A. Lambert

Novel Methylation Markers in a Prostate Cancer Cohort are Associated with Disease Development and Relapse

The paper identifies novel methylation markers in a prostate cancer cohort associated with disease development and relapse, showing their predictive power for recurrence.

Protein restriction associated with high fat induces metabolic dysregulation without obesity in juvenile mice

This study shows that a Western diet with protein restriction in juvenile mice causes metabolic dysregulation without obesity, including hyperglycemia and fatty liver.

Persistent, Private and Mobile genes: a model for gene dynamics in evolving pangenomes

This paper introduces a model for bacterial pangenome evolution and applies it to Salmonella genomes to classify genes based on their evolutionary dynamics.

Hotwiring integrin endocytosis acutely modulates cell interactions

This study uses hot-wired endocytosis to acutely downregulate 5{beta}1 integrins, showing reduced cell area, fibronectin uptake, and slower tumor spheroid compaction.

Phenomics demonstrates cytokines additive induction of epithelial to mesenchymal transition

The paper uses single cell phenomics to show that combining cytokines additively enhances EMT in cancer cell lines, regardless of their baseline EMT state.

How demography shapes linkage disequilibrium with or without recombination

The paper analyzes how demographic factors influence linkage disequilibrium measures under different recombination scenarios and provides recommendations for their use.

Opening the species box: What parsimonious microscopic models of speciation have to say about macroevolution

This paper argues that parsimonious microscopic models of speciation are needed to understand macroevolution, but too detailed models fail to make robust predictions.

The balance between shear flow and extracellular matrix in ovarian cancer-on-chip

This study uses an ovarian tumor-on-chip to investigate how extracellular matrix and shear stress influence tumor cell migration and phenotype, showing ECM's dominant role in migration modes and EMT transition.

Intra-prostatic tumour evolution, steps in metastatic spread and histogenomic associations revealed by integration of multi-region whole genome sequencing with histopathological features

This study integrates multi-region whole genome sequencing with histopathological data to reconstruct tumour phylogenies and identify molecular steps in prostate cancer progression and metastasis.

Evo-Scope: Fully automated assessment of correlated evolution on phylogenetic trees

Evo-Scope is a fast, automated pipeline to assess correlated evolution on phylogenetic trees, improving previous tools and analyzing antibiotic resistance mutations in Streptococcus pneumoniae.

Interpreting the pervasive observation of U-shaped Site Frequency Spectra

The paper analyzes site frequency spectra across species and finds U-shaped patterns, suggesting that multiple merger coalescent models better fit the data than the standard neutral model.

Topology of connective tissues: a key parameter in cellular heterogeneity, beyond composition and stiffness

This study creates ECM models with varied topology, composition, and stiffness to study their impact on cellular phenotypes, showing EMT shifts are multidimensional and not solely dependent on single ECM features.

High-throughput tuning of ovarian cancer spheroids for on-chip invasion assays

This paper develops a microfabricated invasion assay for ovarian cancer spheroids to study tumor invasion and drug response.

EVI/WLS function is regulated by ubiquitination and linked to ER-associated degradation by ERLIN2

This study identifies ERLIN2 as a link between ubiquitination and ERAD in regulating EVI/WLS stability, independent of WNT production levels.

A minimal yet flexible likelihood framework to assess correlated evolution

This paper introduces a likelihood framework to assess correlated evolution between two traits on a phylogenetic tree, showing it performs well with datasets of fewer than 100 species.

Biochemical and mathematical lessons from the evolution of the SARS-CoV-2 virus: paths for novel antiviral warfare

This paper analyzes the evolution of SARS-CoV-2 using probabilistic modeling to link viral genome composition to mutation patterns and host metabolism interactions.

Eco-evolutionary dynamics of nested Darwinian populations and the emergence of community-level heredity

The paper shows how manipulating population structure can impose Darwinian properties on microbial communities, enabling them to reliably reproduce parental phenotypes through developmental correction.

Testing for population decline using maximal linkage disequilibrium blocks

The paper introduces a population genomics method to detect recent population decline using maximal linkage disequilibrium blocks to assess species conservation status.

The genomic view of diversification

This paper introduces a new framework for modeling gene and species lineage evolution, showing it better explains gene flow-driven incongruences than traditional species tree models.

Model-based inference of punctuated molecular evolution

The paper develops a model to detect episodes of fast divergence in molecular evolution and applies it to snake venom protein genes to identify spikes in the phylogeny.

Statistical inference for the evolutionary history of cancer genomes

This paper compares SFS derived from birth-death processes and coalescent models in cancer evolution, showing they can be made comparable and presents a selective sweep model for tumor history analysis.

Population persistence under high mutation rate: from evolutionary rescue to lethal mutagenesis

The paper studies how high mutation rates affect population persistence, showing that moderate increases can aid evolutionary rescue while larger increases lead to extinction via lethal mutagenesis.

Constriction rate modulation can drive cell size control and homeostasis in C. crescentus

This study shows that constriction rate in C. crescentus affects cell size control and homeostasis by regulating elongation during division and compensating for pre-constriction variation.

Pathogen evolution: slow and steady spreads the best

The paper extends life history evolution theory to account for finite population size effects on pathogen virulence evolution, showing demographic stochasticity alters classical deterministic predictions.

Ranked tree shapes, non-random extinctions and the loss of phylogenetic diversity

The paper introduces a model to simulate phylogenetic diversity loss under extinction risks and applies it to bird clades, showing they fall into a 'thin ice zone' where PD loss is sudden.

Accuracy of demographic inferences from Site Frequency Spectrum: The case of the Yoruba population

The paper assesses the accuracy of demographic inferences from the Site Frequency Spectrum (SFS) in the Yoruba population, finding that simple models outperform flexible ones.

The species problem from the modeler’s point of view

The paper explores the species problem by defining three properties for species partitions and shows that any two can be satisfied while the third cannot, proposing algorithms for constructing phylogenies.