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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 Introduction1Video/PPT
Related Concepts3Video/PPT
What we will study?5Video/PPT
Introduction to biological concepts6Video/PPT
DNA and parts7Video/PPT
Structure of DNA8Video/PPT
Data management life cycle9Video/PPT
Data Organization10Video/PPT
DB Architecture11Video/PPT
Data Modeling12Video/PPT
Object Oriented Data Modeling13Video/PPT
Search Engine14Video/PPT
Data Visualization16Video/PPT
Data Model for Bioinformatics17Video/PPT
Computer Vision18Video/PPT
Image Processing19Video/PPT
Image Enhancement - Point Processing20Video/PPT
Image Enhancement - Neighborhood Processing21Video/PPT
Restoration and Segmentation22Video/PPT
Morpholoical Procesing23Video/PPT
Object Recognition24Video/PPT
Medical Imaging25Video/PPT
Introduction- Sequence Alignment26Video/PPT
Distance Measures27Video/PPT
Types of Sequence Alignment28Video/PPT
Dot Plots29Video/PPT
Global Alignment30Video/PPT
Local Alignment31Video/PPT
Database Searching32Video/PPT
BLAST Algorith35Video/PPT
BLAST Variants36Video/PPT
Introduction to Multiple Sequence Alignment37Video/PPT
MSA Approaches38Video/PPT
Assignment No. 1
Progressive alignment methods39Video/PPT
MSA other Methods40Video/PPT
Iterative Methods41Video/PPT
Evolution Introduction42Video/PPT
Introduction to Phylogenetics43Video/PPT
Phylogenetic Tree44Video/PPT
Phylogenetic Tree Basic45Video/PPT
Phylogentic Tree Algorithms46Video/PPT
Distance Base Methods47Video/PPT
Neighbor Join48Video/PPT
Phylogentic analysis50Video/PPT
Molecule Clock51Video/PPT
Neutral Theory52Video/PPT
Genes and Species Tree53Video/PPT
Sequence Acquisition54Video/PPT
MSA for Phylogentics55Video/PPT
Stage 2 - Definitions56Video/PPT
Phylogentic Analysis Stage 357Video/PPT
Phylogenetic Tree Building Methods58Video/PPT
Phylogenetic Bayesian Method59Video/PPT
Automated Tools for Phylogeny Analysis60Video/PPT
Tree Evaluation63Video/PPT
Fitch / Margoliash Algorithm64Video/PPT
Consensus Tree in Phylogenetics65Video/PPT
Distance Matrix for Phylogenetic analysis66Video/PPT
Semantic Web67Video/PPT
Components of Semantic Web68Video/PPT
Components of Semantic Web (Ontology)69Video/PPT
Components of SW71Video/PPT
Open Biomedical Ontologies (OBO)72Video/PPT
Gene Ontology (GO)73Video/PPT
Building Ontology74Video/PPT
Cell Signaling Ontology75Video/PPT
Assignment No. 2
Types of Ontologies76Video/PPT
MBO (Ontology for Molecular Biology)77Video/PPT
Ontology of Austism78Video/PPT
Bio Query Language79Video/PPT
Databank for Biological Data81Video/PPT
Data Integration Techniques82Video/PPT
Databank Generation Challenges83Video/PPT
Databank Generation Steps84Video/PPT
Generation Our Own Data Bank85Video/PPT
Download Server86Video/PPT
Data Processing Engine87Video/PPT
Data Server88Video/PPT
Reporting Server89Video/PPT
Application Area of Bio Informatics90Video/PPT
Introduction of Biotechnology91Video/PPT
Genetically Modified Crops92Video/PPT
Genetic Engineering93Video/PPT
Information Extraction94Video/PPT
Natural Language Processing95Video/PPT
Steps for Natural Language Processing96Video/PPT
Problems for NLP97Video/PPT
Synonym Replacement98Video/PPT
Features Extraction Methods99Video/PPT
Document Classification100Video/PPT
Introduction of Hidden Markov Models101Video/PPT
Markov Chain102Video/PPT
HMM Structure103Video/PPT
HMM Gene Finding104Video/PPT
Limitation of HMM105Video/PPT
Mid Term Examination
Forensic science and Limitation of Thumb finger printing107Video/PPT
DNA Finger Printing/ DNA Profiling108Video/PPT
DNA Fingerprinting109Video/PPT
DNA Profile110Video/PPT
DNA profile Generation Methods111Video/PPT
Short Tandem Repeats112Video/PPT
Variable Numebr Tandem Repeats113Video/PPT
Introduction to Drug Discovery114Video/PPT
