Allen G. Rodrigo
YOU?
Author Swipe
View article: “Gut microbial communities of velvet worm <i>Euperipatoides rowelli</i> (Onychophora) across deadwood microhabitats in southeastern Australia”
“Gut microbial communities of velvet worm <i>Euperipatoides rowelli</i> (Onychophora) across deadwood microhabitats in southeastern Australia” Open
This study investigated the gut microbial community of the velvet worm Euperipatoides rowelli , a saproxylic invertebrate residing in deadwood microhabitats within historical refugia in the Tallaganda forest, New South Wales, Australia. Th…
View article: A digital DNA system favours the superiority of unidirectional inheritance over ‘Lamarckian’ inheritance
A digital DNA system favours the superiority of unidirectional inheritance over ‘Lamarckian’ inheritance Open
In biology, changes to a DNA sequence can impact protein sequence but changes to protein sequences (phenotype) do not flow back into DNA (genotype). A system with bidirectional information flow (i.e., both translation and ‘reverse translat…
View article: Within-host microbial selection and multiple microbial generations buffer the loss of host fitness under environmental change
Within-host microbial selection and multiple microbial generations buffer the loss of host fitness under environmental change Open
The relationship between, and joint selection on, a host and its microbes—the holobiont—can impact evolutionary and ecological outcomes of the host and its microbial community. We develop an agent-based modelling framework for understandin…
View article: Tabelecleucel in Post-transplant Epstein–Barr Virus-Associated Lymphoproliferative Disease: Patient and Oncologist Perspectives
Tabelecleucel in Post-transplant Epstein–Barr Virus-Associated Lymphoproliferative Disease: Patient and Oncologist Perspectives Open
View article: Extending the Hegselmann-Krause Model of Opinion Dynamics to include AI Oracles
Extending the Hegselmann-Krause Model of Opinion Dynamics to include AI Oracles Open
The Hegselmann-Krause (HK) model of opinion dynamics describes how opinions held by individuals in a community change over time in response to the opinions of others and their access to the true value, T, to which these opinions relate. He…
View article: Models of microbiome evolution incorporating host resource provisioning
Models of microbiome evolution incorporating host resource provisioning Open
Multicellular hosts and their associated microbial partners (i.e. microbiomes) often interact in mutually beneficial ways. Consequently, hosts may choose to allocate resources to regulate and recruit appropriate microbes. In doing so, host…
View article: NJGPT: A Large Language Model-Driven, User-Friendly Solution for Phylogenetic Tree Construction
NJGPT: A Large Language Model-Driven, User-Friendly Solution for Phylogenetic Tree Construction Open
Motivation Phylogenetic reconstruction plays an integral part in much of the research in evolutionary biology. Currently, a newly minted phylogeneticist must choose amongst a relatively large array of phylogenetic software, each often with…
View article: A digital DNA system reveals the superiority of unidirectional inheritance over ‘Lamarckian’ inheritance
A digital DNA system reveals the superiority of unidirectional inheritance over ‘Lamarckian’ inheritance Open
In biology, changes to a DNA sequence can impact protein sequence but changes to protein sequence (phenotype) do not flow back into DNA (genotype). A system with bidirectional information flow (i.e. both translation and ‘reverse translatio…
View article: Joint consideration of selection and microbial generation count provides unique insights into evolutionary and ecological dynamics of holobionts
Joint consideration of selection and microbial generation count provides unique insights into evolutionary and ecological dynamics of holobionts Open
The relationship between, and joint selection on, a host and its microbes – the holobiont – can impact evolutionary and ecological outcomes of the host and its microbial community. Here we present a novel agent-based modelling framework fo…
View article: TaxonGPT: Taxonomic Classification Using Generative Artificial Intelligence
TaxonGPT: Taxonomic Classification Using Generative Artificial Intelligence Open
To address the challenges of consistency and quality in taxonomic classifications, we have developed a Python program called TaxonGPT, that utilizes the natural language processing capabilities of generative artificial intelligence (gAI, s…
View article: Mugen-UMAP: UMAP visualization and clustering of mutated genes in single-cell DNA sequencing data
Mugen-UMAP: UMAP visualization and clustering of mutated genes in single-cell DNA sequencing data Open
Background The application of Uniform Manifold Approximation and Projection (UMAP) for dimensionality reduction and visualization has revolutionized the analysis of single-cell RNA expression and population genetics. However, its potential…
View article: Models of microbiome evolution incorporating host resource provisioning
Models of microbiome evolution incorporating host resource provisioning Open
Multicellular hosts and their associated microbial partners (i.e., microbiomes) often interact in mutually beneficial ways. Consequently, hosts may choose to allocate resources to regulate and recruit appropriate microbes. In doing so, hos…
View article: Mugen-UMAP: UMAP visualization and clustering of mutated genes in single-cell DNA sequencing data
Mugen-UMAP: UMAP visualization and clustering of mutated genes in single-cell DNA sequencing data Open
Background The application of Uniform Manifold Approximation and Projection (UMAP) for dimensionality reduction and visualization has revolutionized the analysis of single-cell RNA expression and population genetics. However, its potential…
View article: Penny’s Probably Powerful PhylometerTM and the rise of statistical phylogenetics
Penny’s Probably Powerful PhylometerTM and the rise of statistical phylogenetics Open
View article: MAST: Phylogenetic Inference with Mixtures Across Sites and Trees
MAST: Phylogenetic Inference with Mixtures Across Sites and Trees Open
Hundreds or thousands of loci are now routinely used in modern phylogenomic studies. Concatenation approaches to tree inference assume that there is a single topology for the entire dataset, but different loci may have different evolutiona…
View article: Modelling the evolution of holobionts: an incomplete review
Modelling the evolution of holobionts: an incomplete review Open
A holobiont is a biological individual that consists of a host and its associated microbiome. As a biological individual, a holobiont participates in the evolutionary process, although the dynamics of how it does so are non-trivial. In par…
View article: MAST: Phylogenetic Inference with Mixtures Across Sites and Trees
MAST: Phylogenetic Inference with Mixtures Across Sites and Trees Open
Hundreds or thousands of loci are now routinely used in modern phylogenomic studies. Concatenation approaches to tree inference assume that there is a single topology for the entire dataset, but different loci may have different evolutiona…
View article: Can Stomach Content and Microbiomes of Tuna Provide Near Real-Time Detection of Ecosystem Composition in the Pacific Ocean?
