Richard Neher
@neher.io
Within the syntenic core genome, linkage between SNPs decays rapidly with distance. LD approaches background levels after about 1000 bases. The background level itself is often set by population structure with little linkage within subgroups but genome wide coupling across subgroups.
[4/6]
[4/6]
August 23, 2025 at 4:21 PM
Within the syntenic core genome, linkage between SNPs decays rapidly with distance. LD approaches background levels after about 1000 bases. The background level itself is often set by population structure with little linkage within subgroups but genome wide coupling across subgroups.
[4/6]
[4/6]
Phages are known to recombine with each other and have flexible and fluid genomes. We analyzed diversity within the clusters of the Acinetobacteriophage Database by organizing their genomes into pangenome graphs based on homologous phams (protein families).
[2/6]
[2/6]
August 23, 2025 at 4:21 PM
Phages are known to recombine with each other and have flexible and fluid genomes. We analyzed diversity within the clusters of the Acinetobacteriophage Database by organizing their genomes into pangenome graphs based on homologous phams (protein families).
[2/6]
[2/6]
Numbers came down quickly in early April, but the excess deaths accumulated through March corresponded roughly to the number of people that normally die in half a year.
March 16, 2025 at 10:16 AM
Numbers came down quickly in early April, but the excess deaths accumulated through March corresponded roughly to the number of people that normally die in half a year.
5 years ago, I subscribed to Eco di Bergamo and spent a few hours counting obituaries in Feb/March.
Most cases in northern Europe at the time were travel returnees that didn't get very sick, but the 7x increase in mortality in Bergamo left no doubt what happens if the virus hits the vulnerable.
Most cases in northern Europe at the time were travel returnees that didn't get very sick, but the 7x increase in mortality in Bergamo left no doubt what happens if the virus hits the vulnerable.
March 16, 2025 at 10:16 AM
5 years ago, I subscribed to Eco di Bergamo and spent a few hours counting obituaries in Feb/March.
Most cases in northern Europe at the time were travel returnees that didn't get very sick, but the 7x increase in mortality in Bergamo left no doubt what happens if the virus hits the vulnerable.
Most cases in northern Europe at the time were travel returnees that didn't get very sick, but the 7x increase in mortality in Bergamo left no doubt what happens if the virus hits the vulnerable.
We use the improved estimates of mutation rates to identify regions where synonymous mutations are under purifying selection.
Most clear signals correspond to known structures like the ORF1a/b frameshift and TRSs. But two clear signals lack an explanation (in E and between M/ORF6).
[7/N]
Most clear signals correspond to known structures like the ORF1a/b frameshift and TRSs. But two clear signals lack an explanation (in E and between M/ORF6).
[7/N]
January 11, 2025 at 5:37 PM
We use the improved estimates of mutation rates to identify regions where synonymous mutations are under purifying selection.
Most clear signals correspond to known structures like the ORF1a/b frameshift and TRSs. But two clear signals lack an explanation (in E and between M/ORF6).
[7/N]
Most clear signals correspond to known structures like the ORF1a/b frameshift and TRSs. But two clear signals lack an explanation (in E and between M/ORF6).
[7/N]
A simple linear model with genomic region, 5' and 3' neighborhood, and 2nd pairing explains between 15 and 60% of the fold-variation of the rates.
[6/N]
[6/N]
January 11, 2025 at 5:37 PM
A simple linear model with genomic region, 5' and 3' neighborhood, and 2nd pairing explains between 15 and 60% of the fold-variation of the rates.
[6/N]
[6/N]
The underlying mechanism is a mystery to us (we speculate a bit in the preprint).
Rates also depend on neighboring bases, sometimes by more than 10-fold. These neighbor-dependence is very strand symmetric for some mutations (e.g. T>G and A>C), but not others.
[3/N]
Rates also depend on neighboring bases, sometimes by more than 10-fold. These neighbor-dependence is very strand symmetric for some mutations (e.g. T>G and A>C), but not others.
[3/N]
January 11, 2025 at 5:37 PM
The underlying mechanism is a mystery to us (we speculate a bit in the preprint).
Rates also depend on neighboring bases, sometimes by more than 10-fold. These neighbor-dependence is very strand symmetric for some mutations (e.g. T>G and A>C), but not others.
[3/N]
Rates also depend on neighboring bases, sometimes by more than 10-fold. These neighbor-dependence is very strand symmetric for some mutations (e.g. T>G and A>C), but not others.
[3/N]
Some rates, like C>T(U), are much higher than others. But even for the same mutation type, rates vary dramatically from site to site, sometimes in striking patterns:
A>T mutations are 2-3 fold more common after the start of Spike. C>T drops almost two-fold at the ORF1a/b boundary.
[2/N]
A>T mutations are 2-3 fold more common after the start of Spike. C>T drops almost two-fold at the ORF1a/b boundary.
[2/N]
January 11, 2025 at 5:37 PM
Some rates, like C>T(U), are much higher than others. But even for the same mutation type, rates vary dramatically from site to site, sometimes in striking patterns:
A>T mutations are 2-3 fold more common after the start of Spike. C>T drops almost two-fold at the ORF1a/b boundary.
[2/N]
A>T mutations are 2-3 fold more common after the start of Spike. C>T drops almost two-fold at the ORF1a/b boundary.
[2/N]