#Hi-C
- 3DFAACTS-SNP: Using regulatory T cell-specific epigenomics data to uncover candidate mechanisms of Type-1 Diabetes (T1D) risk
- Comparative 3D Genome Organization in Apicomplexan Parasites
- Mining the wastewater microbiome with a metagenomic Hi-C approach to identify antimicrobial resistance risk in Australia
- qc3C – reference-free quality assessment for Hi-C sequencing data.
#transcription
- 3DFAACTS-SNP: Using regulatory T cell-specific epigenomics data to uncover candidate mechanisms of Type-1 Diabetes (T1D) risk
- A predictive model for commonly-repressed polycomb-target genes dissects DNA sequence from gene expression
- Systematic evaluation for metrics of gene expression variability in single-cell RNA sequencing data
#GWAS
#gene function
- 3DFAACTS-SNP: Using regulatory T cell-specific epigenomics data to uncover candidate mechanisms of Type-1 Diabetes (T1D) risk
- Challenges and Opportunities for Bioinformatics and Computational Biology in Plant Science
- Creating accountability in human population genetics using base editing tools
- Features of functional human genes
- Phage genome bioinformatics
- PhosR enables processing and functional analysis of phosphoproteomic data
- linc2function: Predicting function of lncRNA transcripts using an Artificial Neural Network (ANN) Model
#deep learning
- A Deep Learning Approach to Recover Combination of Biologically Significant Motifs
- Exploring Neural Network models for CNV detection from Exome Data
- Learning Distance-Dependent Motif Interactions: An Interpretable CNN Model of Genomic Events
- Long short-term memory RNN for mirtron identification
- Machine Learning in Dynamic Microscopy
- Molecular barcoding of native RNAs using nanopore sequencing and deep learning
- PACIFIC: A lightweight deep-learning classifier of SARS-CoV-2 and co-infecting RNA viruses
- The landscape of alternative polyadenylation in CD8 T cells in single-cell transcriptome
- linc2function: Predicting function of lncRNA transcripts using an Artificial Neural Network (ANN) Model
#machine learning
- A Deep Learning Approach to Recover Combination of Biologically Significant Motifs
- A machine learning model to predict splice factor expression directly from transcriptome-wide splicing patterns
- A predictive model for commonly-repressed polycomb-target genes dissects DNA sequence from gene expression
- Exploring Neural Network models for CNV detection from Exome Data
- Image-based Predictive Modelling for the Characterisation of Cellular Senescence
- Learning Distance-Dependent Motif Interactions: An Interpretable CNN Model of Genomic Events
- Long short-term memory RNN for mirtron identification
- Machine Learning Prediction of End-stage Kidney Disease for Clinical Decision Support
- Machine Learning in Dynamic Microscopy
- PACIFIC: A lightweight deep-learning classifier of SARS-CoV-2 and co-infecting RNA viruses
- Risk prediction survival model utilising both omics data and clinical data
- The landscape of alternative polyadenylation in CD8 T cells in single-cell transcriptome
- TrackSOM: immunopathogenic temporal mapping through clustering time-series cytometry data
- Transfer learning for data integration of single-cell RNA-seq and ATAC-seq
- ampir: an R package for fast genome-wide prediction of antimicrobial peptides
#sequence analysis
- A Deep Learning Approach to Recover Combination of Biologically Significant Motifs
- Detection and identification of cis-regulatory elements using change-point and classification algorithms
- ampir: an R package for fast genome-wide prediction of antimicrobial peptides
#gene regulation
- A Deep Learning Approach to Recover Combination of Biologically Significant Motifs
- A machine learning model to predict splice factor expression directly from transcriptome-wide splicing patterns
- A predictive model for commonly-repressed polycomb-target genes dissects DNA sequence from gene expression
- An integrated approach for interrogating the dynamics of co-transcriptional splicing with unparalleled depth and minimal bias
- Characterising Diversity in Gene Regulation Across the Indonesian Archipelago
- Comparative 3D Genome Organization in Apicomplexan Parasites
- DNA methylation differences in human placenta from female and male bearing pregnancies
- How does gene expression entropy change along developmental trajectories?
