Sara Goodwin

A comprehensive assessment of tandem repeat genotyping methods for Nanopore long-read genomes

This paper benchmarks 7 TR genotyping tools using Nanopore long-read data, finding that no single tool is best across all metrics, and that sequence-level accuracy is crucial for clinical and population studies.

Multi-site Assessment of Methods for Cell Preservation Upstream of Single Cell RNA Sequencing

This study evaluates three cell preservation methods for scRNA-seq across multiple sites, showing concordant cell type results but platform-specific gene expression differences and better granulocyte retention with preservation methods.

Gapless assembly of complete human and plant chromosomes using only nanopore sequencing

This paper demonstrates that ONT Duplex sequencing combined with Pore-C data can assemble complete, high-quality human and plant chromosomes with base accuracy over 99.999%.

Nanopore sequencing of 1000 Genomes Project samples to build a comprehensive catalog of human genetic variation

The paper uses long-read sequencing on 100 samples from the 1000 Genomes Project to identify structural variants and improve understanding of human genetic variation.

Solanum pan-genomics and pan-genetics reveal paralogs as contingencies in crop engineering

The paper uses pan-genomics and genome editing in Solanum to show that paralog diversification hinders genotype-phenotype predictability in crop domestication.

Exploring the genetic and epigenetic underpinnings of early-onset cancers: Variant prioritization for long read whole genome sequencing from family cancer pedigrees

This study uses long-read whole genome sequencing from family cancer pedigrees to prioritize genetic variants in early-onset cancers, identifying potential disease-causing mutations.

Using deep long-read RNAseq in Alzheimer's disease brain to assess medical relevance of RNA isoform diversity

The paper uses long-read RNAseq to identify new RNA isoforms in Alzheimer's disease brain tissue and demonstrates their medical relevance.

Gene recoding by synonymous mutations creates promiscuous intragenic transcription initiation in mycobacteria

The paper shows that synonymous mutations in mycobacteria can create new transcription start sites within genes, leading to smaller protein isoforms.

Long-read sequencing reveals rapid evolution of immunity- and cancer-related genes in bats

This study uses long-read sequencing to analyze immune and cancer-related gene evolution in bats, finding gene contractions, expansions, and positive selection linked to their unique traits.

The genome of the Wollemi pine, a critically endangered living fossil unchanged since the Cretaceous, reveals extensive ancient transposon activity.

The paper presents the genome of the Wollemi pine, revealing ancient transposon activity and insights into its conservation and evolutionary history.

ACME: an Affinity-based Cas9 Mediated Enrichment method for targeted nanopore sequencing

ACME improves targeted nanopore sequencing by increasing enrichment, depth, and read coverage for specific genomic regions.

High resolution copy number inference in cancer using short-molecule nanopore sequencing

This paper demonstrates that sequencing short DNA molecules with nanopore sequencing improves copy number inference in cancer, offering higher sensitivity and accuracy compared to traditional methods.

Comprehensive analysis of structural variants in breast cancer genomes using single molecule sequencing

This study uses long-read sequencing to identify structural variants in breast cancer genomes, showing high accuracy and sensitivity compared to short-read methods.

Management, Analyses, and Distribution of the MaizeCODE Data on the Cloud

The paper describes the development of a cloud-based platform for managing, analyzing, and distributing MaizeCODE data, enhancing reproducibility and accessibility.

Whole Genome Sequencing and Assembly of the Asian Honey Bee Apis dorsata

This study sequenced and assembled the genome of the Asian honey bee Apis dorsata, identifying unique genes and transposable elements associated with its defensive behavior.

Fast and accurate reference-guided scaffolding of draft genomes

RaGOO rapidly and accurately scaffolds draft genomes using a reference genome, achieving chromosome-scale assemblies and identifying structural variants in tomato and Arabidopsis thaliana.

Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line

The paper uses long-read sequencing to analyze structural variations in the SK-BR-3 breast cancer cell line, revealing complex rearrangements and novel gene fusions.

Oxford Nanopore Sequencing, Hybrid Error Correction, and de novo Assembly of a Eukaryotic Genome

The paper develops a hybrid error correction method for Oxford Nanopore reads and produces a highly contiguous and accurate de novo assembly of the S. cerevisiae genome.