VU Open Course Ware: BioinformaticsVirtual University of Pakistan: Open Course Warehttp://www.vu.edu.pk/BIF401: Bioinformatics IIntroduction to bioinformatics (history, timeline, databases, sequence storage, retrieval and analysis)
Similarity and Homology
Creating alignments (local, global alignment, pairwise and multiple sequence alignments)
Phylogenetic analysis
Dot matrix plots
Dynamic programming algorithm (word (k-tuple) methods, substitution matrices PAM and BLOSUM, scoring algorithms, gap penalties)
Online tools (BLAST, BLAT and FASTA and PDB file structure)http://ocw.vu.edu.pk/CourseDetails.aspx?cat=Bioinformatics&course=BIF401BIF402: Ethical and Legal Issues in BioinformaticsScience Ethics and Values
Cybernetics
Patient-physician relationship
Biotechnology and risk factors
Use of Human Genetic Information
Gene patents in medical genetics
Biosecurity & bioweaponshttp://ocw.vu.edu.pk/CourseDetails.aspx?cat=Bioinformatics&course=BIF402BIF501: Bioinformatics IIIntroduction to genome, gene prediction in prokaryotes and eukaryotes, ORF, TFBS, codon usage table, EST and SNP databases, primer designing, restriction enzyme databases, RNA structure prediction, computational secondary and tertiary protein structure prediction methods, structure optimization and refinement methods, hydrogen bonding, PTMs of proteins, Chou Fasman, PHD and PSIPred, neural network, X-ray crystallography, NMR, ab initio, threading and homology modeling methods, protein fold identification using Pfam (A & B) and other tools.http://ocw.vu.edu.pk/CourseDetails.aspx?cat=Bioinformatics&course=BIF501BIF601: Bioinformatics Computing IDatabases: Data management, networks, geographical scope, communications models, transmissions technology, protocols, bandwidth, topology, hardware, contents, security, ownership, implementation, Search engines. search process, search engine technology, searching and information theory, computational methods, knowledge management, sequence and structure visualization, data mining methods and technology, pattern recognition and discovery, pattern matching, dot matrix analysis, substitution matrices, dynamic programming, Scripting .
Suggested Readings/ Books
1. Book Title: Bioinformatics: Sequence and Genome Analysis
Author: D Mount
Edition: Latest
URL: http://en.bookfi.net/s/?q=Bioinformatics%3A+Sequence+and+Genome+Analysis%2C
2. Book Title: Data Communications and Networking
Author: Behrouz A. Forouzan
Edition: 2nd
ISBN: 0072322047
Publisher: McGraw-Hill Higher Education
3. Book Title: Data Communications and Networking
Author: Behrouz A. Forouzan
Edition: 2nd Edition
Publisher: McGraw-Hill Higher Education
4. Book Title: Data and Computer Communication
Author: William Stallings
Edition: 6th Edition
Publisher: Prentice Hall
5. Book Title: Introduction to Information Retrieval
Author: Christopher D. Manning, Prabhakar Raghavan and Hinrich Schütze
Edition: 1st
Publisher: Cambridge University Press
6. Book Title: Bioinformatics and Functional Genomics
Author: Jonathan Pevsner
Edition: 2nd edition
Publisher: Wiley-Balckwell
------------------------------------------------------------------------------------------------------------------------------------------http://ocw.vu.edu.pk/CourseDetails.aspx?cat=Bioinformatics&course=BIF601BIF602: Bioinformatics Computing IICellular, tissue, organ and system modelling
Simulation
Bio-inspired computation
Evolutionary algorithms
Swarm Intelligence
Neural networks and application of neural networks to Bioinformatics
Applications of machine/ deep learning in predicting diseases
Designing and developing algorithms
Databases for solving biological problems.http://ocw.vu.edu.pk/CourseDetails.aspx?cat=Bioinformatics&course=BIF602BIF731: Advanced Bioinformaticshttp://ocw.vu.edu.pk/CourseDetails.aspx?cat=Bioinformatics&course=BIF731BIF732: Advanced Computing Approacheshttp://ocw.vu.edu.pk/CourseDetails.aspx?cat=Bioinformatics&course=BIF732BIF733: Bioinformatics I (Essentials of Genome Informatics)http://ocw.vu.edu.pk/CourseDetails.aspx?cat=Bioinformatics&course=BIF733BIO301: Essentials of GeneticsIntroduction, heredity and variations, Mendelian and non-Mendelian inheritance, chromosomal structure, chromosomal theory of heredity, multiple allelic, linkage and gene mapping, polygenic inheritance, epitasis, epigenetics, penetrance and expressivity, Sex-linked inheritance, chromosomal aberrations, gene mutation, genetic disorders; DNA polymorphism, cytoplasmic inheritance, population genetics [Hardy-Weinberg equilibrium, selection, inbreeding and heterosis]
Suggested Readings/ Books
1. Book Title: Genetics: Analysis of genes and genomes
Citation: 2008
Author: Daniel L. Hartl and Elizabeth W. Jones.