- Moving beyond RNA sequence: uncovering the functional role of RNA structure
- PhosR enables processing and functional analysis of phosphoproteomic data
- RNA splicing is a hierarchical supernetwork that co-operates to drive osteoblast differentiation
- Single-cell Transcriptional Profiling Reveals Novel Cellular and Molecular Drivers of Cardiovascular Fibrosis
- The role of gene duplication in the evolution of snake venoms
#biomedical informatics
- A comprehensive analysis of code and data availability in biomedical research
- Features that determine 5’ cryptic splice site selection in genetic disorders
- ISOTOPE: ISOform-guided prediction of epiTOPEs in cancer
- Machine Learning Prediction of End-stage Kidney Disease for Clinical Decision Support
- New Insights Of Cancer DNA Methylation By Studies Of Pre-Leukemic Stem Cells In A Mouse Model Of T-Cell Acute Lymphoblastic Leukemia
- Recurrent miscalling of missense variation from short-read genome sequence data
- Risk prediction survival model utilising both omics data and clinical data
- Single-cell and network analyses reveal organ-specific transcriptomic identity of adult fibroblasts
- Understanding Polygenic Disease with BitEpi and EpiExplorer
#reproducibility
- A comprehensive analysis of code and data availability in biomedical research
- Comprehensive analysis of usability and archival stability of RNA-seq tools
- Secondary analysis of publicly available omics data across almost 3 million publications
- pyTCR: a comprehensive cloud-based platform for TCR-Seq data analysis using interactive notebooks to facilitate reproducibility and rigor of immunogenomics research
#open source
- A comprehensive analysis of code and data availability in biomedical research
- An Open Platform for Cannabis Genomics Research
- Best practices for bioinformatics command-line software with Bionitio
- Comprehensive analysis of usability and archival stability of RNA-seq tools
#structural variants
- A comprehensive benchmarking of WGS-based structural variant callers
- Alu Repeat Diversity in the Human Genome
- VIRUSBreakend: Viral Integration Recognition Using Single Breakends
#DNA sequencing
- A comprehensive benchmarking of WGS-based structural variant callers
- Anthroponotic transmission and adaptive introgression underlies cryptic population structure of Cryptosporidium hominis in Africa
- Developing a computational analysis to identify differentially allelic expressed loci in patient-derived stem cells
- Exploring Neural Network models for CNV detection from Exome Data
- Is it a Mammal Thing? Determining When the Change in rDNA Unit Size Occurred in Amniotes
- Recurrent miscalling of missense variation from short-read genome sequence data
- Secondary analysis of publicly available omics data across almost 3 million publications
- Systematic benchmarking of detection tools for CpG methylation from Nanopore sequencing
- VIRUSBreakend: Viral Integration Recognition Using Single Breakends
- clonal tracking as quality control for mutational signature analysis
- genozip: an advanced universal compressor for genomic data files
- qc3C – reference-free quality assessment for Hi-C sequencing data.
#benchmarking
- A comprehensive benchmarking of WGS-based structural variant callers
- A multivariate method to correct for batch effects in microbiome data
- Assessing PacBio long reads and de novo genome assembly tools for useability and suitability to applications where resources are limited.
- Benchmarking single cell RNA-sequencing simulation methods
- Benchmarking single cell transcriptomes with bulk transcriptional atlases.
- Best practices for single-cell expression Quantitative Trait Locus (sc-eQTL) mapping studies from simulated data
- Quick determination of RNA-Seq strandedness with how_are_we_stranded_here
- Reference-free reconstruction and quantification of transcriptomes from Nanopore long-read sequencing
- Systematic Benchmark of aDNA Mapping Bias
- Systematic benchmarking of detection tools for CpG methylation from Nanopore sequencing
- Systematic evaluation for metrics of gene expression variability in single-cell RNA sequencing data
- Using single-cell cytometry to illustrate the generalisable unbiased evaluation of clustering algorithms using Pareto fronts
- clonal tracking as quality control for mutational signature analysis
#pathogens
#long reads
- A high-quality reference genome for the plant pathogen, Phytophthora cinnamomi
- Assessing PacBio long reads and de novo genome assembly tools for useability and suitability to applications where resources are limited.
