Kagan Tuncay

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The Poisson-Boltzmann (PB) equation has been extensively used to analyze the energetics and structure of proteins and other significant biomolecules immersed in electrolyte media. A new highly efficient approach for solving PB-type equations that allows for the modeling of many-atoms structures such as encountered in cell biology, virology, and(More)
BACKGROUND Gene expression microarray and other multiplex data hold promise for addressing the challenges of cellular complexity, refined diagnoses and the discovery of well-targeted treatments. A new approach to the construction and quantification of transcriptional regulatory networks (TRNs) is presented that integrates gene expression microarray data and(More)
Transcriptional regulatory network (TRN) discovery from one method (e.g. microarray analysis, gene ontology, phylogenic similarity) does not seem feasible due to lack of sufficient information, resulting in the construction of spurious or incomplete TRNs. We develop a methodology, TRND, that integrates a preliminary TRN, microarray data, gene ontology and(More)
Although the mechanisms of eukaryotic chromosome segregation and cell division have been elucidated to a certain extent, those for bacteria remain largely unknown. Here we present a computational string model for simulating the dynamics of Escherichia coli chromosome segregation. A novel thermal-average force field accounting for stretching, bending, volume(More)
In one-dimensional (1D) early diagenetic models, bioirrigation is typically represented by a nonlocal mass transfer or bioirrigation coefficient, ␣. Usually, all pore water species are assigned the same ␣. Here, we show that this assumption can lead to significant errors in estimates of bioirrigation intensities. Using a simplified early diagenetic reaction(More)
Transcriptional regulatory network (TRN) discovery using information from a single source does not seem feasible due to lack of sufficient information, resulting in the construction of spurious or incomplete TRNs. A methodology, TRND, that integrates a preliminary TRN, gene expression data and gene ontology is developed to discover TRNs. The method is(More)
cDNA microarray and other multiplex data hold promise for addressing the challenges of cellular complexity, disease progression and drug discovery. We believe that combining transcription kinetic modeling with microarray time series data through information theory will yield more information about the gene regulatory networks than obtained previously. A(More)