I think one of the ones that caused the most buzz in my sphere was the Ion Torrent one. Everyone was waiting for that....

Paper itself: An integrated semiconductor device enabling non-optical genome sequencing

Dan MacArthur's take on it: How accurate is the new Ion Torrent genome, really?

One paper that will influence my work is Stochastic state transitions give rise to phenotypic equilibrium in populations of cancer cells by Gupta et al. Importantly, the authors show that subpopulations of cells purified for a given phenotypic state return towards equilibrium proportions over time, explaining this with Markov models. I would like to examine their conclusions in terms of metabolic diseases, eg type 2 diabetes and dyslipidemia.

I also think that a key event of 2011 is the growing realization that the genome is the basic unit of interrogation. It is increasingly easier to begin to address a biological question by looking genome-wide, then drawing focus on the biological implications of a few select genes.

This paper of Salzberg et al in Genome Research "GAGE: A critical evaluation of genome assemblies and assembly algorithms" (quite recent) is very actual for our research; "Which de novo assembler to choose in short read assembly...and more importantly how to assess which is the best for YOUR situation (e.g. the E-size as alternative/addition for/to N50."

This paper provides some ways to look at it which may be applicable to making a well-understood choice. Not just the choice of the assembler available at the server or because a collegue is using it fine. :-)

• Limitations of next-generation genome sequence assembly
• A Regulatory Archipelago Controls Hox Genes Transcription in Digits

For me this paper made the most difference:

Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies

From protein folding and design:

Computational Design of Proteins Targeting the Conserved Stem Region of Influenza Hemagglutinin

How Fast-Folding Proteins Fold

My two cents:

Technical phosphoproteomic and bioinformatic tools useful in cancer research