- Direct RNA sequencing identifies isoform specific structures
- Is it a Mammal Thing? Determining When the Change in rDNA Unit Size Occurred in Amniotes
- JAFFAL: Detecting fusion genes with long read transcriptome sequencing
- Mapping cancer transcriptomes with long-read sequencing
- Microproteins, Mobile Genetic elements and Strain-level resolution in the microbiome – a path to precision medicine
- Molecular barcoding of native RNAs using nanopore sequencing and deep learning
- Recovery of complete genomes and non-chromosomal replicons from activated sludge enrichment microbial communities using Nanopore long read metagenome sequencing
- Reference-free reconstruction and quantification of transcriptomes from Nanopore long-read sequencing
- Systematic benchmarking of detection tools for CpG methylation from Nanopore sequencing
- The African Orphan Crops Consortium, alleviating stunting due to malnutrition one crop at a time
- Trycycler: working towards the perfect bacterial genome
#plants
- A high-quality reference genome for the plant pathogen, Phytophthora cinnamomi
- A workflow for the detection and phylogenetic placement of eukaryotes from metagenomes
- An Open Platform for Cannabis Genomics Research
- Challenges and Opportunities for Bioinformatics and Computational Biology in Plant Science
- New insights into plant-microbe interactions through Quantitative Trait Locus (QTL) mapping
- Revealing interactions between coding and non-coding transcripts in plants using heterogeneous networks
#RNA splicing
- A machine learning model to predict splice factor expression directly from transcriptome-wide splicing patterns
- An integrated approach for interrogating the dynamics of co-transcriptional splicing with unparalleled depth and minimal bias
- Characterisation of a convergent malignant phenotype in B-cell acute lymphoblastic leukaemia
- Characterisation of transcript expression in placenta across early gestation reveals variable transcript usage
- Features that determine 5’ cryptic splice site selection in genetic disorders
- Learning Distance-Dependent Motif Interactions: An Interpretable CNN Model of Genomic Events
- Moving beyond RNA sequence: uncovering the functional role of RNA structure
#networks
- A machine learning model to predict splice factor expression directly from transcriptome-wide splicing patterns
- An Evolutionary Approach to Network Analysis of Cancer Transcriptomes Reveals Common Indicators of Enhanced Malignancy Across a Range of Solid Tumours
- RNase III-CLASH of multi-drug resistant Staphylococcus aureus reveals a regulatory mRNA 3’UTR required for intermediate vancomycin resistance
- Revealing interactions between coding and non-coding transcripts in plants using heterogeneous networks
- Sex-specific co-expression: a baseline to explore disease
#sponsors
#metagenomics
- A multi-step model for micobiome data with application to Parkinson's disease prediction
- A multivariate method to correct for batch effects in microbiome data
- A workflow for the detection and phylogenetic placement of eukaryotes from metagenomes
- Accurate detection of cell free microbial DNA using a contaminant-controlled analysis framework
- Binning Metagenomic Sequences
- Metagenomic Geolocation with Read Signature Clustering
- Microproteins, Mobile Genetic elements and Strain-level resolution in the microbiome – a path to precision medicine
- Mining the wastewater microbiome with a metagenomic Hi-C approach to identify antimicrobial resistance risk in Australia
- Over 25,000 metagenome assembled genomes reveal the development of the post-weaning pig gut microbial community
- Recovery of complete genomes and non-chromosomal replicons from activated sludge enrichment microbial communities using Nanopore long read metagenome sequencing
- Tampa: interpretable analysis and visualization of metagenomics-based taxon abundance profiles
- The AMPSphere: antimicrobial peptides (AMPs) in the global microbiome
- Viral RNA metagenomics reveals the Australian bovine respiratory virome
#microbiome
- A multi-step model for micobiome data with application to Parkinson's disease prediction
- A multivariate method to correct for batch effects in microbiome data
- Accurate detection of cell free microbial DNA using a contaminant-controlled analysis framework
- Microproteins, Mobile Genetic elements and Strain-level resolution in the microbiome – a path to precision medicine
- Mining the wastewater microbiome with a metagenomic Hi-C approach to identify antimicrobial resistance risk in Australia
- New insights into plant-microbe interactions through Quantitative Trait Locus (QTL) mapping
- Over 25,000 metagenome assembled genomes reveal the development of the post-weaning pig gut microbial community
- The AMPSphere: antimicrobial peptides (AMPs) in the global microbiome
#disease
- A multi-step model for micobiome data with application to Parkinson's disease prediction
- Accurate detection of cell free microbial DNA using a contaminant-controlled analysis framework
- Characterisation of a convergent malignant phenotype in B-cell acute lymphoblastic leukaemia
- Developing a computational analysis to identify differentially allelic expressed loci in patient-derived stem cells
- Features that determine 5’ cryptic splice site selection in genetic disorders
- Implementing an integrated analysis to identify and validate circular RNAs using patient-derived neuronal stem cells.
