Monday, 13th February 44th Lorne Genome Conference 2023

Since the last BGI STOmics™ Lorne Genome workshop, this advanced spatial multi-omics technology has been gaining great momentum globally and in particular in Australia with more users and more data generated contributing to exciting scientific findings. At this year’s workshop we have invited two guest speakers to share their latest findings using Stereo-Seq™, or SpaTial Enhanced REsolution Omics-Sequencing, in their revolutionary life science projects such as oncology, immunology, developmental biology, neuroscience, pathological studies. The workshop will provide breakfast. Please register here.

• Invited Speaker Presentation - Nucleosomes for all! Histone-based chromatin in non-eukaryotic organisms - Karolin Luger
• Invited Speaker Presentation - Specialization of 3D genome structure in different cell types and states - Ana Pombo
• Invited Speaker Presentation - Structural dynamics of condensin for DNA loop extrusion   - Je-Kyung Ryu

• A role for post-translational modifications in epigenetic silencing caused by triplet repeat expansions. - Sridevi Sureshkumar
• Treatment-induced DNA methylation heterogeneity and implications for cell growth in Acute Myeloid Leukaemia - Heather Lee
• A single-cell atlas of transcribed cis-regulatory elements revealed disease associated regulatory modules in distinct cell populations - Chung-Chau Hon
• Deciphering epigenetic alterations in pre-leukemic stem cells during T-cell acute lymphoblastic leukemia development - Feng Yan
• Allosteric regulation of PRC2 by non-histone effectors is required for embryonic development - Samuel C Agius
• Epigenetic signatures of invertebrate CpG island-like sequences - Allegra Angeloni
• Speed talk - Investigating the roles of set-9 and set-26 in transgenerational epigenetic inheritance - Dhruv Monteiro
• Speed talk - Structural and functional insights into Caenorhabditis elegans novel epigenetic pathway components - Carlotta Wills

• The HTLV-1c genomic graveyard reveals host-virus interactions - Natasha Jansz
• CTCF facilitates subset-specific chromatin interactions to limit the formation of memory CD8⁺ T cells - Sara Quon
• Genetic and epigenetic approaches to identify genes contributing to migraine disorders - Heidi G Sutherland
•   Regulation of neural stem cells and cortex development by histone acetylation - Maria I Bergamasco
• Non-random segregation of the therian proto-sex chromosome in platypus - implications for mammalian sex chromosome evolution - Filip Pajpach
• Molecular controls of germline stem cell transcriptional states during homeostasis and regeneration - Robin M Hobbs
• Speed talk - Determining how Hfp prevents ectopic ovarian stem cell niche formation - Madison Barker
• Speed talk - Cic loss-of-function alters the transcriptome of the stem cell niche to non-autonomously drive neural lineage expansion - Brooke Kinsela

As a researcher, it’s essential you learn how to talk and write about your research in a variety of ways and for different audiences. Even the most brilliant research is wasted if no one knows it has been done or if your target audience isn’t able to understand it. In this workshop we’ll consider a number of aspects of research communication. What is the purpose and goal of your communication? How can you hook your audience’s attention and make your research relevant, engaging and accessible to different audiences? What different communication channels and platforms are open to you? What are the benefits to you of communicating effectively about your research?

This workshop will be presented by Associate Professor Jen Martin. A/Prof Martin (@scidocmartin) worked as a field ecologist before founding the University of Melbourne's Science Communication Teaching Program which teaches scientists across all disciplines to be engaging and effective communicators. She also practises what she preaches: she’s been talking about science weekly on 3RRR radio for more than 18 years, hosts podcasts (including @letstalkscicomm), MCs events, teaches as part of the Homeward Bound Faculty, writes for a variety of publications and was named the 2019 Unsung Hero of Australian Science Communication.

• Julian Wells Medal Talk: Statistical bioinformatics enables biomedical discoveries - Gordon Smyth
• Invited Speaker Presentation - Spatially resolved methodologies to understand tissue ecosystems in health and disease     - Joakim Lundeberg

• A GWAS-driven cross-species approach towards a splicing code - Sureshkumar Balasubramanian
• Location, location, location: deciphering spatial gene regulatory networks - Mirana Ramialison
• CHD4 is regulated by autoinhibition and remodels chromatin by decoupling the translocation of entry- and exit-side DNA - Joel Mackay
• Pan-cancer pervasive upregulation of 3' UTR splicing drives tumourigenesis - Yvonne Tay
• Tracking transcriptional evolution in cancer using circulating tumour DNA - Dineika Chandrananda
• CRISPR screens of candidate breast cancer risk genes using a T cell cytotoxicity assay to identify genes implicated in immune-surveillance - Wei Shi

