1000G v disease variants
http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003382
Archive for the 'SciLit' Category
amino acid changes in 1000 Genomes Project Thornton Lab
June 23, 2014A mammalian pseudogene lncRNA at the interface of inflammation and anti-inflammatory therapeutics | eLife
June 22, 2014QT:{{”
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.
“}}
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 !
cancer mutation rates versus chromatin
June 14, 2014Chromatin 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 and systems biology. Ann Biomed Eng. 2006 – PubMed – NCBI
June 14, 2014Bioengineering & #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/).
“}}
Multiscale representation of genomic signals : Nature Methods : Nature Publishing Group
June 14, 2014Interesting 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
Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns
June 13, 2014#Horizontaltransfer of an adaptive chimeric photoreceptor [Neochrome] from bryophytes to #ferns. Careful #phylogeny
http://www.pnas.org/content/111/18/6672.abstract
“An information-theoretic framework for resolving community structure in complex networks.” Proceedings of the National Academy of Sciences
June 12, 2014Rosvall, 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
Genomic Analysis of the Clonal Origins of Relapsed Acute Lymphoblastic Leukemia
June 8, 2014Science. 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
Genetic Maps of the Brain Lead to Surprises – Scientific American
June 8, 2014Neuroscience
Scientific American 310, 70 – 77 (2014)
Published online: 18 March 2014 | doi:10.1038/scientificamerican0414-70
The Genetic Geography of the Brain
Ed Lein & Mike Hawrylycz
http://www.scientificamerican.com/article/genetic-maps-of-the-brain-lead-to-surprises
Data Science and Prediction | December 2013 | Communications of the ACM
June 2, 2014#DataScience & Prediction: Nice overview of the field, emphasizing testable models, even when causation isn’t implied
http://cacm.acm.org/magazines/2013/12/169933-data-science-and-prediction/fulltext
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