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 ABACBS National seminar series is organised by: ABACBS Post-doc Subcommittee.
2025 Seminar program
November 10, 2025
Title: Using omics data to inform drug discovery.
Speaker: A/Prof Sonia Shah
About the speaker: Associate Prof Shah is a National Heart Foundation Future Leader Fellow. She leads the Genomics in Health Group at the Institute for Molecular Bioscience, The University of Queensland. Her group leverages large-scale omic and health data for research that spans across cardiovascular disease, liver transplant and drug discovery. Her talk will focus on using omics data to understand drug effects and inform drug discovery.
Title: Identifying geographical origin of Plasmodium vivax infections.
Speaker: Dr. Hidayat “Anto” Trimarsanto
Abstract: Plasmodium vivax, the most geographically widespread malaria parasite, poses major challenges to control due to its ability to relapse weeks or months after infection and to maintain persistent splenic infections and low-level or asymptomatic parasitemia that often escapes conventional surveillance. Differentiating between local and imported infections is particularly difficult, as reliance on patient travel history is often ineffective. Imported cases can disrupt local control efforts, increase the risk of outbreaks, and contribute to the spread of antimalarial drug resistance.
P. vivax remains understudied at the molecular level because challenges in long-term culture hinder the validation of drug resistance markers. However, identifying the geographical origin of infections provides an important means to track the spread of resistant strains. This study developed a genomic framework for identifying imported infections using a Naive Bayes classifier and a minimal SNP barcode, suitable for both Illumina and Oxford Nanopore platforms. The approach was also evaluated using a recently developed microhaplotype panel for P. vivax.
About the speaker: Hidayat “Anto” Trimarsanto is a final-year PhD candidate at the Menzies School of Health Research, where he studies the genomic epidemiology of Plasmodium vivax. His research combines genomic and bioinformatic approaches to investigate transmission dynamics and the genetic mechanisms underlying antimalarial drug resistance in the Asia–Pacific region. He integrates field data and genomic insights to strengthen surveillance strategies that support malaria elimination efforts and develops open-source tools to enhance local research capacity in endemic countries. Before studying at Menzies, Anto worked at the Eijkman Institute for Molecular Biology in Indonesia, contributing to research on the genomics of malaria, emerging and re-emerging viruses, and human diseases.
August 25, 2025
Title: Unravelling mutational signatures with circulating tumour DNA.
Speaker: Dr. Dineika Chandrananda
Abstract: During the lifetime of a cancer, various environmental and biological processes imprint specific mutation patterns on a patient’s tumour genome. Some of these “mutational signatures”, if correctly detected, can predict sensitivity to specific cancer treatments, enabling personalised treatment strategies to improve clinical outcomes.
Signature analysis requires accurate somatic mutation calls from each patient. Typically, this involves deep sequencing of both tumour and germline samples, incurring substantial costs, long turnaround times, and logistical challenges in biospecimen collection. These barriers have greatly limited the routine adoption of mutational signature analysis in clinical practice.
We have developed MisMatchFinder, an innovative bioinformatics method to address this unmet need. Our algorithm identifies mismatches in sequencing reads relative to the reference genome and removes background noise unrelated to somatic mutations using a series of in silico filters at the read, regional, and positional levels.
Our approach:
Infers somatic variants from low-coverage sequencing (~3x),
Does not require a matched germline sample, and
Is tailored to circulating tumour DNA, short DNA fragments shed into the bloodstream by tumour cells, which can be captured via a simple blood draw.
In a cohort of 375 blood samples across 9 cancer types, we demonstrate that MisMatchFinder accurately infers single-base substitutions, doublet-base substitutions and indels, enabling robust detection of clinically relevant mutational signatures.
