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This Week in Genome Biology: May 8, 2013

Queen Mary University of London's Pedro Cutillas and colleagues from the UK describe phosphoproteomic analyses of cancer cell lines and potential applications of this information in the early, online edition of Genome Biology. When the researchers used mass spectrometry to assess phosphorylation levels at some 2,000 sites in nine cancer cell lines — three representatives apiece from acute myeloid leukemia, lymphoma, and multiple myeloma — they found that cell lines tended to cluster by cancer type. And the team's more in-depth analysis of seven AML lines suggested phosphoproteomics can provide clues to which tumor samples are more or less apt to respond to compounds that inhibit kinase enzymes.

A Wellcome Trust Sanger Institute team outlines a new computational method for surmising the sorts of mutational processes at play in cancer genomes. After applying this probabilistic inference approach, called Emu, to simulated data, the researchers used it to scour sequences from 21 previously sequenced breast cancer samples. Those tumors harbored signs of four main mutational processes, study authors explained. And in conjunction with known functional annotations in the genome, the nature of the mutations and their locations offered clues to some of the biological processes going awry in the tumors.

The human microbiome is home to a range of mobile genetic elements that provide insights into the viral pathogens or plasmids that microbiome members have encountered in the past, according to another Genome Biology study. Researchers from Indiana University and the Roswell Park Cancer Institute sifted through metagenomic sequence data, focusing on spacer sequences at the so-called CRISPR locus, a site in the genome where sequences from potential genetic interlopers are integrated as part of the CRISPR-CAS system used in the bacterial and archaeal immune system. Using data from 95,000 contigs — corresponding to sequences potentially targeted by CRISPR spacers in the metagenomic data — the group was able to tally up and compare the apparent mobile genetic element networks found in the human mouth and gut microbiomes.