STAT115
STAT215 BIO512 BIST298
Introduction to Computational
Biology and Bioinformatics
Spring 2014
Xiaole Shirley Liu
STAT115
STAT 215 BIO512 BIST 298
Student Introduction
• Name, School, Grade, Major
• What do you hope to learn from
this course
Bioinformatics and
Computational Biology
• Interdisciplinary
– Statistics, Biology, Computer Science
• 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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The Protein Sequence and
Structure Wave
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1955: Sanger sequenced bovine insulin
1970: Smith-Waterman algorithm
1973: PDB
1990: BLAST
1994: BLOCKS database
1994-: CASP
1997-: Proteomics
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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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ALL vs AML
• Golub et al, Science 1999.
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ALL vs AML
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“Microarrays” Today
• Infer the expression value of all
the genes from 1000 probes
• High throughput drug screen
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The DNA Sequencing Wave
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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
• Human Genome Project: 1990-2003
– Originally 1990-2005
– Boosted by technology improvement
(automation improved throughput and quality
with reduced cost)
– Competition from Celera
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Human Genome Sequencing
• 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
(automation improved throughput and quality
with reduced cost)
– Competition from Celera
• Informatics essential for both the public and
private sequencing efforts
– Sequence assembly and gene prediction
– Working draft finished simultaneously spring
2000
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Sequencing in 2001
Sequencing in 2007
Sequencing Today
• 1000 Genomes
• Personal genome
sequencing
• HiSeq2500
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Personalized Disease
Susceptibility Test and Treatment
• GWAS Catalog
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• Cancer Genome
Sequencing
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Big Data Challenges
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Is This Course For Me?
• Biologists
• Statistician
• Computer Scientists
• STAT115/STAT215/BIO512/BIST298
• http://stat115.org/
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Class Information
• Professor and Lectures
– Video recording in 2-4 sections
– Tue / Thu 11:30am-1pm, SC221
– Office hours
• Roughly 4 modules
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Gene expression
Transcriptional and epigenetic gene regulation
Human genetics, association studies
Translational cancer bioinformatics
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Class Information
• Teaching Fellows
Yang Li
Lin Liu
• Labs: Wed 6 – 8pm, Science Center 418D
– Tue 5:30 – 7pm, HSPH Kresge 209, Boston?
– Make sure you come tomorrow!
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Class Information
• HW and Grading
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HW 6 * 10 or 6 * 12
Exams (midterm + final) * 10
Class participation: 20
Algorithm videos: 5
Lecture notes: extra 5 points
Late days
• Auditing?
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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