Program
Monday 4th November COMBINE, SBEI, Hackathon, ABACBS welcome reception
Tuesday 5th November ABACBS, Conference dinner
Wednesday 6th November ABACBS
Thursday 7th November Workshops, BioCAsia
Friday 8th November Workshops, BioCAsia
| Monday 4th of November | |||||
| 17:00 | 18:30 | 90 min | Welcome reception | ||
| Tuesday 5th of November | |||||
| 08:00 | 09:00 | Registration open | |||
| Session 1 - 1h 40 min |
Session 1
B2010 Auditorium - Chair: Jean Yang |
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| 09:00 | 09:30 | 30 min | Welcome to Country | ||
| 09:30 | 10:10 | 40 min | International Keynote - Hongyu Zhao (Yale University) | ||
| 10:10 | 10:40 | 30 min | National Keynote - Sarah Kummerfeld (Garvan Institute of Medical Research) | ||
| 10:40 | 11:10 | 30 min | Morning Tea | ||
| Session 2 - 1h 15 min | Session 2 | ||||
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Genomics and Metagenomics
1110 Lecture theatre |
Bioinformatics in Cancer and Immunology
1130 Lecture theatre |
Spatial Transcriptomics
1040 Lecture theatre |
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| Chair: Matt Field | Chair: Alicia Oshlack | Chair: Yue Cao | |||
| 11:10 | 11:25 | 15 min | Predicting Geographic Origins of Buruli Ulcer in Southeastern Australia Using Neural Networks and Genomic Data , Andrew Buultjens (University of Melbourne) | Mapping Chromatin State Dynamics to Unveil Novel Regulatory Regions Underpinning CD8+ T Cell Differentiation , Pushkar Dakle (Monash University) | SemanticST: Spatially informed semantic graph learning for effective clustering, integration, and deconvolution of spatial transcriptomics , Hamid Alinejad-Rokny (UNSW Sydney) |
| 11:25 | 11:40 | 15 min | High-Quality Genomes for Australian Lutjanidae Species , Emma de Jong (University of Western Australia) | Androgen stimulation rapidly reorganizes chromatin structure and nuclear receptor binding to trigger AR-mediated gene activation , Joanna Achinger-Kawecka (Garvan Institute of Medical Research) | SpaNorm: spatially-aware normalisation for Spatial Transcriptomics data , Agus Salim (University of Melbourne) |
| 11:40 | 11:55 | 15 min | Context-Adjusted Proportion of Singletons (CAPS): A robust metric for assessing negative selection and benchmarking variant pathogenicity predictors , Mikhail Gudkov (Garvan Institute of Medical Research) | Serum proteomics in stage III melanoma patients receiving neoadjuvant immunotherapy , Fei Yang (Macquarie University) | clustSIGNAL: a method for cell type clustering using Spatially Informed Gene expression with Neighbourhood Adapted Learning , Pratibha Panwar (University of Sydney) |
| 11:55 | 12:10 | 15 min | Understanding the common genetic architecture of spontaneous coronary artery dissection using genetically related phenotypes , Ingrid Tarr (Victor Chang Cardiac Research Institute) | Mining Targeted Therapies for Pediatric Oncology: Leveraging Gene Dependency and Biomarker Discovery in Pediatric-Focused Multi-Omics AI Cancer Models , Claire Xin Sun (Hudson Institute of Medical Research) | Spatial Sampler: A hypothesis-first collection of how-tos for single-cell spatial transcriptomics analysis , Sarah Williams (Queensland Cyber Infrastructure Foundation) |
| 12:10 | 12:25 | 15 min | Compound processing potential – a new way to examine and quantify metagenome functional potential profiles , Craig Liddicoat (Flinders University) | Capturing Paediatric Cancer Knowledge From ZERO: A Graph Approach , Weilin Wu (Children's Cancer Institute) | Context is important! Identifying context aware spatial relationships with Kontextual , Farhan Ameen (University of Sydney) |
| 12:25 | 13:30 | 65 min | Lunch & AGM | ||
| Session 3 - 1h 15 min | Session 3 | ||||
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Transcriptomics and Functional Genomics
1110 Lecture theatre |
Bioinformatics In Cardiovascular Disease
1130 Lecture theatre |
AI and Machine Learning
1040 Lecture theatre |
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| Chair: Eva Chan | Chair: Andy Tran | Chair: Tony Papenfuss | |||
| 13:30 | 13:45 | 15 min | Exploring human transcriptome using T2T-CHM13 reference and edgeR 4.0 , Xueyi Dong (Walter and Eliza Hall Institute of Medical Research) | Beyond clinical genome: Secondary bioinformatics analysis of patients from the Australian Genomics Cardiovascular Genetic Disorders Flagship , YuChen Chang (Centenary Institute) | The feasibility of LLMs for automated ontology annotation - a semantic task for a semantic language model! , David Kainer (University of Queensland) |
