Pedro A. F. Galante

The complete genome of a songbird

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

Transposable elements shape olaparib response according to BRCA1 status in triple-negative breast cancer

This paper shows that olaparib treatment increases transposable element activity in BRCA1-deficient triple-negative breast cancer cells, leading to genomic instability and immune responses.

TEscape: Defining the human transposable element transcriptome using multiplatform long-read sequencing

TEscape uses long-read sequencing to comprehensively annotate the human transposable element transcriptome, identifying over 83,000 previously unannotated isoforms.

Processed pseudogenes as dynamic substrates of vertebrate genome 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: A global reference genome resource

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

Retrocopy formation and domestication shape genome evolution in sloths and other xenarthrans

This study presents chromosome-level genomes for sloths and anteaters, revealing retrocopy formation and domestication as key drivers of xenarthran genome evolution and physiological specializations.

Transcriptomic entropy reveals tissue-specific patterns in aging and predicts cancer progression

This study examines transcriptomic entropy in aging and cancer, finding tissue-specific entropy changes and its association with cancer progression and survival outcomes.

SERBP1 interacts with PARP1 and is present in PARylation-dependent protein complexes regulating splicing, cell division, and ribosome biogenesis

The paper identifies SERBP1 as a protein involved in PARylation-dependent complexes that regulate splicing, cell division, and ribosome biogenesis, with implications for neurodegenerative diseases.

RCPedia: A global resource for studying and exploring retrocopies in diverse species

RCPedia provides a comprehensive database of retrocopies across 44 species, offering genomic annotations, expression data, and query tools for genomic and evolutionary research.

FREDDIE: A comprehensive tool for detecting exonization of retrotransposable elements in short and long RNA sequencing data

FREDDIE detects exonization of retrotransposable elements in RNA-seq data, identifying chimeric transcripts in cancer cell lines and glioblastoma samples.

Retro-miRs: Novel and functional miRNAs originated from mRNA retrotransposition

This study identifies 17 retroduplicated miRNAs (retro-miRs) originating from mRNA retrocopies, showing they are primate-specific, expressed, and involved in cancer.

Sandy: A user-friendly and versatile NGS simulator to facilitate sequencing assay design and optimization

Sandy generates synthetic NGS reads to help design and optimize sequencing assays by simulating various data features and answering key analytical questions.

Mutational signatures and increased retrotransposon insertions in Xeroderma Pigmentosum variant skin tumors

The paper identifies mutational signatures and retrotransposon insertions in XP-V skin tumors, linking them to UV exposure and tobacco use, and suggests immunotherapy potential.

Molecular dynamics analysis of fast-spreading severe acute respiratory syndrome coronavirus 2 variants and their effects in the interaction with human angiotensin-converting enzyme 2

The paper uses molecular dynamics simulations and SPR assays to analyze how SARS-CoV-2 variants bind to the ACE2 receptor and how this affects viral spread.

Whole-genome sequencing of 1,171 elderly admixed individuals from the largest Latin American metropolis (Sao Paulo, Brazil)

This study presents a high-coverage whole-genome sequencing dataset of 1,171 admixed elderly Brazilians, identifying novel variants and demonstrating the utility of WGS for genomic and clinical research in underrepresented populations.

piRNAdb: A piwi-interacting RNA database

piRNAdb is a database that catalogs piRNAs, their targets, and associated gene ontology terms, providing a user-friendly interface for piRNA research.

Reboot: a straightforward approach to identify genes and splicing isoforms associated with cancer patient prognosis

Reboot identifies genes and splicing isoforms linked to cancer patient prognosis using penalized Cox regression and bootstrap methods, validated on glioblastoma and pancreatic adenocarcinoma datasets.

sideRETRO: a pipeline for identifying somatic and dimorphic insertions of processed pseudogenes or retrocopies

sideRETRO identifies and genotypes somatic and dimorphic retroCNVs from whole-genome or whole-exome sequencing data with high accuracy.

Depletion of Ric-8B leads to reduced mTORC2 activity

This study shows that Ric-8B hypomorphism reduces mTORC2 activity in mice, leading to embryonic defects and impaired GPCR/G protein signaling.