Giulio Formenti

The paper generates high-quality genome assemblies for two manta and devil ray species and identifies structural variations linked to pelagic adaptation.

The paper introduces GBZ-base and GAF-base, indexed pangenome file formats for efficient subgraph and alignment extraction.

Across 325 Darwin Tree of Life genomes, satellite-array and transposon-cluster centromeres are phylogenetically scattered, fitting a model of repeated interconversion; satellites share higher-order repeat structure but not sequence.

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 presents a chromosome-level genome assembly for the European leaf-toed gecko, providing a high-quality reference for studying genome evolution and sex chromosome dynamics.

The paper investigates hatching failure in Alala, the Hawaiian crow, after a near-extinction event, identifying recessive lethal haplotypes as the main cause.

This paper presents the first fully phased, diploid, telomere-to-telomere genome of the zebra finch, revealing new genes and structural features.

T2T-HG002v1.1, a complete diploid HG002 assembly lacking detectable errors over 99.4% of its length, enables genome-based benchmarking of assemblies, sequencing reads, and phased variant calls.

This study investigates speciation in boobies through genomic analysis, finding introgression, divergence patterns, and a neo-sex chromosome linked to coloration diversity.

This paper introduces CAD-C, a new chromatin conformation capture method that improves resolution and efficiency over existing techniques like Micro-C and Hi-C.

This study analyzes interspecies variation in the 45S rDNA locus across vertebrates, revealing lineage-specific differences in organization, copy number, and sequence evolution.

The paper shows processed pseudogenes are dynamic evolutionary elements, not inert, and links their abundance to life-history traits and cancer-related dynamics across vertebrates.

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

The paper identifies convergent evolution of a plant supergene through multiple genomic architectures, showing the same gene is duplicated and co-opted independently in different species.

The paper assesses climate adaptation in Canada lynx populations at their southern trailing edge using genomic data, identifying adaptive loci and highlighting conservation risks.

The paper analyzes chromosome 22q11.2 haplotypes to show how structural variations in specific regions correlate with microdeletion and inversion risks across populations.

The paper presents the first telomere-to-telomere diploid reference genome of the human embryonic stem cell line H9, revealing genomic features and ancestry.

The paper introduces TTT, an algorithm that resolves assembly graph tangles in genomes, improving the accuracy of complex regions in reference assemblies.

The paper uses long-read sequencing to identify pathogenic variants in autism cases, finding three pathogenic mutations and nine candidate structural variants missed by short-read sequencing.

The paper identifies genomic and transcriptomic changes associated with chromosomal instability and seasonal brain size plasticity in the Eurasian common shrew.

The paper identifies a diverse and variable odorant receptor repertoire in birds, including the kiwi, and reveals gene conversion as a mechanism for generating functional diversity in avian olfaction.

The paper analyzes non-B DNA motifs in bird genomes, showing differences in distribution across chromosome types and their potential regulatory roles, while highlighting sequencing challenges.

The paper presents the first chromosome-level genome assembly of the Brazilian merganser, revealing genomic features and population history insights.

The paper introduces rdeval, a tool for efficiently evaluating and visualizing sequencing read metrics, showing improvements in read quality and genome assembly with PacBio data.

The paper shows that placental phenotypes in mammals can be predicted from miRNA repertoires with high accuracy, revealing constrained genetic pathways for convergent evolution.

This study presents a comprehensive mtDNA phylogeny of the barn swallow, identifying new haplogroups, gene flow, and divergence times across all recognized subspecies.

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 describes the European Reference Genome Atlas (ERGA) pilot project, which tests a decentralized model for producing high-quality reference genomes across 98 European species.

The paper presents a reference genome assembly for the Violet Carpenter Bee, including gene annotation and mitochondrial genome, as part of the European Reference Genome Atlas.

This paper presents a new chromosome-scale genome assembly of Littorina saxatilis with improved contiguity and completeness, enabling better study of chromosomal inversions and their role in speciation.