JHU EN.600.749: Computational Genomics: Applied Comparative Genomics
April 15, 2021 · View on GitHub
Project Presentations
Presentations will be a total of 15 minutes: 12 minutes for the presentation, followed by 3 minutes for questions. We will strictly keep to the schedule to ensure that all groups can present in class!
Schedule of Presentations
| Day | Time | Team Name | Students | Title |
|---|---|---|---|---|
| Wed Apr 21 | 1:30-1:45 | Team T-Cell | Hanzhi (Gary) Wang, Sihao (Lynn) Yin | Sequence-Base Prediction of Cross-Reactivity in T Cell agaisnt SARS-COV2 Epitopes |
| Wed Apr 21 | 1:45-2:00 | deMarKate | Margaret Starostik, Katharine Jenike | Identifying RNA modifications in direct RNA sequencing data from Oxford Nanopore |
| Wed Apr 21 | 2:00-2:15 | Daniel's Team | Daniel Borders | Cannabis Project |
| Wed Apr 21 | 2:15-2:30 | Team Blake | Blake Johnson | scCNV from scRNA |
| Wed Apr 21 | 2:30-2:45 | Team Omar | Omar Ahmed | Developing a Realistic Nanopore Signal Simulator Using a Generative Adversarial Network |
| Mon Apr 26 | 1:30-1:45 | The Contextusplicer(s) | Theron Palmer | Single-cell alternative splicing analysis using non-negative matrix factorization and differentially expressed splice junctions. |
| Mon Apr 26 | 1:45-2:00 | The Genome Pals | James Forsmo, Soichiro Asami | Evaluation of Single-Cell Monocle Algorithm with Low Read Coverage |
| Mon Apr 26 | 2:00-2:15 | SIN | Sambit Panda, Ida Shinder, Natalia Rincon | Uncovering the Origin of Polyploidy in Coast Redwood |
| Mon Apr 26 | 2:15-2:30 | Team Amy | Amy Gill | Variant analysis of a whole exome trio to investigate a heritable neurological phenotype |
| Mon Apr 26 | 2:30-2:45 | Team Yanbo | Yanbo Wang | PacBio single-molecule flouorescence resonance energy transfer (FRET) analysis pipeline |
| Wed Apr 28 | 1:30-1:45 | Team Malamutes | Beril Erdogdu, Yuchen Ge | Calling genetic variants from long-read RNA sequencing of SK-BR-3 breast cancer cell line |
| Wed Apr 28 | 1:45-2:00 | Team Bohao | Bohao Tang | Robustness of Single Cell Pseudo-time Reconstruction Methods |
| Wed Apr 28 | 2:00-2:15 | Team Yash | Yash Sonthalia | Applying ML classification models to accurately predict cell-type among datasets using expression data from single-cell RNA seq experiments |
| Wed Apr 28 | 2:15-2:30 | Team Maddy | Maddy Scott | Entropy of DNA |
| Wed Apr 28 | 2:30-2:45 | Team Kathleen | Kathleen Newcomer | Genomic Vis |
Recommended outline for your talk (~1 minute per slide):
- Title Slide: Who are you, title, date
- Intro 1: Whats the big idea???
- Intro 2: More specifically, what are you trying to learn?
- Methods 1: What did you try?
- Methods 2: What is the key idea?
- Data 1: What data are you looking at?
- Data 2: Anything notable about the data?
- Results 1: What did you see!
- Results 2: Does it work?
- Results 3: How does it compare to other methods/data/ideas?
- Discussion 1: What did you learn from this study?
- Discussion 2: What does this mean for the future?
- Acknowledgements: Who helped you along the way?
- Thank you!
I strongly discourage you from trying to give a live demo as they are too unpredictable for a short talk. If you have running software you want to show, use a "cooking show" approach, where you have screen shots of the important steps.