User profiles for David Kainer

David Kainer

Senior Research Fellow, ARC CoE for Plant Success, University of Queensland
Verified email at uq.edu.au
Cited by 2203

[HTML][HTML] Selecting optimal partitioning schemes for phylogenomic datasets

R Lanfear, B Calcott, D Kainer, C Mayer… - BMC evolutionary …, 2014 - Springer
Background Partitioning involves estimating independent models of molecular evolution for
different subsets of sites in a sequence alignment, and has been shown to improve …

Accelerating climate resilient plant breeding by applying next-generation artificial intelligence

AL Harfouche, DA Jacobson, D Kainer, JC Romero… - Trends in …, 2019 - cell.com
Breeding crops for high yield and superior adaptability to new and variable climates is
imperative to ensure continued food security, biomass production, and ecosystem services. …

Plant-derived terpenes: A feedstock for specialty biofuels

R Mewalal, DK Rai, D Kainer, F Chen, C Külheim… - Trends in …, 2017 - cell.com
Research toward renewable and sustainable energy has identified specific terpenes capable
of supplementing or replacing current petroleum-derived fuels. Despite being naturally …

MinIONQC: fast and simple quality control for MinION sequencing data

R Lanfear, M Schalamun, D Kainer, W Wang… - …, 2019 - academic.oup.com
MinIONQC provides rapid diagnostic plots and quality control data from one or more flowcells
of sequencing data from Oxford Nanopore Technologies’ MinION instrument. It can be …

The effects of partitioning on phylogenetic inference

D Kainer, R Lanfear - Molecular Biology and Evolution, 2015 - academic.oup.com
Partitioning is a commonly used method in phylogenetics that aims to accommodate variation
in substitution patterns among sites. Despite its popularity, there have been few systematic …

Multitrait genome‐wide association analysis of Populus trichocarpa identifies key polymorphisms controlling morphological and physiological traits

HB Chhetri, D Macaya‐Sanz, D Kainer… - New …, 2019 - Wiley Online Library
Genome‐wide association studies (GWAS) have great promise for identifying the loci that
contribute to adaptive variation, but the complex genetic architecture of many quantitative traits …

[HTML][HTML] Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models

…, J Streich, JG Felipe Machado Gazolla, D Kainer… - Genome biology, 2020 - Springer
Background A mechanistic understanding of the spread of SARS-CoV-2 and diligent tracking
of ongoing mutagenesis are of key importance to plan robust strategies for confining its …

Identification of novel, replicable genetic risk loci for suicidal thoughts and behaviors among US military veterans

…, NW Hengartner, PC Jones, D Kainer… - JAMA …, 2023 - jamanetwork.com
Importance Suicide is a leading cause of death; however, the molecular genetic basis of
suicidal thoughts and behaviors (SITB) remains unknown. Objective To identify novel, replicable …

Harnessing the MinION: An example of how to establish long‐read sequencing in a laboratory using challenging plant tissue from Eucalyptus pauciflora

M Schalamun, R Nagar, D Kainer… - Molecular ecology …, 2019 - Wiley Online Library
Long‐read sequencing technologies are transforming our ability to assemble highly complex
genomes. Realizing their full potential is critically reliant on extracting high‐quality, high‐…

[HTML][HTML] Assembly of chloroplast genomes with long- and short-read data: a comparison of approaches using Eucalyptus pauciflora as a test case

W Wang, M Schalamun, A Morales-Suarez, D Kainer… - BMC genomics, 2018 - Springer
Background Chloroplasts are organelles that conduct photosynthesis in plant and algal cells.
The information chloroplast genome contained is widely used in agriculture and studies of …