Michael Hiller

This study benchmarks DNA polymerases for long-read sequencing and genome assembly, finding that combining polymerases improves assembly quality and variant calling accuracy.

The paper tests a putative cis-regulatory element near Shox2 in jerboas to see if it affects mouse limb bone length, finding no detectable phenotype.

The paper presents a high-quality genome assembly of the sea stickleback and reveals chromosomal fusions and fissions that reshape understanding of karyotype evolution in sticklebacks.

The paper examines gene-level convergence in placental mammals during evolutionary shifts in torpor and finds that individual genes have low explanatory power, while pathway-level convergence is slightly stronger.

This study integrates genomics and transcriptomics to identify molecular changes in vampire bats adapted to blood-feeding, revealing shifts in gene expression and function across multiple biological pathways.

TOGA2 improves gene annotation and ortholog identification across vertebrate genomes, achieving higher completeness and accuracy than existing methods.

The Vertebrate Genomes Project Phase I provides high-quality reference genomes for 816 species, enabling evolutionary and conservation insights across vertebrates.

The paper uses whole-genome phylogenomic and synteny data to resolve the evolutionary origin of flatfish body asymmetry, finding strong support for a single origin.

The paper uses genomic data to determine whether flatfish asymmetry evolved once or multiple times, finding strong support for a single origin.

The paper shows that prolonged stemness in the tail of Japanese eels drives extreme axis segmentation through delayed Hox13 activation and sustained Oct4 expression.

This study presents seven reference genomes of side-necked turtles, revealing chromosomal dynamics, sex chromosome evolution, and molecular mechanisms underlying skeletal innovation and cancer resistance.

This study investigates the thermogenic adaptations of antelope ground squirrels by analyzing their genome and transcriptome under cold exposure, revealing a shift toward shivering thermogenesis.

The paper identifies convergent and lineage-specific genomic changes in sugar-feeding birds through genome and transcriptome analyses, revealing adaptive mechanisms in metabolic pathways.

The paper tests ancestral diet in Phyllostomidae bats using phylogenetic models, finding support for ancestral omnivory and early evolution of fruit feeding.

The paper compares bat and mouse limb development using single-cell analyses to show how a conserved gene program is repurposed in bat wing formation.

The paper presents haplotype-resolved genomes of six ape species with high accuracy and provides comparative analyses to study evolutionary diversity and gene family evolution.

The paper demonstrates long-read sequencing and genome assembly of ethanol-preserved samples, including challenging organisms like the maned sloth, achieving a 3.1 Gb assembly.

The paper identifies and resolves false population size peaks in PSMC analyses, showing they result from parameter settings and not true population dynamics.

This study examines the evolutionary patterns of dormancy across 1,338 endotherms and finds it is part of a continuum with weak associations to physiological and environmental traits.

This study presents a haplotype-resolved genome and population genomic analysis of the garden dormouse, revealing population structure and isolation patterns that inform conservation strategies.

The paper identifies gene expression differences in jerboa hindfoot muscle loss by comparing intra- and inter-species muscle data, revealing pathways linked to muscle atrophy and potential parallels with human muscle disorders.

This paper introduces GISMO and GISMO-mis metrics to quantify gene loss and missense variation across mammals, identifying essential genes and improving gene-disease associations.

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

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

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

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

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.

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

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.

This paper presents a haplotype-resolved genome assembly of the Nile rat, revealing unique genomic features relevant to type 2 diabetes and metabolic dysfunctions.