Thomas K. F. Wong
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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: piqtree: A Python Package for Seamless Phylogenetic Inference with IQ-TREE
piqtree: A Python Package for Seamless Phylogenetic Inference with IQ-TREE Open
piqtree is an easy to use, open-source Python package that directly exposes IQ-TREE’s phylogenetic inference engine. It offers Python functions for performing many of IQ-TREE’s capabilities including phylogenetic reconstruction, ultrafast …
View article: IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models
IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models Open
IQ-TREE (http://www.iqtree.org) is a widely used open-source software tool for efficiently inferring phylogenetic trees under maximum likelihood. Here, we present IQ-TREE version 3, the third major release of the software. IQ-TREE 3 signif…
View article: MixtureFinder: Estimating DNA Mixture Models for Phylogenetic Analyses
MixtureFinder: Estimating DNA Mixture Models for Phylogenetic Analyses Open
In phylogenetic studies, both partitioned models and mixture models are used to account for heterogeneity in molecular evolution among the sites of DNA sequence alignments. Partitioned models require the user to specify the grouping of sit…
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: GTRpmix: A Linked General Time-Reversible Model for Profile Mixture Models
GTRpmix: A Linked General Time-Reversible Model for Profile Mixture Models Open
Profile mixture models capture distinct biochemical constraints on the amino acid substitution process at different sites in proteins. These models feature a mixture of time-reversible models with a common matrix of exchangeabilities and d…
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: MixtureFinder: Estimating DNA mixture models for phylogenetic analyses
MixtureFinder: Estimating DNA mixture models for phylogenetic analyses Open
In phylogenetic studies, both partitioned models and mixture models are used to account for heterogeneity in molecular evolution among the sites of DNA sequence alignments. Partitioned models require the user to specify the grouping of sit…
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: DecentTree: scalable Neighbour-Joining for the genomic era
DecentTree: scalable Neighbour-Joining for the genomic era Open
Motivation Neighbour-Joining is one of the most widely used distance-based phylogenetic inference methods. However, current implementations do not scale well for datasets with more than 10 000 sequences. Given the increasing pace of genera…
View article: The Phylogeography and Demographic History of the Direct-Developing Coastal Gastropod Haustrum haustorium
The Phylogeography and Demographic History of the Direct-Developing Coastal Gastropod Haustrum haustorium Open
Life history traits can be influential in a species’ evolution, particularly in regards to dispersal ability. Studies have attempted to find a generalized link between particular life history traits and levels of population genetic stru…
View article: Table of Contents
Table of Contents 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: DecentTree: Scalable Neighbour-Joining for the Genomic Era
DecentTree: Scalable Neighbour-Joining for the Genomic Era Open
Summary Neighbour-Joining is one of the most widely used distance-based phylogenetic inference methods. However, current implementations do not scale well for datasets with more than 10,000 sequences. Given the increasing pace of generatin…
View article: Mitochondrial DHODH regulates hypoxia-inducible factor 1 expression in OTSCC.
Mitochondrial DHODH regulates hypoxia-inducible factor 1 expression in OTSCC. Open
Oral tongue squamous cell carcinoma (OTSCC) was one of the most hypoxic tumors with unfavorable outcomes. Hypoxia-inducible factor-1 (HIF-1) signaling was associated with cancer proliferation, lymph node metastasis, angiogenesis and poor p…
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: 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: A minimum reporting standard for multiple sequence alignments
A minimum reporting standard for multiple sequence alignments Open
Multiple sequence alignments (MSAs) play a pivotal role in studies of molecular sequence data, but nobody has developed a minimum reporting standard (MRS) to quantify the completeness of MSAs in terms of completely specified nucleotides or…
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: A minimum reporting standard for multiple sequence alignments
A minimum reporting standard for multiple sequence alignments Open
Multiple sequence alignments (MSAs) play a pivotal role in studies of molecular sequence data, but nobody has developed a minimum reporting standard (MRS) to quantify the completeness of MSAs in terms of completely-specified nucleotides or…
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: 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: 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: 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
Pooling techniques, where multiple sub-samples are mixed in a single sample, are widely used to take full advantage of high-throughput DNA sequencing. Recently, Ranjard et al. [1] proposed a pooling strategy without the use of barcodes. Th…
View article: Reassembling haplotypes in a mixture of pooled amplicons when the relative concentrations are known: A proof-of-concept study on the efficient design of next-generation sequencing strategies
Reassembling haplotypes in a mixture of pooled amplicons when the relative concentrations are known: A proof-of-concept study on the efficient design of next-generation sequencing strategies Open
Next-generation sequencing can be costly and labour intensive. Usually, the sequencing cost per sample is reduced by pooling amplified DNA = amplicons) derived from different individuals on the same sequencing lane. Barcodes unique to each…
View article: Complete mitochondrial genome of the green-lipped mussel, <i>Perna canaliculus</i> (Mollusca: Mytiloidea), from long nanopore sequencing reads
Complete mitochondrial genome of the green-lipped mussel, <i>Perna canaliculus</i> (Mollusca: Mytiloidea), from long nanopore sequencing reads Open
We describe here the first complete genome assembly of the New Zealand green-lipped mussel, Perna canaliculus, mitochondrion. The assembly was performed de novo from a mix of long nanopore sequencing reads and short sequencin…
View article: Mitochondrial DNA and trade data support multiple origins of Helicoverpa armigera (Lepidoptera, Noctuidae) in Brazil
Mitochondrial DNA and trade data support multiple origins of Helicoverpa armigera (Lepidoptera, Noctuidae) in Brazil Open
View article: Predicting RNA Secondary Structures: One-grammar-fits-all Solution
Predicting RNA Secondary Structures: One-grammar-fits-all Solution Open