Welcome to ABACBS2020!

ABACBS 2020 Conference Committee
A welcome and introduction to our conference site, how to use it...

sBeacon: cloud-native genomic data exchange

Yatish Jain, Brendan Hosking, Laurence Wilson, Natalie Twine, Armita Zarnegar, Mercy Rophina, Vinod Scaria, Denis Bauer
The Beacon protocol was published last year (Fiume...

qc3C – reference-free quality assessment for Hi-C sequencing data.

Matthew DeMaere, Aaron Darling
Hi-C is a sample preparation method that enables h...

pyTCR: a comprehensive cloud-based platform for TCR-Seq data analysis using interactive notebooks to facilitate reproducibility and rigor of immunogenomics research

Kerui Peng, Jaqueline Brito, Guoyun Kao, Serghei Mangul
T cells are crucial components of the adaptive imm...

propeller: finding statistically significant differences in cell type proportions in single cell RNA-seq experiments

Belinda Phipson, Evangelyn Sim, Enzo Porrello, Alicia Oshlack
Single cell RNA Sequencing (scRNA-seq) has rapidly...

powerSFS: quantifying the intolerance of genes to mutation with a statistical model of the site frequency spectrum

Loic Thibaut, Eleni Giannoulatou
Scores of genic intolerance such as RVIS, GeVIR an...

linc2function: Predicting function of lncRNA transcripts using an Artificial Neural Network (ANN) Model

Yashpal Ramakrishnaiah, Levin Kuhlmann, Sonika Tyagi
Long Noncoding RNAs (LncRNA) modulate cellular pro...

genozip: an advanced universal compressor for genomic data files

Divon Lan
genozip is a new universal lossless compressor for...

eMST, a scalable and interpretable method for Phylogenetic analysis of hundreds and thousands of SARS-CoV-2 genomes

Sergey Knyazev, Harman Singh, Varuni Sarwal, Ram Ayyala, Daniel Novikov, Roya Hosseini, Serghei Mangul, Alex Zelikovsky
A novel coronavirus, known as SARS-CoV-2, was iden...

clonal tracking as quality control for mutational signature analysis

Christoffer Flensburg, Ian Majewski
High throughput sequencing of cancer samples is an...

ampir: an R package for fast genome-wide prediction of antimicrobial peptides

Legana Fingerhut, Ira Cooke, Jan Strugnell, David Miller, Norelle Daly
Antimicrobial peptides are natural antibiotics, pa...

Whole transcripts in genome assembly, annotation, and assessment: the draft genome assembly of the globally invasive common starling, Sturnus vulgaris

Katarina Stuart, Yuanyuan Cheng, Lee Rollins, Richard Edwards
Native to the Palearctic, the common starling (Stu...

Viral RNA metagenomics reveals the Australian bovine respiratory virome

Barbara Brito Rodriguez, Kay Anantanawat, Tony Batterham, Melinda Frost, Peter Kirkland, Edward Holmes, Aaron Darling
Metagenomic next-generation sequencing is transfor...

VIRUSBreakend: Viral Integration Recognition Using Single Breakends

Daniel Cameron, Anthony Papenfuss
An important cause of disease is the integration o...

Using single-cell cytometry to illustrate the generalisable unbiased evaluation of clustering algorithms using Pareto fronts

Givanna Putri, Irena Koprinska, Thomas Ashhurst, Nicholas King, Mark Read
Clustering is widely used in biological fields suc...

Using equivalence classes for differential transcript usage and variant detection in RNA-seq data

Marek Cmero, Breon Schmidt, Ian Majewski, Paul Ekert, Nadia Davidson, Alicia Oshlack
RNA sequencing (RNA-seq) has enabled high-throughp...

Understanding Polygenic Disease with BitEpi and EpiExplorer

Arash Bayat, Brendan Hosking, Yatish Jain, Cameron Hosking, Milindi Kodikara, Daniel Reti, Natalie Twine, Denis Bauer
Polygenic diseases are driven by a large number of...

Trycycler: working towards the perfect bacterial genome

Ryan Wick, Kathryn Holt
Long-read assembly has progressed rapidly in recen...

