Luis F. Paulin

The paper analyzes genetic variation, ancestry, and DNA methylation in Hispanic/Latino participants using long-read sequencing, identifying novel variants and phenotype associations.

SniffCell assigns somatic variants to cell types using DNA methylation from bulk long-read sequencing, revealing cell-type-specific mutations in human tissues.

T2T-HG002v1.1, a complete diploid HG002 assembly lacking detectable errors over 99.4% of its length, enables genome-based benchmarking of assemblies, sequencing reads, and phased variant calls.

This paper presents near-complete, haplotype-resolved assemblies of a pancreatic cancer genome and normal tissue, identifying extensive somatic variants and epigenetic changes in previously excluded regions.

TumorLens detects genetic and epigenetic alterations in cancer using long reads, revealing key somatic events and methylation patterns across tumor samples.

This study evaluates Oxford Nanopore sequencing's performance in clinical genomics using reference samples, showing high accuracy for SNVs and SVs but challenges with INDELs and CNVs.

This study benchmarks machine learning methods for structural variant filtering in long-read sequencing data, finding that simple models match complex ones in accuracy.

TBAS enables cost-effective long-read sequencing of rare-disease trios with high variant detection accuracy and a 77% potential solve rate.

The paper benchmarks somatic structural variant detection at ultra-low allele fractions using synthetic data and evaluates 12 pipelines, finding long-read sequencing provides higher accuracy than short-read methods.

The paper describes a comprehensive genomic dataset from a tumor-normal pair with broad consent, generated using multiple sequencing technologies for benchmarking somatic variant detection.

The paper introduces a CN caller for KIV-2 repeats using short reads, showing high accuracy and demonstrating its correlation with Lp(a) levels and population-specific CN distributions.

This paper presents a long-read sequencing dataset of cancer samples, showing its ability to resolve structural variants, haplotypes, and methylation patterns in precision medicine.

This paper shows that using a complete reference genome improves the accuracy and reduces false positives in detecting structural variants in cancer genomes.

Sniffles2 improves SV detection accuracy and speed, enabling mosaic and population-level SV calling with applications in neurological disorders.

The paper introduces levioSAM2, a method for accurate lift-over between genome assemblies, improving variant calling accuracy when mapping to older references.

The paper investigates DUP-TRP/INV-DUP genomic rearrangements in neurodevelopmental disorders, identifying four SV haplotypes and refining template switching points using multiple sequencing technologies.

The paper presents the complete sequence of a human Y chromosome, correcting errors in the GRCh38 reference and adding over 30 million base pairs.

The paper introduces FixItFelix and a modified GRCh38 reference to improve variant calling and expression analysis in genes with reference errors, showing benefits across multiple sequencing types and populations.

SVhound predicts regions likely to contain novel structural variations by analyzing population-level SV datasets, showing high correlation with full datasets and applicability across species.

This study identifies PARG's role in promoting meiotic DNA break formation and repair in C. elegans, independent of its catalytic activity.