A5102795329- Data Visualization and Analytics
- Gene expression and cancer classification
- Data Analysis with R
- Malaria Research and Control
- Single-cell and spatial transcriptomics
- Bioinformatics and Genomic Networks
- Genomics and Chromatin Dynamics
- Spaceflight effects on biology
- Space Exploration and Technology
- Reproductive tract infections research
- Advanced Clustering Algorithms Research
- Microbial infections and disease research
- Traffic Prediction and Management Techniques
- Cancer-related molecular mechanisms research
- HIV Research and Treatment
- Evolution and Genetic Dynamics
- Genomics and Phylogenetic Studies
- Algorithms and Data Compression
- Planetary Science and Exploration
- RNA modifications and cancer
- Effects of Radiation Exposure
- Vector-borne infectious diseases
- Bird parasitology and diseases
- Genetic Mapping and Diversity in Plants and Animals
- RNA Research and Splicing
KBR (United States)
2024
Walter and Eliza Hall Institute of Medical Research
2015-2023
Monash University
2016-2022
Technological and Higher Education Institute of Hong Kong
2022
Australian Regenerative Medicine Institute
2022
Hong Kong Institute of Vocational Education
2022
Wyle (United States)
2018-2019
Johnson Space Center
2019
The University of Melbourne
2018
Materials Technology (United Kingdom)
2013
Identification of genomic regions that are identical by descent (IBD) has proven useful for human genetic studies where analyses have led to the discovery familial relatedness and fine-mapping disease critical regions. Unfortunately however, IBD been underutilized in analysis other organisms, including pathogens. This is part due lack statistical methodologies non-diploid genomes addition added complexity multiclonal infections. As such, we developed an methodology, called isoRelate, haploid...
Bioconductor is a widely used R-based platform for genomics, but its host of complex genomic data structures places cognitive burden on the user. For most tasks, GRanges object would suffice, there are gaps in API that prevent general use. By recognizing class follows "tidy" principles, we create grammar transformation, defining verbs performing actions and between interval providing way common analysis tasks through coherent interface to existing infrastructure. We implement this as...
Abstract Motivation Deriving biological insights from genomic data commonly requires comparing attributes of selected loci to a null set loci. The selection this is non-trivial, as it careful consideration potential covariates, problem that exacerbated by the non-uniform distribution features including genes, enhancers, and transcription factor binding sites. Propensity score-based covariate matching methods allow sets pool possible items while controlling for multiple covariates; however,...
Abstract RNA-seq datasets can contain millions of intron reads per library that are typically removed from downstream analysis. Only overlapping annotated exons considered to be informative since mature mRNA is assumed the major component sequenced, especially for poly(A) RNA libraries. In this study, we show informative, and through exploratory data analysis read coverage signal representative both pre-mRNAs retention. We demonstrate how utilized in differential expression using our index...
Abstract Motivation Enrichment analysis is a widely utilized technique in genomic that aims to determine if there statistically significant association between two sets of features. To conduct this type hypothesis testing, an appropriate null model typically required. However, the distribution commonly used can be overly simplistic and may result inaccurate conclusions. Results bootRanges provides fast functions for generation block bootstrapped ranges representing enrichment analysis. As...
Significance Plasmodium vivax is responsible for the most widely distributed recurring human malaria infections whereas falciparum inflicts mortality and morbidity in populations. Malaria parasites enter our blood cells by making proteins that recognize bind to their cognate receptors on red cell surface. Our research describes, knowledge, first crystal structure of PvRBP2a, an erythrocyte-binding protein from P. vivax, which revealed a structural scaffold similar PfRh5, essential ....
Abstract Background Genomic surveillance of malaria parasite populations has the potential to inform control strategies and monitor impact interventions. Barcodes comprising large numbers single nucleotide polymorphism (SNP) markers are accurate efficient genotyping tools, however may need be tailored specific transmission settings, since ‘universal’ barcodes can lack resolution at local scale. A SNP barcode was developed that captures diversity structure Plasmodium vivax Papua New Guinea...