Transfer learning for data integration of single-cell RNA-seq and ATAC-seq

Yingxin Lin, Tung-Yu Wu, Sheng Wan, Jean Yang, Wing H. Wong, Y. X. Rachel Wang
Single-cell transcriptomics profiling with single-...

TrackSOM: immunopathogenic temporal mapping through clustering time-series cytometry data

Givanna H. Putri, Jonathan Chung, Davis N. Edwards, Felix Marsh-Wakefield, Suat Dervish, Irena Koprinska, Nicholas J.C. King, Thomas M. Ashhurst, Mark Read
Disease, and our immune response to it, are dynami...

The role of gene duplication in the evolution of snake venoms

Jack Clarke, Richard Edwards, Vicki Thomson
Snakes are one of the most venomous animals on the...

The landscape of alternative polyadenylation in CD8 T cells in single-cell transcriptome

Lixinyu Liu, Jiayu Wen
Alternative cleavage and polyadenylation (APA) ena...

The African Orphan Crops Consortium, alleviating stunting due to malnutrition one crop at a time

Bernice Waweru
The African Orphan Crops Consortium (AOCC) is a gl...

The AMPSphere: antimicrobial peptides (AMPs) in the global microbiome

Célio Dias Santos-Júnior, Thomas S. B. Schmidt, Anthony Fullam, Peer Bork, Xing-Ming Zhao, Luis Pedro Coelho
Antimicrobial peptides (AMPs) are short peptides t...

Tampa: interpretable analysis and visualization of metagenomics-based taxon abundance profiles

Jaqueline Brito, Varuni Sarwal, Serghei Mangul, David Koslicki
Taxonomic metagenome profiling aims to predict the...

Systematic evaluation for metrics of gene expression variability in single-cell RNA sequencing data

Huiwen Zheng, Atefeh Taherian Fard, Xiao Dong, Jessica Mar, Jan Vijg
During ageing, transcriptional noise has been show...

Systematic benchmarking of detection tools for CpG methylation from Nanopore sequencing

Zaka Yuen, Cameron Jack, Eduardo Eyras
Nanopore sequencing can access native DNA at singl...

Systematic Benchmark of aDNA Mapping Bias

Adrien Oliva, Raymond Tobler, Bastien Llamas, Alan Cooper, Yassine Souilmi
Recent advances in molecular techniques, as well a...

SpicyR - Spatial analysis of in situ cytometry data

Nicolas Canete, Ellis Patrick
Highly multiplexed imaging techniques such as cycl...

Spatial analysis of in situ cytometry data

Ellis Patrick, Nicolas Canete
Understanding the interplay between different type...

Single-cell and network analyses reveal organ-specific transcriptomic identity of adult fibroblasts

Elvira Forte, Mirana Ramialison, Hieu Nim, Milena Furtado
BACKGROUNDS. Organ fibroblasts are essential compo...

Single-cell Transcriptional Profiling Reveals Novel Cellular and Molecular Drivers of Cardiovascular Fibrosis

Malathi S.I. Dona, Micheal A. McLellan, Daniel A. Skelly, Maria Jelinic, Galen T. Squiers, Gabriella E. Farrugia, Anthony Vinh, Taylah L. Gaynor, Charles D. Cohen, Raghav Pandey, Henry Diep, Nadia A. Rosenthal, Grant R. Drummond, Alexander R. Pinto
Fibrosis is a leading factor in the development of...

Single-cell RNA-seq Analysis To Explore Bone-marrow Immune Landscape

Gunjan Dixit, Di Yu, Jiayu Wen
Bone marrow (BM) contains multiple immune cell sub...

Sex-specific co-expression: a baseline to explore disease

Sara Ballouz
Biological states such as cell-type, cell-state, t...

Secondary analysis of publicly available omics data across almost 3 million publications

Nicholas Darci-Maher, Serghei Mangul, Kerui Peng, Dat Duong, Eleazar Eskin, Jaqueline Brito, Anushka Rajesh, Andrew Smith, Reid F. Thompson, Abhinav Nellore, Casey Greene, Jonathan Jacobs
As today’s high throughput sequencing techniques...

