P1252428414rdLoq

1

Bioinformatics Opportunities for KSA_at_IU

Sun Kim School of Informatics Center for
Genomics and Bioinformatics Indiana
University-Bloomington sunkim_at_bio.informatics.ind
iana.edu
2
Bioinformatics A Multidisciplnary Science

• Bioinformatics involves
• Biology
• Computer science
• Statistics
• Chemistry
• Physics

3
CS vs Biology

• An excerpt from a CRA report
• Computation is synthetic in the sense that many
  of the phenomena computer scientists and
  engineers study are created by humans rather than
  occurring naturally in the physical world.
• When one discovers a fact about nature, it is a
  contribution per se, no matter how small. Since
  anyone can create something new in a synthetic
  field, that alone does not establish a
  contribution. Rather, one must show that the
  creation is better.

4
Bioinformatics synthetic but real

• Showing a method is better is easy in an
  environment created by human.
• However, imagine the difficulty in showing a
  method is better in the physical world, combining
  knowledge from multiple disciplines.
• You have an opportunity to overcome all these
  hurdles, e.g, double major in CS and biology.
  Congratulations!

5
Bioinformatics A New Science

• In vivo within living orgnisms
• In vitro outside the living body
• In silico on computer

6
Bioinformatics A New Science

• Washington Post Staff Writer,Wednesday, October
  1, 2003
• With the deepest secrets of life's workings
  seemingly within reach for the first time, the
  National Institutes of Health is initiating a
  major transformation in the way it funds efforts
  to conquer disease, the agency's director
  announced yesterday.joined by physicists,
  material scientists, computer scientists and
  engineers. Those researchers have not
  traditionally been funded by the health agency,
  but their expertise is now seen as crucial if
  recent advances in genetics and cell biology are
  to be put to work in people's bodies.

7
Why Bioinformatics is interesting?

• Bioinformatics is an exciting, challenging
  opportunity
• because it is
• a new science,
• computationally challenging, and
• scientifically sound

8
Transcription and Translation
The central dogma in biology
This makes bioinformatics real.
9
Introns, Exons, and mature mRNAs
10
A Genome Project from Bioinformatics Perspective
11
Computational Challenges

• Problems in biology involve a huge amount of data
  and they are computationally challenging.
• Thus it is highly unlikely single algorithms can
  solve problems in biology.
• It is often tackled as a data mining process,
  which requires careful stepwise tasks.

