| 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.
01/05: ---- Organizational Meeting ----
01/12: Metagenomics -- Katie; Ruzzo
Metagenomic data is inherently high-dimensional, and this is representative: - MI Smith, T Yatsunenko, MJ Manary, I Trehan, R Mkakosya, J Cheng, AL Kau, SS Rich, P Concannon, JC Mychaleckyj, J Liu, E Houpt, JV Li, E Holmes, J Nicholson, et 4 al., "Gut microbiomes of Malawian twin pairs discordant for kwashiorkor." Science, 339, #6119 (2013) 548-54.
[offcampus]
01/19: -- Holiday
01/26: Deep Learning -- Jacob; Noble
The original deep learning paper:
perhaps augmented by snippets from more recent biological
applications such as:
02/02: Compressed Sensing for GWAS -- Scott, Daniel, Haoran; Ruzzo
GWAS is a well studied area where "high
dimensionality" relative to sample sizes is the rule. This paper shows that sparse regression methods work well
once enough samples are present, going through a phase transition in performance, and may be relevant to anyone
using sparse regression:
Also http://arxiv.org/pdf/1310.2264.pdf .
02/09: Alt Splicing -- Aaron, Max; Trapnell
02/16: -- Holiday
02/23: Network Fusion -- Safiye; Lee
- B Wang, AM Mezlini, F Demir, M Fiume, Z Tu, M Brudno, B Haibe-Kains, A Goldenberg, "Similarity network fusion for aggregating data types on a genomic scale." Nat. Methods, 11, #3 (2014) 333-7.
[offcampus]
03/02: T cell signaling -- Alex; Ruzzo
- S Krishnaswamy, MH Spitzer, M Mingueneau, SC Bendall, O Litvin, E Stone, D Pe'er, GP Nolan, "Systems biology. Conditional density-based analysis of T cell signaling in single-cell data." Science, 346, #6213 (2014) 1250689.
[offcampus]
03/09: Cancer Progression -- Nao, Ning; Lee
- AP Parikh, RE Curtis, I Kuhn, S Becker-Weimann, M Bissell, EP Xing, W Wu, "Network analysis of breast cancer progression and reversal using a tree-evolving network algorithm." PLoS Comput. Biol., 10, #7 (2014) e1003713.
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| Other Papers |
Other suggested papers that didn't fit the schedule:
- A really important paper -- compressing dozens to hundreds of variant annotations into a single dimension:
- Using phylogenies to investigate covariation of gene expression values (typically 1000's) across species (perhaps 50 or fewer).
Available as Open Access there, also available as a preprint at: http://arxiv.org/pdf/1302.2978v1.pdf .
The statistical techniques mentioned (Bickel and Levina, also Luo) are not all the popular "regularization"
methods. Another, LASSO, by Robert Tibshirani is explained here: http://statweb.stanford.edu/~tibs/lasso.html .
- One on dynamical biological systems:
- The originally-suggested metagenomics paper
- J Kuczynski, Z Liu, C Lozupone, D McDonald, N Fierer, R Knight, "Microbial community resemblance methods differ in their ability to detect biologically relevant patterns." Nat. Methods, 7, #10 (2010) 813-9.
[offcampus]
- An approach to high dimensional visualization: http://jmlr.csail.mit.edu/papers/volume9/vandermaaten08a/vandermaaten08a.pdf
plus a bio application based on it:
- el-AD Amir, KL Davis, MD Tadmor, EF Simonds, JH Levine, SC Bendall, DK Shenfeld, S Krishnaswamy, GP Nolan, D Pe'er, "viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia." Nat. Biotechnol., 31, #6 (2013) 545-52.
[offcampus]
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