Harnessing the Power of Genomics to Understand Disease

Gene set enrichment analysis for genome-wide DNA methylation data

J Maksimovic, A Oshlack, B Phipson

2021-12-01

DNA methylation is one of the most commonly studied epigenetic marks, due to its role in disease and development. Illumina methyla..

Accuracy of short tandem repeats genotyping tools in whole exome sequencing data

A Halman, A Oshlack

2020-01-01

Background: Short tandem repeats are an important source of genetic variation. They are highly mutable and repeat expansions are a..

Single cell analysis of the developing mouse kidney provides deeper insight into marker gene expression and ligand-receptor crosstalk

AN Combes, B Phipson, KT Lawlor, A Dorison, R Patrick, L Zappia, RP Harvey, A Oshlack, MH Little

2019-06-01

Recent advances in the generation of kidney organoids and the culture of primary nephron progenitors from mouse and human have bee..

Bazam: A rapid method for read extraction and realignment of high-throughput sequencing data

SP Sadedin, A Oshlack

2019-04-18

The vast quantities of short-read sequencing data being generated are often exchanged and stored as aligned reads. However, aligne..

Evaluation of variability in human kidney organoids

B Phipson, PX Er, AN Combes, TA Forbes, SE Howden, L Zappia, HJ Yen, KT Lawlor, LJ Hale, J Sun, E Wolvetang, M Takasato, A Oshlack, MH Little

2019-01-01

The utility of human pluripotent stem cell–derived kidney organoids relies implicitly on the robustness and transferability of the..

STRetch: Detecting and discovering pathogenic short tandem repeat expansions

H Dashnow, M Lek, B Phipson, A Halman, S Sadedin, A Lonsdale, M Davis, P Lamont, JS Clayton, NG Laing, DG MacArthur, A Oshlack

2018-08-21

Short tandem repeat (STR) expansions have been identified as the causal DNA mutation in dozens of Mendelian diseases. Most existin..

Clustering trees: a visualization for evaluating clusterings at multiple resolutions

Luke Zappia, Alicia Oshlack

2018-07-11

Clustering techniques are widely used in the analysis of large datasets to group together samples with similar properties. For exa..

Clinker: visualizing fusion genes detected in RNA-seq data

BM Schmidt, NM Davidson, ADK Hawkins, R Bartolo, IJ Majewski, PG Ekert, A Oshlack

2018-07-01

Background: Genomic profiling efforts have revealed a rich diversity of oncogenic fusion genes. While there are many methods for i..

Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database

L Zappia, B Phipson, A Oshlack

2018-06-01

As single-cell RNA-sequencing (scRNA-seq) datasets have become more widespread the number of tools designed to analyse these data ..

Necklace: combining reference and assembled transcriptomes for more comprehensive RNA-Seq analysis

Nadia M Davidson, Alicia Oshlack

2018-05-02

Background: RNA sequencing (RNA-seq) analyses can benefit from performing a genome-guided and de novo assembly, in particular for ..

Splatter: Simulation of single-cell RNA sequencing data

L Zappia, B Phipson, A Oshlack

2017-09-12

As single-cell RNA sequencing (scRNA-seq) technologies have rapidly developed, so have analysis methods. Many methods have been te..

Gene length and detection bias in single cell RNA sequencing protocols

Belinda Phipson, Luke Zappia, Alicia Oshlack

2017-04-28

Background: Single cell RNA sequencing (scRNA-seq) has rapidly gained popularity for profiling transcriptomes of hundreds to thous..