Amanda Clare

Publications

• No one tool to rule them all: Prokaryotic gene prediction tool performance is highly dependent on the organism of study
• No one tool to rule them all: prokaryotic gene prediction tool annotations are highly dependent on the organism of study
• Constraint-based optimisation tools for semi-automated refinement of genome-scale yeast metabolic models
• Enhanced string factoring from alphabet orderings
• AutoLabDB: a substantial open source database schema to support a high-throughput automated laboratory
• Partridge: An effective system for the automatic classification of the types of academic papers
• Decision Trees for Hierarchical Multilabel Classification
• Hierarchical Multi-classification with Predictive Clustering Trees in Functional Genomics
• Locational distribution of gene functional classes in Arabidopsis thaliana
• The Robot Scientist Adam
• The Automation of Science
• PD5: a general purpose library for primer design software
• Alphabet Reordering for the Lyndon Factorization of Biological Strings
• Machine learning of functional class from phenotype data
• Goldilocks
• An ontology for a Robot Scientist
• Letters - Make way for robot scientists
• Exploring the Generation and Integration of Publishable Scientic Facts Using the Concept of Nano-publications.
• Laboratory Automation in a Functional Programming Language
• Measuring prominence of scientific work in online news as a proxy for impact
• Data mining the yeast genome in a lazy functional language
• Wiki based management of chemometric research projects
• The EXACT description of biomedical protocols
• Towards Robot Scientists for autonomous scientific discovery
• Rhetorical Classification of Anchor Text for Citation Recommendation
• Meta-data analysis of plant trait databases: how are such databases used and how can they be improved?
• MitiGate; an online meta-analysis database for quantification of mitigation strategies for enteric methane emissions
• Integration of genomic and phenotypic data
• An Integrated Laboratory Robotic System for Autonomous Discovery of Gene Function
• Predicting gene function in Saccharomyces cerevisiae
• Scalable Multi-Relational Association Mining
• Evolutionary Search Techniques for the Lyndon Factorization of Biosequences
• Functional bioinformatics for Arabidopsis thaliana
• Measuring scientific impact beyond academia
• Automatically Geotagging Articles in the Welsh Newspapers Online Collection
• StORF-Reporter: Finding Genes between Genes
• FrameRate: learning the coding potential of unassembled metagenomic reads
• A Tool for Multiple Targeted Genome Deletions that Is Precise, Scar-Free, and Suitable for Automation.
• CDˆ2CR
• Confirmation of Data Mining Based Predictions of Protein Function
• How well do we understand the clusters found in microarray data?
• HarriGT
• StORF-Reporter: finding genes between genes
• Replicating complex agent based models, a formidable task
• Recovery of gene haplotypes from a metagenome
• GiraFFe Browse: A lightweight web based tool for inspecting GFF and FASTA data
• Enhanced string factoring from alphabet orderings
• Evaluation of a Permutation-Based Evolutionary Framework for Lyndon Factorizations
• Probabilistic recovery of cryptic haplotypes from metagenomic data
• On the complexity of haplotyping a microbial community
• Accurate prediction of protein functional class from sequence in the Mycobacterium tuberculosis and Escherichia coli genomes using data mining
• Heuristics for the run-length encoded Burrows–Wheeler transform alphabet ordering problem