Monday, 14th February 43rd Lorne Genome Conference 2022

Moderator - Mari Miyamoto, Commercial Director Asia Pacific & Japan, Oxford Nanopore Technologies

Speaker - Warren Bach, Strategic Relationship Manager ANZ, Oxford Nanopore Technologies

Speaker - Seth Cheetham, Mater Research Institute-University of Queensland

Speaker - Josie Gleeson. Centre for Stem Cell Systems, Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC, Australia

Breakfast served from 7:10am

• TBC - Josh Quick
• Integrated single-cell genomics to map immune cell states and predict cellular etiology of autoimmune risk loci. - Hamish W King
• An indigenous Australian genomic sequencing panel uncovers deep population structure and abundant novel variation - Matthew Silcocks
• L1 retrotransposon activation is deeply rooted into the developmental program of a specific neuronal lineage - Gabriela O Bodea

The conference acknowledges the support of:

The conference acknowledges the support of:

• Bayesian Inference for inferring intra-tumoral heterogeneity in single-cell RNA-seq - PuXue Qiao
• InterARTIC: an interactive web application for whole-genome nanopore sequencing analysis of SARS-CoV-2 and other viruses - James M Ferguson
• Detecting genomic variations in COVID-19 virus associated with worse disease outcome - Priya Ramarao-Milne
• SLOW5: a new file format enables massive acceleration of nanopore sequencing data analysis - Hasindu Gamaarachchi
• Comprehensive genetic diagnosis of tandem repeat expansion disorders with programmable targeted nanopore sequencing - Ira Deveson
• Small but mitey: high-quality long-read assembly of a streamlined mite genome from contaminated sequencing data - Richard J Edwards

• De novo design of CRISPR-Cas13b enables efficient silencing of SARS-CoV-2 and tumour pathogenic RNAs with single-base precision - Mohamed MF Fareh
• Manipulating Gene Expression in Eosinophils to Regulate Adipose Tissue Thermogenesis - Kate Quinlan
• Systematic screening reveals the functional circular RNA landscape of Wnt/beta-catenin signaling - Matthew Neve
• Mammalian transcription factors display diverse mechanisms of transactivation - Charles C Bell
• Integrating GWAS and 3D chromatin interactome data to identify multi-cancer risk genes in hormone-related cancers - Sarahi Rivera
• Developmental and post-natal regulation of gene expression by histone 3 lysine 4 merthyltransferases - Francis Stewart

The conference acknowledges the support of:

The conference acknowledges the support of:

• SET-domain proteins in epigenetic inheritance: hidden depths - Alyson Ashe
• PRC2 establishes H3K27me3 at developmental genes in growing oocytes and regulates offspring development via a genetically independent mechanism - Patrick Western
• A new female embryonic stem cell system that reveals the BAF complex as a key regulator of the establishment of X chromosome inactivation - Andrew Keniry
• Maternal SMCHD1 regulates Hox gene expression and patterning in the mouse embryo. - Natalia Benetti
• RNA-binding sites in PRC2 are required for the histone-methylation of chromatin in an RNA-independent manner - Qi Zhang
• Identification of DNA methylation biomarkers for prediction of response to neoadjuvant chemotherapy in triple-negative breast cancer - Braydon Meyer
• Understanding transgenerational epigenetic inheritance dynamics and heterogeneity - Rachel Woodhouse

The conference acknowledges the support of:

• An Aboriginal Australian Genome Project - Ashley Farlow
• Microchromosomes are building blocks of bird, reptile and mammal chromosomes   - Hardip Patel
• National Centre for Indigenous Genomics enabling the inclusion of Indigenous Australians in precision medicine - Hardip Patel
• Genetically Uncoupling Pain Perception from Sleep Defects following UV injury in Fly - Josephine N Massingham
• H3K4me3 and H3K27ac define the gene regulatory landscape during marsupial craniofacial development in the fat-tailed dunnart and provide insights into the drivers of heterochrony. - Laura E Cook
• Single-cell gene expression reveals context-specific and dynamic heritability in immune cell populations - Jose Alquicira Hernandez
• Single-cell eQTL mapping identifies cell type specific genetic control of autoimmune disease - Seyhan Yazar

Tuuli Lappelainen

The conference acknowledges the support of: 