- Integrated transcription factor profiling with transcriptome analysis: identification of L1PA2 transposons as global regulatory modulators in a breast cancer model
- Machine Learning Prediction of End-stage Kidney Disease for Clinical Decision Support
- Mapping cancer transcriptomes with long-read sequencing
- New Insights Of Cancer DNA Methylation By Studies Of Pre-Leukemic Stem Cells In A Mouse Model Of T-Cell Acute Lymphoblastic Leukemia
- Optimising genomic approaches for detection of vancomycin resistant Enterococcus faecium transmission in the hospital environment
- Recurrent miscalling of missense variation from short-read genome sequence data
- Single-cell and network analyses reveal organ-specific transcriptomic identity of adult fibroblasts
- Understanding Polygenic Disease with BitEpi and EpiExplorer
- Using equivalence classes for differential transcript usage and variant detection in RNA-seq data
- clonal tracking as quality control for mutational signature analysis
#nutrition
#statistics
- A multivariate method to correct for batch effects in microbiome data
- A statistical approach for modelling differential distributions in single-cell transcriptomic data
- An automated framework for elucidating hierarchical relationships in high dimensional cytometry data
- Application of mixture model to RNA-seq data to discover ageing regulators
- Integrating multi-modal single-cell studies with a latent component-based approach
- Making sense of heterogeneity in gene expression data
- Navigating through ‘omics data: a multivariate perspective
- New insights into plant-microbe interactions through Quantitative Trait Locus (QTL) mapping
- Nimpress brings polygenic scores to the sequencing era
- powerSFS: quantifying the intolerance of genes to mutation with a statistical model of the site frequency spectrum
- propeller: finding statistically significant differences in cell type proportions in single cell RNA-seq experiments
#batch effects
#epigenetics
#gene expression
- A predictive model for commonly-repressed polycomb-target genes dissects DNA sequence from gene expression
- An Evolutionary Approach to Network Analysis of Cancer Transcriptomes Reveals Common Indicators of Enhanced Malignancy Across a Range of Solid Tumours
- Discovery of Tissue-specific Gene Expression Patterns in CD8 T Cells by Single-cell RNA-seq
- How does gene expression entropy change along developmental trajectories?
- Making sense of heterogeneity in gene expression data
- Single-cell Transcriptional Profiling Reveals Novel Cellular and Molecular Drivers of Cardiovascular Fibrosis
#single cell
- A statistical approach for modelling differential distributions in single-cell transcriptomic data
- An automated framework for elucidating hierarchical relationships in high dimensional cytometry data
- Benchmarking single cell RNA-sequencing simulation methods
- Benchmarking single cell transcriptomes with bulk transcriptional atlases.
- Best practices for single-cell expression Quantitative Trait Locus (sc-eQTL) mapping studies from simulated data
- Challenges and Opportunities for Bioinformatics and Computational Biology in Plant Science
- Discovery of Tissue-specific Gene Expression Patterns in CD8 T Cells by Single-cell RNA-seq
- Exploring mechanisms of nephron maturation using scRNAseq
- Fate specification and variability in cell lineage trees
- How does gene expression entropy change along developmental trajectories?
- Hypothesis generation in the age of cell atlases
- Image-based Predictive Modelling for the Characterisation of Cellular Senescence
- Integrating multi-modal single-cell studies with a latent component-based approach
- Longitudinal single-cell immune profiling revealed distinct innate immune response in asymptomatic COVID-19 patients
- Sex-specific co-expression: a baseline to explore disease
- Single-cell RNA-seq Analysis To Explore Bone-marrow Immune Landscape
- Single-cell Transcriptional Profiling Reveals Novel Cellular and Molecular Drivers of Cardiovascular Fibrosis
- Single-cell and network analyses reveal organ-specific transcriptomic identity of adult fibroblasts
- Spatial analysis of in situ cytometry data
- SpicyR - Spatial analysis of in situ cytometry data
- Systematic evaluation for metrics of gene expression variability in single-cell RNA sequencing data
- The landscape of alternative polyadenylation in CD8 T cells in single-cell transcriptome
- TrackSOM: immunopathogenic temporal mapping through clustering time-series cytometry data
- Transfer learning for data integration of single-cell RNA-seq and ATAC-seq
- Using single-cell cytometry to illustrate the generalisable unbiased evaluation of clustering algorithms using Pareto fronts
- propeller: finding statistically significant differences in cell type proportions in single cell RNA-seq experiments
#transcriptomics
- A statistical approach for modelling differential distributions in single-cell transcriptomic data
- An Evolutionary Approach to Network Analysis of Cancer Transcriptomes Reveals Common Indicators of Enhanced Malignancy Across a Range of Solid Tumours
- Application of mixture model to RNA-seq data to discover ageing regulators
- Benchmarking single cell RNA-sequencing simulation methods
- Benchmarking single cell transcriptomes with bulk transcriptional atlases.
- Characterisation of a convergent malignant phenotype in B-cell acute lymphoblastic leukaemia
- Characterisation of transcript expression in placenta across early gestation reveals variable transcript usage
- Characterising Diversity in Gene Regulation Across the Indonesian Archipelago
- Comprehensive analysis of usability and archival stability of RNA-seq tools
- Developing a computational analysis to identify differentially allelic expressed loci in patient-derived stem cells
- Discovery of Tissue-specific Gene Expression Patterns in CD8 T Cells by Single-cell RNA-seq
- Exploring mechanisms of nephron maturation using scRNAseq
- Features of functional human genes
- Finding signatures of alternative polyadenylation as cancer biomarkers
- How does gene expression entropy change along developmental trajectories?