Drug Discovery Applications115Video/PPT
Pharmacogenetics Applications116Video/PPT
Pharmacogenomics Applications117Video/PPT
Single Nucleotide Polymorphisms118Video/PPT
Drug discovery methods119Video/PPT
Drug Discovery Pipeline120Video/PPT
Biomedical annotated corpora121Video/PPT
Steps for Creation of Biomedical Corpora122Video/PPT
Corpus Design125Video/PPT
Need of Corpora126Video/PPT
DD technologies & Strategies127Video/PPT
Drug Discovery Technologies128Video/PPT
Existing Biomedical Corpora129Video/PPT
Target Discovery Strategy130Video/PPT
Strategies to Identify Possible Drug Targets131Video/PPT
Target validation132Video/PPT
Lead Identification133Video/PPT
Lead Optimization134Video/PPT
Mechanism of Drug Action135Video/PPT
Data/ Image Mining136Video/PPT
Introduction to High performance Computing137Video/PPT
High Performance Computing138Video/PPT
Cloud Computing139Video/PPT
Cloud Computing Architecture140Video/PPT
Cloud Deployment Models141Video/PPT
Cloud computing for MSA143Video/PPT
Biological Data Protection144Video/PPT
eHealth Privacy Concerns145Video/PPT
HIPAA eHealth Privacy147Video/PPT
Health security concerns148Video/PPT
Guidelines for Biological Data Protection149Video/PPT
Adoption Studies150Video/PPT
Phases of Cell Cycle152Video/PPT
Cell Cycle Phase Markers153Video/PPT
Regulations of the Cell Cycle154Video/PPT
Cyclins in Cell Cycle Regulation155Video/PPT
Cell cycle and cancer156Video/PPT
Cell cycle target identification157Video/PPT
Security Actions for Biological Data158Video/PPT
Law and Biological Databases159Video/PPT
Genetic Epidemiology160Video/PPT
Familial aggregation161Video/PPT
Structural Biology & Drugs162Video/PPT
Target identification strategies163Video/PPT
Prediction of important regions164Video/PPT
Validation and Drugability165Video/PPT
Assignment No. 3
VHT in Silico-Screening166Video/PPT
Docking and scoring167Video/PPT
Information retrieval168Video/PPT
Ir models169Video/PPT
QSAR Models170Video/PPT
Ir evaluation measures171Video/PPT
Information retrieval for biological databases172Video/PPT
Ir in bioinformatics173Video/PPT
Search engines-2174Video/PPT
Search Engines in Bioinformatics175Video/PPT
Confusion Matrix176Video/PPT
Existing Hospital Records177Video/PPT
Electronic Health Record178Video/PPT
Knowledge discovery179Video/PPT
Konwledge discovery techniques180Video/PPT
Naive Bayes Classifier181Video/PPT
Decision tree182Video/PPT
Neural networks183Video/PPT
Association rule184Video/PPT
Machine Learning185Video/PPT
ML Concepts186Video/PPT
Ml applications187Video/PPT
Ml other applications188Video/PPT
Computer Programs189Video/PPT
Programming Languages190Video/PPT
Java Introduction191Video/PPT
Anatomy of java program192Video/PPT
Introduction to biojava193Video/PPT
Alphabets, symbols and sequences194Video/PPT
Central Dogma in BioJava195Video/PPT
Sequence input output196Video/PPT
Features and annotations197Video/PPT
Protein structure198Video/PPT
Alignment module199Video/PPT
Introduction to Python200Video/PPT
Python basics201Video/PPT
Introduction to BioPython202Video/PPT
Sequence object203Video/PPT
Phylogenetic tree io204Video/PPT
Protein structure205Video/PPT
Eutils entrez206Video/PPT
Matlab Introduction207Video/PPT
Matlab Basics208Video/PPT
Bioinformatics Toolbox209Video/PPT
Features and Functions210Video/PPT
Bioinformatics Tasks211Video/PPT
Phylogenetic Analysis212Video/PPT
Protein Property Analysis213Video/PPT
Data Integration214Video/PPT
Problems with Data Integration215Video/PPT
Ethic Terminology216Video/PPT
Ethical Issues in Bioinformatics217Video/PPT
Difference between Ethical and Legal Issues218Video/PPT
Bioethics Introduction and Purposes219Video/PPT
Organization for lookup AHIMA-AMIA-HIMSS220Video/PPT
Final Term Examination
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