Introduction#1

Introduction#1 - MCB182 Principles of Genomics(and...

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MCB182 Principles of Genomics (and Bioinformatics)
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General info Location: MWF 1000-1050 Wellman 106 Instructor: Ian Korf Teaching Assistant: Daniël Melters Office Hours (Melters): Thursday 2-3pm SLB 3061 Office Hours (Korf): SmartSite chat room
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Grading • 4 in-class exams, 1 final – 25 points each – Lowest exam is dropped – No make-ups • Extra credit – Ethics paper (1-3 points) – Web assignment (1-2 points) – Class participation (0-2 points) – Online participation (0-2 points) – Good -omics word (0-1 point) – TA recognition (0-1 point)
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Textbook There isn’t any! Notes for each class posted after lecture
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Syllabus 1. Mapping, sequencing, genes, and genomes 2. Information, amino acid similarity, sequence alignment, local alignment statistics 3. Transcriptome, regulome, epigenome 4. Sequence patterns: regex, PWM, Markov models, HMMs, GHMMs 5. Functional genomics, proteomics, metabolomics, ontologies
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Important Dates • 4/9 exam #1 (and photo day) • 4/23 exam #2 • 4/26 movie day (essay assigned) • 5/7 exam #3 • 5/10 ethics day (essay due) • 5/21 exam #4 • 5/31 Memorial Day (no class) • 6/7 final exam (8 am)
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Bioinformatics/Genomics Laboratory Unofficial laboratory companion to MCB182. Learn how to program. Experience -omic biology first-hand. Tues-Thurs 3:40-5:30 Hart 1102 Seats available! Sign up for MCB198 Sec 015
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Epitome Main Entry: epit·o·me Pronunciation: Function: noun Etymology: Latin, from Greek epitomE, from epitemnein to cut short, from epi- + temnein to cut -- more at TOME 1 a : a summary of a written work b : a brief presentation or statement of something 2 : a typical or ideal example : EMBODIMENT <the British monarchy itself is the epitome of tradition -- Richard Joseph> 3 : brief or miniature form -- usually used with in -ep·i·tom·ic / / or ep·i·tom·i·cal /- adjective From Merriam Webster Online A Zijlstra, JE Testa, JP Quigley, Targeting the proteome / epitome , implementation of subtractive immunization, Biochem Biophys Res Commun 303(3): 733- 744, Apr. 11, 2003 epitomics : A new field of science that studies all epitopes of the proteome in an organism What the heck are they talking about? What the heck are they talking about? What the heck are they talking about? What the heck are they talking about?
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Gene, genome, genomics Genome is an old word. It was first used in 1920 by Hans Winkler. Genomics is a turn-of-the-century buzz word. Genomics is so cool that everyone wants their own -ome and -omics . Gene is an old word. Ludvig Johannsen first used the word as a unit of inheritance in 1909. Gene comes from the Greek term "gives birth to". Gregor Mendel studied inheritance in the mid 1800s. He didn't use the term "gene".
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Transcriptome Proteome Proteomics Metabolome Metabolomics ORFeome Pseudogenome Epigenome Epigenomics Regulome Morphome Interactome Interactomics Transportome Secretome Transductome Translatome Degredome Degredomics Allergenome Allergenomics
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Introduction#1 - MCB182 Principles of Genomics(and...

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