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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.
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STAT115STAT215 BIO512 BIST298 Introduction to Computational Biology and BioinformaticsSpring 2014 Xiaole Shirley Liu
STAT115STAT 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 STAT115
The Protein Sequence and Structure Wave • 1955: Sanger sequenced bovine insulin • 1970: Smith-Waterman algorithm • 1973: PDB • 1990: BLAST • 1994: BLOCKS database • 1994-: CASP • 1997-: Proteomics STAT115
The Microarray Wave • Microarray contains hundreds to millions of tiny probes • Simultaneously detect how much each gene is expressed STAT115
ALL vs AML • Golub et al, Science 1999. STAT115
ALL vs AML STAT115
“Microarrays” Today • Infer the expression value of all the genes from 1000 probes • High throughput drug screen STAT115
The DNA Sequencing Wave • 1953: DNA structure • 1972: Recombinant DNA • 1977: Sanger sequencing • 1985: PCR • 1988: NCBI • 1990: BLAST STAT115
Sequencing in the 1970s STAT115
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 STAT115
Human Genome Sequencing • Clone-by-clone and whole-genome shotgun STAT115
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 STAT115
Sequencing Today • 1000 Genomes • Personal genome sequencing • HiSeq2500 STAT115
Personalized Disease Susceptibility Test and Treatment • GWAS Catalog • Cancer Genome Sequencing STAT115
Big Data Challenges STAT115
Is This Course For Me? • Biologists • Statistician • Computer Scientists • STAT115/STAT215/BIO512/BIST298 • http://stat115.org/ STAT115
Class Information • Professor and Lectures • Video recording in 2-4 sections • Tue / Thu 11:30am-1pm, SC221 • Office hours • Roughly 4 modules • Gene expression • Transcriptional and epigenetic gene regulation • Human genetics, association studies • Translational cancer bioinformatics STAT115
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! STAT115
Class Information • HW and Grading • HW 6 * 10 or 6 * 12 • Exams (midterm + final) * 10 • Class participation: 20 • Algorithm videos: 5 • Lecture notes: extra 5 points • Late days • Auditing? STAT115
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