• TBC - Tuuli Lappalainen

• Immune repertoire sequencing enables accurate clonality determination - Selva Kumari Ramasubramanian
• A hidden Markov model to identify inherited disease-causing variants using shared genetic markers  - Erandee Robertson
• Understanding The Tumour Microenvironment And Metastasis On Triple-negative Breast Cancer - Laura Rodriguez de la Fuente
• The BTR and Aurora B complexes regulate chromosome end dynamics during mitotic telomere deprotection - Samuel Rogers
• Accessing high-throughput functional assay data via MaveDB - Alan F Rubin
• Modelling XY intersex conditions through reprograming of patient fibroblasts into testicular Sertoli cells - Janelle Ryan
• The C.elegans TRIM protein NHL-2 regulates let-7 miRNA pathways through RNA binding domain - Nasim Saadati
• Yap regulates an SGK1/mTOR/SREBP-dependent lipogenic program to fuel liver cancer - Talhah Salmi
• Liver cryoinjury as novel localised acute liver injury method in the zebrafish - Marcos Sande-Melon
• Diagnosis of Australasian neuromuscular disease patients: insights from a comprehensive panel approach - Carolin K Scriba
• Quantifying the dynamics of exon ligation reveals long-distance coordination of co-transcriptional splicing  - Aditya J Sethi
• Towards Cas13-mediated transcriptional repression of tumour drivers with single-nucleotide precision - Carolyn E Shembrey
• Engineered barcode iPSCs coupled with unsupervised data analysis pipelines for scalable analysis of multi-lineage cell differentiation - Sophie Shen
• Diffusional variance signatures of single molecule dynamics in the translation complex profiling data - Nikolay E. Shirokikh
• Glucocorticoid regulation of primary ciliogenesis in the developing mouse kidney - Kelly L Short
• Methods for differential nucleosome occupancy detection in NOMe-Seq - Brandon Signal
• The role of Poly(A) polymerase – Pla1 in the MTREC complex mediated exosome targeting of CUTs - Anusree Lakshmi Sivadas
• Signatures of mutational processes in human nuclear and mitochondrial DNA evolution - Hamid Alinejad Rokny
• Benchmarking methods for the identification of spatially variable genes in spatial transcriptomics data sets - Natalie C Charitakis
• Total recall: one step recognition of moleculer barcodes, genes or gene Segments using deep convolutional networks  - Tansel Ersavas
• LRRC15 suppresses SARS-CoV-2 infection and controls collagen production - Lipin Loo
• Correlated histone FLIM-FRET and SPT microscopy: a method to determine nuclear protein dynamics within the chromatin nanoscale landscape. - Jieqiong Lou
• KLF1 acts as a pioneer transcription factor via SMARCA4 to open chromatin and facilitate recruitment of a settler transcription factor complex containing GATA1 and SCL - Graham Magor
• Robust differential composition and variability analysis for multisample single-cell and microbiome data - Stefano Mangiola
• Nonsense-mediated decay is highly divergent in the malaria parasite Plasmodium falciparum - Emma McHugh
• Regulatory mRNA-mRNA interactions are prevalent and coordinate gene expression in methicillin-resistant Staphylococcus aureus - Daniel G Mediati
• Combination of small non-coding RNAs as an efficient strategy for targeting oncogenic pathway - Melodie Migault
• TYRO3 controls Sertoli cell proliferation and germ cell survival in the testis - Zhenhua Ming
• Analysis of population genetic and phenotypic diversity reveal a predictable organisation of gene programs in the cell - Dalia Mizikovsky
• Investigating the impact of set-9, set-26, and Y73B3A.1 on transgenerational epigenetic inheritance. - Dhruv D Monteiro
• Whole-genome CRISPR-activation screen  identifies new genes that can control SARS-CoV-2 infection - Cesar Moreno
• FUBP1/Psi functions in the niche to non-autonomously control neural stem cell fate - Damien Muckle
• The cytopathological mechanisms caused by dj-1 loss in the d discoideum parkinsons disease model - Vanessa J Musco
• Improved identification of cell-free droplets and damaged cells in single-cell RNA-seq data - Walter Muskovic
• The eyes absent family of tyrosine phosphatases regulates mitosis through dephosphorylation of PLK1 - Christopher B Nelson
• Robust public computational services supporting Genome Assembly and Annotation for Australian Researchers - Tiffanie Nelson
• Building a spatial single-cell multi-omics atlas and cellular interactome for skin cancer - Guiyan Ni
• Finding needles in a haystack: using cis-regulatory elements to define heart-associated genes - Hieu T Nim
• The potency state of a stem cell governs replication stress management and tolerance - Aisling O'Connor
• Altered epigenetic programming of oocytes modulates offspring growth and accelerates bone development - Ruby Oberin
• Loss of Keap1 triggers Nrf2-mediated aberrant lysosomal biogenesis and post-developmental lethality - Athena Jessica S Ong
