Prof Usman Sumo F. Tambunan Dr. Rer. Nat. Arli Aditya Parikesit Hilyatuz Zahroh.,Ssi. MA

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Prof Usman Sumo F . Tambunan Dr. rer. nat. Arli Aditya Parikesit Hilyatuz Zahroh.,Ssi. MA
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OUTLINE
1. Introduction 2. History of Bioinformatics 3. Bioinformatics techniques 4. Areas in bioinformatics 5. Applications 6. Related Computer T echnology 7. Bioinformatics and Patent 8. Reference
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The fast growth of biological researches has produced huge amount of biological data
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Growth of GenBank:
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Genomic researches has given rise to a new field of science, BIOINFORMATICS

Genomic research makes it possible to look at biological phenomena on a scale not previously possible: all genes in a genome, all transcripts in a cell, all metabolic processes in a tissue. One feature that all of these approaches share is the production of massive quantities of data. GenBank, for example, now accommodates >1010 nucleotides of nucleic acid sequence data and continues to more than double in size every year. New technologies for assaying gene expression patterns, protein structure, protein-protein interactions, etc., will provide even more data. How to handle these data, make sense of them, and render them accessible to biologists working on a wide variety of problems is the challenge facing bioinformaticsan emerging field that seeks to integrate computer science with applications derived from molecular biology. We are swimming in a rapidly rising sea of data. . . how do we this keep from drowning? Network Free Powerpoint Template Click here to download powerpoint template : Human Computers
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Roos (2001). Science. 291:1260
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Definition:
(Molecular) bio informatics: bioinformatics is conceptualising biology in terms of molecules (in the sense of Physical chemistry) and applying informatics techniques (derived from disciplines such as applied maths, computer science and the statistics) to understand and organise information associated with these molecules, on a large scale. In short, bioinformatics is a management information system for molecular biology and has many practical applications.
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Bioinformatics:
Bioinformatics Position in Computers Network Free Powerpoint Template Click here to download this powerpoint template : Human For more : Powerpoint Backgrounds
relation with other fields of science
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What we study with Bioinformatics Tools:
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Bioinformatics:
Bioinformatics is the integrated discipline formed from the combination of biology, computer science, and information technology. "The mathematical, statistical and computing methods that aim to solve biological problems using DNA and amino acid sequences and related information. Frank Tekaia
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Bioinformatics:
Bioinformatics is based on the fact that DNA sequencing is cheap, and becoming easier and cheaper very quickly.
the Human Genome Project cost roughly $3 billion and took 12 years (1991-2003). Sequencing James Watsons genome in 2007 cost $2 million and took 2 months Today, you could get your genome sequenced for about $100,000 and it take a month. would The Archon X prize: you win $10 million if you can sequence 100 human genomes in 10 days, at a cost of $10,000 per genome. It is realistic to envision $100 per genome within 10 years: everyones genome could be sequenced if they wanted or needed it. Click here to download this powerpoint template : Human Computers Network Free Powerpoint T emplate
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Brief history of bioinformatics: Databases

The first biological database - Protein Identification Resource was established in 1972 by Margaret Dayhoff Dayhoff and co-workers organized the proteins into families and superfamilies based on degree of sequence similarity
Idea of sequence alignment was introduced as well as special tables that reflected the frequency of changes observed in the sequences of a group of closely related proteins
Currently there are several huge Protein Banks : SwissProt, PIR International, etc. The first DNA database was established in 1979. Currently there are several powerful databases: GenBank, EMBL, DDBJ, etc.
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Brief history of bioinformatics: evolutionary reconsructions
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Brief history of bioinformatics: other important steps

Development of sequence retrieval methods (1970-80s)
Development of principles of sequence alignment (1980s)

Prediction of RNA secondary structure (1980s) Prediction of protein secondary structure and 3D (1980-90s) The FASTA and BLAST methods for DB search (1980-90s) Prediction of genes (1990s) Studies of complete genome sequences (late 1990s 2000s)
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Related Field: Computational Biology

The study and application of computing methods for classical biology Primarily concerned with evolutionary, population and theoretical biology, rather than the cellular or molecular level
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Related Field: Medical Informatics

The study and application of computing methods to improve communication, understanding, and management of medical data Generally concerned with how the data is manipulated rather than the data itself
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Related Field: Cheminformatics

The study and application of computing methods, along with chemical and biological technology, for drug design and development
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Related Field: Genomics