Risk prediction survival model utilising both omics data and clinical data

Yunwei Zhang, Jean Yang, Samuel Mueller, Graham Mann
Utilisation of omics data such as gene expression ...

Revealing interactions between coding and non-coding transcripts in plants using heterogeneous networks

Joel Robertson, Stephen Davis, Nitin Mantri, Alice Johnstone
Once thought to be junk genetic material, non-codi...

Reference-free reconstruction and quantification of transcriptomes from Nanopore long-read sequencing

Ivan de la Rubia, Joel Indi, Silvia Carbonell-Sala, Julien Lagarde, Mar Alba, Eduardo Eyras
Single-molecule long-read sequencing with Nanopore...

Recurrent miscalling of missense variation from short-read genome sequence data

Matt Field, Dan Andrews
Short-read resequencing of genomes produces abunda...

Recovery of complete genomes and non-chromosomal replicons from activated sludge enrichment microbial communities using Nanopore long read metagenome sequencing

Rohan Williams, Krithika Arumugam, Irina Bessarab, Mindia Haryono, Xianghui Liu, Rogelio Montanez, Samarpita Roy, Guanglei Qiu, Daniela Drautz-Moses, Yingyu Law, Stefan Wuertz, Federico Lauro, Daniel Huson
New long read sequencing technologies offer huge p...

RNase III-CLASH of multi-drug resistant Staphylococcus aureus reveals a regulatory mRNA 3’UTR required for intermediate vancomycin resistance

Daniel G. Mediati, Julia L. Wong, Wei Gao, Stuart MacKellar, Chi Nam Ignatius Pang, Sylvania Wu, Winton Wu, Brandon Sy, Ian Monk, Joanna Richmond, Benjamin Howden, Tim P. Stinear, Sander Granneman, Jai J. Tree
Treatment of methicillin-resistant Staphylococcus ...

RNA splicing is a hierarchical supernetwork that co-operates to drive osteoblast differentiation

Angel Liang
Splicing is essential for the proper expression of...

Quick determination of RNA-Seq strandedness with how_are_we_stranded_here

Beth Signal, Tim Kahlke
RNA-Seq is a commonly performed method to analyse ...

Population dynamics of rDNA copy number in yeast and humans

Diksha Sharma, Sylvie Hermann Le Denmat, Nicholas Matzke, Lauri Saag, Katherine Hannan, Ross Hannan, Herwati Sudoyo, Murray Cox, Justin Sullivan, Austen Ganley
In most eukaryotes the ribosomal RNA genes (rDNA) ...

PhosR enables processing and functional analysis of phosphoproteomic data

Jieun Kim, Taiyun Kim, Nolan J Hoffman, Di Xiao, David James, Sean J Humphrey, Pengyi Yang
Mass spectrometry (MS)-based phosphoproteomics has...

Phage genome bioinformatics

Robert Edwards
Phages, viruses that infect bacteria, experience u...

PACIFIC: A lightweight deep-learning classifier of SARS-CoV-2 and co-infecting RNA viruses

Pablo Acera Mateos, Renzo Balboa, Simon Easteal, Eduardo Eyras, Hardip Patel
Viral co-infections occur in COVID-19 patients, po...

Over 25,000 metagenome assembled genomes reveal the development of the post-weaning pig gut microbial community

Daniela Gaio, Matthew Z. DeMaere, Kay Anantanawat, Toni A. Chapman, Steven P. Djordjevic, Aaron E. Darling
Building on a new lower-cost metagenome sequencing...

Optimising genomic approaches for detection of vancomycin resistant Enterococcus faecium transmission in the hospital environment

Charlie Higgs, Claire Gorrie, Norelle Sherry, Ben Howden
Objectives:

Vancomycin-resistant Enteroco...

Nimpress brings polygenic scores to the sequencing era

Mark Pinese, Emilie Wilkie, Mark Cowley
Polygenic scores enable the quantitative predictio...

New insights into plant-microbe interactions through Quantitative Trait Locus (QTL) mapping

Charlotte Francois
Like humans, plants are colonised by bacteria on v...

