Biology subjects

Potter, B. I.

Publications and source records attributed to Potter, B. I..

3 recordsLinked to original sources

bioRxiv2026

baltic: the Backronymed Adaptable Lightweight Tree vIsualisation Code

For ten years, baltic (Backronymed Adaptable Lightweight Tree vIsualization Code) has been used to make annotated phylogeny figures in molecular epidemiology, including during the West African Ebola epidemic, the Zika epidemic in the Americas, and the SARS-CoV-2 pandemic, as well as other fields. At its core, baltic is a Python library used for the efficient parsing, traversal, manipulation, and visualisation of phylogenetic trees. It is a small library with few dependencies that reads tree formats common in phylodynamic analyses and gives the user leverage to interact with a lightweight tree data structure to produce publication-ready figures with matplotlib. We present baltic v1.0, its first formally released and documented version. baltic reads and writes BEAST Nexus, Newick, and Nextstrain/Auspice JSON, and can process large BEAST posterior tree files in parallel to extract user-defined posterior statistics. The same objects are used for tree manipulation and for plotting in a single script. New to this release: a set of rooting methods (midpoint rooting, rerooting on any branch, and root-to-tip regression); support for reticulate evolution, with reassortment and recombination edges; and composite figures that combine a tree with other data, such as Muller plots, skygrid plots, tanglegrams, and plots connecting trees to maps. The release includes a documentation site with an API reference, tutorials, and a matplotlib-style gallery of worked examples.

bioinformatics↗

bioRxiv2019

Gene balance predicts transcriptional responses immediately following ploidy change in Arabidopsis thaliana

The Gene Balance Hypothesis postulates that there is selection on gene copy number (gene dosage) to preserve stoichiometric balance among interacting proteins. This presupposes that gene product abundance is governed by gene dosage, and that the way in which gene product abundance is governed by gene dosage is consistent for all genes in a dosage-sensitive network or complex. Gene dosage responses, however, have rarely been quantified and the available data suggest that they are highly variable. We sequenced the transcriptomes of two synthetic autopolyploid accessions of Arabidopsis thaliana and their diploid progenitors, as well as one natural tetraploid and its synthetic diploid produced via haploid induction, to estimate transcriptome size and gene dosage responses immediately following ploidy change. We demonstrate that overall transcriptome size does not exhibit a simple doubling in response to genome doubling, and that individual gene dosage responses are highly variable in all three accessions, indicating that expression is not strictly coupled with gene dosage. Nonetheless, putatively dosage-sensitive gene groups (GO terms, metabolic networks, gene families, and predicted interacting protein pairs) exhibit both smaller and more coordinated dosage responses than do putatively dosage-insensitive gene groups, suggesting that constraints on dosage balance operate immediately following whole genome duplication. This supports the hypothesis that duplicate gene retention patterns are shaped by selection to preserve dosage balance.

plant biology↗

bioRxiv2019

Evolution and rapid spread of a reassortant A(H3N2) virus that predominated the 2017-2018 influenza season

The 2017-2018 North American influenza season caused more hospitalizations and deaths than any year since the 2009 H1N1 pandemic. The majority of recorded influenza infections were caused by A(H3N2) viruses, with most of the viruss North American diversity falling into the A2 clade. Within A2, we observe a subclade which we call A2/re that rose to comprise almost 70% of A(H3N2) viruses circulating in North America by early 2018. Unlike most fast-growing clades, however, A2/re contains no amino acid substitutions in the hemagglutinin (HA) segment. Moreover, HI assays did not suggest substantial antigenic differences between A2/re viruses and viruses sampled during the 2016-2017 season. Rather, we observe that the A2/re clade was the result of a reassortment event that occurred in late 2016 or early 2017 and involved the combination of the HA and PB1 segments of an A2 virus with neuraminidase (NA) and other segments a virus from the clade A1b. The success of this clade shows the need for antigenic analysis that targets NA in addition to HA. Our results illustrate the potential for non-HA drivers of viral success and necessitate the need for more thorough tracking of full viral genomes to better understand the dynamics of influenza epidemics.

genomics↗