FUBAR - Fast Unconstrained Bayesian AppRoximation

From the authors that brought you BUSTED (Branch-site Unrestricted Statistical Test for Episodic Diversification), behold FUBAR: Fast Unconstrained Bayesian AppRoximation. (Doubly from the authors in this case, as the first author gave the tip-off.)

Despite it’s intranym status, FUBAR gets an extra geek hat-tip for being a homonym of “foo bar”. (Although in looking that up, I came across the original FUBAR acronym, which is hopefully not reflective of their method!)

Abstract

Model-based analyses of natural selection often categorize sites into a relatively small number of site classes. Forcing each site to belong to one of these classes places unrealistic constraints on the distribution of selection parameters, which can result in misleading inference due to model misspecification. We present an approximate hierarchical Bayesian method using a Markov chain Monte Carlo (MCMC) routine that ensures robustness against model misspecification by averaging over a large number of predefined site classes. This leaves the distribution of selection parameters essentially unconstrained, and also allows sites experiencing positive and purifying selection to be identified orders of magnitude faster than by existing methods. We demonstrate that popular random effects likelihood methods can produce misleading results when sites assigned to the same site class experience different levels of positive or purifying selection–an unavoidable scenario when using a small number of site classes. Our Fast Unconstrained Bayesian AppRoximation (FUBAR) is unaffected by this problem, while achieving higher power than existing unconstrained (fixed effects likelihood) methods. The speed advantage of FUBAR allows us to analyze larger data sets than other methods: We illustrate this on a large influenza hemagglutinin data set (3,142 sequences). FUBAR is available as a batch file within the latest HyPhy distribution (http://www.hyphy.org), as well as on the Datamonkey web server (http://www.datamonkey.org/).

• Murrell B, Moola S, Mabona A, Weighill T, Sheward D, Kosakovsky Pond SL & Scheffler K (2013). FUBAR: a fast, unconstrained bayesian approximation for inferring selection. Mol Biol Evol. 30(5):1196-205. PMID: 23420840

SANTA - Spatial Analysis of NeTwork Associations

A festive bioinformatics acronym today: SANTA - Spatial Analysis of NeTwork Associations. The authors don't make a big deal of the acronym in the paper but it seemed contrived enough for a Christmas ORCA entry.

Abstract

Linking networks of molecular interactions to cellular functions and phenotypes is a key goal in systems biology. Here, we adapt concepts of spatial statistics to assess the functional content of molecular networks. Based on the guilt-by-association principle, our approach (called SANTA) quantifies the strength of association between a gene set and a network, and functionally annotates molecular networks like other enrichment methods annotate lists of genes. As a general association measure, SANTA can (i) functionally annotate experimentally derived networks using a collection of curated gene sets and (ii) annotate experimentally derived gene sets using a collection of curated networks, as well as (iii) prioritize genes for follow-up analyses. We exemplify the efficacy of SANTA in several case studies using the S. cerevisiae genetic interaction network and genome-wide RNAi screens in cancer cell lines. Our theory, simulations, and applications show that SANTA provides a principled statistical way to quantify the association between molecular networks and cellular functions and phenotypes. SANTA is available from http://bioconductor.org/packages/release​/bioc/html/SANTA.html.

Ref: Cornish AJ & Markowetz F (2014) SANTA: Quantifying the Functional Content of Molecular Networks. PLoS Comput Biol 10(9): e1003808.

MUSIC - MUltiScale enrIchment Calling

Over on the ACGT blog, Keith Bradnam has another JABBA Award (and a nice new JABBA logo):

MUSIC - Multiscale Enrichment Calling.

I'm not sure what the connection between MUSIC and ChIP-Seq is but the authors seemed pretty determined. His post is actually a twofer, as it also draws attention to an equally contrived an unfathomable intranym:

MuSiC - Multiple Sequence Alignment with Constraints

Read more at Keith’s blog!

PEPPER - Protein complex Expansion using Protein-Protein intERactions

Another offering from the ever-fruitful world of bioinformatics today - with a fruit, fittingly enough.

PEPPER - Protein complex Expansion using Protein-Protein intERactions - pulls out all the stops when it comes to contriving a functional word, skipping words and using internal letters.

For the curious, PEPPER is available from the Cytoscape App Store and is:

“designed to identify protein complexes as densely connected subnetworks from seed lists of proteins derived from proteomic studies. Pepper identifies connected subgraph by using multi-objective optimization involving two functions: (i) the coverage, a solution must contain as many proteins from the seed as possible, (ii) the density, the proteins of a solution must be as connected as possible, using only interactions from a proteome-wide interaction network.”

Despite its use of “seed lists”, I don’t think there is a direct connection with peppers, so PEPPER is being classified as an ad hoc intranym.

I’m not sure if there’s a bigger version of the logo available but if you look carefully, you can see the little chilli peppers.

Winterhalter C et al. (2014) PEPPER: cytoscape app for protein complex expansion using protein-protein interaction networks. Bioinformatics. Aug 18. pii: btu517. [Epub ahead of print]

HOTAIR - HOX Transcript Antisense RNA

According to Wikipedia:

HOTAIR (for HOX antisense intergenic RNA) is a human gene located on chromosome 12. It is the first example of an RNA expressed on one chromosome that has been found to influence transcription on another chromosome.

However, Wikipedia itself cites Genecards, which has a slightly different metanym expansion (without any missing letters) for HOTAIR: HOX Transcript Antisense RNA. Either way, a very interesting gene and, though ad hoc intranym, certainly contrived enough for ORCA!

(HOTAIR possibly needs a new ORCA classification because both “metanym” sub-acronyms - HOX (Homeobox) and RNA (Ribonucleic acid) are themselves “itranyms”, as is HOTAIR.)

TARDIS - TARDigrades In Space

Yesterday’s TARDIS post was preamble for another TARDIS: Tardigrades in Space. This TARDIS is science rather than science fiction and you can read about it at the Tardigrades In Space blog.

Tardigrades In Space or “TARDIS” is the first research project to evaluate the ability of tardigrades to survive under open space conditions. TARDIS is one of the projects within the Biopan-6 research platform provided by European Space Agency (ESA), and will be sent into space with the russian FOTON-M3 mission.

Apparently, Tardigrades (a.k.a. “waterbears” or "moss piglets") can survive the vacuum and cosmic radiation of space.

h/t: This one is a submission from reader vardis.

CLARITY - Clear, Lipid-exchanged, Anatomically Rigid, Imaging/immunostaining compatible, Tissue hYdrogel

Another one that popped up in a journal Table of Contents (this time Science), CLARITY is the spectacularly contrived Clear, Lipid-exchanged, Anatomically Rigid, Imaging/immunostaining compatible, Tissue hYdrogel. As an acronym, it falls down at the end, so this one is being classed as an “intranym” but as CLARITY is a brain-imaging technique, I think it deserves pre hoc status. CLARITY was runner-up for Science journal’s Breakthrough of the Year.

ADAN - prediction of protein-protein interAction of moDular domAiNs

The ADAN Database - prediction of protein-protein interAction of moDular domAiNs - breaks the rules, really, as it is not technically an acronym. To be honest, I am not really sure what it is but it seemed so contrived that it warranted an ORCA entry. To add to the confusion, I do not know what “Adan” (the word rather than the database) is nor its relevance to protein-protein interactions, which is one of my own research areas.

As the database seems to be hosted by Universidad Miguel Hernández in Spain, the only thing I can think is that it is a backronym homage to Spanish footballer, Antonio Adán!

h/t: Nico.