New Insights Of Cancer DNA Methylation By Studies Of Pre-Leukemic Stem Cells In A Mouse Model Of T-Cell Acute Lymphoblastic Leukemia

Feng Yan, David J. Curtis, Francine E. Garrett-Bakelman, Nicholas C. Wong, Pieter Van Vlierberghe
The role of DNA methylation in the initiation and ...

Navigating through ‘omics data: a multivariate perspective

Kim-Anh Lê Cao
Technological improvements have allowed for the co...

Moving beyond RNA sequence: uncovering the functional role of RNA structure

Vincent Corbin, Phillip Tomezko, Paromita Gupta, Margalit Glasgow, Sitara Persad, Lachlan McIntosh, Anthony Papenfuss, Silvia Rouskin
RNA is unique among biomolecules in its possession...

Molecular barcoding of native RNAs using nanopore sequencing and deep learning

Martin A. Smith, Tansel Ersavas, James Ferguson, Huanle Liu, Morghan C. Lucas, Oguzhan Begik, Lilly Bojarski, Kirston Barton, Eva Maria Novoa
Nanopore sequencing enables direct measurement of ...

Mining the wastewater microbiome with a metagenomic Hi-C approach to identify antimicrobial resistance risk in Australia

Johanna Wong, Ethan Wyrsch, Daniel Bogema, Faisal Hai, Jawad Al-Rifai, Kay Anantanawat, Matthew DeMaere, Sotirios Vasileiadis, Erica Donner, Steven Djordjevic, Aaron Darling
The rise of antimicrobial resistance (AMR) poses a...

Microproteins, Mobile Genetic elements and Strain-level resolution in the microbiome – a path to precision medicine

Ami Bhatt
From climate change to agriculture, and human hea...

Metagenomic Geolocation with Read Signature Clustering

Timothy Chappell, Shlomo Geva, James Hogan, David Lovell, Dimitri Perrin, Andrew Trotman
Metagenomic sequencing produces large quantities o...

Mapping cancer transcriptomes with long-read sequencing

Stephen Kazakoff, Pamela Mukhopadhyay, Futoshi Kawamata, Catherine Bond, Katia Nones, Akinobu Takeomi, Vicki Whitehall, Ann-Marie Patch
Whilst tissue-specific transcript expression is hi...

Making sense of heterogeneity in gene expression data

Jessica Mar
Any model that we apply makes assumptions. But how...

Machine Learning in Dynamic Microscopy

Khelina Fedorchuk, Damien Hicks, Sarah Russel, Kajal Zibaei
The tracking of individual, proliferating cells ov...

Machine Learning Prediction of End-stage Kidney Disease for Clinical Decision Support

Dan Andrews, Aaron Chuah
Chronic kidney disease (CKD) is a major source of ...

Longitudinal single-cell immune profiling revealed distinct innate immune response in asymptomatic COVID-19 patients

Yue You
Recent studies have characterized the single-cell ...

Long short-term memory RNN for mirtron identification

Ke Ding, Jiayu Wen
MicroRNAs are small regulatory RNAs mediate extens...

Learning Distance-Dependent Motif Interactions: An Interpretable CNN Model of Genomic Events

Thomas Quinn, Dang Nguyen, Phuoc Nguyen, Sunil Gupta, Svetha Venkatesh
In most biological studies, prediction is used pri...

JAFFAL: Detecting fusion genes with long read transcriptome sequencing

Nadia Davidson, Ying Chen, Jonathan Göke, Alicia Oshlack
Genomic rearrangements are common in the cancer la...

Is it a Mammal Thing? Determining When the Change in rDNA Unit Size Occurred in Amniotes

Emma Macdonald, Austen Ganley, Richard Edwards
The ribosomal RNA genes in eukaryotes are organise...

Integrating multi-modal single-cell studies with a latent component-based approach

Al J Abadi, Kim-Anh Lêcao
Single-cell multi-modal sequencing offers unpreced...

Integrated transcriptional and chromatin accessibility profiling uncovers sex-specific adipose tissue imprinting of regulatory T cells

David Chisanga, Ajith Vasanthakumar, Wei Shi, Axel Kallies
Integrated transcriptional and chromatin accessibi...

Integrated transcription factor profiling with transcriptome analysis: identification of L1PA2 transposons as global regulatory modulators in a breast cancer model

Jiayue-Clara Jiang, Joe Rothnagel, Kyle Upton
LINE1 retrotransposons occupy approximately 17% of...

