A5051156900- Scientific Computing and Data Management
- Genetics, Bioinformatics, and Biomedical Research
- Research Data Management Practices
- Genomics and Phylogenetic Studies
- RNA and protein synthesis mechanisms
- Plant Pathogenic Bacteria Studies
- Advanced Proteomics Techniques and Applications
- CRISPR and Genetic Engineering
- Evolution and Genetic Dynamics
- Bacterial Genetics and Biotechnology
- DNA and Biological Computing
- Plant Virus Research Studies
- Software Engineering Research
- RNA modifications and cancer
Wellcome Sanger Institute
2016-2024
University of Canterbury
2014-2018
University of Otago
2018
Noncoding RNAs are integral to a wide range of biological processes, including translation, gene regulation, host-pathogen interactions and environmental sensing. While genomics is now mature field, our capacity identify noncoding RNA elements in bacterial archaeal genomes hampered by the difficulty de novo identification. The emergence new technologies for characterizing transcriptome outputs, notably RNA-seq, improving identification expression quantification. However, major challenge...
The pan-genome is defined as the combined set of all genes in gene pool a species. Pan-genome analyses have been very useful helping to understand different evolutionary dynamics bacterial species: an open often indicates free-living lifestyle with metabolic versatility, while closed pan-genomes are linked host-restricted, ecologically specialized bacteria. A detailed understanding species has also instrumental tracking phylodynamics emerging drug resistance mechanisms and drug-resistant...
Computational biology provides software tools for testing and making inferences about biological data. In the face of increasing volumes data, heuristic methods that trade speed accuracy may be employed. We have studied these trade-offs using results a large number independent benchmarks, evaluated whether external factors, including speed, author reputation, journal impact, recency developer efforts, are indicative accurate software.We find citations age unreliable predictors accuracy. This...
Abstract Background Computational biology provides widely used and powerful software tools for testing making inferences about biological data. In the face of rapidly increasing volumes data, heuristic methods that trade speed accuracy may be employed. We are have studied these trade-offs using results a large number independent benchmarks, evaluated whether external factors indicative accurate software. Method extracted ranks from benchmarks different bioinformatic tools, speed, author...
Abstract The pan-genome is defined as the combined set of all genes in gene pool a species. Pan-genome analyses have been very useful helping to understand different evolutionary dynamics bacterial species: an open often indicates free-living lifestyle with metabolic versatility, while closed pan-genomes are linked host-restricted, ecologically specialised bacteria. A detailed understanding species has also instrumental tracking phylodynamics emerging drug resistance mechanisms and resistant...
Abstract The reactions of functional molecules like proteins and RNAs to mutation affect both host cell viability biomolecular evolution. These are considered robust if function is maintained despite mutations. Proteins have different structural characteristics that their robustness, date, comparisons between them been theoretical. In this work, we test the relative mutational robustness RNA protein pairs using three approaches: evolutionary, structural, functional. We compare nucleotide...