James McInerney
@jomcinerney.bsky.social
Writing a book about horizontal gene transfer and non treelike evolution. Bioinformatics, Evolutionary Biology. Pangenomes. Chair in Evolutionary Biology. 🇮🇪 http://github.com/mol-evol/panGPT
Another really bad graphic on the BBC website at the moment. Anybody see anything wrong with this one?
November 12, 2025 at 10:12 AM
Another really bad graphic on the BBC website at the moment. Anybody see anything wrong with this one?
A pangenome influence graph. How much does the presence or absence of a gene influence the presence or absence of another in a genome? Somewhere in here is some of the answer.
May 15, 2025 at 11:51 AM
A pangenome influence graph. How much does the presence or absence of a gene influence the presence or absence of another in a genome? Somewhere in here is some of the answer.
There is also an option to "convert" your input sequences into an "optimized" set of sequences using a variety of approaches. Obviously, these do not guarantee sequence optimization, but the functionality might be useful to some people.
April 28, 2025 at 12:14 PM
There is also an option to "convert" your input sequences into an "optimized" set of sequences using a variety of approaches. Obviously, these do not guarantee sequence optimization, but the functionality might be useful to some people.
there are other outputs that might be interesting, such as a correlation matrix for the various metrics.
April 28, 2025 at 12:14 PM
there are other outputs that might be interesting, such as a correlation matrix for the various metrics.
so, for instance, if you zoom in, you can see the G and C-ending codons tend to be rarely used, while the T and A-ending codons are used more frequent. Just hover over a cell and you can see the underlying data.
April 28, 2025 at 12:14 PM
so, for instance, if you zoom in, you can see the G and C-ending codons tend to be rarely used, while the T and A-ending codons are used more frequent. Just hover over a cell and you can see the underlying data.
This is a new bit. It is an RSCU Heatmap. Every row is a codon, every column is a gene and the colour is how high or low its RSCU value is. You can see the plot is a bit "banded", this is because alternative -neighboring - codons in this organism are either highly or lowly used
April 28, 2025 at 12:14 PM
This is a new bit. It is an RSCU Heatmap. Every row is a codon, every column is a gene and the colour is how high or low its RSCU value is. You can see the plot is a bit "banded", this is because alternative -neighboring - codons in this organism are either highly or lowly used
These plots pop up in a browser and are a bit interactive (see plotly for all this goodness). This is a plot (of the Plasmodium falciparum protein coding genes) of Effective Number of Codons versus the GC3s content of the gene - sometimes called "Wrights Plot" doi.org/10.1016/0378...
April 28, 2025 at 12:14 PM
These plots pop up in a browser and are a bit interactive (see plotly for all this goodness). This is a plot (of the Plasmodium falciparum protein coding genes) of Effective Number of Codons versus the GC3s content of the gene - sometimes called "Wrights Plot" doi.org/10.1016/0378...
and it can do nice interactive visualizations like this (this is the default correspondence analysis of codon usage, showing the outlier genes whose codon usage is not quite the "canonical" usage pattern).
April 28, 2025 at 12:14 PM
and it can do nice interactive visualizations like this (this is the default correspondence analysis of codon usage, showing the outlier genes whose codon usage is not quite the "canonical" usage pattern).
it has a "proper" old fashioned interface, but can run on the command line.
April 28, 2025 at 12:14 PM
it has a "proper" old fashioned interface, but can run on the command line.
Happy saint patricks day to all who celebrate it.
March 17, 2025 at 8:37 PM
Happy saint patricks day to all who celebrate it.
Author unknown.
February 14, 2025 at 9:41 AM
Author unknown.
This day four years ago we got some very good news about the COVID vaccinations. I was asked to do a small interview with Irish TV about it. This is the response to the post on twitter 🤣
December 2, 2024 at 8:04 PM
This day four years ago we got some very good news about the COVID vaccinations. I was asked to do a small interview with Irish TV about it. This is the response to the post on twitter 🤣
Bluesky. The other Bluesky.
November 16, 2024 at 6:45 PM
Bluesky. The other Bluesky.
Latest paper. We show that evolution repeats itself in predictable ways. This directly addresses the assertion by Stephen Jay Gould that evolution is not predictable. The answer is more nuanced than a simple yes/no. www.pnas.org/doi/10.1073/...
December 30, 2023 at 6:32 PM
Latest paper. We show that evolution repeats itself in predictable ways. This directly addresses the assertion by Stephen Jay Gould that evolution is not predictable. The answer is more nuanced than a simple yes/no. www.pnas.org/doi/10.1073/...