- Hypothesis generation in the age of cell atlases
- Implementing an integrated analysis to identify and validate circular RNAs using patient-derived neuronal stem cells.
- Integrated transcription factor profiling with transcriptome analysis: identification of L1PA2 transposons as global regulatory modulators in a breast cancer model
- Integrated transcriptional and chromatin accessibility profiling uncovers sex-specific adipose tissue imprinting of regulatory T cells
- JAFFAL: Detecting fusion genes with long read transcriptome sequencing
- Long short-term memory RNN for mirtron identification
- Longitudinal single-cell immune profiling revealed distinct innate immune response in asymptomatic COVID-19 patients
- Mapping cancer transcriptomes with long-read sequencing
- Molecular barcoding of native RNAs using nanopore sequencing and deep learning
- PACIFIC: A lightweight deep-learning classifier of SARS-CoV-2 and co-infecting RNA viruses
- Quick determination of RNA-Seq strandedness with how_are_we_stranded_here
- RNA splicing is a hierarchical supernetwork that co-operates to drive osteoblast differentiation
- RNase III-CLASH of multi-drug resistant Staphylococcus aureus reveals a regulatory mRNA 3’UTR required for intermediate vancomycin resistance
- Reference-free reconstruction and quantification of transcriptomes from Nanopore long-read sequencing
- Revealing interactions between coding and non-coding transcripts in plants using heterogeneous networks
- Sex-specific co-expression: a baseline to explore disease
- Single-cell RNA-seq Analysis To Explore Bone-marrow Immune Landscape
- Single-cell Transcriptional Profiling Reveals Novel Cellular and Molecular Drivers of Cardiovascular Fibrosis
- Single-cell and network analyses reveal organ-specific transcriptomic identity of adult fibroblasts
- Systematic evaluation for metrics of gene expression variability in single-cell RNA sequencing data
- The landscape of alternative polyadenylation in CD8 T cells in single-cell transcriptome
- Using equivalence classes for differential transcript usage and variant detection in RNA-seq data
- Viral RNA metagenomics reveals the Australian bovine respiratory virome
- Whole transcripts in genome assembly, annotation, and assessment: the draft genome assembly of the globally invasive common starling, Sturnus vulgaris
- linc2function: Predicting function of lncRNA transcripts using an Artificial Neural Network (ANN) Model
- propeller: finding statistically significant differences in cell type proportions in single cell RNA-seq experiments
#phylogenetics
- A workflow for the detection and phylogenetic placement of eukaryotes from metagenomes
- AusTrakka – Working towards integrated pathogen genomics for SARS-CoV-2
- Confidence and truth in phylogenomics
- Detection of recombination amongst SARS-CoV-2 strains
- Evaluation of recombination detection methods for viral sequence analysis
- How bioinformatics and genomics helped Australia’s COVID response
- eMST, a scalable and interpretable method for Phylogenetic analysis of hundreds and thousands of SARS-CoV-2 genomes
#phylogenomics
- A workflow for the detection and phylogenetic placement of eukaryotes from metagenomes
- Confidence and truth in phylogenomics
- eMST, a scalable and interpretable method for Phylogenetic analysis of hundreds and thousands of SARS-CoV-2 genomes
#cell free DNA
#cancer
- Accurate detection of cell free microbial DNA using a contaminant-controlled analysis framework
- An Evolutionary Approach to Network Analysis of Cancer Transcriptomes Reveals Common Indicators of Enhanced Malignancy Across a Range of Solid Tumours
- Characterisation of a convergent malignant phenotype in B-cell acute lymphoblastic leukaemia
- Finding signatures of alternative polyadenylation as cancer biomarkers
- ISOTOPE: ISOform-guided prediction of epiTOPEs in cancer
- Integrated transcription factor profiling with transcriptome analysis: identification of L1PA2 transposons as global regulatory modulators in a breast cancer model
- JAFFAL: Detecting fusion genes with long read transcriptome sequencing
- Making sense of heterogeneity in gene expression data
- Mapping cancer transcriptomes with long-read sequencing
- New Insights Of Cancer DNA Methylation By Studies Of Pre-Leukemic Stem Cells In A Mouse Model Of T-Cell Acute Lymphoblastic Leukemia
- Using equivalence classes for differential transcript usage and variant detection in RNA-seq data
- clonal tracking as quality control for mutational signature analysis
#evolution
- Alu Repeat Diversity in the Human Genome