• Simultaneous identification of m6A and m5C reveals coordinated RNA modification at single-molecule resolution - Eduardo Eyras
• First report of RNA editing in human retina – a process central to photoreceptor health, and a risk factor for both AMD and rarer macular degeneration - Brendan R E Ansell
• FitnessTracker identifies transcriptional programs driving clonal evolution from barcoded single-cell RNA-sequencing data - David L Goode
• Resolving spatial boundaries in the lateral plate mesoderm  - Lisa N Waylen
• Computing spatial mutation intolerance to assess selective pressure across the human proteome - Aaron Kovacs
• scATACPop: simulating population scale single-cell ATAC seq data  - Sagrika Chugh

• Invited Speaker Presentation - Investigating enhancer-mediated gene expression regulation in the human brain, and its role in brain development  - Irina Voineagu

• Investigation of Novel Gene Therapies for ACTA1-Related Nemaline Myopathy - Christina M Vo
• Dissecting SR Protein Function Using A Unique Model System - Jordyn P Coutts
• Investigating the epigenetic regulator SMCHD1 as a potential therapeutic target for the treatment of Prader-Willi Syndrome and Schaaf-Yang Syndrome - Megan Iminitoff
• Investigating H3.3 in B cell subsets upon stimulation - Clarissa R Chakma
• Genome-wide unresolved double-strand breaks underpin mitotic lethality following ablative radiotherapy - Lucy French
• N6-methyldeoxyadenine (N6mA) DNA methylation plays a role in transgenerational epigenetic inheritance - Natalya Frolows
• Mechanisms of intronic trinucleotide repeat expansion in A. thaliana - Giulia Folini
• Meta-regression on sex-specific epigenetic ageing - Mandhri Abeysooriya
• Optimising gene therapy vectors using nanopore direct RNA sequencing - Kathleen Zeglinski
• Transcriptional Steps in Megakaryocyte Commitment and Maturation - AnneMarie Welch
• CRISPR gene editing of Krüppel-like factor 1 to cure sickle cell disease - Stephanie Anderson
• DNA replication timing predicts transcription factor binding and the rate of enhancer turnover - Carina Paola Cornejo Paramo
• Residual Bodies: Wasteland or Treasure Island? - Mohd Nazmul Hasan Apu
• Identifying alternative polyadenylation signatures in the human heart with polyApiper - Akriti Varshney
• Statistical modelling for single cell ATAC-seq data - Aaron Wing Cheung Kwok
• Chromatin regulation in thermal responses - Sourav Mukherjee
• Unravel the role of nucleic binding ability of the epigenetic regulator SMCHD1 - Ruifeng Hu
• An annotation-guided deep neural-network method for factor analysis of single-cell RNA-seq data - Sandeep Santhosh Kumar
• Mutations of histone H3.3 and Krebs cycle genes inhibit the role of H3K9/K36 KDM4 histone demethylase in telomere maintenance - Maheshi I Udugama
• 3’UTR splicing may contribute to gastric cancer development - Xiaonan Fan
• Analysing arrayed CRISPR screen data - Waruni Abeysekera
• KLF3 represses inflammatory gene expression in macrophages through interactions with the pioneering transcription factor PU.1 - Jessica Salmon
• Comparison of haematopoietic cell identity across vertebrates using single-cell transcriptomics - Davide Vespasiani
• Mechanisms producing novel polyadenylated isoforms of ncRNA RPPH1 - Kiarna Kavanagh-Beck
• VIVID: a web application for variant interpretation and visualisation in multidimensional analyses - Swapnil Tichkule
• Functional characterisation of active enhancers in human astrocytes using a CRISPRi screen - Nicole FO Green
• Shorter 3’UTR signatures as biomarkers for triple-negative breast cancer - Nitika Kandhari
• Ultra-long and targeted nanopore sequencing to resolve human macrosatellite epigenetics in health and disease - Quentin Gouil
• Investigating the variability of gene expression in the human brain using BITHub - Urwah Nawaz
• Genome Wide Association Studies on Splicing at individual splice-sites in Humans - Aiswarya Balakrishnan
• Riccia small plants big genus - Tom Fisher
• Heterogeneity of cancer cell telomere biology revealed by analysis of 976 cell lines - Dale Cross
• CaraVaN: Prioritising Cardiac Variants in the Non-coding genome using Gradient Boosting algorithm. - Gulrez Chahal
• Exquisite timing and mechanistic diversity of gene expression changes in response to a prototypical nutritional stress   - Yoshika Janapala
