2012: that was the Genome Biology year that was


2012 was ominous in Genome Biology parlance: the dreaded 'Volume 13'. But, happily, our luck remained in good order as we saw our Impact Factor soar to 9.04, while our publications  continued to intrigue, inform and enthuse our readership.

January: figure of the year?

January opened the year with a human population genetics flavor, courtesy of studies on the Amhara and Ashkenazi Jews, and also provided the popular Uberon cross-species anatomy ontology with a home in the scientific record.

In February, the software title 'All Your Base' was finally claimed by the Bioinformatics community, following 12 years of missed opportunities. Elsewhere in the issue, Pauline Ng updated her SIFT tool, which predicts the functional consequences of mutations, for application to frameshifting indels, and Hunter Fraser and Michael Kobor used HapMap cell lines to investigate the population specificity of DNA methylation.

February: internet meme or superlative base caller?

Two of the most highly accessed articles of 2012 featured in our March issue: a library prep protocol for microbial RNA-seq and the Transcription Factor Encyclopedia. These were joined by Ben Raphael's GASVPro method for identifying structural variation and a hugely improved Drosophila genetic deficiency kit.

April was notable for the inaugural Genome Biology publication in the field of 'babypoopomics'. We also dipped our toes gingerly into the waters of the Great RNA Editing Debate, with a comparison between 15 lab mouse strains. And in May we went old school, as Paul Nurse revisited some of his Nobel-prize winning work with tools of the -omics era.

The Human Microbiome Project published its findings in June, with the digestive tract-focused component appearing in Genome Biology. Matched blood and brain samples from the same individuals made for an interesting study design, as Jon Mill investigated how DNA methylation varies between, and within, humans. More methylation from the Oshlack lab: their SWAN method normalizes Illumina 450k chip data.

August: are tomatoes the new Arabadopsis?

Review content on autism genetics and on the aging epigenome proved hugely popular in July, while in August Wolf Reik and Shankar Balasubramanian developed a new method to produce the first high resolution map of 5fC, AKA the 7th base. Another method in the issue, ggbio, introduces a new graphics grammar to genomics – so that R can be harnessed to create funkier figures than ever before. And there were genomics figures aplenty in two articles describing stem cell-associated and lncRNA gene expression signatures in cancer.

September was ENCODE month, and Genome Biology joined together with Nature, Genome Research and BMC Genetics to publish the functional annotation of the human genome. Alexander Meissner stepped in as Guest Editor for October's special issue on epigenomics, which included a few surprises – not least the identification of DNA methylation in nematodes and ciliates. Particularly popular in the special issue were articles describing a gene module responsive to human aging, a viewpoint heralding a new era of epitranscriptomics, and a software tool for ChIP-seq QC.

December: transmission dynamics in two hospital superbugs

We summed up November on this blog as "germs, junk and jumping genes", which was shorthand for "microbiome, pseudogenes and endogenous retroviruses". And we rounded off the year in December with a clutch of cancer genomics articles: mutational signatures in gastric cancer genomes, telomeric DNA in pediatric cancer genomes, a Lincoln Stein method for identifying prognostic gene signatures, and a Sohrab Shah/Samuel Aparicio/Carlos Caldas method for analyzing somatic driver mutations in transcriptional networks.

It goes without saying that not one of these articles would have been published were it not for the 1000s of collective (wo)man-hours consumed by our armies of peer reviewers and editorial advisors, for which we are very grateful. We also thank all the researchers who chose to submit the produce of their blood, sweat and tears to Genome Biology in 2012. And a final thank you to our readers, especially those who engaged with our publications on the blogosphere, Twitter and elsewhere. Happy publishing in 2013!

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