Syllabus 2024
Please post questions on Piazza if you have any questions on class, assignments, exams etc.
| Date | Day | Lecture/Lab | Lecturer | Assignment due (policies) |
| 1/17/24 | Wed | Genomics basics I slides Reading Materials: Popejoy & Fullerton 2016 Green et al. 2020 Astley et al. 1996 Wang et al. 2022 | Wang | |
| 1/19/24 | Fri | LAB 1: Introduction of statistical models and Python programming Assignment 1 2024 Lab 1 Slides | TAs | |
| 1/22/24 | Mon | Genomics basics II slides Reading Materials: Shendure et al. 2017 Miga et al. 2020 Javris et al. 2022 Nurk et al. 2022 Liao et al. 2023 | Wang | |
| 1/24/24 | Wed | Sequencing technology slides Reading Materials: Stergachis et al. 2020 Wang et al. 2021 Kovaka et al. 2023 | Wang | |
| 1/26/24 | Fri | LAB 2: Sequence technology Assignment 2 2024 Lab 2 Slides | LAB 1: Introduction of statistical models and Python programming | |
| 1/29/24 | Mon | Homology I slides Reading Materials: 4_HomologyReading_1_STATISTICAL-ERRORS.pdf 4_HomologyReading_2_Designing-comparative-experiments.pdf 4_HomologyReading_3_Stormo_HomologySearch.pdf 4_HomologyReading_4_Eddy_HMM.pdf 4_HomologyReading_5_Eddy_DynamicProgramming.pdf 4_HomologyReading_6_Eddy_BLOSUM62.pdf 4_HomologyReading_7_Eddy_Bayesian.pdf 4_HomologyReading_8_Zhang_Chromap.pdf | Wang | |
| 1/31/24 | Wed | Homology II | Wang | |
| 2/2/24 | Fri | LAB 3: Sequence comparison 2024_Assignment3 2024_Lab_3_slides | TAs | LAB 2: Sequence technology |
| 2/5/24 | Mon | Epigenetics I slides Reading Materials: paper_1 paper_2 paper_3 paper_4 paper_5 paper_6 Liang et al 2024 Lawson et al. 2023 Precision Medicine Pathway.Introduction | Wang | |
| 2/7/24 | Wed | Epigenetics II | Wang | |
| 2/9/24 | Fri | LAB 4: Epigenomics assignment 4 assignment 4 slides | TAs | LAB 3: Sequence comparison |
| 2/12/24 | Mon | Gene Expression I slides | Lawson | |
| 2/14/24 | Wed | Gene Expression II slides | Lawson | |
| 2/16/24 | Fri | LAB 5: Gene Expression 2024_Assignment5 Lab-5-Lecture_Slides | TAs | LAB 4: Epigenomics |
| 2/19/24 | Mon | Chromatin Dynamics I slides | Meers | |
| 2/21/24 | Wed | Chromatin Dynamics II slides | Meers | |
| 2/23/24 | Fri | LAB 6: Chromatin Dynamics 2024_Assignment6 2024_lab_6_slides example | TAs | LAB 5: Gene Expression |
| 2/26/24 | Mon | Single cell genomics I slides supplementary paper: Zebrafish heatshock single cell multiplexing (Dorrity et al., 2022) | Morris | |
| 2/28/24 | Wed | Single cell genomics II slides Supplemental reading: Biddy et al., 2018 (original CellTag paper) Jindal et al., 2022 (newer CellTag with larger barcode and chromatin capture compatibility) | Morris | |
| 3/1/24 | Fri | Lab 7: Single cell analysis Lab-7 instructions Lab-7 slides | TAs | LAB 6: Chromatin Dynamics |
| 3/4/24 | Mon | Genetic variation I – slides Reading materials: Latorre-Pellicer et al., 2016 Ebert et al., 2021 Nurk et al., 2022 | Jin | |
| 3/6/24 | Wed | Genetic variation II – slides Reading materials: Koboldt, 2020 De Coster et al., 2021 | Jin | |
| 3/8/24 | Fri | MIDTERM EXAM Last year’s midterm for practice (2023) Midterm equations sheet1 Midterm equations sheet2 Lab 8: Genetic variation Lab 8 Instructions Lab 8 video lecture | ||
| 3/11/24 | Spring Break | |||
| 3/13/24 | Spring Break | |||
| 3/15/24 | Spring Break | |||
| 3/18/24 | Mon | Methods for variant analysis I slides Reading materials: Lee, S. et al., (2014) All of Us (2024) | Jin | |
| 3/20/24 | Wed | Methods for variant analysis II slides Reading materials: Eilbeck et al., 2017 Cohen et al., 2006 | Jin | |
| 3/22/24 | Fri | LAB 9: Variant analysis Lab 9 Instructions Lab 9 Slides | TAs | LAB 7: Single cell analysis LAB 8: Genetic variation |
| 3/25/24 | Mon | Proteogenomics I – slides Reading materials: Steen and Mann, 2004 Gessulat et al., 2019 Aebersold and Mann, 2016 | Goldfarb | |
| 3/27/24 | Wed | Proteogenomics II – slides Reading materials: Nesvizhskii, 2014 Mani et al., 2022 Deutsch et al., 2019 | Goldfarb | |
| 3/29/24 | Fri | LAB 10: Proteogenomics Assignment Slides | TAs | LAB 10: Proteogenomics |
| 4/1/24 | Mon | Functional assays I – slides post-lecture slides Readings: Taskiran et al, 2024 Taskiran et al, 2023 Helpful reading for homework: Wong et al, 2018 | White | |
| 4/3/24 | Wed | Functional assays II – slides post-lecture slides | White | |
| 4/5/24 | Fri | LAB 11: Identify Expression-Modulating Variants Assignment Slides | TAs | LAB 10: TBD |
| 4/8/24 | Mon | Metagenomics I slides Readings: Handelsman et al, 1998 Metagenomics_NIH_2007 | Wu | |
| 4/10/24 | Wed | Metagenomics II slides | Wu | |
| 4/12/24 | Fri | LAB 12: Metagenomics Assignment Slides | TAs | LAB 11: Identify Expression-Modulating Variants |
| 4/15/24 | Mon | Comparative genomics I slides | Buchser | |
| 4/17/24 | Wed | Comparative genomics II | Buchser | |
| 4/19/24 | Fri | LAB 13: Cis-regulatory evolution Assignment Slides | TAs | LAB 12: Metagenomics |
| 4/22/24 | Mon | Review | No Class | |
| 4/24/24 | Wed | Review | No Class | |
| 4/26/24 | Fri | FINAL EXAM Last year’s final exam (2023) Final equations sheet | LAB 13: Cis-regulatory evolution |