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BIF731 : Advanced Bioinformatics

Course Overview

Course Synopsis

In this course students will be familiar with the importance and role of Bioinformatics in following Areas; Forensic sciences, Drug discovery, Biotechnology, Genetic Engineering, Phylogenetic analysis, Medical imaging also students will be able to perform extraction and retrieval of Biological data and students will have better Understanding of annotation, integration, knowledge discovery and semantic web of biological data. More ever students will able to learn Combination of Bioinformatics with other domains such as statistics, mathematics, cloud computing and database management systems.

Course Learning Outcomes

At the end of the course, students will have good understanding of following Areas

  • Phylogeny and Phylogeny Algorithms
  • Microarray Data Analysis
  • Markov Hidden Models and their usability in bioinformatics
  • Human Disease
  • Drug Discovery: Technology and Strategies
  • Computer-aided Drug Design
  • Real life Applications of Bioinformatics
  • Role of bioinformatics in forensic
  • Role of bioinformatics and genetic engineering in agriculture
  • Medical Imaging
  • Computational Model of Human Brain
  • Dealing with large scale Biological Data
  • Informatics and Statistics in Biopharmaceutical Research
  • Database Management system for Biological Data
  • Generation of Databank For Biological Data
  • Development of Search Engine for Biological Data
  • Semantic interpretation of biological data

Course Calendar

Instructor Introduction1
Related Concepts3
What we will study?5
Introduction to biological concepts6
DNA and parts7
Structure of DNA8
Data management life cycle9
Data Organization10
DB Architecture11
Data Modeling12
Object Oriented Data Modeling13
Search Engine14
Data Visualization16
Data Model for Bioinformatics17
Computer Vision18
Image Processing19
Image Enhancement - Point Processing20
Image Enhancement - Neighborhood Processing21
Restoration and Segmentation22
Morpholoical Procesing23
Object Recognition24
Medical Imaging25
Introduction- Sequence Alignment26
Distance Measures27
Types of Sequence Alignment28
Dot Plots29
Global Alignment30
Local Alignment31
Assignment No. 1
Database Searching32
BLAST Algorith35
BLAST Variants36
Introduction to Multiple Sequence Alignment37
MSA Approaches38
Progressive alignment methods39
MSA other Methods40
Iterative Methods41
Evolution Introduction42
Introduction to Phylogenetics43
Phylogenetic Tree44
Phylogenetic Tree Basic45
Phylogentic Tree Algorithms46
Distance Base Methods47
Neighbor Join48
Phylogentic analysis50
Molecule Clock51
Neutral Theory52
Genes and Species Tree53
Sequence Acquisition54
MSA for Phylogentics55
Stage 2 - Definitions56
Phylogentic Analysis Stage 357
Phylogenetic Tree Building Methods58
Phylogenetic Bayesian Method59
Automated Tools for Phylogeny Analysis60
Tree Evaluation63
Fitch / Margoliash Algorithm64
Consensus Tree in Phylogenetics65
Distance Matrix for Phylogenetic analysis66
Assignment No. 2
Semantic Web67
Components of Semantic Web68
Components of Semantic Web (Ontology)69
Components of SW71
Open Biomedical Ontologies (OBO)72
Gene Ontology (GO)73
Building Ontology74
Cell Signaling Ontology75
Types of Ontologies76
MBO (Ontology for Molecular Biology)77
Ontology of Austism78
Bio Query Language79
Databank for Biological Data81
Data Integration Techniques82
Databank Generation Challenges83
Databank Generation Steps84
Generation Our Own Data Bank85
Download Server86
Data Processing Engine87
Data Server88
Reporting Server89
Application Area of Bio Informatics90
Introduction of Biotechnology91
Genetically Modified Crops92
Genetic Engineering93
Information Extraction94
Natural Language Processing95
Steps for Natural Language Processing96
Problems for NLP97
Synonym Replacement98
Features Extraction Methods99
Document Classification100
Introduction of Hidden Markov Models101
Markov Chain102
HMM Structure103
HMM Gene Finding104
Limitation of HMM105
Forensic science and Limitation of Thumb finger printing107
DNA Finger Printing/ DNA Profiling108
DNA Fingerprinting109
DNA Profile110
Mid Term Examination
DNA profile Generation Methods111
Short Tandem Repeats112
Variable Numebr Tandem Repeats113
Introduction to Drug Discovery114
Drug Discovery Applications115
Pharmacogenetics Applications116
Pharmacogenomics Applications117
Single Nucleotide Polymorphisms118
Drug discovery methods119
Drug Discovery Pipeline120
Biomedical annotated corpora121
Steps for Creation of Biomedical Corpora122
Corpus Design125
Need of Corpora126
DD technologies & Strategies127
Drug Discovery Technologies128
Existing Biomedical Corpora129
Target Discovery Strategy130
Strategies to Identify Possible Drug Targets131
Target validation132
Lead Identification133
Lead Optimization134
Mechanism of Drug Action135
Data/ Image Mining136
Assignment No. 3
Introduction to High performance Computing137
High Performance Computing138
Cloud Computing139
Cloud Computing Architecture140
Cloud Deployment Models141
Cloud computing for MSA143
Biological Data Protection144
eHealth Privacy Concerns145
HIPAA eHealth Privacy147
Health security concerns148
Guidelines for Biological Data Protection149
Adoption Studies150
Cell Cycle: Key to Drug Discovery151
Phases of Cell Cycle152
Cell Cycle Phase Markers153
Regulations of the Cell Cycle154
Cyclins in Cell Cycle Regulation155
Cell cycle and cancer156
Cell cycle target identification157
Security Actions for Biological Data158
Law and Biological Databases159
Genetic Epidemiology160
Familial aggregation161
Structural Biology & Drugs162
Target identification strategies163
Prediction of important regions164
Validation and Drugability165
VHT in Silico-Screening166
Docking and scoring167
Information retrieval168
Ir models169
QSAR Models170
Ir evaluation measures171
Information retrieval for biological databases172
Ir in bioinformatics173
Search engines-2174
Search Engines in Bioinformatics175
Confusion Matrix176
Existing Hospital Records177
Electronic Health Record178
Knowledge discovery179
Konwledge discovery techniques180
Naive Bayes Classifier181
Decision tree182
Neural networks183
Association rule184
Machine Learning185
ML Concepts186
Ml applications187
Ml other applications188
Assignment No. 4
Computer Programs189
Programming Languages190
Java Introduction191
Anatomy of java program192
Introduction to biojava193
Alphabets, symbols and sequences194
Central Dogma in BioJava195
Sequence input output196
Features and annotations197
Protein structure198
Alignment module199
Introduction to Python200
Python basics201
Introduction to BioPython202
Sequence object203
Phylogenetic tree io204
Protein structure205
Eutils entrez206
Matlab Introduction207
Matlab Basics208
Bioinformatics Toolbox209
Features and Functions210
Bioinformatics Tasks211
Phylogenetic Analysis212
Protein Property Analysis213
Data Integration214
Problems with Data Integration215
Ethic Terminology216
Ethical Issues in Bioinformatics217
Difference between Ethical and Legal Issues218
Bioethics Introduction and Purposes219
Organization for lookup AHIMA-AMIA-HIMSS220
Final Term Examination
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