Scoring alignments by embedding vector similarity.

Sequence similarity is of paramount importance in biology, as similar sequences tend to have similar function and share common ancestry. Scoring matrices, such as PAM or BLOSUM, play a crucial role in all bioinformatics algorithms for identifying similarities, but have the drawback that they are fixed, independent of context. We propose a new scoring method for amino acid similarity that remedies this weakness, being contextually dependent.

Evolution of Transcript Abundance is Influenced by Indels in Protein Low Complexity Regions.

Protein Protein low complexity regions (LCRs) are compositionally biased amino acid sequences, many of which have significant evolutionary impacts on the proteins which contain them. They are mutationally unstable experiencing higher rates of indels and substitutions than higher complexity regions. LCRs also impact the expression of their proteins, likely through multiple effects along the path from gene transcription, through translation, and eventual protein degradation.

Sequence signatures within the genome of SARS-CoV-2 can be used to predict host source.

We conducted an analysis to better understand the potential factors impacting host adaptation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in white-tailed deer, humans, and mink due to the strong evidence of sustained transmission within these hosts. Classification models trained on single nucleotide and amino acid differences between samples effectively identified white-tailed deer-, human-, and mink-derived SARS-CoV-2. For example, the balanced accuracy score of Extremely Randomized Trees classifiers was 0.

Seq-InSite: sequence supersedes structure for protein interaction site prediction.

Motivation: Proteins accomplish cellular functions by interacting with each other, which makes the prediction of interaction sites a fundamental problem. As experimental methods are expensive and time consuming, computational prediction of the interaction sites has been studied extensively. Structure-based programs are the most accurate, while the sequence-based ones are much more widely applicable, as the sequences available outnumber the structures by two orders of magnitude.

A 14th century CE Brucella melitensis genome and the recent expansion of the Western Mediterranean clade.

Brucellosis is a disease caused by the bacterium Brucella and typically transmitted through contact with infected ruminants. It is one of the most common chronic zoonotic diseases and of particular interest to public health agencies. Despite its well-known transmission history and characteristic symptoms, we lack a more complete understanding of the evolutionary history of its best-known species-Brucella melitensis.

Reply to Barton et al: signatures of natural selection during the Black Death.

Barton . raise several statistical concerns regarding our original analyses that highlight the challenge of inferring natural selection using ancient genomic data. We show here that these concerns have limited impact on our original conclusions.

Low Complexity Regions in Proteins and DNA are Poorly Correlated.

Low complexity sequences (LCRs) are well known within coding as well as non-coding sequences. A low complexity region within a protein must be encoded by the underlying DNA sequence. Here, we examine the relationship between the entropy of the protein sequence and that of the DNA sequence which encodes it.

Decision Tree Ensembles Utilizing Multivariate Splits Are Effective at Investigating Beta Diversity in Medically Relevant 16S Amplicon Sequencing Data.

Developing an understanding of how microbial communities vary across conditions is an important analytical step. We used 16S rRNA data isolated from human stool samples to investigate whether learned dissimilarities, such as those produced using unsupervised decision tree ensembles, can be used to improve the analysis of the composition of bacterial communities in patients suffering from Crohn's disease and adenomas/colorectal cancers. We also introduce a workflow capable of learning dissimilarities, projecting them into a lower dimensional space, and identifying features that impact the location of samples in the projections.

Emergence, continuity, and evolution of Yersinia pestis throughout medieval and early modern Denmark.

The historical epidemiology of plague is controversial due to the scarcity and ambiguity of available data. A common source of debate is the extent and pattern of plague re-emergence and local continuity in Europe during the 14th-18th century CE. Despite having a uniquely long history of plague (∼5,000 years), Scandinavia is relatively underrepresented in the historical archives.

Plagued by a cryptic clock: insight and issues from the global phylogeny of Yersinia pestis.

Plague has an enigmatic history as a zoonotic pathogen. This infectious disease will unexpectedly appear in human populations and disappear just as suddenly. As a result, a long-standing line of inquiry has been to estimate when and where plague appeared in the past.

Evolution of immune genes is associated with the Black Death.

Infectious diseases are among the strongest selective pressures driving human evolution. This includes the single greatest mortality event in recorded history, the first outbreak of the second pandemic of plague, commonly called the Black Death, which was caused by the bacterium Yersinia pestis. This pandemic devastated Afro-Eurasia, killing up to 30-50% of the population.

Examining pathogen DNA recovery across the remains of a 14th century Italian friar (Blessed Sante) infected with Brucella melitensis.

Objective: To investigate variation in ancient DNA recovery of Brucella melitensis, the causative agent of brucellosis, from multiple tissues belonging to one individual MATERIALS: 14 samples were analyzed from the mummified remains of the Blessed Sante, a 14 century Franciscan friar from central Italy, with macroscopic diagnosis of probable brucellosis.

Methods: Shotgun sequencing data from was examined to determine the presence of Brucella DNA.

Results: Three of the 14 samples contained authentic ancient DNA, identified as belonging to B.

Computing Maximal Covers for Protein Sequences.

