| 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.
10/03: -- ---- Organizational Meeting ----
10/10: RNAseq Benchmarks -- Katie; Ruzzo
- M Teng, MI Love, CA Davis, S Djebali, A Dobin, BR Graveley, S Li, CE Mason, S Olson, D Pervouchine, CA Sloan, X Wei, L Zhan, RA Irizarry, "A benchmark for RNA-seq quantification pipelines." Genome Biol., 17, (2016) 74.
[offcampus]
- M Teng, MI Love, CA Davis, S Djebali, A Dobin, BR Graveley, S Li, CE Mason, S Olson, D Pervouchine, CA Sloan, X Wei, L Zhan, RA Irizarry, "Erratum to: A benchmark for RNA-seq quantification pipelines." Genome Biol., 17, #1 (2016) 107.
[offcampus]
10/17: Variant Calling Benchmarks -- Scott; Ruzzo
- S Hwang, E Kim, I Lee, EM Marcotte, "Systematic comparison of variant calling pipelines using gold standard personal exome variants." Sci Rep, 5, (2015) 17875.
[offcampus]
10/24: Single-cell RNA-seq in melanoma -- Alex; Lee
- I Tirosh, B Izar, SM Prakadan, MH Wadsworth, D Treacy, JJ Trombetta, A Rotem, C Rodman, C Lian, G Murphy, M Fallahi-Sichani, K Dutton-Regester, JR Lin, O Cohen, P Shah, et 22 al., "Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq." Science, 352, #6282 (2016) 189-96.
[offcampus]
10/31: Predicting Ribosome Footprints -- Cody, Pat; Noble
11/07: Functional relationships from DNA contact maps -- Arman, Jacob; Noble
11/14: Synthetic lethality and other genetic interactions -- Daniel; Haynor
11/21: Deep learning for circadian rythms -- Dave, Farah; Noble
Erratum:
11/28: Histone Methylation and Metabolism -- Safiye; Wang
This (not yet peer reviewed) paper describes a new computational analysis integrating DNA methylation and gene
expression data from The Cancer Genome Atlas to predict both overall and locus-specific DNA methylation levels based
on the expression of key metabolic genes:
A somewhat related paper (more experimental than computational) could be an interesting read - it relates metabolic
perturbation and histone methylation: - SJ Mentch, M Mehrmohamadi, L Huang, X Liu, D Gupta, D Mattocks, P Gómez Padilla, G Ables, MM Bamman, AE Thalacker-Mercer, SN Nichenametla, JW Locasale, "Histone Methylation Dynamics and Gene Regulation Occur through the Sensing of One-Carbon Metabolism." Cell Metab., 22, #5 (2015) 861-73.
[offcampus]
12/05: Multi-trait prediction -- Damon; Kannan
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