• Applying single-cell multi-omics approach to discover changes in circulating immune cells under long-term venetoclax treatment - Hongke Peng
• Classifying whole slide images based on Tumor Infiltrating Lymphocytes using deep learning  - Rashindrie Perera
• The DNA methylome of excitatory neurons in human sporadic Alzheimer’s disease - Thalia Perez-Suarez
• Polycomb-dependent epigenetic programming in the oocyte modulates brain development and behaviour in offspring - Sigrid Petautsching
• Significant and pervasive effects of RNA degradation on Nanopore direct RNA sequencing - Sefi Prawer
• Key regulators of adipose-resident eosinophil-driven metabolic homeostasis - Annalise M Psaila
• Targeted Degradation of β-Catenin and Wnt Pathway Suppression in Human Colorectal Cancer Cells Using a βTrCP-Derived bioPROTAC - Jacob Purcell
• Identification of a novel chromosome 14 deletion/duplication in a large Australian pedigree presenting with autosomal dominant slowly progressive late onset ataxia - Haloom Rafehi
• Alternative splicing in the human parasites Plasmodium falciparum and Toxoplasma gondii - Stuart A Ralph
• Cic function in the neural stem cell niche is essential to control stem cell fate - Brooke Kinsela
• Fusion to Alu strengthens L1 mobility and restraint - Nathan Smits
• Machine learning pipeline, VariantSpark + BitEpi, reveals novel variants and epistatic interactions associated with coronary artery disease - Letitia M.F. Sng
• Understanding the regulation of bivalent chromatin using unbiased functional genomics - Christina E Sparbier
• Screening for regulators of LINE-1 retroelements. - Jenny Steiner
• A genetic perspective on rapid adaptation in the globally invasive European starling (Sturnus vulgaris) - Katarina C Stuart
• Large field-of-view, high-resolution spatially resolved transcriptomics using DNA nanoball patterned array - Stephanie Sun
• Using consortium-level epigenetic data to identify cell type-specific genes provides a computational anchor to define biological diversity in single cell data   - Yuliangzi Sun
• Comprehensive evaluation of deconvolution methods for human brain gene expression - Gavin J Sutton
• UnNrf(2)ing the adaptive transcriptional responses following liver injury and during liver regeneration - Vicky Tan
• Characterising changes in ribosomal DNA chromatin during malignant transformation - Thejaani Udumanne
• Accurate identification of human microRNA-target interaction using machine learning  - Korawich Uthayopas
• Finding treatments for chromatin disorders: early postnatal interventions to improve neurodevelopmental outcomes - Hannah Vanyai
• Identifying non-genetic determinants of malignant clonal fitness at single cell resolution - Dane Vassiliadis
• Scalable and Highly Sensitive Single Cell RNA-seq through Combinatorial Barcoding   - Jiyoti Verma
• NT2/D1-cas9: a novel in vitro manipulatable model for male sex development - Brittany Vining
• Immune regulation of adipose tissue beiging – exploring the role of transcription factor Krüppel-like Factor 3 (KLF3) - Emily J Vohralik
• Genetic sex determination in a reptile departs from the classical amniote model while DNA methylation defines expression of key sex genes - Susan Wagner
• Investigating the relationship between alternative splicing and back-splicing in the human brain - Juli Wang
• A novel breast cancer risk-associated lncRNA named K-LNC promotes apoptosis of cancer cells. - Lu Wang
• Shining a light on the epigenetic modifier Smchd1 - Iromi Wanigasuriya
• dedUCE: efficient identification of ultraconserved elements and applications to genome assembly completeness - Cadel Watson
• Computational investigation of embryonic boundaries in the developing zebrafish from spatially resolved transcriptomes - Lisa N Waylen
• Long-read sequencing technologies unveil unexpected sequence, structure, and methylation variability in ribosomal RNA gene repeats   - Emiliana Weiss
• Erythrocyte chromatin accessibility throughout vertebrates - AnneMarie Welch
• Mapping DNA repair complexes at stalled and broken replication forks using super resolution microscopy - Donna R Whelan
• Gene-environment interactions underpinning temperature induced sex reversal in a dragon lizard   - Sarah Whiteley
• Uncovering the small RNA interactome and its roles in antibiotic tolerance in Staphylococcus aureus - Winton Wu
• SRP19 as a target in cancers with hemizygous loss of APC - Xinqi Xi
• The histone lysine acetyltransferase HBO1 (KAT7) regulates haematopoietic stem cell quiescence and self-renewal - Yuqing Yang
• NanoSplicer: Accurate identification of splice junctions using Oxford Nanopore sequencing - Yupei You
• Streamlined sequencing of hybridomas and single B cells with Oxford Nanopore long-reads - Kathleen Zeglinski
• Evaluation of clonality in lentigo maligna - Peinan Zhao