Implementing an integrated analysis to identify and validate circular RNAs using patient-derived neuronal stem cells.

Oak Hatzimanolis, Alan Mackay-Sim, Alexandre Cristino
In recent years it has been determined that a larg...

Image-based Predictive Modelling for the Characterisation of Cellular Senescence

Ebony Watson, Atefeh Taherian Fard, Farhad Soheilmoghaddam, Ernst Eolvetang, Jessica Mar
Senescence is a cellular stress response character...

ISOTOPE: ISOform-guided prediction of epiTOPEs in cancer

Juan Luis Trincado, Eduardo Eyras
Immunotherapies provide effective treatments for p...

Hypothesis generation in the age of cell atlases

Fabio Zanini, Julie Thoms, Bojk Berghuis, Racquel Domingo-Gonzales, Zhiyuan Yao, Shirit Einav, Cristina Alvira, David Cornfield, Stephen Quake, John Pimanda
While many laboratories are driven by computationa...

How does gene expression entropy change along developmental trajectories?

Elisabeth Roesch, Anissa Guillemin, Michael P.H. Stumpf, Megan Anne Coomer
The differentiation of stem or progenitor cells is...

How bioinformatics and genomics helped Australia’s COVID response

Torsten Seemann
This talk will tell the story of how Victoria...

How Ancient genomes can help Aboriginal Australian communities: lessons from the Cape York project

Sally Wasef, Joanne Wright, Michael Westaway, Clarence Flinders
Paleogenetics is a relatively new and promising fi...

Finding signatures of alternative polyadenylation as cancer biomarkers

Nitika Kandhari, Paul Harrison, Kaylene Simpson, David Powell, Traude Beilharz, Iva Nikolic, Robert Vary, Karla Cowley
Alternative transcript cleavage and Polyadenylatio...

Features that determine 5’ cryptic splice site selection in genetic disorders

Ruebena Dawes, Sandra Cooper
Background:
Splicing variants are a common cau...

Features of functional human genes

Paul Gardner, Helena Cooper
Proteins and non-coding RNAs are functional produc...

Fate specification and variability in cell lineage trees

Caleb Lau, Terry Speed, Sarah Russell, Damien Hicks
Cell lineage trees provide a blueprint for underst...

Exploring mechanisms of nephron maturation using scRNAseq

Sarah Williams, Rachel Lam, Yasmin Neirijnck, Pauline Sararols, Chloé Mayère, Serge Nef, Alex Combes
Three paired kidney structures arise sequentially ...

Exploring Neural Network models for CNV detection from Exome Data

Simon Sadedin
In recent years many methods have been developed t...

Evaluation of recombination detection methods for viral sequence analysis

Frederick Jaya, Barbara Brito-Rodriguez, Aaron Darling
To accurately infer the evolutionary history of vi...

Discovery of Tissue-specific Gene Expression Patterns in CD8 T Cells by Single-cell RNA-seq

Ying Zheng, Di Yu, Jiayu Wen
The current most effective clinical cancer treatme...

Direct RNA sequencing identifies isoform specific structures

Yue Wan
The ability to correctly assign structure informat...

Developing a computational safeguard to detect gene drive systems in wild populations

Aidan Tay, Cameron Hosking, Brendan Hosking, Suzanne Scott, Daniel Reti, Aidan O'Brien, Denis Bauer, Laurence Wilson
Genome editing technologies such as CRISPR-Cas9, h...

Developing a computational analysis to identify differentially allelic expressed loci in patient-derived stem cells

Daniel Russell, Alexandre S. Cristino
Epigenetics is the inherited and acquired modifica...

Detection of recombination amongst SARS-CoV-2 strains

Cameron Hosking, Daniel Reti, Brendan Hosking, Suzanne Scott, Aidan Tay, Denis Bauer, Laurence Wilson
The emergence and spread of the SARS-CoV-2 virus h...

Detection and identification of cis-regulatory elements using change-point and classification algorithms

Dominic Maderazo, Jennifer Flegg, Manjula Algama, Mirana Ramialison, Jonathan Keith
Transcriptional regulation is primarily mediated b...

