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    BIO 531-Computational Biology-Aziz Mithani

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    This document provides information about the Computational Biology course offered at Lahore University of Management Sciences in Fall 2018. The course is 3 credit hours and will meet twice a week for 1 hour and 15 minutes lectures. Grading will be based on assignments, quizzes, attendance, midterm and final exams. The course introduces computational tools for DNA and protein sequence analysis, phylogenetic analysis, and biological networks. The course is intended to provide foundational knowledge in key computational biology concepts and techniques.

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    BIO 531-Computational Biology-Aziz Mithani

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    Anonymous sF8ZuiG
    111 views3 pages
    This document provides information about the Computational Biology course offered at Lahore University of Management Sciences in Fall 2018. The course is 3 credit hours and will meet twice a week for 1 hour and 15 minutes lectures. Grading will be based on assignments, quizzes, attendance, midterm and final exams. The course introduces computational tools for DNA and protein sequence analysis, phylogenetic analysis, and biological networks. The course is intended to provide foundational knowledge in key computational biology concepts and techniques.

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    This document provides information about the Computational Biology course offered at Lahore University of Management Sciences in Fall 2018. The course is 3 credit hours and will meet twice a week for 1 hour and 15 minutes lectures. Grading will be based on assignments, quizzes, attendance, midterm and final exams. The course introduces computational tools for DNA and protein sequence analysis, phylogenetic analysis, and biological networks. The course is intended to provide foundational knowledge in key computational biology concepts and techniques.

    Copyright:

    © All Rights Reserved
    Download as PDF, TXT or read online from Scribd
    Download as pdf or txt
    111 views3 pages

    BIO 531-Computational Biology-Aziz Mithani

    Uploaded by

    Anonymous sF8ZuiG
    This document provides information about the Computational Biology course offered at Lahore University of Management Sciences in Fall 2018. The course is 3 credit hours and will meet twice a week for 1 hour and 15 minutes lectures. Grading will be based on assignments, quizzes, attendance, midterm and final exams. The course introduces computational tools for DNA and protein sequence analysis, phylogenetic analysis, and biological networks. The course is intended to provide foundational knowledge in key computational biology concepts and techniques.

    Copyright:

    © All Rights Reserved
    Download as PDF, TXT or read online from Scribd
    Download as pdf or txt
    of 3

    Lahore University of Management Sciences

    BIO 531 –Computational Biology


    Fall 2018
    Instructor Dr Aziz Mithani
    Room No. 9-319A
    Office Hours Mondays and Tuesdays 9am to 10am
    Email [email protected]
    Telephone 8397
    Secretary/TA Madiha Shabbir
    TA Office Hours
    Course URL (if any)

    Course Basics
    Credit Hours 3
    Lecture(s) Nbr of Lec(s) Per Week 2 Duration 1hr 15 mins
    Recitation (per week) Nbr of Rec (s) Per Duration
    Week
    Lab (if any ) per week Nbr of Session(s) Per Duration
    Week
    Tutorial (per week) Nbr of Tut(s) Per Duration
    Week

    Course Distribution
    Core Yes
    Elective
    Open for Student Category Any
    Closed for Student Category

    COURSE DESCRIPTION
    This course provides introduction to computational biology introducing the tools and techniques important to study and analyze genomic data.
    This course emphasises on the fundamentals of nucleic acid and protein sequence analysis, phylogenetic analysis and the analysis of biological
    networks.

    COURSE PREREQUISITE(S)

    •
    •

    COURSE OBJECTIVES

    • To provide introduction to computational biology and bioinformatics


    • To introduce tools and techniques useful for DNA and protein sequence analysis
    • To enable students to program in perl to solve problems in bioinformatics

    Learning Outcomes
    After the course, the student should:
    • Have knowledge of key computational biology/bioinformatics concepts and techniques.
    • Understand the inner working of some of the most widely-used bioinformatics methods, such as sequence analysis and
    comparison, and protein structure and function analysis.
    • Be able to solve moderate complexity problems related to bioinformatics
    Lahore University of Management Sciences
    Grading Breakup and Policy

    Assignment(s): 20% (4 assignments, equal weightage)


    Home Work:
    Quiz(s): 15% (4 quizzes, equal weightage)
    Class Participation:
    Attendance: 5%
    Midterm Examination: 25%
    Project:
    Final Examination: 35%

    Examination Detail

    Yes/No: Yes
    Combine Separate: Combine
    Midterm
    Duration: 2 hrs
    Exam
    Preferred Date:
    Exam Specifications:

    Yes/No: Yes
    Combine Separate: Combine
    Final Exam
    Duration: 2 hrs
    Exam Specifications:

    COURSE OVERVIEW
    Lecture/ Recommended Objectives/
    Topics
    Module Readings Application
    1 Introduction, Analysing DNA Sequences – GC Content,
    Base Frequencies, Codon Bias
    Module 1: Sequence Comparison and Alignment
    2 Pairwise Alignment - Global
    3 Pairwise Alignment - Local, Repeat / Overlap
    4 Pairwise Alignment - Affine Gap, Scoring Matrices
    5 Multiple Sequence Alignment
    6 BLAST and e-value Distribution
    7 Markov Chains/Hidden Markov Models
    8 Sequence Alignment using Pair HMM
    9 Profile HMM
    Module 3: Phylogenetics
    10 UPGMA and Neigbour Joining
    11 Parsimony, Evolution Models - JC69 & K2P
    12 Estimating the Number of Substitutions between DNA
    Sequences
    13 Maximum Likelihood
    Module 4: RNA
    14 RNA Secondary Structure Prediction I
    15 RNA Secondary Structure Prediction II
    Module 5: Proteins
    16 From DNA to Protein Sequences
    17 Protein Secondary Structures
    18 Protein Structure Visualization
    19 Protein Structure Classification
    Lahore University of Management Sciences
    20 Protein Structure Comparison I - Introduction
    21 Protein Structure Comparison II - Singular Value
    Decomposition
    22 Protein Structure Comparison III - Sequence based Structure
    Alignment
    Module 6: Biological Networks
    23 Introduction to Biological Networks
    24 Representing Biological Networks
    25 Boolean Networks
    26 Extracting Information from Biological Networks
    27 Biological Networks in Diseases
    28 Moving towards Systems Biology

    Textbook(s)/Supplementary Readings
    • Bioinformatics, Sequence and Genome Analysis, Second Edition, David W Mount, Cold Spring Harbor Laboratory Press, 2004.
    • Developing Bioinformatics Computer Skills, Cynthia Gibas and Per Jambeck, O'Reilly, 2001
    • Biological Sequence Analysis. Probabilistic Models of Proteins and Nucleic Acids, Richard Durbin, Sean R. Eddy, Anders Krogh, Graeme
    Mitchison. Cambridge University Press, 1998.
    • Inferring Phylogenies, 2nd Ediition, Joseph Felsenstein. Sinauer Associates, 2003.
    • Introduction to Computational Biology. An Evolutionary Approach. Bernhard Haubold, Thomas Wiehe. Birkhauser,Verlag 2006.
    • Microarray Bioinformatics. Dov Sketel. Cambridge University Press. 2003

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