- An Evolutionary Approach to Network Analysis of Cancer Transcriptomes Reveals Common Indicators of Enhanced Malignancy Across a Range of Solid Tumours
- Anthroponotic transmission and adaptive introgression underlies cryptic population structure of Cryptosporidium hominis in Africa
- Features of functional human genes
- Is it a Mammal Thing? Determining When the Change in rDNA Unit Size Occurred in Amniotes
- New Insights Of Cancer DNA Methylation By Studies Of Pre-Leukemic Stem Cells In A Mouse Model Of T-Cell Acute Lymphoblastic Leukemia
- The role of gene duplication in the evolution of snake venoms
#genomics
- Alu Repeat Diversity in the Human Genome
- An Open Platform for Cannabis Genomics Research
- AusTrakka – Working towards integrated pathogen genomics for SARS-CoV-2
- CRISPR, faster, better - The Crackling method for whole-genome target detection
- Challenges In Aboriginal health in the genomics era
- Challenges and Opportunities for Bioinformatics and Computational Biology in Plant Science
- Characterising Diversity in Gene Regulation Across the Indonesian Archipelago
- DNA methylation differences in human placenta from female and male bearing pregnancies
- Developing a computational safeguard to detect gene drive systems in wild populations
- Features of functional human genes
- How Ancient genomes can help Aboriginal Australian communities: lessons from the Cape York project
- How bioinformatics and genomics helped Australia’s COVID response
- Microproteins, Mobile Genetic elements and Strain-level resolution in the microbiome – a path to precision medicine
- Nimpress brings polygenic scores to the sequencing era
- Optimising genomic approaches for detection of vancomycin resistant Enterococcus faecium transmission in the hospital environment
- Phage genome bioinformatics
- The role of gene duplication in the evolution of snake venoms
- Understanding Polygenic Disease with BitEpi and EpiExplorer
- Whole transcripts in genome assembly, annotation, and assessment: the draft genome assembly of the globally invasive common starling, Sturnus vulgaris
- powerSFS: quantifying the intolerance of genes to mutation with a statistical model of the site frequency spectrum
- pyTCR: a comprehensive cloud-based platform for TCR-Seq data analysis using interactive notebooks to facilitate reproducibility and rigor of immunogenomics research
- sBeacon: cloud-native genomic data exchange
#transposable elements
- Alu Repeat Diversity in the Human Genome
- Integrated transcription factor profiling with transcriptome analysis: identification of L1PA2 transposons as global regulatory modulators in a breast cancer model
#Cannabis
#cytometry
- An automated framework for elucidating hierarchical relationships in high dimensional cytometry data
- Spatial analysis of in situ cytometry data
- SpicyR - Spatial analysis of in situ cytometry data
- TrackSOM: immunopathogenic temporal mapping through clustering time-series cytometry data
- Using single-cell cytometry to illustrate the generalisable unbiased evaluation of clustering algorithms using Pareto fronts
#splicing dynamics
#introgression
- Anthroponotic transmission and adaptive introgression underlies cryptic population structure of Cryptosporidium hominis in Africa
- Characterising Diversity in Gene Regulation Across the Indonesian Archipelago
#recombination
- Anthroponotic transmission and adaptive introgression underlies cryptic population structure of Cryptosporidium hominis in Africa
- Detection of recombination amongst SARS-CoV-2 strains
- Evaluation of recombination detection methods for viral sequence analysis
#non-model organisms
- Anthroponotic transmission and adaptive introgression underlies cryptic population structure of Cryptosporidium hominis in Africa
- Comparative 3D Genome Organization in Apicomplexan Parasites
- Developing a computational safeguard to detect gene drive systems in wild populations
- Is it a Mammal Thing? Determining When the Change in rDNA Unit Size Occurred in Amniotes
- The role of gene duplication in the evolution of snake venoms
- Whole transcripts in genome assembly, annotation, and assessment: the draft genome assembly of the globally invasive common starling, Sturnus vulgaris
#ageing
- Application of mixture model to RNA-seq data to discover ageing regulators
- Image-based Predictive Modelling for the Characterisation of Cellular Senescence
- Making sense of heterogeneity in gene expression data
- Systematic evaluation for metrics of gene expression variability in single-cell RNA sequencing data
#genome assembly
- Assessing PacBio long reads and de novo genome assembly tools for useability and suitability to applications where resources are limited.
