Slides contain information about why bioinformatics appeared,
who bioinformaticians are, what they do, what kind of cool applications and challenges in bioinformatics there are.
Slides were prepared for the Bioinformatics seminar 2016, Institute of Computer Science, University of Tartu.
7. Cell size and scale
http://learn.genetics.utah.edu/content/cells/scale/
8. Central dogma
What is DNA?
What is the difference
between DNA and RNA?
Image credit: Genome Research Limited
100 000 different proteins
23 000 genes
12. Each cell has its own gene
expression profile
Gene Expression
profile
Expression
level
G1 OFF 0
G2 ON 30
G3 ON 20
G4 OFF 0
Gene Expression
profile
Expression
level
G1 OFF 0
G2 ON 30
G3 ON 20
G4 ON 20
HEALTHY CELL CANCER CELL
13. Single Nucleotide polymorphism
• variation in a single nucleotide that occurs at a specific position in the
genome, where each variation is present to some appreciable degree
within a population (e.g. >1%)
• underlie differences in our susceptibility to disease
Image credit: Wikipedia
22. Why do we need bioinformaticians?
• Amount of generated biological data
requires sophisticated data analysis and
management
• Programmers & statisticians lack biological
knowledge
• Biologists don’t program
• These two don’t understand each other
Slide is inspired by from “How to be a bioinformatician” by Christian Frech
23. Biologist talks to statistician
http://www.youtube.com/watch?v=Hz1fyhVOjr4
25. What do bioinformaticians do?
Word cloud from manuscript titles published in
Bioinformatics from Jan 2013 to April 2014
Slide credit: “How to be a bioinformatician” by Christian Frech
65. Data storage
The amount of sequencing data created is growing at
a faster rate than economically available storage
http://geschwindlab.neurology.ucla.edu/protocols/next-generation-sequencing
66. N Goldman et al. Nature 000, 1-4 (2013) doi:10.1038/nature11875
Using DNA as a digital archive media
store sequenced DNA information in … DNA
67. N Goldman et al. Nature 000, 1-4 (2013) doi:10.1038/nature11875
Scaling properties of DNA-based
storage
If the cost of DNA synthesis falls by two orders of magnitude,
it will become a sensible way to store data for the medium term
(below 50 years)
68. Challenges
• Need of new compression methods
• Data integration methods
• Lack of specialists
• Need for new:
– Analysis pipelines
– Methodology
– Algorithmic solutions
– Tools
69. Challenges of being
bioinformatician
• Biology is complex, not black and white
– As many exceptions as rules (e.g.: define “gene”)
– No single optimal solution to a problem
– Results interpretable in many ways (story telling, cherry picking)
• Understanding the biological question
• Field is moving incredibly fast
– Lack of standards, immature/abandoned software
– Much time spent on collecting/cleaning-up data, troubleshooting
errors
• Hundreds of software tools and databases out there
– Easy to get lost
– Important to understand their strengths and weaknesses
81. Genes
are
us…
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EUROPEAN,BIOINFORMAT,ICS,INSTITUTE
Genes
are
us…
and them.SOURCE:,JAVIER,HERRERO,,EUROPEAN,MOLECULAR,BIOLOGY,LABORATORY—
EUROPEAN,BIOINFORMAT,ICS,INSTITUTE
Genes
are
us…
and them.SOURCE:,JAVIER,HERRERO,,EUROPEAN,MOLECULAR,BIOLOGY,LABORATORY—