Can Stomach Content and Microbiomes of Tuna Provide Near Real-Time Detection of Ecosystem Composition in the Pacific Ocean? Open
This preliminary study used DNA metabarcoding to test whether the stomach content and gut microbiome of tuna could be a viable near real-time monitoring tool for detecting composition and change in oceanic ecosystems. The gut content of sk…
View article: Genetic Variants of CLPP and M1AP Are Associated With Risk of Non-Small Cell Lung Cancer
Genetic Variants of CLPP and M1AP Are Associated With Risk of Non-Small Cell Lung Cancer Open
Background Single nucleotide polymorphisms (SNPs) are often associated with distinct phenotypes in cancer. The present study investigated associations of cancer risk and outcomes with SNPs discovered by whole exome sequencing of normal lun…
View article: An assembly-free method of phylogeny reconstruction using short-read sequences from pooled samples without barcodes
An assembly-free method of phylogeny reconstruction using short-read sequences from pooled samples without barcodes Open
A current strategy for obtaining haplotype information from several individuals involves short-read sequencing of pooled amplicons, where fragments from each individual is identified by a unique DNA barcode. In this paper, we report a new …
View article: pgHMA: Application of the Heteroduplex Mobility Assay Analysis in Phylogenetics and Population Genetics
pgHMA: Application of the Heteroduplex Mobility Assay Analysis in Phylogenetics and Population Genetics Open
The Heteroduplex mobility assay (HMA) has proven to be a robust tool for the detection of genetic variation. Here, we describe a simple and rapid application of the HMA by microfluidic capillary electrophoresis, for phylogenetics and popul…
View article: The draft genome sequence of<i>Eucalyptus polybractea</i>based on hybrid assembly with short- and long-reads reads
The draft genome sequence of<i>Eucalyptus polybractea</i>based on hybrid assembly with short- and long-reads reads Open
Eucalyptus polybractea is a small, multi-stemmed tree, which is widely cultivated in Australia for the production of Eucalyptus oil. We report the hybrid assembly of the E. polybractea genome utilizing both short- and long-read technology.…
View article: An assembly-free method of phylogeny reconstruction using short-read sequences from pooled samples without barcodes
An assembly-free method of phylogeny reconstruction using short-read sequences from pooled samples without barcodes Open
A current strategy for obtaining haplotype information from several individuals involves short-read sequencing of pooled amplicons, where fragments from each individual is identified by a unique DNA barcode. In this paper, we report a new …
View article: Correction to: Effective machine-learning assembly for next-generation amplicon sequencing with very low coverage
Correction to: Effective machine-learning assembly for next-generation amplicon sequencing with very low coverage Open
Following publication of the original article [1], the author reported that there are several errors in the original article;
View article: Effective machine-learning assembly for next-generation amplicon sequencing with very low coverage
Effective machine-learning assembly for next-generation amplicon sequencing with very low coverage Open
View article: Mineralogical characterization and comparative study of two processing methods of iron ore from the Anini deposit (NE Algeria)
Mineralogical characterization and comparative study of two processing methods of iron ore from the Anini deposit (NE Algeria) Open
The objective of this article is to study the possibilities of enrichment of the iron ore from Jebel Anini and to develop these mineral resources in order to use them in the metallurgical complex of Annaba. Representative samples were take…
View article: HaploJuice : accurate haplotype assembly from a pool of sequences with known relative concentrations
HaploJuice : accurate haplotype assembly from a pool of sequences with known relative concentrations Open
View article: Application of liquid biopsies in metastatic gastrointestinal cancer to identify candidate therapeutic targets
Application of liquid biopsies in metastatic gastrointestinal cancer to identify candidate therapeutic targets Open
[Background]: Next-generation sequencing (NGS) of cell-free tumor DNA (ctDNA) has great potential for liquid biopsy in cancer diagnostics and to identify patients with actionable genomic alteration. This study, a prospective longitudinal s…
View article: Effective Machine-Learning Assembly For Next-Generation Sequencing With Very Low Coverage
Effective Machine-Learning Assembly For Next-Generation Sequencing With Very Low Coverage Open
In short-read DNA sequencing experiments, the read coverage is a key parameter to successfully assemble the reads and reconstruct the sequence of the input DNA. When coverage is very low, the original sequence reconstruction from the reads…
View article: Neutral models of short-term microbiome dynamics with host subpopulation structure and migration limitation
Neutral models of short-term microbiome dynamics with host subpopulation structure and migration limitation Open