- Binning Metagenomic Sequences
- Microproteins, Mobile Genetic elements and Strain-level resolution in the microbiome – a path to precision medicine
- Mining the wastewater microbiome with a metagenomic Hi-C approach to identify antimicrobial resistance risk in Australia
- Over 25,000 metagenome assembled genomes reveal the development of the post-weaning pig gut microbial community
- The African Orphan Crops Consortium, alleviating stunting due to malnutrition one crop at a time
- Trycycler: working towards the perfect bacterial genome
- Whole transcripts in genome assembly, annotation, and assessment: the draft genome assembly of the globally invasive common starling, Sturnus vulgaris
#COVID-19
- AusTrakka – Working towards integrated pathogen genomics for SARS-CoV-2
- Detection of recombination amongst SARS-CoV-2 strains
- How bioinformatics and genomics helped Australia’s COVID response
- Longitudinal single-cell immune profiling revealed distinct innate immune response in asymptomatic COVID-19 patients
- PACIFIC: A lightweight deep-learning classifier of SARS-CoV-2 and co-infecting RNA viruses
- eMST, a scalable and interpretable method for Phylogenetic analysis of hundreds and thousands of SARS-CoV-2 genomes
- sBeacon: cloud-native genomic data exchange
#epidemiology
- AusTrakka – Working towards integrated pathogen genomics for SARS-CoV-2
- Optimising genomic approaches for detection of vancomycin resistant Enterococcus faecium transmission in the hospital environment
#software development
#methods
- Best practices for bioinformatics command-line software with Bionitio
- Comprehensive analysis of usability and archival stability of RNA-seq tools
- Fate specification and variability in cell lineage trees
- Long short-term memory RNN for mirtron identification
- Molecular barcoding of native RNAs using nanopore sequencing and deep learning
- Quick determination of RNA-Seq strandedness with how_are_we_stranded_here
- genozip: an advanced universal compressor for genomic data files
#eQTL
#graph algorithms
- Binning Metagenomic Sequences
- Revealing interactions between coding and non-coding transcripts in plants using heterogeneous networks
- eMST, a scalable and interpretable method for Phylogenetic analysis of hundreds and thousands of SARS-CoV-2 genomes
#genome editing
- CRISPR, faster, better - The Crackling method for whole-genome target detection
- Developing a computational safeguard to detect gene drive systems in wild populations
#CRISPR
#indigenous genomics
#indigenous health
#ethics
#gene annotation
- Challenges and Opportunities for Bioinformatics and Computational Biology in Plant Science
- Whole transcripts in genome assembly, annotation, and assessment: the draft genome assembly of the globally invasive common starling, Sturnus vulgaris
#alternative splicing
- Characterisation of transcript expression in placenta across early gestation reveals variable transcript usage
- Direct RNA sequencing identifies isoform specific structures
- ISOTOPE: ISOform-guided prediction of epiTOPEs in cancer
- Mapping cancer transcriptomes with long-read sequencing
- Using equivalence classes for differential transcript usage and variant detection in RNA-seq data
#development
- Characterisation of transcript expression in placenta across early gestation reveals variable transcript usage
- Exploring mechanisms of nephron maturation using scRNAseq
- Fate specification and variability in cell lineage trees
- How does gene expression entropy change along developmental trajectories?
- Hypothesis generation in the age of cell atlases
- RNA splicing is a hierarchical supernetwork that co-operates to drive osteoblast differentiation
#pregnancy
- Characterisation of transcript expression in placenta across early gestation reveals variable transcript usage
- DNA methylation differences in human placenta from female and male bearing pregnancies
#malaria
#3D genome
#single cell genomic
#long-reads
#single cell multi-omics
#transcriptomic
#uncertainty
#DNA editing
#population genetics
#selection
#DNA methylation
- DNA methylation differences in human placenta from female and male bearing pregnancies
- New Insights Of Cancer DNA Methylation By Studies Of Pre-Leukemic Stem Cells In A Mouse Model Of T-Cell Acute Lymphoblastic Leukemia
- Systematic benchmarking of detection tools for CpG methylation from Nanopore sequencing
#sex differences
- DNA methylation differences in human placenta from female and male bearing pregnancies
- Integrated transcriptional and chromatin accessibility profiling uncovers sex-specific adipose tissue imprinting of regulatory T cells
- Sex-specific co-expression: a baseline to explore disease
#sequence alignment
- Detection and identification of cis-regulatory elements using change-point and classification algorithms
- Systematic Benchmark of aDNA Mapping Bias
#classification algorithms
#epigenomics
#biosecurity
#RNA structure