A of a or of length , which we model as an array , is a repeating substring of such that "many" positions in lie within occurrences of . A -introduced in 2018 by Mhaskar and Smyth as -is a partial cover that, over all partial covers , maximizes the positions covered. Applying data structures also introduced by Mhaskar and Smyth, our software MAXCOVER for the first time enables efficient computation of for any -in particular, as described here, for protein sequences of Arabidopsis, , and humans.

A 16 century Escherichia coli draft genome associated with an opportunistic bile infection.

Escherichia coli - one of the most characterized bacteria and a major public health concern - remains invisible across the temporal landscape. Here, we present the meticulous reconstruction of the first ancient E. coli genome from a 16 century gallstone from an Italian mummy with chronic cholecystitis.

Low Complexity Regions in Mammalian Proteins are Associated with Low Protein Abundance and High Transcript Abundance.

Low Complexity Regions (LCRs) are present in a surprisingly large number of eukaryotic proteins. These highly repetitive and compositionally biased sequences are often structurally disordered, bind promiscuously, and evolve rapidly. Frequently studied in terms of evolutionary dynamics, little is known about how LCRs affect the expression of the proteins which contain them.

LANDMark: an ensemble approach to the supervised selection of biomarkers in high-throughput sequencing data.

Background: Identification of biomarkers, which are measurable characteristics of biological datasets, can be challenging. Although amplicon sequence variants (ASVs) can be considered potential biomarkers, identifying important ASVs in high-throughput sequencing datasets is challenging. Noise, algorithmic failures to account for specific distributional properties, and feature interactions can complicate the discovery of ASV biomarkers.

Genomic inversions in alter gene expression and are associated with nucleoid protein binding sites.

Genomic reorganization, such as rearrangements and inversions, influences how genetic information is organized within the bacterial genomes. Inversions, in particular, facilitate genome evolution through gene gain and loss, and can alter gene expression. Previous studies have investigated the impact inversions have on gene expression induced inversions targeting specific genes or examine inversions between distantly related species.

Resampling the pool of genotypic possibilities: an adaptive function of sexual reproduction.

Background: Natural populations harbor significant levels of genetic variability. Because of this standing genetic variation, the number of possible genotypic combinations is many orders of magnitude greater than the population size. This means that any given population contains only a tiny fraction of all possible genotypic combinations.

Towards advancing scientific knowledge of climate change impacts on short-duration rainfall extremes.

A large number of recent studies have aimed at understanding short-duration rainfall extremes, due to their impacts on flash floods, landslides and debris flows and potential for these to worsen with global warming. This has been led in a concerted international effort by the INTENSE Crosscutting Project of the GEWEX (Global Energy and Water Exchanges) Hydroclimatology Panel. Here, we summarize the main findings so far and suggest future directions for research, including: the benefits of convection-permitting climate modelling; towards understanding mechanisms of change; the usefulness of temperature-scaling relations; towards detecting and attributing extreme rainfall change; and the need for international coordination and collaboration.

The Location of Substitutions and Bacterial Genome Arrangements.

Increasing evidence supports the notion that different regions of a genome have unique rates of molecular change. This variation is particularly evident in bacterial genomes where previous studies have reported gene expression and essentiality tend to decrease, whereas substitution rates usually increase with increasing distance from the origin of replication. Genomic reorganization such as rearrangements occur frequently in bacteria and allow for the introduction and restructuring of genetic content, creating gradients of molecular traits along genomes.

American mastodon mitochondrial genomes suggest multiple dispersal events in response to Pleistocene climate oscillations.

Pleistocene glacial-interglacial cycles are correlated with dramatic temperature oscillations. Examining how species responded to these natural fluctuations can provide valuable insights into the impacts of present-day anthropogenic climate change. Here we present a phylogeographic study of the extinct American mastodon (Mammut americanum), based on 35 complete mitochondrial genomes.

DELPHI: accurate deep ensemble model for protein interaction sites prediction.

Motivation: Proteins usually perform their functions by interacting with other proteins, which is why accurately predicting protein-protein interaction (PPI) binding sites is a fundamental problem. Experimental methods are slow and expensive. Therefore, great efforts are being made towards increasing the performance of computational methods.

The origins and genomic diversity of American Civil War Era smallpox vaccine strains.

Vaccination has transformed public health, most notably including the eradication of smallpox. Despite its profound historical importance, little is known of the origins and diversity of the viruses used in smallpox vaccination. Prior to the twentieth century, the method, source and origin of smallpox vaccinations remained unstandardised and opaque.

The role of introgression and ecotypic parallelism in delineating intraspecific conservation units.

Parallel evolution can occur through selection on novel mutations, standing genetic variation or adaptive introgression. Uncovering parallelism and introgressed populations can complicate management of threatened species as parallelism may have influenced conservation unit designations and admixed populations are not generally considered under legislations. We examined high coverage whole-genome sequences of 30 caribou (Rangifer tarandus) from across North America and Greenland, representing divergent intraspecific lineages, to investigate parallelism and levels of introgression contributing to the formation of ecotypes.