EUROPEAN,BIOINFORMAT,ICS,INSTITUTE
Genes
are
us…
and them.SOURCE:,JAVIER,HERRERO,,EUROPEAN,MOLECULAR,BIOLOGY,LABORATORY—
EUROPEAN,BIOINFORMAT,ICS,INSTITUTE
Genes
are
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and them.SOURCE:,JAVIER,HERRERO,,EUROPEAN,MOLECULAR,BIOLOGY,LABORATORY—
EUROPEAN,BIOINFORMAT,ICS,INSTITUTE
Genes
are
us…
and them.SOURCE:,JAVIER,HERRERO,,EUROPEAN,MOLECULAR,BIOLOGY,LABORATORY—
EUROPEAN,BIOINFORMAT,ICS,INSTITUTE
Genes
are
us…
and them.SOURCE:,JAVIER,HERRERO,,EUROPEAN,MOLECULAR,BIOLOGY,LABORATORY—
EUROPEAN,BIOINFORMAT,ICS,INSTITUTE
Genes
are
us…
and them.SOURCE:,JAVIER,HERRERO,,EUROPEAN,MOLECULAR,BIOLOGY,LABORATORY—
EUROPEAN,BIOINFORMAT,ICS,INSTITUTE
Genes
are
us…
and them.SOURCE:,JAVIER,HERRERO,,EUROPEAN,MOLECULAR,BIOLOGY,LABORATORY—
EUROPEAN,BIOINFORMAT,ICS,INSTITUTE
82. Genes
are
us…
and them.SOURCE:,JAVIER,HERRERO,,EUROPEAN,MOLECULAR,BIOLOGY,LABORATORY—
EUROPEAN,BIOINFORMAT,ICS,INSTITUTE
Genes
are
us…
and them.SOURCE:,JAVIER,HERRERO,,EUROPEAN,MOLECULAR,BIOLOGY,LABORATORY—
EUROPEAN,BIOINFORMAT,ICS,INSTITUTE
Genes
are
us…
and them.SOURCE:,JAVIER,HERRERO,,EUROPEAN,MOLECULAR,BIOLOGY,LABORATORY—
EUROPEAN,BIOINFORMAT,ICS,INSTITUTE
Genes
are
us…
and them.SOURCE:,JAVIER,HERRERO,,EUROPEAN,MOLECULAR,BIOLOGY,LABORATORY—
EUROPEAN,BIOINFORMAT,ICS,INSTITUTE
Genes
are
us…
and them.SOURCE:,JAVIER,HERRERO,,EUROPEAN,MOLECULAR,BIOLOGY,LABORATORY—
EUROPEAN,BIOINFORMAT,ICS,INSTITUTE
Genes
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us…
and them.SOURCE:,JAVIER,HERRERO,,EUROPEAN,MOLECULAR,BIOLOGY,LABORATORY—
EUROPEAN,BIOINFORMAT,ICS,INSTITUTE
Genes
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us…
and them.SOURCE:,JAVIER,HERRERO,,EUROPEAN,MOLECULAR,BIOLOGY,LABORATORY—
EUROPEAN,BIOINFORMAT,ICS,INSTITUTE
Genes
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us…
and them.SOURCE:,JAVIER,HERRERO,,EUROPEAN,MOLECULAR,BIOLOGY,LABORATORY—
EUROPEAN,BIOINFORMAT,ICS,INSTITUTE
Genes
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us…
and them.SOURCE:,JAVIER,HERRERO,,EUROPEAN,MOLECULAR,BIOLOGY,LABORATORY—
EUROPEAN,BIOINFORMAT,ICS,INSTITUTE
Genes
are
us…
and them.SOURCE:,JAVIER,HERRERO,,EUROPEAN,MOLECULAR,BIOLOGY,LABORATORY—
EUROPEAN,BIOINFORMAT,ICS,INSTITUTE
83. Genes
are
us…
and them.SOURCE:,JAVIER,HERRERO,,EUROPEAN,MOLECULAR,BIOLOGY,LABORATORY—
EUROPEAN,BIOINFORMAT,ICS,INSTITUTE
Genes
are
us…
and them.SOURCE:,JAVIER,HERRERO,,EUROPEAN,MOLECULAR,BIOLOGY,LABORATORY—
EUROPEAN,BIOINFORMAT,ICS,INSTITUTE
Genes
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and them.SOURCE:,JAVIER,HERRERO,,EUROPEAN,MOLECULAR,BIOLOGY,LABORATORY—
EUROPEAN,BIOINFORMAT,ICS,INSTITUTE
Genes
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and them.SOURCE:,JAVIER,HERRERO,,EUROPEAN,MOLECULAR,BIOLOGY,LABORATORY—
EUROPEAN,BIOINFORMAT,ICS,INSTITUTE
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and them.SOURCE:,JAVIER,HERRERO,,EUROPEAN,MOLECULAR,BIOLOGY,LABORATORY—
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and them.SOURCE:,JAVIER,HERRERO,,EUROPEAN,MOLECULAR,BIOLOGY,LABORATORY—
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and them.SOURCE:,JAVIER,HERRERO,,EUROPEAN,MOLECULAR,BIOLOGY,LABORATORY—
EUROPEAN,BIOINFORMAT,ICS,INSTITUTE
Genes
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and them.SOURCE:,JAVIER,HERRERO,,EUROPEAN,MOLECULAR,BIOLOGY,LABORATORY—
