 6_proteinStructure.ppt sample_questions  
HW6

  

* Note: A (minor) clarification was added in question 3 of HW2 (it is marked in blue). Good luck.

** HW3 is due to March 2nd 2008. Please submit it on the lesson (there is no exercise on that week) or to Tal Pupko's post box in Britannia building 2nd floor near 222.

*** HW5 is due to March 30th. Please submit it to Tal Pupko's post box.