Author

Sophie Octavia

UNSW SydneyORCID 0000-0001-8506-9127Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

Click to filter author papers

Genomics· 2 Microbiology· 2 Bioinformatics· 1

Signature Assays, Organisms & Methods

Click to filter · or open tag

Assay:whole-genome sequencing· 5 Organism:bacteria (other)· 4 Research Focus:database / resource· 4 Approach:statistical model· 4 Research Focus:benchmarking· 2 Research Focus:genome assembly· 2 Approach:benchmark study· 1 Approach:deep learning· 1

Frequent Co-Authors

Lijuan LuoiD· 3 shared Mark M. TanakaiD· 3 shared Michael PayneiD· 3 shared Ruiting LaniD· 3 shared Sandeep KauriD· 3 shared Vitali SintchenkoiD· 3 shared Arti KapiliD· 2 shared Assaf RokneyiD· 2 shared

Activity by Year

2021-2025 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 21 mutual co-author links

Click any collaborator node to inspect or filter shared papers

Focal author (center)Selected co-authorORCID co-authorUnlinked name

Curved chords = mutual co-authorship

3 shared papersGenomics

Lijuan LuoORCID

Mutual co-authors in cluster

Author profile →

5 papers

Recent·Most cited

MicrobiologyGenome MedicinePeer-reviewedOct 24, 2025

✦ In-depth digest

Typhi Mykrobe: fast and accurate lineage identification and antimicrobial resistance genotyping directly from sequence reads for the typhoid fever agent Salmonella Typhi

Danielle J. Ingle, Jane Hawkey, Martin Hunt…·Kathryn E. Holt

Mykrobe k-mer panel genotypes Salmonella Typhi lineages, antimicrobial resistance (AMR) markers and plasmids from Illumina or nanopore reads, matching mapping-based lineage calls for 99.8% of genomes.

12 citationstop 5%

bacteria (other)human

𝕏 PostBluesky

MicrobiologyGenome MedicinePeer-reviewedMay 9, 2025

The TyphiNET data visualisation dashboard: Unlocking Salmonella Typhi genomics data to support public health

Zoe A. Dyson, Louise Cerdeira, Vandana Sharma…·Jackie Wright

The paper introduces TyphiNET, a dashboard for exploring Typhi genomics data to support public health decisions on antimicrobial resistance and vaccine implementation.

13 citations

bacteria (other)whole-genome sequencing

𝕏 PostBluesky

GenomicsMicrobiology SpectrumPeer-reviewedJan 10, 2023

Genomic epidemiology and multilevel genome typing of Australian Salmonella enterica serovar Enteritidis

Lijuan Luo, Michael Payne, Qinning Wang…·Ruiting Lan

This study uses multilevel genome typing to analyze Australian Salmonella Enteritidis isolates, finding strong epidemiological links to Asian strains and a local outbreak linked to European isolates.

10 citations

whole-genome sequencingstatistical model

𝕏 PostBluesky

BioinformaticsDatabasePeer-reviewedJan 1, 2022

MGTdb: A web service and database for studying the global and local genomic epidemiology of bacterial pathogens

Sandeep Kaur, Michael Payne, Lijuan Luo…·Ruiting Lan

MGTdb provides a web service for assigning and analyzing multilevel genome types of bacterial isolates, supporting epidemiological studies of Salmonella and Vibrio species.

14 citations

bacteria (other)whole-genome sequencing

𝕏 PostBluesky

GenomicsMicrobial GenomicsPeer-reviewedJul 22, 2021

Elucidation of global and local genomic epidemiology of Salmonella enterica Enteritidis through multilevel genome typing

Lijuan Luo, Michael Payne, Sandeep Kaur…·Ruiting Lan

This study develops a multilevel genome typing method for Salmonella Enteritidis and analyzes 26,670 genomes to reveal global and local genomic epidemiology, including multidrug resistance and outbreak patterns.

24 citations

bacteria (other)whole-genome sequencing

𝕏 PostBluesky