About the speaker: Dr. Dineika Chandrananda is a Senior Research Officer at the Peter MacCallum Cancer Centre, where she leads the bioinformatics arm of the Molecular Biomarkers and Translational Genomics Laboratory. She develops AI-driven methods to integrate multi-omic circulating tumour DNA (ctDNA) data for the early detection and monitoring of cancer via liquid biopsy. She has secured over $5.5 million in national and international funding, including an NHMRC Ideas Grant, MRFF support, and previously held a VCA Early Career Fellowship. Her contributions have been recognised with the Lea Medal for research excellence and leadership in translational genomics.
Title: Disruption and rewiring of multicellular gene regulatory networks in cancer.
Speaker: Dr. David Goode
Abstract: The emergence of multicellularity involved evolution of complex gene regulatory networks (GRNs) to control activity of essential cellular growth pathways inherited from unicellular ancestors. Many features of multicellularity, such as lineage specificity and coordinated growth, are lost in cancer cells. Our lab investigates how GRNs that evolved to support multicellular life are altered in cancer.
Using phylogenomics, we established the evolutionary ages of human genes to categorize them as having unicellular or multicellular origins. RNA-sequencing data from The Cancer Genome Atlas reveal widespread downregulation of genes involved in multicellular processes across solid cancers. In contrast, many genes of unicellular origins are selectively up-regulated in tumours. Concordantly, ‘hubs’ linking unicellular and multicellular genes in human GRNs are enriched in driver mutations.
Gene co-expression analysis indicated co-regulation of unicellular and multicellular genes is disrupted in cancer. Connections are lost between many unicellular and multicellular genes, while novel connections form between unicellular and multicellular genes not expressed together in normal tissues. Such patterns that become stronger as tumours progress from benign to malignant states.
Our findings suggest alteration of GRNs as cancer develops tilts gene expression in favour of activation of highly-conserved growth-promoting processes that enhance tumour malignancy. The loss of multicellularity perspective can make sense of complex transcriptional changes in cancer and uncover evolutionarily-informed biomarkers for predicting risk of disease progression in patients.
About the speaker: Dr Goode is a Laboratory Head in the Department of Biochemistry and Molecular Biology at Monash University and part of the Monash Biomedicine Discovery Institute (BDI). His group’s core mission is to understand how cancer cells adapt and evolve. This is achieved by integrating aspects of molecular evolution, network analysis and machine learning with data from longitudinal sampling and cohort studies of cancer. Dr Goode’s research has appeared in Science, Nature Genetics, Lancet Oncology, PNAS, Genome Biology and eLife. He has received funding from the NHRMC, MRFF, Victorian Cancer Agency and the CASS Foundation.
June 2, 2025
Title: Understanding microbiomes to develop novel therapeutic interventions for inflammatory bowel disease
Speaker: A/Prof Samuel Forster
About the speaker: A/Professor Samuel Forster is a CSL Centenary Fellow and Research Group Head at the Hudson Institute of Medical Research. He leads the Microbiota and Systems Biology group, focusing on the role of the microbiome in health and disease, particularly in areas like antimicrobial resistance, IBD, gastroenteritis, and COVID-19. His research integrates microbiology, immunology, and computational biology to develop targeted microbiome-based therapies. A/Prof Forster has pioneered methods for culturing gut bacteria and modelling microbiome dynamics, and he established Australia's first public microbiome culture collection. He collaborates closely with industry partners, including BiomeBank, to translate microbiome science into clinical treatments.
Title: Capturing cancer fusions at single-cell resolution
Speaker: Dr. Jovana Maksimovic
About the speaker: Dr. Jovana Maksimovic is a Senior Research Associate in bioinformatics and computational biology in the Oshlack Lab at the Peter MacCallum Cancer Centre. Her research has focused on epigenetics and transcriptomics data analysis, with a strong influence in methylation array analysis as the co-creator of the widely used missMethyl Bioconductor package. She was a lead computational investigator on a Chan Zuckerberg Initiative Paediatric Cell Atlas Network Grant, contributing to the development of a globally accessible cell atlas of the healthy paediatric airway. Currently, she holds an NHMRC EL2 Investigator Grant and is focused on developing analytical approaches for multi-sample, multi-condition single-cell transcriptomics experiments.
