Justin Zobel

Automatic Consistency Assurance for Literature-based Gene Ontology Annotation

This paper introduces a method to automatically detect inconsistencies in gene ontology annotations using text mining models, achieving high precision on synthetic data.

GeneMates: an R package for Detecting Horizontal Gene Co-transfer between Bacteria Using Gene-gene Associations Controlled for Population Structure

GeneMates identifies horizontal gene co-transfer in bacteria using WGS data and controls for population structure to avoid spurious associations.

Automated Detection of Records in Biological Sequence Databases that are Inconsistent with the Literature

The paper develops an algorithm to detect inconsistent biological sequence database records by comparing them with literature, achieving moderate precision and recall.

Literature Consistency of Bioinformatics Sequence Databases is Effective for Assessing Record Quality

The paper assesses sequence database quality by analyzing literature consistency, finding that 25% of records not previously flagged as erroneous are inconsistent with the literature.

Duplicates, redundancies, and inconsistencies in the primary nucleotide databases: a descriptive study

This study assesses the scale, types, and impact of duplicates in INSDC nucleotide databases through a benchmark dataset of 67,888 merged groups.

Benchmarks for Measurement of Duplicate Detection Methods in Nucleotide Databases

The paper develops new benchmarks for evaluating duplicate detection methods in nucleotide databases, highlighting the limitations of existing benchmarks and the importance of diverse, curated data.

Bandage: interactive visualisation of de novo genome assemblies

Bandage visualizes de novo genome assembly graphs, allowing users to interact with contig connections and perform BLAST searches within the tool.

SRST2: Rapid genomic surveillance for public health and hospital microbiology labs

SRST2 is a tool for rapid and accurate detection of genes and alleles from whole genome sequencing data, outperforming assembly-based methods in public health and hospital settings.