Alexander V. Predeus

HARP integrates PBMC data from multiple studies to create a reference atlas with consensus annotations and identifies age, sex, and disease-related cellular modules.

The paper presents the Human Gut Cell Atlas v1.0, a unified reference of gut cell diversity, revealing how tissue structure influences cellular composition and enabling disease and organoid analysis.

The paper integrates multiple single-cell and single-nucleus RNA-sequencing datasets to create a comprehensive Human Kidney Cell Atlas, identifying cell types, states, and disease-associated populations.

The paper builds a spatiotemporal map of human pilosebaceous unit development using single-cell multiomics and machine learning, showing how epithelial-mesenchymal interactions drive organogenesis and how sebaceous gland programs are disrupted in tumors.

This paper creates an integrated multimodal atlas of the female reproductive system across the lifespan, identifying cell types and linking them to gynaecological pathologies.

This study creates a comprehensive spatial atlas of the human ovarian cortex, revealing molecular mechanisms of primordial follicle activation and follicle niche organization.

This paper analyzes 100,526 GWAS to identify pleiotropic genes and their therapeutic implications, finding that highly pleiotropic genes are associated with safety liabilities and that combining PAV support with intermediate pleiotropy improves therapeutic success.

Human Developmental Cell Atlas integrates ~4.6 million cells/nuclei from 4-22 post-conception weeks into 454 refined cell types and maps 114 spatial niches across 6PCW whole-embryo sections.

This paper presents a single-cell and spatial proteotranscriptomic atlas of human oral tissues, identifying fibroblasts as key immunoregulatory hubs and revealing changes in disease states.

This study creates a spatially-resolved molecular atlas of human skin and uses deep learning to identify 26 niches, revealing novel immune memory structures in inflammatory skin diseases.

This study identifies that the unique lipopolysaccharide (LPS) of Salmonella Typhimurium ST313 reduces pyroptosis and inflammasome activation in human macrophages, contributing to its pathogenicity.

This study creates a spatial genomics atlas of human skin fibroblasts in health and disease, identifying six major populations and three disease-specific subtypes.

This study investigates pleiotropy across species and trait types, finding common features and selection pressures in highly pleiotropic genes.

The paper integrates single-cell RNA-seq datasets across the GI tract to identify epithelial metaplasia in inflammatory diseases, showing its role in inflammation through immune cell interactions.

The paper integrates exome data from 7,452 Russian samples to create a population-specific allele frequency reference, identifying rare variants and clusters within the Russian population.

This study investigates the role of two type III secretion systems in Providencia alcalifaciens, showing their differential contributions to host interactions and pathogenicity.

This study creates a developmental cell atlas of the human thyroid gland using single-cell sequencing, revealing cell type heterogeneity and its implications in thyroid disorders and cancer.

This study constructs a multiomic atlas of human early skeletal development using single-nuclei transcriptomics, epigenomics, and spatial transcriptomics to uncover regulatory mechanisms and cell states involved in bone and joint formation.

This study evaluates the impact of adapter trimming on germline variant calling accuracy using WGS and WES data, finding negligible effects in most cases and highlighting method-specific dependencies.

This study uses single-cell transcriptomics to map the early placental response to three pathogens in first-trimester human placenta, identifying coordinated inflammatory responses and pathogen-specific effects.

The paper identifies a new sublineage of Salmonella Typhimurium ST313 in Malawi with a gene expression signature and increased fitness compared to its parent lineage.

The paper introduces a method to determine X-inactivation states in single-cell transcriptomes and uses it to infer cellular phylogenies in human females.

The paper benchmarks variant calling pipelines on gold standard datasets, finding DeepVariant performs best and highlighting the need for diverse reference genomes.

This study identifies population-specific protein-truncating variants and introduces LoFfeR, a tool that improves the annotation of low-confidence loss-of-function alleles by filtering more variants with the same false positive rate.

This study systematically evaluates coverage biases in whole-exome and whole-genome sequencing, finding that some WES platforms outperform others and that WES can match WGS in variant discovery.

This study uses GWAS summary statistics to identify pleiotropic loci across the human phenome, revealing shared genetic components and novel genes involved in complex traits.

The paper was withdrawn by the authors due to lack of full consent, and is not intended for citation.

The paper analyzes genomic and phylogenetic data of Salmonella Typhimurium and monophasic variants from Colombia to understand their population structure, evolution, and antibiotic resistance.