Chambers Hall, Room 3146 (Mac Computer Lab)
Class meets every Monday, Wednesday and Friday, 11:30 AM - 12:20 PM
Unit One: Genome Sequences - Making sense of ATCG... |
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| Day | Chapter | Pre-Class Reading | Pre-class Homework Discovery Questions |
| M, Aug 27 | Course introduction Class photo |
none | none |
| W, Aug 29 | What's wrong with my child? (case study 1) 1.1 First Patients 1.2 The next steps in understanding the disease, the need for a model animal system (intro.) |
Web: BIO309 Syllabus Web: Assignment Help Guide Text: 3 - 9 (stop at "What was the Other Protein...") |
Homework 1-1 6, 7, 10, Math Minute 1.1-1, 14 |
| F, Aug 31 | Genome sequence acquisition and analysis 2.1 How are genomes sequenced? |
Text: 34 - 45 (stop at "Can We Predict...") | Homework 1-2 2*, 10, 11, Math Min. 2.1-1, 14, 15 a (*Note: DQ 2 does not require an answer) |
| M, Sept 3 | Genome sequence acquisition and analysis 2.1 How are genomes sequenced? (cont.) |
Text: 45 - 59 (stop at 2.2) | Homework 1-3 17, 22, 27, 28, 31, 38 |
| W, Sept 5 | Genome sequence acquisition and analysis 2.2 What have we learned from unicellular genomes? |
Text: 59 - 65; 78 (start at "Is There a Model...") - 83 (stop at 2.3) |
Homework 1-4 48, 52, 53, 70, 71 |
| F, Sept 7 | Genome sequence acquisition and analysis 2.3 What have we learned from metazoan genomes? |
Text: 90 - 109 | Homework 1-5 80, 86, Math Min. 2.5-2, 90, 92 |
| M, Sept 10 | Comparitive genomics in Evolution and Medicine 3.1 Comparitive genomics |
Text: 114 - 123 | Homework 1-6 2, 3, 8, 12, 14 |
| W, Sept 12 | Comparitive genomics in Evolution and Medicine 3.2 Evolution of genomes |
Text: 126 - 138 (stop at "Are We Related...") | Homework 1-7 23, 24, 25, 30, 32, 35 |
| F, Sept 14 | Comparitive genomics in Evolution and Medicine 3.2 Evolution of genomes |
Text: 138 - 145 (stop at 3.3) | Homework 1-8 36, 37, 39, 41, 42, 43 |
| M, Sept 17 | Comparitive genomics in Evolution and Medicine 3.4 Biomedical genome research |
Text: 162 - 172 | Homework 1-9 69, 70, 73, 75, 80, 81 |
| W, Sept 19 | Genomic variations 4.1 Environmental case study 4.2 Human genomic variation |
Text: 178 - 182; 186 (start at 4.2) - 187; Math Minute 4.3; 192 (start at "Do Any SNPs...") - 198 (stop at 4.3) | Homework 1-10 Math Min. 4.1-2, 2, 9, 20, 23a, 23b, 32 |
| F, Sept 21 | Review session TAKE-HOME EXAM 1 - Due Wed. Sept. 26, 3 pm |
none | none |
| M, Sept 24 | Lab conference day, No lecture | none | none |
| W, Sept 26 | Exam recovery | Turn in exam | none |
Unit Two: Genome Expression - Microarrays and proteomics |
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| Day | Chapter | Pre-Class Reading | Discovery Questions |
| F, Sept 28 | No class, presenting out of town | none | none |
| M, Oct 1 | Basic Research With DNA Microarrays 6.1 Introduction to microarrays |
Text: 234 - 245 (stop at "Can Chips Reveal...") | Homework 2-1 3, 6a-b, Math Min. 6.3-1, Math Min. 6.3-2, 10, 12 |
| W, Oct 3 | Basic Research With DNA Microarrays 6.1 Introduction to microarrays (cont.) |
Text: 245 - 254 | Homework 2-2 16, 25, 28, 33a-b, 34, 43 |
| F, Oct 5 | Basic Research with DNA Microarrays 6.2 Alternative uses of DNA Microarrays |
Text: 254 (start at 6.2) - 261 | Homework 2-3 45, 48, 49, 55, 56, 68, 77 |
| M, Oct 8 | Applied research with DNA microarrays 7.1 Cancer and genomic microarrays |
Text: 264 - 269 | Homework 2-4 3, 5, 9, 14, 19, 24a-b |
| W, Oct 10 | Applied research with DNA microarrays 7.2 Improving healthcare with DNA microarrays |
Text: 270 - 277 (stop at "What Happens When...") | Homework 2-5 30, 36, 40, 43, 48, 56, 61 |
| F, Oct 12 | Why can't I just take a pill to lose weight? (case study 2) 5 Hungry for knowledge Applied research with DNA microarrays 7.2 Improving healthcare with DNA microarrays |
