Definitions, History, Biological databases, Scope of Bioinformatics, Applications
Computational Biology, Intro to Computational Biology
Distributed Computing And Networking, Databases And Data Structures, Client /Server Technology, 'C' Programming Language, Perl, elementary commands and protocols, ftp, telnet, http. Primer on information theory, Operating System, Windows, Unix, Linux, Advanced Operating Systems, Software Tool for Biological Data Analysis,
Biological preliminaries, Intro Molecular Biology, Introduction, References, Exercises, Answers,
Concept of Randomization, Importance of Randomization, Noise and Signal in Biological Data
Normalization, Scoring Matrices, Heuristics, Pre-Processing, Quality Control and Reliability,
Analysis of Data -I, Data -II, Data -III, Data -IV, Case Studies on Analysis
Algorithms-Brief Overview of Various Computer Science Algorithms
Global Alignment, Multiple Sequence Alignment, Needle man and Wunsch Algorithm
Alignment Statistics of Alignment Score, Local Alignment, Concept of Matrices in Sequence Alignment
Analysis of Motifs and Patterns, Pattern and Motif Search, Blast and Fasta
Fasta and Blast Versions and Their Options, Dot Plots, Multiple Sequence Alignment
Intro to Other Searching Techniques Such As Suffix Trees
Biological Databases; Hidden Markov Models, Hidden Markov Models2
Hidden Markov Model, Markov Chain, Random Walk
Hmm Design for Protein Profiling and Gene Profiling
Algorithmic Approaches Relevant To Evolutionary Analysis
Distances - Clustering Methods, Rooted and Non Rooted Tree Representation
Bootstrapping Strategies, Phylip and Clustalw, Ensemble Learning
Boosting, Bagging and Support Vector Machines
Analysis of individual sequences
Intro. Helical wheels, amphipatic helices and coiled-coils Ref. Exercises
Pairwise Sequence Alignment, Pairwise sequence comparison, Algorithms for Pair wise And MSA
Dot plots Sequence Alignment References Exercises Answers
Algorithms for the comparison of two sequences
Intro., Type I and type II alignments, Type I alignment, Type II alignment, General gap functions for type II alignments, Minimum distance alignments,Minimum distance alignment score as a metric on sequences, Ref.
Introduction, Suboptimal points, Suboptimal Alignments, Stability, Application, References
Variants of the dynamic programming algorithm
Introduction, Free end-gaps, Local Alignments, Suboptimal Alignments, Similarity and Distance, Parametric Alignments, Linear in Space Algorithm, Practical on Pairwise Alignments, Alignment Applet, Alignment Quiz
Multiple Sequence Alignment, Multiple sequence alignment1, Introduction, References, Exercises
Local Multiple Sequence Alignment, Algorithms for SP-optimal multiple alignments
Definition, Motivation, Score functions, Problem
The exact solution, saving space, affine gap-costs, Reduction of search space
Divide-and-Conquer Alignment, References
Proteomics Intro to Proteomics, Proteomics1, Intro to Amino acids, a a. as Building Blocks of Proteins
Proteins and Their Structures, Proteins and Their Structures 2, Interatomic Forces and Protein Structure, Protein Structure Related to Function, Protein Function, Protein Structure
Structural Classification of Proteins, Protein Structure Classification
Protein Information Resources, Secondary Databases, Gene Expression Databases
Normalization and Processing the Data to Get Expression Levels
2-D Gel Analysis, 2d Gel Electrophoresis for Proteomics Tutorial
Application of Proteomic Technologies in the Drug Development Process
Protein Modeling Predicting Protein Structure and Function from Sequence
Intro to Secondary Structure Prediction, Secondary structure prediction
Secondary Structure Predictions and Prediction Servers, Predicting 3D Structure
Tertiary Structure Prediction, Tertiary Structure Prediction and Prediction Servers
Domain Databases, Protein folding, Protein Folding Prediction, Protein Threading
Structural Alignment of Proteins,
3-D structure Visualization and Operation, Protein Structure Optimization
Protein Analysis Tools, Protein structure Analysis- Alpha Amylase as an Example
Introduction, Different Levels of Protein Structure, Prediction Methods
Protein Structure Prediction from Primary Sequence, Protein Structure Prediction
Secondary Structure Prediction, Comparative Modelling References, Related Links, Exercises
Phylogenetic Analysis, Phylogenetic Analysis2, Evolution, Species, Taxonomy and Biosystematics,
Molecular Evolution and Biodiversity, Phylogenetic Analysis and Sequence Analysis,
Phylogenetic Trees and Multiple Alignments, Evolution, Ultrametric Trees, Iterative alignment strategy, Additive trees, Reconstruction of additive trees,Approximating additive metrics, Heuristics, Parsimony, Character-based methods for Phylogeny Construction
Gene and Genome Analysis
Data Mining, RNA Secondary Structure Prediction
Sequence Assembly Techniques, Searching Sequence Databases
Gene Prediction, Gene Predictions2, Genome Comparison
Genome Annotation - Algorithms, Software and Projects, Molecular predictions with DNA strings.
