1. INTRODUCTION TO BIOINFORMATICS
Dilvan Moreira (based on Prof. André Carvalho presentation)

2. Objectives Learning of: Basic concepts Main tecniques
Future prospects and
Application in Bioinformatics
André de Carvalho - ICMC/USP
11/05/2018

3. Content Molecular Biology Sequence analysis Gene recognition
Sequence alignment
Use of Markov chains in biological data
Variation among and inside specie
André de Carvalho - ICMC/USP
11/05/2018

4. Content Natural selection in molecular level Phylogenetic analysis
Genome comparison
Gene expression analysis
Identification of regulatory sequences
André de Carvalho - ICMC/USP
5/11/2018

5. In the end of the course, you will be able to
Understand statistical and algorithmic approaches to sequence and gene expression analyses.
Understand the role of computation in the modern biology
Read and comprehend recent articles about genome, in particular the aspects associated to data analysis
Become familiar with standard problems and tools, beyond the area current and future objectives
Access and handle real genomic data
André de Carvalho - ICMC/USP
5/11/2018

6. About the course Course directed to problems
The book reading is indispensable!
Experimental
Discussion classes based on the didactic material
Weekly homework
André de Carvalho - ICMC/USP
5/11/2018

7. Bibliography
Nello Cristianini and Matthew W. Hahn: Introduction to Computational Genomics: A Case Studies Approach, Cambridge, 2007
Neil C. Jones and Pavel A. Pevzner: An Introduction to Bioinformatics Algorithms, MIT Press, 2004
André de Carvalho - ICMC/USP
5/11/2018

8. Bibliography Site: www.computational-genomics.net
André de Carvalho - ICMC/USP
11/05/2018

11. Bioinformatics
Research and development of computational, mathematical and statistical tools to solve problems from Biology
Molecular Biology
A Computação está para a Biologia da mesma
forma que a Matemática está para a Física.
Harold Morowitz
André de Carvalho - ICMC/USP
11/05/2018

12. Bioinformatics Areas from Bioinformatics
Development of new techniques and algorithms for research in biological database
Development and implementation of tools which allow efficient management and access of several kinds of information
André de Carvalho - ICMC/USP
5/11/2018

13. Bioinformatics Historical 1960: first aminoacid sequences databases
: development of algorithms do analyze those data
1980: launch of GeneBank and other public database
With analyses tools
1990: Huge growth of DBs GenBank and PDB
André de Carvalho - ICMC/USP
5/11/2018

14. Bioinformatics Research benefits several areas Medicine
Medicine - Pharmacy - Agriculture
Medicine
Improve disease diagnosis
Detect genetic propensity to diseases
Use gene therapy as medicine
Allow the development of “personal medicine”, based on individual genetical profile
André de Carvalho - ICMC/USP
11/05/2018

15. Bioinformatics First step to understand the cell operation:
To know of its nucleotide sequence (DNA)
It defines the entire organism genome
Set of all its DNA
André de Carvalho - ICMC/USP
5/11/2018

16. Bioinformatics Genomics ground zero
Publication of the hole sequencing of a free-living organism (Science, 1995)
Haemophilus influenza bacterium
The Institute for Genomic Research (TIGR)
Craig Venter
Until then, only small viral organism or small parts of other genomes
First genomic sequence (Phage virus phiX174) in 1978
André de Carvalho - ICMC/USP
5/11/2018

17. Bioinformatics Haemophilus influenza
Causer of several clinical diseases
Menigite and septicemia, both usually occur in children, infeccion of middle ear, etc
Until 1933, it was incorrectly consider as the cause of common flu (influenza)
Chosen because one of the leaders of the project had been working with it from decades
They could build high qualities DNA libraries
DNA base pairs in one single circular chromosome
André de Carvalho - ICMC/USP
11/05/2018

18. Bioinformatics
Few months later, TIGR published another bacterium genome
Mycoplasma genitalium
Causer of pelvic inflamation
TIGR created revolutionary computational methods to obtain and assemble genome sequences
Soon after, by other group, it was published the first eukaryote sequence
Sacharomyces cerevisiae fungi (yeast)
André de Carvalho - ICMC/USP
11/05/2018

19. Bioinformatics January 2008 TIGR creates synthetic bacterium genome
Utilizes parts of Mycoplasma genitalium
Plan: insert in a living cell and create the first artificial organism
André de Carvalho - ICMC/USP
11/05/2018

21. Bioinformatics In the last years several genomes were sequenced
Generating a great amount of data
Until January 2008:
More than 3500 sequencing projects
Around 700 organisms had been completely sequenced
André de Carvalho - ICMC/USP
11/05/2018

22. Bioinformatics André de Carvalho - ICMC/USP 11/05/2018
Source:
André de Carvalho - ICMC/USP
11/05/2018

23. Bioinformatics André de Carvalho - ICMC/USP 11/05/2018
Source:
André de Carvalho - ICMC/USP
11/05/2018

24. Growth of Nucleotide Sequences Database
Moore's
Law
DNA
André de Carvalho - ICMC/USP
11/05/2018

25. Bioinformatics André de Carvalho - ICMC/USP 11/05/2018
Source:
André de Carvalho - ICMC/USP
11/05/2018

26. Ongoing Genome Projects
Total EUA UE Japão Outros Indústrias
Archaea
Procaryote
Eucaryote
2007
Archaebacteria:
Unicell procariotes organisms
Considered an intermediate group between eucaryote and procaryote
André de Carvalho - ICMC/USP
11/05/2018

