S. A. Smith

Identification and Characterization of a Novel Nematode Pan Allergen (NPA) from Wuchereria bancrofti and their Potential Role in Human Filarial Tropical Pulmonary Eosinophilia (TPE)

The paper identifies a novel nematode allergen, NPA, from Wuchereria bancrofti that may contribute to the pathology of TPE by inducing histamine release, cytokine secretion, and eosinophil accumulation.

Sculpting the tumour microenvironment by combining radiotherapy and ATR inhibition for curative-intent anti-PD-L1- and anti-NKG2A-based adjuvant immunotherapy

This study combines ATR inhibition with radiotherapy and immune checkpoint blockade to enhance antitumour immunity in HNSCC preclinical models.

Genome duplications, genomic conflict, and rapid phenotypic evolution characterize the Cretaceous radiation of Fagales

This study examines the relationship between phenotypic and genomic evolution in Fagales, finding an 'early burst' model of diversification linked to gene duplication and genomic conflict during the Cretaceous.

HIV, asymptomatic STI, and the rectal mucosal immune environment among young men who have sex with men

This study examines the immunologic effects of HIV and asymptomatic bacterial STIs on the rectal mucosa in YMSM, finding HIV alters cellular composition while STIs increase pathogenic bacteria and inflammation in HIV-positive individuals.

Molecular early burst associated with the diversification of birds at the K-Pg boundary

The paper identifies a molecular early burst in avian evolution around the K-Pg boundary, linked to shifts in substitution rates and allometric scaling relationships.

Identifying climatic drivers of hybridization in Heuchereae (Saxifragaceae)

This study identifies climatic factors driving hybridization in Heuchereae by analyzing phylogenetic data and paleoclimatic records.

Compositional shifts associated with major evolutionary transitions in plants

The paper examines compositional shifts in DNA and amino acids across plant clades, finding shifts at major evolutionary transitions and shared directional changes within clades.

Stable Isotope Tracing In Vivo Reveals A Metabolic Bridge Linking The Microbiota To Host Histone Acetylation

This study uses stable isotope tracing to show that gut microbiota supply carbon for host histone acetylation, linking microbial metabolism to host epigenetic regulation.

Genomic characterization of metastatic patterns from prospective clinical sequencing of 25,000 patients

The paper analyzes genomic data from 25,000 patients to identify associations between genomic alterations and metastatic patterns across 50 tumor types, finding chromosomal instability correlates with metastatic burden in some cancers.

Categorical edge-based analyses of phylogenomic data reveal conflicting signals for difficult relationships in the avian tree

This study uses edge-based analysis to examine phylogenomic conflicts in avian evolution, revealing gene-specific biases and data type effects that impact resolution of contentious nodes.

Gene duplications and phylogenomic conflict underlie major pulses of phenotypic evolution in gymnosperms

This study links genomic changes like WGD and gene duplication to phenotypic innovation and diversification in gymnosperms, showing ecological factors also drive diversification after angiosperms.

Dichotomous regulation of lysosomes by MYC and TFEB controls hematopoietic stem cell fate

This study shows that lysosomes are regulated by TFEB and MYC to balance catabolic and anabolic processes in hematopoietic stem cells, influencing their fate and activation.

The evolutionary assembly of forest communities along environmental gradients: recent diversification or sorting of pre-adapted clades?

The paper investigates how environmental gradients shape community assembly through immigration and sorting of pre-adapted clades versus recent diversification, finding clade sorting dominates species turnover along elevational gradients.

Mapping the Cellular Origin and Early Evolution of Leukemia in Down Syndrome

This study identifies the cellular origin and mechanisms of leukemia predisposition in Down syndrome by analyzing gene mutations and their effects in fetal hematopoietic cells.

Phylogenomic conflict coincides with rapid morphological innovation

The paper examines the relationship between phylogenomic conflict and phenotypic innovation across six clades, finding a correlation between high conflict regions and elevated rates of phenotypic innovation.

Understanding how an amphicarpic species with a mixed mating system responds to fire: a population genetic approach

This study investigates whether belowground seeds of an amphicarpic species recolonize fire-disturbed sites, finding that selfed seeds from belowground flowers predominantly recolonize after fire.

Disentangling Sources of Gene Tree Discordance in Phylogenomic Datasets: Testing Ancient Hybridizations in Amaranthaceae s.l.

The paper investigates gene tree discordance in Amaranthaceae s.l. using multiple methods, finding that ancient hybridizations and rapid lineage diversification may contribute to the discordance.

Disentangling biological and analytical factors that give rise to outlier genes in phylogenomic matrices

The paper identifies four factors causing outlier genes in phylogenomic matrices and shows how excluding them can mislead evolutionary inferences.

Intragenic conflict in phylogenomic datasets

The paper examines intragenic conflict in phylogenomic datasets, finding high variability in conflict rates and identifying alignment errors as a major source.

A consensus phylogenomic approach highlights paleopolyploid and rapid radiation in the history of Ericales

This study uses a consensus phylogenomic approach to analyze Ericales' evolutionary history, finding unresolved ancient relationships and evidence of a whole genome duplication.

Phylogenetic conflicts, combinability, and deep phylogenomics in plants

The paper dissects phylogenetic signal in a plant dataset to resolve conflicts and identify unresolved relationships, finding support for certain placements but uncertainty in others.

Exploring the phylogeny of rosids with a five-locus supermatrix from GenBank

The paper constructs a five-locus supermatrix from GenBank data to explore rosid phylogeny, finding improved resolution but also highlighting sampling biases and limitations in current data.

Evolution of Portulacineae marked by gene tree conflict and gene family expansion associated with adaptation to harsh environments

This study reconstructs the phylogeny of Portulacineae and examines molecular evolution correlates with adaptation to harsh environments, identifying gene duplications and expansions linked to stress responses.

Analyzing contentious relationships and outlier genes in phylogenomics

The paper identifies outlier genes causing conflict between supermatrix and coalescent-based species trees in two datasets and proposes a framework for examining alternative edges in phylogenomic analyses.

Pan-arthropod analysis reveals somatic piRNAs as an ancestral defence against transposable elements

The paper analyzes piRNA pathways across 20 arthropod species, finding somatic piRNAs as an ancestral defense against transposable elements.

The Past Sure Is Tense: On Interpreting Phylogenetic Divergence Time Estimates

The paper investigates how prior assumptions in divergence time estimation can lead to inaccurate age estimates for angiosperms, even without data, highlighting issues with calibration densities and prior distributions.

Quartet Sampling distinguishes lack of support from conflicting support in the plant tree of life

The paper introduces Quartet Sampling (QS), a method to distinguish conflicting support from poor support in plant phylogenies, showing it effectively identifies discordant evolutionary relationships.

Bayesian and likelihood phylogenetic reconstructions of morphological traits are not discordant when taking uncertainty into consideration. A comment on Puttick et al.

The paper critiques Puttick et al.'s conclusion that Bayesian methods are superior for phylogenetic reconstruction from morphological traits, arguing that their comparison was flawed and that ML and Bayesian methods are concordant when uncertainty is properly considered.

Widespread paleopolyploidy, gene tree conflict, and recalcitrant relationships among the carnivorous Caryophyllales

The paper uses phylogenomic data to analyze relationships among carnivorous Caryophyllales, finding gene tree conflict, paleopolyploidy events, and unresolved relationships.

Inhibition of microbial biofuel production in drought stressed switchgrass hydrolysate

This study investigates how drought stress in switchgrass affects biofuel production by inhibiting yeast fermentation due to the formation of toxic compounds during pretreatment.