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- GENOME-TILING ARRAYS, DNA-REPLICATION, HISTONE MODIFICATIONS, MAMMALIAN-CELLS, PROTEIN MATRIX, CHROMATIN LOOP, HELA-CELLS, IDENTIFICATION, ORGANIZATION, CHROMOSOME (1)
- Integrins, prostate cancer, protein expression, computer software (1)
- Support vector machines, intrinsically disordered proteins, protein structure, sequence databases (1)
Articles 1 - 3 of 3
Full-Text Articles in Life Sciences
Dispredict: A Predictor Of Disordered Protein Using Optimized Rbf Kernel, Sumaiya Iqbal, Md Tamjidul Hoque
Dispredict: A Predictor Of Disordered Protein Using Optimized Rbf Kernel, Sumaiya Iqbal, Md Tamjidul Hoque
Computer Science Faculty Publications
Intrinsically disordered proteins or, regions perform important biological functions through their dynamic conformations during binding. Thus accurate identification of these disordered regions have significant implications in proper annotation of function, induced fold prediction and drug design to combat critical diseases. We introduce DisPredict, a disorder predictor that employs a single support vector machine with RBF kernel and novel features for reliable characterization of protein structure. DisPredict yields effective performance. In addition to 10-fold cross validation, training and testing of DisPredict was conducted with independent test datasets. The results were consistent with both the training and test error minimal. The use …
Pcaanalyser: A 2d-Image Analysis Based Module For Effective Determination Of Prostate Cancer Progression In 3d Culture, Md Tamjidul Hoque, Louisa C. E. Windus, Carrie J. Lovitt, Vicky M. Avery
Pcaanalyser: A 2d-Image Analysis Based Module For Effective Determination Of Prostate Cancer Progression In 3d Culture, Md Tamjidul Hoque, Louisa C. E. Windus, Carrie J. Lovitt, Vicky M. Avery
Computer Science Faculty Publications
Three-dimensional (3D) in vitro cell based assays for Prostate Cancer (PCa) research are rapidly becoming the preferred alternative to that of conventional 2D monolayer cultures. 3D assays more precisely mimic the microenvironment found in vivo, and thus are ideally suited to evaluate compounds and their suitability for progression in the drug discovery pipeline. To achieve the desired high throughput needed for most screening programs, automated quantification of 3D cultures is required. Towards this end, this paper reports on the development of a prototype analysis module for an automated high-content-analysis (HCA) system, which allows for accurate and fast investigation of …
Nuclear Scaffold Attachment Sites Within Encode Regions Associate With Actively Transcribed Genes, Christopher M. Taylor, Mignon A. Keaton, Ryan M. Layer, Anindya Dutta
Nuclear Scaffold Attachment Sites Within Encode Regions Associate With Actively Transcribed Genes, Christopher M. Taylor, Mignon A. Keaton, Ryan M. Layer, Anindya Dutta
Computer Science Faculty Publications
The human genome must be packaged and organized in a functional manner
for the regulation of DNA replication and transcription. The nuclear
scaffold/matrix, consisting of structural and functional nuclear
proteins, remains after extraction of nuclei and anchors loops of DNA.
In the search for cis-elements functioning as chromatin domain
boundaries, we identified 453 nuclear scaffold attachment sites
purified by lithium-3,5-iodosalicylate extraction of HeLa nuclei across
30 Mb of the human genome studied by the ENCODE pilot project. The
scaffold attachment sites mapped predominately near expressed genes and
localized near transcription start sites and the ends of genes but not
to …