| 13:45 | 14:00 | 15 min | Precise Modelling of Drug-Resistant Epilepsy for Drug Screening Using Patient-Derived Brain Organoids and Single-Cell Transcriptomics , Huiwen Zheng (The University of Queensland) | Leveraging rare pathogenic variants in GPCR genes from the UK Biobank to understand gut microbiome-host communication in cardiovascular diseases , Leticia Camargo Tavares (Monash University) | An Integrative, Pharmacologically-Informed AI Model for Predicting Drug Synergy in Combinational Therapies , Parvin Mansouri (UNSW Sydney) |
| 14:00 | 14:15 | 15 min | Preparation protocols for long-read RNA-seq influence expression and structure of transcripts , Rotem Aharon (Peter MacCallum Cancer Centre) | Single-cell Transcriptional Profiling Reveals Novel Cellular and Molecular Drivers of Cardiovascular Fibrosis , Malathi Imiyage Dona (Baker Heart and Diabetes Institute) | A Machine Learning Approach to Automated Analysis of High-Dimensional Flow Cytometry Data , Benjamin Mashford (Australian National University) |
| 14:15 | 14:30 | 15 min | Enabling clinical translation and modelling of high-throughput functional assay data , Alan F. Rubin (The Walter and Eliza Hall Institute of Medical Research) | Investigating heart disease by analysing spatial transcriptomics data using VR-Omics , Denis Bienroth (Murdoch Children's Research Institute) | Multifaceted Representation of Genes via Deep Learning of Gene Expression Networks , Zheng Su (UNSW Sydney) |
| 14:30 | 14:45 | 15 min | A Computational Approach for Exploring Cryptons in the Search for Novel Therapeutics , Pablo Acera Mateos (Children's Cancer Institute) | Mass cytometry analysis comparing immune profiles of patients on statins, Matthew Shu (University of Sydney) | Leveraging AI in predicting protease-specific substrate cleavage sites, Fuyi Li (University of Adelaide) |
| 14:45 | 15:15 | 30 min | Afternoon Tea | ||
| Session 4 - 1h 45 min |
Session 4
B2010 Auditorium - Chair: Dominik Beck |
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| 15:15 | 15:55 | 40 min | International Keynote - Jingyi Jessica Li (University of California, Los Angeles) | ||
| 15:55 | 16:25 | 30 min | National Keynote - Jasmin Straube (QIMR Berghofer Medical Research Institute) | ||
| 16:25 | 16:55 | 30 min | Fast forward presentations (Chair: Ellis Patrick) | ||
| 17:00 | 18:00 | 60 min | Poster session A | ||
| 18:15 | 22:30 | Dinner | ABACBS dinner (Thai Pothong Restaurant) | ||
| Wednesday 6th of November | |||||
| 08:30 | 09:10 | Registration open | |||
| Session 5 - 1h 25min |
Session 5
B2010 Auditorium - Chair: Eleni Giannoulatou |
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| 09:10 | 09:50 | 40 min | International Keynote - Hannah Carter (University of California San Diego) | ||
| 09:50 | 10:20 | 30 min | National Keynote - Timo Lassman (Telethon Kids Institute) | ||
| 10:20 | 10:35 | 15 min | Best COMBINE Talk | ||
| 10:35 | 11:10 | 30 min | Morning Tea | ||
| Session 6 - 1h 15min | Session 6 | ||||
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Indigenous Genomics and Health Equity
1110 Lecture theatre |
Proteomics and Structural Bioinformatics
1130 Lecture theatre |
Spatial Transcriptomics and Imaging
1040 Lecture theatre |
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| Chair: Jimmy Breen | Chair: Rebecca Poulos | Chair: Farhan Ameen | |||
| 11:10 | 11:25 | 15 min | A draft pangenome reference for Indigenous Australians , Hyungtaek Jung (Australian National University) | The Proteomic Analyst Suites: Streamlining Proteomic Data Analysis and Visualisation , Laura Perlaza-Jimenez (Monash University) | Spatial analysis of in situ cytometry data in R , Shreya Rajesh Rao (Westmead Institute for Medical Research) |
| 11:25 | 11:40 | 15 min | Investigating type 2 diabetes status in Indigenous South Australians using supervised clustering techniques , Anna Liza Kretzschmar (Telethon Kids Institute) | Highly efficient protein structure alignment with segment-level representations and block-sparse optimization , Thomas Litfin (Griffith University) | Deciphering patterns in spatial transcriptomics data from zebrafish embryos , Hieu Nim (Murdoch Children's Research Institute) |
