#Ontologies in Quantitative Biology
http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1000374 Nice example (RTKs) showing utility of #DAGs & good normalized #bibliometrics
RTK = receptor Tyr Kinase
norm pub stats = Hits per million in pubmed
The “Grep” Command But Not FusionMap, FusionFinder or ChimeraScan Captures the CIC-DUX4 Fusion Gene from Whole Transcriptome Sequencing Data on a Small Round Cell Tumor with t(4;19)(q35;q13)
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0099439
1000G v disease variants
http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003382
QT:{{”
We identify an lncRNA pseudogene, Lethe (named after the mythological river of forgetfulness, for its role in negative feedback), which is expressed in response to proinflammatory cytokines TNFα and IL-1β, and the anti-inflammatory agent, dexamthasone, but is not responsive to microbial components, and is primarily found on the chromatin. Lethe is regulated by RelA, independent of pseudogene family members and proximal genes. Additionally, Lethe is dramatically downregulated in aged spleen. Finally, Lethe binds directly to RelA to inhibit NF-κB DNA binding activity. These findings suggest that Lethe may function as a novel negative regulator of NF-κB, to help fine tune the inflammatory response.
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A mammalian #pseudogene #lncRNA at the interface of inflammation… Lethe may down-regulate NF-kB via binding to RelA
http://elifesciences.org/content/2/e00762
No use of Gencode pgenes !
Chromatin organization is a major influence on regional mutation rates in human cancer cells
Benjamin Schuster-Böckler & Ben Lehner
http://www.nature.com/nature/journal/vaop/ncurrent/abs/nature11273.html
Bioengineering & #systemsbiology. Classic def’n in terms of the “4 M’s”—Measurement, #Mining, Modeling & Manipulation
http://www.ncbi.nlm.nih.gov/pubmed/16474915
QT:{{”
Systems Biology can also be defined operationally, as
by the MIT Computational & Systems Biology Initiative,
in terms of the “4 M’s”—Measurement, Mining, Modeling,
and Manipulation—illustrated schematically in Fig. 1 (see
http://csbi.mit.edu/).
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Interesting but addressing mappability issue is key! Might want to also use a non-analytic stat test….
Compared to wavelets, non-independence betw. scales, perhaps key for allowing pruning.
Multiscale representation of #genomic signals. Fold changes & peaks at different scales; better expression prediction
http://www.nature.com/nmeth/journal/v11/n6/full/nmeth.2924.html
#Horizontaltransfer of an adaptive chimeric photoreceptor [Neochrome] from bryophytes to #ferns. Careful #phylogeny
http://www.pnas.org/content/111/18/6672.abstract
Rosvall, Martin, and Carl T. Bergstrom. “An information-theoretic framework for resolving community structure in complex networks.” Proceedings of the National Academy of Sciences 104.18 (2007): 7327-7331.
Info-theoretic framework for… community structure in complex #networks. Compression v modularity, former better?
http://www.pnas.org/content/104/18/7327.short
Science. 2008 Nov 28;322(5906):1377-80. doi: 10.1126/science.1164266.
Mullighan CG1, Phillips LA, Su X, Ma J, Miller CB, Shurtleff SA, Downing JR.
Interesting older paper
Genomic analysis of the clonal origins of relapsed ALL
http://www.sciencemag.org/content/322/5906/1377.abs Older paper, describing relapse as arising from minor subclone
linkstream2 microblog 