• CaraVaN: Prioritising Cardiac Variants in the Non-coding genome using boosting algorithm - Gulrez Chahal
• Is the TREX-2 complex an unidentified mRNA export receptor? - Yoona Kim
• SMCHD1 at the human 15q11.2-13 locus. Exploring mechanisms of silencing - Anna LeFevre
• Screening for genetic determinants of female-specific pluripotency and differentiation in mouse embryonic stem cells. - Ryan J Hall
• Genetic and transcriptomic sequencing analysis unveil the molecular genetics of neuromuscular disorders: a selection of case studies - Chiara Folland
• Planting ideas for medicine: What can plants teach us about Friedreich’s ataxia?   - Rucha Sarwade
• Aberrant Non-Coding RNA Polyadenylation is an Early Stress Response in Saccharomyces cerevisiae - Calvin A Kraupner-Taylor
• Genomic evolution of ricciocarpos natans - a monoecious liverwort derived from dioecious ancestor  - Shilpi Singh
• ZMYND8 knock-out leads to widespread transcriptional changes and impaired brain organoid development - Juli Wang
• Unraveling the mechanisms involved in the co-regulation of breast cancer associated genes at the 6q25.1 locus - Amie Siemonek
• Absence of a telomere maintenance mechanism in Ewing sarcoma - Karen L MacKenzie
• Revealing the real R-loop landscape in the S. pombe genome - Jing Zhang
• Gene expression and chromatin accessibility at single cell resolution in lung alveolar stem cells with age and exercise - Qing Wang
• Whole genome Nanopore DNA sequencing shows that chronic corticosterone supplementation in mice results in altered sperm DNA methylation in exposed animals and their offspring. - Coralina Collar Fernandez
• Non-reference genome transposable elements (TEs) have a significant impact on the progression of the Parkinson’s disease - Sulev Koks
• SSSavi: A modular dCas9-based recruitment platform for combinatorial epigenome editing - Tessa Swain
• RNA Polymerase I inhibition as a treatment strategy towards H3.3 mutated gliomas - Andrew Garvie
• CRISPR-ChIP delineates a Menin-dependent oncogenic DOT1L complex in MLL leukaemia    - Omer Gilan
• Interpretation of exercise-induced changes in human skeletal muscle mRNA expression depends on the timing of the post-exercise biopsies - Jujiao Kuang
• VR-Omics: Spatially Resolved Transcriptomics Exploration in Virtual Reality - Denis Bienroth
• Genomic Occupancy of the Bromodomain Protein Bdf3 Is Dynamic during Differentiation of the African trypanosome   - Danae Schulz
• Survey of activation-induced genome architecture reveals a novel enhancer of Myc - Timothy Johanson
• Understanding mechanisms of aging in human brain organoids and in vivo. - Julio Aguado
• Iroquois 3 plays an essential role in odontogenesis   - Anrizandy Narwidina
• A comparison of epithelial cell content of oral samples estimated using cytology and DNA methylation - Yen Ting Wong
• Title:  Single-molecule simultaneous profiling of DNA methylation and DNA-protein interactions with Nanopore-DamID. - Yohaann M.A Jafrani
• METTL3-dependent m⁶A RNA methylation regulates inflammasome activation - Natalia Pinello
• A cellular and spatial atlas of mammalian tongue - Alistair Forrest
• Chromatin mobility and relocalization in DNA repair at centromeres - Anna Gonzalez Manjon
• Epigenetic Reprogramming of Tumor Associated Macrophages - Helen M McRae
• Elucidating the transcriptional landscape of oligodendroglioma - Elizabeth M Troy
• Novel Y chromosome-PML nuclear body disrupted in ATRX syndrome model - Vincent Harley
• A novel PCR-based molecular tool for the screening of hypermethylated genes associated with endometrial cancer, using Thinprep®   - Vinod Benjamin
• Investigating the role of developmentally-regulated genes in the genetic architecture of psychiatric disorders - Gavin j Sutton
• Novel activatable glucocorticoid receptor agonists as novel treatments for preterm birth - Rutu Dhavan
• Systematic loss of function screens identify pathway specific functional circular RNAs - Matthew Neve
• DNA methylation differences between two types of skeletal muscle fibre at rest and in response to high intensity interval training. - Andrew Palmer
• Mechanism and evolution of the ovarian somatic piRNA pathway in Diptera - Rippei Hayashi
• Enhancer-promoter interactome drives neuronal cell differentiation and contextualizes Alzheimer’s associated polymorphisms - Leaw Chui Li