Winston Timp

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

The paper identifies a bimodal m6A code in cardiac development, showing how m6A stoichiometry and context regulate metabolic switches and gene expression.

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

The paper shows that human centromeres and neocentromeres evolve epigenetically, with instability linked to loss of heterochromatin boundaries and CENP-A overexpression.

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.

The paper uses a complete diploid human genome to study centromeric chromatin organization, revealing that DNA methylation regulates centromere structure and plasticity.

The paper uses long-read RNA sequencing to study dynamic mRNA isoform changes during human retinal organoid development, revealing splicing patterns and allelic imbalance.

The paper shows CTCF controls chromatin boundary permeability through a dynamic conformational ensemble, not static occupancy, influencing cohesin capture probabilities.

This paper introduces a 'write-and-read' framework using synthetic DNA modifications to enable nanopore sequencing to detect chemically altered nucleotides and expand the sequence alphabet.

The paper analyzes long-read sequencing data from the All of Us Research Program to identify structural variants and their associations with diseases in a large cohort of Black or African American participants.

This study uses single-cell long-read sequencing to profile experience-induced gene and isoform expression in mouse hippocampal cells, identifying 1,266 experience-variable isoforms.

The paper introduces a method to detect protein-DNA binding in single molecules using antibody-guided methylation, generating identifiable methylation patterns near binding sites.

This study presents three chromosome-level genome assemblies of Lomentospora prolificans, revealing a chromosomal translocation event between strains.

Uncalled4 improves nanopore signal alignment for DNA and RNA modification detection, identifying more modifications than existing tools in human cell lines.

This study uses single-cell RNA sequencing to show that clonal CHO-K1 cells exhibit subpopulation heterogeneity in production stability over time.

The paper introduces a new soft decoder for nanopore sequencing that improves throughput and read density while maintaining low error rates for DNA and RNA.

The paper uses long-read sequencing to identify structural variants and their impacts on gene expression and methylation in diverse human brain samples.

This study uses Tn-seq to analyze genetic and epigenetic variation in Candida glabrata strains, revealing structural differences, resistance mechanisms, and subtelomeric chromatin accessibility.

The paper produces a high-quality genome sequence for whitebark pine and identifies NLR genes associated with resistance to white pine blister rust.

This study shows LARP1 binds free ribosomal subunits to repress TOP mRNAs, coordinating ribosome protein synthesis with cellular demand.

The paper develops a pooled library screening method with a Bayesian approach to improve prediction of split protein behavior using light-inducible Cre recombinase.

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

This study uses nanopore sequencing to show that mtDNA deletion mutations increase exponentially with age and map to a wider genomic region, with novel algorithms improving detection accuracy.

This study presents a genome and transcriptome analysis of ruby-throated hummingbirds, identifying metabolic adaptations related to energy turnover and glucose regulation.

The paper describes a method using in vitro transcribed guideRNAs for targeted nanopore sequencing to study structural variations in pancreatic cancer cell lines.

This paper develops a scalable protocol for Oxford Nanopore long-read sequencing, achieving high SNP and structural variant detection with haplotype-resolved methylation calls, suitable for large-scale genomics projects.

The paper introduces modbamtools, a tool for analyzing single-molecule epigenetic data, enabling visualization, manipulation, and downstream analysis of base modifications in long-read sequencing data.

This paper introduces a method to sequence mtDNA using Cas9-guided adaptor ligation and nanopore long reads, enabling mutation phasing and detection of age-induced deletions in a patient with mtDNA-linked syndrome.

The paper uses a complete human genome assembly to analyze epigenetic patterns in previously uncharacterized genomic regions, revealing methylation and chromatin accessibility features in satellite DNA and centromeres.

A gapless 3.055 billion bp human genome from HiFi and ultra-long nanopore reads resolves all centromeric arrays and acrocentric p-arms, adding 182 Mbp of new sequence.