Alicia Oshlack

The paper compares RNA sequencing protocols using long-read sequencing, finding significant changes in isoform structure and abundance due to RNA processing steps.

This study uses scRNA-seq on amniotic fluid to create a cell atlas of healthy fetal cells, revealing gestational age-related changes in cell composition and gene expression.

This study shows that ambient RNA correction can reduce doublet detection accuracy and recommends detecting doublets before correction, except when using CellBender.

The paper introduces a probe-based workflow to detect oncogenic gene fusions in single-cell RNA-seq, validated in cancer cell lines and pediatric B-ALL cohorts.

barbieQ is an R package for analysing barcode count data from clonal tracking experiments, providing statistical tests for differential barcode proportion and occurrence.

This study benchmarks normalization methods for differential binding analysis in CUT&RUN, finding data-driven normalization to be most robust and highlighting variable performance of spike-in normalization.

This paper develops a large biobank of patient-derived MOC organoids and screens them for drug efficacy, finding resistance to standard therapies and effectiveness of less commonly used drugs.

This study benchmarks Nanopore long read RNA sequencing in human cell lines, showing improved isoform resolution compared to short reads.

Damsel provides an R package for end-to-end analysis of DamID sequencing data, including quantification, testing, and visualization of protein-DNA interactions.

TALLSorts classifies T-ALL samples using bulk RNA-seq data with high accuracy across four international cohorts.

This study benchmarks seven HTO demultiplexing tools using datasets with genetic variant-based ground truth, finding similar performance on high-quality data but poor performance on lower quality data for bimodal distribution methods.

Toblerone detects exon deletions in RNA-seq data, specifically applied to IKZF1 in B-ALL samples, identifying deletions associated with poor prognosis.

propeller tests for differences in cell type proportions between experimental conditions using scRNA-seq data, showing significant changes in heart development, ageing, and COVID-19 severity.

The paper uses scRNA-seq and flow cytometry to identify novel immune and epithelial cell populations in preschool CF patients' bronchoalveolar lavage.

STRipy simplifies STR genotyping in HTS data by providing a user-friendly tool that targets all known disease-causing STRs and handles long alleles.

JAFFAL detects fusion genes from long-read transcriptome sequencing with high accuracy, outperforming existing methods and enabling single-cell resolution.

splatPop simulates population-scale scRNA-seq data with eQTL effects and batch effects for method testing.

MINTIE identifies novel structural and splice variants in transcriptomes using RNA-seq data, outperforming existing methods in detecting a wide range of variants.

ALLSorts classifies B-ALL samples into 18 subtypes and five meta-subtypes using RNA-Seq data with high accuracy.

This paper introduces SuperFreq, a method to detect copy number alterations from RNA-Seq data, showing high agreement with DNA-based calls in cancer genomes.

The paper introduces two new methods for gene set testing in DNA methylation data and shows they outperform existing approaches.

Sierra identifies differential transcript usage from polyA-captured scRNA-seq data, validated against bulk RNA-seq and showing 3UTR shortening in cardiac fibroblasts.

This study evaluates four short tandem repeats genotyping tools on whole exome sequencing data, finding varying performance based on repeat type and filtering parameters.

SuperFreq detects mutations and tracks clones in cancer samples without requiring matched normal samples, achieving high accuracy in identifying clones and mutations.

Bazam extracts and realigns high throughput sequencing data efficiently, reducing realignment time by up to 90% compared to standard methods.

This paper introduces a pooled-parent exome sequencing strategy to prioritize de novo variants in genetic disease, showing it effectively filters variants while reducing costs.

The paper introduces a method for differential transcript usage analysis using equivalence class counts, showing comparable sensitivity and speed to exon-level counts.

The paper uses single-cell RNA-seq to analyze developing mouse kidney and human kidney organoids, identifying cell clusters and revealing insights into kidney development and organoid maturation.

Ximmer improves CNV calling accuracy and consistency from exome data through systematic quality control, parameter adjustment, and confidence calibration.

STRetch detects pathogenic short tandem repeat expansions in whole genome sequencing data, revealing novel disease-causing STRs with low false discovery rate.