12
An Example of Computational Challenges
A genome content can be better understood by
comparing it to other genomes that we can have
more information about. Imagine a task of
comparing the human genome to the mouse Genome
(each is of 3 billion encrypted characters).
gtgi28525800refNT_039683.1Mm19_39723_30 Mus
musculus chromosome 19 genomic contig, strain
C57BL/6J GCCTGCTCTCCTAGGAGTACCGAGAATCATGGGTCCCAGAC
ACTAAAGGGGAAAGGAACTTGGCCAGTGG ACCAAAGTCACAGTTACGAG
CTCAGCTACACTGCAAAGCAACTGGAGTTCACCCTGTACCTGGAAGAGAA
GAATTTGGCTTAGATTTGCGGGAAGGGTGGTGtttagagacctgggctc
cccatgttgctcaggctagat tggaatccctgagcgaaccatcctccag
tgacagcctcccgagggtggccaggagagtgcacaccacTTA CTGCCCA
AGCTGAAGAGACTTCACTAAGGAGGTGAGAgccagacaatggtgacatac
atctttaatccca gcattcaggaggcagaggcaggtaaataaatctctg
agtttgaggccaacctggcctacagagctagttc caggacagccagggc
tacacaaagaaacgctgcctcaaaaaaagcaaaaCAGAAGGAGGAGGAGG
TGAGG ACGTCTAACGGCCTGGATTGATCGCCATGAAAGCTTCAGCGGAT
AAAGCGGTGCACCCGTCTATAATCCC TACAGTTACCATGAAGCAATTAG
ACAACAACAACAAAAGGCTGGGCTGAGTTCCTGGCTTGAGAGGAGGG AA
GGGGGTCAGCCAGGGCTTGAGAGGCAGTGTACAAGGGCCCTGGGATCTCC
TGACTTGGGTTTGAGCCA CCTGAGTGGTAAGACAAATGAATATCTCCCC
CCAAGCCAGCCCCTCCTCAGTGCTCAGTGCTGTGAAAGT CACCAGTGGC
TTTATTAAGGCTTAAAGCAGGAACACCAGCCAGGCTGCCTTCACAGTAAT
CTTTCTGTGT TTTGCTTGTCAAGGTCCCTCTTCTCGCCTCCTTTGGTGC
CCCCGCCCGTCACCTCCAGAGCCCTCTTGGC CTCTGGATCCAATTCCCA
GCCAGGGAAGCCCGCCCTGGGCAAATTACTGCTGTCAATTAGATTGCCAG
CA TGTCTGCCCTGCAAATTAATGAGTCCACTCATCAGCTCATAAATCAC
CTCCTGCCACAAGCCTGGCCTGG TCCCAGGAGAGTGTCCAGGCTCAGAC
CAGGATATAAGAAGAACAGTGTCCCCAAACTACATTCCTGGGAA CCTGC
CCCTCCCTGGCAGGTGTGTAGAGCAAGCCTGAGTCTACAGGACATCACCA
TGCAGGACTTGTTAC CATGCAGGACTTGTCACCATGCAGGACTTGTCAG
AGGTTCGACCATGCCTGAGGAACCATGGCTTCCTGC AGCAGCATCACGG
AGGGCTGGCTGGTCAGAGTGTTGATGAGCAGTTTGCAAGTGTTCAGGGAG
CTGGGCT TGGGGGCACACAAGcaggcagtagagacaggaggattgggga
ttcaggatcagcctgatctaactgagac catgtctcaaaacaaaTgggc
tgaacagatggctcagcagttaagaacattctctgcttctgtagatggc
aggggttcggttcccagcaccctcatggccacagcacacagcatctgtaa
ctccagctccaggaagtctg acaccctctgctggctgcggtaagcactg
cacacacttggggcactgatgatcaggcagattcacaccca cgagataa
aaataaagctGACTAAATAAGTAAACACAACTGACAGAGGAGCTGCCAGC
CTGACTGGGAAG CTGAAGCCTGGGACCATCAACAGCACTCAGCTGCACA
GGGTGCAAAGTCAGAGCCCACAGAGCCAAGAGC
gtgi6004447refNT_002446.1Hs22_2567 Homo
sapiens 22q11.2 sequence. GATCTGATAAGTCCCAGGACTTCA
GAAGAGCTGTGAGACCTTGGCCAAGTCACTTCCTCC TTCAGGAACATTG
CAGTGGGCCTAAGTGCCTCCTCTCGGGACTGGTATGGGGACGGTCAT GC
AATCTGGACAACATTCACCTTTAAAAGTTTATTGATCTTTTGTGACATGC
ACGTGGGT TCCCAGTAGCAAGAAACTAAAGGGTCGCAGGCCGGTTTCTG
CTAATTTCTTTAATTCCAA GACAGTCTCAAATATTTTCTTATTAACTTC
CTGGAGGGAGGCTTATCATTCTCTCTTTTG GATGATTCTAAGTACCAGC
TAAAATACAGCTATCATTCATTTTCCTTGATTTGGGAGCCT AATTTCTT
TAATTTAGTATGCAAGAAAACCAATTTGGAAATATCAACTGTTTTGGAAA
CC TTAGACCTAGGTCATCCTTAGTAAGATCTTCCCATTTATATAAATAC
TTGCAAGTAGTAG TGCCATAATTACCAAACATAAAGCCAACTGAGATGC
CCAAAGGGGGCCACTCTCCTTGCT TTTCCTCCTTTTTAGAGGATTTATT
TCCCATTTTTCTTAAAAAGGAAGAACAAACTGTGC CCTAGGGTTTACTG
TGTCAGAACAGAGTGTGCCGATTGTGGTCAGGACTCCATAGCATTT CAC
CATTGAGTTATTTCCGCCCCCTTACGTGTCTCTCTTCAGCGGTCTATTAT
CTCCAAG AGGGCATAAAACACTGAGTAAACAGCTCTTTTATATGTGTTT
CCTGGATGAGCCTTCTTT TAATTAATTTTGTTAAGGGATTTCCTCTAGG
GCCACTGCACGTCATGGGGAGTCACCCCC AGACACTCCCAATTGGCCCC
TTGTCACCCAGGGGCACATTTCAGCTATTTGTAAAACCTG AAATCACTA
GAAAGGAATGTCTAGTGACTTGTGGGGGCCAAGGCCCTTGTTATGGGGAT
G AAGGCTCTTAGGTGGTAGCCCTCCAAGAGAATAGATGGTGAATGTCTC
TTTTCAGACATT AAAGGTGTCAGACTCTCAGTTAATCTCTCCTAGATCC
AGGAAAGGCCTAGAAAAGGAAGG CCTGACTGCATTAATGGAGATTCTCT
CCATGTGCAAAATTTCCTCCACAAAAGAAATCCT TGCAGGGCCATTTTA
ATGTGTTGGCCCTGTGACAGCCATTTCAAAATATGTCAAAAAATA TATT
TTGGAGTAAAATACTTTCATTTTCCTTCAGAGTCTGCTGTCGTATGATGC
CATACC AGAGTCAGGTTGGAAAGTAAGCCACATTATACAGCGTTAACCT
AAAAAAACAAAAAACTG TCTAACAAGATTTTATGGTTTATAGAGCATGA
TTCCCCGGACACATTAGATAGAAATCTG GGCAAGAGAAGAAAAAAAGGT
CAGAGTTTAATCCTCATTCCTAAGTTATGTAAACCAAAA ATAAAATTCT
GAAGATGTCCTGATCATCTGAATGGACCCTTCCTCTGGACCAGGGCATTC

13
Major in Bioinformatics?

• M.S in Bioinformatics, Ph.D program in proposal
• Ph.D minor in Bioinformatics
• You should take courses in biology, informatics,
  CS, statistics,
• Who to contact
• Gary Wiggins
• Director, Chemical Informatics ProgramInterim
  Director, Bioinformatics Program
• Linda Hostetter Recorder/Graduate Administrator