BIF401 Merged Slides 1-125

Lecture 01

Modern Biology:

• Humans have over 25,000 genes.
• The genes may produce > 250,000 different proteins.
• Each protein may further take up multiple modifications.
• But then, there are numerous organelles & intermediary molecules as well
• The scale and speed of biomolecular interactions, reactions & transport is simply bewildering!

Experiments in Biology:

Brisk enhancements in instrumentation:

• Next Generation Sequencers
• High Resolution Mass Spectrometers
• Nuclear Magnetic Resonance Spectroscopy

Digitalization of Biology:

• Modern biological experiments produce data which is stored on computers.
• The data includes text, numbers, symbols and images.

Speed of Data Growth:

Data is being accumulated at an exponentially increasing rate E.g. Genome sequences in genome databases are doubling every few years!

• Humans are limited in recalling information from their memory
• So, we need the help of computers to store & recall this data!
• Computers can also quickly process this information and help in its manipulation.

END · Lecture 02 · Introduction to Bioinformatics: · Motivation:

1. An interdisciplinary field
2. New but rapidly developing field
3. Low requirement on infrastructure & research equipment
4. Vast opportunities for scientific discovery.

Scope of Bioinformatics:

Use of computational algorithms and techniques for:

1. Storage,
2. Organization,
3. Analysis, and
4. Representation of biological information

Activities:

1. Developing algorithms 2. Writing software 3. Data processing pipelines 4. Statistical evaluation of data 5. Data visualization

Moving ahead…

Learn the available bioinformatics concepts, algorithms & tools Advance these concepts by developing novel ideas Apply these ideas to forward the understanding of biology & life.

• The benefits of studying bioinformatics in Pakistan • New degree programs in several universities • Opportunity for cutting edge discoveries in a resourcelimited setting.

Lecture 03 · Need for Bioinformatics - I · Motivation:

1. An interdisciplinary field 2. New but rapidly developing field 3. Low requirement on infrastructure and research equipment 4. Vast opportunities for scientific discovery

• Since genome and proteome information is publically available, you can process this information after downloading it • If you carefully search this online data, with a little bit of biology background, it is a gold mine!

Lecture 04 · Need for Bioinformatics - II · Quote:

Biology easily has 500 years of exciting problems to work on. Donald Knuth, Professor, Stanford University.

What can bioinformatics deliver?

• Life, evolution and disease can be better understood
• Drugs can be better developed after understanding molecular basis of life

Possible contributions:

• Solve important problems related to life
• Handle mammoth quantities of experimental data
• Develop efficient solutions towards these goals • From gene sequences to protein sequences Bioinformatics is the way forward. • Protein structure, protein-protein interactions & systems biology are other research areas in bioinformatics.

Lecture 05

Applications of Bioinformatics - I

• Where can bioinformatics be applied specifically?

• What are the avenues in biology that can benefit from this science?

• What benefits can it deliver to the society?

1. Genomics: · DNA Sequencing · Gene Finding · Genome Assembly · Variation in Genomes · Transcription Data · Databases · 2. Evolutionary Studies: · • Evolutionary relationships · • Evolutionary distances · • Phylogenetics · • Tree of life · 3. Proteomics: · • Protein Sequencing · • Post-translational Modifications · • Protein-Protein Interactions · • Database Development · 4. Systems Biology: · • Model protein and gene interactions · • Dynamical analysis of such models · • Understand system properties · • Predict system level behaviors · • Genomics · • Proteomics · • Metabolomics · • Structural Proteomics · • Drug Design · • Systems Biology · • Personalized Medicine · Lecture 06 · Applications of Bioinformatics - II

• Genomics
• Proteomics
• Metabolomics
• Structural Proteomics
• Drug Design
• Systems Biology
• Personalized Medicine
• Bioinformatics techniques have enabled us to generate ‘omic’ data and its utilization!
• Step by step application of bioinformatics from genome level to entire biosystems.

Small to Big:

• Gene finding, function prediction • Structure prediction, modeling • Predicting Molecular (Protein) interaction • Biological network building & modeling • Cell level modeling & simulation • Cell signaling modelling & simulation • Tissue & morphology modelling • Biological network building & modeling • Models integrate biological data • Simulations help validate testable hypotheses • Moreover, these simulations can also predict disease progression & outcomes Conclusion: Bioinformatics not only organizes, stores and analyzes biological data, but can also validate novel hypotheses. Modern day bioinformatics also helps predict disease outcomes as well as drugs to treat them!

Lecture 07

Frontiers in Bioinformatics – I

Introduction: Bioinformatics is a relative young scientific area. It is rapidly expanding to cater for the variety and scale of biological data. • Several unresolved challenges exist in this expansion!

Frontiers in Genomics

• Next generation sequencing of whole genomes • Massive amounts of data (Tera byte files) • Handling & analysis of this data • Genome assembly & prediction

Frontiers in Transcriptomics:

• Identification of hitherto unknown types as a roles of RNA • Understanding the regulatory dynamics of these RNA molecules • Interactions of the RNA molecules.

Frontiers in Proteomics:

• Identification of low abundance proteins in patient tissue samples • Large scale protein identification • Identification of known as well as novel posttranslational modifications.

• Bioinformatics is full of challenges and opportunities. • Amongst other frontiers in bioinformatics, there are protein structures, systems biology and personalized medicine!