Tomi Pastinen

The paper uses long-read sequencing to analyze telomere inheritance patterns in human trios, finding parent-of-origin effects and heritable influences on telomere length.

Owl quantifies microsatellite instability from long-read data, identifying MSI-high genomes and motif-specific patterns in cancer samples.

The paper introduces a data model and dataset for rare disease research, enabling interoperable multi-omic data integration across clinical sites.

This study presents a comprehensive bulk and single-cell transcriptional dataset of 69 pediatric leukemia patients, demonstrating its utility in improving leukemia characterization and clinical testing.

DeepSomatic is a deep learning method for detecting somatic variants from short-read and long-read sequencing data, outperforming existing callers, especially for indels.

The paper expands the human genomic imprinting map using long-read sequencing and GWAS integration, revealing new disease-associated loci and maternal/paternal imprinting patterns.

The paper identifies altered sperm DNA methylation in overweight men linked to transposable element regulation and potential impacts on offspring neurodevelopmental risks.

The paper characterizes the structural variation and diversification of the NPIP gene family in humans using long-read sequencing and identifies evidence of positive selection and novel gene models.

Severus detects and characterizes somatic structural variations in tumor genomes using long reads, outperforming existing methods in accuracy and revealing clinically relevant rearrangements.

This paper expands methylome analysis and detects quantitative trait loci by long-read sequencing of personal DNA, revealing tens of thousands of methylation QTLs associated with structural variants.

STRkit is a software tool for accurate STR genotyping using long reads and single-nucleotide variants, achieving high F1 scores and Mendelian inheritance rates.

The paper develops Paraphase, a HiFi-based method to resolve highly similar paralogous genes, revealing genetic diversity and de novo events in segmental duplications.

The paper analyzes segmental duplications in human genomes using long-read sequencing, identifying structurally polymorphic events and novel genes associated with copy number variation.

StarPhase diplotypes 21 pharmacogenes using long-read sequencing with high accuracy, updating 26.2% of existing diplotypes and highlighting gaps in pharmacogenomic databases.

This study shows that HiFi long-read sequencing can detect clinically relevant structural variants in pediatric leukemia, improving subtype classification.

The paper investigates the expansion, selection, and hypervariability of the TBC1D3 gene family in humans using long-read sequencing data, revealing multiple duplications, copy number variation, and expression patterns.

This study quantifies polygenic liability in rare disease probands and finds associations between rare disease phenotypes and polygenic scores, supporting complex trait influences on Mendelian variant interpretation.

The paper introduces OSMP, a tool for one-sided genomic matchmaking in rare disease patients, which efficiently filters variant occurrences to prioritize clinically relevant matches.

The paper identifies a common flanking variant linked to increased meiotic stability at the FGF14-SCA27B repeat locus.

The paper uses long-read whole genome sequencing and polygenic scores to identify structural variants linked to rare diseases and prioritize candidate genes for functional validation.

The paper introduces EpiVar Browser, a tool for exploring epigenomics data under controlled access, enabling genotype-chromatin phenotype analysis without releasing identifiable information.

The paper uses pangenome graphs to improve detection of rare structural variants in a rare disease cohort, identifying novel diagnostic variants.

The paper uses HiFi sequencing to identify hypermethylation outliers in a rare disease cohort, finding allele-specific loss of regulatory elements linked to disease.

The paper introduces TRGT, a tool for tandem repeat genotyping, and a database of 937,122 TRs across 100 genomes, achieving high concordance and detecting repeat expansions, methylation, and mosaicism.

The paper uses genome graphs to detect polymorphic mobile elements in active epigenomic states during influenza infection, revealing novel peaks and modifying quantitative trait loci estimates.

This paper describes a platform for generating patient-derived organoids to evaluate personalized antisense oligonucleotide therapeutics for rare diseases, showing reversal of disease phenotypes in Duchenne muscular dystrophy models.

The paper identifies monoallelic DHX9 variants as a cause of neurodevelopmental disorders and Charcot-Marie-Tooth disease, showing genotype-phenotype correlations and cellular dysfunction.

This paper develops a single-molecule long-read sequencing method to detect single-strand DNA mismatches and damage, revealing their relationship to double-strand mutations and providing insights into mutation mechanisms in cancer and aging.

The paper develops Paraphase, a method using long-read sequencing to accurately determine SMN1 and SMN2 haplotypes and copy numbers, improving silent carrier detection in spinal muscular atrophy.

The paper identifies differentially methylated regions in children after liver transplant that are associated with rejection, highlighting immune-related pathways and potential therapeutic targets.