| 11:40 | 11:55 | 15 min | GeneGuardian: Empowering Participants with Dynamic Consent for Ethical Genomic Data Management, Adrien Oliva (CSIRO) | Investigating mRNA-protein correlations in cancer to inform precision medicine, Urwah Nawaz (Children's Medical Research Institute) | Viewing the zebrafish embryo in 4D , Jialin Ding (University of Melbourne) |
| 11:55 | 12:10 | 15 min | Personalised Prediction of Essential Genes in Cancer Using Driver Prioritisation and Synthetic Lethality , Rhys Gillman (James Cook University) | Do Protein Language Models Learn Phylogeny? , Sanjana Tule (The University of Queensland) | Assessing interpretability of Vision Transformers on image mass cytometry data , Joshua Pople (University of Sydney) |
| 12:10 | 12:25 | 15 min | A Novel Deep Transfer Learning Model for Predicting Post-gestational Type 2 Diabetes through Integrating Multi-omics Data , Coco Xiaoge Huang (UNSW Sydney) | Background correction in imaging-based spatial proteomics datasets , Dharmesh D. Bhuva (South Australian Immunogenomics Cancer Institute) | Spotlight on 10x Visium: a multi-sample protocol comparison of spatial technologies , Mei Du (Murdoch Children's Research Institute) |
| 12:25 | 13:45 | 80 min | Lunch / Poster session B | ||
| Session 7 - 1h 15min | Session 7 | ||||
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Single Cell Analytics
1110 Lecture theatre |
Epigenetics
1130 Lecture theatre |
Data Analytics and Omics Integration
1040 Lecture theatre |
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| Chair: Jess Mar | Chair: Dominik Beck | Chair: Shila Ghazanfar | |||
| 13:45 | 14:00 | 15 min | Building a Comprehensive Multi-Tissue Paediatric Airway Atlas with Flex Single-cell RNA-seq Analysis , Gunjan Dixit (Peter MacCallum Cancer Centre) | A paediatric pan-cancer hierarchical classifier using DNA methylation for precision medicine , Ben Curran (Children's Cancer Insitute of Australia) | Novel method for validating reproducibility of bioinformatics and computational biology workflows , Ignatius Jeppe Menzies (Garvan Institute of Medical Research) |
| 14:00 | 14:15 | 15 min | wSIR: Weighted Sliced Inverse Regression for supervised dimension reduction of spatial transcriptomics and single cell gene expression data , Max Woollard (University of Sydney) | realfreq: real-time base modification analysis for nanopore sequencing , Suneth Samarasinghe (UNSW Sydney) | Utilisation of Kolmogorov-Arnold Networks to provide more eXplAInability about relationships in large omics datasets for complex traits, James Temple (University of Tasmania) |
| 14:15 | 14:30 | 15 min | Isopod: Detecting differential isoform usage between cell types from long-read single cell data , Michael Nakai (Peter MacCallum Cancer Centre) | Genetic Variants Associated with Schizophrenia Change Epigenetic Regulation Leading to Allele-Specific Expression , Daniel J Russell (Griffith University) | EDAmame: exploratory data analysis for everyone , Tim C. Hewitt (Australian National University) |
| 14:30 | 14:45 | 15 min | Prioritisation of novel transcription factor targets that improve adoptive T cell therapy using an in silico perturbation framework , Jesse Armitage (University of Western Australia) | Hi-Cing Double: Differential analysis of haplotype-resolved HiC data , Hannah Coughlan (The Walter and Eliza Hall Institute of Medical Research) | PLSKO: a robust knockoff generator to control false discovery rate in omics variable selection , Guannan Yang (University of Melbourne) |
| 14:45 | 15:00 | 15 min | BARBIE: An R software package for analysing barcode count data from clonal tracking experiments , Liyang Fei (Peter MacCallum Cancer Centre) | Evaluating the reproducibility of public bioinformatic databases for m6A peak calls , Gavin Sutton (University of Sydney) | A knowledge-embedded deep learning framework for multi-parameter cytometry data , Elijah Willie (University of Sydney) |
| 15:00 | 15:30 | 30 min | Afternoon Tea | ||
| Session 8 - 1h 40min |
Session 8
B2010 Auditorium - Chair: Ellis Patrick |
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| 15:30 | 16:10 | 40 min | International Keynote - Davide Risso (University of Padova) | ||
| 16:10 | 16:40 | 30 min | National Keynote - Matt Field (James Cook University) | ||
| 16:40 | 17:00 | 20 min | Closing session, and ABACBS conference awards | ||