30.6k citations
Counting papers with at most 25 authors, so collaboration author lists do not stand in for the people here.
- The University of MelbourneAU12 papers
- City University of Hong KongHK4 papers
- Institut National de la Recherche ScientifiqueCA4 papers
- Monash UniversityAU4 papers
- RMIT UniversityAU4 papers
- Swinburne University of TechnologyAU4 papers
- Xi'an Institute of Optics and Precision MechanicsCN4 papers
- University of AucklandNZ3 papers
- University of Electronic Science and Technology of ChinaCN3 papers
- Australian Institute of Tropical Health and MedicineAU2 papers
- National University of Ireland, MaynoothIE2 papers
- SIB Swiss Institute of BioinformaticsCH2 papers
21 papers
Mathematical models of Plasmodium vivax transmission: a scoping review
Md Nurul Anwar, Lauren Smith, Angela Devine +8
Plasmodium vivax is one of the most geographically widespread malaria parasites in the world due to its ability to remain dormant in the human liver as hypnozoites and subsequently…
Quantifying the HIV reservoir with dilution assays and deep viral sequencing
Sarah C. Lotspeich, Brian D. Richardson, Pedro L. Baldoni +2
People living with HIV on antiretroviral therapy often have undetectable virus levels by standard assays, but "latent" HIV still persists in viral reservoirs. Eliminating these res…
Photonic single perceptron at Giga-OP/s speeds with Kerr microcombs for scalable optical neural networks
Mengxi Tan, Xingyuan Xu, David J. Moss
Optical artificial neural networks (ONNs) have significant potential for ultra-high computing speed and energy efficiency. We report a novel approach to ONNs that uses integrated K…
Optical neuromorphic processing at Tera-OP/s speeds based on Kerr soliton crystal microcombs
Mengxi Tan, Xingyuan Xu, David J. Moss
Convolutional neural networks (CNNs), inspired by biological visual cortex systems, are a powerful category of artificial neural networks that can extract the hierarchical features…
Soliton crystal Kerr microcombs for high-speed, scalable optical neural networks at 10 GigaOPs/s
Xingyuan Xu, Mengxi Tan, David J. Moss
Optical artificial neural networks (ONNs) have significant potential for ultra-high computing speed and energy efficiency. We report a new approach to ONNs based on integrated Kerr…
11 TeraFLOPs per second photonic convolutional accelerator for deep learning optical neural networks
Xingyuan Xu, Mengxi Tan, Bill Corcoran +9
Convolutional neural networks (CNNs), inspired by biological visual cortex systems, are a powerful category of artificial neural networks that can extract the hierarchical features…
Sample Path Properties of the Average Generation of a Bellman-Harris Process
Gianfelice Meli, Tom S. Weber, Ken R. Duffy
Motivated by a recently proposed design for a DNA coded randomised algorithm that enables inference of the average generation of a collection of cells descendent from a common prog…
A thermodynamic framework for modelling membrane transporters
Michael Pan, Peter J. Gawthrop, Kenneth Tran +2
Membrane transporters contribute to the regulation of the internal environment of cells by translocating substrates across cell membranes. Like all physical systems, the behaviour…
Bond graph modelling of the cardiac action potential: Implications for drift and non-unique steady states
Michael Pan, Peter J. Gawthrop, Kenneth Tran +2
Mathematical models of cardiac action potentials have become increasingly important in the study of heart disease and pharmacology, but concerns linger over their robustness during…
The cardiac Na/K ATPase: An updated, thermodynamically consistent model
Michael Pan, Peter J. Gawthrop, Joseph Cursons +2
The Na/K ATPase is an essential component of cardiac electrophysiology, maintaining physiological Na and K concentrations over successive heart beats. Terkildsen et…
RLE Plots: Visualising Unwanted Variation in High Dimensional Data
Luke C. Gandolfo, Terence P. Speed
Unwanted variation can be highly problematic and so its detection is often crucial. Relative log expression (RLE) plots are a powerful tool for visualising such variation in high d…
Long-term sustained malaria control leads to inbreeding and fragmentation of Plasmodium vivax populations
Andreea Waltmann, Cristian Koepfli, Natacha Tessier +13
Plasmodium vivax populations are more resistant to malaria control strategies than Plasmodium falciparum, maintaining high genetic diversity and gene flow even at low transmission.…
Permutation p-values should never be zero: calculating exact p-values when permutations are randomly drawn
Belinda Phipson, Gordon K. Smyth
Permutation tests are amongst the most commonly used statistical tools in modern genomic research, a process by which p-values are attached to a test statistic by randomly permutin…
Site-specific recombinatorics: in situ cellular barcoding with the Cre Lox system
Tom S. Weber, Mark Dukes, Denise Miles +3
Cellular barcoding is a significant, recently developed, biotechnology tool that enables the familial identification of progeny of individual cells in vivo. Most existing approache…
Robust hyperparameter estimation protects against hypervariable genes and improves power to detect differential expression
Belinda Phipson, Stanley Lee, Ian J. Majewski +2
One of the most common analysis tasks in genomic research is to identify genes that are differentially expressed (DE) between experimental conditions. Empirical Bayes (EB) statisti…
Assessing Technical Performance in Differential Gene Expression Experiments with External Spike-in RNA Control Ratio Mixtures
Sarah A. Munro, Steve P. Lund, P. Scott Pine +30
There is a critical need for standard approaches to assess, report, and compare the technical performance of genome-scale differential gene expression experiments. We assess techni…
Rotating-crystal Malaria Diagnosis: Pre-clinical validation
Agnes Orban, Adam Butykai, Zsofia Prohle +8
Improving the efficiency of malaria diagnosis is one of the main goals of current malaria research. We have recently developed a magneto-optical (MO) method which allows high-sensi…
featureCounts: An efficient general-purpose program for assigning sequence reads to genomic features
Yang Liao, Gordon K Smyth, Wei Shi
Next-generation sequencing technologies generate millions of short sequence reads, which are usually aligned to a reference genome. In many applications, the key information requir…
Count-based differential expression analysis of RNA sequencing data using R and Bioconductor
Simon Anders, Davis J. McCarthy, Yunshen Chen +4
RNA sequencing (RNA-seq) has been rapidly adopted for the profiling of transcriptomes in many areas of biology, including studies into gene regulation, development and disease. Of…
Guidelines for the next 10 years of proteomics
Marc R Wilkins, Ron D Appel, Jennifer E Van Eyk +13
In the last ten years, the field of proteomics has expanded at a rapid rate. A range of exciting new technology has been developed and enthusiastically applied to an enormous varie…
A multivariate empirical Bayes statistic for replicated microarray time course data
Yu Chuan Tai, Terence P. Speed
In this paper we derive one- and two-sample multivariate empirical Bayes statistics (the -statistics) to rank genes in order of interest from longitudinal replicated d…