April 7, 2025
Title: snPATHO-seq, a versatile FFPE single-nucleus RNA sequencing method to unlock pathology archives.
Speaker: Dr. Michael Roach
Abstract: Clinical tissue biopsies are routinely preserved as formalin-fixed paraffin-embedded (FFPE) samples. These FFPE samples can be preserved for decades in biobanks and there are millions of historical samples preserved worldwide. This valuable resource is often used in retrospective studies, but is currently underutilised in single-cell omics research due to low RNA quality and difficulty dissociating individual cells from this preservation method. In this study, leveraging a recent advance in single-cell genomic technology, we introduce snPATHO-seq, a versatile method to derive high-quality single-nucleus transcriptomic data from FFPE samples. We benchmarked the performance of the snPATHO-seq workflow against existing 10x 3’ and Flex assays designed for frozen or fresh samples and highlighted the consistency in snRNA-seq data produced by all workflows. The snPATHO-seq workflow also demonstrated high robustness when tested across a wide range of healthy and diseased FFPE tissue samples. When combined with FFPE spatial transcriptomic technologies such as FFPE Visium, the snPATHO-seq provides a multi-modal sampling approach for FFPE samples, allowing more comprehensive transcriptomic characterization.
About the speaker: Michael is the Bioinformatics program lead within Bioplatforms and Bioresources at the Flinders Health and Medical Research Institute (FHMRI). His research interests include developing new tools and methods to expand the capabilities of emerging 'omics technologies. Michael previously worked at the Australian Wine Research Institute (AWRI) where he assembled the Chardonnay genome and developed the new gold standard for grapevine clonal marker discovery. He wrote the pipeline Purge Haplotigs for heterozygous diploid assembly cleanup, and contributed to many other various yeast genomics projects. Michael completed a post-doc at the Flinders Accelerator for Microbiome Exploration (FAME), where they applied metagenomics to obtain a better understanding of the microbiomes associated with various environmental and human health issues. Most recently, Michael worked at the Adelaide Centre for Epigenetics (ACE) and South Australian immunoGENomics Cancer Institute (SAiGENCI) developing new bioinformatics software and methods for single cell and spatial 'omics.
Title: Capturing cancer fusions at single-cell resolution.
Speaker: Dr. Ciccy Wang
Abstract: Immune checkpoint blockade (ICB) has improved treatment success in triple negative breast cancer (TNBC), but it is still unclear as to which tumours will respond to treatment. As ICB blocks specific cell-cell interactions, we investigated whether the arrangement of cells in the TME could predict ICB response and explored how ICB remodels the tumour microenvironment during the course of treatment. We used imaging mass cytometry to profile the in situ expression of 43 proteins in tumours from patients in a randomised trial of neoadjuvant ICB, sampled at three timepoints (baseline biopsy, n = 243; early on-treatment biopsy, n = 207; post-treatment surgical excision, n = 210). At baseline, proliferating CD8+TCF1+T cells and MHCII+ cancer cells, and cancer–immune interactions with B cells and granzyme B+ T cells were significant predictors of combined chemotherapy-immunotherapy response. Immunotherapy resistance early on-treatment was characterised by CD15+ expression on cancer cells. Response was best predicted by combining tissue features before and on-treatment, showing a potential role for early biopsies in guiding adaptive therapy.
About the speaker: Ciccy is currently a computational biologist at the Data Science Platform at the Garvan Institute of Medical Research. She completed her PhD at the Cancer Research UK Cambridge Institute with Dr. Raza Ali investigating biomarkers of immunotherapy response in breast cancer. Prior to this, she had a primarily wet lab background in immunology, virology and genomics research during her undergraduate and MPhil at the University of Sydney and the Westmead Institute for Medical Research.