M. L. Smith

Short lifespan is one's fate, long lifespan is one's achievement: lessons from Daphnia

This study examines baseline longevity of Daphnia magna clones under various conditions, finding strong genotype-by-environment interactions and differences in lifespan extension responses to caloric restriction.

Selection leads to false inferences of introgression using popular methods

This study shows that popular methods for detecting migration can falsely infer introgression when selection is present, highlighting the need for more robust methods.

Resolving haplotype variation and complex genetic architecture in the human immunoglobulin kappa chain locus in individuals of diverse ancestry

The paper uses long-read sequencing to resolve haplotype variation and genetic architecture in the human IGK locus across diverse ancestries, identifying novel variants and population-specific allele frequencies.

Honey bees perform fine-scale detailing that continuously reduces comb area after nest expansion

Honey bees continuously reduce comb area after nest expansion by trimming edges, showing dynamic nest modification beyond initial construction.

Virally induced lipid droplets are a platform for innate immune signalling complexes

This study shows that virally induced lipid droplets host antiviral signaling proteins and undergo dynamic proteome and lipidome changes to support innate immune responses.

Honey bee drones are synchronously hyperactive inside the nest

This study tracks honey bee drones inside the nest and finds they exhibit synchronized hyperactivity in the afternoon, influenced by weather and social cues.

Phylogenetic inference using Generative Adversarial Networks

This paper introduces phyloGAN, a GAN for phylogenetic inference, and evaluates its performance on small-scale datasets.

Deep learning for histopathological subtyping and grading of lung adenocarcinoma

This study develops CNNs to subtype and grade lung adenocarcinoma, achieving high accuracy and outperforming most pathologists in grading prediction.

FLAIRR-seq: A novel method for single molecule resolution of near full-length immunoglobulin heavy chain repertoires

FLAIRR-seq provides high-resolution, single-molecule characterization of immunoglobulin heavy chain repertoires, including constant region features, and identifies novel alleles.

Multistate structures of the MLL1-WRAD complex bound to H2B-ubiquitinated nucleosome

The paper determines structures of the MLL1-WRAD complex bound to H2B-ubiquitinated nucleosomes using cryo-EM and mass spectrometry-crosslinking, revealing multiple states and the role of ubiquitin in complex assembly.

A BALB/c IGHV Reference Set, defined by haplotype analysis of long-read VDJ-C sequences from F1 (BALB/c / C57BL/6) mice

The paper defines a BALB/c IGHV reference set by analyzing long-read VDJ-C sequences from F1 mice, identifying strain-specific variations and germline alleles not present in existing genome references.

Using all gene families vastly expands data available for phylogenomic inference

The paper evaluates the impact of using all gene families instead of single-copy orthologs in phylogenomic analysis, finding increased data availability and consistent results across methods and datasets.

Learning to embed lifetime social behavior from interaction dynamics

The paper introduces a temporal matrix factorization model to learn temporally consistent functional roles from social interaction networks in honey bees, enabling comparison of individual roles across time and colonies.

The dominant axes of lifetime behavioral variation in honey bees

This study quantifies behavioral variation in honey bees over their lifetimes and under environmental changes, identifying two dominant behavioral axes and showing individual consistency and colony-level adaptability.

Deep oncopanel sequencing reveals fixation time- and within block position-dependent quality degradation in FFPE processed samples

This study identifies FFPE processing errors in oncology panel sequencing by analyzing variants from technical artifacts in FFPE samples with varying fixation times and block positions.

Social networks predict the life and death of honey bees

The paper develops a method to predict honey bee task allocation, survival, and behavior using social network descriptors without interfering with colonies.

The frequency and topology of pseudoorthologs

This paper models the probabilities and topologies of pseudoorthologs in a three-taxon species tree, showing they are rare and unlikely to mislead phylogenetic inference.

A comparison of immunoglobulin IGHV, IGHD and IGHJ genes in wild-derived and classical inbred mouse strains

The paper compares immunoglobulin gene diversity in wild-derived and classical inbred mouse strains, finding novel alleles and highlighting genetic complexity in IGH loci.

Clonal evolution and genome stability in a 2,500-year-old fungal individual

The paper estimates the age and size of a long-lived fungal individual and reports low mutation rates in its somatic cells over 2,500 years.

Tensional homeostasis in multicellular clusters: effects of geometry and traction force dynamics

This study investigates how cluster size and focal adhesion dynamics affect traction field variability in multicellular clusters, finding that cluster size has a major influence while shape has a minor effect.

Disentangling the process of speciation using machine learning

This paper introduces delimitR, a machine learning tool for inferring species boundaries and evaluating speciation processes using genomic data.