Edition: 7th
Publisher: Jones & Bartlett Learning
URL: https://books.google.com.pk/books/about/Genetics.html?id=cfvILxY9tCIC&redir_esc=y
2. Book Title: Human Genetics: Concepts and Applications
Citation: 2009
Author: Ricki Lewis
Edition: 9th
Publisher: McGraw-Hill Education
3. Book Title: An introduction to genetic analysis
Author: Anthony Griffiths
Edition: 8th edition
Publisher: W. H. Freemanhttp://ocw.vu.edu.pk/CourseDetails.aspx?cat=Bioinformatics&course=BIO301BIO401: BiostatisticsIntroduction to Bio Statistics
Data
Measurements Scale
Statistics
Sampling and Types of Sampling
Probability Sampling
probability Sampling
Non-Probability Sampling
Organizing Data
Data Presentation-I
Data Presentation-II
Data Presentation-III
Data presentation-IV
Data presentation-V
Centeral Tendeency
Measure of Dispersion
Measure of Dispersion
Set Theory
Probability
Baye's Theorem
Laws of Expectation
Discrete Distribution
Measure of Locations
Quantiles
Measure of Dispersion
Absolute Measure of Dispersion
Relative Measure of Dispersion
Measure of Dispersion
Counting Rules
Discrete Distribution
Sampling Distribution of Means
Estimation
Correlation
Correlation-II
Correlation-III
Regression
A Tutorial to SPSS-I
A Tutorial to SPSS-II
A Tutorial to SPSS-III
A Tutorial to SPSS-IV
A Tutorial to SPSS-V
A Tutorial to SPSS-VI
A Tutorial to SPSS-VIIhttp://ocw.vu.edu.pk/CourseDetails.aspx?cat=Bioinformatics&course=BIO401CS620: Modelling and SimulationIntroduction to modeling and evaluation, bench marking, performance evaluation of high parallel systems architecture, measurement techniques, hardware monitoring, software monitoring, hybrid monitoring, fundamentals of queuing models, structure and performance parameters, operational analysis of queuing models, general features of queuing models, birth and death processes, m/m/i and m/g/1 systems, dependability modeling, analysis of reliable, available and high assurance systems, fault-tolerant techniques, software reliability modeling, adaptive modeling, agent based modeling, Types of simulations, applications of simulations
Suggested Readings/ Books
1. Book Title: INTRODUCTION TO MODELING AND SIMULATION
Author: W. A. Menner
Edition: 1995
URL: https://www.jhuapl.edu/Content/techdigest/pdf/V16-N01/16-01-Menner.pdf
2. Book Title: System Design, Modeling, and Simulation
Editor: Claudius Ptolemaeu
ISBN: 978-1-304-42106-7
Edition: 2014
URL: https://ptolemy.berkeley.edu/books/Systems/PtolemyII_DigitalV1_02.pdfhttp://ocw.vu.edu.pk/CourseDetails.aspx?cat=Bioinformatics&course=CS620