Francisco Pereira Lobo

Common germline polymorphisms and somatic cancer mutations exhibit non-random positional overlap across the human genome

The paper identifies non-random positional overlap between common germline polymorphisms and somatic cancer mutations, suggesting intrinsically vulnerable genomic loci.

Transcription factors SP5 and SP8 drive primary cilia formation

This study identifies SP5 and SP8 as transcription factors that drive primary cilia formation through genetic and transcriptomic analyses in mouse embryos.

Sp Transcription Factors Establish the Signaling Environment in the Neuromesodermal Progenitor Niche During Axial Elongation

The paper identifies Sp5/8 as essential regulators of neuromesodermal progenitor maintenance through their role in sustaining Wnt/Fgf signaling and repressing retinoic acid activity.

Phylogeny-informed transfer learning with protein language models for epitope prediction

This paper improves epitope prediction by using phylogeny-informed transfer learning with protein language models, showing better performance than existing methods.

Phylogeny-aware linear B-cell epitope predictor detects candidate targets for specific immune responses to Monkeypox virus

The paper develops a phylogeny-aware model to predict linear B-cell epitopes for Monkeypox virus, identifying nine specific peptides as potential diagnostic targets.

Phylogeny-aware modeling uncovers molecular functional convergences associated with complex multicellularity in Eukarya

This study identifies molecular functional convergences in complex multicellular eukaryotes by analyzing genomic and phylogenetic data across 49 species.

CALANGO: a phylogeny-aware comparative genomics tool for discovering quantitative genotype-phenotype associations across species

CALANGO identifies genotype-phenotype associations across species by integrating genomic, evolutionary, and phenotypic data to uncover biologically relevant molecular mechanisms.

Cross-species prediction of essential genes in insects through machine learning and sequence-based attributes

This paper develops a machine learning method to predict essential genes in insects using sequence-based attributes, validated on Drosophila and Tribolium, and shows cross-species predictive capability.

Admixture/fine-mapping in Brazilians reveals a West African associated potential regulatory variant (rs114066381) with a strong female-specific effect on body mass- and fat mass-indexes

The paper identifies a West African-associated regulatory variant with a strong female-specific effect on BMI and fat mass in Brazilian admixed populations.

Recounting the FANTOM Cage Associated Transcriptome

The paper presents FC-R2, an expanded transcriptome atlas of over 109,000 genes, including lncRNAs, and demonstrates its utility in analyzing gene expression across normal and diseased human samples.