Best 2013 genetics and evolution papers (a personal selection)

At this time of the year I usually screen the papers I have printed/downloaded/read during the year, as an exercise to recall what has been discovered this year. I thought that it would be a good idea to create a list of my favourite 2013 papers and post it in this blog. Obviously, this is a very personal list, and the selection is completely biased. Also, the list is not about the best discoveries or the most famous findings, so don’t expect microbrains or Lenski’s experiments. Hope you find this list, at least, informative.

But before the list, I want to stress from which journals I have downloaded/read most of the papers. These are the top 10 journals: PLoS ONE, PLoS Genetics, Genetics, MBE, PNAS, NAR, arXiv, Science, BMC Genomics and Genome Res. Clearly, PLoS ONE and arXiv have a substantial impact in my field.

Out of 500+, this is my small selection (with no particular order):

• “An Experimental Test on the Probability of Extinction of New Genetic Variants” by Ivo Chelo et al. This paper test the predictions from classical population genetics about the fixation probability of alleles in C. elegans. Very interesting combination of theoretical evolution with experimental biology.
• “Why Transcription Factor Binding Sites Are Ten Nucleotides Long” by Alexander Stewart, Sridhar Hannenhalli and Joshua Plotkin. It develops a population genetics model which predicts the observed length distribution of regulatory motifs. May or may not be realistic, you may like it or not, but the paper is worth reading.
• “Fungal Small RNAs Suppress Plant Immunity by Hijacking Host RNA Interference Pathways” by Arne Weiberg et al. This is a demonstration that genes in one species do regulate genes in a species of a different kingdom in nature. Quite amazing!
• “Genomic evidence for elevated mutation rates in highly expressed genes” by Chungoo Park, Wenfeng Qian and George Zhang. High transcription implies high mutation rates. Straightforward observation with deep implications in evolutionary genetics.
• “Sequencing mRNA from Cryo-Sliced Drosophila Embryos to Determine Genome-Wide Spatial Patterns of Gene Expression” by Peter Combs and Michael Eisen. In my opinion, one of the technical breakthroughs of the year (together with the CRISPR/Cas9 system). I feel that there will be interesting applications, but I still don’t know which ones.
• “Integration of new genes into cellular networks, and their structural maturation” by György Abrusán. This year has been the year of de novo emerged genes. This is, as far as I know, the first systematic exploration of the functional consequences on novel gene emergence.
• “Linking Stochastic Fluctuations in Chromatin Structure and Gene Expression” by Christopher Brown et al. Using a yeast system, the authors add a new layer of complexity in gene expression profiles, the random component from stochastic chromatin structures.

Happy new year!

Tags: arxiv, evolution, genetics, plos one, research papers