Text: 219 - 224 Text: 277 (start at "What Happens When...") - 282 |
Homework 2-6 Chpt. 5: 4, 12, 18 Chpt. 7: 68, 71, 76, 78 |
| M, Oct 15 | FALL BREAK, no class | ---- | ---- |
| W, Oct 17 | Proteomics 8.1 Introduction |
Text: 286 - 295 | Homework 2-7 2, 5, 15, 18, 20, 23 |
| F, Oct 19 | Proteomics 8.2 Protein 3D structures |
Text: 295 - 299 | Homework 2-8 26, 28, 30, 32 |
| M, Oct 22 | Proteomics 8.3 Protein interaction networks |
Text: 299 - 307 | Homework 2-9 33, 36, 38a-b, 40, 42, 43 |
| W, Oct 24 | Proteomics 8.4 Measuring proteins |
Text: 307 - 315 | Homework 2-10 47a-c, 48, Math Min. 8.3-1, 51, 52 |
| F, Oct 26 | Proteomics 8.4 Measuring proteins (cont.) |
Text: 316 - 327 | Homework 2-11 55, 57, 58, 60, 64a-c, 66 |
| M, Oct 29 | Proteomics websites Guided tour/ review in class DNA microarray research in Drosophila Guest speaker Julie Goodliffe, UNCC |
Web: Dr. Goodliffe's page | none |
| W, Oct 31 | Review session TAKE-HOME EXAM 2 - Due Fri. Nov. 2, 5 pm |
Prepare questions to ask | none |
| F, Nov 2 | Exam recovery (5 pm) | Turn in exam | none |
Unit Three: Whole Systems Perspective - Constructing the big picture |
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| Day | Chapter | Pre-Class Reading | Discovery Questions |
| M, Nov 5 | Lab conference day, no lecture | none | none |
| W, Nov 7 | What's wrong with my child? (case study 1, revisited) 1.2 The next steps in understanding the disease |
Text: 9 (start at "The next steps...") - 19 | Homework 3-1 15, 19, 20a-d, 22, 26, 27, 31 |
| F, Nov 9 | Genomic circuits in single genes 10.1 Dissecting a gene's circuitry |
Text: 342 - 354 | Homework 3-2 2, 4, 7, 9, 11, 13 |
| M, Nov 12 | Genomic circuits in single genes 10.1 Dissecting a gene's circuitry (cont.) 10.2 Integrating single-gene circuits |
Text: 354 - 367 | Homework 3-3 |
| W, Nov 14 | Integrated genomic circuits 11.1 Natural gene circuits |
Text: 370 - 378 (stop at "Does memory...") | Homework 3-4 2, 3, 5, 6, 7 |
| F, Nov 16 | Integrated genomic circuits 11.1 Natural gene circuits (cont.) |
Text: 378 (start at "Does memory...") - 391 (stop at "Can we understand...") | Homework 3-5 9, 11, 13, 16, 18, 22, 27 |
| M, Nov 19 | Integrated genomic circuits 11.1 Natural gene circuits (cont.) |
Text: 391 (start at "Can we understand ...") - 394 (stop at 11.2) Web: CellDesigner.org: Process Diagram Web: about Systems Biology Markup Language (SBML) |
Homework 3-6 28, 30, 31, 33 |
| W, Nov 21 | THANKSGIVING BREAK, no class | none | none |
| F, Nov 23 | THANKSGIVING BREAK, no class | none | none |
| M, Nov 26 | Integrated genomic circuits 11.2 Synthetic biology |
Text: 394 - 400 (stop at "Can synthetic devices...") | Homework 3-7 |
| W, Nov 28 | Integrated genomic circuits |
Text: 400 (start at "Can synthetic devices...") - 407 | Homework 3-8 44, 46, 47, 51, 53, 55 |
| F, Nov 30 | Why can't we cure more dieases? 9 How are new medications developed? |
Text: 331 - 340 | Homework 3-9 7, 11, 14, 17, 21, 22 |
| M, Dec 3 | Genomic variations 4.3 The ultimate genomic phenotype--Death? 4.4 Ethical consequences of genomic variations |
Text: 198 - 214 | Homework 3-10 40, 43, 45, 49, 50, 57, 60 |
| W, Dec 5 | Modeling whole-genome circuits 12.1 Is genomics a new perspective? 12.2 Can we model entire eukaryotes with a systems approach? 12.3 Will systems biology go systemic? |
Text: 410 - 419 | none |
| F, Dec 7 | Review session
Course survey |
Prepare questions to ask | End of Fall '07 Genomics Lectures! |
| M, Dec 10 | Lab conference day, no lecture | ---- | ---- |
| W, Dec 12 | FINAL EXAM - Due Tues. Dec. 18, 3 pm End of classes |
Final exam will be e-mailed to you at 11:30 am. | ---- |
| T, Dec 18 | Exam recovery (3 pm) | Turn in exam at my office (black & white, signed) and by e-mail (color version) | ---- |
Davidson Academic Calendar - http://www3.davidson.edu/cms/x7693.xml