Blog

Mechanisms of Protein Evolution SMBE Satellite Meeting, Denver February 2013

Several members of the Bioinformatics and Molecular Evolution Unit attended the second “Mechanisms of Protein Evolution” meeting in Denver Colorado in February 2013. The agenda for the meeting is here:   http://www.proteinevolution.org/wp-content/uploads/2012/09/Agenda_MPEII_5Feb13.pdf   During the meeting a video was made where a number of the speakers gave a brief overview of what they were speaking […]

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Bioenergetics and The Major Evolutionary Transitions

I spoke at a meeting organised by Nick Lane at Chichley Hall, home of the Kavli Royal Society International Centre, Buckinghamshire. This was a wonderful meeting, full of diverse talks and with a lot of people interested in major evolutionary transitions on the planet. The programme for the meeting can be picked up here. I gave […]

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Introgressive descent

For some time, it has become apparent that many evolving entities (genes, cells, viruses, plasmids, genomes, etc.) are mosaic.  That is to say, we cannot describe their evolutionary history without telling more than one story about it. Genes can be chimaeric and indeed, it is arguable that it is almost impossible for them not to […]

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Our letter in the Irish Times today

Here I reproduce our letter in the Irish Times:   Sir, – Ireland’s poor success rate in winning grants from the European Research Council (Business+Technology, August 16th) comes as no surprise to many of us in the Irish scientific community, given recent warnings from a number of international funding agencies. What is of particular concern […]

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The five biggest evolutionary transitions?

Have been thinking recently about what the five biggest evolutionary transitions might be.  Naturally, there are several transitions and indeed it is arguable that at every speciation event, there has been a transition – indeed at every mutational event, even. But which ones are the biggest?  Also, in this vein – what evolves and what […]

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Society for Molecular Biology and Evolution Annual Meeting 2012

The society for Molecular Biology and Evolution held their annual meeting in Dublin from June 23-26 in the Convention Centre Dublin. The meeting was attended by 1,300 delegates, 44 from Irish institutions and the rest were from international institutions.  The value to the Irish economy is estimated at approximately €3,000,000. Some of the outcomes of […]

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Is there any treelikeness in prokaryotic phylogenetic history

Right now there are some very valid questions being asked about how treelike we might expect to find the history of prokaryotes.  Conflicting phylogenetic trees derived from homologs-that-look-like-orthologs are probably in large part due to horizontal (or lateral if you prefer) gene transfer.  Some might be due to hidden paralogy, poor phylogenetic models and maybe […]

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Pervasive horizontal gene transfer in Chlamydia

The genome era has really taught us something impressive about the plasticity of bacterial genomes. Gene exchange between strains of the same species and gene exchange between different species is not limited to special categories of genes and is not limited to ‘oddball’ species.  It is pervasive, frequent and it is also a public health […]

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BI101

Transcription: The first video is an introduction to the structure of a gene and its transcription into messenger RNA. Click here:   This video follows on from the first transcription video and completes the section on transcription. Click here:   Translation: This first translation video introduces the various components required for translation of an mRNA […]

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Two conferences in Colorado in one week

The research unit decamped to Colorado this week to attend the first MMPE (Molecular Mechanisms of Protein Evolution), which was held in the University of Colorado Denver medical school and the 12th ISCB Regional Meeting, which was held in Snowmass Colorado in the Silvertree Hotel. Speaking at the meeting were: Dr. Davide Pisani, Dr. James […]

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H-Index, M-Index and google citations

Today I downloaded and installed the r program for analysing Google Scholar citation metrics (you can pick it up here). There is a lot of talk about the various metrics being used to analyse the productivity of scientists and there seems to be no really good way to do it.  A simple point-statistic doesn’t do […]

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Post-doctoral applicants sought for IRCSET grants.

post-doc applicants wanted We are looking for post-doctoral applicants for the upcoming IRCSET grant deadline. The name of the programme is EMPOWER and it is aimed at relatively early-stage postodoctoral applicants. Here is some of the information form the website: EMPOWER: Government of Ireland Postdoctoral Fellowships in Science, Engineering and Technology IRCSET will continue to […]

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Survival of the sexiest

This is to announce that on Tuesday next (the 15th of November), there will be a talk given by Dr. James McInerney in JH2 in the John Hume Building at NUI Maynooth at 7:30pm, entitled:   Survival of the sexiest: Why females want a mate with a good sense of humour, a brightly coloured tail […]

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SMBE2012 in Dublin

The annual meeting of the Society for Molecular Biology and Evolution will be held in Dublin next June from the 23rd to the 26th. In the coming week we will make the decisions on which symposia will be included in the final programme. This will be a great thing on one hand, because we get […]

