Biology subjects

Andrew, S. C.

Publications and source records attributed to Andrew, S. C..

4 recordsLinked to original sources

bioRxiv2025

GeneWhisperer: Enhancing manual genome annotation with large language models

Genome annotation is critical for understanding functional elements within genomes. Manual curation is a common practice for identifying the functions of genes, particularly those missed by automated annotation pipelines. However, this process is notoriously labour-intensive and time-consuming. In response to these challenges, we present GeneWhisperer, an innovative assistant system designed to facilitate the manual gene functional annotation process. Utilizing a large language model (LLM) agent, GeneWhisperer provides users access to tools appropriate for specific curation tasks in genome annotation. Featuring a conversational interface, GeneWhisperer fosters effective collaboration between human experts and AI. By synergizing the capabilities of AI with human expertise, GeneWhisperer offers a promising approach to advancing our understanding of gene functions and streamlining the gene annotation process.

bioinformatics↗

bioRxiv2024

OzWheat: a genome-to-phenome platform to resolve complex traits for wheat pre-breeding and research.

For over a century, Australian wheat breeders have successfully adapted wheat to a broad range of climatic conditions and crop management practices. The OzWheat genome-to-phenome (G2P) platform was established to capture this breeding history and explore traits, genes, and their interactions with the environment to enable ongoing research and deliver targets for wheat improvement. A panel of 285 cultivars and landraces were chosen through knowledge of breeding pedigrees to represent both global diversity and the historic flow of genetic variation over more than 100 years of selective breeding in Australia. Genetic characterisation of the panel included identification of genome-wide sequence variants and gene expression profiling across environments. Important traits for adaptation (flowering time and plant height) were assayed in controlled environments and at multiple field sites and years, with genome-wide association analyses (GWAS) using linear mixed models detecting both known and novel loci. Here, we report establishment of the OzWheat G2P platform as a powerful tool to integrate wheat genomes and phenomes and demonstrate its use to identify candidate genes and understand gene by environment interactions. This provides the wheat research and breeding community a new resource to support future cultivar development.

genomics↗

bioRxiv2021

AusTraits: a curated plant trait database for the Australian flora

We introduce the AusTraits database - a compilation of measurements of plant traits for taxa in the Australian flora (hereafter AusTraits). AusTraits synthesises data on 375 traits across 29230 taxa from field campaigns, published literature, taxonomic monographs, and individual taxa descriptions. Traits vary in scope from physiological measures of performance (e.g. photosynthetic gas exchange, water-use efficiency) to morphological parameters (e.g. leaf area, seed mass, plant height) which link to aspects of ecological variation. AusTraits contains curated and harmonised individual-, species- and genus-level observations coupled to, where available, contextual information on site properties. This data descriptor provides information on version 2.1.0 of AusTraits which contains data for 937243 trait-by-taxa combinations. We envision AusTraits as an ongoing collaborative initiative for easily archiving and sharing trait data to increase our collective understanding of the Australian flora.

ecology↗

bioRxiv2020

Areas of global importance for terrestrial biodiversity, carbon, and water

Summary paragraphTo meet the ambitious objectives of biodiversity and climate conventions, countries and the international community require clarity on how these objectives can be operationalized spatially, and multiple targets be pursued concurrently1. To support governments and political conventions, spatial guidance is needed to identify which areas should be managed for conservation to generate the greatest synergies between biodiversity and natures contribution to people (NCP). Here we present results from a joint optimization that maximizes improvements in species conservation status, carbon retention and water provisioning and rank terrestrial conservation priorities globally. We found that, selecting the top-ranked 30% (respectively 50%) of areas would conserve 62.4% (86.8%) of the estimated total carbon stock and 67.8% (90.7%) of all clean water provisioning, in addition to improving the conservation status for 69.7% (83.8%) of all species considered. If priority was given to biodiversity only, managing 30% of optimally located land area for conservation may be sufficient to improve the conservation status of 86.3% of plant and vertebrate species on Earth. Our results provide a global baseline on where land could be managed for conservation. We discuss how such a spatial prioritisation framework can support the implementation of the biodiversity and climate conventions.

ecology↗