Browsing by Author "van Heusden, Peter A."

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    COMBAT-TB-NeoDB: Fostering tuberculosis research through integrative analysis using graph database technologies
    (Oxford University Press, 2020) Lose, Thoba; van Heusden, Peter A.; Christoffels, Alan G.
    Tuberculosis (TB) is a significant global health threat, with onethird of the population infected with its causative agent Mycobacterium tuberculosis (M.tb). Globally, researchers have been responding with a plethora of heterogeneous TB databases with each focusing on different subsets of TB data and present limited options for data integration thus impeding the chances of integrative analysis. Although each database can provide answers to certain questions in its scope, it falls short in answering questions that require federated queries across multiple domains of biological knowledge.
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    The contribution of exon-skipping events on chromosome 22 to protein coding diversity
    (Cold Spring Harbor Laboratory Press, 2001) Hide, Winston A.; Babenko, Vladimir N.; van Heusden, Peter A.
    Completion of the human genome sequence provides evidence for a gene count with lower bound 30,000–40,000. Significant protein complexity may derive in part from multiple transcript isoforms. Recent EST based studies have revealed that alternate transcription, including alternative splicing, polyadenylation and transcription start sites, occurs within at least 30–40% of human genes. Transcript form surveys have yet to integrate the genomic context, expression, frequency, and contribution to protein diversity of isoform variation. We determine here the degree to which protein coding diversity may be influenced by alternate expression of transcripts by exhaustive manual confirmation of genome sequence annotation, and comparison to available transcript data to accurately associate skipped exon isoforms with genomic sequence. Relative expression levels of transcripts are estimated from EST database representation. The rigorous in silico method accurately identifies exon skipping using verified genome sequence. 545 genes have been studied in this first hand-curated assessment of exon skipping on chromosome 22.