Old idea or miRNS sponging applied to a new class of RNAs — circRNAs
http://www.nature.com/nature/journal/vaop/ncurrent/full/nature11993.html?WT.ec_id=NATURE-20130228
Archive for the 'SciLit' Category
circRNAs can be functionally important
February 28, 2013Predicting the Binding Patterns of Hub Proteins: A Study Using Yeast Protein Interaction Networks
February 24, 2013used the singlish/multi concept. Then used machine learning to predict whether a protein is singlish or multi
PLOS ONE
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0056833
Taner Z. Sen
Developmental Milestones Punctuate Gene Expression in the Caenorhabditis Embryo
February 19, 2013http://www.cell.com/developmental-cell/abstract/S1534-5807%2812%2900142-6
Michal Levin, Tamar Hashimshony, Florian Wagner, and Itai Yanai.
Developmental milestones punctuate gene expression in the
Caenorhabditis embryo. Developmental Cell (May 2012)
Nice disussion of the phylotypic stage .
Figure 4S-E have stage mapping between dmel and celegans
Abstractions for genomics – how data processing can be layered, including separating evidence from interference
February 17, 2013Abstractions for genomics
Communications of the ACM
Volume 56 Issue 1, January 2013
Pages 83-93
http://cseweb.ucsd.edu/~varghese/PAPERS/querythegenome.pdf
http://dl.acm.org/citation.cfm?id=2398376
PLOS Computational Biology: Large-Scale Trends in the Evolution of Gene Structures within 11 Animal Genomes
February 16, 2013intron & exon length distributions
http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.0020015
Human Mobility Characterization from Cellular Network Data | January 2013 | Communications of the ACM
February 14, 2013Thoughts on “A few useful things to know about machine learning”
February 14, 2013Some thoughts on a good paper giving intuition on machine learning approaches
http://homes.cs.washington.edu/~pedrod/papers/cacm12.pdf
http://dl.acm.org/citation.cfm?id=2347755
In particular, the paper gives good intuition about:
– overfitting (e.g. how it’s related to multiple testing & bias v variance)
– the curse of dimensionality (in high-D all neighbors look the same)
– the non-practicality of theoretical guarantees
– how different frontiers can give the same prediction
– ensembles (which reduce variance greatly without increasing bias that much)
– ensembles vs Bayesian model averaging (which essentially select the best model)
A Phylotypic Stage for All Animals?
February 13, 2013http://www.sciencedirect.com/science/article/pii/S1534580712001980
> Michal Levin, Tamar Hashimshony, Florian Wagner, and Itai Yanai. > Developmental milestones punctuate gene expression in the
> Caenorhabditis embryo. Developmental Cell (May 2012)
Retro CNVs
February 3, 2013transposable element common to both human and fruit fly
January 30, 2013The Human THAP9 Gene Encodes an Active P-Element DNA Transposase http://www.sciencemag.org/content/339/6118/446.abstract
linkstream2 microblog 