DNA methylation differences in human placenta from female and male bearing pregnancies

Qianhui Wan, Melanie Smith, Konstantinos Bogias, Tanja Jankovic-Karasoulos, Dale McAninch, Dylan McCullough, Shalem Leemaqz, Jimmy Breen, Claire Roberts
Sex differences in fetal growth and development ar...

Creating accountability in human population genetics using base editing tools

Keolu Fox
Appropriate empirical-based evidence and detailed ...

Confidence and truth in phylogenomics

Robert Lanfear
How do you estimate a good phylogeny? How do you k...

Comprehensive characterization of single cell full-length isoforms in human and mouse with long-read sequencing

Luyi Tian, Jafar Jabbari, Matthew Ritchie
Alternative splicing shapes the phenotype of cells...

Comprehensive analysis of usability and archival stability of RNA-seq tools

Karishma Chhugani, Dhrithi Deshpande, Serghei Mangul
As technology has advanced, RNA-seq methods have b...

Comparative 3D Genome Organization in Apicomplexan Parasites

Evelien Bunnik, Aarthi Venkat, Ferhat Ay, Karine Le Roch
The malaria parasite, Plasmodium falciparum, is a ...

Characterising Diversity in Gene Regulation Across the Indonesian Archipelago

Irene Gallego Romero
Title: Genetic Drivers Of Gene Expression And DNA ...

Characterisation of transcript expression in placenta across early gestation reveals variable transcript usage

Konstantinos Bogias, Stephen Pederson, Qianhui Wan, Melanie Smith, James Breen, Claire Roberts
The human placenta is a rapidly developing, highly...

Characterisation of a convergent malignant phenotype in B-cell acute lymphoblastic leukaemia

Adria Closa, Marina Reixachs, Eduardo Eyras
Acute lymphoblastic leukaemia (ALL) is the most co...

Challenges and Opportunities for Bioinformatics and Computational Biology in Plant Science

Seung Rhee
Plants make up the biggest biotic component of the...

Challenges In Aboriginal health in the genomics era

Alex Brown
Engagement in the genomic era poses significant co...

CRISPR, faster, better - The Crackling method for whole-genome target detection

Jacob Bradford, Timothy Chappell, Brendan Hosking, Laurence Wilson, Dimitri Perrin
CRISPR-Cas9 systems have become a leading tool for...

Binning Metagenomic Sequences

Yu Lin
Metagenomics studies have provided key insights in...

Best practices for single-cell expression Quantitative Trait Locus (sc-eQTL) mapping studies from simulated data

Christina Azodi, Davis McCarthy
Advances in single-cell (sc) technologies have mad...

Best practices for bioinformatics command-line software with Bionitio

Bernard Pope, Peter Georgeson, Anna Syme, Jessica Chung, Michael Milton, Harriet Dashnow, Andrew Lonsdale, Clare Sloggett, David Powell
The results-driven focus of bioinformatics means t...

Benchmarking single cell transcriptomes with bulk transcriptional atlases.

Yidi Deng, Kim-Anh Lê Cao, Choi Jarny, Christine Wells

Single cell RNA sequencing (scRNA-seq) allows...

Benchmarking single cell RNA-sequencing simulation methods

Yue Cao, Pengyi Yang, Jean Yang
Single cell RNA-sequencing (scRNA-seq) is a powerf...

AusTrakka – Working towards integrated pathogen genomics for SARS-CoV-2

Clare Sloggett, Torsten Seemann, Anders Goncalves Da Silva
The COVID-19 pandemic has highlighted the need for...

Assessing PacBio long reads and de novo genome assembly tools for useability and suitability to applications where resources are limited.

Chelsea Matthews, Nathan Watson-Haigh
Due to the further development of long read sequen...

Application of mixture model to RNA-seq data to discover ageing regulators

Sasdekumar Loganathan, Atefeh Taherian Fard, Jessica Mar, Ameya Kulkarni
Ageing is a complex process where the combined eff...

Anthroponotic transmission and adaptive introgression underlies cryptic population structure of Cryptosporidium hominis in Africa

Swapnil Tichkule, Aaron Jex, Cock Van Oosterhout, Simone Cacciò
INTRODUCTION: Cryptosporidiosis is a major cause o...

