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Full-Text Articles in Life Sciences
Automating Dicentric Chromosome Detection From Cytogenetic Biodosimetry Data., Peter K Rogan, Yanxin Li, Asanka Wickramasinghe, Akila Subasinghe, Natasha Caminsky, Wahab Khan, Jagath Samarabandu, Ruth Wilkins, Farrah Flegal, Joan H Knoll
Automating Dicentric Chromosome Detection From Cytogenetic Biodosimetry Data., Peter K Rogan, Yanxin Li, Asanka Wickramasinghe, Akila Subasinghe, Natasha Caminsky, Wahab Khan, Jagath Samarabandu, Ruth Wilkins, Farrah Flegal, Joan H Knoll
Biochemistry Publications
We present a prototype software system with sufficient capacity and speed to estimate radiation exposures in a mass casualty event by counting dicentric chromosomes (DCs) in metaphase cells from many individuals. Top-ranked metaphase cell images are segmented by classifying and defining chromosomes with an active contour gradient vector field (GVF) and by determining centromere locations along the centreline. The centreline is extracted by discrete curve evolution (DCE) skeleton branch pruning and curve interpolation. Centromere detection minimises the global width and DAPI-staining intensity profiles along the centreline. A second centromere is identified by reapplying this procedure after masking the first. Dicentrics …
A Framework For Organizing Cancer-Related Variations From Existing Databases, Publications And Ngs Data Using A High-Performance Integrated Virtual Environment (Hive), Tsung-Jung Wu, Amirhossein Shamsaddini, Yang Pan, Krista Smith, Daniel J. Chrichton, Vahan Simonyan, Raja Mazumder
A Framework For Organizing Cancer-Related Variations From Existing Databases, Publications And Ngs Data Using A High-Performance Integrated Virtual Environment (Hive), Tsung-Jung Wu, Amirhossein Shamsaddini, Yang Pan, Krista Smith, Daniel J. Chrichton, Vahan Simonyan, Raja Mazumder
Biochemistry and Molecular Medicine Faculty Publications
Years of sequence feature curation by UniProtKB/Swiss-Prot, PIR-PSD, NCBI-CDD, RefSeq and other database biocurators has led to a rich repository of information on functional sites of genes and proteins. This information along with variation-related annotation can be used to scan human short sequence reads from next-generation sequencing (NGS) pipelines for presence of non-synonymous single-nucleotide variations (nsSNVs) that affect functional sites. This and similar workflows are becoming more important because thousands of NGS data sets are being made available through projects such as The Cancer Genome Atlas (TCGA), and researchers want to evaluate their biomarkers in genomic data. BioMuta, an integrated …