Ivo Glynne Gut

This study uses ancient whole-genome data to show geographically structured selection during the Neolithic transition in Western Eurasia, involving both farmer and hunter-gatherer alleles.

This study uses non-invasive genomic sampling to analyze genetic diversity in wild gorillas, revealing population clusters and migration patterns, and predicts geographic origins with high accuracy.

This paper constructs a single-cell atlas of circulating immune cells to understand inflammation across diseases and develops a classifier for inflammatory diseases.

CBIcall provides a configuration-driven framework for standardized variant calling across large sequencing cohorts, ensuring reproducibility and consistency in pipeline execution.

The paper examines transcriptomic responses to thermal stress in shallow and mesophotic red coral populations, finding distinct gene expression patterns suggesting local adaptation influences thermal resilience.

The paper analyzes the genomes of spider monkeys and northern muriquis to assess genetic diversity, load, and divergence, finding no alignment between genetic diversity and endangerment status, higher genetic load in wild populations, and divergence linked to environmental factors.

The paper reanalyzes exome sequencing data from rare disease cases to identify previously undetected copy number variants, resulting in diagnoses for 51 families and partial explanations for 34 individuals.

This study identifies mitochondrial dysfunction and mtDNA damage as early triggers of immune response in PM-Mito and IBM, linking mitochondrial abnormalities to inflammation and disease progression.

FixNCut is a reversible fixation and dissociation method that preserves RNA integrity and cellular composition in human and mouse tissues, enabling robust single-cell and spatial analyses.

The paper presents a chromosome-level genome assembly for the common octopus, O. vulgaris, which spans 2.8 billion basepairs and supports a karyotype of 1n=30 chromosomes.

The paper uses primate genetic data to predict human variant pathogenicity with a deep learning classifier trained on 4.3 million common missense variants.

This study presents whole-genome data from 233 primate species, revealing patterns of genetic diversity, mutation rates, and recurrent missense mutations across primate clades.

The paper maps DNA methylation and transcriptomes across human stomach regions, showing limited transcriptomic regulation by methylation and identifying region-specific transcription factors.

This paper introduces a method to sequence full-length human mitochondrial genomes using Cas9 and long-read sequencing, enabling accurate detection of heteroplasmy and deletion patterns.

The paper summarizes methods and lessons from assembling 16 vertebrate genomes, highlights the importance of long-read sequencing, and introduces the Vertebrate Genomes Project to generate complete reference genomes for all vertebrate species.

The paper analyzes ACE2 gene sequences in strepsirrhine primates to assess their susceptibility to SARS-CoV-2, finding high variability and potential risk in some species.

This study examines 3D genome architecture changes during B cell differentiation and in B cell neoplasias using Hi-C and multi-omic data, revealing dynamic compartment shifts and tumor-specific chromatin reorganization.

SPOTlight integrates spatial transcriptomics with single-cell RNA-seq to deconvolute cell types and states in tissues, showing accurate predictions in mouse brain and human pancreatic cancer.

The paper introduces a framework for assessing the quality of whole genome cancer sequences using a star rating system based on five QC measures, providing a tool for researchers to evaluate and exclude low-quality data.

The paper uses Nanopore sequencing to track antibiotic resistance plasmid evolution and transfer between bacterial species in a hospital setting, identifying plasmid fusion and gene rearrangements.

This study benchmarks 13 scRNA-seq protocols to evaluate their effectiveness in characterizing cell types and states for cell atlas projects.

The paper introduces the Cancer LncRNA Census (CLC), a curated resource of lncRNAs with causative roles in cancer, and shows their genomic and evolutionary features.

ActivePathways integrates multivariate omics data to identify enriched pathways, revealing cancer driver genes and prognostic pathways in breast cancer.

The paper uses single cell transcriptomics to show that transdifferentiation and reprogramming can be uncoupled in pre-B cells based on their intrinsic plasticity.

The paper develops a method to sequence and assemble a human Y chromosome of African origin using native DNA and nanopore sequencing, achieving high continuity and enabling epigenetic modification detection.

The paper identifies DNA methylation oscillations as a marker for enhancer classification, showing high predictive power compared to other methods.

The paper introduces pheno-seq, a method that links morphological features to gene expression in 3D cell cultures, showing its ability to identify morphology-specific genes and regulatory states not captured by scRNA-seq.

The paper introduces GEMBS, a high-throughput processing tool for DNA methylation data from WGBS, aiming to improve efficiency for large datasets.

The paper predicts the first eigenvector of the Hi-C matrix from whole genome bisulfite sequencing data, showing that methylation variability better predicts chromatin compartments than methylation levels.

bigSCale is a scalable framework for analyzing large single-cell RNA sequencing datasets, showing improved speed and accuracy in differential expression analysis and identifying rare cell populations.