An integrated approach for interrogating the dynamics of co-transcriptional splicing with unparalleled depth and minimal bias

A.J. Sethi, Rippei Hayashi
Although dysregulated alternative splicing underli...

An automated framework for elucidating hierarchical relationships in high dimensional cytometry data

Adam Chan, Ellis Patrick, Jean Yang
With the progressive influx of high dimensional cy...

An Open Platform for Cannabis Genomics Research

Locedie Mansueto, Ramil Mauleon, Tobias Kretzschmar, Graham King
Recent global appreciation of the therapeutic prop...

An Evolutionary Approach to Network Analysis of Cancer Transcriptomes Reveals Common Indicators of Enhanced Malignancy Across a Range of Solid Tumours

David Goode, Anna Trigos, Rick Pearson, Tony Papenfuss
Despite diverse origins and significant genomic he...

Alu Repeat Diversity in the Human Genome

Renzo Balboa, Simon Easteal, Hardip Patel
More than half of the human genome is comprised of...

Accurate detection of cell free microbial DNA using a contaminant-controlled analysis framework

Enrique Zozaya-Valdés, Stephen Q. Wong, Jeanette Raleigh, Athena Hatzimihalis, Sarah Ftouni, Anthony T. Papenfuss, Shahneen Sandhu, Mark A. Dawson, Sarah-Jane Dawson
The human microbiome plays an important role in ca...

A workflow for the detection and phylogenetic placement of eukaryotes from metagenomes

Heroen Verbruggen, Bobbie Shaban
Microbial eukaryotes (protists) play key roles in ...

A statistical approach for modelling differential distributions in single-cell transcriptomic data

Malindrie Dharmaratne, Ameya Kulkarni, Atefeh Taherian Fard, Ernst Wolvetang, Nir Barzilai, Jessica C Mar
Single cell RNA sequencing (scRNA-seq) allows the ...

A predictive model for commonly-repressed polycomb-target genes dissects DNA sequence from gene expression

Emma Gail, Sonika Tyagi, Chen Davidovich
BACKGROUND: Histone H3 lysine 27 trimethylation (H...

A multivariate method to correct for batch effects in microbiome data

Yiwen Wang, Kim-Anh Lê Cao
Microbial research has become critical to investig...

A multi-step model for micobiome data with application to Parkinson's disease prediction

Xiangnan Xu, Samuel Mueller, Jean Yang, Michal Lubomski, Ryan Davis, Andrew Holmes, Carolyn Sue
Parkinson's disease (PD) is one of the most common...

A message from ABACBS2020 Gold Sponsor CSL

A message from ABACBS2020 Gold Sponsor CSL

A machine learning model to predict splice factor expression directly from transcriptome-wide splicing patterns

A.J. Sethi, Pablo Acera Mateos, Renzo Balboa, Emiliana Weiss, Attila Horvath
Dysregulated splicing is a major driver of cancer ...

A high-quality reference genome for the plant pathogen, Phytophthora cinnamomi

Amy Longmuir, Peter Beech, Mark Richardson
The plant pathogen, Phytophthora cinnamomi results...

A comprehensive benchmarking of WGS-based structural variant callers

Varuni Sarwal, Sebastian Niehus, Ram Ayyala, Eleazar Eskin, Jonathan Flint, Serghei Mangul
Structural variants (SVs) are genomic regions that...

A comprehensive analysis of code and data availability in biomedical research

Dhrithi Deshpande, Ruiwei Guo, Serghei Mangul
In biomedical research, it is not only imperative ...

A Deep Learning Approach to Recover Combination of Biologically Significant Motifs

Tarun Bonu, Sonika Tyagi
DNA or RNA motifs are short (5-20 bp) recurring pa...

3DFAACTS-SNP: Using regulatory T cell-specific epigenomics data to uncover candidate mechanisms of Type-1 Diabetes (T1D) risk

Ning Liu, Timothy Sadlon, Ying Ying Wong, Stephen Pederson, Simon Barry, Jimmy Breen
Background
Genome-wide association studies (GW...