From the following article:
Initial sequencing and analysis of the human genome
International Human Genome Sequencing Consortium
Nature 409, 860-921(15 February 2001)
doi:10.1038/35057062
Alu age distribution
http://www.nature.com/nature/journal/v409/n6822/fig_tab/409860a0_F18.html
System-wide analyses have underestimated #protein abundances… Corrected protein conc. better correlated w/ #mRNA
https://peerj.com/articles/270
…once a non linear bias in mass spec. data is corrected, the concentration of the factor expressed at the median level is present at 70,000 molecules per cell. ….
Li, J, Bickel, P.J. and Biggin M.D. (2014) System Wide Analyses have Underestimated Protein Abundances and the Importance of Transcription in Mammals. PeerJ DOI10.7717/peerj.270
PARADIGM-SHIFT predicts… function of mutations in… #cancers using pathway[s]. #Network-based gene prioritization
http://bioinformatics.oxfordjournals.org/content/28/18/i640
http://www.nature.com/nmeth/journal/v11/n1/full/nmeth.2732.html
From the paper:
QT:{{”
2. Pseudogenes represent less than 0.1% of the total search space, yet a surprisingly large number, 36%, of human novel peptides mapped to pseudogenes (Fig. 2b). These findings are supported by recent peptide-level evidence of pseudogenes in mouse6. In humans, the observation of lineage- and cancer-specific expression of pseudogenes at the RNA level indicates biological relevance17. Our data suggest that pseudogenes may be not only transcribed but also translated. An interesting particular example was the pseudogene MYH16, identified by 20 peptides (Fig. 3), which were validated by LC-MS using synthetic peptides (Supplementary Fig. 15). The protein-coding capacity of MYH16 was previously shown to have been lost through double base deletion (resulting in a premature stop codon) during divergence of the human lineage from other primates18. However, our data show that, in the A431 cell line, the MYH16gene is actively encoding a shorter protein isoform with its translation initiation site downstream from the aforementioned double base deletion.
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Integrating genotype from many callers & indication of where they differ. Might be useful for the personal diploid genome.
http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.2835.html
Best Practices for Scientific #Computing. Well known but useful pts, eg vers. control, asserts, interface comments…
http://www.plosbiology.org/article/info:doi%2F10.1371%2Fjournal.pbio.1001745
http://www.plosbiology.org/article/info:doi%2F10.1371%2Fjournal.pbio.1001745
What is a support vector machine? A nice overview w/o equations, just pictures. Great for #teaching!
http://www.nature.com/nbt/journal/v24/n12/abs/nbt1206-1565.html #SVM .@GenomeNathan YES, but see
http://noble.gs.washington.edu/papers/noble_what.html …, which has an expanded, “free” version.
http://noble.gs.washington.edu/papers/noble_what.html
http://www.nature.com/nbt/journal/v24/n12/abs/nbt1206-1565.html
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