27. Bioinformatics Pace of genome projects
Examples of complete published genomes
Human
Mouse
Drosophila melanogaster
Arabidopsis thaliana
Yeast
Domestic animals genome
André de Carvalho - ICMC/USP
11/05/2018

28. Bioinformatics Most known sequencing: Made by two groups
Humans: trillions of cells
Yeast: 1 cell
Made by two groups
Human genome project
Public
International consortia
Celera Genomics
Private
André de Carvalho - ICMC/USP
5/11/2018

29. The Human Genome Project
Officially initiated in 1990
Originally planned for during 15 years
Technological advances brought the conclusion to 2003
Coordinated by U.S. Department of Energy and for National Institutes of Health
André de Carvalho - ICMC/USP
5/11/2018

30. G16 Human Genome Sequencing Consortium
1. Baylor College of Medicine, Houston, Texas, USA
2. Beijing Human Genome Center, Institute of Genetics, Chinese Academy of Sciences, Beijing, China
3. Gesellschaft für Biotechnologische Forschung mbH, Braunschweig, Germany
4. Genoscope, Evry, France
5. Genome Therapeutics Corporation, Waltham, MA, USA
6. Institute for Molecular Biotechnology, Jena, Germany
7. Joint Genome Institute, U.S. Department of Energy, Walnut Creek, CA, USA
8. Keio University, Tokyo, Japan
9. Max Planck Institute for Molecular Genetics, Berlin, Germany
10. RIKEN Genomic Sciences Center, Saitama, Japan
11. The Sanger Centre, Hinxton, U.K.
12. Stanford DNA Sequencing and Technology Development Center, Palo Alto, CA, USA
13. University of Washington Genome Center, Seattle, WA, USA
14. University of Washington Multimegabase Sequencing Center, Seattle, WA,USA
15. Whitehead Institute for Biomedical Research, MIT, Cambridge, MA, USA
16. Washington University Genome Sequencing Center, St. Louis, MO, USA
Funding: National Institutes of Health (US) , Department of Energy (US) , Medical Research Council of Great Britain and Northern Ireland (UK) Wellcome Trust (UK)
André de Carvalho - ICMC/USP
11/05/2018

31. The Human Genome Project
Main objectives:
To identify all human DNA genes
To determine the base pars sequence which compose the human DNA
Store this information in a DB
To improve tools to data analysis
To transfer acquired technology to the private sector
To address the ethical, legal and social themes that would arise from the project
André de Carvalho - ICMC/USP
5/11/2018

32. The Human Genome Project
Some results
Number of bases: 3 billions
A's, C's, G's and T's
The exact number of genes is still unknown
Currently between and genes
André de Carvalho - ICMC/USP
5/11/2018

33. Human Genome Cromosomes
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11/05/2018

34. The Human Genome Project
More recently numbers
Released in October 2004
It was identified genes possibles genes
Less than the rice
to (shorter genes)
A little more than the nematode
genes
André de Carvalho - ICMC/USP
5/11/2018

35. Bioinformatics Nematode (Caenorhabditis elegans) Worm
More than genes
Already gave hints about diabetes, aging process and cancer development
Has a gene that regulates the organ formation
Can increase the development of artificial organs
André de Carvalho - ICMC/USP
5/11/2018

36. Bioinformatics Some results of human genome project
One gene have around bases
The sizes vary a lot
Major known human gene has 2.4 millions of bases
The genes are concentrated in random areas through the genome
The function of more than 50% of the genes is unknown
André de Carvalho - ICMC/USP
5/11/2018

37. Bioinformatics Some results of human genome project
Around 2% of the genome codes for instructions for the protein synthesis
More than 40% of the expected human proteins show similarities with worm and house flies proteins
The genomes from human and chimp are 98.5% genetically identical
André de Carvalho - ICMC/USP
5/11/2018

38. Bioinformatics Objetctive of Genetic community:
Equivalent to the sequencing of all human genome for US$1,000
News from “Terra” website, January 22, 2008
The American genetic research company 23andMe, sponsored by google, offers on Europe the internet dispatch of a personalized copy of DNA by internet
around US$ 999
EI4802,00.html
André de Carvalho - ICMC/USP
5/11/2018

39. Genomes
Several specie genomes and individuals from the same specie are available
Scientists are comparing them
André de Carvalho - ICMC/USP
5/11/2018

40. Global sells in Bioinformatics
Global Market
Global sells in Bioinformatics
$6,000
$5,000
$4,000
$3,000
$2,000
$1,000 $0
Millions of dollars
Year
André de Carvalho - ICMC/USP
11/05/2018

41. Bioinformatics Generated data need to be analyzed
Progressive emphasis change
Accumulation  interpretation
Laboratorial Analysis: expensive and hardworking
Need of sophisticated computational tools
André de Carvalho - ICMC/USP
11/05/2018

42. Bioinformatics Bioinformatics Artificial Intelligence Computational
Theory
Bio inspired
Computing
Data
Structure
Bioinformatics
Optimization
Computer
Network
Internet
Graphic
Computing
Parallel
Computing
Image
Processing
Software
Engineering
Database
André de Carvalho - ICMC/USP
5/11/2018

43. Questions?