R. Baker

Stable isotopes disentangle niche partitioning and species co-occurrence in a multi-level marine mutualism

The paper uses stable isotope analysis to show that co-occurring crustacean symbionts in a marine mutualism have distinct trophic niches, supporting niche theory over neutral theory.

GLS1 is a Protective Factor Rather than a Molecular Target in ARID1A-Mutated Ovarian Clear Cell Carcinoma

The paper investigates GLS1 expression in ARID1A-mutated ovarian clear cell carcinoma and finds it is not correlated with ARID1A loss and is associated with better clinical outcomes.

Genetic and behavioral adaptation of Candida parapsilosis to the microbiome of hospitalized infants revealed by in situ genomics, transcriptomics and proteomics

This study identifies genetic and behavioral adaptations of C. parapsilosis in the gut microbiome of hospitalized infants using in situ genomics, transcriptomics, and proteomics.

Competitive binding of MatP and topoisomerase IV to the MukB dimerization hinge

The paper shows MatP and topoisomerase IV ParC compete for binding to the MukB dimerization hinge, with matS binding displacing MatP from the hinge.

Infant gut strain persistence is associated with maternal origin, phylogeny, and functional potential including surface adhesion and iron acquisition

The paper investigates factors influencing gut microbiome strain persistence in infants, finding maternal origin and specific genetic functions are associated with strain survival.

Monitoring the microbiome for food safety and quality using deep shotgun sequencing

The paper uses deep shotgun sequencing to analyze food microbiomes, identifying microbial genera and observing shifts related to ingredient composition, but finds limited correlation between RNA sequencing and Salmonella growth.

A computer vision approach for studying fossorial and cryptic crabs

This paper introduces a non-invasive computer vision protocol for studying fossorial and cryptic crabs using image-based sampling and open-source software.

Continuum descriptions of spatial spreading for heterogeneous cell populations: theory and experiment

This study uses a continuum model to analyze how cell size heterogeneity affects spatial spreading in cell populations, finding that simple models work well for certain distributions but not others.

Patterns of fish utilisation in a tropical Indo-Pacific mangrove-coral seascape, New Caledonia

This study examines fish utilization patterns in a mangrove-coral seascape using underwater video cameras, revealing differences in fish assemblages between mangrove edge and interior habitats.

Necrotizing enterocolitis is preceded by increased gut bacterial replication, Klebsiella, and fimbriae-encoding bacteria that may stimulate TLR4 receptors

The paper identifies microbial features predictive of necrotizing enterocolitis (NEC) in premature infants using metagenomic analysis and machine learning.

Dynamic architecture of the Escherichia coli structural maintenance of chromosomes (SMC) complex, MukBEF

The paper examines how nucleotide binding and ATP hydrolysis affect the architecture of the Escherichia coli SMC complex MukBEF.

Shifts in microbial transcription patterns prior to onset of Necrotizing enterocolitis may indicate low oxygen levels in the gut

The paper identifies shifts in microbial transcription patterns in preterm infants prior to NEC onset, suggesting hypoxic conditions in the gut.

Using experimental data and information criteria to guide model selection for reaction--diffusion problems in mathematical biology

This study uses Bayesian analysis and information criteria to select a reaction-diffusion model for cell invasion, showing that model complexity and residual errors should both be considered.

Mechanistic and experimental models of cell migration reveal the importance of intercellular interactions in cell invasion

This paper uses experimental and modeling approaches to show that intercellular interactions, particularly pushing, significantly influence cell invasion.

Strain-level overlap between infant and hospital fungal microbiomes revealed through de novo assembly of eukaryotic genomes from metagenomes

The paper analyzes metagenomic data from premature infants and NICUs to identify fungal strains and their genetic diversity, revealing high similarity between infant and hospital-associated fungi.

The developing premature infant gut microbiome is a major factor shaping the microbiome of neonatal intensive care unit rooms

The paper investigates how the gut microbiome of premature infants shapes the microbial composition of NICU rooms over time.

Hospitalized premature infants are colonized by related bacterial strains with distinct proteomic profiles

This study examines microbial colonization in premature infants, finding distinct proteomic profiles among related bacterial strains and correlations with NEC development.

Asymmetric MukB ATPases are regulated independently by the N- and C-terminal domains of MukF kleisin

The paper shows that MukF's N- and C-terminal domains independently regulate the two MukB ATPases in the MukBEF complex, forming an asymmetric tripartite structure during ATP cycles.

Co-operation, competition and crowding: a discrete framework linking Allee kinetics, nonlinear diffusion, shocks and sharp-fronted travelling waves

The paper develops a discrete model of invasion processes with different birth, death, and movement rates for individuals in or out of the bulk population, showing shock-fronted travelling waves under strong Allee effect and nonlinear diffusion.