- Direct RNA sequencing identifies isoform specific structures
- Moving beyond RNA sequence: uncovering the functional role of RNA structure
#RNA function
#immunology
- Discovery of Tissue-specific Gene Expression Patterns in CD8 T Cells by Single-cell RNA-seq
- ISOTOPE: ISOform-guided prediction of epiTOPEs in cancer
- Longitudinal single-cell immune profiling revealed distinct innate immune response in asymptomatic COVID-19 patients
- Machine Learning in Dynamic Microscopy
- Single-cell RNA-seq Analysis To Explore Bone-marrow Immune Landscape
- The landscape of alternative polyadenylation in CD8 T cells in single-cell transcriptome
- TrackSOM: immunopathogenic temporal mapping through clustering time-series cytometry data
- pyTCR: a comprehensive cloud-based platform for TCR-Seq data analysis using interactive notebooks to facilitate reproducibility and rigor of immunogenomics research
#viruses
- Evaluation of recombination detection methods for viral sequence analysis
- Hypothesis generation in the age of cell atlases
- Moving beyond RNA sequence: uncovering the functional role of RNA structure
- PACIFIC: A lightweight deep-learning classifier of SARS-CoV-2 and co-infecting RNA viruses
- Phage genome bioinformatics
- VIRUSBreakend: Viral Integration Recognition Using Single Breakends
- Viral RNA metagenomics reveals the Australian bovine respiratory virome
#differentiation
#non-coding RNA
- Features of functional human genes
- Long short-term memory RNN for mirtron identification
- Revealing interactions between coding and non-coding transcripts in plants using heterogeneous networks
- linc2function: Predicting function of lncRNA transcripts using an Artificial Neural Network (ANN) Model
#sequence variation
- Features that determine 5’ cryptic splice site selection in genetic disorders
- New insights into plant-microbe interactions through Quantitative Trait Locus (QTL) mapping
- Nimpress brings polygenic scores to the sequencing era
- Population dynamics of rDNA copy number in yeast and humans
- Understanding Polygenic Disease with BitEpi and EpiExplorer
- clonal tracking as quality control for mutational signature analysis
- powerSFS: quantifying the intolerance of genes to mutation with a statistical model of the site frequency spectrum
#polyadenylation
#ancient DNA
- How Ancient genomes can help Aboriginal Australian communities: lessons from the Cape York project
- Systematic Benchmark of aDNA Mapping Bias
#clustering
- Hypothesis generation in the age of cell atlases
- Metagenomic Geolocation with Read Signature Clustering
- RNA splicing is a hierarchical supernetwork that co-operates to drive osteoblast differentiation
- TrackSOM: immunopathogenic temporal mapping through clustering time-series cytometry data
- Using single-cell cytometry to illustrate the generalisable unbiased evaluation of clustering algorithms using Pareto fronts
#image analysis
- Image-based Predictive Modelling for the Characterisation of Cellular Senescence
- Machine Learning in Dynamic Microscopy
- Spatial analysis of in situ cytometry data
- SpicyR - Spatial analysis of in situ cytometry data
#senescence
#circular RNAs
#chromatin
#rDNA
- Is it a Mammal Thing? Determining When the Change in rDNA Unit Size Occurred in Amniotes
- Population dynamics of rDNA copy number in yeast and humans
#model interpretation
#clinical genomics
- Machine Learning Prediction of End-stage Kidney Disease for Clinical Decision Support
- Risk prediction survival model utilising both omics data and clinical data
#microscopy
#geolocation
#gene funcion
#data integration
#biomarkers
#QTL
#bacteria
- New insights into plant-microbe interactions through Quantitative Trait Locus (QTL) mapping
- RNase III-CLASH of multi-drug resistant Staphylococcus aureus reveals a regulatory mRNA 3’UTR required for intermediate vancomycin resistance
- Trycycler: working towards the perfect bacterial genome
#resistance
- Optimising genomic approaches for detection of vancomycin resistant Enterococcus faecium transmission in the hospital environment
- RNase III-CLASH of multi-drug resistant Staphylococcus aureus reveals a regulatory mRNA 3’UTR required for intermediate vancomycin resistance
#agriculture
- Over 25,000 metagenome assembled genomes reveal the development of the post-weaning pig gut microbial community
- Viral RNA metagenomics reveals the Australian bovine respiratory virome
#phages
#proteomics
- PhosR enables processing and functional analysis of phosphoproteomic data
- RNA splicing is a hierarchical supernetwork that co-operates to drive osteoblast differentiation
#phylodynamics
#wastewater
#reference-free
#data sharing
#spatial analysis
#visualization
#taxonomy
#antimicrobial peptides
- The AMPSphere: antimicrobial peptides (AMPs) in the global microbiome
- ampir: an R package for fast genome-wide prediction of antimicrobial peptides
#plant genomics
#homology
#data compression
#reference-free. Benchmarking
#abacbs
#welcome