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Xiaole Shirley Liu

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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Xiaole Shirley Liu

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  1. STAT115STAT215 BIO512 BIST298 Introduction to Computational Biology and BioinformaticsSpring 2014 Xiaole Shirley Liu

  2. STAT115STAT 215 BIO512 BIST 298 Student Introduction Name, School, Grade, Major What do you hope to learn from this course

  3. 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

  4. 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

  5. The Microarray Wave • Microarray contains hundreds to millions of tiny probes • Simultaneously detect how much each gene is expressed STAT115

  6. ALL vs AML • Golub et al, Science 1999. STAT115

  7. ALL vs AML STAT115

  8. “Microarrays” Today • Infer the expression value of all the genes from 1000 probes • High throughput drug screen STAT115

  9. The DNA Sequencing Wave • 1953: DNA structure • 1972: Recombinant DNA • 1977: Sanger sequencing • 1985: PCR • 1988: NCBI • 1990: BLAST STAT115

  10. Sequencing in the 1970s STAT115

  11. 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

  12. Human Genome Sequencing • Clone-by-clone and whole-genome shotgun STAT115

  13. 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

  14. Sequencing in 2001

  15. Sequencing in 2007

  16. Sequencing Today • 1000 Genomes • Personal genome sequencing • HiSeq2500 STAT115

  17. Personalized Disease Susceptibility Test and Treatment • GWAS Catalog • Cancer Genome Sequencing STAT115

  18. Big Data Challenges STAT115

  19. STAT115

  20. Is This Course For Me? • Biologists • Statistician • Computer Scientists • STAT115/STAT215/BIO512/BIST298 • http://stat115.org/ STAT115

  21. 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

  22. 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

  23. 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

  24. 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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