http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.2645.html
Archive for the 'SciLit' Category
Accounting for technical noise in single-cell RNA-seq experiments : Nature Methods : Nature Publishing Group
October 2, 2013Thoughts on Network deconvolution as a general method to distinguish direct dependencies in networks
September 29, 2013The opposite of clique completion: #Network deconvolution.. to distinguish direct dependencies http://go.nature.com/dVzNwC via @taziovanni
Network deconvolution as a general method to distinguish direct dependencies in networks
Soheil Feizi, Daniel Marbach, Muriel Médard & Manolis Kellis
http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.2635.html
My thoughts:
Indirect relationships in a network can confound the inference of true direct relationships in a network. T, so this paper sought to develop a quantitative framework, termed network deconvolution (ND), to infer direct relationships and remove false positives in a network by quantifying and then removing indirect transitive relationship effects. The mathematical framework assumes that (1) an indirect relationship (edge) can be approximated as the product of its component direct edges and that (2) the observed edge weights are the sum of the direct and indirect edge weights – a linear dependency. The main application seems to be in mutual information (MI) and
correlation-based (COR) networks. They applied ND to various scenarios such as local network connectivity prediction (FFL
prediction), gene regulatory network prediction (in E. coli), prediction of interacting amino acids in protein structures (MI network) and coauthorship relationship network and found that (1) it can be used with various networks beyond just MI and COR (2) it can be used alone or more powerfully in combination with existing
methods/algorithms to improve predictions. In a sense it is the opposite of clique and module completion approaches (such as k-core).
Exosomes mediate the cell-to-cell transmission of IFN-α-induced antiviral activity
September 28, 2013Rare tRNAs driving protein folding paper
September 26, 2013The gist is that it is important for protein folding to choose optimal and non-optimal synonymous codons, at different locations.
http://www.nature.com/nsmb/journal/v20/n2/full/nsmb.2466.html
An interesting paper! Nice to see codon usage revisited again. Another revisiting of codons (my own) is at
http://papers.gersteinlab.org/papers/revisit-cai
Evolutionary conservation of codon optimality reveals hidden signatures of cotranslational folding
Sebastian Pechmann & Judith Frydman
Nature Structural & Molecular Biology 20, 237–243 (2013) doi:10.1038/nsmb.2466
BrainSpan related paper
September 22, 2013Appears to use the data set
Cell, Volume 154, Issue 3, 1 August 2013, Pages 518–529
Spatial and Temporal Mapping of De Novo Mutations in Schizophrenia to a Fetal Prefrontal Cortical Network
http://www.sciencedirect.com/science/article/pii/S0092867413008313#
Network-based stratification of tumor mutations
September 21, 2013http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.2651.html
Network-based stratification of tumor mutations
Matan Hofree,
John P Shen,
Hannah Carter,
Andrew Gross
& Trey Ideker
Nature Methods(2013)doi:10.1038/nmeth.2651
Distributed variation prefers the golden mean – Gene Expression | DiscoverMagazine.com
September 16, 2013#Variation prefers the golden mean: Moderate selection involves many loci v weak & strong, few http://bit.ly/18MgU6p via @drbachinsky
Moderate selection, many loci; Weak or strong selection, few loci.
http://blogs.discovermagazine.com/gnxp/2013/09/distributed-variation-prefers-the-golden-mean/#.UjJTHmSG1MF
Systematic identification of trans eQTLs as putative drivers of known disease associations
September 15, 2013http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.2756.html
“They found SNPs that regulate one gene (Ikaros) in different cell types, meaning they found different cis-regulatory regions for a single gene, that map to different pathways…. they used the cell-type specific information from ENCODE data.”
Papers about retroduplications (variable pseudogenes)
September 13, 2013here are three more relevant papers about retroduplications :
http://www.nature.com/nmeth/journal/v9/n2/full/nmeth.1810.html http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003242 http://genomebiology.com/content/14/3/R22
Cancer on left and right sides
September 13, 2013I guess it is peer-reviewed paper
http://www.jaad.org/article/S0190-9622(10)00614-6/abstract
Skin cancer correlates with handedness of car driving
linkstream2 microblog 