Class meets M/W/F 9:30-10:40 in PSB 305
For a list of past/present lecture notes please see the lecture_notes
| Number | Date | Topic | Lecturer | Lecture Notes | Note taker 1 | Note taker 2 | Slides |
| 1 | 30 Mar | Course overview & introduction | Green/Karplus | 03-30-2015 | Dudek | Eisenhart | |
| 2 | 1 Apr | The biology of the banana slug | Leonard / Pearse | 04-01-2015 | Matthew | Saremi | |
| 3 | 3 Apr | Disection and sequencing libraries | Weber / Green | 04-03-2015 | Richardson | Hussain | Banana slug genome project |
| 4 | 6 Apr | De novo genome assembly I | Prost | 04-06-2015 | Kan | Chaves | genomics_workshop_ucsc.pdf |
| 5 | 8 Apr | De novo genome assembly II | Prost | 04-08-2015 | Hussain | jolespin | genomics_workshop_ucsc.pdf |
| 6 | 10 Apr | De novo genome assembly III | Prost | 04-10-2015 | Musselman-Brown | jolespin | genomics_workshop_ucsc.pdf |
| 7 | 13 Apr | Illumina sequencing technology | Green | 04-13-2015 | Hussain | Eisenhart | Illumina slides |
| 8 | 15 Apr | k-mer spectra analysis | Green | 04-15-2015 | Musselman-Brown | Cole | k-mer slides |
| 9 | 17 Apr | Genome assembly - theory and practice | Green | 04-17-2015 | Hussain | Cole | DBG-assembly slides |
| 10 | 20 Apr | Team 1 report | Team 1 | 04-20-2015 | Chaves | Calef | Meraculous: Team 1 Report |
| 11 | 22 Apr | Team 2 report | Team 2 | 04-22-2015 | McGovern | Cole | SOAPdenovo: Team 2 Report |
| 12 | 24 Apr | Team 3 report | Team 3 | 04-24-2015 | Richardson | Houser | SGA: Team 3 Report |
| 13 | 27 Apr | Team 4 report | Team 4 | 04-26-2015 | Houser | Chaves | ABySS: Team 4 Report |
| 14 | 29 Apr | Team 5 report | Team 5 | 04-29-2015 | Richardson | Kan | Discovar de novo: Team 5 Report |
| 15 | 1 May | Population genetics / PSMC | Green | 05-01-2015 | Saremi | Markello | |
| 16 | 4 May | Mate-pair libraries | Weber/O'Connell | 05-04-2015 | Musselman-Brown | Cole | Mate Pair Libraries |
| 17 | 6 May | RNAseq | Katzman | 05-06-2015 | Dudek | Chaves | RNA-seq; Trapnell et al., 2010 |
| 18 | 8 May | Strategy session | Karplus/class | 05-08-2015 | Saremi | Markello | |
| 19 | 11 May | Team 1 report | Team 1 | 05-11-2015 | Eisenhart | Matthew | bme235_meraculous_report_2.pdf |
| 20 | 13 May | Team 2 report | Team 2 | 05-13-2015 | Feal | Calef | Team 2 SOAPdenovo2 update |
| 21 | 15 May | Team 3 report | Team 3 | 05-15-2015 | Chaves | Calef | |
| 22 | 18 May | Team 4 report | Team 4 | 05-18-2015 | Musselman-Brown | McGovern | |
| 23 | 20 May | Team 5 report | Team 5 | 05-20-2015 | jolespin | Saremi | discovar_team_presentation_2.pdf |
| 24 | 22 May | Assembly of Repeat regions | 05-22-2015 | JaredC | Saremi | ||
| - | 25 May | Holiday | N/A | N/A | N/A | N/A | |
| 25 | 27 May | Genome Annotation Annotation Review paper | Prost | 05-27-2015 | Kan | Feal | annotation_workshop_ucsc.pdf |
| 26 | 29 May | Jellyfish internals for kmer counting | Karplus | 05-29-2015 | Kan | JaredC | |
| 27 | 1 Jun | Burrows-Wheeler transform (guts of most mappers) | Karplus | 06-01-2015 | JaredC | Markello | |
| 28 | 3 Jun | Presentation for donor & final analysis I | 06-03-2015 | Feal | Calef | ||
| 29 | 5 Jun | Presentation for donors & final analysis II | Green | 06-05-2015 | JaredC | Dudek | finalpresentation_bme235.pdf bs-het-v1.pptxbs-het-v1.pdf |