Federica Di Palma

Genome-wide chromatin accessibility during early embryogenesis in a generalist cichlid fish

This study maps genome-wide chromatin accessibility in A. calliptera embryos across three stages, revealing dynamic changes in regulatory elements and transcription factor activity during early development.

Evolution of chromatin accessibility associated with traits of cichlid phenotypic diversity

This study links chromatin accessibility divergence to phenotypic diversity in cichlid fishes by analyzing ATAC-seq and transcriptomes across multiple tissues and species.

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.

Genome-wide characterisation of pathogenicity-related proteins in Mycena citricolor, the causal agent of the American Leaf Spot in coffee

This study identifies pathogenicity-related genes in Mycena citricolor by comparing its genome to saprophytic relatives, finding expanded virulence factor copies and candidate genes involved in plant interaction.

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.

Chromatin accessibility associated with aquaculture relevant traits in tilapia

The paper identifies regulatory variants associated with aquaculture traits in tilapia using ATAC-seq and genetic data.

Evolution of miRNA binding sites and regulatory networks in cichlids

The paper investigates miRNA and TF binding site evolution in cichlids, linking regulatory site turnover to GRN rewiring and adaptive traits.

A new genome allows the identification of genes associated with natural variation in aluminium tolerance in Brachiaria grasses

This study identifies genes and molecular responses associated with aluminium tolerance in Brachiaria grasses using a new reference genome and QTL analysis.

Sequencing smart: De novo sequencing and assembly approaches for non-model mammals.

The paper evaluates de novo genome assembly methods for a low-quality non-model mammal sample, finding that more data types do not always improve assembly quality.

Regulatory network analysis of Paneth cell and goblet cell enriched gut organoids using transcriptomics approaches

The paper uses transcriptomics and network analysis to study regulatory networks in Paneth and goblet cell enriched gut organoids, identifying key regulators and their links to inflammatory bowel disease.

A Galaxy-based training resource for single-cell RNA-seq quality control and analyses.

The paper develops Galaxy-based tools for scRNA-seq quality control and analysis, making the process more accessible through simple scripts and a user-friendly interface.

A quantitative model for characterizing the evolutionary history of mammalian gene expression

The paper uses an OU process to model gene expression evolution across mammals and identifies expression pathways under different selection pressures.

Integrative analysis of Paneth cell proteomic and transcriptomic data from intestinal organoids reveals functional processes dependent on autophagy

The paper integrates proteomic and transcriptomic data from intestinal organoids to identify autophagy-dependent processes in Paneth cells, showing that autophagy impairment affects protein abundance and key cellular functions.

An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations.

W2RAP: a pipeline for high quality, robust assemblies of large complex genomes from short read data

The paper introduces a pipeline for generating high-quality genome assemblies from short read data, demonstrating its effectiveness on plant and human datasets.