Abigail Lind

A novel clonal and axenic isolation pipeline for the human gut protist Blastocystis reveals within-subtype strain coexistence

This study develops a new cultivation method for Blastocystis, revealing that multiple strains can coexist within a single host.

Quantitative detection of gut microbial eukaryotes with EukDetect2 reveals global distribution of commensal protists and association with distinct microbial community structure

EukDetect2 improves eukaryote detection in metagenomes with a larger database and quantitative metrics, revealing Blastocystis and Dientamoeba as prevalent gut eukaryotes.

Vocal learning-associated convergent evolution in mammalian proteins and regulatory elements

The paper identifies proteins and regulatory elements associated with vocal learning by analyzing bat neural activity and epigenomic data.

Integrating gene annotation with orthology inference at scale

TOGA integrates gene annotation and orthology inference across hundreds of genomes, improving ortholog detection and creating large comparative gene resources.

Relating enhancer genetic variation across mammals to complex phenotypes using machine learning

A machine learning approach identifies enhancer-phenotype associations across mammals, revealing links to brain size and behavior evolution.

Insights into mammalian TE diversity via the curation of 248 mammalian genome assemblies

The paper curates TE content in 248 mammalian genomes, finding trends in recent TE accumulation and associations with dietary habits.

Evolutionary constraint and innovation across hundreds of placental mammals

A 240-species placental mammal alignment resolves constraint to single bases, estimating at least 10.7% of the human genome is constrained, with 48.5% of constrained bases unannotated.

Title: Leveraging Base Pair Mammalian Constraint to Understand Genetic Variation and Human Disease

The paper uses evolutionary constraint scores to identify functional genomic regions and finds they are enriched for variants associated with common diseases.

Chiropterans are a hotspot for horizontal transfer of DNA transposons in Mammalia

The paper identifies bats as a hotspot for horizontal transfer of DNA transposons, finding over 200 putative elements and shared transposons across mammals and reptiles.

Accurate and sensitive detection of microbial eukaryotes from whole metagenome shotgun sequencing

EukDetect identifies microbial eukaryotes in shotgun metagenomic data, revealing their distribution in the human gut and Baltic Sea, and their transcriptional activity in stool samples.

A high-resolution, chromosome-assigned Komodo dragon genome reveals adaptations in the cardiovascular, muscular, and chemosensory systems of monitor lizards

The paper presents a high-resolution chromosome-assigned genome of the Komodo dragon, identifying adaptations in cardiovascular, muscular, and chemosensory systems through comparative genomics.

A robust phylogenomic timetree for biotechnologically and medically important fungi in the genera Aspergillus and Penicillium

The paper constructs a robust phylogenomic timetree for Aspergillus and Penicillium fungi using multiple genome datasets and phylogenetic methods to identify incongruent branches and estimate divergence times.

Drivers of genetic diversity in secondary metabolic gene clusters within a fungal species

This study identifies five types of genetic variation in secondary metabolic gene clusters across 66 strains of Aspergillus fumigatus and links them to evolutionary drivers like mutation, recombination, and horizontal gene transfer.