EUROPEAN,BIOINFORMAT,ICS,INSTITUTE
Genes
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and them.SOURCE:,JAVIER,HERRERO,,EUROPEAN,MOLECULAR,BIOLOGY,LABORATORY—
EUROPEAN,BIOINFORMAT,ICS,INSTITUTE
84. Genes
are
us…
and them.SOURCE:,JAVIER,HERRERO,,EUROPEAN,MOLECULAR,BIOLOGY,LABORATORY—
EUROPEAN,BIOINFORMAT,ICS,INSTITUTE
Genes
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us…
and them.SOURCE:,JAVIER,HERRERO,,EUROPEAN,MOLECULAR,BIOLOGY,LABORATORY—
EUROPEAN,BIOINFORMAT,ICS,INSTITUTE
Genes
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and them.SOURCE:,JAVIER,HERRERO,,EUROPEAN,MOLECULAR,BIOLOGY,LABORATORY—
EUROPEAN,BIOINFORMAT,ICS,INSTITUTE
Genes
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and them.SOURCE:,JAVIER,HERRERO,,EUROPEAN,MOLECULAR,BIOLOGY,LABORATORY—
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Genes
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and them.SOURCE:,JAVIER,HERRERO,,EUROPEAN,MOLECULAR,BIOLOGY,LABORATORY—
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and them.SOURCE:,JAVIER,HERRERO,,EUROPEAN,MOLECULAR,BIOLOGY,LABORATORY—
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and them.SOURCE:,JAVIER,HERRERO,,EUROPEAN,MOLECULAR,BIOLOGY,LABORATORY—
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EUROPEAN,BIOINFORMAT,ICS,INSTITUTE
Genes
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and them.SOURCE:,JAVIER,HERRERO,,EUROPEAN,MOLECULAR,BIOLOGY,LABORATORY—
EUROPEAN,BIOINFORMAT,ICS,INSTITUTE
Genes
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us…
and them.SOURCE:,JAVIER,HERRERO,,EUROPEAN,MOLECULAR,BIOLOGY,LABORATORY—
EUROPEAN,BIOINFORMAT,ICS,INSTITUTE
85. Genes
are
us…
and them.SOURCE:,JAVIER,HERRERO,,EUROPEAN,MOLECULAR,BIOLOGY,LABORATORY—
EUROPEAN,BIOINFORMAT,ICS,INSTITUTE
Genes
are
us…
and them.SOURCE:,JAVIER,HERRERO,,EUROPEAN,MOLECULAR,BIOLOGY,LABORATORY—
EUROPEAN,BIOINFORMAT,ICS,INSTITUTE
Genes
are
us…
and them.SOURCE:,JAVIER,HERRERO,,EUROPEAN,MOLECULAR,BIOLOGY,LABORATORY—
EUROPEAN,BIOINFORMAT,ICS,INSTITUTE
Genes
are
us…
and them.SOURCE:,JAVIER,HERRERO,,EUROPEAN,MOLECULAR,BIOLOGY,LABORATORY—
EUROPEAN,BIOINFORMAT,ICS,INSTITUTE
Genes
are
us…
and them.SOURCE:,JAVIER,HERRERO,,EUROPEAN,MOLECULAR,BIOLOGY,LABORATORY—
EUROPEAN,BIOINFORMAT,ICS,INSTITUTE
Genes
are
us…
and them.SOURCE:,JAVIER,HERRERO,,EUROPEAN,MOLECULAR,BIOLOGY,LABORATORY—
EUROPEAN,BIOINFORMAT,ICS,INSTITUTE
Genes
are
us…
and them.SOURCE:,JAVIER,HERRERO,,EUROPEAN,MOLECULAR,BIOLOGY,LABORATORY—
EUROPEAN,BIOINFORMAT,ICS,INSTITUTE
Genes
are
us…
and them.SOURCE:,JAVIER,HERRERO,,EUROPEAN,MOLECULAR,BIOLOGY,LABORATORY—
EUROPEAN,BIOINFORMAT,ICS,INSTITUTE
Genes
are
us…
and them.SOURCE:,JAVIER,HERRERO,,EUROPEAN,MOLECULAR,BIOLOGY,LABORATORY—
EUROPEAN,BIOINFORMAT,ICS,INSTITUTE
Genes
are
us…
and them.SOURCE:,JAVIER,HERRERO,,EUROPEAN,MOLECULAR,BIOLOGY,LABORATORY—
EUROPEAN,BIOINFORMAT,ICS,INSTITUTE
Genes
are
us…
and them.SOURCE:,JAVIER,HERRERO,,EUROPEAN,MOLECULAR,BIOLOGY,LABORATORY—
EUROPEAN,BIOINFORMAT,ICS,INSTITUTE
Genes
are
us…
and them.SOURCE:,JAVIER,HERRERO,,EUROPEAN,MOLECULAR,BIOLOGY,LABORATORY—
EUROPEAN,BIOINFORMAT,ICS,INSTITUTE
Genes
are
us…
and them.SOURCE:,JAVIER,HERRERO,,EUROPEAN,MOLECULAR,BIOLOGY,LABORATORY—
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