Abstract Summary CTCF (CCCTC-binding factor) is an 11-zinc-finger DNA binding protein which regulates much of the eukaryotic genome’s 3D structure and function. The diversity motifs has led to a fragmented landscape data. We collected position weight matrices defined strand-oriented sites in human mouse genomes, including recent Telomere mm39 assemblies. included selected experimentally determined predicted sites, such as CTCF-bound cis-regulatory elements from SCREEN ENCODE. recommend...
The growth of omic data presents evolving challenges in manipulation, analysis, and integration. Addressing these challenges, Bioconductor
ABSTRACT Pathogen genomic surveillance demands rapid, low-cost genotyping solutions for tracking infections. Here we use single nucleotide polymorphism (SNP) barcodes to generate practical information malaria and control. Using 91 Plasmodium falciparum genomes from three provinces of Papua New Guinea (PNG), assessed SNP panels with different allele frequency characteristics. A 191 ‘local’ barcode captured similar patterns population structure evident 5786 ‘whole genome’ SNPs. Geographically...
In high-dimensional data analysis, the curse of dimensionality reasons that points tend to be far away from center distribution and on edge space. Contrary this, is projected tends clump at center. This gives a sense any structure near projection obscured, whether this true or not. A geometric transformation reverse curse, defined in article, which uses radial transformations data. It integrated seamlessly into grand tour algorithm, we have called it burning sage tour, indicate reverses...
Radiotherapy injury to cells of the skin and subcutaneous tissue is an inevitable consequence external beam radiation for treatment cancer. This sublethal normal tissues plays a significant role in development fibrosis, lymphedema, impaired wound healing, recurrent infections. To elucidate transcriptional changes that occur soft after radiotherapy injury, we performed genome-wide RNA-sequencing comparing irradiated (10Gy) with non-irradiated (0Gy) controls human dermal fibroblasts,...
The Transportation Operations Coordinating Committee’s System for Managing Incidents and Traffic (TRANSMIT) is an operational test that uses vehicles equipped with tags of the E-ZPass electronic toll collection system as traffic probes surveillance incident detection. TRANSMIT detection algorithm based on statistical comparison real-time estimates travel times continuously updated historical same time period day type (weekday, Saturday, Sunday, or holiday). probability detecting false-alarm...
RNA-seq datasets can contain millions of intron reads per sequenced library that are typically removed from downstream analysis. Only overlapping annotated exons considered to be informative since mature mRNA is assumed the major component sequenced, especially when examining poly(A) RNA samples. In this paper, we demonstrate and pre-mRNA source signal. Making use signal, our index method combines differential expression analyses exon counts categorise changes observed in each count set,...
ABSTRACT In this preliminary study, mathematical models based on Quantitative Structure Property Relationships (QSPR) were applied in order to analyze how molecular structure of chloroprene rubber accelerators relates their rheological and mechanical properties. QSPR developed disclose which structural features mainly affect the mechanism vulcanization. such a way can help faster more parsimonious design new curative molecules. Regression calibrated two properties (scorch time optimum cure...
Non-linear dimensionality reduction (NLDR) methods such as t-distributed stochastic neighbour embedding (t-SNE) are ubiquitous in the natural sciences, however, appropriate use of these is difficult because their complex parameterisations; analysts must make trade-offs order to identify structure visualisation an NLDR technique. We present visual diagnostics for pragmatic usage by combining them with a technique called tour. A tour sequence interpolated linear projections multivariate data...
Abstract Identification of genomic regions that are identical by descent (IBD) has proven useful for human genetic studies where analyses have led to the discovery familial relatedness and fine-mapping disease critical regions. Unfortunately however, IBD been underutilized inanalysis other organisms, including pathogens. This is in part due lack statistical methodologies non-diploid genomes addition added complexity multiclonal infections. As such, we developed an methodology, called...