STAT115/215 BIO282/BST282

Introduction to Computational
Biology and Bioinformatics
Spring 2019

Xiaole Shirley Liu

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 The Microarray Wave
• Microarray contains hundreds to millions of
tiny probes
• Simultaneously detect how much each gene
is expressed

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 Acute Lymphoblastic Leukemia
vs Acute Myeloid Leukemia
• Golub et al, Science 1999.

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 “Microarrays” Today
• Infer the expression value of all the genes
from 1000 probes
• Connectivity Map: 1.5M expression profiles
upon 3K gene & 5K drug perturbations

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 The DNA Sequencing Wave
• 1953: DNA structure
• 1972: Recombinant DNA
• 1977: Sanger sequencing
• 1985: PCR
• 1988: NCBI
• 1990: BLAST

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 Sequencing in the 1970s

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 The Human Genome Race
• Clone-by-clone and whole-genome shotgun

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 The Human Genome Race
• Human Genome Project: 1990-2003
– Originally 1990-2005
– Boosted by technology improvement and
automation
– Competition from Celera
• Informatics essential for both the public and
private sequencing efforts
– Sequence assembly and gene prediction
– Working draft finished simultaneously spring 2000
– Complete human genome 2003

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 Sequencing in 2001

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 Sequencing in 2007

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 Sequencing Today

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Cost of Sequencing Human Genomes

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 Personalized Disease Susceptibility
Test and Treatment

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 Big Data Challenges

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 Difference between Bioinformatics
and Computational Biology
• Computational biology = the study of biology
using computational techniques. The goal is
to learn new biology, knowledge about living
systems. It is about science.
• Bioinformatics = the creation of tools
(algorithms, databases) that solve problems.
The goal is to build useful tools that work on
biological data. It is about engineering.
• Used interchangeably in this course

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 Levels of Bioinfo / CB
• Level 0: Modeling for modeling’s sake
• Level 1: Use published tools to analyze data
and generate hypotheses for experimentalists
• Level 2 (Bioinfo): Develop algorithms and
databases for data analyses on new
technologies, data integration and reuse.
• Level 3 (CompBio): Make biological
discoveries from public data integration and
modeling
• Level X: Integrative studies from big consortia

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 Bioinformatics and Computational
Biology
• Interdisciplinary
– Statistics, Biology, Computer Science
– Change in emphasis over time
• Applied
– From freshman to postdocs
– Useful training for many
– The more you practice, the better you get
• Moves with technology development

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 Is This Class for me?
• Computer: R and Python
• Biology: molecular biology, genomics
• Statistics: hypothesis testing, distributions,
intuition
• Major questions and and major solutions in
computational biology
• Hands on skills of data analyses and
programming
• It is not for statistical theories or deductions

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 Course Organization

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 All biology is becoming
computational, much the same way
it has became molecular …
Otherwise “low input, high
throughput and no output science”
--- Sydney Brenner
2002 Nobel Prize

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 Course Information
• Sign up for
Odyssey
account online
• Check course
website
instead of
syllabus for
updated
information

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 Class Website
• Course website:
– 2019: videos, slides, labs, HW
[Link]
urse-schedule

– Last year:
[Link]
– Videos for software usage:
[Link]
eo-tutorials-for-bioinformatics-software

• Take / audit the course remotely

• Teaching fellows
– Andy Shi, Yushi Tang, Mingrui Xu (grader)

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 HW and Grading
• Discuss and submit each HW on Canvas
• HW: HW1 is 8 points; HW2-6 are 15 points
each for STAT115 and 20 points each for
graduate level courses.
• Survey after each HW: 0.25 point each
• Final: 10 points open book classroom exam
• Bonus credits: online videos
• HW1 will be released today and due on
Sunday 2/10
• 6 total late days
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