Papers, 5 minute

RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming
http://bioinformatics.oxfordjournals.org/content/26/18/i460.full
- it's fast, uses threshold-cut to limit search space
CopyMap: localization and calling of copy number variation by joint analysis of hybridization data from multiple individuals.
http://bioinformatics.oxfordjournals.org/content/26/21/2776.long
- compare many things at the same time, so better accuracy?
Using Sequence-Specific Chemical and Structural Properties of DNA to Predict Transcription Factor Binding Sites
http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1001007
- uses machine learning, lower false positive rate, compared with other methods, Match, MATRIX SEARCH, QPMEME, method of Berg and von Hippel, data from ChIP-chip assays to measure transcription binding on DNA sequences of Fis (TF), binding sites obtained from RegulonDB
-  A long-standing problem has been how to identify new TF binding sites given known binding sites.

SmashCommunity: a metagenomic annotation and analysis tool
http://bioinformatics.oxfordjournals.org/content/26/23/2977.full
- SmashCommunity (Simple Metagenomics Analysis SHell for microbial communities) to annotate shotgun metagenomes with inbuilt tools for quantitative and comparative analyses.
- Each task in metagenomic analysis, such as sequence assembly or gene prediction, is implemented as a module that is a wrapper around a software program that implements this task.

BigWig and BigBed: enabling browsing of large distributed datasets
http://bioinformatics.oxfordjournals.org/content/26/17/2204.full
- BigWig and BigBed files are compressed binary indexed files containing data at several resolutions that allow the high-performance display of next-generation sequencing experiment results in the UCSC Genome Browser
- BigBed and BigWig files are similar in many ways to BAM files (Li et al., 2009), which are commonly used to store mappings of short reads to the genome.
- http://samtools.sourceforge.net/ SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments.
MulteeSum: A Tool for Comparative Spatial and Temporal Gene Expression Data
http://gvi.seas.harvard.edu/paper/multeesum-tool-comparative-spatial-and-temporal-gene-expression-data
- Comparision of different Drosophila embryos (for morphological studies) from different Drosophila species, eg. Dmel, Dpse (Drosophila pseudoobscura, second species to be sequenced)
- Developed using the Processing language (Processing.org), based on PointCloudXplor
- http://multeesum.org/

Networks of gene sharing among 329 proteobacterial genomes reveal differences in lateral gene transfer frequency at different phylogenetic depths.
http://mbe.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=21059789
- Using a minimal lateral network approach, we compared LGT rates at different phylogenetic depths.
- Hence our results indicate that the rate of gene acquisition per protein family are similar at the level of species (by recombination) and at the level of classes (by LGT).
is-rSNP: a novel technique for in silico regulatory SNP detection
http://bioinformatics.oxfordjournals.org/content/26/18/i524.short
- Determining the functional impact of non-coding disease-associated single nucleotide polymorphisms (SNPs) identified by genome-wide association studies (GWAS) is challenging. Many of these SNPs are likely to be regulatory SNPs (rSNPs): variations which affect the ability of a transcription factor (TF) to bind to DNA.

Modeling associations between genetic markers using Bayesian networks
http://bioinformatics.oxfordjournals.org/content/26/18/i632.short
- Many coefficients were proposed for measuring the degree of LD, but they provide only a static view of the current LD structure. Generative models (GMs) were proposed to go beyond these measures, giving not only a description of the actual LD structure but also a tool to help understanding the process that generated such structure.
- method is based on learning optimal BN structures (weighted) from haplotype data, extracting equivalence structure classes (PDAGs) and using them to model LD.
- HapMap database
- These plots provide a nice visualization of how single nucleotide polymorphisms (SNPs) travel together in human subpopulations and samples due to linkage disequilibrium (LD).
- http://www.goldenhelix.com/SNP_Variation/Manual/svs7/using_ld_plots.html
- http://bioinformatics.oxfordjournals.org/content/23/6/774/F1.medium.gif
- snp.plotter: an R-based SNP/haplotype association and linkage disequilibrium plotting package