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Planctomycetes and Eukaryotes are both interesting, but not specifically related

We have finally published our analysis of the relationships between Planctomycetes, Verrucomicrobia and Chlamydia (the so-called PVC group) and Eukaryotes.  In other words, we have shown that these two groups of organisms share superficial similarities, but have no close relationship.  The manuscript has been published in BioEssays and you can access it here [1]. If […]

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Research returns to Ireland far exceed investment

by Dick Ahlstrom, Irish Times Financial returns from Ireland’s expenditure in research have easily outstripped the original investment, according to a study released on 19 September. It claims that while the Exchequer put in almost €1.2 billion over the period 2000-2006 the returns amounted to about €1.8bn. The study by PA Consulting said that the […]

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PVC bacteria are not half-way to being eukaryotes

Over the past few years, manuscripts have been appearing in the literature that have been suggesting that PVC (Planctomycetes, Verrucomicrobia, Chlamydia) bacteria are in many ways like Eukaryotes and consequently, they are an excellent system for understanding eukaryote biology and indeed this group of bugs actually gave rise to modern eukaryotes. This is complete nonsense. […]

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Clans, clades and unrooted trees

A few years back, Mark Wilkinson at The Natural History Museum, London came up with the idea that we should really have a more precise language for groups that we can see on unrooted trees. The problem stemmed from the fact that on an unrooted tree a clade is not defined. A clade is a […]

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TIGER: Identifying rapidly-evolving characters in evolutionary data.

TIGER: Identifying rapidly-evolving characters in evolutionary data. About TIGER TIGER is open source software for identifying rapidly evolving sites (columns in an alignment, or characters in a morphological dataset). It can deal with many kinds of data (molecular, morphological etc.). Sites like these are important to identify as they are very often removed or reweighted […]

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Pisani lab work on Tardigrades.

Today the Irish Independent ran a nice report on Davide Pisani’s recent publication on the phylogenetic position of Tardigrades.  The work is reported in Proceedings of the National Academy of Sciences, USA.  Here’s the link.

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Goods thinking versus tree-thinking

Goods-thinking versus Tree-thinking In the famous Monty Python “Dead Parrot” sketch, John Cleese returns to a pet shop where he has just bought a parrot and asks for his money back.  The reason being that the parrot is in fact dead. This seems to be a not unreasonable request on the part of the purchaser […]

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CLANN: Software for inferring phylogenetic supertrees.

CLANN: Software for inferring phylogenetic supertrees. What is clann? Clann (the Irish word for “family”), is a free software program designed and written by Chris Creevey at the Bioinformatics and Molecular Evolution Unit at NUI Maynooth. The purpose of the program is to implement methods of determining the optimal phylogenetic supertree, given a set of […]

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Scientific American Article features Our Cancer Evolution Work

Carl Zimmer has written a very nice article for Scientific American where he discusses the influence of evolution on cancer.  He interviewed Dr. McInerney about his work with Dr. Mary O’Connell of DCU on how natural selection influences genes that are known to be involved in cancer.  The article can be read by clicking on […]

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ModelGenerator: amino acid and nucleotide substitution model selection

ModelGenerator is a a free, easy-to-use model selection program, designed and written by Thomas Keane, that selects optimal amino acid and nucleotide substitution models from Fasta or Phylip alignments. ModelGenerator supports 56 nucleotide and 96 amino acid substitution models. Modelgenerator uses the Akaike Information Criterion (AIC), the Bayesian Information Criterion (BIC) and hierarchical Likelihood-ratio tests […]

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CRANN: Software for inferring selection

CRANN Crann (pronounced ‘crown’) is the Irish word for ‘tree’. The program Crann has been developed in order to provide fast heuristic methods of detecting adaptive evolution in protein-coding genes. It is important that the user understands the advantages and limitations of these methods. It is also important for the user to know that the […]

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PutGaps : DNA gapped file from Amino Acid alignment

PutGaps : DNA gapped file from Amino Acid alignment Copyright © David Fitzpatrick, Melissa Pentony 2004 PutGaps is a free software program designed and written by David Fitzpatrick and Melissa Pentony. The purpose of the program is to add gaps to a DNA alignment file based on its Amino Acid equivalent. PutGaps has been written […]

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GCUA: General Codon Usage Analysis

GCUA: General Codon Usage Analysis GCUA was initially written while working at the Natural History Museum, London, however it is now being developed at the University of Manchester. The pdf describing the program can be downloaded here. Click on the appropriate link below to download the program: [wpdm_package id=’2526′] [wpdm_package id=’2537′] [wpdm_package id=’2536′]   Purpose: This program is […]

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