ABACBS National Seminar Series
The ABACBS national seminar series aims to highlight the work of bioinformaticians across the spectrum of career stages, located in both urban and regional universities.
The seminars are held every few months from 12-1pm EST on Mondays via Zoom. Each seminar features two speakers, with each talk running for approximately 25 minutes, followed by 5 minutes of Q&A time.
The next seminar is scheduled to take place Monday June 22nd, 12pm-1pm AEST.
Register for the next seminar via https://abacbs.org/seminarzoom
The ABACBS National seminar series is organised by: ABACBS Post-doc Subcommittee.
2026 Seminar program
june 22, 2026
Title: AI-driven discovery of serum microRNA biomarkers for Johne’s disease
Speaker: Dr. Carlos Miranda Rodrigues
Abstract: Johne’s disease remains difficult to diagnose, particularly during subclinical infection, limiting effective disease control in cattle. In this seminar, I will present an AI-driven bioinformatics pipeline for discovering serum microRNA biomarkers of infection using RNA-seq data from cattle in Australia and New Zealand. By combining differential expression analysis, feature selection, and machine learning classification, we identified a three-microRNA signature associated with MAP infection. I will discuss how this computational workflow supported biomarker discovery and translation into a diagnostic RT-qPCR assay, highlighting the broader potential of bioinformatics and AI to advance host-response diagnostics in infectious disease.
Bio: Dr Carlos is a Research Scientist at ACDP/CSIRO (Geelong), where he applies next-generation sequencing and machine learning to develop more efficient pipelines for identifying biomarkers in infectious diseases. Before joining the Host Response team, he was a postdoctoral fellow at the Baker Institute and the University of Queensland, focusing on using machine learning to identify protein binding sites, assess the effects of genetic mutations on protein–protein interaction networks and disease, detect drug-resistant mutations in tuberculosis, and model the impact of genetic variation in SARS-CoV-2. His work sits at the intersection of bioinformatics, infectious disease, and translational data science.
Title: Understanding plasmid-mediated dissemination of antimicrobial resistance
Speaker: Dr. Leah Roberts
Abstract: The rapid rise in antimicrobial resistance (AMR) among clinically-important bacteria threatens our ability to treat and manage infections. Plasmids are known to be key drivers of AMR, owing to their ability to transfer horizontally between bacterial cells. Despite this well known phenomenon, plasmid investigations have lagged due to the difficulty in resolving them from short-read sequencing techniques. However, with the advent of long-read sequencing, our ability to interrogate plasmid biology with detailed precision has become a reality. Here, I will present three stories of how we have applied long-read sequencing to investigate plasmid-mediate AMR dissemination among a diverse group of pathogens, outlining novel bioinformatic techniques to resolve and compare plasmids.
Bio: Dr Leah Roberts is an NHMRC EL1 investigator fellow based at UQ's Frazer Institute (Herson Campus). She leads a bacterial genomics research team with a strong focus on investigating mobile genetic elements, particularly plasmids, and their role in bacterial adaptation and transmission of antimicrobial resistance. Previously, she has led large collaborative international projects in the United Kingdom, Vietnam, and South Africa, focused on the genomic investigation of clinically-important bacteria such as carbapenemase-producing Enterobacteriaceae and Mycobacterium tuberculosis. She is also invested in the development of novel bioinformatics tools, and has contributed to the development of MicroPipe, Pling, and Celebrimbor, among others.
April 13, 2026
Title: Resolving allele-specific HLA dysregulation in lung cancer.
Speaker: Dr. Clare Puttick
Abstract: Disruption of the class I human leukocyte antigen (HLA) molecules has important implications for immune evasion and tumor evolution. We developed major histocompatibility complex loss of heterozygosity (LOH), allele-specific mutation and measurement of expression and repression (MHC Hammer). We identified extensive variability in HLA allelic expression and pervasive HLA alternative splicing in normal lung and breast tissue. In lung TRACERx and lung and breast TCGA cohorts, 61% of lung adenocarcinoma (LUAD), 76% of lung squamous cell carcinoma (LUSC) and 35% of estrogen receptor-positive (ER+) cancers harbored class I HLA transcriptional repression, while HLA tumor-enriched alternative splicing occurred in 31%, 11% and 15% of LUAD, LUSC and ER+ cancers. Consistent with the importance of HLA dysfunction in tumor evolution, in LUADs, HLA LOH was associated with metastasis and LUAD primary tumor regions seeding a metastasis had a lower effective neoantigen burden than non-seeding regions. These data highlight the extent and importance of HLA transcriptomic disruption, including repression and alternative splicing in cancer evolution.
About the speaker: Dr Clare Puttick established her laboratory at the Garvan Institute of Medical Research in February 2026, where her research sits at the intersection of computational biology, cancer immunology, and genomics. Dr Puttick’s research focuses on understanding how tumours evade immune detection, with a particular emphasis on the HLA genes. These genes play a central role in both the adaptive and innate immune systems, regulating antigen presentation as well as antigen-independent activating and inhibitory signalling. The HLA genes are frequently disrupted across many cancer types, including lung cancer, at both the genomic and epigenetic levels. However, their extreme polymorphism makes them computationally challenging to study, requiring the development of specialised analytical approaches.
Title: Snippy-NG - unified microbial variant calling and phylogenomics for heterogenous sequence data.
Speaker: Dr. Wytamma Wirth
Abstract: Snippy-NG is a next-generation reimplementation of Snippy designed to keep the familiar SNP-calling workflow while making the system more modular, extensible, and suitable for modern datasets. It supports short reads, long reads, and assemblies within a shared architecture built from reusable stages and pipelines. Here I will detail the development progress of Snippy-NG, new features, and initial benchmarks.
About the speaker: Dr Wytamma Wirth is a technical biologist in the Centre for Pathogen Genomics at the Peter Doherty Institute. His work focuses on genomic epidemiology, phylodynamics, and bioinformatics. Wytamma’s role spans basic research, tool development, analysis of large scale real world datasets, and contributions to national genomics infrastructure. In his current Essential Open Source Software for Science funded position, Wytamma works with Associate Professor Torsten Seemann as a core developer of the microbial variant caller Snippy-NG, helping build the next generation of microbial bioinformatics tools.