Advanced Bioinformatics
Drug Designing, Drug discovery, Virtual drug development
Genomes for Medicine, Intro to Genomics and Proteomics, Proteomics and Pharmacogenomcis
Genetic Network, E-cell- Complete Pathway Simulation
Neural Network Concepts, Neural Network and its Application in Bioinformatics
Systems Biology, Nutri-Genomics: Exploiting Systems Biology in the Nutrition and Health Arena
Pharmacogenomic Cancer Pharmacogenomics: Current and Future Applications
Pharmacogenomics-Drug Disposition, Drug Targets, and Side Effects
The Pharmacogenomics of Alzheimer's disease
Metabolomics and Metabolic Modelling Intro to metabolic pathways, databases, and Metabolomics
A Data Analysis Application on Scaling Properties of Biochemical Pathways
An Overview of Metabolism and Bioenergetics, Harvesting Biologically Useful Energy, Metabolic Networks, Network Properties, Metabolic Engineering,Ingredients of a Metabolic Model, Structural Network Models, Stoichiometric Network Models, Carbon Flux Models, Nonstationary Mechanistic Models,Metabolic Maps of E. coli
Principles of Metabolic Flux Analysis, Fluxanalyzer: Exploring Structure, Pathways,And Fluxes In (Bio) Chemical Reaction Networks, Metabolic Control Analysis, New Approaches to Modelling and Analysis of Biochemical Reactions, Pathways and Networks
Enzyme Kinetics, Enzyme Reactions and Inhibition, Activation, Ph, Kinetics, Mechanism, Summary
Gene Regulatory Networks (Grns), Construction of a Genetic Toggle Switch in Escherichia Coli
Transcriptional Regulatory Networks in Saccharomyces Cerevisiae, Integrated Genomic and Proteomic Analyses of A Systematically Perturbed Metabolic Network, Computer Simulation of Grns Modeling and Simulation of Genetic Regulatory Networks, Method for Qualitative Modeling and Simulation,Implementation and Application of the Method, Boolean Network, Generalized Logical Networks, Dynamic Networks, Non Linear Differential Equation and Modeling via Differential Equations, Some Applications, Control Theory, Deciphering Gene Expression Regulatory Networks, Pathways Databases Reverse Engineering of Regulatory Networks
Reverse Engineering in Systems Biology, Software Tools for Molecular Modeling
Various Databases Relevant To Metabolic Modelling
Microarrays - The Cutting Edge Technology
Origins of Microarrays-Some Controversies, Background Techniques
Microarray Image Analysis, Microarrays Technology, Methods of Construction
Types of Microarrays Chips, Microarray Analysis, Microarray Software -I, Microarray Software -II
Uses for Microarrays, Case Studies and Practical Applications
Role of DNA Microarrays in Drug Discovery and Development
Bioinformatics Tutorial, Tutorial 1
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