Analysis and comparison of the entire genome of a single species or of multiple species A genome is the set of all genes possessed by an organism Genomics existed before any genomes were completely sequenced, but in a very primitive state
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Related Field: Proteomics

Study of how the genome is expressed in proteins, and of how these proteins function and interact Concerned with the actual states of specific cells, rather than the potential states described by the genome
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Related Field: Pharmacogenomics

The application of genomic methods to identify drug targets For example, searching entire genomes for potential drug receptors, or by studying gene expression patterns in tumors
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Related Field: Pharmacogenetics

The use of genomic methods to determine what causes variations in individual response to drug treatments The goal is to identify drugs that may be only be effective for subsets of patients, or to tailor drugs for specific individuals or groups
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Pharmaceutical:
Biobanks
A biobank is a type of biorepository which stores human biological samples (including tissue providers, others include genetic profiling) for use in research. Since the late 1990s: a key resource for supporting many types of contemporary research, e.g. genomics and personalized medicine. Drivers: the need to accelerate the discovery and development of drugs. As that industry shifts to more-personalised medicine, the need for highquality, well-maintained biospecimens intensifies.
Veterinary Science/ Animal Health

Divided into Production animals and companion animals, the animal health market covers diagnostics, medicines and vaccines for farmed animals and pets. Drivers:growing demand for animal proteins, as well as a strong Click here to download this powerpoint template : Human Computers Network Free Powerpoint T emplate consumer need for companion animal health care. For more : Powerpoint Backgrounds Page 22
Medical Implications:
Pharmacogenomics Not all drugs work on all patients, some good drugs cause death in some patients So by doing a gene analysis before the treatment the offensive drugs can be avoided Also drugs which cause death to most can be used on a minority to whose genes that drug is well suited volunteers wanted! Customized treatment Gene Therapy Replace or supply the defective or missing gene E.g: Insulin and Factor VIII or Haemophilia
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Diagnosis of Disease:
Diagnosis of disease
Identification of genes which cause the disease will help detect disease at early stage e.g. Huntington disease -
Symptoms uncontrollable dance like movements, mental disturbance, personality changes and intellectual impairment Death in 10-15 years The gene responsible for the disease has been identified Contains excessively repeated sections of CAG So once analyzed the couple can be counseled
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Drug Design:
Can go up to 15yrs and $700million One of the goals of bioinformatics is to reduce the time and cost involved with it. The process
Discovery Computational methods can improves this Testing
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Drug Discovery:
Target identification
Identifying the molecule on which the germs relies for its survival Then we develop another molecule i.e. drug which will bind to the target So the germ will not be able to interact with the target. Proteins are the most common targets
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Drug Discovery:
For example HIV produces HIV protease which is a protein and which in turn eat other proteins This HIV protease has an active site where it binds to other molecules So HIV drug will go and bind with that active site Easily said than done!
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What well learn in this semester:

Topic Introduction Bioinformatics How to use SCELE - Navigation and database searching 2 - Similarity searching 3 Multiple Sequence Alignment dan Phylogenetic tree 4 PCR Primer Design 5 Host Mapping 6-7 Vaccine Design 8 Homology Modeling 9-10 Molecular Docking and Dynamics 11 Introduction to Epigenomic Computation 12 Introduction to Transcriptomic Computation Click here to download this powerpoint template : Human Computers Network Free Powerpoint T emplate For more : Powerpoint Backgrounds 13 Experimental Exam 14 Final T est Page 28
Week: 1

Prof Usman Sumo F. Tambunan Dr. Rer. Nat. Arli Aditya Parikesit Hilyatuz Zahroh.,Ssi. MA

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Click here to download this powerpoint template : Human Computers Network Free Powerpoint T emplate For more : Powerpoint

Genomic researches has given rise to a new field of science, BIOINFORMATICS

Roos (2001). Science. 291:1260

relation with other fields of science

What we study with Bioinformatics Tools:

Brief history of bioinformatics: Databases

Brief history of bioinformatics: evolutionary reconsructions

Brief history of bioinformatics: other important steps

Development of principles of sequence alignment (1980s)

Related Field: Computational Biology

Related Field: Medical Informatics

Related Field: Cheminformatics

Related Field: Genomics

Related Field: Proteomics

Related Field: Pharmacogenomics

Related Field: Pharmacogenetics

Veterinary Science/ Animal Health

What well learn in this semester:

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