Bioinformatics Notes

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

Smith-Waterman 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.

Suboptimal Alignments

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

The Escherichia Coli Mg1655 In Silico Metabolic Genotype: Its Definition, Characteristics, And Capabilities

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

Problems with Microarrays

Bioinformatics Tutorial, Tutorial 1

Bioinformatics Terms

Bioinformatics in India