| Papers, etc. |
 Note on Electronic Access to Journals
The UW Library is generally a paid subscriber to non-open-access journals we cite. You can freely access these
articles from on-campus computers. For off-campus access, follow the "[offcampus]" links below or look at the
library "proxy server" instructions. You will be
prompted for your UW net ID and password.
10/04: -- ---- Organizational Meeting ----
10/11: -- No Class
10/18: Benchmark Biases -- Ayse, Chris; Ruzzo
10/25: Optimizing Protein Production -- Addie, Erin
- Caitlin Gamble, Drew Bryant, Damian Carrieri, Eli Bixby, Jason Dang, Jacob Marshall,
David Doughty, Lucy Colwell, Marc Berndl, James Roberts, Michael Frumkin,
"Machine Learning Optimization of Photosynthetic Microbe Cultivation and Recombinant Protein Production,"
https://www.biorxiv.org/content/10.1101/2021.08.06.453272v1
11/01: Perils of Dimension Reduction -- Anna, Pascal
11/08: Hierarchical Hypotheses -- Gian Marco; Ruzzo
11/15: Contrastive PCA -- Ethan
11/22: Sequence -> Function: Regulation -- Alyssa; Meuleman
11/29: Sequence -> Function: Enhancer-Promoter Interactions & ATAC-seq -- Ian, Xinming; Mostafavi
- Lu, Y.Y., Noble, W.S. A wider field of view to predict expression. Nat Methods 18, 1155--1156 (2021).
https://doi.org/10.1038/s41592-021-01259-4 [offcampus]
- Avsec, Ž., Agarwal, V., Visentin, D. et al. Effective gene expression prediction from sequence by
integrating long-range interactions. Nat Methods (2021). https://doi.org/10.1038/s41592-021-01252-x [offcampus]
- Han Yuan, David R Kelley, "scBasset: Sequence-based modeling of single
cell ATAC-seq using convolutional neural networks,"
https://www.biorxiv.org/content/10.1101/2021.09.08.459495v1
12/06: Sequence -> Function: Chromatin Accessibility & Histone Mods -- Bingbing; Mostafavi
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